Conservation Genetics by kR3B0u

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									      Conservation Genetics
• Why should we be concerned with
  genetic diversity when more severe
  threats threaten entire systems?
• First, the rate of evolutionary change in
  a population is proportional to the
  amount of genetic diversity available
• Fundamental Theorem of Natural
  Selection
      Conservation Genetics
• Second, diversity as measured at the
  level of genes or quantitative genetic
  traits represents the primary level of
  biodiversity
• Every biochemical product, every
  growth pattern, every instinctive
  behavior, every color morph is encoded
  in the in the ‘genetic library’ of each
  species
     Conservation Genetics
• Third, there are many conservation
  challenges that benefit from the
  guidance and direction that genetic
  data, collected and interpreted with the
  constructs of sound population genetic
  theory, can furnish
      Conservation Genetics
• The basic link from genetics to
  conservation is that of small populations,
  which tend to lose genetic diversity over
  time
• The power of conservation genetics
  comes in the form of tools which allow
  one to identify unique evolutionary
  lineages, monitor dispersal movements,
  estimate population size, or trace
  genetic changes through time
     Conservation Genetics
• In this chapter we will go over the
  principles of genetics and how they may
  aid in conservation
• Next, we will provide a board overview
  of contemporary efforts and
  controversies in conservation genetics
Conservation Genetics
         Genetic Variation
• A species’ pool of genetic diversity
  exists on 3 levels: variation within an
  individual, differences among individuals
  w/in a pop(n), differences among
  popuations
Conservation Genetics
       Conservation Genetics
     variation w/in the individual
• Chromosomes consist of long sequences
  of nucleotides, some of which code for
  molecules that create the structure and
  the physiological functions of an
  organism
• A gene represents a specific segment of
  DNA of a specific chromosome pair that
  (1) codes for the primary structure of
  proteins
       Conservation Genetics
     variation w/in the individual
• (2) codes for the formation of
  ribonucleic acid (RNA), or (3) regulates
  the location and time of gene expression
• The majority of genetic material does
  not code for any product (thus not
  subject to NS, unless linked)
• This is termed neutral genetic variation
  and is frequently analyzed when
  examining evolution change…problem?
       Conservation Genetics
     variation w/in the individual
• One such problem is you may be asking
  questions pertaining to adaptive
  variation (i.e. genes under selection)
• So while we are very concerned with
  maintaining the adaptive variation, we
  usually don’t know where in the genome
  that exists (see Box 11.1)
       Conservation Genetics
     variation w/in the individual
• A physical or behavioral character
  (phenotype) can be expressed directly
  as a trait may be entirely due to
  genotype (e.g. eye color) or environment
  (nutritional regime), but more likely a
  combination of both (e.g. skin color)
• Quantitative genetics are helpful in
  determining how much of the phenotype
  is attributable to genes (Box 11.1)
       Conservation Genetics
     variation w/in the individual
• The ultimate source of variation is
  mutation
• Mutations range from a change in a
  single base, deletion or duplication of a
  group of nucleotides, to large-scale
  changes such as deletion, duplication, or
  translocation of large parts of the
  chromosome (or the entire chromosome)
• Are they good, bad, or ugly?
        Conservation Genetics
       variation w/in the individual
• Recombination is another source of variation,
  requires sexual recombination
• At the population level, a given locus is either
  monomorphic (both copies always found
  without variation) or polymorphic (two or
  more types of the alleles possible)
• The overall level of heterozygosity (the
  proportion loci in an individual that contains
  alternative)
       Conservation Genetics
      variation w/in the individual
• What is the value of focusing on genetic
  variation within individuals?
• First, heritable genetic variation is the
  basis for evolutionary change and the
  individual is where NS operates
• Second, the individual is where problems
  associated with inbreeding occur
       Conservation Genetics
      variation w/in the individual
• Third, knowledge of individual genotypes
  may be important in some captive
  breeding programs
• Finally, genetic variation is always
  measured in individuals and can only be
  estimated for collections (i.e.
  populations) through statistical
  summaries
       Conservation Genetics
      variation among individuals
• Variation among individuals, or pop-level
  variation, consists of the types of
  alleles present and their relative
  frequencies across all members of a
  population considered together (the
  gene pool)
        Conservation Genetics
       variation among individuals
• Which has the highest mean Hp? Why are
  other populations (e.g. Litchfield) so low?
       Conservation Genetics
      variation among individuals
• Are gene frequencies constant?
• They frequently change over time due
  to mutation, NS, and random processes
  such as genetic drift, non-random
  mating, small pop size, and I & E (gene
  flow)
       Conservation Genetics
      variation among individuals
• There have been a number of attempts
  to link ecological characteristics ad
  levels of genetic variation
• Not surprisingly, widespread organisms
  tend to have higher levels of genetic
  diversity while small range, small
  populations or large body size are
  correlated with low diversity (see Table
  11.3)
Conservation Genetics
variation among individuals
       Conservation Genetics
      variation among populations
• Species rarely exist as single, randomly
  interbreeding, or panmictic populations
  spread across large areas (or there is
  structure within and among populations)
       Conservation Genetics
      variation among populations
• Diversity is variable, but also higher
  than any individual site
       Conservation Genetics
      variation among populations
• Thus, genetic diversity among a set of
  populations consists of within-population
  diversity and among-population
  divergence
• Thus a simple genetic diversity model is:
             HT = HP + DPT
  where HT = total genetic variation, HP=
  average diversity within pop(n), and DPT
  = average divergence among pop(n)
       Conservation Genetics
     variation among populations
• Divergence may result from a number of
  processes including random processes
  (e.g. founder effects, genetic drift,
  episodic population bottlenecks) and
  from local selection
• Again, important to remember we can
  quantify within and among-population
  diversity components
      Conservation Genetics
     variation among populations
• RCWO has mean heterozygosity of 7.8%
  which is typical
• Of total variation, 14%
  consists of among- and 86%
     consists of within pop(n)
• The among is higher than
  most species, which tend to
  be more site-specific than
  many other sp
       Conservation Genetics
      variation among populations
• Ecological correlates can subsequently
  influence genetic structure by
  influencing movement
• E.g. white-tail deer vs. Alpine Ibex
       Conservation Genetics
      variation among populations
• One frequent question is if current
  mortality rates are negatively impacting
  the health of the population (use
  previous approach)
• The type of genetic marker has issues:
  molecular markers are usually neutral but
  are used as a proxy for adaptive
  variation…(because gene not known)
• Adaptive divergence may not be the
  same as adaptive variation
       Conservation Genetics
    variation at the metapopulation
• We have utilized the metapopulation
  paradigm to describe populations on a
  fragmented landscape
• By definition, metapopulations interact,
  thus influencing the genetic structure
  of the populations
• Metapopulations lose genetic variation
  more rapidly than a single large pop(n)
      Why is Genetic Diversity
            Important?
• The amount of adaptive variation in a
  population should be related to the
  health of a population, or to its ability
  to withstand stresses and challenges
• There have been a number of general
  correlates of genetic variation among
  populations (Table 11.5)
Why is Genetic Diversity
      Important?
     Why is Genetic Diversity
           Important?
• There is mixed results on the actual
  importance of adaptive genetic diversity
• There is no absolute value of
  heterozygosity that indicates a
  population’s health, although it may be
  correlated with individual fitness
  (taxonomic comparisons see Table 11.4)
     Why is Genetic Diversity
           Important?
• However, while the absolute level of
  heterozygosity may not provide a clear
  level of risk, loss of it does indicate
  serious problems
• E.g. low RS following inbreeding is usually
  accompanied by low HP
• There is some evidence
• E.g. Drosophila and inc. salinity & HP
     Why is Genetic Diversity
           Important?
• Among-population divergence may play a
  critical role in local fitness and
  population survival
• First, pop(s) may be locally adapted (?)
• Second, coadapted gene complexes may
  arise in local pop(s) (Essay 11.1)
   Forces that Affect Genetic
      Variation w/in Pop(s)
• When making predictions about likely
  changes in allele frequency, not the
  difference between N and Ne (effective
  populatiton size)
• Ideal is large, panmictic, 1:1 sex ratio
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Mutations are the ultimate source of
  new genetic variation with mutations
  being rare and most being neutral
• This is generally not a problem until
  popo(s) become small…why?
• The gradual accumulation of deleterious
  mutations results in the mutational
  meltdown (mean viability lowered, and
  pop(s) become smaller, with fixation)
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Genetic drift is the random fluctuation
  of gene frequencies over time due to
  chance alone
• Because of sexual mating (and only one
  copy being passed on) there is a high
  chance that not all alleles will not be
  passed on
• Drift can occur very quickly in small
  pop(s)
    Forces that Affect Genetic
       Variation w/in Pop(s)
• Average % of
  genetic variance
  remains over 10
  generation in a
  theoretical, idealized
  pop(n) at various
  genetically effective
  pop(n) size Ne
    Forces that Affect Genetic
       Variation w/in Pop(s)
• Ultimately, in any small pop(n) is genetic
  drift will result in the fixation of one
  allele at 100%
• The likelihood of that occurring is equal
  to the initial allele frequency (e.g. 0.8)
   Forces that Affect Genetic
      Variation w/in Pop(s)
• When a demographic bottleneck occurs,
  the magnitude of the genetic loss
  depends not only on the size of the
  bottleneck but also on the growth rate
  of the population afterward
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Recovery is
  quickest when
  pop(s) have a
  high growth
  rate (r) and
  when
  bottleneck is
  less severe
    Forces that Affect Genetic
       Variation w/in Pop(s)
• Rare alleles are lost from small, isolated
  populations
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Gene flow is the movement of genes
  from one population to another
• Measuring gene flow is problematic
  – Not all breed
  – Cannot account for historical dispersal
  – Similarity could be recent ancestor
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Inbreeding can lead to decreased
  fitness (inbreeding depression) either
  by the expression of deleterious
  recessive alleles or the loss of
  heterozygosity
    Forces that Affect Genetic
       Variation w/in Pop(s)
• Data from
  domestic
  animals
  indicate a 10%
  increase in
  inbreeding
  coefficient will
  result in a 5-
  10% decline in
  ind RS
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Lab studies of land snails and white-
  footed mice were inbred and outbred
  and released…
• Results of WFM
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Not all low levels of heterozygosity or
  even inbreeding should be alarming
• Some natural populations have
  apparently experienced low levels of
  inbreeding for several generation with
  little to no harm
   Forces that Affect Genetic
      Variation w/in Pop(s)
• Outbreeding depression can
Forces that Affect Genetic
   Variation w/in Pop(s)
Forces that Affect Genetic
   Variation w/in Pop(s)
Forces that Affect Genetic
   Variation w/in Pop(s)
Forces that Affect Genetic
   Variation w/in Pop(s)
Why is Genetic Diversity
      Important?
Why is Genetic Diversity
      Important?
  Conservation Genetics
variation at the metapopulation

								
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