Questions?

1. Questions?

2. Genetics & Population Ecology

3. For wildlife studies, genetic tools can help: • Who/What Are they (Taxonomy) • Where are they? (Spp. ID & Distribution) • How many are there? (Abundance) • Are they increasing? (Trends) • How much movement among populations? (Connectivity) • Effects of small population size (inbreeding) • Forensics

4. A few Definitions • Phenotypic Expression • A function of genetic makeup and • Epigenetic processes • Environment • Genes • Stretches of DNA along chromosomes

5. A few Definitions • Locus • The location of a gene on a chromosome • Alleles • Different forms of a gene • Vary in specific sequence of DNA nucleotides

6. Brief history of genetic sampling • Pre 1960: Breeding experiments only. • 1960: Protein electrophoresis • Direct measure of Gen. Var., but lethal sampling. • 1980: PCR coupled with direct analysis of DNA allowed non-invasive sampling to occur!

7. Protein electrophoresis: Good for taxonomic questions. Low resolution Logistically challenging. Destructive. DNA High resolution Logistical advantages Possible: Non-destructive Non-invasive Comparison of molecular markers

8. NUCLEAR For each gene: one allele inherited from each parent. One copy per cell. Some Uses: individual identification, population-level variation, etc. MITOCHONDRIAL (mtDNA) Maternally inherited 100’s to 1,000’s copies per cell. Some Uses: Species ID with poor quality samples, also gene flow. Two main classes of DNA

9. Neutral vs. adaptive variation NEUTRAL • Non-coding • Useful for forensics, cases where we want to know effects of genetic drift (eg inbreeding, gene flow). • Not connected to fitness ADAPTIVE • Reveals functional genes that code for variation under selection. • Phenotypes are functions of genes and environment. • Most often multiple genes make up traits.

10. Most DNA markers are PCR-based • Fragment analysis: compare size of DNA among individuals. (nuclear or mtDNA) • Microsatellite analysis: a form of fragment analysis using nuclear DNA. • PCR amplifies regions with 1-10 bp repeated 10 – 50 times [e.g. “CA” repeated 17 times]. • Different alleles have different number of repeat units. • SNPs • Genomics/transcriptomics/sequencing.

11. A side note on Taq polymerase: • THE KEY to successful PCR, which is in turn perhaps the greatest revolutionary advance for wildlife conservation ever invented. • Was formerly an unknown slime in Yellowstone National Park. A fitting quote from John Varley (YNP): “Here in the world’s most popular geothermal region, an obscure, primitive, hot spring bacterium is discovered that contains an even more obscure enzyme that in turn establishes a procedure that promises to change the world for the better…The fact is that Thermus aquaticus was available for discovery there in Mushroom Pool because the feature and its basin were not available for more destructive, short-term uses… Our celebration of Taq is thus tinged with a vague sense of waste: what else, around the world, have we lost already, and how much more can we afford to lose?”

12. Polymerase Chain Reaction (PCR) • Put isolated DNA in tubes w/ primers, nucleotides, and Taq polymerase. • Each cycle: PCR machine separates DNA strands (denature), then cools to anneal primers, then heats a bit to attach nucleotides (extend).

13. When PCR is used, sufficient DNA (nuclear or mtDNA) can be obtained non-invasively from: • Old samples • 120 million-year-old weevil • 20,000 year old saber-toothed cat bones • Museum specimens • Field samples of low quality &/or quantity. • Feathers, fish scales, feces, urine, egg shells, hairs, sloughed skin, blood

14. Hardy-Weinberg equilibrium

15. Remember: Genetic markers complement ecological approaches.

16. Next: estimating Abundance