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Cons Gen Lecture 2 Overview

Cons Gen Lecture 2 Overview. Effective Population Size Genetic processes Genetic Structure Fst ESUs. What is effective population size?. Size of the “ideal population” that would lose variation or ‘drift’ at the same rate observed in the real biological population. Why do we care about Ne?.

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Cons Gen Lecture 2 Overview

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  1. Cons Gen Lecture 2 Overview • Effective Population Size • Genetic processes • Genetic Structure • Fst • ESUs

  2. What is effective population size? • Size of the “ideal population” that would lose variation or ‘drift’ at the same rate observed in the real biological population.

  3. Why do we care about Ne?

  4. How rapidly does variation decline in a population? • Heterozygosity is lost at a rate of 1/(2Ne) per generation. • Ht = H0 [1 – 1/(2Ne)]t Ne=1000 Ne=100 Ne=10

  5. 2 Main Approaches to Estimating Ne • Demographic (ecological) approach • Genetic approach

  6. Demographic parameters • Unequal sex ratio (Wright 1938) • Fluctuating population size (Wright 1938) • Variance in family size (Wright 1938, Crow and Morton 1955)

  7. Effective Population Size • Not all individuals in a population leave offspring • Ne/N ratio 0.1 - 0.7. • Male brown bear reproductive success in Brooks Range, AK. • Each circle is one male. Colored is proportion of 36 cubs left by that individual. Craighead et al. 1994 (J of Heredity)

  8. Effects of Sex Ratio on Ne • Ne = 4NmNf / Nm + Nf • Nm is number of breeding males, • Nf is the number of breeding females

  9. Converting from Real to Ideal Populations • Skewed sex ratio (either real, or from mating system eg. elk, African lions, Prairie Chickens) Ne = 4*Nm*Nfemales Nm + Nf Example from Prairie Chicken Population: census breeding females 30 30 males 30 4 total 60 34 Ne =

  10. Effects of Population Fluctuations on Ne • 1/Ne = 1/t (1/N1 + 1/N2 + ..... + 1/Nt), the harmonic mean or • Ne = t/summation (1/Ni) • t = time in generations • N = population census

  11. 1/Ne = (1/t) (1/N1 + 1/N2 + …+ 1/Nt) where t is the number of generations Ne = t/ Σ (1/N) Example, N 1 through 4 = 100, 100, 10, 100

  12. Effects of variance in family size • Ne = 4N/(2 + 2), where 2 equals the variance in family size among females • Higher variance = smaller Ne

  13. Variance in # of Progeny • Ne = 4N • 2 + Var where Var = variance in # of progeny between individuals Large Variance (eg Frogs) Small Variance (eg. bats) N=100, Var=10 N=100, Var=1

  14. MeasuringPatterns and Process at the Genetic Level

  15. Gene flow

  16. A theoretical population panmixia

  17. Population Sub-division (eg. glaciation)

  18. Gene Flow • In the absence of other evolutionary forces, gene flow would eventually homogenize two populations completely. • Drift causes divergence and thus counteracts gene flow. Gene Flow Drift

  19. Mainland/Island Model Equal Island model

  20. Sustainability BreakDNA fingerprinting to stop illegal loggingwww.cosmosmagazine.com/node/1135 Australia introduced the world’s first DNA testing for the origin of timber in 2007 to avoid purchasing illegally logged wood. Simmonds Lumber invested developing DNA testing for timber audits with Singapore-based company Cerisource. DNA profile taken for each tree in legally managed forest. Then harvested logs are matched and certified for export

  21. Why should we worry about genetic structure?

  22. How is gene flow and population structure measured? 1) Fst 2) Phylogenetic Analysis And much, much more

  23. Fst • FST measures how much of the total variation (heterozygosity) is partitioned into sub-populations. • Fst - Ht - Hs Ht How does Fst differ from Gst? Complete pamixia Complete isolation 0 1 Higher gene flow Lower gene flow

  24. Population Structure Pairwise FST8 microsatellite loci Red-and-green Macaw 1000km Scarlet Macaw 125 km

  25. Key NIDGS SIDGS Extirpated NIDGS Adams Extirpated SIDGS 400 m. 3000 m. Valley Washington Payette Gem Yensen and Sherman 1997 Idaho Ground Squirrels (Spermophilus brunneus)

  26. Southern Idaho Ground Squirrels nDNA connectivity 10 usat loci 10 km HB RH / HC MC Sk PFS FST < 0.1 HG FST > 0.2 CP BC SB SH

  27. Isolation by Distance Model Bighorn sheep Wolves Brown bears Forbes & Hogg 1999

  28. Using Fst to estimate Gene flow • Under an infinite islands model where migration between any two groups is equally likely, FST = 1 / (4Nm+1) (where Nm = absolute # of migrants / generation)

  29. Examples

  30. Brown Bear Examples FST=0.033 Nm=7.5 West Slope East Slope FST=0.33 Nm=0.5 Kodiak Island Kuskokwim Mts. These values are approximate, long term averages !

  31. Building a Phylogeny Use genetic data to reconstruct evolutionary relationships and to evaluate how genetic variation is partitioned across the range of a species

  32. Waits et al. 1998 • 317 brown bears • 294 nucleotides of mtDNA sequence • 28 unique sequences

  33. Waits et al 1998

  34. U.S. ENDANGERED SPECIES ACT ESA defines “species” as a species, subspecies or distinct population segment (amendment 1978). But gives no criteria for defining. In 1996, NMFS and USFWS agreed that Evolutionary Significant Units are are a reasonable interpretation of Distinct Population Segment.

  35. What are Evolutionary Significant Units (ESUs)? Concept introduced by Ryder in 1986 Why? • Preserve the range of diversity within a species • Provide a guide for transplantation and reintroduction

  36. ESU Definitions Waples (1991, 1995)An ESU is a population (or group of populations) that is (1) substantially reproductively isolated from other conspecific population units, and (2) represents an important component in the evolutionary legacy of the species. Isolation does not have to be absolute but gene flow has to be restricted to the point that evolutionarily important differences occur. Evaluated by genetic data and tagging studies and biogeography

  37. Waples (1991, 1995) Evolutionary legacy is defined as “genetic variability that is the product of past evolutionary events and that represents the reservoir upon which future evolutionary potential depends.” Evaluated using genetic data, ecology, life history traits/adaptive differences

  38. ND5 SD18 ND3 ND6 SK10 SD14 ND1 SD17 MB3 ND10 ND2 SD20 AB4 MI12 MD6 ME6 NC3 DE2 MD3 MD7 MD1 NJ16 RI1 NC8 DE1 RI3 NY18 NC1 NC2 QB1 PL8 PI2 PI3 PI6 QB2 MD9 NY3 ME2 NY7 NY9 NY17 NC4 NY1 NY4 NY2 ME3 ME4 TURNST. Inland The Genetic Approach to ESUs Moritz 1994 ESUs should be reciprocally monophyletic for mtDNA alleles and show significant divergence of allele frequencies at nuclear loci. Atlantic

  39. Example – Reed Buntings (Emberiza schoeniclus) in Europe – one or two ESUs?(Grapputo et al 1998) • Northern pops migratory • Collected 515 bp of mtDNA sequence data • 4 nDNA microsatellite loci Bill size by pop.

  40. mtDNA tree • S group of pops is intermedia • N group of pops is schoeniclus

  41. Microsatellite Results • Allele frequencies significantly different between N and S groups • Fst = 0.045 between N and S groups, 0.02 among S and 0.03 among N pops

  42. ESU based on Moritz criteria? • ESU based on Waples criteria?

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