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

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 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

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:

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

    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