Intro to Systematics Part 2 Synapomorphy

● Shared derived feature

How do systematists infer phylogeny?

● Gather morphological and molecular data
(genes and biochemistry) of living
organisms and analyze fossil records
● Seek morphological and molecular
homologies
○ Homologies = phenotypic and
genetic similarities due to shared
ancestry
○ Organisms with similar
morphologies or DNA sequences
are likely to be more closely related
than organisms with different
structures or sequences
● Is the similarity a result of homology or
analogy?
○ Homology is similarity due to
shared ancestry
○ Analogy is similarity due to
Phylogenetic Trees
convergent evolution
● Represents a hypothesis about evolutionary
Morphological homologies
relationships
Homologies
Branch point
● Similarities due to common ancestry
● Represents divergence between two
○ Arms, forelegs, wings, and flippers
species
of mammals
● Tree branches can be rotated around a
Convergent evolution
branch point without changing the
● Occurs when similar environmental
evolutionary relationships
pressures and natural selection produce
Sister Taxa
similar (analogous) adaptions in
● Groups that share an immediate common
organisms from different evolutionary
ancestor
lineages.
Rooted tree
● Convergence - Stem succulent and “spines”
● Includes a branch to represent the last
in Cactaceae and Euphorbia spp.
common ancestor of all taxa in the tree
Basal taxon
Primary tenet of phylogenetic systematics?
● Diverges early in the history of a group
● Taxa (Operational Taxonomic Units) can be
● Originates near the common ancestor of
grouped by apomorphies because these
the group
represent unique evolutionary events
● Most primitive
Recency of common ancestry?
Polytomy
● Premise: All forms of life share a common
● A branch from which two branches emerge
ancestor
Pre-existing Feature
● Taxa that share a common ancestor more
Plesiomorphy
recent in time are more closely related to
● Ancestral feature
one another than they are to a taxon whose
Symplesiomorphy
common ancestor is further back in time.
● Shared ancestral feature

New Feature
Apomorphy
● Derived feature
 ○ The analysis of how species may
be group into clades is called
cladistics. (Will Hennig,
Phylogenetic Systematics, 1966)

Types of clades or groupings

Monophyletic clade
● Consists of a common ancestor and all its
descendants
○ Single tribe
○ Only monophyletic groups qualify
Is C most closely related to D or F? ad legitimate taxa derived from
● Taxon D is more related to taxon C cladistics
● D was related to C
Is C more closely related to E or to B?
● Take note of their common ancestor
● C is more closely related to E than to B
● Because C and E share a common ancestor
Is C most closely related to A or B?
● C is more closely related to A
● Common ancestor
● B is only derived from A

Molecular homologies
● DNA and RNA sequences of nucleic acids ● All systemasists are aiming to reach
● Each change in a nuclelic acid is equal to monophyletic grouping
one evolutionary event Paraphyletic clade
○ The more events, the more
disstantly related are the species
○ Fewer events mean that a species
if more closely related
● Systematists use computer programs and
mathemathical tools when analyzing
comparable DNA segments from different
organisms.

● Consists of an ancestor and some but not

all of the descendants
● Does not meet the cladistic criterion
● Descendants that are yet to be discovered
Polyphyletic clade

A phylogenetic tree is also called a cladogram

● Each brancg in the tree is called a clade
● Clade is a group of species that includes a
common ancestor and all its descendants
 ● Consists of various species with different
ancestors; lacks a common ancestor
● Fails the cladistic test
● Only monophyletic group is acceptable in
cladistic analysis
a. A species that is closely related to
the species under study, the
outgroup has a shared primitive
character that is common to all
species.
3. Construct a character table and tabulate
the data.
a. The more shared characters, the
more closely related are the
species
4. Construct a cladogram based on the
number of shared characters

Constructing cladograms
1. Identify homologies
a. Shared characteristics derived
from one ancestor
2. When constructing a cladogram, the
greater the number of homologous paarts
between two organisms, the more closely
related they are
3. The classification scheme must reflect the
Classification Schemes
similarities
1. Classical/Artificial
Similarities can either be:
a. Based on few observable
a. Shared primitive characters
characters
i. Homologous characters that are
i. Linnaeus Sexual System
shared by more than one taxon
and Theophrastus from
ii. (example) backbone is shared by
system of plant
mammals and reptiles
classification
b. Shared derived characteristics
ii. Theophrastus -
i. An evolutionary novelty that is
classification system of
unique for a particular clade
plants, made use of plant
ii. The more derived characters that a
habit only, classified
species has, the more
plants according to the
evolutionarily unique it is
habitat
Steps to construct a cladogram
2. Phenetics/Natural
1. Select your species for which you want to
a. Constructs phenohgrams based
make a cladogram. These are called the
on overall similarity, largely
ingroup. They have shared primitive and
phenotypic, without regard to
derived characters.
2. Select an outgroup
 evolutionary history; all characters Development of Plant Classification System
are given equal weights ● Premolecular classification
i. Sneath and Sokal ○ Artifical
Numerical Taxonomy ○ Natural
(1973) ■ Sneath and Sokal
ii. Builds a phenogram Numerical Taxonomy is
3. Cladistics an appilication of natural
a. Constructs cladograms anchored classification
on assumed phylogenetic ○ Phylogenetic
relationships ● Molecular classification
i. Willi Henning ○ Phylogenetic
Phylogenetic Systematics ● Postmolecular classifications
(1966) ○ Phylogenetic based on a wide array
of characters including the
molecular and
micromorphological level (based
on the Angiosperm Phylogeny
Group [APG])
○ APG - group of scientists working
on classification of flowering
plants

Drawing of Phylogenetic classifications

● Baesd on Darwin’s Natural Selection theory
○ On The Origin of Species by Means
of Natural Selection on the
Preservation of Favoured Races in
the Struggle for Life Classification of Life: The Five-Kingdom System (R.
○ Published 1859 Whittaker & L. Margulis 1969)
Phylogenetic classifications
● Charles Bessey (1845-1915)
○ Proposed the Phylogenetic
Taxonomy of Flowering Plants
○ Based classification on 28 guiding
dicta to determine the level of
being simple/complex,
primitive/advanced
Classification of Life: The Three-Domain/ Eight
Kingdom System (Campbell, 1996)
Classification of Life: The
Two-Empire/Eight-Kingdom System
(May 1997)
Six-Kingdom Classification (Woese, 1977)
● Accepted
● Kingdom Eubacteria (domain Bacteria)
● Kingdom Protista (domain Eukarya)
● Kingdom Fungi (domain Eukarya)
● Kingdom Plante (domain Eukarya)
● Kingdom Animalia (domain Eukarya)
September 8, 2022 - Species, Species Concepts
and Speciation
General Ideas on Species
● Latin for “kind” or “appreance”
● Species: organisms belonging to the same
kind
How many species are there?
● No one knows
● Estimate 3.6 to 111 million species
● Normally used working figure is often 10 to
15 million
Development of species concept
Species Fixity
● Concept that each species remain
unchanged since its creation
● Began by Plato (428-348 BC)
○ Theory of Forms
○ There is a perfect form for every
organism, any deviation from that
would be considered an
imperfection
○ Perfect vs imperfect forms;
variations are imperfections
● Reinforced by Aristotle
○ Theory of types
○ Species reflect existence of
unchanging ideal form the
universal or type
○ Variations are imperfections
● St. Augustine (AD 345-430)
○ Adhered to the Aristotelian fixity of
species
○ “In the beginning were created
only germs or causes of the forms
of life which were afterwards to be
developed in gradual course”
■ St. Augustine from De
Genesi (Literal meaning of
Genesis)
● St. Thomas Aquinas (1225-1274)
○ Design in nature is evidence of
benevolence, omnipotence, and
existence of God as Creator of the
existing order (Argument from
design)
● Caroulus Linnaeus (1707-1778)
○ An entire species could be
represented by one type specimen
(holotype)
● Typological species concept =
Morphological Species Concept (Linneaus)
○ Species is a set of organisms that
resemble one another and is
distinct from other sets
○ Species are groups of individuals
that are morphologically similar
and clearly distinguishable from
individuals of other groups
Species as Evolving Entities
● Charles Darwin (1809-1882)
○ Origin of Species* (1859)
○ Central dogma of Biological
Studies
○ 2000+ years of certainty in fixed
species ended
 ○ Species Problem was born
The Modern Species Problem
● Problem of competing species concepts
○ Biological Species Concept
○ Paleontological Species Concept
○ Ecological Species Concept
○ Phylogeneic Species concept
○ Etc..
The Biological Species Concept
● Ernst Mayr’s biological species concept
defines species as…
“...groups of actually or potentially interbreeding natural
populations which are reproductively isoloated from
other such groups.”
● In short, members of a population mate
with each other and procude fertile
offspring
Reproductively isolated
● Populations whose members do not mate
with each other or who cannot produce
fertile offspring
● Reproductive isolating mechanisms:
barriers to successful reproduction
○ Geographic (prezygotic)
○ Behavioral (prezygotic)
○ Mechanical (prezygotic)
○ Ecological (prezygotic)
○ Temporal (prezygotic)
○ Gamete fusion (prezygotic)
○ Postzygotic (Once fertilization is
successfully carried out)
Prezygotic Isolating Mechanism
○ Fireflies recognize signals of their
own species
○ Frogs have calls that only attract
their own species
○ Birds have songs that only attract
their own species
Temporal isolation
● Species reproduce in different seasons or
at different timmes of the day
○ Frog species mate at different
seasons
Mechanical isolation
● Structural differences between species
prevent mating
○ Flowers of varied nature of corolla
are likely visted by dissimilar
pollinators
○ Insects whose copulatory organs
may not fit together, so no sperm
wpuld be transferred
Prevention of gamete fusion
(Gametic/gametophytic isolation)
● Gametes of one species functions poorly
with the gametes of another species or
within the reproductive tract of another
species
○ Failure of egg to recognize sperm
from another species among
aquatic species
○ Failure of pollen germination
between different flowering plant
species

Lions and tigers are GEOGRAPHICALLY (1) &

ECOLOGICALLY (2) isolated
● Also morphologically separated
● No zygote may be formed between two
distantly located organisms

Behavioral isolation
● Species differ in their mating rules

1. Reduced Hybrid Viability
a. Hybrid zygotes fail to develop or
fail to reach sexual maturity
2. Reduced hybrid fertility
a. Even if hybrids are vigorous, they
may be sterile
3. Hybrid breakdown
a. Offspring of hybrids have reduced
viability or fertility
Limitations of biological species concept
● Interspecific hybridization among animals
● 10% of bird species have hybridized in
nature
● Many plants naturally hybridize
● Concept applies to sexual species only,
excludes fossils and asexual organisms
such as prokaryotes
Other species concepts
Paleontological Species Concept
● Focuses on morphologically discrete
species known only from fossil record
Phylogenetic Species Concept
● Defines a species as a set of organisms
with a unique genetic history-that is, as
one branch on the tree of life
Ecological Species Concept
● Views a species in terms of its ecological
niche, its role in a biological community
Real Species Problems
● Asexual populations
● Prokaryotes
● Interspecific hybrids
● Endosymbionts
● Are all organisms assignable to species?
How are Species formed?
Speciation
● The process by which new species arise
either by
○ Anagenesis - Transformation of
one species into another
○ Cladogenesis - Splitting of one
ancestral species into two
descendant species
 b. Speciation that takes place in
geographically overlapping
populations
c. Chromosomal changes and
nonrandom mating reduce gene
flow
3. Parapatric Speciation
a. Adjacent populations evolve into
distinct species while maintaining
contact along a common border
Remember: Species arise when individuals in a
population become isolated from one another

Modes of speciation

1. Allopatric Speciation
a. “Patric” = country
b. Speciation that takes place in
populations with geographically
separate ranges
c. Gene flow is interrupted and new
species evolve
2. Sympatric Speciation
a. “Same country”

Examples of Sympatric Speciation
● Speciation that takes place
geographically overlapping populations
○ Occur by chromosomal changes
and nonrandom mating. Both can
reduce gene flow between
organisms and cause populations
to evolve to new species
Polyploidy
● Greater than 2 sets of chromosomes
● Most common in plants
Autopolyploidy arises from gene duplication
Causes of genome duplication
a. Meotic non-reduction of gametes (in both
egg and sperm)
b. Genome duplication w/o cytokinesis (after
fertilization)
● Autopolyploids are fertile because each
chromosome has a partner with which it
can pair during meiosis, the process in
which gametes are produced
● Duplicated genomes are tertraploid when
the cell contains 4 copies of each
chromosome. It is diploid when it contains
only 2 copies of each,
● Autopoluploidy in some plants can result in
cells with more than a hundred
in
chromosomes
Allopolyploidy arises from hybridization plus
genome duplication
Allopolyploidy Origin of Life, Geologic Time, Speciation,
● Chromosomes in the new species come Extinction
from two different (but related ancestral)
species Theories on the origin of life

Panspermia
● Seeds everywhere
● Life exists throughout the Universe,
distributed by space dust, meteoroids,
asteroids, comets, planetoids, and also by
contaminated spacecraft
● Deinococcus radiodurans
○ Extremophilic bacterium and one
of the most radiation-resistant
organisms known. It can survive
cold, dehydration, vacuum, and
acid. It has been listed as the
world’s toughest known bacterium
in The Guinness Book of World
Records.
○ Found to withstand harsh
environmental conditions present
in outer space. Deinococcus
radiodurans was exposed for 1 year
outside the International Space
Station with Tanpopo orbital
mission (Microbiome, 2020)

Spontaneous Generation Theory (Abiogenesis)

● Life can arise from nonliving matter.
● Aristotle (384-322 BC) proposed that life
arose from nonliving material if the
material contained pneuma (vital heat)
● Evidences
○ Bivalves/fishes from
spontaneously in mud or sand
 ○ Insects generated on dew falling
on leaves
Spontaneous Generation - 19th Century
Lamarck (1724-1829)
● Each species arose from an independent
event of spontaneous generation
● Spontaneous generation continues today
Spontaneous generation was first refuted by
Pasteur (1822-1895)
● Demonstrated experimentally that
microbes would not appear in flasks
protected from dust and other small
particles
Chemosynthesis
● The biological production of organic
compounds from C-1 compounds and
nutrients, using the energy generated by
the oxidation of inorganic (e.g. hydrogen
gas, hydrogen sulfide, ammonium,) or C-1
organic (e.g. methane, methanol)
molecules.
● Implies that the development of life is
probable wherever the proper physical and
chemical conditions are in place
Conditions on early Earth made the origin of life
possible
● Earth formed about 4.6 billion years ago,
along with the rest of the solar system
● Bombardment of Earth by rocks and ice
likely vaporized water and prevented seas
from forming before 4.2 to 3.9 billion years
ago
● Earth’s early atmosphere likely contained
water vapor and chemicals released by
volcanic eruptions (nitrogen, nitrogen
oxides, carbon dioxide, methane, ammonia,
hydrogen, hydrogen sulfide)
○ The atmosphere was devoid of
oxygen = reducing oxygen
Synthesis of Organic Compounds on Early Earth
● In the 1920’s, A.I. Oparin and J.B.S. Haldane
hypothesized that the early atmosphere
was a reducing environment and could
produce organics
● In 1953, Stanley Miller and Harold Urey
conducted lab experiments that showed
that the abiotic synthesis of organic
molecules (amino acids) in a reducing
atmosphere is possible
The key building blocks of life are not hard to
come by
● Amino acids have also been found in
meteorites
● RNA monomers have been produced
spontaneously from simple molecules
● In water, lipids and other organic molecules
can spontaneously form vesicles with a
lipid bilayer
● Adding clay can increase the rate of vesicle
formation
● Vesicles exhibit simple reproduction and
metabolism and maintain an internal
chemical environment
○ Result —> protocells
Chemical and physical processes on early Earth
may have produced very simple cell through a
sequence of stages
a. Abiotic synthesis of small organic
molecules
b. Joining of these small molecules into
macromolecules
c. Packaging of molecules into protocells
d. Origin of self-replicating molecules
molecules
The rise and fall of groups of organisms reflect
differences in speciation and extinction rates.
● Not only geologic time but also continental
movement had profound effects on these
rates
○ A continent’s climate can change
as it moves north or south
○ Separation of land masses can
lead to allopatric speciation
 What died: 86% of species and 57% of genera
(Trilobites, corals, etc)
What thrived best: Sponges

Devonian
When (MYA): 359-380
Why: Climate change for >20 million plus years:
volcanic activity in Siberia, reduced oxygen levels in
the oceans
What died: 75% of species and 35% of genera;
placoderms, corals, trilobites
What thrived best: Small vertebrates, tetrapods,
amphibians, reptiles, mammals

Permian
When (MYA): 251
Why: Volcanic activity in Siberia; global warming;
apocalypse unfolded over a span of about 50,000
years
What died: 96% of species and 35% of genera; vast
forests; amphibians; marine life
What thrived best: Fungi; early ancestors of
dinosaurs

Permian extinctions
A number of factors might have contributed to these
extinctions
Mass Extinctions 1. Intense volcanism in what is now Siberia
● The fossil record shows that most species 2. Global warming resulting from the
that have ever lived are now extinct emission of large amounts of Co2 from the
● At times, the rate of extinction has other volcanoes
increased dramatically and caused a mass 3. Reduced temperature gradient from
extinction, and is the result of disruptive equator to poles
global environmental changes
Triassic
When (MYA): 201
Why: Massive volcanic eruptions in what would
become the Atlantic Ocean
What died: 80% of Species and 47% of genera;
ribbonlike fish conodont, reptiles
What thrived best: Dinosaurs

Cretaceous
When (MYA): 65.5
Why: Asteroid; volcanic eruptions
The “Big Five” Mass Extinction Events What died: 76% of species and 40% of genera;
● In each of the five mass extinction events, dinosaurs, ammonites, etc..
more than 50% of the Earth’s population What thrived best: Mammals
became extinct
Cretaceous extinction
Ordovician 1. Dinosaurs went extinct after living for ca.
When: (MYA): ca. 443 165 MY on earth
Why: Climate change (first icy, then ice melted)
2. Planetwide volcanism; large-scale volcanic
eruption in the Indian Deccan Traps
a. A spike in carbon dioxide and a
drop in ocean oxygen levels
3. An asteroid (or comet) hit the earth and
created a cloud of debris that blocked out
sunlight for months. Temperatures dropped
and plants died.

Is a Sixth Mass Extinction Under Way?

● Scientists estimate that the current rate of
extinction is 1,000 to 10,000 times the
typical background rate (IUCN)
○ Background extinction = normal
1997 Core - Tiny Creatures Tell a Big Story extinction rate, refers to the
number of species that would be
expected to go extinct over a
period of time, based on
non-anthropogenic (non-human)
factors.
○ Species-level life span
○ The baseline extinction rate is
about one species per one million
species per year.
○ For mammals
■ Background extinction: 1
species / 200 years
■ Current: 89 species from
past 400 years alone
 ● Speciation has generated the diversity of
life
● Eukaryotes are “cells within cells”
● Photosynthesis changed the course of
evolution - and the planet
● Multicellular organisms developed
relatively late in Earth's history

Major threats to biodiversity are:

● Habitat destruction and degradation
● Over-exploitation (extraction, hunting,
fishing, etc)
● Pollution
● Disease
● Invasions of alien species (e.g. cats and
rats on islands)
● Global climate change (changes in
migratory species, coral bleaching)

Data suggest that a sixth mass extinction is already

underway and speeding up unless dramatic action
is taken.
● Cause: Anthropogenic
● Extinction rates speeded up since the
1800s (Industrial Age)

Consequences of Mass Extinctions

Mass extinction can pave the way for adaptive
radiations
● Mammals underwent adaptive radiation
after the extinction of terrestrial dinosaurs
● Other notable radiations include
photosynthetic prokaryotes, large predators
in the Cambrian, land plants, insects, and
tetrapods

Evolutionary Milestones
● Life arose from nonlife
○ Involved a lot of chemical
processes in between
○ Chemosynthetic process
● The first organisms were single cells