Lecture 1 - Ecological and Evolutionary Genetics

what parts of the genome are uniparentally inherited?

mitochondrial DNA and Y chromosome

what parts of the genome are biparentally inherited?

autosomes and X chromosomes

what parts of the genome are present in all members of the population?

mitochondrial DNA, autosomes and X chromosomes

what parts of the genome are only present in half of the population?

Y chromosomes

what areas are inherited as a unit?

low recombination areas

what areas are inherited independently?

high recombination areas

how are maternal lineages tracked?

tracked by using mitochondrial genome

how are paternal lineages tracked?

tracked by using Y chromosomes

how can uniparental and biparental genome tracking be applied together?

by using genetic markers to understand evolutionary process and use behavioral data and ecology to understand patterns of data

what kind of social system do elephants have?

fluid social system because females tend to live as a group but males are kicked out at adolescence

male elephants

leave natal group at adolescence, attracted to females in estrous, long reproductive lifespan

what is the first hypothesis concerning how male elephants avoid inbreeding?

they have evolved inbreeding avoidance because inbreeding depression is severe

what is the second hypothesis concerning how male elephants avoid inbreeding?

selection has not led to inbreeding avoidance because inbreeding depression is weak and/or male reproductive success is highly variable

why is measuring inbreeding depression or fitness directly not possible?

because gestation is 22 months and lifespan is 62 yrs

what alternative approach is used to measure inbreeding depression and fitness in elephants?

using genetic markers to apply an inferential approach via genetic markers

litmus test

quantifying behavior by assessing if inbreeding is directed to kin or not by observing elephant behavior

what are the 3 possible outcomes of the litmus test?

• no difference between kin and non kin

• inbreeding preference

• inbreeding avoidance

what was the result of the breeding behavior?

majority of breeding is directed to non relatives showing evidence of inbreeding avoidance

what deduction can be made from the litmus test in elephants?

inbreeding depression is most likely high in elephants and females may have some choice and avoid mating with close relatives

inbreeding depression

the reduced survival and fertility of offspring of related individuals

what features of new york rats’ ecology do we use to understand their genetics?

• they rely on human resources that vary across New York

• live in a highly social colony and have small home ranges throughout their life

SNP

single nucleotide polymorphism, section of the genome where there is a polymorphism in the genome

what genomic characteristics are unique to midtown rats?

higher inbreeding, lower observed than expected heterozygosity and lots of pairwise nucleotide differences

what caused the high amount of pairwise nucleotide differences in midtown rats?

caused by a lack of gene flow, higher inbreeding coefficients, reduced heterozygosity and occasional immigration from other neighborhoods

pairwise nucleotide differences

differences between paired stretches of DNA repeated a bunch of times

why is the expected heterozygosity in midtown rats lower than what is observed?

due to occasional immigration from uptown and downtown rats but this is eliminated by inbreeding

how do we know rats live in social groups?

due to high relatedness at short distances, gene flow only present between nearby colonies

what shapes the patterns of genomic variation observed within and between populations?

gene flow (behavior + mating system) + inbreeding

how does human food trash effect genetic variation?

creates habitat availability for the rats creating barrier to their dispersal

patrilocality

females move to the location of their male reproductive partner

matrilocality

males move to the location of their female reproductive partner

in what instances do we expect to see higher matrilocality variation patterns ?

mtDNA differentiation between population and Y chromosome variation within populations

in what instances do we expect to see higher patrilocality variation patterns?

y chromosome differentiation between populations and mtDNA variation within populations

Fst

allele frequency differences

Y chromosome genetic differentiation

as populations become more distant from each other there is more allele frequency differences

what do we observe when Fst is higher at long distances

there is less male gene flow

what do we observe when there is lower Fst at long distances?

more female gene flow

what is the correlation between Y chromosome and mtDNA differentiation?

• gene flow among populations is similar for males and females

• siilar rates of divergence for Y chromosome and mtDNA being a little faster

what do regional level studies conclude about the results?

dispersal is female biased and patrilocality is the dominant variation pattern

Hill people of northern thailand

same geographic region, speak related Sino Tibetan languages, practice similar modes agriculture

what approach is suggested to reconcile the conflicting results?

compare genetic diversity on mtDNA and Y chromosome for matrilocal and patrilocal ethnic groups in the same region

y-str

targets STR regions on the male chromosome that is passed down through the paternal lineage by targeting the Y chromosome, can be unmasked in the presence of female DNA

what causes barriers to human migration

Sahara Desert, Himalayas, Mediterranean, genetic differences mainly within geographic populations