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Rachit Jain(2011084)
Rishabh Kwatra(2011087) .
Abstract
Genetic Diversity in Modern human is the result of
demographic history(study of human population in the
past) and selective effects that have acted to adapt dierent populations with respect to environment.Global Diversity can be explained on the basis of geographical location(geography),climate and many more factors.Global
Diversity Pattern is also based on out of africa model
of early human evolution.Natural Selection,climate,diet,
pathogens is responsible for population differences after
study is done on loci(specific location of a gene or DNA
sequence on a chromosome).
Introduction
Aim of human population genetics is to explain current
patterns of genetic diversity on the basis of population history and how humans adapted the enviroment or in other
words globe successfully.Goal is to study the effects/causes
of human genetic diversity. We will discuss developments
by studying human genetic diversity with the help of samples,computing FST on 2 population,SNP Plot and finally
dietary and climatic adaption by human population.
0.1 Mating
Mating can occur in two forms, with different consequences. One form of nonrandom mating isinbreeding,
0.3 Distribution
A species with a broad distribution rarely has the same
genetic makeup over its entire range. For example, individuals in a population living at one end of the range may
live at a higher altitude and encounter different climatic
conditions than others living at the opposite end at a lower
altitude. What effect does this have? At this more extreme
boundary, the relative allele frequency may differ dramatically from those at the opposite boundary. Distribution is
one way that genetic variation can be preserved in large
populations over wide physical ranges, as different forces
will shift relative allele frequencies in different ways at either end.
If the individuals at either end of the range reconnect
and continue mating, the resulting genetic intermixing can
contribute to more genetic variation overall. However, if
the range becomes wide enough that interbreeding between
opposite ends becomes less and less likely, and the different forces acting at either end become more and more pronounced, and the individuals at each end of the population
range may eventually become genetically distinct from one
another.
0.4 Migration
Migration basically is the transfer of alleles from gene
pool of one population to the other. Allele frequency will
change if migration occurs into or away from the population. It is more possible in animals than plants as they are
mobile and hence more capable of meeting genetically distinct species. Gene flow or migration leads to combining
of two gene pools, and even though this reduces variation,
it helps maintain genetic diversity. After mating is established between the migrating and destination individuals,
the migrating individuals will contribute gametes carrying
alleles that can alter the existing proportion of alleles in the
destination population.
0.2 Allele
One of a number of alternative forms of the same gene
or same genetic locus (generally a group of genes). different alleles can result in different observable phenotypic
traits, such as different pigmentation. However, many variations at the genetic level result in little or no observable
variation.
Fixation Index
The fixation index is the average coefficient of inbreeding in a population. In case of random mating, the probability that an offspring would have exactly the same two
ancestral alleles at a locus is (1/2)N, where N is the number of diploid individuals in the population. The probability of having two different alleles at the same locus is
1 (1/2)N. The coefficient of inbreeding of the first generation of this population is also (1/2)N by definition of
inbreeding. In each succeeding generation, the non-inbred
part of the population will have a chance to produce offspring with an allele pair identical by descent. Therefore,
the coefficient of inbreeding in the next generations will be
(1/2)N + [(1 (1/2)N] x F, where F is the inbreeding coefficient of the preceding generation. After the gth generation
the coefficient of inbreeding of this population will be: Fg
= (1/2)N + [1 (1/2)N]Fg1 and this is called the index of
fixation.
Figure 2:
Figure 2
The values of Fst for pairwise population comparisons
of 34 genes among the three most commonly defined human continental population groups (African, Asians, and
Europeans) are shown in Figure 2.If the value fell within
the 95(Cavalli-Sforza et al. 1994) value, then the degree of
genetic diversity for this gene between these two populations was considered to be not significantly different from
that expected from the reference value (indicated as R in
the table). Values greater than the upper confidence limit
could reflect the effects of positive or diversifying natural selection leading to increased diversity between populations. Values of Fst below the 95on the other hand, might
result from balancing selection (especially for alleles at or
near fixation), or could be due to chance.
SNP
We took samples from 1000genome project with following constraints Linkage Disequilibrium Data Focus:
Variant rs311685 (dbSNP 137)
Figure 6:
Figure 8:
Figure 9:
Figure 10:
Figure 12: rs12213727
Adaption to Environment
0.1 Climate
They refer to adaptations in a living organism in response to change in climate, habitat and surroundings.
This includes physical changes like the change in skin/fur
color; or behavioral changes like hibernating during winters. Africans, living in the tropics were exposed to direct sunlight, which meant a darker skinned population.
On the other hand, the migrants settled in colder environments, with lesser sunlight, resulting in a lighter skin tone.
Bergmanns Rule
It states that populations having less massive individuals
are more often found in warm climates near the equator,
while those with greater mass, are found further from the
equator in colder regions. This is due to the fact that big
animals generally have larger body masses which result in
more heat being produced. The greater amount of heat results from there being more cells. A normal byproduct of
metabolism in cells is heat production. Subsequently, the
more cells an animal has, the more internal heat it will produce. Also, larger animals usually have a smaller surface
area relative to their body mass and, therefore, are comparatively inefficient at radiating their body heat off into the
surrounding environment.
Allens Rule
He noted that among warm-blooded animals, individuals
in populations of the same species living in warm climates
near the equator tend to have longer limbs than populations living further away from the equator in colder environments. This is due to the fact that a body with relatively long appendages is less compact and subsequently
has more surface area. Greater the surface area, the faster
body heat will be lost to the environment.
0.2 Diet
A dietary adaptation is a morphological trait of a species
which relates to the diet of the species.
For example, the shape of primate molars and premolars are adapted to the diet of the species, Insectivores
have pointed teeth for piercing insect exoskeletons Herbivores have ridged teeth which cut teeth in a scissor-like
fashion Dietary adaptations arent just limited to the teeth.
Cows have evolved a stomach which has 4 compartments;
the rumen, the reticulum, the omasum and the abomasum,
which allows for increased efficiency of plant matter digestion compared to a simple stomach. There are many
differences in how effectively our bodies process particular
foods. Some people live a healthy life on diets that would
be at a starvation level for others. Also people eat different
food to suit the surroundings. For example, people living
Contribution
Rachit conceived the idea and organized it , and surfed
the net for data of SNP and Fst, downloaded the data and
found out softwares to compute the data and generated
the result of Snp. Priyam performed the analysis of fst
and generated the results of FST using perl and surfed the
net for Human genetic factors. Rishabh has done work
on adaptation and genetic factors(only theory). All three
wrote paper on basis of work done by each. Priyam converted the proposal and report in IEEE format.
References
[1] Jobling M.A., Hurles M.E., Tyler-Smith C. Human
Evolutionary Genetics: Origins, Peoples and Disease.
New York, Abingdon: Garland Science; 2004.
[2] Rosenberg N.A. Standardized subsets of the HGDPCEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs
of close relatives. Ann. Hum. Genet. 2006;70:841-847.
[3] bio-bwa.sourceforge.net/
[4] samtools.sourceforge.net/
[5] www.broadinstitute.org/igv/
[6] 1000genomes.org