Genetics in Domesticated Species

Question 1

domestication

Answer 1

selection for traits of genetic tameness; domestic animals can tolerate close and continual human presence w/o exhibiting stress or fight or flight and can mate and reproduce in proximity to humans

Question 2

Belayev’s Farm Fox Experiment

Answer 2

foxes selected for tameness started wagging their tails in 4 generations and developing white splotches; foxes display traits of domestication syndrome within 6 generations

Question 3

3 pathways of domestication

Answer 3

Commensal, Prey, Directed

Question 4

Commensal domestication

Answer 4

these aren’t animals that were kept in kennels these were dogs and cats that started hanging around humans because of scavenging or because of rodent populations and in turn selected for animals that were comfortable around people and didn’t get stressed around them

Question 5

Directed domestication pathway

Answer 5

Remove animals from the wild and select for certain traits to develop a domestic species

Question 6

Prey domestication pathway

Answer 6

If hunting an animals is easier to do this if controlling the landscape where the animals live then enentually start breeding them

Question 7

pig domestication pathway

Answer 7

were domesticated twice one through commensal pathway once through prey pathway; domesticated in Near East and East Asia; key domesticate of Polynesians, used for food, hide, bone, bristles, and control refuse (garbage); came from wild boar can still hybridize with them

Question 8

Domestication syndrome plants

Answer 8

• loss of seed dispersal
• increased grain/ fruit size (we selected for bigger, better tasting fruit)
• loss of environmental sensitivity
• synchronous ripening
• compact growth
• enhanced culinary chemistry
• Reduced armor
• Reduced Toxins

Question 9

Domestication syndrome animals

Answer 9

• Increased docility
• Coat color changes
• Reduced tooth size
• Craniofacial changes
• Ear/ Tail modifications
• Nonseasonal estrus
• Hormonal changes
• Prolonged juvenile behavior
• Reduced brain size

Question 10

What underlies domestication syndrome in animals?

Answer 10

Neural crest hypothesis: reduction in neural crest cell migration may underlie most of the conditions in DS meaning these traits were not individually selected for but rather they all sort of go together because they are related to neural crest cells; this is because all these traits are linked to neural crest cell migration changes; see effect of reduced neural crest cell migration by loos of pigment at tips of face, paws, tail, and ventral surface

Question 11

Dog domestication

Answer 11

First human domesticated species (even before plants) they were likely domesticated in Asia from Eurasian grey wolves; started as commensal domestication (self-domestication) then became obligate scavengers and humans could take them into communities and breed for roles as hunting/ guard dogs/ pets ect; most dogs today live as semi-feral commensal village dogs many live as pets/ working dogs and some are truly feral dingos

Question 12

dingos

Answer 12

these are dogs that are truly feral they were domestic and ended up loosing domestication and becoming wild again

Question 13

Natural and artificial selection in dogs

Answer 13

gray wolves most natural selection -> indigenous village dogs (branching to feral dogs and street dogs)-> traditional bred dogs -> registered dog breeds (branching to mixed breeds)= most artificial selection least natural selection (ie natural selection for pure breeds is that they have to stay alive)
- artificial selection basically for personality and then morphological traits such as size, appearance, earlier age of reproduction

Question 14

domestication and artificial selection

Answer 14

• domestication selected for behavioral changes, smaller body size, earlier age of retro, probs evolved with tameness bc obligate scavengers
• barking likely arose early
• Adapted diet
• modern breeds founded from local dogs or breeds or cross breeding (breeding shifted a lot when focus switched to pure breeds)

Question 15

roles dogs were bred for

Answer 15

• livestock (gaurd, herding ect)
• sporting- hunting
• service- guard dogs, sled dogs, rescue dogs, tracking dogs, pets, housework, barge, cart, carriage, travois
• Production- meat and fiber

Question 16

Phenotypic diversity in dogs

Answer 16

huge phenotypic diversity in dogs; great for maping traits like body size; also behavioral diversity but genes not mapped

Question 17

Cat domestication

Answer 17

• came from middle east
• not as many breeds of cats as of dogs bc cats not as motivated for us to breed purpose into them mostly do rodent control
• mostly selection for coat color variation
• some breeds, most are hybrids (ie Bengal, Savanah Cat ect)

Question 18

Bovid domestication

Answer 18

• sheep and goats domesticated in near east
• cattle (taurine) domesticated in near est; Zebu cattle (indices) domesticated in Indus valley
• selective sweeps not shared between taurine and indicine cattle (ie cattle domesticated twice once for each of these populations)
• Cattle have been improved via marker assisted seleciton

Question 19

Camelid domestication

Answer 19

• Evolved in North America during Eocene, old world and new world camels diverted
• Dromedaries= domesticated in Arabia= no longer in wild
• Bactrain= domesticated in Central Asia= still in wild but critically endagnered= 6 subspecies exist
• camels used for draft animal, saddle animal, milk, hair, dung, blood
• Llama and alpaca domesticated from guanaco and vicuna; were in North America then went to South America llama used for meat and pack animal

Question 20

horse domestication

Answer 20

horse evolved in North America, dispersed into old world then went extinct in new world; new world has feral horse populations again

Question 21

Rabbit domestication

Answer 21

domesticated fairly recently maybe by monks in France to eat on Fridays per pope ok to eat them and fish on Friday; now about 50 breeds; used for pets, pelts, food, and research animals

Question 22

Guinea pig

Answer 22

domesticated in South America used for food until imported to Europe where used for pets and research animals

Question 23

Chicken domesticato

Answer 23

domesticated in Asia; most prolific bird in the world; depends from red jungle fowl but has yellow feet from recessive mutation from gray junglefowl (indicating hybridization early on); large domestication sweep around thyroid stimulating hormone for increased egg laying capacity; sweeps in roasters vs egg layers

Question 24

Turkey

Answer 24

domesticated in Mexico; these were main poultry meat source in new world

Question 25

Pigeon

Answer 25

- domesticated from rock dove near Mesopotamia - were bred for food now for fancy of homing - MANY breeds bust most are feral (racing/ homing/ carrier most closely related to feral) - Selective sweep in EphB2 controls head crest - many breeds; used to draw picture of what you wanted and breed based on that and behavior

Question 26

Large amounts of differentiation between dogs and wolves

Answer 26

domesticatio; mainly drift at certain loci; drift accelerated in breed dogs vs village dogs because small effective population size in breed dogs; dogs and wolves are v different species although they can interbreed

Question 27

differentiations between village dog populations

Answer 27

little differentiation; large population size

Question 28

Basenjis and drift

Answer 28

so much drift Basenjis are equally related to Congo village dogs and gray wolves

Question 29

Skeletal and coat variation in the dog (and other domesticates)

Answer 29

- these variants are much older than breed barriers; it is possible that a trait shared among breeds will mean the breeds also share variant underlying the trait (ie shared trait bc of same gene mutation) - skeletal and coat traits are under intense selection so alleles contributing to variation are likely to rise in frequency and become fixed in select populations; high Fst associated with these traits under extreme selection - highly mappable traits

Question 30

mapping skeletal and coat traits in dogs

Answer 30

highly feasible b/c: 1. Tremendous phenotypic signal (lots of diversity) 2. Huge #s of breeds each selected based on skeletal and coat traits 3. Individual breeds subject to selection and drift and likely to be fixed for one or two loci/ trait so genetic diversity reduced making mapping easier - general idea is take big phenotypic signal and pick up on major genes driving the trait

Question 31

Gene architecture for body size in dogs vs people

Answer 31

look at 10k people and barely find significant genes for body size, look at 2k dogs and find quite a few significant traits bc these genes have major effect on size phenotype (explain 90% of variation is size and weight)

Question 32

IGF-1

Answer 32

every individual in small size breed has same sweep haplotype at IGF-1

Question 33

Complex diseases

Answer 33

- don't know much about genetics of complex dx in dogs - pleiotropic? (gene affects multiple traits) - dx alleles subject to hitchhiking/ genetic drift (risk alleles occurring at higher or lower frequency in some breeds) - dx alleles frequency in breeds bc drift - driven by single loci or many minor loci cumulatively? - risk for complex dx driven by alleles segregating at many loci? - due to small Ne seems many dx alleles will be fixed because of simple drift in breeds even if not under selection

Question 34

Mapping canine complex dx

Answer 34

- diff breeds vary in prevalence of some dx suggesting strong genetic component - Risk alleles could be fixed in breeds were dx is prevalent - unrelated breeds most likely don't share many of sam risk alleles (at least for large effect loci which are young, rare, and deleterious) - related breeds share some dx causing variants - need to use cross-breed mapping (look at breeds with high dx prevalence and breeds with low to try to figure out what is causing that dx)

Question 35

why do domestic species differ in population and genome structures from wild species

Answer 35

- small effective population size - intense artificial selection - differentiation into breeds fixed for desirable traits

Question 36

what traits do breeds differ most on

Answer 36

- coat - body size - often other skeletal traits - sometimes behavior

Question 37

complex trait mapping gin domesticates

Answer 37

feasible to map especially when trait selected and genetically simplified by breed structure things that have been selected for tend to be easiest things to map

Question 38

domestication effect on population size

Answer 38

when a species is domesticated its population size is likely to dramatically shrink and that means drift will be powerful in subsequent smaller population; small pop size and founding bottle neck means more closely related members of population than before

Question 39

fixation in new population

Answer 39

genetic diversity goes down after bottle neck (fewer haplotypes at any particular locus than there were before); some markers will loose all but one allele which will go to fixation in new small population

Question 40

selective breeding

Answer 40

humans control matings to try to fix a trait or set of traits in a population and select who to mate to get those traits

Question 41

natural selection under domestication

Answer 41

is relaxed; get more diverged coat traits where in wild populations they are v similar because natural selection acting upon them for camouflage and signaling; we protect domestic species from predators so they don't have to worry about camaflogue or running down food ect. We may even like a new fur pattern and select to fix it in the breed

Question 42

adaptations that would be maladaptive under natural selection can be __ __ under artificial selection

Answer 42

highly adaptive

Question 43

why is mapping in dogs so effiecient

Answer 43

there are multiple traits under intense positive selection by breeders which have strong genetic signals that aid in mapping them; more variation means more phenotypic signal (variants with large effects have been actively selected thus just a few large effect variants can explain substantial portion of the variants we see)