Inbreeding Flashcards
Identity by descent
inbreeding is the inheritance of identical chromosome segments (chunk of chromosome same between individuals); if mutation in one chromosome it will also be in other;
inbreeding affects all
finite population to some degree; particularly strong in small populations and populations (of any size) where matings between close relatives occur
inbreeding measured by
inbreeding coefficient (f); can be estimated from a pedigree or calculated from genetic data
inbreeding increases
homozygosity so it can increase expression of homozygous recessive alleles which may be deleterous
inbreeding depression
caused by increase of deleterious recessive alleles
coefficient of relatedness
r (how related are two individuals) identical twins 1 parent-offspring: .5 full siblings: .5 grandparent-grandchildren: .25 half siblings: .25 First cousins: .125 Second cousins: .0325
why are you approximately 25% related to grandma?
because you are 50% related to each parent but because of recombination could have little more or a little less from grandma or grandpa
coefficient of relatedness and coefficient of inbreeding
coefficient of inbreeding is half of coefficient of relatedness
outbred identical twins selfing inbreeding coefficient
Have coefficient of relatedness of 1 with self the offspring are going to have f=.5 because recombination
inbred identical twins selfin
f=1; for inbred parents the coefficient of relatedness is the same as coefficient of inbreeding
if parents are related inbreeding coefficient in relation to coefficient of relatendess
will be half plus more if parents are related
if parents are unrelated offspring will be
outbred (f=0) even if parents are inbred
if parents are related (COR=x) offspring will be
inbred (f=x/2 or more if parents are inbred)
Drawbacks to pedigree based estimates of relatedness and inbreeding
- they’re just estimates; amount of genomic sharing btwn to individuals depends on actual chromosomal segments transmitted (ie can have distant ancestors who made no genetic contribution if far enough back)
- might be wrong if pedigree is wrong (paternity?)
- only capture IBD as far back as pedigree is recorded (usually 5-10 generations max)
far back pedigree
starting with only a few ancestors contributing same hapolotypes differences appear with recombination events
run of homozygosity
look for this when calculating relatedness and inbreeding; run of homozygosity is continuous length of homozygous genotype present in genome that is shared
- looking at this generally captures inbreeding tracts inherited in last ~100 generations
f with subscript ROH
proportion of genome that is shared; chunk of chromosome that is shared btwn related individuals with no mutations
Inbreeding and Hardy-Weinberg
- effect of inbreeding is a loss of heterozygosity (locus can’t be heterozygous if it occurs in inbreeding tract)
- inbreeding tracts can’t contain heterozygosity so f determines amount of loss in heterozygosity
- inbreeding is violation of random mating assumption of hardy-weinberg equilibrium
expected heterozygosity under hardy-weinberg equilibrium
Ho=2pq
observed heterozygosity
=H
Inbreeding coefficient f=(Ho-H)/Ho
inbreeding hardy-weinbrg frequencies
AA p^2 + fpq
AB 2pq(1-f)
BB q^2 + fpq
f=(Ho-H)/ Ho same as
H=Ho(1-f)
when allele frequency is low and there is inbreeding
it increases number of homozygous genotypes by a large factor if inbreeding is .2 then frequency of recessive allele is now 20x higher than it was before this is why we see more recessive alleles in purebred animals (more inbreeding)
is inbreeding harmful?
Goldens with inbreeding loops in last 10 generations did not live as long and had smaller litter size but there are organisms that have evolved to live in highly inbred populations which works because if inbreeding/ selfing has occurred for many many generations the most deleterious recessive alleles have been exposed to selection and lost
INBREEDING IS NOT HARMFUL IT IS ONLY HARMFUL WHEN IT UNMASKS HARMFUL RECESSIVE VARIANTS
inbreedign in domestic animals
causes inbreedng depression because it unmasks deleterious recessive variants (inbreeding occurs in all domestic animals and is almost always associated with decreased fitness bc it unmasks deleterious recessive alleles)
warnings re genomic testing
- don’t try to use inbreeding to purge deleterious alleles, use genetic testing
- don’t blindly use genomic tools to pedigrees to simply maximize outcrossing; small differences in relatedness/ inbreeding may not be meaningful need to consider other things such as are both parents health and conforming to breed standards (a poor poodle crossed with a poor lab doesn’t make good little or labradoodles)
labradoodles
many are inbred because only if its a lab x poodle vs labradoodle x labradoodle can you say its not inbred and even lab x poodle can make crappy dog if crappy genes
conservation genomics and outcrossing
distant relatives/ lines may be adapted to different purpose/ environment and outcrossing them may make something adapted to neither which is not good in conservation genomics
inbreeding is ___ the relatedness of parents in outbred population
half; can be more in inbred populations
inbreeding (and relatedness) can be accurately calculated from
genome-wide data (dense genotyping arrays or sequencing)
how to estimate inbreeding and relatedness without genomic data
use a pedigree, if no pedigree use molecular markers
