Molecular markers in conservation genetics

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Molecular markers in conservation genetics
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Introduction
Biodiversity is genetic diversity. One goal of
conservation biology is to preserve genetic
diversity. Another goal is to promote the
continuance of ecological and evolutionary
processes that foster and sustain biodiversity.
Genetic drift, gene flow, natural selection,
sexual selection, speciation, and hybridization
are examples of natural and dynamic evolutionary
processes that orchestrate how genetic diversity
is arranged. How can molecular markers
contribute to assessments of genetic diversity
and natural processes in ways that are
serviceable to the field of conservation biology?
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The most general answer is simple Molecular
genetic tools help us to understand the nature of
life. Molecular markers offer conservation
applications in assessments of genetic variation
within populations, biological parentage,
kinship, gender identification, population
structure, phylogeography, wildlife forensics at
various levels, speciation, hybridization,
introgression, and phylogenetics.
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Within-population heterozygosity issues
Conservation genetics have focused on how best to
preserve variability within rare of threatened
populations. A common assumption - higher mean
heterozygosity enhances a populations survival
probability over ecological or evolutionary time.
Management of H in captive populations -
breeding programs designed to avoid intense
inbreeding, either by maintaining populations
above some minimum viable population size or
by exchanging breeding individuals among sites.
For natural populations - ensure adequate
habitat - effective population sizes remain above
levels at which inbreeding becomes pronounced -
facilitate natural dispersal and gene flow among
populations. Thus, concerns about inbreeding
depression in small populations, both captive and
wild, have motivated much of the work in
conservation genetics.
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• With the advent of molecular techniques, more
  direct estimates of heterozygosity were made
  possible.
• These estimates typically involve assays of
  multiple marker loci (such as allozymes of
  microsatellites).
• Such molecular heterozygosity estimates raise two
  major conservation-related issues
• Is molecular variability reduced significantly
  in rare of threatened populations?
• If so, is this reduction a cause for serious
  concern about the future of those populations?

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Molecular variability in rare and threatened
species
In the mid-1800s, indiscriminate commercial
harvests of northern elephant seals (Mirounga
angustirostris) reduced this formerly abundant
species to dangerously low levels. Fewer than 30
individuals survived through the 1890s (all on a
single remote island west of Baja California),
but following legislative protection by Mexico
and the United States, the species rebounded and
now numbers tens of thousands of individuals,
distributed among several rookeries. Bonnell and
Selander (1974) first surveyed 24 allozyme loci
in 159 of these seals from five rookeries and
observed absolutely no genetic variability, a
striking finding given the high heterozygosities
reported for most other species similarly assayed
by protein electrophoretic methods.
Several additional molecular analyses have since
confirmed and extended these finding of an
exceptional paucity of genetic variation in
northern elephant seals.
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Hillis et al. (1991) employed allozyme markers to
estimate genetic variability in the Florida tree
snail (Liguus fasciatus), many of whose
populations are threatened or already extinct.
Among 34 genes monitored in 60 individuals,
only one locus was polymorphic, and mean
heterozygosity was only 0.002. Surprisingly,
the lack of appreciable variation at the allozyme
level contrasts diametrically with this species
exuberant morphological variability, especially
with regard to genetically based shell patterns.
Results highlight the fact that mean
heterozygosity (as registered by molecular
markers) and magnitude of phenotypic variation
(even that which is genetically encoded) are not
necessarily similar.
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Another endangered species assayed extensively
for molecular genetic variability is the cheetah
(Acinonyx jubatus).
The South African subspecies of this large cat
was first surveyed at 47 allozyme loci, all of
which proved to be monomorphic, and at 155
abundant soluble proteins revealed by
two-dimensional gel electrophoresis, at which
heterozygosity also proved to be low (H 0.013
OBrien et al. 1983). Subsequent assays of more
allozyme markers and of RFLPs at the major
histocompatibility complex (MHC) gave further
support to the notion that this population is
extremely genetically depauperate. Additional
confirmation came from the fact that these cats
fail to acutely reject skin grafts from
unrelated conspecifics. The low molecular
genetic variation documented in cheetahs cannot
be attributed to some inherent property
characteristic of all cats, because other species
of Felidae often exhibit normal to high levels of
genic heterozygosity in these same kinds of
assays.
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Later surveys of rapidly evolving molecular
systems (mtDNA and VNTR nuclear loci) did uncover
modest genetic variation in cheetahs across their
broader range, but the overall magnitude remained
low, leading Menotti-Raymond and OBrien ( 1993)
to conclude that the heterozygosity present today
could be due to post-bottleneck mutational
recovery over a time frame of roughly 6,000 to
20,000 years.
OBrien et al. (1987) proposed that the cheetah
experienced at least two population bottlenecks
one approximately 10,000 years ago, prior to
geographic isolation of the two recognized
subspecies (which are highly similar genetically)
and a second within the last century, which may
have produced the exceptional genetic
impoverishment of the South African form.
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In a review of 38 endangered mammals, birds,
fishes, insects, and plants, Frankham (1995)
reported that 32 species (84) displayed lower
genetic diversity, as estimated by molecular
markers (usually allozymes), than did closely
related non-endangered species. A similar trend
subsequently was reported in DNA-level appraisals
(VNTRs, RAPDs, AFLPs, or STRs) of threatened
species versus their more common relatives. The
magnitudes of these reductions in H were not
invariable great, but there are many examples of
rare or threatened populations that reportedly
show extremely low molecular variation. In most
of these instances, results were provisionally
attributed to effects of genetic drift attending
historical bottlenecks in population size.
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In theory, the demographic details of population
bottlenecks (such as their size, duration, and
periodicity) should exert important influences on
the severity of expected reductions in neutral
genetic variability. For example, the loss in
mean heterozygosity can be minimal if populations
size increases rapidly following a single
bottleneck of short duration. An empirical
example of a sever population reduction that, for
suspected demographic reasons, did not results in
low heterozygosity involves the endangered
on-horned rhinoceros (Rhinocero unicornis).
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The particular molecular markers employed can
also dramatically influence estimates of genetic
heterozygosity (allozymes vs. microsatellites).
STR loci have high mutation rates and tend to
recover genetic variation quickly, so the
molecular footprints of population bottlenecks on
these loci should be less long-lasting than on
allozyme loci.
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Does reduced molecular variability matter?
Heterozygosity is reduced in many (though
certainly no all) rare or threatened populations
and species. In general, there are several
reasons for exercising caution in interpreting
low molecular heterozygosities reported for rare
species Most of the reductions in genetic
variation presumably have been outcomes, rather
than causes, of population bottlenecks at least
a few widespread and successful species also
appear to have low H values as estimated by
molecular methods. In some endangered species
(such as the northern elephant seal), low genetic
variation has not seriously inhibited population
recovery form dangerously low levels (at least to
the present).
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Fitness costs of inbreeding are known to vary
widely among species - some taxa are highly
susceptible, but others relatively immune, to
fitness depression effects from consanguineous
matings.
Caution is indicated in drawing firm universal
conclusions about levels of molecular variation
as they might relate on a populations
susceptibility to extinction.
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The argument has been made that demographic,
ecological, and behavioral considerations should
often be of greater immediate importance than
genetic (i.e., heterozygosity) issues in the
formulation of conservation plans for endangered
species. On the other hand, some authors have
forcefully argued that heterozygosity, as
measured by molecular markers, is important to a
populations health and continued survival and
should be monitored accordingly in enlightened
management programs. Several years ago, a
disease (feline infectious peritonitis, or FIP,
caused by a coronavirus) swept through several
captive cheetah colonies and caused 50-60
moralit y over a 3-year period. This same virus
in domestic cats (which have normal levels of MHC
variation, as indicated by graft rejections and
molecular assays) has an average mortality rate
of only 1.
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In general, enhanced susceptibility to infectious
diseases or parasitic agents probably constitutes
one of the most serous challenges faced by a
population with low genetic variation. In
conclusion, especially when large numbers of loci
are monitored and multiple assays are performed
(e.g. of allozymes, MHC loci, and
microsatellites), molecular markers can provide
quite reliable estimates of genome-wide
heterozygosity, which in turn are theoretically
interpretable in terms of historical effective
population sized. Thus, molecular analysis can
help to identify natural or captive populations
that display severe genetic impoverishments from
past population bottlenecks or inbreeding. Less
clear molecular heterozygosity is a reliable
gauge of a populations short-term survival and
long-term adaptive potential.
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Managing captive or natural populations for
genetic heterozygosity - not at the expense of
behavioral, ecological, or environmental factors.
Management programs for rare or endangered
species often promote heterozygosity preservation
through captive breeding programs designed to
avoid close inbreeding or via habitat
preservation that promotes larger effective
population sizes in the wild. So, genetic
heterozygosity issues are typically just one of
several reinforcing elements in a nexus of
management considerations for endangered taxa.
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Inbreeding depression
Inbreeding depression is the decrease in growth,
survival, or fertility often observed following
mating among relatives. The phenomenon is of
special concern in conservation biology because
inbreeding is likely to be severe in small
populations. Genetically inbred populations
have reduced heterozygosity (increased
homozygosity) due to increased probabilities that
individuals carry alleles that are identical by
descent (stem from the same ancestral copy in
earlier generations of a pedigree).
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