Individual genotype: Individual Identity and Capture Mark Recapture by Genotype

Marker: a gene or DNA sequence that allows us to detect variation among individuals or between alleles

Brief overview of Mendelian inheritance

  • all cells in mammals and birds, except sperm, eggs, and RBC in mammals, are diploid (they have two copies of each type of chromosome)

  • Chromosome: a distinct piece of DNA (and associated proteins) containing many genes (23 dif chromosomes in humans, 2n=46)

    • you inherit one copy of each chromosome from your mother and one from your father, therefore you have two alleles at every locus

  • Allele: genetic variant or alternative form of a gene (think yellow or green in peas)

  • Genotype: the specific alleles present in an individual at a particular locus or many loci (or the entire genetic makeup of an individual)

Markers: need to be variable

  • common types of variable DNA markers

    • SNPs

    • Microsatellites

    • DNA sequences and AFLPs (will cover later on)

    • RFLPs and many others that we won’t discuss

SNPs

  • Single nucleotide polymorphism: single base pair positions that vary among individuals (PCR-based)

  • Genetically characterize individuals and populations

  • SNPs plentiful: every 200-500 bp for non-coding DNA and every 500-1000 bp for coding DNA

  • SNPs are becoming more common bc of new methodological approaches, can obtain 1000s of SNP markers - very powerful

Microsatellites (msats)

  • diploid marker

  • Short Repeats (ex. ATATATATATAT)

    • present in most organisms and highly variable: can detect differences among pops or closely related individuals

    • Fast mutation rates: can look at short-term changes (not good for changes in the distant past)

    • Neutral “junk” DNA

      • Advantages: PCR-based so almost any tissue can be used. Tiny amounts of tissue required

      • Disadvantages: Primer of known sequence required. Can be expensive and time-consuming to develop

  • probably most common approach for conservation genetics

  • One Locus

  • Homozygous vs heteroxygous

Examples of microsatellite data

  • to estimate Nc (census size)

  • to assess parentage/familial relationships

Using genetics to estimate Nc

  • number of individuals in a pop is a fundamental characteristic

  • why not use traditional methods?

  • can use genetics to estimate Nc

    • rarefaction

    • capture-mark-recapture

Rarefaction

  • estimate minimum pop size by counting the number of unique genotypes

  • ex. 30 unique genotypes out of 115 coyote feces samples

  • estimate can be corrected to take into account the probability of not sampling individuals

Capture-mark-recapture - Individual ID: Match probability

  • match the genotype of a sample to an individual

    • ex. match a hair to an individual bear to recognize a recapture or a new individual

  • use highly polymorphic markers and then compute a match probability based on allele frequencies from the reference pop

Capture-mark-recapture

  • can be used with genetic data

  • Multilocus genotypes are the permanent marks

  • Nc = (N1 x N2)/R

    • N1 = number of individuals int he first sample

    • N2 = the number of individuals in the second sample

    • R = number of animals recaptured

  • Ex: 10 animals caught in first, 10 caught in second, 5 animals capture in the second sample were marked

    • Nc = (10×10)/5 = 20

Problems with the method

  • failure to distinguish individuals (not enough loci, loci not variable enough) = underestimate pop size

  • Genotyping errors produce false unique genotypes = overestimate pop size

Bears - Northern Continental Divide Ecosystem

  • more sophisticated: not just estimating abundance but long-term monitoring of pop growth rates (lambda) and distribution

Grizzly Bears

  • listed under the ESA since 1975

  • Monitoring consisted of opportunistic sightings of females with cubs, distribution of females with young, and human-caused mortalities

  • Inadequate: no reliable estimates of pop size, trend, or distribution

  • 2006: Montana draft grizzly bear management plan: pop trend info will guide management decisions

  • Radiotrack 25 females in perpetuity

  • Live capture of bears is:

    • expensive

    • logistically difficult in remote areas

    • requires specialized training

    • has inherent risk to bears and trappers

    • may be subject to intense scrutiny and potential moratoria on public lands

Non-invasive genetic sampling

  • barbed wire on bear rubs

  • Species ID, individual identity, and sex via nuclear DNA extracted from hair follicles

  • 7 msats

Objectives

  • power to detect gender-specific and pop-wide declines in pop abundance

  • precision and relative bias of growth rate estimates

  • Sampling effort required to achieve 80% power to detect a decline within 10 years

Results

  • model simulations showed annual bear rub surveys would exceed 80% power to detect 3% annual decline within 6 years

  • rate of decline rapid enough to require management intervention, but slight enough to require a powerful monitoring method

Parentage Analysis

  • can use individual genotypes to identify mothers and fathers bc we know that one allele at each locus comes from the mother with the other allele comes from the father

  • can do with a specific group of individuals

    • ex. nestlings where the mother is known

  • or for a pop without a pedigree

    • here you need many and highly variable loci

    • can assign probable parents for each individual and build a pedigree