1.1: Ecological and Evolutionary Genetics

Question 1

what is the genome

Answer 1

the total DNA

Question 2

mitochondria (mtDNA), sex chromosomes and autosomes are all apart of

Answer 2

the genome

Question 3

the mitochondrial and chloroplast dna are transmitted through

Answer 3

the female parent (uniparentally inherited)

Question 4

for humans and fruitflies, males are the heterogametic sex with XY where all members have the X chromosome. what is the difference for birds or lepidoptera

Answer 4

all members have the Z and the heterogametic sex are females with ZW

Question 5

which group of species have Z and W sex chromosomes

Answer 5

birds and lepidoptera

Question 6

which types of chromosomes can undergo recombination

Answer 6

autosomes

Question 7

contrast the results of genetic exchange between the high and low recombination rates

Answer 7

high recombination - likely inherited independently
low recombination - inherited as a unit thus the evolutionary fates are tied together

Question 8

can recombination happen in all population members

Answer 8

yes

Question 9

different parts of the genome have alternative modes of transmission, some parts are uniparentally inherited and others are biparentally. which parts of the genome belong to which?

Answer 9

uniparent: mt, Y
bi parent: autosomes, X

Question 10

areas of low recombination will be inherited _______, while recombination will break up areas of high recombination to be inherited _____________

Answer 10

inherited as a unit, inherited independently

Question 11

how can genomic data be used - for both biparental and uniparental and combined

Answer 11

• use regions of the genome that are inherited biparentally to infer the contributions of both parents
• use uniparentally inhertied genomes tack specific contributions of one parent: mtDNA trakc mternal lineages, Y chromosomes track paternal lineages
• combined: use genetic markers to understand the evolutionary process and use data about behaviour and ecology to understand patterns in genetic data

Question 12

we can use regions of the genome that are inherited __________ to infer the contributions of both parents

Answer 12

biparentally

Question 13

define inbreeding depression

Answer 13

reduced fitness of inbred offpsring to non inbred

Question 14

what is estrous

Answer 14

the receptive part of the reproductive cycle

Question 15

describe some characteristics of an elephants natal group

Answer 15

the natal group is the group they were born into: 2-20 maternal kin, composed of females and juveniles, males leave at adolescence

Question 16

why would experiments with elephants be impossible and what is the solution

Answer 16

gestation is 22 months, 64 lifespan and so measuring inbreeding depression or fitness directly is infeasible thus the use of genetic markers allows an inferential approach

Question 17

state the litmus test for assessing the elephant experiment

Answer 17

do males behave in a way that suggests inbreeding avoidance

Question 18

for the question, “do males behave in a way that suggests inbreeding avoidance” what would the two hypotheses be

Answer 18

1. yes, male elephants have evolved inbreeding avoidance because inbreeding depression is severe
   2: selection has not led to inbreeding avoidance because inbreeding depression is weak and/or male reproductive success is so highly variable (mating w relative is better than not mating at all)

Question 19

how was “do males behave in a way that suggests inbreeding avoidance” measured or what steps were taken to answer it

Answer 19

• observe elephant behaviour (who they direct behaviour to)
• quantify mating behaviours and assess whether they are directed away from kin
• maternity is a certainty and paternity requires genetics == extracted dna non invasively through poop and did patenrity analysis in the lab with genetic markers

Question 20

(maternity/paternity) is a certainty, (maternity/paternity) requires genetics

Answer 20

maternity is a certainty and paternity requires genetics

Question 21

in this question, “do males behave in a way that suggests inbreeding avoidance” what are the null and alt hypothesis.

Answer 21

null: nether inbreeding avoidance or preference
two sided: inbreeding preference and inbreeding avoidance

Question 22

what is the result of: “do males behave in a way that suggests inbreeding avoidance”. how do they know

Answer 22

result: elephants avoid their kin – the results even hold for paternal kin (paternal half siblings: male elephants avoid female half siblings that share a father)
observed the behaviours of following, guarding, copulating, and siring and compared these behaviours with natal fam/close kin vs not and saw much less for kin

Question 23

contrast between genetic differentiation and genetic variation

Answer 23

genetic differentiation: differences BETWEEN pops in allele freq
genetic variation: amount of variation WITHIN populatoins

Question 24

list examples of genetic variaiton

Answer 24

nucleotide diffs, heterozygosity, proportion of polymorphic loci, etc

Question 25

gene flow will _______ differences between populations

Answer 25

erode

Question 26

restricting gene flow will lead to the __________ of genetic differences

Answer 26

accumulation

Question 27

to answer the question, “how do barriers affect genetic structure in coyotes”, what methods did they use

Answer 27

collected ~1000 scats in the greater seattle area (its divided by roads, major water ways), and dna was extracted from scats for microsatellite analysis

Question 28

what are microsatellites

Answer 28

repetitive dna motifs that can be used as genetic markers

Question 29

state the null and alternative hypotheses for the following question, “how do barriers affect genetic structure in coyotes”

Answer 29

null: natural and human barriers have no effect on coyote patterns of genetic variation
alt1: natural and human barriers lead to genetic differences between coyote pop (presumably because of reduced gene flow)
alt2: natural and human barriers lead to slight genetic diff between coyote pop (presumably because of reduced gene flow)

Question 30

describe Fst

Answer 30

it is one measurement metric for genetic differentiation. it ranges from 0 (pan-mixia) and 1 (complete genetic differentiation – allelic freq completely diff)

in coyotes it was 0.08 == not strong pattern (it’s the slope on genetic distance (y) and variable (x))

Question 31

how can genetic differentiation be genetically measured

Answer 31

fst

Question 32

what do the values of fst mean

Answer 32

it ranges from 0 (pan-mixia) and 1 (complete genetic differentiation – allelic freq completely diff)

Question 33

list 2 dispersal barriers that affect human populations

Answer 33

1. culture
2. physical (oceans, mountains)

Question 34

will dispersal barriers affect different components of genome is the same way? explain.

Answer 34

not necessarily. these features might have differential effects on different components of our genomes - mtDNA, Y chro, X chro, autosomes

Question 35

define patrilocality and matrilocality (2 common human trends)

Answer 35

patrilocality: females move to the location of their male reproductive partner
matrilocality: males move to the location of their female reproductive partner

Question 36

predict the effects of patrilocality and matrilocality on y chro and mt dna differentiation and variation

Answer 36

patrilocality:
- y chro variation: lower
- y chro differentiation: higher
- mtdna variation: higher
- mtdna differentiation: lower
matrilocality:
- y chro variation: higher
- y chro differentiation: lower
- mtdna variation: lower
- mtdna differentiation: higher
*the variations and differentiations are paired, use that to ascertain trends

Question 37

in the early new of human genetic DIFFERENTIATION, what would the fst tell us

Answer 37

for patrilocality: higher y chro than mtdna
for matrilocality: higher mtdna, lower y chro

Question 38

in the later view, (with better markers) considering human differentiation. what is the correlation between y chromosome and mtdna (in fst)

Answer 38

• gene flow among populations is similar for males and females
• similar rates of divergence for y chromosomes and mtdna (slightly faster rate in mtdna)

Question 39

an approach is the use of genetic markers, what can this help us infer

Answer 39

mating, fitness (mating and paternity), movement, human migration – and illuminate the evolutionary process in long lived organisms

Question 40

combining the knowledge of which 2 key factors will affect differentiation

Answer 40

habitat barriers, genomic transmission

Question 41

human ________ will affect patterns of genetic differentiation and diversity among and within populations

Answer 41

social behaviour

Question 42

there are conflicting results in many papers that aim to describe sex biased dispersal patterns. however, state the trend in the majority of REGIONAL level studies

Answer 42

female biased dispersal (patrilocality)

Question 43

since there are conflicting results in many papers that aim to describe sex biased dispersal patterns, what factor would influence this a lot

Answer 43

cultural variation

Question 44

for the hill people of northern thailand (same georgraphic region, speak related sino-tibetan languages, practice similar modes of agriculture). describe the approach to assess human differentiation

Answer 44

compare genetic diversity on mtdna and y chromosomes for matrilocal and patrilocal ethnic groups in the same region

Question 45

for the hill people of nothern thailand, state the trends in variation results

Answer 45

patrilocal: lower y chrom variation, higher mtdna
matrilocal: higher y chrom variation, lower mtdna
(this makes sense)