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Crowdsourcing ConGen – A Reading List

This is a little different from my usual Crowdsourcing ConGen posts. I recently completed my qualifying exams for PhD candidacy, so have a very large reading list compiled for population and conservation genetics. So, if you’re interested in the field, you should check out some of these papers, and if you know of any others that should be included, please let me know in the comments.

Textbooks

Allendorf FW and Luikart G (2006) Conservation and the Genetics of Populations. Wiley-Blackwell.

Carroll SP and Fox CW eds. 2008. Conservation Biology: Evolution in Action. Oxford University Press.

Hartl DL and Clark AG (2006) Principles of Population Genetics, Fourth Edition. Sinauer Associates, Inc.

Wakeley J (2008) Coalescent Theory: An Introduction. Roberts and Company Publishers.

Historical/Seminal

Felsenstein J (1985) Phylogenies and the comparative method. Am Nat 125:1-15.

Hill WG (1974) Estimation of linkage disequilibrium in randomly mating populations. Heredity 33: 229-239.

Kimura M and Weiss GH (1964) The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49: 561-576.

Lewontin RC (1988) On Measures of Gametic Disequilibrium. Genetics 120: 849-852.

Slatkin M (1981) Estimating levels of gene flow in natural populations. Genetics 99: 323-335.

Slatkin M (1985) Gene Flow in Natural Populations. Annu. Rev. Ecol. Syst. 16: 393-430.

Wright S (1943) Isolation by distance. Genetics 28: 114-138.

Wright S (1965) The Interpretation of Population Structure by F-Statistics with Special Regard to Systems of Mating. Evolution 19: 395-420.

Conservation and Population Genetics

Gebremedhin B et al (2009) Frontiers in identifying conservation units: from neutral markers to adaptive genetic variation. Animal Conservation 12: 107-109.

Hedrick PW (2001) Conservation genetics: where are we now? Trends in Ecology and Evolution 16: 629-636.

Pearse DE and Crandall KA (2004) Beyond FST: Analysis of population genetic data for conservation. Conservation Genetics 5: 585-602.

Stockwell et al. 2003 Contemporary evolution meets conservation biology. TREE 18:94-101

Methodology and Theory

Bazin E, Glemin S, and Galtier N (2006) Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals. Science 312: 570-572.

Beaumont MA and Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol 13: 969-980.

Emerson BC, Paradis E, and Thébaud C (2001) Revealing the demographic histories of species using DNA sequences. Trends in Ecology & Evolution 16: 707-716.

Falush D, Stephens M, and Pritchard JK (2003) Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies. Genetics 164: 1567-1587.

Foll M and Gaggiotti O (2006) Identifying the Environmental Factors That Determine the Genetic Structure of Populations. Genetics 174: 875-891.

Gaggiotti OE et al (2009) Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic Herring as a case study. Evolution 63: 2939-2951.

Hubisz MJ, Falush D, Stephens M, and Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9: 1322-1332.

Lehmann L, Feldman MW, and Rousset F (2009) On the evolution of harming and recognition in finite panmictic and infinite structured populations.  Evolution 63: 2896-2913.

Lieberman E, Hauert C, and Nowak MA (2005) Evolutionary dynamics on graphs. Nature 433: 312-316.

Luikart G and Cornuet J (1999) Estimating the Effective Number of Breeders from Heterozygote Excess in Progeny. Genetics 151: 1211-1216.

Manel S, Schwartz MK, Luikart G, and Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution 18: 189-197.

Mühlenbein H and Mahnig T (2002) Evolutionary computation and Wright’s equation. Theoretical Computer Science 287: 145-165.

Nordborg M and Tavaré S (2002) Linkage disequilibrium: what history has to tell us. Trends in Genetics 18: 83-90.

Orr HA and Betancourt AJ (2001) Haldane’s Sieve and Adaptation from the Standing Genetic Variation. Genetics 157: 875-884.

Pelletier F, Clutton-Brock T, Pemberton J, Tuljapurkar S, and Coulson T (2007) The Evolutionary Demography of Ecological Change: Linking Trait Variation and Population Growth. Science 315: 1571-1574.

Pritchard JK, Stephens M, and Donnelly P (2000) Inference of Population Structure Using Multilocus Genotype Data. Genetics 155: 945-959.

Rosenberg, Noah A, and Magnus Nordborg (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews. Genetics 3: 380-390.

Selkoe KA and Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters 9: 615–629.

Smedbol RK, McPherson A, Hansen MM, and Kenchington E (2002) Myths and moderation in marine ‘metapopulations’? Fish and Fisheries 3: 20-35.

Sunnucks P (2000) Efficient genetic markers for population biology. Trends in Ecology & Evolution 15: 199-203.

Templeton AR, Maxwell T, Posada D, Stengård JH et al (2005) Tree Scanning: A Method for Using Haplotype Trees in Phenotype/Genotype Association Studies. Genetics 169: 441.

Thorne JL, Choi SC, Yu J, Higgs PG, and Kishino H (2007) Population Genetics Without Intraspecific Data. Mol Biol Evol 24: 1667-1677.

Wagner AP, Creel S, and Kalinowski ST (2006) Estimating relatedness and relationships using microsatellite loci with null alleles. Heredity 97: 336-345.

Waples RS and Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15: 1419-1439.

Waples R. (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J Hered 89: 438-450.

Whitham TG et al (2006) A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet 7: 510-523.

Whitlock MC and Phillips PC (2000) The exquisite corpse: a shifting view of the shifting balance. Trends in Ecology and Evolution 15: 347-348.

Wilkins JF (2004) A Separation-of-Timescales Approach to the Coalescent in a Continuous Population. Genetics 168: 2227-2244.

Statistics

Beaumont MA (2005) Adaptation and speciation: what can Fst tell us? Trends in Ecology and Evolution 20: 435-440.

Beaumont MA and Rannala B (2004) The Bayesian revolution in genetics. Nat Rev Genet 5: 251-261.

Galtier N, Nabholz B, Glemin S, and Hurst GDD (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18: 4541-4550.

Guillot G, Leblois R, Coulon A, and Frantz AC (2009) Statistical methods in spatial genetics. Molecular Ecology: 9999.

Heller R and Siegismund HR (2009) Relationship between three measures of genetic differentiation GST, DEST and GST: how wrong have we been? Molecular Ecology 18: 2080-2083.

Holsinger KE and Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nat Rev Genet 10: 639-650.

Jost L (2008) GST and its relatives do not measure differentiation. Molecular Ecology 17: 4015-4026.

Jost L (2009) D vs. GST: Response to Heller and Siegismund (2009) and Ryman and Leimar (2009). Molecular Ecology 18: 2088-2091.

Molitor J, Marjoram P, and Thomas D (2003) Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping. Genetic Epidemiology 25: 95-105.

Novembre J and Stephens M (2008) Interpreting principal component analyses of spatial population genetic variation. Nat Genet 40: 646-649.

~Southern Fried Scientist

Ryman N and Leimar O (2009) GST is still a useful measure of genetic differentiation – a comment on Jost’s D. Molecular Ecology 18: 2084-2087; discussion 2088-2091.

Hypothesis Testing and Applications

Beebee TJC (2009) A comparison of single-sample effective size estimators using empirical toad (Bufo calamita) population data:  genetic compensation and population size-genetic diversity correlations. Molecular Ecology: 9999.

Carlsson J (2008) Effects of Microsatellite Null Alleles on Assignment Testing. J Hered 99: 616-623.

Cushman SA, McKelvey KS, Hayden J, and Schwartz MK (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am. Nat 168: 486-499.

Gomez-Uchida D, Knight TW, and Ruzzante DE (2009) Interaction of landscape and life history attributes on genetic diversity, neutral divergence and gene flow in a pristine community of salmonids. Molecular Ecology: 9999.

Handley LJL, Manica A, Goudet J, and Balloux F (2007) Going the distance: human population genetics in a clinal world. Trends in Genetics 23: 432-439.

Rosindell J and Cornell SJ (2007) Species-area relationships from a spatially explicit neutral model in an infinite landscape. Ecology Letters 10: 586-595.


Deep-sea biologist, population/conservation geneticist, backyard farm advocate. The deep sea is Earth's last great wilderness.


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