Below are the references of papers to be read for class, plus some additional references that I came across when I prepared for lecture. These can serve as an introduction to a specific area when you want to work in it. The additional references are also ones I used for my slides.
Waples RS, Gaggiotti OE (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.
Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: Causes, consequences and solutions. Nature Reviews Genetics 6, 847-859.
Excoffier L, Heckel G (2006) Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics 7, 745-758.
Ewen KR, Bahlo M, Treloar SA, et al. (2000) Identification and analysis of error types in high-throughput genotyping. American Journal of Human Genetics 67, 727-736.
Montgomery GW, Campbell MJ, Dickson P, et al. (2005) Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues. Twin Research and Human Genetics 8, 346-352.
Pearse DE, Crandall KA (2004) Beyond FST: Analysis of population genetic data for conservation. Conservation Genetics 5, 585-602.
Ryman N, Jorde PE (2001) Statistical power when testing for genetic differentiation. Molecular Ecology 10, 2361-2373.
Raymond M, Vaanto RL, Thomas F, Rousset F, deMeeus T, Renaud F (1997) Heterozygote deficiency in the mussel Mytilus edulis species complex revisited. Marine Ecology-Progress Series 156, 225-237.
Waples R (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J Hered 89, 438-450.
Taylor BL, Dizon AE (1999) First policy then science: why a management unit based solely on genetic criteria cannot work. Molecular Ecology 8, S11-S16.
Neigel JE (2002) Is F-ST obsolete? Conservation Genetics 3, 167-173.
Wilson AJ, Hutchings JA, Ferguson MM (2004) Dispersal in a stream dwelling salmonid: Inferences from tagging and microsatellite studies. Conservation Genetics 5, 25-37.
Kalinowski ST (2002) Evolutionary and statistical properties of three genetic distances. Mol Ecol 11, 1263-1273.
Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144, 389-399.
Palsboll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends in Ecology & Evolution 22, 11-16.
Ryman N, Palm S, Andre C, et al. (2006) Power for detecting genetic divergence: differences between statistical methods and marker loci. Molecular Ecology 15, 2031-2045.
Garcia, L. V. 2004. Escaping the Bonferroni iron claw in ecological studies. Oikos 105(3):657-663.
Narum SR (2006) Beyond Bonferroni: Less conservative analyses for conservation genetics. Conservation Genetics 7, 783-787. (Erratum: Conservation Genetics 7, 811).
Neuhauser M (2003) Tests for genetic differentiation. Biometrical Journal 45, 974-984. Rice WR (1989) Analyzing tables of statistical data. Evolution 43, 223-225.
Verhoeven KJF, Simonsen KL, McIntyre LM (2005) Implementing false discovery rate control: increasing your power. Oikos 108, 643-647.
Turkheimer FE, Smith CB, Schmidt K (2001) Estimation of the number of "true" null hypotheses in multivariate analysis of neuroimaging data. Neuroimage 13, 920-930.
Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA (2005) Serial SimCoal: A population genetics model for data from multiple populations and points in time. Bioinformatics 21, 1733-1734.
Balloux F (2001) EASYPOP (version 1.7): A computer program for population genetics simulations. Journal Of Heredity 92, 301-302.
Excoffier L, Novembre J, Schneider S (2000) SIMCOAL: A general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. Journal Of Heredity 91, 506-509.
Laval G, Excoffier L (2004) SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20, 2485-2487.
Ryman N, Palm S (2006) POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. Molecular Ecology Notes 6, 600-602.
Wilson AJ, Ferguson MM (2002) Molecular pedigree analysis in natural populations of fishes: approaches, applications, and practical considerations. Canadian Journal of Fisheries and Aquatic Sciences 59, 1696-1707.
Veliz D, Duchesne P, Bourget E, Bernatchez L (2006) Genetic evidence for kin aggregation in the intertidal acorn barnacle (Semibalanus balanoides). Molecular Ecology 15, 4193-4202.
Blouin MS (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends In Ecology & Evolution 18, 503-511.
Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Molecular Ecology 12, 2511-2523.
Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: Causes, consequences and solutions. Nature Reviews Genetics 6, 847-859.
Bonin A, Bellemain E, Eidesen PB, et al. (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology 13, 3261-3273.
Slate J, Marshall T, Pemberton J (2000) A retrospective assessment of the accuracy of the paternity inference program CERVUS. Molecular Ecology 9, 801-808.
Valiere N, Bonenfant C, Toigo C, et al. (2007) Importance of a pilot study for non-invasive genetic sampling: genotyping errors and population size estimation in red deer. Conservation Genetics 8, 69-78.
Waits JL, Leberg PL (2000) Biases associated with population estimation using molecular tagging. Animal Conservation 3, 191-199.
Bentzen P, Olsen JB, McLean JE, Seamons TR, Quinn TP (2001) Kinship analysis of Pacific salmon: Insights into mating, homing, and timing of reproduction. Journal of Heredity 92, 127-136.
Wang JL (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166, 1963-1979.
Konovalov DA, Manning C, Henshaw MT (2004) KINGROUP: a program for pedigree relationship reconstruction and kin group assignments using genetic markers. Molecular Ecology Notes 4, 779-782.
Emery AM, Wilson IJ, Craig S, Boyle PR, Noble LR (2001) Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Molecular Ecology 10, 1265-1278.
Wang JL (2005) Estimation of effective population sizes from data on genetic markers. Philosophical Transactions Of The Royal Society B-Biological Sciences 360, 1395-1409.
Turner TF, Wares JP, Gold JR (2002) Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops ocellatus). Genetics 162, 1329-1339.
Fraser DJ, Hansen MM, Ostergaard S, et al. (2007) Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems. Molecular Ecology 16, 3866-3889.
(Excellent paper comparing different methods to estimate Ne in different population systems. Highly recommended)
Hedrick P (2005) Large variance in reproductive success and the Ne/N ratio. Evolution 59, 1596-1599.
(Interesting paper investigating the relationship between the number of successful breeders and Ne.)
Palstra FP, Ruzzante DE (2008) Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? Molecular Ecology 17, 3428-3447.
Cornuet JM, Luikart G (1996) Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks From Allele Frequency Data. Genetics 144, 2001-2014. (Description of methods in Bottleneck)
Lin J, Quinn TP, Hilborn R, Hauser L (2008) Fine-scale differentiation between sockeye salmon ecotypes and the effect of phenotype on straying. Heredity 101, 341-350.
Ruzzante DE, Mariani S, Bekkevold D, et al. (2006) Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring. Proceedings Of The Royal Society B-Biological Sciences 273, 1459-1464.
Hauser L, Seamons TR, Dauer M, Naish KA, Quinn TP (2006) An empirical verification of population assignment methods by marking and parentage data: hatchery and wild steelhead (Oncorhynchus mykiss) in Forks Creek, Washington, USA. Molecular Ecology 15, 3157-3173.
Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology 13, 55-65.
Baums IB, Miller MW, Hellberg ME (2005) Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata. Molecular Ecology 14, 1377-1390.
Manel S, Gaggiotti OE, Waples RS (2005) Assignment methods: matching biological questions techniques with appropriate techniques. Trends in Ecology & Evolution 20, 136-142.
Manel S, Berthier P, Luikart G (2002) Detecting wildlife poaching: Identifying the origin of individuals with Bayesian assignment tests and multilocus genotypes. Conservation Biology 16, 650-659.
Storfer A, Murphy MA, Evans JS, et al. (2006) Putting the `landscape' in landscape genetics. Heredity advance online publication 1 November 2006; doi: 10.1038/sj.hdy.6800917.
Frantz AC, Pourtois JT, Heuertz M, et al. (2006) Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population. Molecular Ecology 15, 3191-3203.
Rolf H, Helene HW (2006) A brief guide to Landscape Genetics. Landscape Ecology 21, issue 6. Special Issue on Landscape Genetics, including some fairly basic reviews but also interesting application. You should definitely consult this issue if you are interested in the topic.
Manel, S., Schwartz, M.K., Luikart, G. and Taberlet, P. (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution 18, 189-197.
Hutchison, D.W. and Templeton, A.R. (1999) Correlation of pairwise genetic and geographic distance measures: Inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution 53, 1898-1914.
Angers, B., Magnan, P., Plante, M. and Bernatchez, L. (1999) Canonical correspondence analysis for estimating spatial and environmental effects on microsatellite gene diversity in brook charr (Salvelinus fontinalis). Molecular Ecology 8, 1043-1053.
Case, R.A.J., Hutchinson, W.F., Hauser, L., Van Oosterhout, C. and Carvalho, G.R. (2005) Macro- and microgeographic variation in pantophysin (PanI) allele frequencies in NE Atlantic cod Gadus morhua. Marine Ecology Progress Series 301, 267-278.
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap,A, King K, Bergmann S, Nelson MR, Stephens M, Bustamante CD (200) Genes mirror geography within Europe. Nature 456, 98-101. Fascinating paper about landscape genetics in European human populations.
Note - Thursday lecture cancelled because of GSS
Vasemägi A, Nilsson J, Primmer CR (2005) Expressed sequence tag-linked microsatellites as a source of polymorphism for detecting signatures of divergent selection in Atlantic salmon, Slamo salar L). Molecular Biology and Evolution 22, 1067-1076.
Jensen JD, Wong A, Aquadro CF (2007) Approaches for identifying targets of positive selection. Trends in Genetics 23, 568-577.
Nielsen R (2005) Molecular signatures of natural selection. Annual Reviews of Genetics 39, 197-218.
Hemmer-Hansen J, Nielsen EE, Frydenberg J, Loeschke V (2007) Adaptive divergence in a high gene flow environment: Hsc70 variation in the European flounder (Platichtys flesus L.). Heredity 99, 592-600.
Grant WS, Bowen BW (2006) Living in a tilted world: climate change and geography limit speciation in Old World anchovies (Engraulis; Engraulidae). Biological Journal of the Linnean Society 88, 673-689.
Palstra FP, O'Connell MF, Ruzzante DE (2007) Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history. Molecular Ecology 16, 4504-4522.
Rosenberg NA, Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics 3, 380-390.
Hänfling B, Weetman D (2006) Concordant genetic estimators of migration reveal anthropogenically enhanced source-sink population structure in the River Sculpin, Cottus gobio. Genetics 173, 1487.
Hey J, Machado CA (2003) The study of structured populations - New hope for a difficult and divided science. Nature Reviews Genetics 4, 535-543.
Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions Of The Royal Society Of London Series B-Biological Sciences 359, 183-195.
Templeton AR (2002) Out of Africa again and again. Nature 416, 45-51.
Knowles LL (2008) Why does a method that fails continued to be used? . Evolution 62, 2713-2717.