Inbreeding

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Inbreeding
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What is inbreeding? Inbreeding is the mating of
individuals related by ancestry. It is measured
as the probability that two alleles at a locus
are identical by descent (F). Inbreeding
increases homozygosity and exposes rare alleles.
When parents of an individual share one or more
common ancestors (i.e. are related), the
individual is inbred.
Inbred matings include self-fertilization, mating
of brother with sister, father with daughter,
mother with son, cousins, etc. Inbreeding is
unavoidable in small populations as all
individuals become related by descent over time.
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Conservation concerns with inbreeding
Inbreeding reduces reproductive fitness in
essentially all well-studied populations of
outbreeding animals and plants. Example Ralls
Ballou (1983) found higher mortality in inbred
progeny than in in outbred progeny in 41 of 44
mammal populations. In the pygmy hippopotamus,
inbred offspring had 55 juvenile mortality,
while outbred offspring had 25 mortality. On
average, progeny of brother-sister (fullsib)
matings resulted in a 33 reduction in juvenile
survival.
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Inbreeding coefficient (F)
The consequence of matings between relatives is
that offspring have an increased probability of
inheriting alleles that are recent copies of the
same DNA sequence. These recent copies of the
same allele are referred to as identical by
descent, or autozygous. An offspring resulting
from a brother sister mating may inherit two
copies of allele A1 from its grandparent. The
grandparents are said to be common ancestors
meaning that they are ancestors of both the
mother and the father of the individual. The
inbreeding coefficient (F) is used to measure
inbreeding. The inbreeding coefficient of an
individual is the probability that both alleles
at a locus are identical by descent.
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As F is a probability, it ranges from 0 to 1, the
former being outbreds and the latter completely
inbred. Identity by descent is related to, but
distinct from homozygosity. Individuals
carrying two alleles identical by descent are, of
course, homozygous. However, not all homozygotes
carry alleles that are identical by descent, i.e.
homozygotes include both autozygous and
allozygous types (where the two alleles do not
originate form a recent common ancestor).
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The inbreeding coefficient of an individual
resulting from self-fertilization (selfing) is ½
and that for an individual resulting from
brother-sister (full-sib) mating is ¼ . To
calculate inbreeding coefficients from first
principles, each non-inbred ancestor is labeled
as having unique alleles (A1A2, A3A4, etc.). The
probability that an individual inherits two
alleles identical by descent (A1A1, or A2A2 etc)
is computed from the paths of inheritance,
assuming normal Mendelian segregation.
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Example, with selfing the inbreeding coefficient
is the probability that offspring X inherits
either two A1 alleles by descent or two A2
alleles. Individual X inherits either two A1
alleles by descent, or two A2 alleles.
Individual X has ½ chance of inheriting it
through the pollen. Consequently, the probability
that X inherits two identical A1 alleles is ½ x ½
¼. Similarly the chance that X inherits two A2
alleles is also ½ x ½ ¼. The inbreeding
coefficient is then the probability of inheriting
either A1A1 or A2A2 ¼ ¼ ½. The inbreeding
coefficient, measures the probability of alleles
at a locus being identical by decent within an
individual. Inbreeding increases the frequency
of homozygotes, and so exposes deleterious
recessives.
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Inbreeding in small populations
While a minority of plants routinely
self-fertilize, animals normally do not self.
In spite of many opportunities for relatives to
mate due to the proximity of siblings, offspring
or parents, inbred matings are generally less
than expected - many species have evolved
inbreeding-avoidance mechanisms. In species
that do not deliberately inbreed, the majority of
inbreeding arises as an inevitable consequence of
small population sizes. In small closed
populations all individuals eventually become
related by descent, so inbreeding is unavoidable.
This can be understood by considering numbers
of ancestors. We each have two parents, four
grandparents, eight great-grandparents and 2t
ancestors t generations in the past. The number
of ancestors rapidly exceeds the historical
population size, so individuals must have common
ancestors and be related.
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For example, 10 generations back we each have
1024 ancestors. Our parents each have 512
ancestors, so the minimum population size for
them to have no common ancestors 10 generations
ago would be 1024. If the population size was
less than this, then our parents must share
common ancestors, and we must be inbred to some
degree. Many threatened species have population
sizes less than this (a size below 1000 adults is
sufficient for a population to be included in the
IUCN vulnerable category), or have had
generations where the size was less than this.
Consequently, individuals are more likely
to be inbred in small than in large
populations. In a very large random mating
population, inbreeding is close to zero as
there is very little chance of mating with a
relative.
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Indirect estimates of population inbreeding
coefficients.
In most populations, levels of inbreeding are
unknown. However, the relationship between
genotype frequencies and inbreeding coefficients
can be used to estimate levels of inbreeding. A
deficiency of heterozygotes provides and
indication that a population is inbreeding,
rather than mating randomly. The deficiency of
heterozygotes, compared to Hardy-Weinberg
equilibrium expectations, provides an estimate of
F.
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A second estimate of the average inbreeding
coefficients for a population can be obtained
from the loss of genetic diversity over time.
Many polymorphic loci should be used to
estimate effective inbreeding coefficients.
This is particularly important if the
inbreeding coefficient of an individual is being
estimated, as there is wide variation in
homozygosity among loci due to the chance effects
involved in Mendelian segregation.
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Fitness consequences of inbreeding and
outbreeding
In diploids the genetic relatedness between the
parents of an individual can be viewed as a
continuum along which there may be changing
fitness consequences for the offspring.
Typically, inbred offspring are less fit
(inbreeding depression) and outbred offspring
more fit (heterosis) The underlying processes
responsible for inbreeding depression and
heterosis probably include increased homozygosity
for deleterious recessive mutations and
overdominance. The fitness consequences of
inbreeding are a major concern in conservation
biology of species now dependent on captive
breeding or intensive management.
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Although a species may show inbreeding depression
or heterosis in the laboratory, we often do not
know how common inbreeding events are in nature,
and therefore whether laboratory observations are
of any consequence in the wild. There is
considerable debate in the literature as to what
level of relatedness constitutes inbreeding in
natural populations. There is substantial
evidence that inbreeding depression may interact
with environmental conditions, so that laboratory
measurements may not reflect effects found in the
wild. There is a suite of questions about how
inbreeding depression varies with the kind of
trait studied (e.g. early-expressed versus
late-expressed, sexually selected versus not),
which are largely untouched in natural
populations.
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Previous studies of inbreeding in natural
populations have adopted on of two routes. In
one approach, pedigrees are drawn up for
individuals within long-term studies, usually of
wild vertebrates from which individual inbreeding
coefficients (F) are estimated and correlated
with individual measures of various fitness
component or fitness-related traits. Well known
examples of this approach include prairie dogs in
South Dakota and song sparrows on Mandarte
Island. This approach is only feasible for some
species and in some circumstances. Advent of
molecular methods for determining parentage has
generally reduced the confidence with which
parentage can be inferred from behavioral
observations, even for apparently monogamous
species.
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An alternative approach is to analyse individual
mean heterozygosity at a sample of codominant
molecular markers, which should be inversely
correlated with inbreeding coefficient. This
approach has been investigated extensively with
allozymes. Reviews tend to favor a positive
association between individual heterozygosity and
measures of fitness. An obvious advantage of
microsatellites is that individual heterozygosity
measured by microsatellites should be more
closely related to the degree of inbreeding than
that measured by allozymes.
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The stepwise mutation process of microsatellites
offer a second, more interesting approach to
measuring inbreeding and outbreeding. The
difference in repeat units between two alleles at
a locus is related to their time since
coalescence. Working at the population level,
Goldstein (1995) have shown that this distance
squared, averaged over many loci, is linearly
correlated with the time since two populations
diverged.
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