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.  Ne 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 Ne?

Unequal proportions of females and males

Sex ratios distorted by mating system

Stochastic variation in small populations

Anthropogenic effects

Ne = 4Nef x Nem/ Nef +Nem


Deviations from 1:1 lead to reduction in Ne


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



High rates of mutation in animals

Universal primers available

No recombination

Different regions evolve at

    different rates

Easy to amplify from non-invasive




Organellar: Mitochondrial DNA



Only tells you about female


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 Ho
(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


Indirect estimates of gene flow

Population sizes in each fragment

Migration rates b/n fragments

Dispersal capacity of individual

    organisms (along ecological




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

Hi = average observed heterozygosity across subpopulations

Hs = average expected heterozygosity across subpopulations

Ht= expected heterozygosity of the total population


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


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


FST = (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:

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

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


FST = 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



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