Effective population size in a conservation context'

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Effective population size in a conservation
context.
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Population sizes
The concept of effective population size is
relevant to many conservation efforts. Frankel
(1980) and Soulé (1980) suggested that a minimum
effective population size of 50 individuals would
be required to stem inbreeding depression, and
Frankel (1980) added that an effective population
size of 500 would prevent the long-term erosion
of variability by genetic drift. Lande (1995)
and Lynch and Lande (1998) concluded from further
theoretical considerations that these numbers
were about one or two orders of magnitude too
small. All such recommendations are
assumption-laden and provide only crude
guidelines for population management, but they
do illustrate the kind of attention that has
been devoted to estimating Ne in a conservation
context.
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Average molecular heterozygosity (H) and
long-term effective population size (evolutionary
Ne) are interrelated under models that assume
selective neutrality for genetic variation. If
average mutation rates are known or assumed, and
if the current standing crop of variation in
those markers has been assayed - provisional
estimates of Ne for that population by several
statistical procedures.
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• Marker-based appraisals of the temporal dynamics
  of population demographic history - results must
  be interpreted with great caution because they
  rest critically on several underlying
  assumptions
• that the focal population has been genetically
  closed and spatially unstructured
• that mutation rate estimates are reliable
• that genealogies are estimated with considerable
  accuracy
• and that the particular molecular markers
  employed are appropriate for the ecological or
  evolutionary time frame presumable covered by the
  analysis.

Marker-based estimates of historical population
sizes and their temporal dynamics normally have
major uncertainties and wide biological
confidence limits.
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Molecular markers can also be employed to
estimate generation-by-generation Ne in modern or
contemporary time. One such method requires
that neutral allele frequencies be monitored
across two or more generation. Then, effective
population size for that time interval can be
estimated by statistical procedures that relate
Ne to any of several molecular outcomes that
might be empirically observed reductions in
heterozygosity due to inbreeding changes in
allele frequencies due to genetic drift
rates of decay of linkage disequilibrium among
loci
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Tracking individuals in wildlife management

• Wildlife movements - monitored - physical devices
  (such as fin tags placed on fish, leg bands on
  birds, or radio collars on mammals) or by field
  observations of individuals that are
  distinguishable by natural phenotypic markings
  (such as variable color patterns or scars on
  whales).
• Protein and DNA molecules provide specimen tags
• Advantages
• All species come ready-made with these natural
  labels
• Genetic tags - transmitted across generations
• PCR - make it routinely possible to obtain
  genotypes from shed hair, feathers, eggshells,
  feces, etc.
• Population genetic variation in sexual species
  is normally so high that molecular markers from
  multiple hypervariable loci are expected to
  distinguish individuals with high probability.

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One of the largest molecular studies of this sort
involved black bears and brown bears in western
Canada, for which Woods et al. (1999) used hair
traps (barbed wire attached to trees) to collect
nearly 2,000 hair samples from the wild.
Following PCR, these samples were genotyped at
the mtDNA control region, at a Y-chromosome
segment, and at six autosomal microsatellite
loci. Each genotypic match was deemed to be a
repeat collection from the same individual,
whereas distinct genotypes clearly came from
different specimens. Through these genetic
analyses, the authors were able to identify the
species, sex, and individuality of each sample
without the need to capture or even observe
these free-ranging animals directly.
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Apart from obviating the need to disturb (or be
disturbed by) such large and difficult-to-observe
animals, another rationale for this kind of
individual tracking by non-invasive molecular
markers is to estimate current population size.
For example, based on microsatellite analyses
of coyote fecal samples systematically collected
within a 15-km2 region of the Santa Monica
Mountains near Los Angeles, California, Kohn et
al. (1999) estimated a population size of N 38
for these other wise difficult-to-count animals.
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Parentage and kinship
Molecular studies of genetic paternity and
kinship often have conservation or management
relevance. For example, microsatellite
paternity analyses in one group of captive
chimpanzees showed that the dominant male had
sired most (but not all) offspring (Houlden et
al. 1997). If these results are typical, they
suggest that particular males might generally
dominate reproduction in captivity, in which case
Ne in each zoo population could be far lower than
might otherwise have been assumed. By contrast,
a similar marker-based study of wild chimpanzees
revealed that slightly more than 50 of analyzed
offspring had been fathered by males from outside
the focal group. Thus, managers might wish to
consider the occasional exchanges of male
chimpanzees (or at least their sperm for
artificial insemination) between zoos, both to
diminish inbreeding within captive colonies and
perhaps to mimic natural behavioral and genetic
conditions more closely.
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Molecular data on parentage and kinship have been
used to verify breeding records and correct
studbook errors for several captive or
reintroduced endangered species, such as the
Waldrapp. Such analyses can also be used to help
decide which specific individuals in a captive
population of known pedigree should have breeding
priority when the goal is to maximize population
genetic variation. Marker-based studies related
to parentage and kinship can often provide
conservation-relevant information on managed
non-captive populations as well.
Perhaps the greatest value of molecular parentage
and kinship analyses in conservation effort lies
in their ability to reveal otherwise unknown
aspect of the reproductive biology and natural
history of threatened (and other) species in the
wild.
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Gender identification
Many endangered species in captive breeding
programs are sexually nondimorphic in their
visible features, so sex-linked molecular
markers can play a key role in identifying
gender. In the critically endangered black
stilt of New Zealand, knowledge gained through
molecular sexing was used to avoid same-sex
pairings in a recovery program that began with
only about a dozen adult birds. By estimating
the gender of otherwise unknown individuals in
any populations, molecular markers can also
provide information suitable of estimating
effective population size, because the relative
number of breeding adults of the two genders is
an important determinant of Ne.
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Estimating historical population size
Most high-gene-flow species with large numbers of
living individuals show far less molecular
genetic variation than might have been expected.
Molecular markers sometimes register an
entirely different relationship between inferred
historical population size and contemporary
census size in species that today are rare or
endangered.
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Dispersal and gene flow
Management strategies for natural populations can
often benefit from knowledge about the movement
patterns of organisms (and their gametes) from
their natal sites and the magnitudes of realized
gene flow (i.e., successful reproduction) that
such dispersal entails. Molecular markers can
assist greatly in these analyses, and the
findings often have conservation
implications. One case in point involves marine
protected areas, or MPAs. A sad truth is that
negative human impacts, including pollution and
overharvesting, have radically degraded the
worlds oceans. This situation has triggered
calls for efforts to protect and restore marine
ecosystems.
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How large should MPAs be, and how should they be
spaced? To a considerable degree, the answers
depend on each species dispersal and recruitment
patterns, and in particular, on magnitudes of
larval production and transport. Using
molecular markers applied to many marine taxa,
scientist are examining genetic patterns in the
sea and beginning to interpret results in the
context of MPA design.
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Microsatellites in conservation genetics
Knowledge of the demographic history of
populations is important when making informed
decisions about population management. For
example, there may be concerns about the level of
inbreeding within a populations, the ration of
effective population size to census size, and the
effective population size itself. To ameliorate
possible deleterious consequences of inbreeding
depression and the risks posed by maintaining
monocultures, it might be decided to move animals
from different populations. However, this raises
questions of which populations should be used to
exchanged individuals, and which should be
maintained as genetically distinct.
Microsatellites can be used to answer a number
of these questions.
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• Microsatellites are, however, slightly
• restricted in their potential application,
• largely due to their inappropriateness for
• phylogenetic studies.
• The main areas
• Studies of hybridization
• Population history
• Phylogeography,
• Detecting population bottlenecks and inbreeding
• Assessing the impact of reproductive behaviour,
  social structure, and dispersal on the genetic
  structure of endangered populations.

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