Evolutionary Biology

Class 1

#You can submit a report: Publication grade article –term paper; can be done on

 Number of species in the world- All Kingdoms

Ref: Mora et al. 2011
 Zhang (ed.) 2011, Zootaxa 3148:1-237

Breakdown of Phylum Arthropoda (80% of total) –

Coleoptera, Diptera,Lepidoptera,Hymenoptera,Hemiptera (In order of number
of species)

Arhtropoda, Arachnida,Mollusca, Craniata (In order of species diversity)

Wilson’s species-scape <EO Wilson- Biodiversity>

Biomass in a rainfoerest- insects predominate the biomass distribution-

comparable with trees

Evolution of life diversity through time <Penn State University>

Geological time scales-Chinese Owls Seldom Defeat Clas Pigeons,

They Just Chase Past Each Other Making Perposterous Puns:- Ha

PERIOD:Cambrian, Ordovician, Silurian, Devonian, Carboniferous, Permian,

(PALEOZOIC);Triassic, Jurassic, Cretaceous, (MESOZOIC) Tertiary, Quarternary
(CENOZOIC) (ERA)

Tertiary- EPOCHS: Paleocene,, Eocene,Oligocene,Miocene,Pliocene

Quartenray-EPOCHS: Pleistocene, Holocene

Archean:
 Origin of life molecules; 1st fossil evidence at 3500 mya; Photosynthesis;
Aerobic respiration

Proterozoic – origin of eukaryotes, evolution of multicellularity- annelids and

arthropods

(Ref: Dawkins’ Blind Watchmaker- building components that can come together
to build complexity- origin of eukaryota- hybridization events- endosymbiosis)

Accelerated rates of evolution with time- early steps more gradual which then
build up leading to increased rates over time due to availablity of more building
blocks

Cambrian explosion: Earliest agnathan fishes

Ordovician: Echinoderms radiate-
Mass extinction

Silurian: Jawed fish – earliest terrestrial vascular plants-arthropods, insects

Devonian: Trilobites, ammonoids, insects, ferns, seed plants

Mass extinction

Carboniferous-lycopsid forests, tree ferns

Early orders of winged insects, amphibians diversify,
First reptiles

Permian-
Pangaea, glaciation,diverse insects, amphibian decline, reptiles diversify
(mammal like forms of reptiles)
Major Mass Extinction

Triassic-
Continents begin to separate, Marine diversity increases, gymnosperms
dominant, reptiles diversify, 1st dinosaurs and mammals

Jurassic-
Dinosaurs diversify, birds originate, early mammals, origin of Angiosperms,
Ammonoid radation

Cretaceous-
Angisperms radiate, mammals and birds diversify
Mass extinction dinosaurs and ammonoids extinct

Tertiary-
Cool and Dry
Angiosperms radiate, pollinating insects, odern fishes, mammals and birds

Quarternary-
Continents in modern position
Glaciation oscillations- lowering of sea levels : due to earths revolution pattern
10,000 year breaks (interglacials) between glaciations
Extinctions in giant mammals and flightless birds
Evolutions of hominids

### Living fossils:

Name 5 living fossils: Coelacanth, Ginkgo, Nautilus…
**** Look up JBS Haldane

Class 2

Mass extinctions

Rohde and Muller.205.Nature,434:208-210

Loss of known diversity during mass extiinctions

Why is there greater diversity in modern times-

 Taxonomic resolution better for more recent fossils compared to more
ancient fossils regarding which we have really limited biological
information. Thus fossils coming from multiple different organisms can
be grouped into a single category due to lack of better taxonomic
categorizations. Modern animals can be easily classified giving rise to
higher diversity.
 Older fossils are less likely to survive as compared to newer ones. Fossil
record is incomplete.

Pseudo-genes and molecular evolution, recreation of entire extinct genes and

gene families using phylogenetic methods

Chronospecies and real species difference

Eg. Homo erectus and Homo sapiens

Difficult to separate polymorphisms within a species from forms that represent

distinct species. Eg. Sexual dimorphism within the same species might skew
interpretation

Eldredge and Gould(>1972): Punctuated equilibrium- fossil records of cetain

invertebrates that evolution follows a punctuated equilibrium- Equilibrium or
stasis – unchanging phenotypes over extended periods of geological time, which
is punctuated by rapid evolution of traits- Characters in equilibrium or stasis-
anagenesis evolution within a species ; cladogenesis: a branching event, i.e
evolution of a new species

Morphological evolution is correlated with speciation

Graph of phenotype change vs time- random brownian motion type variation for
long time periods followed by rapid branching or change- in bursts

Infinite small steps vs large rapid steps

Punctuted equilibrium contrasts with phyletic gradualism(characters evolve
gradually over time)
Lecture 2

Concepts of species and phylogenetics

Diversity at the level of functional, morphological and genetic diversity, species,

organizational levels and principles
No theoretical barrier to considering the existence of a single global species on
earth
Bacteria and plants do not follow the biological species concept
Horizontal gene exchange

Class 3

Birds have specific alarm calls for different predators- classification- taxonomy is
not completely human/contrived artifact
Linnaean system of taxonomical nomenclature- pre Darwinian- no concept of
evolution

Evolutionary thinking in taxonomy and systematics is recent ~c.1950

Are species real?- Biological species concept- Ernst Mayr, Theo Dobzhansky

Reproductive isolation??? Horse, donkey!

Definition of genus is subjective

Reproductive isolation in allopatric species- plants

Asexually reproducing species- how do you define a species- entire slopes of

plants may be a single clone reproducing vegetatively

Phylogenetic species concept- monophyletic groups

Smallest monophyletic group –species
Percentage divergence/differences between individuals- are they different
species- variation between individuals within a species as compared to variation
across individuals from different species- intra species vs inter species
divergence

Population differentiation – is a continuous evolutionary process with nodal

stages commonly seen in diverse or incipient groups.

Species are sometimes real and sometimes not!!!

Consequences of hybridization- evolutionary consequences range from neutral

introgression to hybrid speciation
Hybridization can occur at the level of species to at the level of genera-
Populations at a nodal stage in divergence ? can they be classified as different
species.
Are subspecies real?
Some birds, mammals, and butterflies- that have been extensively characterised

Geographically structured variation within species with little reproductive

isolation within the polytypic species

Subspecies do not neccessrily go on to form new species

Are subspecies incipient species- No not necessarily

Population to species continuum!!

Plot of distnace (any environmental gradient) vs gene/phenotype frequency

Stepcline- threshold difference or gradual-cline

, sympatry, parapatry

Genomic island- how much gene flow is enough to categorise populations as

different species

Hybrid swarms between populations A and B- characters vs frequency plot

A and B have distinct characters-

i> these characters might overlap
ii> might not overlap at all.
These 2 pecies hybridise – with a swarm of hybrids that share the 2 characters-
does that constitute a new species

Long term consequences of introgresion to hybrid speciation( rivers and buckets

analogy)

“Speciation” is a continuous process (if one believes in species)

(diversification)

Haeckel’s classification(1866) of phylogeny

Numerical taxonomists: Pheneticists: Sokal, Sneath, Camin

Phylogenetic systematics: cladists: Willi Hennig
Phylogeny should be central to systematics-
Phylogenies may be reconstructed from comparisons of extant species based on
synapomorphies
Classification should be based directly on phylogeny

Mathematical and molecular biologists- Fitch and Felsenstein

Molecular data and computational power-c1990 – Hillis et al.

Diversification may be dichotomous but network methods are beinf explored for
horizintal gene transfer

Basal (primitive, lower) and derived (advanced, higher) lineages: humans and
modern bacteria are equally advanced.

Components of phylogenetic trees

Terminal nodes, peripheral branch, internal branch, node, root

Trees based on character matrix- genetic or molecular data

Trees built using a dissimilarity among various taxa

Informative and non informative characters(invariable characters, variation

shared within and across species)

Plesiomorphy- ancestral state

Symplesiomorphy-shared ancestral state
Apomorphy-derived state
Autapomorphy-unique derived state
Synapomorphy shared derivative state
Homology-
Homoplasy – convergent evolution

Branches may be rotated around the nodes without changing the relationships

MRCA (Most Recent Common Ancestor)

Monophyly
Paraphyly: members of a clade excluding some
Polyphyly: pulling out members of different clades into one group

Reptiles are paraphyletic wrt birds. Butterflies are moths (Moths are
paraphyletic wrt to butterflies)

Rooted trees may be more phylogenetically informative

Ingroup and outgroup- outgroups are important in rooting a tree.

Sister group concepts

Branch lengths and phylograms: length of a branch indicates the amount of

evolution- may or may not be related to its absolute age in time (faster vs slower
evolving genes, adaptive radiations, time-calibrated trees …)

Species trees vs gene trees

Class 4

Population genetics

Fusion of natural selection, mendelian genetics and mathematics during modern

synthesis
Fisher, Haldane, Sewall-Wright

Population genetics models form null models for evolution- influenced molecular
evolution

Null models and neutral processes-

Origin, spread and fixation of mutations and traits in asexual and sexual
populations

Phenotype: morphology, behavior, physiology, biochemistry, external and

anatomical characters-may be based on genotype, environment, or a
combination of the two (environment can be internal or external)

Genotype: can be a single base or a large collection of molecular markers

Canalisation of phenotypes:

https://en.wikipedia.org/wiki/Canalisation_(genetics)#cite_note-1

< Canalisation (or canalization) is a measure of the ability of a population to

produce the same phenotype regardless of variability of its environment
or genotype. In other words, it means robustness. The term canalisation was
coined by C. H. Waddington, who used the word to capture the fact that
"developmental reactions, as they occur in organisms submitted to natural
selection...are adjusted so as to bring about one definite end-result regardless of
minor variations in conditions during the course of the reaction". He used this
word rather than robustness to take into account that biological systems are not
robust in quite the same way as, for example, engineered systems.
Biological robustness or canalisation comes about when developmental
pathways are shaped by evolution. Waddington introduced the epigenetic
landscape, in which the state of an organism rolls "downhill" during
development. In this metaphor, a canalised trait is illustrated as a valley enclosed
by high ridges, safely guiding the phenotype to its "fate". Waddington claimed
that canals form in the epigenetic landscape during evolution, and that this
heuristic is useful for understanding the unique qualities of biological
robustness>

Silent molecular variation

Alternate genotypes may produce same phenotype
Alternate phenotypes may be produced by same genotype

Locus
Physical location on a chromosome: can be of a single base to large portions of
the chromosome

Gene: DNA sequence producing a functional product

Allele and haplotype: haplotypes (a set of any number of genetic determinants

located on a single chromosome) can be a variation of different SNPs

< A haplotype is a group of genes within an organism that was inherited together
from a single parent. The word "haplotype" is derived from the word "haploid,"
which describes cells with only one set of chromosomes, and from the word
"genotype," which refers to the genetic makeup of an organism. A haplotype can
describe a pair of genes inherited together from one parent on one chromosome,
or it can describe all of the genes on a chromosome that were inherited together
from a single parent. This group of genes was inherited together because of
genetic linkage, or the phenomenon by which genes that are close to each other
on the same chromosome are often inherited together. In addition, the term
"haplotype" can also refer to the inheritance of a cluster of single nucleotide
polymorphisms (SNPs), which are variations at single positions in the DNA
sequence among individuals.
By examining haplotypes, scientists can identify patterns of genetic variation
that are associated with health and disease states. For instance, if a haplotype is
associated with a certain disease, then scientists can examine stretches of DNA
near the SNP cluster to try to identify the gene or genes responsible for causing
the disease >

Difference between allele frequency and genotype frequency

Frequency of individual alleles vs frequency of combinations of alleles that form
genotypes

Transitions, transversions, mutations, substitutions, synonymous and non

synonymous, mutations in 1st, 2nd and 3rd bases in codons, changes in amino
acids
Forward mutations- common, back mutation (very rare); recurrent
mutations(rare)

Evolution is change in allele frequency over time

Epigenetic changes such as changes in methylation patterns defy this rule

Individuals do not evolve ;populations evolve!!

Evolution does not have any direction

Evolution may proceed due to random genetic drift, selection or a combination of

the two- evolution does not necessarily need to invoke natural selection

Cladogenesis vs Anagenesis
Genetic variation is the fuel for evolution- tremendous standing gegetic variation
for almost any trait in natural populations
-historically believed to be low (organisms on adaptive peaks)
-allozymes and sequencing change this view (Lewontin)
Mutations are random-
No increase in mutation rate under stressful conditions(absence of DNA repair)
No directed mutations towards a desirable outcome
Mutations are blind to the future or a highly selective environment
(selective environment does not induce advantageous mutations)

Contrast between the rates of mutation and the rates of fixation

Mutation rates do vary across genes, chromosomes , populations and species and
in time and space : what are thr intrinsic and extrinsic factors that explain this
variation

Mutational hotspots- CpG islands

Class 5

In absence of evolution, standing genetic variation depends on-

-population size- = +ve correlation
-mutation rate- = +ve correlation

a new mutation in the population is likely to go to fixation or extinction in the

population with some frequency
At any time, an allele’s probability of fixation is its current frequency.

Most mutations are likely to go to extinction over a small numberof generations:

if an allele is represented by a singe copy, its frequency in a diploid population is
pt=1/2N and this is also its likelihood of going to fixation(p=1);
This likelihood is greater in smaller populations

In a small population, spread or loss of variation depends much more on chance

effects. Drift is stronger in smaller populations and can override natural
selection.

Drift leds to loss of variation over time (reduced heterozygosity) at all loci,
although different loci and populations in a cluster will lose different variation

Overall genetic diversity may be maintained in a cluster of populations but each

population will have low level of genetic variation and heterozygosity under
random genetic drift
Drift may purge mildly advantageous alleles from a pop. Or drive to fixation a
mildly deleterios allele and may therefore reduce the average fitness of a
population

Genetic bottlenecks , inbreeding, and fixation of deleterios alleles: hexadactyly in

American Germans disease frequency among Parsis. Founder effects and
expansion of previously small populations

<Genetic Bottleneck: population bottleneck

A population bottleneck is an event that drastically reduces the size of a
population. The bottleneck may be caused by various events, such as an
environmental disaster, the hunting of a species to the point of extinction, or
habitat destruction that results in the deaths of organisms. The population
bottleneck produces a decrease in the gene pool of the population because many
alleles, or gene variants, that were present in the original population are lost.
Due to the event, the remaining population has a very low level of genetic
diversity, which means that the population as a whole has few genetic
characteristics.
Following a population bottleneck, the remaining population faces a higher level
of genetic drift, which describes random fluctuations in the presence of alleles in
a population. In small populations, infrequently occurring alleles face a greater
chance of being lost, which can further decrease the gene pool. Due to the loss of
genetic variation, the new population can become genetically distinct from the
original population, which has led to the hypothesis that population bottlenecks
can lead to the evolution of new species>

Population size (N) is usually larger than the “effective population size” (Ne). In
lekking species such as elephant seals, 10% of the males get more than 90% of
the matings, so their Ne is much smaller than N. Greater discrepancy between N
and Ne strengthens drift and loss of heterozygosity.

Ne<N if
-individuals have variable numbers of progeny
-sex ratio departs from 1:1
-generations overlap or populations are structured,both of which are likely to
lead to inbreeding
-populations fluctuate in time, in which case Ne is a harmonic mean of the
populations sizes rather than the arithmetic mean(former is smaller than the
latter)

Kimura (1968) showed that the rates of evolution of amino acid sequences of
many proteins are similar , concluding that these proteins had evolved at a
similar rate in different lineages.
He proposed that such constancy of rates indicate that neutral processes such as
mutation and drift govern rates of molecular evolution

Later(1983) he published an influential book on the “neutral theory of molecular

evolution “ – molecular clock concept
Tenets-
-Most observed molecular variation is a result of mutation and drift. Neutral
variation is of little adaptive significance
-Observed molecular variation is a result of mutation and drift in finite
populations which can be explained from basic principles of neutral population
genetics
-molecular evolution will follow the established patterns of bases in codons ,
coding vs non-coding regions of the genome

Absolute null model: every single base in the genome is equally likely to undergo
mutation

In a diploid population new mutation if fixed takes 4Ne generations to fix

In large effective populations newer mutations will arise before previous

mutations go to fixation. In which case each mutation has a probability of fixation
of 1/2Ne, with a steady substitution of one allele for another. Thus, any locus will
be polymorphic during this process(remember that most loci show considerable
molecular variation, supporting the neutral theory)
As a result of the constant mutation rates and a small population sizes, selection
will be negligible and drift will be string for most molecular variation

As a result of constant mutation rates and small population sizes, selection will
be negligible and drift will be strong for most molecular variation

Hardy Weinberg equilibrium-

Panmictic,inifinetly large (N~Ne),close-no gene flow, no differential mortality, no
mutations, no natural selection, no meiotic drives, allele frequencies do not
change over generations, freq of genotypes after random mating in a single gene
two alelle model is p2:2pq:q2

Class 2 popilation genetics:

Spread and purge of dominant vs recessive alleles under natural selection!!!!!

Linkage disequilibrium:
Genes on the same chromosome are physically linked (non-physical linkage
between genes on different chromosomes)
This linkage causes association between various genetic and phenotypic traits
called linkage disequilibrium (LD)

LD breaks down with increasing rate of recombination between the loci, but LD
may be maintained by selection , lethality, etc.
<Linkage disequilibrium — the nonrandom association of alleles at different loci
— is a sensitive indicator of the population genetic forces that structure a
genome. Because of the explosive growth of methods for assessing genetic
variation at a fine scale, evolutionary biologists and human geneticists are
increasingly exploiting linkage disequilibrium in order to understand past
evolutionary and demographic events, to map genes that are associated with
quantitative characters and inherited diseases, and to understand the joint
evolution of linked sets of genes. This
article(http://www.nature.com/nrg/journal/v9/n6/full/nrg2361.html)
introduces linkage disequilibrium, reviews the population genetic processes that
affect it and describes some of its uses. At present, linkage disequilibrium is used
much more extensively in the study of humans than in non-humans, but that is
changing as technological advances make extensive genomic studies feasible in
other species

In population genetics, linkage disequilibrium is the non-random association

of alleles at different loci. Loci are said to be in linkage disequilibrium when the
frequency of association of their different alleles is higher or lower than what
would be expected if the loci were independent and associated randomly.[1]
Linkage disequilibrium is influenced by many factors, including selection, the
rate of recombination, the rate of mutation, genetic drift, the system of
mating, population structure, and genetic linkage. As a result, the pattern of
linkage disequilibrium in a genome is a powerful signal of the population genetic
processes that are structuring it.

In spite of its name, linkage disequilibrium may exist between alleles at different
loci without any genetic linkage between them and independently of whether or
not allele frequencies are in equilibrium (not changing with time) Furthermore,
linkage disequilibrium is sometimes referred to as gametic
phase disequilibrium, however, the concept also applies to asexual organisms
and therefore does not depend on the presence of gametes>

<http://scienceblogs.com/tfk/2007/10/21/the-panglossian-paradigm-or-as/>

Class 6
<Allometry, in its broadest sense, describes how the characteristics of living
creatures change with size. The term originally referred to the scaling
relationship between the size of a body part and the size of the body as a whole,
as both grow during development. However, more recently the meaning of the
term allometry has been modified and expanded to refer to biological scaling
relationships in general, be it for morphological traits (e.g., the relationship
between brain size and body size among adult humans), physiological traits (e.g.,
the relationship between metabolic rate and body size among mammal species)
or ecological traits (e.g., the relationship between wing size and flight
performance in birds). Indeed, allometric relationships can be described for
almost any co-varying biological measurements, resulting in broad usage of the
term. However, a unifying theme is that allometry describes how traits or
processes scale with one another. The study of allometry concerns the functional
mechanisms that generate these scaling relationship, how they impact ecology,
and how they respond to and influence evolution

For more refer:

http://www.nature.com/scitable/knowledge/library/allometry-the-study-of-
biological-scaling-13228439 >

Linkage disequilibrium can make 2 traits evolve when there is selection on one
closely located loci: genetic hitchiking leading to fixation- change without
adaptation-

Phenotypic plasticity

< Exaptation (a replacement for the teleologically-loaded term "pre-adaptation")

and the related term co-option describe a shift in the function of a trait
during evolution. For example, a trait can evolve because it served one particular
function, but subsequently it may come to serve another. Exaptations are
common in both anatomy and behaviour. Bird feathers are a classic example:
initially they may have evolved for temperature regulation, but later were
adapted for flight. Interest in exaptation relates to both the process and products
of evolution: the process that creates complex traits and the products (functions,
anatomical structures, biochemicals, etc.) that may be imperfectly developed>

<https://en.wikipedia.org/wiki/Exaptation>

<Any aspect of an organism that has not changed over a certain period of time
could be considered to provide evidence for "constraint" of some sort. To make
the concept more useful, it is therefore necessary to divide it into smaller units.
First, one can consider the pattern of constraint as evidenced
by phylogenetic analysis and the use of phylogenetic comparative methods; this
is often termed phylogenetic inertia, or phylogenetic constraint. It refers to the
tendency of related taxa sharing traits based on phylogeny. Charles Darwin
spoke of this concept in his 1859 book "On the Origin of Species", as being "Unity
of Type" and went on to explain the phenomenon as existing because organisms
do not start over from scratch, but have characteristics that are built upon
already existing ones that were inherited from their ancestors; and these
characteristics likely limit the amount of evolution seen in that new taxa due to
these constraints.
If one sees particular features of organisms that have not changed over rather
long periods of time (many generations), then this could suggest some constraint
on their ability to change (evolve). However, it is not clear that mere
documentation of lack of change in a particular character is good evidence for
constraint in the sense of the character being unable to change. For example,
long-term stabilizing selection related to stable environments might cause stasis.
It has often been considered more fruitful, to consider constraint in its causal
sense: what are the causes of lack of change?>

Phenotype without genotype- Eg. Shell shape due to environmental constraints

Selection but no adaptation. Find out examples

Class 7

Genetic drift diagram!

Linkage in genetic variation

Drift, variation and selection pressures, forms of selection(directional,

disruptive, stabilizing, positive and negative
Concept of fitness

Phenotype space vs frequency curves

Normal distribution under normal conditions

Skewing of phenotype distribution uder conditions of directional slection. Eg.

Body size in cold climate-
Distribution might not remain normal

Stabilizing selection- towards the mean

With loss of heterozygosity, selection without evolution

Gegetic variability and stochastic events

Positive selection- when a phenotype is being selected for

<Purifying selection- In natural selection, negative selection or purifying

selection is the selective removal of alleles that are deleterious. This can result in
stabilizing selection through the purging of deleterious variations that arise>

Fitness:
Fecundity is an absolute measure, fitness is relative
Fitness at the allelic level- allele frequency increase: since selection acts at the
allelic level

You need effective population size to get an estimate of fitness

Allele fitness vs individual fitness

Fitness of a female is easier to measure compared to fitness of a male

Fitness: adaptive value, fecundity, genotype based

Same allele may have different fitness coefficients based on environment: Eg.
Summer and winter forms of insects

Fisher’s Fundamental theorem

Rate of increase in (average) fitness of a species is equal to its genetic variance in
fitness
Natural slection would usually drive fitness to a greater value
This works only if loci are not linked (linkage equilibrium), there are no epistatic
interactions , no frequency dependence and the environemnt reliably and stably
selects for one optimum
-fitness can decrease when selection acts on two linked loci that have epistatic
effects on fitness
fluctuating environments and periodicity affects rates

Fitness landscape: fitness vs gene or phenotype1 vs gene or phenotype2

Sewall wrights adaptive landscape: Khan 2010.Discover -Surfplot- fitness valleys

and fitness peaks
n-dimesnional fitness lanscape

The rate of change in allele frequency depends on steepness of the gradient in

average fitness of the population, i.e dW/dq , where W is the average fitness of
the population and q is allele frequency

Rugged landscape- more number of fitness peaks

Size of mutational steps ~ fitness impact (+ve or –ve)
< http://www.pnas.org/content/112/24/7345.full.pdf

http://www.nature.com/nrg/journal/v15/n7/abs/nrg3744.html >

Adaptive evolution may be rapid with a combination of temporally divided

populations, drift, migration, and selection- 3 phases
1. genetic drift allows a locally adapted sub population to move from one fitness
peak across an adaptive valley towards a higher adaptive peak
2. natural slection will take the population to the higher peak
3. Better adapted subpopulations then expand its range and outcompetes other
subpopulations, causing the spread of new adaptations and movement of the
global population towards the new fitness peak

Shifting balance theory

<The shifting balance theory is a theory of evolution proposed in 1932 by Sewall
Wright, suggesting that adaptive evolution may proceed most quickly when
a population divides into subpopulations with restricted gene flow. The name of
the theory is borrowed from Wright's metaphor of fitness
landscapes (evolutionary landscapes), attempting to explain how a population
may move across an adaptive valley to a higher adaptive peak. According to the
theory, this movement occurs in three steps:
Genetic drift allows a locally adapted subpopulation to move across an adaptive
valley to the base of a higher adaptive peak.
Natural selection will move the subpopulation up the higher peak.
This new superiorly adapted subpopulation may then expand its range and
outcompete or interbreed with other subpopulations, causing the spread of
new adaptations and movement of the global population toward the new fitness
peak.
Although shifting balance theory has been influential in evolutionary biology,
inspiring the theories of quantum evolution and punctuated
equilibrium, little empirical evidence exists to support the shifting balance
process as an important factor in evolution>

<http://www.nature.com/scitable/topicpage/sewall-wright-and-the-
development-of-shifting-30508>

Class 8

Fisher’s geometric model

<Fisher's geometric model (FGM) is an evolutionary model of the effect sizes and
effect on fitness of spontaneous mutations proposed by Ronald Fisher to explain
the distribution of effects of mutations that could contribute
to adaptative evolution>

Gradual vs saltatory evolution; phenotypes from one or multiple genees(QTL);

mutations of small effects vs large effects (“major genes”)

<’Hopeful monsters’ also known as the hopeful monsters hypothesis is

a biological theory which suggests that major evolutionary transformations have
occurred in large leaps between species due to macromutations
Stephen Jay Gould (1941 – 2002) had attempted to update the ideas of
Goldschmidt by redefining the concept of "hopeful monster" in a way that can be
kept in the neo-Darwinian framework via an extension In an article titled The
Return of Hopeful Monsters (1977) Gould argued that the recent discovery of
regulatory genes offered new evidence which supported some of Goldschmidt's
postulates and that small changes in the embryological "contraint systems" can
produce large morphological transformation in the adult, and possibly macro-
evolutionary pathways. Gould's re-definition of the hopeful monster is different
to that of Goldschmidt and they should not be confused with each other>
<http://www.dartmouth.edu/~dietrich/NRG2003.pdf>
<http://www.evolocus.com/publications/theissen2009.pdf> *********

Fisher’s geometric mpdel of adaptation (change in size of mutations towards an

adaptive peak)
<http://www.nature.com/nrg/journal/v10/n8/pdf/nrg2603.pdf>
<http://www.nature.com/nrg/journal/v6/n2/pdf/nrg1523.pdf> ***********

<A selective sweep is the reduction or elimination of variation among

the nucleotides in neighboring DNA of a mutation as the result of the
recent fixation of a beneficial allele due to strong positive natural selection.
A selective sweep can occur when a rare or previously non-existing allele that
increases the fitness of the carrier relative to other members of
the population increases rapidly in frequency due to natural selection. As the
prevalence of such a beneficial allele increases, genetic variants present on the
genomic background of the beneficial allele will also become more prevalent.
This phenomenon is called genetic hitchhiking. A selective sweep due to a
strongly selected allele, which arose on a single genomic background therefore
results in a region of the genome with a large reduction of genetic variation in
that chromosome region. The idea that strong positive selection could reduce
nearby genetic variation due to hitchhiking was proposed by Maynard-Smith and
Haigh in 1974.
It is now recognized that not all sweeps reduce genetic variation in the same
way. Sweeps can be categorized in three main categories.
The "classic selective sweep" or "hard selective sweep" is expected to occur
when beneficial mutations are rare, but once a beneficial mutation has occurred
it increases in frequency rapidly, thereby drastically reducing genetic variation
in the population.
A so-called "soft sweep from standing genetic variation" occurs when a
previously neutral mutation that was present in a population becomes beneficial
because of an environmental change. Such a mutation may be present on several
genomic backgrounds so that when it rapidly increases in frequency, it doesn't
erase all genetic variation in the population.
Finally, a "multiple origin soft sweep" occurs when mutations are common (for
example in a large population) so that the same or similar beneficial mutations
occurs on different genomic backgrounds such that no single genomic
background can hitchhike to high frequency

https://en.wikipedia.org/wiki/Selective_sweep

http://rspb.royalsocietypublishing.org/content/early/2012/07/17/rspb.2012.0
799

http://www.nature.com/nrg/journal/v12/n4/full/nrg2978.html

http://www.genetics.org/content/genetics/189/1/213.full.pdf>
Alleles on a chromosome plotted vs LOD score gives an estimate of
1> Distance / separation of linked alleles: further you go, lesser correlation
between what is under selection and what is not
2> Recombination rate( recombinational hotspots and coldspots: )
3> Single gene vs polygenic (not as important)
4> Strength of selection: low selection and low recombination vs high
selection low recombination
5> Age of mutation: time for which an allele exists positively correlates with
the number of combinations and associations it makes (which increases
wih time)

y-axis is a measure of the correlation between genotype and phenotype/fitness

benefits

<The LOD score (logarithm (base 10) of odds), developed by Newton Morton, is a
statistical test often used for linkage analysis in human, animal, and plant
populations. The LOD score compares the likelihood of obtaining the test data if
the two loci are indeed linked, to the likelihood of observing the same data
purely by chance. Positive LOD scores favor the presence of linkage, whereas
negative LOD scores indicate that linkage is less likely. Computerized LOD score
analysis is a simple way to analyze complex family pedigrees in order to
determine the linkage between Mendelian traits (or between a trait and a
marker, or two markers).
The method is described in greater detail by Strachan and Read [1]. Briefly, it
works as follows:
Establish a pedigree
Make a number of estimates of recombination frequency
Calculate a LOD score for each estimate
The estimate with the highest LOD score will be considered the best estimate
The LOD score is calculated as follows:
{\displaystyle {\begin{aligned}LOD=Z&=\log _{10}{\frac {\mbox{probability of
birth sequence with a given linkage value}}{\mbox{probability of birth sequence
with no linkage}}}=\log _{10}{\frac {(1-\theta )^{NR}\times \theta

^{R}}{0.5^{(NR+R)}}}\end{aligned}}}
NR denotes the number of non-recombinant offspring, and R denotes the
number of recombinant offspring. The reason 0.5 is used in the denominator is
that any alleles that are completely unlinked (e.g. alleles on separate
chromosomes) have a 50% chance of recombination, due to independent
assortment. 'θ' is the recombinant fraction, i.e. the fraction of births in which
recombination has happened between the studied genetic marker and the
putative gene associated with the disease. Thus, it is equal to R / (NR + R)
By convention, a LOD score greater than 3.0 is considered evidence for linkage,
as it indicates 1000 to 1 odds that the linkage being observed did not occur by
chance. On the other hand, a LOD score less than -2.0 is considered evidence to
exclude linkage. Although it is very unlikely that a LOD score of 3 would be
obtained from a single pedigree, the mathematical properties of the test allow
data from a number of pedigrees to be combined by summing their LOD scores.
However, this traditional cut-off of LOD score > +3 is arbitrary, and in certain
types of linkage studies, such as analyses of complex genetic traits with hundreds
of markers, this criterion should probably be modified to a higher cut-off (for
example, by applying a Bonferroni correction)>

Class 9

Malthusian Disasters

< https://en.wikipedia.org/wiki/Malthusian_catastrophe>

< https://en.wikipedia.org/wiki/Malthusian_trap>

<http://rescuingbiomedicalresearch.org/wpcontent/uploads/2015/04/Malthus
-1798.pdf>

< https://en.wikipedia.org/wiki/The_Population_Bomb>

<http://projectavalon.net/The_Population_Bomb_Paul_Ehrlich.pdf>

 Rate of increase in resources lower than rate of increase in population

size: famines inevitable
 Struggle for existence: competition for resources
 Fitness is a consequence of ability to acquire more resources , defend it,
and/or convert it most efficiently to offspring

Intrinsic growth rate (r) , population size (N)

Nt = Nort

Carrying capacity K : density dependence. An abstract notion of how many

individuals a habitat can support
Stability, resileince, equilibrium, stochastic effects

Graph of #adults vs time – oscillations in populations observed

Density dependent vs density independent growth rate

Intrinsic and extrinsic

Sex-ratio : intrinsic

External regulation: predation, parasitism

Top Down vs Bottom up control

< http://www.yellowstonepark.com/wolf-reintroduction-changes-ecosystem/>

< http://www.pbs.org/wnet/nature/in-the-valley-of-the-wolves-reintroduction-
of-the-wolves/213/>

< https://en.wikipedia.org/wiki/Wolf_reintroduction>

< http://nationalgeographic.org/encyclopedia/keystone-species/>

<http://www.smithsonianmag.com/science-nature/shrinking-keystone-
180959748/?no-ist>

< https://www.washington.edu/research/pathbreakers/1969g.html>

< http://www.asnailsodyssey.com/LEARNABOUT/SEASTAR/seasKeys.php>

<file:///Users/rishav/Downloads/Lafferty%20and%20Suchanek%202016%20
(1).pdf>

< Reintroducing a top predator like the wolf will not only affect prey populations,
but it will influence the complexity of interacting species, including indirect
effects. Food webs are an essential feature of every ecosystem and consumer-
prey interactions are a fundamental linkage among species (Estes, 1996).
Ecologists divide ecosystem interactions and predator-prey relationships into
bottom-up and top-down processes (Hunter and Price, 1992 cited in Estes,
1996). A bottom-up systemconcentrates attention on how resources (space and
nutrients) influence higher trophic forms. A top-down system focuses on
interactions at top level consumers (predators) and their prey influence on
lower trophic forms (Estes, 1996). In other words, the structure of bottom-up
systems is food or resource limited, and the structure of top-down systems is
driven by predation (Kay, 1998). McLaren (1994) states that a top-down trophic
model predicts changes in density at one trophic level caused by opposite
changes in the next higher trophic level, and such inverse correlations cascade
down the food chain. In a forested ecosystem, top-down control means that plant
growth rates are regulated by cycles in herbivore density and respond to
increased potential for primary productivity only when released from herbivory
by wolf predation (McLaren, 1994).
Through top-down control, wolves can indirectly affect plant communities. For
example, if predators are missing, herbivore populations tend to overgraze their
habitat with adverse consequences for the ecosystem (Primack, 1993 cited in
Breitenmoser, 1998). Wolves can affect spatial organization and therefore
browsing patterns of ungulates (Ripple and Larson, 2000). Browsing patterns
and tendencies have a great impact on the vegetation and rate of regeneration.
However, it is important to note that although overgrazing may shift ecosystems
(e.g., short-grass prairie to desert), sterility is not the result. From the
perspective of the new organisms, the shift in plant communities may be
advantageous.
In North America there are also cases of strong interactions between herbivores
and plants: deer and caribou on Alaskan islands, elk in Yellowstone (Servheen
and Knight, 1993 cited in Estes, 1996), and large herbivores in North American
grasslands (Mack and Thompson, 1882 cited in Estes, 1996). Skow (1989) writes
that no wolves in Yellowstone meant too many elk and as a result, the elk were
starving by the thousands in winter die-offs because of such high densities and
the limited resources available. Understanding the structure of the ecosystem is
critical in terms environmental management. Predators are seen as balance
wheels in ecosystems. Therefore reintroduction is going to have profound effects
on species at each following trophic level. The Nez Perce living near Yellowstone
described the return of the wolf as "making the circle whole again (Chadwick,
1998)." The return of the wolf results in a cascade of effects within the circle.
The role of the wolf in its ecosystem in turn forces the question of whether the
wolf should be reintroduced after the ecosystems have changed dynamically in
the absence of wolves. In the early 1900's humans eliminated the wolf from its
ecosystem, and the system was forced to adapt and change such that new
carnivores and competitors dominated, ungulate population densities shifted,
and food chain cycles adjusted. Now, over 60 years later, the wolf has been
thrown back into the mix where it will naturally reclaim its top spot. The
ecosystem will again change to support the wolf's return, but one can't help
wondering how much can humans rightly interfere with nature, and is it too late
to try and fix the natural ecosystem where we once stole a key member?>

< The dichotomy between top-down and bottom-up forces acting on populations
and communities has informed and motivated research in ecology over its entire
history. Early practitioners emphasized the importance of bottom-up control
because of the apparent association between many species and the supply of
resources from the environment. Consumers and predators, the sources of top-
down control, were often assumed to exert little influence over the composition
of communities or the dynamics of ecosystems. Thomas Huxley’s famous
assertion in 1883 that “all the great sea fisheries, are inexhaustible; that is to say,
that nothing we do seriously affects the number of the fish” reflects the general
impression about the effects of many consumers, including humans, on
populations of their prey (“The abundance of the seas,” New York Times, 17
November 1895). Predators were considered to be agents of natural selection,
removing unfit individuals but having little impact on the numbers of their prey,
which were often thought to be capable of mounting effective defensive
strategies and prodigious reproduction. Top-down regulation became a strong
contender as an alternative to bottom-up control in the 1960s, when theoretical
and empirical evidence began to accumulate that consumers exert considerable
influence over the ecosystems they inhabit. Since then a much-richer picture has
emerged of how, where, and when top-down and bottom-up forces come into
play and of the interaction between the two. This article deals with approaches
to disentangling the effects of predators and resources on communities and
ecosystems and what they have revealed about the structure and dynamics of
nature>

R and K selection

< https://en.wikipedia.org/wiki/R/K_selection_theory>

<http://www.bio.miami.edu/tom/courses/bil160/bil160goods/16_rKselection.
html>

R selected K selected
Size Small Large
Fecundity High Low
Parental care No Yes
Lifespan Short Long
Age at maturity Early Late
Gestation Short Long
Predation High Low

# Bouts of High Low

reproduction
Metabolism High Low
Population size Large Small
Sexual No/less Yes/greater
selection/dimorphism

Bet hedginng:

<Biological bet hedging occurs when organisms suffer decreased fitness in

"normal" conditions in exchange for increased fitness in stressful conditions.
Biological bet hedging was originally proposed to explain the observation of
a seed bank, or a reservoir of ungerminated seeds in the soil. For example,
an annual plant's fitness is maximized for that year if all of its seeds germinate.
However, if a drought occurs that kills germinated plants, but not ungerminated
seeds, plants with seeds remaining in the seed bank will have a fitness
advantage. Therefore, it can be advantageous for plants to "hedge their bets" in
case of a drought by producing some seeds that germinate immediately and
other seeds that lie dormant. Other examples of biological bet hedging
include female multiple mating, foraging behavior in bumble bees, nutrient
storage in rhizobia, and bacterial persistence in the presence of antibiotics.
Bet hedging traits are, by definition, neutral or slightly deleterious in the
"normal" environment, and beneficial in a less common, often more stressful,
environment or condition. Therefore, the conditions under which a bet
hedging allele may be favored due to natural selection are slightly more
complicated than for a globally advantageous allele. First, a bet hedging mutant
must persist in the "normal" environment due to genetic drift long enough for
the alternative environment, in which the bet hedger has an advantage, to occur.
At that point selection may sweep the allele to fixation>

< http://rspb.royalsocietypublishing.org/content/276/1669/2963>
< http://rspb.royalsocietypublishing.org/content/277/1685/1153>

Strategies under competition:

-Grow fast
-survive lean times

Predicted environmental correlates: temporal stability

Suite of biotic and abiotic factors necessary for an organisms survival and
reproduction

Hutchinson's "niche" (a description of the ecological space occupied by a species)

is subtly different from the "niche" as defined by Grinnell (an ecological role, that
may or may not be actually filled by a species—see vacant niches). A niche is a
very specific segment of ecospace occupied by a single species.

< https://en.wikipedia.org/wiki/Ecological_niche>

< http://www.pnas.org/content/106/Supplement_2/19659.full>

Fundamental vs Realised Niche

Some species are not able to occupy their entire niche because of the presence or
absence of other species.
Interspecific competition occurs when two different species attempt to utilize
the same resource and there is not enough of the resource for both species.
Observation of this phenomenon in nature has led to the concepts
of fundamental and realized niches.
Fundamental niche: the set of resources a population is theoretically capable of
using under ideal conditions
Realized niche: the resources a population actually uses
The realized niche may be smaller than the fundamental niche because of
interspecific interactions such as:
-Competition
-Predation

< Fundamental and realized niche refers to the environmental conditions or

positions of different species in an ecosystem. These two niches refer to the
conditions needed for the persistence of different species and their ecological
roles in the system.
They are two different aspects and differ in many ways. Let us look at some of
the differences between a fundamental and a realized niche.
A fundamental niche can be defined as the range of environmental conditions in
which each of the species survives. The realized niche can be termed as the range
of environmental conditions in which a species is really found.
While a fundamental niche elaborates on the various roles of the species, the
realized niche elaborates on what the species actually do. The fundamental niche
refers to a range of conditions, roles, and resources under which a species
survives, grows, and reproduces. This niche describes the experiences of the
species and how it tolerates a particular condition.
The fundamental niche is larger than the realized niche. It can be said that as the
realized niche grows, the fundamental niche also grows accordingly. The realized
niche can be called as a subset of fundamental niche.
When the species comes across various interactions and pressures from others,
they are forced to go for a narrower niche, and thus the realized niche is formed.
It is in the realized niche that a species will be well adopted, and so this niche is
where the species actually exist.

1.Fundamental and realized niche refers to the environmental conditions or

positions of different species in an ecosystem.
2.A fundamental niche can be defined as the range of environmental conditions
in which each of the species survives. 3.The realized niche can be termed as the
range of environmental conditions in which a species is really found.
4.The fundamental niche is larger than the realized niche. The realized niche can
be called a subset of the fundamental niche. It can be said that as the realized
niche grows, the fundamental niche also grows accordingly.
5.While a fundamental niche elaborates on the various roles of species, the
realized niche elaborates on what the species actually do.
6.It is in the realized niche that a species will be well adopted, and so this niche is
where the species actually exist.
7.The fundamental niche refers to a range of conditions, roles, and resources
under which a species survives, grows, and reproduces.>

Bob Holt’s
< http://www.pnas.org/content/106/Supplement_2/19659.full.pdf>
Class10

Class11

Optimal foraging theory

< Optimal foraging theory (OFT) is a model that helps predict how an animal
behaves when searching for food. Although obtaining food provides the animal
with energy, searching for and capturing the food require both energy and time.
The animal wants to gain the most benefit (energy) for the lowest cost
during foraging, so that it can maximize its fitness. OFT helps predict the best
strategy that an animal can use to achieve this goal.
OFT is an ecological application of the optimality model. This theory assumes
that the most economically advantageous foraging pattern will be selected for in
a species through natural selection. When using OFT to model foraging behavior,
organisms are said to be maximizing a variable known as the currency, such as
the most food per unit time. In addition, the constraints of the environment are
other variables that must be considered. Constraints are defined as factors that
can limit the forager's ability to maximize the currency. The optimal decision
rule, or the organism's best foraging strategy, is defined as the decision that
maximizes the currency under the constraints of the environment. Identifying
the optimal decision rule is the primary goal of the OFT>

What should you eat?

When should you eat?
How should you eat?
When should you switch to something new?

 Competition
 Ecological oppurtunity
 gut symbionts
 ancestral constraints
 adaptive potential
 fitness benefits
 behavioral decisions

Meta populations, Sources and Sinks

Saccheri et al., 1998 , Nature

< http://www.life.illinois.edu/ib/451/Saccheri%20(1998).pdf>

< A metapopulation consists of a group of spatially separated populations of the

same species which interact at some level. The term metapopulation was coined
by Richard Levins in 1969 to describe a model of population dynamics of insect
pests in agricultural fields, but the idea has been most broadly applied to species
in naturally or artificially fragmented habitats. In Levins' own words, it consists
of "a population of populations".
A metapopulation is generally considered to consist of several distinct
populations together with areas of suitable habitat which are currently
unoccupied. In classical metapopulation theory, each population cycles in
relative independence of the other populations and eventually goes extinct as a
consequence of demographic stochasticity (fluctuations in population size due to
random demographicevents); the smaller the population, the more chances of
inbreeding depression and prone to extinction.
Although individual populations have finite life-spans, the metapopulation as a
whole is often stable because immigrants from one population (which may, for
example, be experiencing a population boom) are likely to re-colonize habitat
which has been left open by the extinction of another population. They may also
emigrate to a small population and rescue that population from extinction
(called the rescue effect). Such a rescue effect may occur because declining
populations leave niche opportunities open to the "rescuers".
The development of metapopulation theory, in conjunction with the
development of source-sink dynamics, emphasised the importance of
connectivity between seemingly isolated populations. Although no single
population may be able to guarantee the long-term survival of a given species,
the combined effect of many populations may be able to do this.
Metapopulation theory was first developed for terrestrial ecosystems, and
subsequently applied to the marine realm. In fisheries science, the term "sub-
population" is equivalent to the metapopulation science term "local population".
Most marine examples are provided by relatively sedentary species occupying
discrete patches of habitat, with both local recruitment and recruitment from
other local populations in the larger metapopulation. Kritzer & Sale have argued
against strict application of the metapopulation definitional criteria that
extinction risks to local populations must be non-negligible.
Finnish biologist Ilkka Hanski of the University of Helsinki was an important
contributor to metapopulation theory.>

< http://www.helsinki.fi/~ihanski/Articles/Biol_J_Linn_Soc_42.pdf>

< http://www.helsinki.fi/~ihanski/Articles/Nature%201998%20Hanski.pdf>

< https://www.jstor.org/stable/pdf/2463046.pdf>

< http://www.annzool.net/PDF/anzf42/anzf42-347.pdf>

Interspecific competition

Lotka-Volterra equations:

< http://www.tiem.utk.edu/~gross/bioed/bealsmodules/competition.html>

< http://www.math.harvard.edu/library/sternberg/slides/11809LV.pdf>
Competitive exclusion

< In ecology, the competitive exclusion principle, sometimes referred to

as Gause's law of competitive exclusion or just Gause's law, is a proposition that
states that two speciescompeting for the same resource cannot coexist at
constant population values, if other ecological factors remain constant. When
one species has even the slightest advantage or edge over another then the one
with the advantage will dominate in the long term. One of the two competitors
will always overcome the other, leading to either the extinction of this
competitor or an evolutionary or behavioral shift toward a different ecological
niche. The principle has been paraphrased into the maxim "complete
competitors cannot coexist">

<http://lubmengelab.oregonstate.edu/sites/default/files/BAMpubs/Menge%20
1972%20Ecology.pdf>

< http://www.asnailsodyssey.com/LEARNABOUT/SEASTAR/seasComm.php>

Interference competition vs exploitative competition

< In exploitation competition, organisms use up resources directly. Once used,

the resource is no longer available for other species to use. In interference
competition, one organism prevents other organisms from using the resource. Of
the two mechanisms, exploitation competition is the more common>

closely related species often compete more: niche conservatism?

Ecological ratios and coexistence

1.2X difference needed for co-existence of sympatric species

Character displacement refers to the phenomenon where differences among

similar species whose distributions overlap geographically are accentuated in
regions where the species co-occur, but are minimized or lost where the species'
distributions do not overlap.

Competitive release occurs when one of two species competing for the same
resource disappears, thereby allowing the remaining competitor to utilize the
resource more fully than it could in the presence of the first species.

Niche conservatism :
John Wiens et al., 2010, Ecol.Letters
https://damschenlab.zoology.wisc.edu/Pubs/Wiens%20et%20al.%202010.pdf

Adaptive radiation in Cichlids in African Lakes

< http://www.sciencedirect.com/science/article/pii/S0960982207017046>
< https://www.hindawi.com/journals/ijeb/2011/620754/>

Darwins finches on Galapagos

< http://www.nature.com/news/2009/091116/full/news.2009.1089.html>

< http://bioscience.oxfordjournals.org/content/53/10/965.full>

<http://www.d.umn.edu/~jetterso/IBS8012/documents/EvolCharacterdisplace
mentDarwinfinchGandG2007.pdf>

Character diplacement: Less competitive species displaces character

< https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279117/pdf/nihms-
354836.pdf>

Competition affects multiple axes

Lopez-Fernandez et al. 2013, Evolution

< http://onlinelibrary.wiley.com/doi/10.1111/evo.12038/epdf>
Class12

Predation

Yoshida et al, 2007 , Plos Biology

<
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050235>

Tritrophic interaction vs Ditrophic interaction cycles … syncing across trophic

levels

R selected species used for most experimental evolution studies

Classic prey predator cycles
Coevolution alters dynamics

Multiple prey options drive one to extinction (rarer species go extinct)

Single prey population drive the predator to extinction

Parasitism

Yanoviak at al., 2008, American Naturalist

< http://www.journals.uchicago.edu/doi/pdfplus/10.1086/528968>

< https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674981/pdf/jane0084-
0723.pdf>

Barbero et al. 2009 Science

<http://sci-hub.io/10.1126/science.1163583>

Host parasite interactions

Parasites may manipulate behaviour of host :

<https://www.newscientist.com/article/dn22599-parasite-makes-mice-
fearless-by-hijacking-immune-cells/>

Mutualism/Cooperation

Endosymbiosis
Gut-microbiome
Pollination
Limiting factors- Eg. Abiotic
Competitive superiority vs predator/parasite susceptibility
Environmental fluctuations (Eg. Mammals could be active through the night due
to homeothermy , mammals could swallow and breathe simultaneously unlike
reptiles(seasonally fluctuating fitness))
Temporal niche partitioning
Microhabitats

Intra and inter species continuum

Niche partitioning , competition, coexistence

Intraspecific mutualism : Sexual reproduction

Generalist vs specialist evolution

Frequency and density depenence

< https://parasiteecology.wordpress.com/2014/02/26/parasite-transmission-
density-dependent-frequency-dependent-or-neither/>

< https://parasiteecology.wordpress.com/2013/10/17/density-dependent-vs-
frequency-dependent-disease-transmission/>

< https://en.wikipedia.org/wiki/Density_dependence>

< https://www.boundless.com/biology/textbooks/boundless-biology-
textbook/population-and-community-ecology-45/environmental-limits-to-
population-growth-251/density-dependent-and-density-independent-
population-regulation-931-12187/>

< https://en.wikipedia.org/wiki/Frequency-dependent_selection>

< Apostatic selection is negative frequency-dependent selection. It describes the

survival of individual prey animals that are different (through mutation) from
their species in a way that makes it more likely for them to be ignored by
their predators. It operates on polymorphic species, species which have different
forms. In negative frequency-dependent selection, the common forms of a
species are preyed on more than the rarer forms, giving the rare forms
a selective advantage in the population.
Apostatic selection was used in 1962 by Bryan Clarke in reference to predation
on polymorphic grove snails and since then it has been used interchangeably
with negative frequency-dependent selection.
Apostatic selection can also apply to the predator if the predator has various
morphs. There are multiple concepts that are closely linked with apostatic
selection. One is the idea of prey switching, which is another term used to look at
a different aspect of the same phenomenon, as well as the concept of a 'search
image'. Apostatic selection is important in evolution because it can sustain a
stable equilibrium of morph frequencies, and hence maintains large amounts of
genetic diversity in natural populations>

< https://en.wikipedia.org/wiki/Apostatic_selection>

Multiple selection pressures

Population regulation from various sources

Niche conservatism ~ Phylogenetic inertia

< The term phylogenetic niche conservatism has seen increasing use in recent
years in the scientific literature, though the exact definition has been a matter of
some contention. Fundamentally, phylogenetic niche conservatism refers to the
tendency of species to retain their ancestral traits. When defined as such,
phylogenetic niche conservatism is therefore nearly synonymous
with phylogenetic signal. The point of contention is whether or not
"conservatism" refers simply to the tendency of species to resemble their
ancestors, or implies that "closely related species are more similar than expected
based on phylogenetic relationships".If the latter interpretation is employed,
then phylogenetic niche conservatism can be seen as an extreme case of
phylogenetic signal, and implies that processes that prevent divergence are in
operation in the lineage under consideration. Despite efforts by Losos to end this
habit, however, the former interpretation appears to frequently motivate
scientific research. In this case, phylogenetic niche conservatism might best be
considered a form of phylogenetic signal reserved for traits with broad-scale
ecological ramifications (i.e. related to the Hutchinsonian niche). Thus,
phylogenetic niche conservatism is usually invoked with regards to closely
related species occurring in similar environments>

< The degree to which plants and animals retain their ancestral ecological traits
and environmental distributions ('niche conservatism') is hotly debated, in part
because of its relevance to the fate of modern species facing climate change. A
tendency towards conservatism has been demonstrated previously on the local
and regional scales, and now a study of more than 11,000 plant species from
across the Southern Hemisphere confirms a similar phenomenon on a global
scale. Only 3.6% of the evolutionary divergences observed involved a shift of
biome, suggesting that many species have only a limited capacity to adapt to new
biomes, making them particularly susceptible to ecological change>
< http://www.nature.com/nature/journal/v458/n7239/pdf/nature07764.pdf>

< http://www.sciencedirect.com/science/article/pii/S1369848610001068>

< https://en.wikipedia.org/wiki/Phylogenetic_inertia>

Communities

Pioneer species

Lichens as pioneer species

Ecological succession and climax communities

Community assembly dispersal vs selection

Neutral theory of biodiversity

< https://en.wikipedia.org/wiki/Unified_neutral_theory_of_biodiversity>

< http://link.springer.com/article/10.1007/s11515-008-0008-z>

< http://press.princeton.edu/chapters/s7105.pdf>

< http://bioscience.oxfordjournals.org/content/53/2/124.full>

Community assembly rules

< https://en.wikipedia.org/wiki/Assembly_rules>

< http://www.annualreviews.org/doi/pdf/10.1146/annurev-ecolsys-110411-
160411>

< https://sites.lifesci.ucla.edu/eeb-kraft/wp-
content/uploads/sites/56/2016/01/Kraft_Ackerly_2014_assembly_chapter.pdf>

< https://usucommassembly.wordpress.com/2013/10/09/stochastic-and-
deterministic-mechanisms-of-assembly/>

< https://usucommassembly.files.wordpress.com/2013/09/vellend-2010-
conceptual-sysnthesis-of-comm-ecol.pdf>

< http://mmbr.asm.org/content/77/3/342.full.pdf+html>
< https://www.scientificamerican.com/article/interview-with-steve-hubb/>

<
http://www.scholarpedia.org/article/Unified_neutral_theory_of_biodiversity_an
d_biogeography>

<http://www.cfbiodiv.org/userfiles/2011_TREE_Rosindell_The%20Unified%20
Neutral%20Theory%20of%20Biodiversity%20and%20Biogeography%20at%2
0Age%20Ten.pdf>

Habitat selection vs random dispersal (Steve Hubbel, BCI forest plots)

< https://en.wikipedia.org/wiki/Barro_Colorado_Island>

Ecological equivalence; Turnover rates

Keystone species

< http://nationalgeographic.org/encyclopedia/keystone-species/>

Ecological equivalence
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759543/pdf/pone.0007460
.pdf>

< ecological equivalents Unrelated organisms that occupy similar habitats and
resemble each other. Ecological equivalents result from convergent evolution.
For example, sharks (fish) and dolphins (mammals) live in a marine habitat and
superficially resemble each other. "ecological equivalents.">

< https://www.ncbi.nlm.nih.gov/pubmed/16869413>

Interaction Networks

Cambrian food web (Burgess Shale)

<http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060102
>

Class 13

Refer
The American Naturalist: Homage to Santa Rosalia or Why are there so many
kinds of animals by G F Hutchinson 1959
< http://courses.pbsci.ucsc.edu/eeb/bioe108/wp-
content/uploads/2016/01/Homage-to-Santa-Rosalia.pdf>

< http://www.kharms.biology.lsu.edu/AHernandez_Re_Hutchinson.pdf>

What are species?

Biological species concept (Dobzhansky, Mayr.. post 1930)
Groups of actually or potentially interbreeding natural populations that are
reproductively isolated from other such groups
Restricted to sexually reproducing organisms only- Problems defining species in
Prokaryotes and certain groups of pants; isolated populations in different
regions; evolutionary terms( where do you daw the line?)- how much genomic
distinction and difference in critical characters muct exist?

Phylogenetic species concept (1980s onwards)-

Smallest monophyletic group with diagnosable characters and clear ancestor-
descendent relationships

What is a diagnostic differentiating marker- from phenotypic to molecular

markers

Variation may be distriuted among individuals, populations, subspecies or

species. This is another biological continuum where drawing of a line at species
may be arbitrary , even theoretically .
Anagenesis and cladogenesis may be contiguous processes

Any divergence results from reproductive barriers, which may be due to intrinsic
(biological, perhaps population level processes) and/or extrinsic (eg. Abiotic,
such as geographical isolation) factors

Geographic isolation has historically been considered the most important form
of isolation that has resulted in most biodiversity on earth. Three important
speciation concepts based on geography:-allopatric speciation; parapatric
speciation; sympatric speciation

** Plasmids can measure upto a third of the entire genome in bacteria- many of
which define the bacterium’s ecology and phenotypic characteristics-and can
even be exchanged; how does one then differentiate between different species

Geographical modes of speciation

Allopatric speciation: Vicariance. Often considered the most parsimonious mode
of separation. This can happen under selection or drift. Examples:
<Vicariance (from Latin vicarius, derived from vicis; change, alternation, stead)
is a process by which the geographical range of an individual taxon, or a
whole biota, is split into discontinuous parts by the formation of a physical or
biotic barrier to gene flow or dispersal
Vicariance of whole biotas occurs following large-scale geophysical events such
as the uplift of a mountain chain, or the separation of continents. A well-
documented example of vicariance in the marine realm was the formation of
the Isthmus of Panama about 3 million years ago, which resulted in the evolution
of related (geminate) species pairs on the Atlantic and Pacific sides. Another well
known example of vicariance in continental ecosystems was the separation of
South America from Africa about 100 million years ago, which isolated many
taxa on either side of the newly forming South Atlantic.
Historically vicariance has been contrasted with biological dispersal as a means
of explaining the patterns of distribution among related species. For example, the
occurrence of some plant genera in both Africa and Australia may be explained in
one of two different ways:
The genus may have a Gondwanan origin; that is, it may have arisen before
Africa and Australia separated into distinct continents. What was once a
contiguous range was broken into a widely disjunct distribution by continental
drift; this is an example of vicariance.
The genus may be much younger, having arisen on one continent, and
subsequently established populations on the other by long-distance seed
dispersal.
Once a species has been split by vicariance into multiple populations with little
to no genetic exchange, the populations begin to driftindependently. Thus
vicariance is a necessary precursor to allopatric speciation.
In biogeography, vicariance can be contrasted with geodispersal, which is the
erosion of barriers to gene flow and biological dispersal. The relative importance
of these different factors has long been a subject of debate.
In contrast to 'geographic' vicariance (see above) where physical or biotic
barriers lead to the fragmentation of a population or taxon, ecological
vicariance is the process by which an initially continuous and often widespread
population (or taxon) becomes fragmented through ecological barriers.>

Parapatric speciation
“Speciation in neighbourhood “. Clinal variation.

Cichlid species pairs along water depth in African Lakes.

< http://evolution.berkeley.edu/evolibrary/news/090301_cichlidspeciation>

< http://www.nature.com/nature/journal/v439/n7077/pdf/nature04325.pdf>
<
http://bbcd.bio.uniroma1.it/clone_bbcd/sites/default/files/file%20lezioni/barl
uenga%20%26%20meyer%202004.pdf>

< http://ac.els-cdn.com/S0960982206014102/1-s2.0-S0960982206014102-
main.pdf?_tid=b360977a-b163-11e6-9467-
00000aacb35f&acdnat=1479895425_f985c08125adcd0a51790854a4fe1903>

< http://ac.els-cdn.com/S0960982212011475/1-s2.0-S0960982212011475-
main.pdf?_tid=bcc8c47c-b163-11e6-bb73-
00000aacb362&acdnat=1479895440_9c3626f2364613a71223613f16f8227e>

< Clinal variation : A gradual change in an inherited characteristic across the

geographic range of a species, usually correlated with an environmental
transition such as altitude, temperature, or moisture>

Speciation can occur in the space of a few hundred generations and not always
take thousands of generations in different conditions

Small ecological changes can have vast changes on speciation

Sympatric speciation – “Speciation in house” . Rhagoletis fruit flies (hawthorn

and apple maggots); hybrid species
-happens necessarily under selection
-historically the most difficult mode of speciation to explain , resistance from
theoretical biologists
-problems of continued gene flow

< http://www.natureworldnews.com/articles/17860/20151030/speciation-
fruit-fly-evolution-causes-cascading-changes-wasp-species.htm>

< http://www.nature.com/nature/journal/v407/n6805/pdf/407739a0.pdf>

 Incipient species vs sympatric speciation

< Incipient speciation is the evolutionary process in which new species form but
are still capable of interbreeding; it can be the first part of the larger process of
speciation>

Hybrid Zones : Hybridization and introgression

<Introgression: the transfer of genetic information from one species to another
as a result of hybridization between them and repeated backcrossing>

< https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2173880/>

< There is strong evidence for the introgression of Neanderthal genes and
Denisovan genes into parts of the modern human gene pool.
Further information: Archaic human admixture with modern humans
One important example of introgression has been observed in butterfly mimicry.
Genus Heliconius has been studied. This genus includes 43 species and many
races with different color patterns. Congeners exhibiting overlapping
distributions show similar color patterns. The distribution of the subspecies H.
melpomene amaryllis and H. melpomene timareta ssp. nov. overlap. Using the
ABBA/BABA test, some researchers have observed that there is ≈2-5%
introgression between the pair of subspecies. It is important to know that this is
not random introgression. They saw important introgression in chromosomes
15 and 18, where important mimicry loci are located (loci B/D and N/Yb). They
compared both subspecies with H. melpomene agalope, which is a subspecies
near H. melpomene amaryllis in entire genome trees. The result of this
experiment was that there is no relation between those two species and H.
melpomene agalope in the loci B/D and N/Yb. Moreover, they performed the
same experiment with two other species with overlapping distributions, H.
timareta florencia and H. melpomene agalope. They demonstrated introgression
between the two taxa, especially in the loci B/D and N/Yb. Finally, they
concluded their experiments with sliding-window phylogenetic analyses,
estimating different phylogenetic trees depending on the different regions of the
loci. When a locus is important in the color pattern expression, there is a close
phylogenetic relationship between the species. When the locus is not important
in the color pattern expression, the two species are phylogenetically distant
because there is no introgression at such loci.
Introgression could be an important conservation problem for wild species
through hybridisation, for instance, between wild and domestic cats or
among wild canids and domestic dogs.[15] Another important example has been
studied by Arnold & Bennett 1993: iris species from southern Louisiana>

< http://link.springer.com/article/10.1007/s12080-011-0118-0>

< http://sci-hub.io/10.1111/j.1469-185X.1953.tb01379.x>

< http://krishikosh.egranth.ac.in/bitstream/1/2047200/1/ANAND-29.pdf>

< file:///Users/rishav/Downloads/ncomms13158.pdf>

< https://www.sciencedaily.com/releases/2012/08/120807104820.htm>

< http://www.nytimes.com/2007/01/09/science/09bison.html>
Class 14

Isolation by distance and Ring species

Populations may diverge in space as a product of local selection ( eg. Clinal

variation)

Populations of ring species – may interbreed with neighbouring species except in

areas where the ring closes
Eg. Asian leaf warblers, Phylloscopus trochiloides and N american salamanders
Ensantina eschscholtzii

< In biology, a ring species is a connected series of neighboring populations that

can interbreed with relatively closely related populations, but for which there
exist at least two "end" populations in the series that are too distantly related to
interbreed

A ring species is a situation in which two populations which do not interbreed

are living in the same region and connected by a geographic ring of populations
that can interbreed.
Famous examples of ring species are the herring and lesser black-backed gulls in
northern Europe and the Ensatina salamanders of California.
A ring species can be best imagined like this:
Consider a species that is geographically distributed in a straight line from east
to west across America: it is possible that the forms in the east and west are so
different that they could not interbreed. Now imagine taking the line and
bending it into a circle, such that the end points (formerly in the east and west)
come to overlap in space.
If they do not interbreed then the geographic distribution of the species will be
in the shape of a ring, and they will be 'ring species': the extreme forms do not
interbreed in the region of overlap. A ring species has an almost continuous set
of intermediates between two distinct species, and these intermediates happen
to be arranged in a ring. At most points in the ring, there is only one species; but
there are two where the end-points meet.
The image opposite is of the herring and lesser black-backed gulls in northern
Europe: while they are two reproductively isolated species, there is a continuous
set of interbreeding forms between them.
>

< http://www.actionbioscience.org/evolution/irwin.html>

< http://www.pnas.org/content/110/13/5080.full.pdf>

< http://www.nature.com/nature/journal/v409/n6818/pdf/409333a0.pdf>

< https://www.zoology.ubc.ca/~irwin/PDFs/IrwinIrwin%26Price2001.pdf>
Reproductive barriers

Dobzhansky : prezygotic and postzygotic reproductive barriers

Prezygotic barriers-

 Ecological isolation(different habitats, breeding phenologies)

 Behavioral isolation (contact or copulation difficult eg. Courtship displays,

pheromones)

 Post mating isolation (mechanical isolation from lock and key mechanism,
gametic isolation)

Postzygotc isolating mechanisms:

o Hybrid inviability (gametic incompatibility)

o Hybrid sterility (mules)

o Ecological inviability (hybrids in adaptive valleys)

o Endosymbiont incompatibility (genotype-environment effects)

o Reproductive incompatibility with either parent or siblings

Species differences

What kind of genetic differences separate species?

(few major-effect vs many small-effect)

Species difference arise as-

-by-product of neutral accumulated mutations
-divergent adaptation
-adaptive evolution of isolating mechanisms to prevent fitness lost via hybrids
(reinforcement: pre zygotic isolating mechanism)

< http://www.nature.com/hdy/journal/v83/n5/full/6886320a.html>

< https://whyevolutionistrue.wordpress.com/2010/12/08/reinforcement-and-
the-origin-of-species/>

<
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC535571/pdf/pbio.0020420.pd
f>

< Reinforcement is the process by which natural selection increases

reproductive isolation.
Reinforcement can occur as follows:
When two populations which have been kept apart, come back into contact, the
reproductive isolation between them might be complete or incomplete.
If it is complete, speciation has occurred.
If it is incomplete, hybrids would be produced.
If the hybrids had lower fitness than either parental form, selection would act to
increase the reproductive isolation because each form would do better not to
mate with the other and form the disadvantageous hybrids. Speciation might
then be speeded up by favoring genes which caused individuals to avoid mating
with hybrids.
Reinforcement is a necessary requirement for both the parapatric and sympatric
theories of speciation: it is the process by which a hybrid zone develops into a
full species barrier.
• Secondary reinforcement:
Reinforcement is known as secondary reinforcement if the reproductive
isolation has partly evolved allopatrically, and is then reinforced when the two
populations come into secondary contact. Reinforcement could occur whenever
two forms coexist, and the hybrids between them have lower fitness than crosses
within each form.
• Artificial selection experiments:
Reinforcement can be simulated by artificial selection experiments. By
continually selecting for assortative mating it has been possible to obtain
significant changes in prezygotic isolation mechanisms. However, the theoretical
conditions for speciation to take place by reinforcement are difficult and it is
controversial whether the process takes place in nature>

< http://ac.els-cdn.com/S096098221401046X/1-s2.0-S096098221401046X-
main.pdf?_tid=8306aeca-b2f3-11e6-98ae-
00000aab0f27&acdnat=1480067142_9e472434f87cdbca2162864ae5f960a6>
Gradual accumulation of Differences

Wu and Ting (2004, Nat Rev Gen)

< https://www.ncbi.nlm.nih.gov/pmc/articles/PMC514461/>

< http://sci-hub.cc/10.1038/nrg2718>

Hybrid incompatibility

Presgraves (2010, Nat Rev Gen)

< https://www.ncbi.nlm.nih.gov/pubmed/20051985>-

Nup96 adaptive evolution

Nup96,98-muclear pore complex

< http://mbe.oxfordjournals.org/content/24/1/306.long>

Snowball effect Moyle and Nakazato 2010, Science

<
http://www.nature.com/news/2010/100916/full/news.2010.476.html?s=news
_rss>

< http://sci-hub.cc/10.1126/science.1193063> =

< https://www.ncbi.nlm.nih.gov/pubmed/20847271>

Polyploidy and speciation

Wood et al 2009 PNAS

< http://www.pnas.org/content/106/33/13875.full.pdf>

Hybridization and introgression

Kunte et al 2011, Plos Genetics
Haldane’s Rule : Wallace’s Reinforcement

<
https://cienciasbiologicas.uniandes.edu.co/genetica/archivos/uploads/22.pdf>

<
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207414/pdf/ge14331485.pd
f>

Haldane’s Rule: among hybrids, the heterogametic sex is more likely to be

inviable or infertile

Reinforcement : reproductive isolation to avoid interbreeding that leads to

inviable ot infertile hybrids

Prezygotic isolation more common in sympatric species, postzygotic more

common in allopatric species
-Coyne and Corr 1989,1997

Speciation Genes

Nosil and Schluter (2011, Trends in Ecol and Evol)

< http://ac.els-cdn.com/S0169534711000024/1-s2.0-S0169534711000024-
main.pdf?_tid=c1c6bd38-b2fa-11e6-adb3-
00000aacb35e&acdnat=1480070254_75b151983cd9e51f362e6393155544ee>

< https://en.wikipedia.org/wiki/Coalescent_theory>

Class 15

Population genetics and Molecular evolution

First principles of population genetics largaely determine the tempo and mode of
molecular evolution

Drift, population size and mode of reproduction (seual vs asexual) determine the
spread of mutations, heterozygosity and overall composition of genomes as a
neutral process

Strength of selection, response to selection, standing genetic variation, genomic

architecture, (Eg. Number of chromosomes, inversions , centromeres) ets
determine molecular evolution under selection
Mutation-selection balance

Genotype : single base/ large collection of molecular markers

Genetic variation is the fuel for evolution: tremendous standing genetic variation
for almost any trait in natural population-historically believed to be low
-allozymes and sequencing changed this view (Lewontin)

Gene duplication and evolution

Gene duplication-
Unequal crossing over
Retrotransposition
Replication slippage
Polyploidy- genome duplication (plants and yeast)

Homologs, orthologs and paralogs

Fate of dupicated genes:

Neofunctionalization : adaptive process, paralogs evolve new functions. Anti
freeze zoarcid fish –Sialic acis synthase (SAS) gene

< The evolution of the antifreeze protein in the Antarctic zoarcid fish provides a
prime example of Neofunctionalization after gene duplication. In the case of the
Antarctic zoarcid fish type III antifreeze protein gene diverged from a parologus
copy of sialic acid synthase (SAS) gene. The ancestral SAS gene was found to have
both sialic acid synthase and rudimentary ice-binding functionalities. After
duplication one of the paralogs began to accumulate mutations that lead to the
replacement of SAS domains of the gene allowing for further development and
optimization of the antifreeze functionality. The new gene is now capable of
noncolligative freezing-point depression, and thus is neofunctionalized. This
specialization allows Antarctic zoarcid fish to survive in the frigid temperatures
of the Antarctic Seas>

< http://www.pnas.org/content/107/50/21593.full.pdf>

Subfunctionalization: paralogs specialize on parts- hox genes- haemoglobin

< Human hemoglobin provides a variety of subfunctionalization examples. For

instance, the gene for hemoglobin α-chain is undoubtedly derived from a
duplicate copy of hemoglobin β-chain. However, neither chain can function
independently to form a monomeric hemoglobin molecule; that is a molecule
consisting entirely of α-chains or entirely of β-chains. Conversely, hemoglobin
consists of both α and β chains; with α2β2 being among the most efficient forms
of hemoglobin in the human genome. This is a prime example of
subfunctionalization. Another good example is the emergence of fetal
hemoglobin from embryonic hemoglobin after duplication of the hemoglobin γ-
chain. This example of subfunctionalization illustrates how different forms of
hemoglobin are present at various developmental stages. In fact, there is distinct
hemoglobin at each developmental stage:ζ2 ε2 and α 2ε2 in the embryo, α2γ2 in
the fetus, and α2β2 and α2δ2 in adults. Each type of hemoglobin has advantages
that are particular to the developmental stage in which it thrives. For example,
embryonic and fetal hemoglobin have higher oxygen affinity than adult
hemoglobin giving them improved functionality in hypoxic environments such as
the uterus>

< Specialization is a unique model of subfunctionalization, in which paralogs

divide into various areas of specialty rather than function. In this model both
gene copies perform exactly the same ancestral function. For instance, while the
ancestral gene may have performed its function in all tissues, developmental
stage, and environmental conditions, the paralogous genes become specialists,
dividing themselves among different tissues, developmental stages, and
environmental conditions. For example, if the ancestral gene is responsible for
both digestive and lymphatic regulatory processes, after gene duplication one of
the paralogs would claim responsibility for lymphatic regulation and the other
for digestive regulation. Specialization is also unique in the fact that it is a
positive rather than neutral mutation process. When a gene specializes among
different tissues, developmental stages, or environmental conditions it acquires
an improvement in function. Isozymes are a good example of this because they
are gene products of paralogs that catalyze the same biochemical reaction.
However, different members have evolved particular adaptations to different
tissues or different developmental stages that enhance the physiological fine-
tuning of the cell>

Pseudogenes: ghost genes- may play a regulatory function??

https://en.wikipedia.org/wiki/Pseudogene#Examples

< http://pseudogene.org/background.php>

< http://naturalselection.0catch.com/Files/pseudogenes.html>

< http://www.nature.com/scitable/topicpage/origins-of-new-genes-and-
pseudogenes-835>

Loss of a copy because of cost of replication

Mobile genetic elements

B chromosomes

< In addition to the normal karyotype, wild populations of many animal, plant,
and fungi speciescontain B chromosomes (also known
as supernumerary or accessory chromosomes). By definition,
these chromosomes are not essential for the life of a species, and are lacking in
some (usually most) of the individuals. Thus a population would consist of
individuals with 0, 1, 2, 3 (etc.) supernumeraries.
Most B chromosomes are mainly or entirely heterochromatic (and so would be
largely non-coding), but some, such as the B chromosomes of maize, contain
sizeable euchromaticsegments. In general it seems unlikely that
supernumeraries would persist in a species unless there was some positive
adaptive advantage, which in a few cases has been identified. For instance, the
British grasshopper Myrmeleotettix maculatus has two structural types of B
chromosomes: metacentrics and submetacentrics. The supernumeraries, which
have a satellite DNA, occur in warm, dry environments, and are scarce or absent
in humid, cooler localities.
B chromosomes are not to be confused with marker chromosomes or additional
copies of normal chromosomes as they occur in Trisomies>

<
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692730/pdf/10724453.pdf>

Transposable elements

Lateral gene transfer

Repetitive elements

Evo-Devo is the holy grail of how genotypes relate to phenotypes as a function of

genetic and environmental regulations during development

Gene families: hox genes and the evolution of the animal body plan from worms
and lies to mice

Developmental pathways: sometimes even small tweaks in the timing and

activity placement of hox genes dramatically alter the body plan

The altered body plans may be selectively favoured in different environmental

conditions or selection regimes: ‘Hopeful monsters’
Class 16

Modularity (compartmentalization) and evolution of the animal body plans: fly

limbs , six legged vs eight legged insects, lepidopteran caterpillars vs sawfly
larvae, eye spot development on butterfly wings

Serial homology : eg. Eye spot is a homologous structure

Module duplication and compartmentalization

Haeckel’s Biogenetic Law

Ontogeny recapitulates phylogeny

Heterochrony

A comparative approach to study development

< In evolutionary developmental biology, heterochrony is defined as a

developmental change in the timing or rate of events, leading to changes in size
and shape. There are two main components, namely (i) the onset and offset of a
particular process, and (ii) the rate at which the process operates>

< Heterochrony can be defined as “change to the timing or rate of developmental

events, relative to the same events in the ancestor” (Alberch et al. 1979;
McKinney and McNamara 1991). All organisms have an ontogeny. This is their
life history, from the time of conception until death. While organisms increase in
size as they grow, from an initial egg, through larval or embryonic stages, to
juvenile and then adult stages, they also change in shape. You, for instance, look
very different now from what you looked like when you were born, for the
simple reason that many parts of your body have changed in relative shape
during your ontogeny. Most organisms have a finite period of growth, which
usually ends at the onset of sexual maturity, both size and shape slowing down
markedly, or stopping. Within populations of a single species, individuals do not
all grow and develop at the same rate or for the same duration; individuals grow
at slightly different rates and for slightly different durations. The same holds for
many species, where, between closely related species, the main morphological
differences arise from variations to the rate and duration of growth.
Certain parts of a single individual may grow for relatively different lengths of
time and at different relative rates. Thus, in many vertebrates, for instance, the
rate of growth of the head is relatively greater than growth of the trunk or limbs
during the embryonic phase of growth>

< http://link.springer.com/article/10.1007/s12052-012-0420-3>

Developmental onset and termination of a particular process are shifted but the
developmental rate remains constant ( predisplacement and post displacement)
-growth rate increases but the developmental onset and terminations are
proportionally decreased ( acceleration and neoteny)

-developmetal window is prolonged

the developmental window is prolonged but the rate remains constant (brain
and head growth in chimps and humans

both developmental window and growth rate increases hypermorphosis and

progenesis

external gills in juvenile salamanders are retained in adult axolotl

< Predisplacement and postdisplacement: If a developmental process, such as

the growth of a tail in the embryo of "species A", starts earlier and ends earlier
than that of "species B", but the rate of growth is the same for both, the final
result may basically be the same, although the tail of species A develops earlier
than the one of species B. The earlier exhibits predisplacement, and the later
species exhibits postdisplacement.
Neoteny: if the rate of growth is increased, and the time between the start and
end of development is decreased proportionally, the tail will end up the same
size. The species with faster growth exhibits acceleration, and the species with
slower exhibits neoteny.
Hypermorphosis: if the end of development is delayed and the rate is unaffected,
development progresses further, and the tail will be also larger. The species that
develops further exhibits hypermorphosis, and the species that does not develop
as far exhibits progenesis>

< http://izt.ciens.ucv.ve/ecologia/Archivos/References-I-biol/books-
biol/Biology/Briggs_Crowther-Paleobiology_a_Synthesis/Pages%20111-
130,%20Section%202.pdf>

Allometry

Geometric scaling of body parts in relation to body size, often represented as a

power law or log values for non-linear relationships

Y=ax+b or log y = alog x + log b or y=bxa

where y is organ size, x is body size and b is the y intercept, and a is the slope of the line or the allometric
coefficient

isometry or equal growth i.e., m or alpha =1

unequal growth, i. m<1 (negative allometry) or >1 (positive allometry)
Changes in the intercept and slope of relationships (lengths of forelimbs and
hindlimbs of human vs chimp vs bat)
Allometry and developmental changes ( heterochrony” developmental windows
and growth rates)
Allometric relationships are important not only in external traits but also in
physiology

Spatially and Temporally Variable Environments

Environments in which organisms live and evolve is variable because of the

latitudinal , altitudinal , local and temporal (daily, seasonal, yearly) variation in
temperature water, food availability etc

Evolutionary response to variation is based on-

Mean and variance of variable conditions
Frequency or periodicity of climatic or biotic oscillations (daily , seasonal)
Predictability (onset of monsoons, spring etc)

Organisms adapt with-

Habitat selection
Homeostasis
Local movements- migrations (monarchs); hibernation (polar bear)
Plasticity including behavioral (eg food intake), physiological, seasonal
polyphenism

Phenotype tolerance Environment Evolutionary outcome

Broad Fine grained Intermediate generalist
phenotype
Broad Coarse grained Intermediate generalist
phenotype
Narrow Fine grained One or more specialist
phenotype
Narrow Coarse grained Mixture of specialist
phenotypes

Phenotypic plasticity

Ability of the same genome to express different phenotypes

Papilio polytes green/brown pupae depending on substrate

Daphnai water fleas spike/helmet depending on predator presence
White Pieridae butterflies are darker in spring and monsoon broods than in
summer broods
Regular vs cannibalistic larvae in tiger salamanders

Specific alternative phenotype expressed is the reaction norm. These are often
threshold dependent
-intrinsic / physiological chemical cues that triger change in a normally buffered
environment

Variable DSFs in Chiladespandava

Kunte and Tiple (2009, NewsLep, Soc); Tiple et al (2009, Curr. Sci)

< Apostatic selection is negative frequency-dependent selection. It describes the

survival of individual prey animals that are different (through mutation) from
their species in a way that makes it more likely for them to be ignored by
their predators. It operates on polymorphic species, species which have different
forms. In negative frequency-dependent selection, the common forms of a
species are preyed on more than the rarer forms, giving the rare forms
a selective advantage in the population.
Apostatic selection was used in 1962 by Bryan Clarke in reference to predation
on polymorphic grove snails and since then it has been used interchangeably
with negative frequency-dependent selection.
Apostatic selection can also apply to the predator if the predator has various
morphs. There are multiple concepts that are closely linked with apostatic
selection. One is the idea of prey switching, which is another term used to look at
a different aspect of the same phenomenon, as well as the concept of a 'search
image'. Apostatic selection is important in evolution because it can sustain a
stable equilibrium of morph frequencies, and hence maintains large amounts of
genetic diversity in natural populations

Prey switching is the concept that predators sometimes switch from primary
prey to an alternative food source for various reasons. This is related to apostatic
selection because when a rare morph is being selected for, it is going to increase
in abundance in a specific population until it becomes recognized by a predator.
Prey switching, therefore, seems to be a result of apostatic selection. Prey
switching is related to prey preference as well as the abundance of the prey

The concept of a ‘search image’ in predatory birds is that they only look for a
single cryptic food even though there are other cryptic alternatives that may be
as equally beneficial. A search image defined by Luuk Tinbergen as a typical
image of a prey that a predator can remember and use to spot prey when that
image is common. Having a search image can be beneficial because it increases
proficiency of a predator in finding a common morph type.
Because of this, it makes it more advantageous to be a less common morph of a
species, so apostatic selection occurs on these less common morphs.
Experiments have been done on hawks to show that because of the fact that they
are of high intelligence, formation of a search image is plausible and a reasonable
hypothesis is the relationship of apostatic selection and polymorphism >

Bond and Kamil, 1998, Nature

< http://www.nature.com/nature/journal/v395/n6702/abs/395594a0.html>

Predators learn a particular cryptic pattern of the prey and develop a ‘search
image’

If a prey is variable, negative density dependenc offers fitnesss advantages to

less common forms.
This may produce oscillations in phenotypic variations

Balance polymorphism

<Balanced polymorphism is a situation in which two different versions of a gene

are maintained in a population of organisms because individuals carrying both
versions are better able to survive than those who have two copies of either
version alone>

Class 17

Seasonal forms in Chilades pandava Tiple et al. (2009, Curr. Sci)

<http://biodiversitylab.org/sites/default/files/images/website/TipleEtal09Chil
adesPolyphenismCurrSci.pdf>

Life history evolution

Variation in developmental and reproductive strategies

Some organisms produce a single egg and others hundreds of thousands- Kiwi
relatively largest egg among birds
- produce a single egg-chick per year- with mortality it comes to less than 1
offspring per year
Some organisms live mostly as juveniles (cicadas), others mostly as asults
(reptiles, furs, giant sequoias)
Some live and reproduce in a matter of hours and die, others live and reproduce
for hundreds of years( mayflies vs tortoises)

Some are semelparous (bamboos, cicadas, octopus, agave) most are iteroparous

Newborns in some species are almost independent from birth i.e they are
precocious (most invertebrates, some birds)
Organisms modulate the timing of and investment in development, reproduction
and death over their lifetimes and life spans in response to selection to maximise
their fitness. This is usually species-specific but may be variable within
populations and specific environments

Life history evolutions is an optimization problem- given specifc ecological

factors , limited resources, trade offs and strong selection, how to partitiion
various life stages to maximise reproductive success

Several important factors play a role in life history evolution-

-Vx : age specific expectation of future offspring-
-ex : expectation of life at age x
-Ix : probability of surviving from birth to age class x
-mx : the expected number of offspring in age class x
alpha-age at 1st reproduction
omega- age at last reproduction
Euler lotka equation
1= integral from alpha to omega e to the power –rx.dx

< In the study of age-structured population growth, probably one of the most important equations is
the Lotka–Euler equation. Based on the age demographic of females in the population and female
births (since in many cases it is the females that are more limited in the ability to reproduce), this
equation allows for an estimation of how a population is growing.

http://users-deprecated.aims.ac.za/~doriano/research/postgrad/essay.pdf

https://www.cpp.edu/~djmoriarty/b418/b418%20derivation%20of%20Euler
%20eqn.pdf

>

Optimal solutions should lead to Darwinian Demons that reproduce fom birth
produce an infinite number of offspring and live practically forever

< A Darwinian Demon is a hypothetical organism which can maximize all aspects
of fitness simultaneously and would exist if the evolution of species was entirely
unconstrained.[1] It is named for Charles Darwin. Such organisms
would reproduce directly after being born, produce infinitely many offspring,
and live indefinitely. Even though no such organisms exist, biologists use
Darwinian Demons in thought experiments to understand different life
history strategies among different organisms

Natural selection is shown to be an extended instance of a Maxwell's demon

device. A demonic selection principle is introduced that states that organisms
cannot exceed the complexity of their selective environment. Thermodynamic
constraints on error repair impose a fundamental limit to the rate that
information can be transferred from the environment (via the selective demon)
to the genome. Evolved mechanisms of learning and inference can overcome this
limitation, but remain subject to the same fundamental constraint, such that
plastic behaviors cannot exceed the complexity of reward signals. A natural
measure of evolutionary complexity is provided by mutual information, and
niche construction activity--the organismal contribution to the construction of
selection pressures--might in principle lead to its increase, bounded by
thermodynamic free energy required for error correction.

http://sci-hub.cc/10.1063/1.3643064

>

Trade offs may arise- antagonistic selection on traits, or from genetic

constraints- antagonistic pleiotropy, linkage disequilibrium

Developmental times and spans, timing of and efforts in reproduction,

number/size of propagules,

Reproductive sacrifice, parental care and death!

< https://en.wikipedia.org/wiki/Sexual_cannibalism>

< https://en.wikipedia.org/wiki/Filial_cannibalism>

Major trade offs-

Current reproduction vs survival /current vs future reproduction

Number vs size of offspring (r and k selection)
Frequency of reproduction (semelparity vs iteroparity)
Nature of young (precocious vs altricial)

<
https://web.stanford.edu/group/stanfordbirds/text/essays/Precocial_and_Altri
cial.html>

reproductive effort usually increases with age (age dependent life expectancy
and future reproductive effort declines with age)

If mortality increases in all age classes, reproductive effot should be greater early
in life and age at maturity should decrease

Important themes in life histoy evolution-

Evolution of semelparity
Evolution of clutch size
Evolution of body size: body size of the species and the sexes may be related to
fecundity selection (anurans) or sexual selection (grouse)
Sex allocation and offspring production
Evolution of senescence

< Sexual size dimorphism (SSD) is one of the most common ways in which males
and females differ. Male-biased SSD (when males are larger) is often attributed
to sexual selection favouring large males. When females are larger (female-
biased SSD), it is often argued that natural selection favouring increased
fecundity (i.e. larger clutches or eggs) has coevolved with larger female body
size. Using comparative phylogenetic and multispecies regression model
selection approaches, we test the hypothesis that among-species variation in
female fecundity is associated with the evolution of female-biased SSD. We also
ask whether the hypothesized relationship between SSD and fecundity is relaxed
upon the evolution of parental care. Our results suggest a strong relationship
between the evolution of fecundity and body size, but we find no significant
relationship between fecundity and SSD. Similarly, there does not appear to be a
relationship between fecundity and the presence or absence of parental care
among species. Thus, although female body size and fecundity coevolve,
selection for increased fecundity as an explanation for female-biased SSD is
inconsistent with our analyses. We caution that a relationship between female
body size and fecundity is insufficient evidence for fecundity selection driving
the evolution of female-biased SSD

http://sci-hub.cc/10.1111/jeb.12695

https://web.stanford.edu/group/stanfordbirds/text/essays/Sexual_Selection.ht
ml

http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-27

http://biorxiv.org/content/biorxiv/early/2015/02/23/015586.full.pdf

>

Iteroparity and increased reproductive lifespan are favored when adult survival
is high and adult fecundity or juvenile survival is low-
High adult survival offers greater number of reproductive events per lifetime,
and low juvenile survival reduces fitness that selects compensatory frequent
reproductive effort

Semelparity and decreased reproductive lifespan are favored when adult

survival is low and juvenile survival is high. If reproductive effort yields
decreasing returns or greater chances of mortality, maximal reproductive effort
and semelparity are favored
Semelparous organisms usually have very large reproductive effort pe
reproductive event than iterparous organisms

Semelparous organisms usually reproduce after prime number of years (3,7,13)

or after longer time periods than their predators lifetimes (70 or 120 years),
presumably to prevent co-evolutionary response from predators

<https://en.wikipedia.org/wiki/Life_history_theory>

How many eggs should one lay? As many as possible? – life history evolutionary
theory would predict a different solution

Clutch size vs number of surviving offspring plot- gives a quadratic curve –

inverted u
Half clutch size corresponds to optimal survival of offspring

< Group selection is a proposed mechanism of evolution in which natural

selectionacts at the level of the group, instead of at the more conventional level
of the individual.
Early authors such as V. C. Wynne-Edwards and Konrad Lorenz argued that the
behavior of animals could affect their survival and reproduction as groups.
From the mid 1960s, evolutionary biologists such as John Maynard Smith argued
that natural selection acted primarily at the level of the individual. They argued
on the basis of mathematical models that individuals would
not altruistically sacrifice fitness for the sake of a group. They persuaded the
majority of biologists that group selection did not occur, other than in special
situations such as the haplodiploidsocial insects like honeybees (in
the Hymenoptera), where kin selection was possible.
In 1994 David Sloan Wilson and Elliott Sober argued for multi-level selection,
including group selection, on the grounds that groups, like individuals, could
compete. In 2010 three authors including E. O. Wilson, known for his work
on social insects especially ants, again revisited the arguments for group
selection, provoking a strong rebuttal from a large group of evolutionary
biologists. As of yet, there is no clear consensus among biologists regarding the
importance of group selection
Once Darwinism had been accepted, animal behavior was glibly explained with
unsubstantiated hypotheses about survival value, which was largely taken for
granted. The naturalist Konrad Lorenz had argued loosely in books like On
Aggression (1966) that animal behavior patterns were "for the good of the
species", without actually studying survival value in the field; the ethologist Niko
Tinbergen praised Lorenz for his interest in the survival value of behavior, and
naturalists enjoyed Lorenz's writings for the same reason.[2] In 1962, group
selection was used as a popular explanation for adaptation by the zoologist V. C.
Wynne-Edwards

https://en.wikipedia.org/wiki/Group_selection
Food limitation and nest predation hypotheses. David Lack observed a direct
relationship between latitude and avian clutch size. Birds near the equator laid
approximately half as many eggs as those that resided in northern temperate
habitats.

https://en.wikipedia.org/wiki/Avian_clutch_size

http://www2.hawaii.edu/~taylor/z652/VanderWerf.pdf

https://www.jstor.org/stable/pdf/3494101.pdf

http://www.zoo.ox.ac.uk/group/west/pdf/singlesexI99.pdf

https://en.wikipedia.org/wiki/Mate_choice

>

Is it better to be a secondary wife to a superior male than chose an inferior male?

Avian clutch sizes and parasitoid brood sizes

Class 18

Life history evolution II

Reproductive allocation based on fitness consequences of producing fewer or

more offspring of specific quality and fitness

Do females invest more in reproduction (gametes) than males???

< http://biomed.brown.edu/Courses/BIO48/18.Sexual.Selection.HTML>

< http://icb.oxfordjournals.org/content/45/5/848.full>

Fecundity selection may drive evolution of female body size when larger females
produce more or better quality offspring

Investing in sons vs daughters : sex ratio vs operational sex ration

Normal sex ratio is 1:1 in most organisms at birth

Eg. Of organisms with departure from 1:1

Trivers-Willard hypothesis:
High-status parents (parasite loads, physiological condition, social status)
preferentially invest in sons whereas low status parents preferentially invest in
daughters (females almost always mate and reproduce, males are unlikely to)
-parental condition is correlated with offspring condition
-condition affects fecundity
-sex ratios of offspring can be manipulated

In polygynous or lekking species, females in good condition should produce

more males and females in poor conditions should produce more females
In sex reversed species, females in good condition produce more females than
males

< In evolutionary biology and evolutionary psychology, the Trivers–Willard

hypothesis, formally proposed by Robert Trivers and Dan Willard, suggests that
female mammals are able to adjust offspring sex ratio in response to their
maternal condition. For example, it may predict greater parental investment in
males by parents in "good conditions" and greater investment in females by
parents in "poor conditions" (relative to parents in good condition). The
reasoning for this prediction is as follows: Assume that parents have information
on the sex of their offspring and can influence their survival differentially. While
pressures exist to maintain sex ratios at 50%, evolution will favor local
deviations from this if one sex has a likely greater reproductive payoff than is
usual.
Trivers and Willard also identified a circumstance in which reproducing
individuals might experience deviations from expected offspring reproductive
value—namely, varying maternal condition. In polygynous species males may
mate with multiple females and low-condition males will achieve fewer or no
matings. Parents in relatively good condition would then be under selection for
mutations causing production and investment in sons (rather than daughters),
because of the increased chance of mating experienced by these good-condition
sons. Mating with multiple females conveys a large reproductive benefit,
whereas daughters could translate their condition into only smaller benefits. An
opposite prediction holds for poor-condition parents—selection will favor
production and investment in daughters, so long as daughters are likely to be
mated, while sons in poor condition are likely to be out-competed by other males
and end up with zero mates (i.e., those sons will be a reproductive dead end).
The hypothesis was used to explain why, for example, Red Deer mothers would
produce more sons when they are in good condition, and more daughters when
in poor condition. In polyandrous species where some females mate with
multiple males (and others get no matings) and males mate with one/few
females (i.e., "sex-role reversed" species), these predictions from the Trivers–
Willard hypothesis are reversed: parents in good condition will invest in
daughters in order to have a daughter that can out-compete other females to
attract multiple males, whereas parents in poor condition will avoid investing in
daughters who are likely to get out-competed and will instead invest in sons in
order to gain at least some grandchildren

The Trivers–Willard hypothesis rests on certain assumptions:

Parental condition is associated with offspring condition;
Differences in offspring condition will persist into adulthood;
Being in condition differentially affects the mating success of one sex more than
it does the other.
Evolutionary biologists predict a Trivers–Willard effect where these conditions
hold, and no effect when these conditions do not hold. In polygynous species
where some males have multiple mates and others have none (i.e., greater
variance in mating success among males than females), being in good condition
affects males more than females. This is reversed in polyandrous species, and
possibly in species where condition is based on social status and males disperse.
In their original paper, Trivers and Willard were not yet aware of the
biochemical mechanism for the occurrence of biased sex ratios. Eventually,
however, Melissa Larson et al. (2001)[3] proposed that a high level of
circulating glucose in the mother's bloodstream may favor the survival of
male blastocysts. This conclusion is based on the observed male-skewed survival
rates (to expanded blastocyst stages) when bovine blastocysts were exposed to
heightened levels of glucose. As blood glucose levels are highly correlated with
access to high-quality food,[4] blood glucose level may serve as a proxy for
"maternal condition". Thus, heightened glucose functions as one possible
biochemical mechanism for observed Trivers–Willard effects.
Wild and West published a paper describing a mathematical model built on the
Trivers–Willard hypothesis that allows precise predictions of alterations in sex-
ratio under different circumstances>

< http://rspb.royalsocietypublishing.org/content/283/1830/20160126>

< http://rspb.royalsocietypublishing.org/content/271/1549/1723.short>

< http://ac.els-cdn.com/S016953479901592X/1-s2.0-S016953479901592X-
main.pdf?_tid=14383104-c373-11e6-859f-
00000aacb361&acdnat=1481881151_f90fdf2b04860176abb60b0d46ad2de3>

< Fisher's principle is an evolutionary model that explains why the sex ratio of
most species that produce offspring through sexual reproduction is
approximately 1:1 between males and females. It was famously outlined
by Ronald Fisher in his 1930 book The Genetical Theory of Natural Selection (but
incorrectly attributed to Fisher as original). Nevertheless, A. W. F. Edwards has
remarked that it is "probably the most celebrated argument in evolutionary
biology". Specifically, Fisher couched his argument in terms of parental
expenditure, and predicted that parental expenditure on both sexes should be
equal. Sex ratios that are 1:1 are hence known as "Fisherian", and those that are
not 1:1 are "non-Fisherian" or "extraordinary" and occur because they break the
assumptions made in Fisher's model. Many eusocial wasps, such as the Polistes
fuscatus and the Polistes exclamans seem to exhibit such a ratio at times
W.D. Hamilton gave the following basic explanation in his 1967 paper on
"Extraordinary sex ratios",[3] given the condition that males and females cost
equal amounts to produce:
Suppose male births are less common than female.
A newborn male then has better mating prospects than a newborn female, and
therefore can expect to have more offspring.
Therefore parents genetically disposed to produce males tend to have more than
average numbers of grandchildren born to them.
Therefore the genes for male-producing tendencies spread, and male births
become more common.
As the 1:1 sex ratio is approached, the advantage associated with producing
males dies away.
The same reasoning holds if females are substituted for males throughout.
Therefore 1:1 is the equilibrium ratio.
In modern language, the 1:1 ratio is the evolutionarily stable strategy (ESS)>

< http://www.zoo.ox.ac.uk/group/west/pdf/Sheldon&West_02.pdf>

Evolution of senescence and death

Organisms try to increase fitness until they die, sometimes they die because of
the reproductive effort
-Some insectivorous marsupial males mate until they die of stress , immune
system collapse and exhaustion- females are iteroparous and males are
semelparous ( Fisher et al. 2013)

<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816400/pdf/pnas.2013106
91.pdf>

- male spiders and praying mantids being eaten by their mates

-matriphagous spiders (Eg. Stegodyphous lineatus, Amaurobius ferox),
pseudoscorpions (Paratemnoides nidificator) and Adactylidium mites( adult
female mites feed on insect eggs, their daughters grow inside their bodies along
with one son, who mates with his sisters while they are all inside their mother
and feeding on her

Death may be an outcome of the end of reproduction

Evolution of senescence
Post reproductive survival and lifespan are beyond the influence of natural
selection as the fitness of the organism is not affected
(exception: grand parental care in humans)
Therefore, natural selection cannot optimize post reproductive survival and
lifespan

Senescence (ageing) is physiological degeneration of body with age: healing of

wounds takes longer with age
Harmful compounds (eg toxins) from metabolism accumulate with age causing
eventual tissue damage (metabolic rates and senescence)

Genes that negatively affect physiological processes related to survival and

reproduction may be expresses only after reproductive stage, e.g geneticaly
dominant allele for Huntington’s Disease causing neurological degenration is
expressed after 30-40 years

Two major hypotheses

1. Deleterious mutations that affect later age classesaccumulate in

populations at higher frequency compared to mutations that affect early
age classes (Medawar 1952: <http://web.csulb.edu/~acarter3/course-
evolution/files/Medawar.pdf>)
-selection is weak against late than early mutations
-greater genetic variation in fitness related traits in late rather
than early life

< http://www.programmed-
aging.org/theories/medawar_hypothesis.html>

< http://www.senescence.info/evolution_of_aging.html>

2. Antagonistic pleiotropy of genes that increase survival and reproduction

early in life and decrease survival and reproduction late in life (Williams
1957)
-trade-offs of reproducing early rather than late in life

< The theory of antagonistic pleiotropy is based on two assumptions. First, it is

assumed that a particular gene may have an effect not only on one trait, but on
several traits of an organism (pleiotropy). The second assumption is that these
pleiotropic effects may affect individual fitness in opposite (antagonistic) ways.
This theory was first proposed by George Williams in 1957, who noticed that
"natural selection may be said to be biased in favor of youth over old age
whenever a conflict of interests arises" (Williams, 1957).
According to Williams, this conflict arises from "pleiotropic genes . . . that have
opposite effects on fitnesses at different ages. . . . Selection of a gene that confers
an advantage at one age and a disadvantage at another will depend not only on
the magnitudes of the effects themselves, but also on the times of the effects. An
advantage during the period of maximum reproductive probability would
increase the total reproductive probability more than a proportionately similar
disadvantage later on would decrease it. So natural selection will frequently
maximize vigor in youth at the expense of vigor later on and thereby produce a
declining vigor (aging) during adult life." (Williams). These verbal arguments
were later proved mathematically by Brian Charlesworth (1994).
Williams was suggesting the existence of so-called pleiotropic genes (those
demonstrating favorable effects on fitness at a young age and deleterious ones at
old age), which could explain the aging process. Such genes are maintained in the
population due to their positive effect on reproduction at a young age, despite
their negative effects at a post-reproductive age (their negative effects in later
life will look exactly like the aging process).
For the purpose of illustration, suppose that there is a gene that increases the
fixation of calcium in bones. Such a gene may have positive effects at a young age,
because the risk of bone fracture and subsequent death is decreased, but
negative effects in later life, because of increased risk of osteoarthritis due to
excessive calcification. In the wild, such a gene would have no actual negative
effect, because most animals would die long before its negative effects could be
observed. There is then a trade-off between an actual positive effect in young
individuals and a potential negative one in old individuals: this negative effect
may become important only if animals live in protected environments such as
zoos or laboratories.
Antagonistic pleiotropy theory explains why reproduction may come with a cost
for species longevity, and may even induce death (see the story on bamboo
plants and salmon life cycles at the beginning of this article). Indeed, any
mutations favoring more intensive reproduction (more offspring produced) will
be propagated in future generations even if these mutations have some
deleterious effects in later life. For example, mutations causing overproduction
of sex hormones may increase the sex drive, libido, reproductive efforts, and
reproductive success— and therefore be favored by selection, despite causing
prostate cancer (in males) and ovarian cancer (in females) later in the life. Thus,
the idea of reproductive cost, or, more generally, of trade-offs between different
traits follows directly from antagonistic pleiotropy theory.
The trade-offs between reproduction (reproductive success, fitness, vigor) and
longevity were predicted by Williams as "testable deductions from the theory."
Specifically, he predicted, "rapid individual development should be correlated
with rapid senescence. Reproductive maturation is the most important landmark
in the life-cycle for the evolution of senescence. Senescence may theoretically
begin right after this stage in development. So the sooner this point is reached,
the sooner senescence should begin, and the sooner it should have demonstrable
effects." Another prediction of the trade-offs between reproductive capacity
(vigor) and longevity was made by Williams in the following way: "successful
selection for increased longevity should result in decreased vigor in youth."
These predictions were confirmed later in selection experiments using the fruit
fly, Drosophila melanogaster. By restricting reproduction to later ages, the
intensity of selection on the later portions of the life span was increased. This
selection for late reproduction extended the longevity of the selected
populations. Furthermore, a reduced fecundity was observed among the long-
lived flies, supporting the idea of a trade-off between fertility and survival, as
predicted by the antagonistic pleiotropy theory. A similar trade-off between
fecundity and longevity was observed when fruit flies were selected directly for
longevity. In another selection experiment with different levels of extrinsic
mortality, the descendants from populations with low extrinsic mortality
demonstrated increased longevity, longer development times, and decreased
early fecundity. The general finding from these selection experiments in fruit
flies is that increased longevity is associated with depression of fitness (vigor) in
early life, just as Williams predicted.
Trade-offs between longevity and reproduction have also been found in
experiments with soil-dwelling round worms (the nematode Caenorhabditis
elegans), where a number of long-lived mutants have been identified. When
long-lived mutants were reared together with normal (wild-type) individuals
under standard culture conditions, neither of them exhibited a competitive
advantage, contrary to theoretical predictions. However, when cultures were
exposed to starvation cycles (alternatively fed and starved)— mimicking field
conditions in nature—the wild type quickly outcompeted (outnumbered) the
long-lived mutant. These findings demonstrate that mutations that increase life
span do indeed exhibit some fitness cost, thereby supporting the antagonistic
pleiotropy theory of aging.
Studies on humans, however, have been less convincing. One study found that
long-lived people (women in particular) did have impaired fertility at a young
age—as predicted, in general, by antagonistic pleiotropy theory, and in
particular, by disposable soma theory. However, serious methodological flaws
were later found in that study, and its findings proved to be inconsistent with
findings of many other researchers, including historical demographers analyzing
human data (see reviews in Gavrilov and Gavrilova, 1999; Le Bourg, 2001).
Therefore, more additional studies on this subject are required>

< http://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-12-
160>

< https://en.wikipedia.org/wiki/Evolution_of_ageing>

Class19

Missed

Class 20

Cornell lab of ornithology youtube channel

< https://www.youtube.com/watch?v=YTR21os8gTA>

Sexual selection

Darwins most original and unique contribution to biology

Distinguishes adaptations needed for successfully finding mates and increasing
reproductive output rather than survival
-a subset of natural selection
-must always work under the influence of natural selection
-sexually selected traits may originally evolve under natural selection for
ecological demands

Basic assumptions of Sexual selections-

1.Male investment in reproduction (gamete production) is minimal, females
invest in reproduction tremendously
2.The sexual inequality in reproductive investment makes males the courting sex
and females the choosing sex
3.Competition among males (intrasexual selection) leads to the evolution of male
weapons, whereas mate choice (intersexual selection) leads to the evolution of
male ornaments
4. Traits may evolve in males that increase their fitness at the cost of reduction in
female fitness ( Drosophila seminal fluid reduces fertility in females)

< http://www.news.cornell.edu/stories/2008/01/seminal-fluid-can-impact-
female-fruit-flys-fertility>

<
http://ase.tufts.edu/biology/labs/lewis/publications/documents/2011South.pd
f>

Species with paternal care

-Social matching
-resource availability
-resource defense (males are more aggressive towards intruding males than
females and vice versa)

Species without paternal care: especially lekking species

< A lek is an aggregation of males gathered to engage in competitive

displays, lekking, that may entice visiting females who are surveying prospective
partners for copulation. Leks are commonly formed before or during
the breeding season. A lekking species is characterised by male displays, strong
female mate choice, and the conferring of male indirect benefits. Although
lekking is most prevalent among avian species, lekking behavior is found in
insects, amphibians, and mammals as well>

< https://en.wikipedia.org/wiki/Lek_mating>

-Good genes hypothesis

< http://www.pnas.org/content/103/44/16343.full>
< https://www.britannica.com/science/good-genes-hypothesis>
-Sexy son hypothesis
< The sexy son hypothesis in evolutionary biology and sexual selection—
proposed by Ronald Fisher in 1930—states that a female's ideal mate
choice among potential mates is one whose genes will produce
male offspring with the best chance of reproductive success and implies that a
potential mate's capacity as a parental caregiver or any other direct benefits the
father can offer the mother such as nuptial gifts, or good territory are irrelevant
to his value as the potential father of the female's offspring. Fisher's
principle means that the sex ratio (except in certain eusocial insects) is always
1:1 between males and females, yet what matters most are her "sexy sons"'
future breeding successes, more likely if they have a promiscuous father, in
creating large numbers of offspring carrying copies of her genes.[1] This sexual
selection hypothesis has been researched in species such as the European pied
flycatcher>

< https://en.wikipedia.org/wiki/Sexy_son_hypothesis>

< https://rajpersaud.wordpress.com/2015/04/16/the-sexy-sons-hypothesis-
why-women-get-better-sex-with-men-other-women-fancy-by-dr-raj-persaud/>

-parasite resistance hypothesis

< http://ib.berkeley.edu/courses/ib160/past_papers/smyth.html>

< http://sci-hub.io/10.1016/0169-5347(88)90115-2>

<
https://en.wikipedia.org/wiki/Major_histocompatibility_complex_and_sexual_se
lection>

< http://ndt.oxfordjournals.org/content/15/9/1269.full>

Species with or without paternal care

-Handicap Principle (Zahavi)
< Zahavi's handicap principle is an argument for sexual selection in which the
costliness of the male character, such as a peacock's tail for example, is positively
useful to the female. The argument, originally suggested by the biologist Amotz
Zahavi runs as follows:
In a population in which males vary in their quality, some of the males possess a
handicap - a costly or deleterious character which reduces survival. If only males
with high quality genes can survive possessing a handicap, a female who mates
preferentially with handicapped males will only mate with males with good
genes.
Provided the advantage through the superior genes outweighs the cost of the
handicap then the net quality of the choosy female's offspring will be higher than
those of the randomly mating female.
The handicap acts as an indicator of genetic quality and has to be costly to
guarantee that signalling is honest: otherwise low quality males could equally
well advertise and females would be unable to distinguish between them>
< In the early 1970's, biologist Amotz Zahavi struggled to understand why
animals often produce costly and extravagent displays or physical ornaments.
Why to peacocks have such spectacular plumage? Why do baby birds beg so
loudly? Why do gazelles jump up and down when they see a lion?
To answer this question, Zahavi proposed that these extravagences are signals to
other individuals. For example, a peacock's tail may be a signal used by
prospective mates in order to estimate the individual's overall condition and/or
genetic quality:
"An individual with a well developed sexually selected character [such as a
peacock's flashy tail] is an individual which has survived a test. A female which
could discriminate between a male possessing a sexually selected character,
from one without it, can discriminate between a male which has passed a test
and one which has not been tested. Females which selected males with the most
developed characters can be sure that they have selected from among the best
genotypes of the male population. " (Zahavi 1975)
Zahavi named his theory "the handicap principle," and suggested that there was
something about costly behaviors or physical features that made for inherently
reliable signals. But what is it about these costly traits - handicaps, as he called
them - that makes them believable?
This became a topic of great debate over the next fifteen years.
>

< https://en.wikipedia.org/wiki/Handicap_principle>

< https://www.ethz.ch/content/dam/ethz/special-interest/gess/chair-of-
sociology-dam/documents/icsd2013/07_1_zahavi.pdf>

< https://en.wikipedia.org/wiki/Signalling_theory>

-Sensory Exploitation (Endler and Ryan)

< http://nekhbet.com/ss_textbook.pdf>

< http://web.biosci.utexas.edu/ryan/Publications/1990/1990Evolution44-
305.pdf>

< https://www.allaboutbirds.org/why-so-red-mr-cardinal-nestwatch-
explains/>

< http://beheco.oxfordjournals.org/content/10/1/80.full>

< https://www.scientificamerican.com/article/why-are-male-birds-more-c/>

< https://www.jstor.org/stable/pdf/2409409.pdf>

< http://www.nature.com/nature/journal/v343/n6253/pdf/343066a0.pdf>
< http://www.sekj.org/PDF/anzf27/anz27-087-100.pdf>

< http://www.smithsonianmag.com/science-nature/frogs-mating-call-also-
attracts-predators-180949463/>

< http://www.livescience.com/42803-frog-mating-ripples-attract-bats.html>