Conservation genetics

 
I.  Major Issues

•Inbreeding depression

•Loss of genetic diversity

•Fragmentation of populations and loss of gene flow

•Genetic issues with captivity and  reintroduction

•Resolving taxonomic uncertainties

•Understanding species biology

II.  Management uses

•Minimizing inbreeding and loss of genetic diversity

•Resolving population structure

•Understanding species biology

•Choosing the best populations for reintroduction

•Resolving taxonomic uncertainties

•Defining management units w/in species

•Detecting hybridization

•Non-intrusive sampling

•Wildlife forensics

•Breeding captive species

III.  Genetics underlying conservation

1.  N_e is a key parameter - usually less than census size in most populations

                                    estimated from demographic data

                                    also from genetic data (short, long term)

Size of an idealized population that would lose genetic diversity (or become inbred) at the same rate as the actual population

2.  What factors influence estimates of N_e?

•Unequal proportions of females and males

•Sex ratios distorted by mating system

•Stochastic variation in small populations

•Anthropogenic effects

_•N_e = 4N_ef x N_em/ N_ef +N_em

_•Deviations from 1:1 lead to reduction in N_e

2.  Molecular marker: defined segments of DNA in genome

Can be protein coding and non-coding à selectively neutral

Measuring genetic diversity: polymorphism

Chromosomal/immunological (1900s): first techniques, karyotyping, DNA-DNA hybridization as measure of genetic similarity

Proteins (1960s): enzyme (allozyme) electrophoresis

    distinguish alternate allelic forms by changes in mobility

Organellar - Mitochondrial DNA

Advantages:

•High rates of mutation in animals

•Universal primers available

•No recombination

•Different regions evolve at

    different rates

•Easy to amplify from non-invasive

    samples

Organellar: Mitochondrial DNA

Disadvantages

•Only tells you about female

    evolution

•Is only a single locus

•Nuclear translocated copies (Numts)

•Variable types of selection

•Heteroplasmy: more than

   one sequence

What Are Microsatellites?

•Genetic markers based on variation of unique DNA sequences

•1-6 nucleotide core element tandemly repeated, e.g.

                        atatatatatatatatatat = (at)₁₀

•Allele size based on repeat number of core elements

Primer Design

Observed heterozygosity H_o
(using allele frequencies)

Provides a null model to identify whether evolutionary processes are occurring

Basic Assumptions of HWE: random mating, no migration, infinitely large population size & no migration

Can calculate expected heterozygosity for two alleles with frequencies p and q à HWE equation

                                    p² + 2pq + q² = 1

p² = frequency of allele A

2pq = frequency of heterozygote Aa

q² = frequency of allele a

Estimating allele frequencies at a locus

Studies of gene flow integral to species biology

•Meta-population structure

•Estimators of population

•differentiation

•Indirect estimates of gene flow

•Population sizes in each fragment

•Migration rates b/n fragments

•Dispersal capacity of individual

    organisms (along ecological

    gradients?)

IV.  Wright’s F statistics based on average and observed heterozygosity:

H_i = average observed heterozygosity across subpopulations

H_s = average expected heterozygosity across subpopulations

H_t= expected heterozygosity of the total population

F_IS= (Hs – Hi)/ Hs à measures the degree of inbreeding (homozygosity excess) of individuals within their subpopulation

F_IT = (Ht – Hi)/ Ht à  measures the overall level of inbreeding of an individual relative to the total population (not commonly used)

F_ST = (Ht – Hs)/ Ht àthe “fixation index”, measures the degree of inbreeding of subpopulations relative to the total population, is a common estimator of subpopulation differentiation (i.e. population structure

Wright’s F statistics based on average and observed heterozygosity:

F_IS= measures the degree of inbreeding of individuals within their subpopulation

ranges from 0 (no inbreeding) to 1 (full inbreeding)

F_ST = measures the degree of inbreeding of subpopulations relative to the total population

Ranges from 0 (no population structure) to 1 (fully separate populations)

Values > 0.2 are considered to reflect strong structuring

III.  Genetic distance: genetic relatedness based on the number of allelic substitutions per locus

Character-based approach:

Conservation units identified based on presence/absence of nucleotide substitutions

Tree-based approach:

Conservation units identified based on ‘reciprocal monophyly’

•Phascolarctus cinereus – diverse morphology – differentiated into 3 subspecies

IV.  Other uses of genetic knowledge for conservation

Captive breeding

•Maximize the number of founders

•Maximize no. of breeders/generation

•Stimulate growth to carrying capacity

•Maximize Ne/N ratios

•Selection of individuals for

    reintroduction

Cloning of endangered animal species

Species biology and natural history

•Relatedness and social behavior

•Paternity and reproductive success

•Predator-prey relationships

•Local population dynamics

Identifying hybridization

•Occurs at several levels (species, subspecies and populations)

•Produces offspring of mixed ancestry

•May be morphologically/ genetically intermediate

•Extensive hybridization; progeny not distinguishable from parental types

•“Genetic swamping” of rare/threatened species

•Outbreeding depression