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Unformatted text preview: CONSERVATION GENETICS Zebra shark Ecological Genetics ECL242_PHR242 February 10, 2010 Ernest Lec 9b Assigned readings • Ch 8 • Conservation Genomics by Ouborg 2009 CONSERVATION GENETICS
SMALL POPULATIONS = GENETICALLY THREATENED
•Genetic drift •Inbreeding •Deleterious alleles •Genetic load •PVA / PHVA
•Inbreeding depression & outbreeding depression •Genetic restoration •Management and Conservation Units •IUCN categories, ESU and MSU CONSERVATION GENETICS INTRODUCTION
Evolutionary theory: very small populations face dangers —inbreeding depression — low genetic variation — Leading to fitness decreases (inbreeding depression
…that keep them from recovering, despite efforts to preserve them Passenger Pigeon 1920 Chromolithograph by Hayashi and Toda Conservation Genetics: Merging of Fields population genetics, molecular ecology, biology, evolutionary biology, systematics, etc. Several levels to conserve biodiversity Genetics Species diversity Ecosystem diversity CONSERVATION GENETICS INTRODUCTION
Conservation of genetic variability important to overall health of populations •Decreased genetic variability → extinctions •Molecular techniques utilize individuals’ genetics to assess a population variation •Research may suggest steps to fix or reverse the factors that lead to extinction, or reduced biodiversity. Passenger Pigeon 1920 Chromolithograph by Hayashi and Toda CONSERVATION GENETICS ROLES FOR MOLECULAR MARKERS Distinctions among Current survival probability Evolutionary potential Neutral genetic variation vs. adaptive/functional/expressed genomic variation
(Ouborg etal 2009 paper for today) Emerging pathogens Signals of effects of global climate change Physical changes in landscape habitat CONSERVATION GENETICS – ROLES FOR MOLECULAR MARKERS Ne, Effective pop size Gene flow ID Pop bottlenecks recent vs distant past Reln between gen diversity and pop viability Only recently non-invasive sampling practical 10-15 years ago – needed destructive sampling to obtain suffic. sample for allozymes, mtDNA Ne - effective population size Population size varies over time Suppose there are t non-overlapping generations, then Ne is given by the harmonic mean of the population sizes: Harmonic mean often most appropriate for rates Ne population size , N N = 10, 100, 50, 80, 20, 500 for six generations (t = 6). Effective population size is the harmonic mean Ne population size , N N = 10, 100, 50, 80, 20, 500 for six generations (t = 6). Then effective population size is the harmonic mean of these, giving: = 0.032 Ne = 30.8 Note this is less than the arithmetic mean of the population size, which in this example is 126.7. Of particular concern is the effect of a population bottleneck. CONSERVATION GENETICS INBREEDING AND GENETIC LOAD Inbreeding (breeding among relatives) → increased homozygosity → fixation of mildly delet. Alleles → increase genetic load Decline in fitness In offspring of close relatives “Inbreeding depression” Increasing deleterious recessive alleles Reduced survivorship and repro rates Heterosis (hybrid vigor) = increased fitness due to outbreeding When a decline in fitness occurs due to outbreeding the result is referred to as outbreeding depression. CONSERVATION GENETICS INBREEDING AND GENETIC LOAD Large pop When rare delet. alleles maintained in heterozygotes effects of inbreeding depression most severe to pop Small pop Increasing homozyg of slightly del. Alleles Drift to fixation With time, accumulation of mutations, increased genetic load – decline in fitness relative to an optimal genotype CONSERVATION GENETICS GENETIC LOAD Inbreeding avoidance mechanisms in natural populations Recognition and avoidance of kin mating Sex diff’s in dispersal, age of sexual maturity Extra-pair fertilizations Optimal outbreeding Difficult to maintain in small fragmented population Pedigree analysis in captive pops Inbreeding coefficient, F You’ve also seen analogous index: FIS Probability that both alleles at a locus are IBD 0=fully outbred (neither allele IBD) 1 = completely inbred (both alleles IBD) Example – 2 outbred heterozygotes Parents with alleles [ab] x [cd] = gen 1 generation 2: all offspring are het and have 50% chance of sharing one allele with a sibling genotypes are ac ad bc bd If gen 2’s mate example ac x bc F=0.25 that next gen 3 offspring will have 2 IBD alleles: ab ac bc cc – so prob of IBD (cc) is 0.25 Conservation Genetics Inbreeding and genetic load
Breeding among relatives For alleles of major deleterious effects (MDE) - Can be most severe among related individuals in large population When rare recessive alleles can persist in heterozygotes Homozygotes purged out, therefore low effect at population level In small populations – MDE alleles as homozygotes will be purged out Conservation Genetics Small inbred populations
increasing homozygosity of mild deleterious alleles Mildly delet. Alleles accum as homozyg and contrib to reduced fitness Genetic load = decline in fitness relative to “optimal” genotype “Mutational meltdown” – extinction vortex Reduction of mean survivorship and/or reproduction rates (Higgins* and Lynch 2001)
•UCD Ecology PhD graduate http://www.pnas.org/content/98/5/2928.full Inbreeding avoidance mech Recog and avoidance of kin as mates Avoidance mech’s compromised small pops captive breeding programs Pedigree analysis to lower inbreeding and raise Ne Text example of wild dogs of S. Africa (page 255) Estimating loss of genetic diversity Low population sizes = faster het. Decline Inbreeding decreases het Increased homozygosity But no change in allele frequencies Therefore HW disequilibrium Inbreeding HW discord Inbreeding increases each generation inversely in relation to pop size Genetics as measure of endangered species “health” What are other indicators of how populations are faring? Census numbers – ex: transect counts, bird counts Polled class – sex ratios, age distributions, etc…. What genetic indices are useful? Relationship between genetic diversity & population viability Identification of population units Number, distribution, relationships among populations Ne Character of populations Single panmictic; metapopulation; isolation by distance, etc Pedigree reconstruction…natural and captive populations Optimize breeding regimes PVA’s and genetics Population Viability Analysis Methods to evaluate risks of extinction and potential recovery strategies modeling populations on the question of evaluating species persistence. Vortex http://www.cbsg.org/cbsg/vortex/ http://www.vortex9.org/vortex.html GENES software for pedigree analysis and management http://www.vortex9.org/genes.html Captive Breeding specialist group http://www.cbsg.org/cbsg/ Conservation Genetics Article ID of management units Palsboll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends in Ecology & Evolution 22, 11-16. IUCN The variety of species - product of 3.5 billion years of evolution, and influenced by… radiation, speciation, extinction more recently, the impacts of people Current estimates of the number of species 5 to 30 million, working estimate of 8 to 14 million of these, only around 1.8 million have been described. By 2008, 44,837 species have been assessed and 38% have been classified as threatened.
http://www.iucn.org/about/work/programmes/species/red_list/review IUCN SOURCE http://cmsdata.iucn.org/downloads/the_iucn_red_list_a_key_conservation_tool_factsheet_en.pdf IUCN http://cmsdata.iucn.org/downloads/state_of_the_world_s_species_factsheet_en.pdf IUCN bird species survival http://cmsdata.iucn.org/downloads/state_of_the_world_s_species_factsheet_en.pdf IUCN - Marine Millions of sharks caught each year for fi ns used to make Asian delicacy shark fin soup. http://cmsdata.iucn.org/downloads/status_of_the_world_ © John Nightingale s_marine_species.pdf Marine environment Stock structure Defining management units (Moritz 1994) Shark migration varies greatly Genetic structure assoc. with vagility (movement) Circum-global (whale shark) Highly restricted (benthic angel shark) Dissociation of gen. structure and vagility Viviparous reproduction Female natal philopatry to pupping grounds Oviparous repro Zebra shark Life history Sometimes called “leopard shark” Genetic subdivision within regions Source-sink Low recruitment to areas of high exploitation
Zebra shark egg Regional dispersal – larvae not pelagic Demersal Bottom-dwelling; living on seabed Shallow water; (correction)-reef associated
• Dudgeon et al .2009
Photo Aquarium of the Pacific | 100 Aquarium Way, Long Beach, CA http://www.aquariumofpacific.org/blogs/comments/egg_id/ Zebra shark Life history Seasonal aggregations Capable of long distance movements At least 150 km Restricted by deep-water tranches, currents Pleistocene land bridges Summer, large reproductively mature adults
Zebra shark egg •Chris Dudgeon et al .2009 Zebra Shark
*Species No. 630 127 26 613150 629 126 25 5 Conservation Genetics DISTRIBUTION
Indo-West Pacific: Red Sea and East Africa to New Caledonia, north to southern Japan, south to New South Wales, Australia
Source: AquaMaps and FISHBASE Zebra shark life history
Pleistocene land bridges http://users.monash.edu.au/~mcoller/SahulTime/explore.html Zebra shark Ecol. Genetics Questions
Zebra shark egg Are IUCN classification zones supported by genetic groupings? Is there fine scale genetic structure within regions? ID prominent population boundaries Zebra Shark IUCN classifications Least concern Vulnerable • Dudgeon et al .2009 ND4 sequence 13 microsat. 180 individuals 13 locations Indo-west Pacific Some of most exploited and least exploited chondrichthyan populations mtDNA indices Number of haplotypes Haplotype diversity (h) % nucleotide diversity (π) mtDNA indices Haplotype: Combination of nucleotide sequences Haplotype diversity (h) h=N(1-Σxi2)/(N-1) xi is the haplotype frequency of each haplotype in the sample N is the sample size. Haplotype diversity is given for each sample. mtDNA indices Nucleotide diversity (π) Mean number of nucleotide differences per site between two random haplotypes in the sample. π=[n/n-1](Σxi*xj*πij) xi is the frequency of the haplotype i in the sample, xj is the frequency of the haplotype j in the sample, πij is the number of sequence differences between the haplotypes i and j n = number of the haplotypes tested in the sample. Nucleotide diversity is given for each sample and is expressed in a value of (%). Haplotype:
combination of nucleotide sequences Haplotype diversity (h)
Resampling of the microsatellite data set to assess the effect of low sample numbers on IUCN regional pairwise FST comparisons. y-axis. Conservation Genetics Mean pairwise FST values () (scale on the primary y-axis) were calculated for 10 random resamples at 10% increments of the full data set. axis. Corresponding mean significance values () are shown on the secondary yDudgeon et al. 2009 Mol Ecol Sharks
Distribution of ND4 haplotypes and microsatellite groups
identified by Bayesian clustering analysis. Conservation Genetics • Dudgeon et al. 2009 Mol Ecol The most probable ancestral haplotype is indicated by a rectangle. Haplotypes are labeled H1 to H8 and the number of individuals with each haplotype indicated in brackets. Each line connecting two haplotypes represents a single mutation. Ouborg et al paper-1 What is the conservation genetics paradigm? First 2 pages What are 3 main conclusions of studies to find empirical evidence for this paradigm? 2nd page Explain FST and QST and relevance to paper Explain the effects of drift relative to the cons. Gen paradigm (3rd page) Explain expectations of neutral markers (3rd page, 2nd column) What ecogenomic approaches are suggested? 4th pg What are the challenges for these methods ?- QTL Ouborg et al paper-2 How does author present inbreeding depression as example of how cons genetics and –omics can get together? Pg 5 What points are they making about interactions between genetics and envir? Pg 6 How do they suggest Designing modern ecogenomic tools? Pg 6-7 ...
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This note was uploaded on 03/02/2010 for the course ECL 242 taught by Professor Holly during the Winter '10 term at UC Davis.
- Winter '10