popgen_notes.bib

@article{charlesworth:09,
  title={Effective population size and patterns of molecular evolution and variation},
  author={Charlesworth, Brian},
  journal={Nature Reviews Genetics},
  volume={10},
  number={3},
  pages={195},
  year={2009},
  publisher={Nature Publishing Group}
}

@article{janicke:16,
  title={Darwinian sex roles confirmed across the animal kingdom},
  author={Janicke, Tim and H{\"a}derer, Ines K and Lajeunesse, Marc J and Anthes, Nils},
  journal={Science advances},
  volume={2},
  number={2},
  pages={e1500983},
  year={2016},
  publisher={American Association for the Advancement of Science}
}

@article{rands:14,
  title={8.2\% of the human genome is constrained: variation in rates of turnover across functional element classes in the human lineage},
  author={Rands, Chris M and Meader, Stephen and Ponting, Chris P and Lunter, Gerton},
  journal={PLoS genetics},
  volume={10},
  number={7},
  pages={e1004525},
  year={2014},
  publisher={Public Library of Science}
}


@book{kimura:83,
  title={The neutral theory of molecular evolution},
  author={Kimura, Motoo},
  year={1983},
  publisher={Cambridge University Press}
}

@article{king:69,
  title={Non-darwinian evolution},
  author={King, Jack Lester and Jukes, Thomas H},
  journal={Science},
  volume={164},
  number={3881},
  pages={788--798},
  year={1969}
}

@article{kimura:68,
  title={Evolutionary rate at the molecular level},
  author={Kimura, Motoo},
  journal={Nature},
  volume={217},
  number={5129},
  pages={624--626},
  year={1968}
}


@article{li:08,
  title={Worldwide human relationships inferred from genome-wide patterns of variation},
  author={Li, Jun Z and Absher, Devin M and Tang, Hua and Southwick, Audrey M and Casto, Amanda M and Ramachandran, Sohini and Cann, Howard M and Barsh, Gregory S and Feldman, Marcus and Cavalli-Sforza, Luigi L and others},
  journal={science},
  volume={319},
  number={5866},
  pages={1100--1104},
  year={2008},
  publisher={American Association for the Advancement of Science}
}

@article{rosenberg:02,
  title={Genetic structure of human populations},
  author={Rosenberg, Noah A and Pritchard, Jonathan K and Weber, James L and Cann, Howard M and Kidd, Kenneth K and Zhivotovsky, Lev A and Feldman, Marcus W},
  journal={science},
  volume={298},
  number={5602},
  pages={2381--2385},
  year={2002},
  publisher={American Association for the Advancement of Science}
}

@article{lawson:18,
  title={A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots},
  author={Lawson, Daniel J and Van Dorp, Lucy and Falush, Daniel},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={3258},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{alvarez:09,
  title={The role of inbreeding in the extinction of a European royal dynasty},
  author={Alvarez, Gonzalo and Ceballos, Francisco C and Quinteiro, Celsa},
  journal={PLoS One},
  volume={4},
  number={4},
  pages={e5174},
  year={2009},
  publisher={Public Library of Science}
}

@article {Sams:18,
	author = {Sams, Aaron J and Boyko, Adam R},
	title = {Fine-scale resolution and analysis of runs of homozygosity in domestic dogs},
	year = {2018},
	doi = {10.1101/315770},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Inbreeding and consanguinity leave distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (\> 5 megabase (Mb)) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long versus short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied. In domestic dogs, nearly 200 mutations are known to cause recessive diseases, most of which can be efficiently assayed using SNP arrays. By examining genome-wide data from over 200,000 markers, including 150 recessive disease variants, we built high-resolution ROH density maps for nearly 2,500 dogs, recording ROH down to 500 kilobases. We observed over 500 homozygous deleterious recessive genotypes in the panel, 90\% of which overlapped with ROH inferred by GERMLINE. Although most of these genotypes were contained in ROH over 5 Mb in length, 14\% were contained in short (0.5 - 2.5 Mb) tracts, a significant enrichment compared to the genetic background, suggesting that even short tracts are useful for computing inbreeding metrics like the coefficient of inbreeding estimated from ROH (FROH). In our dataset, FROH differed significantly both within and among dog breeds. All breeds harbored some regions of reduced genetic diversity due to drift or selective sweeps, but the degree of inbreeding and the proportion of inbreeding caused by short versus long tracts differed between breeds, reflecting their different population histories. Although only available for a few species, large genome-wide datasets including recessive disease variants hold particular promise not only for disentangling the genetic architecture of inbreeding depression, but also evaluating and improving upon current approaches for detecting ROH.},
	URL = {https://www.biorxiv.org/content/early/2018/05/07/315770},
	eprint = {https://www.biorxiv.org/content/early/2018/05/07/315770.full.pdf},
	journal = {bioRxiv}
}


@article{novembre:08,
  title={Interpreting principal component analyses of spatial population genetic variation},
  author={Novembre, John and Stephens, Matthew},
  journal={Nature genetics},
  volume={40},
  number={5},
  pages={646},
  year={2008},
  publisher={Nature Publishing Group}
}

@article{bradburd:16,
  title={A spatial framework for understanding population structure and admixture},
  author={Bradburd, Gideon S and Ralph, Peter L and Coop, Graham M},
  journal={PLoS genetics},
  volume={12},
  number={1},
  pages={e1005703},
  year={2016},
  publisher={Public Library of Science}
}

@article{alcaide:14,
  title={Genomic divergence in a ring species complex},
  author={Alcaide, Miguel and Scordato, Elizabeth SC and Price, Trevor D and Irwin, Darren E},
  journal={Nature},
  volume={511},
  number={7507},
  pages={83},
  year={2014},
  publisher={Nature Publishing Group}
}

@article{becquet:07,
  title={Genetic structure of chimpanzee populations},
  author={Becquet, Celine and Patterson, Nick and Stone, Anne C and Przeworski, Molly and Reich, David},
  journal={PLoS genetics},
  volume={3},
  number={4},
  pages={e66},
  year={2007},
  publisher={Public Library of Science}
}


@article{vonHoldt:11,
author = {vonHoldt, Bridgett M. and Pollinger, John P. and Earl, Dent A. and Knowles, James C. and Boyko, Adam R. and Parker, Heidi and Geffen, Eli and Pilot, Malgorzata and Jedrzejewski, Wlodzimierz and Jedrzejewska, Bogumila and Sidorovich, Vadim and Greco, Claudia and Randi, Ettore and Musiani, Marco and Kays, Roland and Bustamante, Carlos D. and Ostrander, Elaine A. and Novembre, John and Wayne, Robert K.}, 
title = {A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids},
year = {2011}, 
doi = {10.1101/gr.116301.110}, 
URL = {http://genome.cshlp.org/content/early/2011/05/12/gr.116301.110.abstract}, 
eprint = {http://genome.cshlp.org/content/early/2011/05/12/gr.116301.110.full.pdf+html}, 
journal = {Genome Research} 
}

@article{lewontin:94,
author = "Lewontin, R. C.",
doi = "10.1214/ss/1177010492",
fjournal = "Statistical Science",
journal = "Statist. Sci.",
month = "05",
number = "2",
pages = "259--262",
publisher = "The Institute of Mathematical Statistics",
title = "[DNA Fingerprinting: A Review of the Controversy]: Comment: The Use of DNA Profiles in Forensic Contexts",
url = "https://doi.org/10.1214/ss/1177010492",
volume = "9",
year = "1994"
}


@article{chen:16,
title = "Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay",
journal = "Current Biology",
volume = "26",
number = "21",
pages = "2974 - 2979",
year = "2016",
issn = "0960-9822",
doi = "https://doi.org/10.1016/j.cub.2016.08.062",
url = "http://www.sciencedirect.com/science/article/pii/S0960982216310077",
author = "Nancy Chen and Elissa J. Cosgrove and Reed Bowman and John W. Fitzpatrick and Andrew G. Clark",
keywords = "habitat fragmentation, gene flow, inbreeding depression, population genetics, conservation genomics"
}

@article{Aguillon:17,
    author = {Aguillon, Stepfanie M. AND Fitzpatrick, John W. AND Bowman, Reed AND Schoech, Stephan J. AND Clark, Andrew G. AND Coop, Graham AND Chen, Nancy},
    journal = {PLOS Genetics},
    publisher = {Public Library of Science},
    title = {Deconstructing isolation-by-distance: The genomic consequences of limited dispersal},
    year = {2017},
    month = {08},
    volume = {13},
    url = {https://doi.org/10.1371/journal.pgen.1006911},
    pages = {1-27},
    abstract = {Author summary Dispersal is a fundamental component of the life history of most organisms and therefore influences many biological processes. Dispersal is particularly important in creating genetic structure on the landscape. We often observe a pattern of decreased genetic relatedness between individuals as geographic distances increases, or isolation-by-distance. This pattern is particularly pronounced in organisms with extremely short dispersal distances. Despite the ubiquity of isolation-by-distance patterns in nature, there are few examples that explicitly demonstrate how limited dispersal influences spatial genetic structure. Here we investigate the processes that result in spatial genetic structure using the Florida Scrub-Jay, a bird with extremely limited dispersal behavior and extensive genome-wide data. We take advantage of the long-term monitoring of a contiguous population of Florida Scrub-Jays, which has resulted in a detailed pedigree and measurements of dispersal for hundreds of individuals. We show how limited dispersal results in close genealogical relatives living closer together geographically, which generates a strong pattern of isolation-by-distance at an extremely small spatial scale (<10 km) in just a few generations. Given the detailed dispersal, pedigree, and genomic data, we can achieve a fairly complete understanding of how dispersal shapes patterns of genetic diversity over short spatial scales.},
    number = {8},
    doi = {10.1371/journal.pgen.1006911}
}

@article{algee:16,
  title={Individual identifiability predicts population identifiability in forensic microsatellite markers},
  author={Algee-Hewitt, Bridget FB and Edge, Michael D and Kim, Jaehee and Li, Jun Z and Rosenberg, Noah A},
  journal={Current Biology},
  volume={26},
  number={7},
  pages={935--942},
  year={2016},
  publisher={Elsevier}
}


@incollection{box:79,
  title={Robustness in the strategy of scientific model building},
  author={Box, George EP},
  booktitle={Robustness in statistics},
  pages={201--236},
  year={1979},
  publisher={Elsevier}
}

@article{Meredith:09,
    author = {Meredith, Robert W. AND Gatesy, John AND Murphy, William J. AND Ryder, Oliver A. AND Springer, Mark S.},
    journal = {PLOS Genetics},
    publisher = {Public Library of Science},
    title = {Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals},
    year = {2009},
    month = {09},
    volume = {5},
    url = {https://doi.org/10.1371/journal.pgen.1000634},
    pages = {1-12},
    abstract = {Author Summary Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin's theory of descent with modification.},
    number = {9},
    doi = {10.1371/journal.pgen.1000634}
}

@article {Wright:05,
	author = {Wright, Stephen I. and Bi, Irie Vroh and Schroeder, Steve G. and Yamasaki, Masanori and Doebley, John F. and McMullen, Michael D. and Gaut, Brandon S.},
	title = {The Effects of Artificial Selection on the Maize Genome},
	volume = {308},
	number = {5726},
	pages = {1310--1314},
	year = {2005},
	doi = {10.1126/science.1107891},
	publisher = {American Association for the Advancement of Science},
	abstract = {Domestication promotes rapid phenotypic evolution through artificial selection. We investigated the genetic history by which the wild grass teosinte (Zea mays ssp. parviglumis) was domesticated into modern maize (Z. mays ssp. mays). Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4\% of these genes experienced artificial selection. The remaining genes retain evidence of a population bottleneck associated with domestication. Candidate selected genes with putative function in plant growth are clustered near quantitative trait loci that contribute to phenotypic differences between maize and teosinte. If we assume that our sample of genes is representative, \~{}1200 genes throughout the maize genome have been affected by artificial selection.},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/308/5726/1310},
	eprint = {http://science.sciencemag.org/content/308/5726/1310.full.pdf},
	journal = {Science}
}


@article{Hudson:15,
    author = {Hudson, Richard R.},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {A New Proof of the Expected Frequency Spectrum under the Standard Neutral Model},
    year = {2015},
    month = {07},
    volume = {10},
    url = {https://doi.org/10.1371/journal.pone.0118087},
    pages = {1-5},
    number = {7},
    doi = {10.1371/journal.pone.0118087}
}

@article{Sankararaman:12,
    author = {Sankararaman, Sriram AND Patterson, Nick AND Li, Heng AND Pääbo, Svante AND Reich, David},
    journal = {PLOS Genetics},
    publisher = {Public Library of Science},
    title = {The Date of Interbreeding between Neandertals and Modern Humans},
    year = {2012},
    month = {10},
    volume = {8},
    url = {https://doi.org/10.1371/journal.pgen.1002947},
    pages = {1-9},
    number = {10},
    doi = {10.1371/journal.pgen.1002947}
}

@article{Laurie:07,
    author = {Laurie, Cathy C AND Nickerson, Deborah A AND Anderson, Amy D AND Weir, Bruce S AND Livingston, Robert J AND Dean, Matthew D AND Smith, Kimberly L AND Schadt, Eric E AND Nachman, Michael W},
    journal = {PLOS Genetics},
    publisher = {Public Library of Science},
    title = {Linkage Disequilibrium in Wild Mice},
    year = {2007},
    month = {08},
    volume = {3},
    url = {https://doi.org/10.1371/journal.pgen.0030144},
    pages = {1-9},
    number = {8},
    doi = {10.1371/journal.pgen.0030144}
}


@article{jennings:05,
  title={Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees},
  author={Jennings, W Bryan and Edwards, Scott V},
  journal={Evolution},
  volume={59},
  number={9},
  pages={2033--2047},
  year={2005},
  publisher={Wiley Online Library}
}



@article{paaby:14,
  title={A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life-history adaptation},
  author={Paaby, Annalise B and Bergland, Alan O and Behrman, Emily L and Schmidt, Paul S},
  journal={Evolution},
  volume={68},
  number={12},
  pages={3395--3409},
  year={2014},
  publisher={Wiley Online Library}
}


@article{wright:46,
  title={Genetics of natural populations. XII. Experimental reproduction of some of the changes caused by natural selection in certain populations of Drosophila pseudoobscura},
  author={Wright, Sewall and Dobzhansky, Theodosius},
  journal={Genetics},
  volume={31},
  number={2},
  pages={125},
  year={1946},
  publisher={Genetics Society of America}
}


@article{richards:00,
  title={Inbreeding depression and genetic rescue in a plant metapopulation},
  author={Richards, Christopher M},
  journal={The American Naturalist},
  volume={155},
  number={3},
  pages={383--394},
  year={2000},
  publisher={The University of Chicago Press}
}



@article{Haldane:37,
author = {Haldane, J. B. S.},
title = {The Effect of Variation of Fitness},
journal = {The American Naturalist},
volume = {71},
number = {735},
pages = {337-349},
year = {1937},
doi = {10.1086/280722},

URL = { 
        https://doi.org/10.1086/280722
    
},
eprint = { 
        https://doi.org/10.1086/280722
    
}
,
    abstract = { In a species in equilibrium variation is mainly due to two causes. Some deleterious genes are being weeded out by selection at the same rate as they are produced by mutation. Others are preserved because the heterozygous form is fitter than either homozygote. In the former case the loss of fitness in the species is roughly equal to the sum of all mutation rates and is probably of the order of 5 per cent. It is suggested that this loss of fitness is the price paid by a species for its capacity for further evolution. }
}




@article{darwin:1876,
  title={The effect of cross and self fertilization in the vegetable kingdom: Murray},
  author={Darwin, Charles},
  journal={London, UK},
  year={1876}
}


@article{lek:16,
  title={Analysis of protein-coding genetic variation in 60,706 humans},
  author={Lek, Monkol and Karczewski, Konrad J and Minikel, Eric V and Samocha, Kaitlin E and Banks, Eric and Fennell, Timothy and O’Donnell-Luria, Anne H and Ware, James S and Hill, Andrew J and Cummings, Beryl B and others},
  journal={Nature},
  volume={536},
  number={7616},
  pages={285},
  year={2016},
  publisher={Nature Publishing Group}
}


@article{macarthur:12,
  title={A systematic survey of loss-of-function variants in human protein-coding genes},
  author={MacArthur, Daniel G and Balasubramanian, Suganthi and Frankish, Adam and Huang, Ni and Morris, James and Walter, Klaudia and Jostins, Luke and Habegger, Lukas and Pickrell, Joseph K and Montgomery, Stephen B and others},
  journal={Science},
  volume={335},
  number={6070},
  pages={823--828},
  year={2012},
  publisher={American Association for the Advancement of Science}
}


@article{francioli:14,
  title={Whole-genome sequence variation, population structure and demographic history of the Dutch population},
  author={Francioli, Laurent C and Menelaou, Androniki and Pulit, Sara L and Van Dijk, Freerk and Palamara, Pier Francesco and Elbers, Clara C and Neerincx, Pieter BT and Ye, Kai and Guryev, Victor and Kloosterman, Wigard P and others},
  journal={Nature genetics},
  volume={46},
  number={8},
  pages={818},
  year={2014},
  publisher={Nature Publishing Group}
}


@article{Toews:16,
title = "Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers",
journal = "Current Biology",
volume = "26",
number = "17",
pages = "2313 - 2318",
year = "2016",
issn = "0960-9822",
doi = "https://doi.org/10.1016/j.cub.2016.06.034",
url = "http://www.sciencedirect.com/science/article/pii/S096098221630673X",
author = "David P.L. Toews and Scott A. Taylor and Rachel Vallender and Alan Brelsford and Bronwyn G. Butcher and Philipp W. Messer and Irby J. Lovette"
}


%Crew B. (2013). In North American katydids, green isn’t the dominant colour, pink is. Scientific American Blog Network. (3 September 2015).
@Misc{Crew:13,
  OPTkey = 	 {}, 
  OPTauthor = 	 {Crew, B.},
  title = 	 {In North American katydids, green isn’t the dominant colour, pink is.},
  howpublished = {Scientific American Blog Network.},
 URL = {https://blogs.scientificamerican.com/running-ponies/in-north-american-katydids-green-isne28099t-the-dominant-colour-pink-is/},
  OPTmonth = 	 {},
  year = 	 {2013},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Wheeler:07,
 ISSN = {00030147, 15375323},
 URL = {http://www.jstor.org/stable/2454781},
 author = {William Morton Wheeler},
 journal = {The American Naturalist},
 number = {492},
 pages = {773--780},
 publisher = {[University of Chicago Press, American Society of Naturalists]},
 title = {Pink Insect Mutants},
 volume = {41},
 year = {1907}
}




@article {Barrett:08,
	author = {Barrett, Rowan D. H. and Rogers, Sean M. and Schluter, Dolph},
	title = {Natural Selection on a Major Armor Gene in Threespine Stickleback},
	volume = {322},
	number = {5899},
	pages = {255--257},
	year = {2008},
	doi = {10.1126/science.1159978},
	publisher = {American Association for the Advancement of Science},
	abstract = {Experimental estimates of the effects of selection on genes determining adaptive traits add to our understanding of the mechanisms of evolution. We measured selection on genotypes of the Ectodysplasin locus, which underlie differences in lateral plates in threespine stickleback fish. A derived allele (low) causing reduced plate number has been fixed repeatedly after marine stickleback colonized freshwater from the sea, where the ancestral allele (complete) predominates. We transplanted marine sticklebacks carrying both alleles to freshwater ponds and tracked genotype frequencies over a generation. The low allele increased in frequency once lateral plates developed, most likely via a growth advantage. Opposing selection at the larval stage and changing dominance for fitness throughout life suggest either that the gene affects additional traits undergoing selection or that linked loci also are affecting fitness.},
	issn = {0036-8075},
	URL = {http://science.sciencemag.org/content/322/5899/255},
	eprint = {http://science.sciencemag.org/content/322/5899/255.full.pdf},
	journal = {Science}
}


@article{houde:94,
  title={Effect of artificial selection on male colour patterns on mating preference of female guppies},
  author={Houde, Anne E},
  journal={Proc. R. Soc. Lond. B},
  volume={256},
  number={1346},
  pages={125--130},
  year={1994},
  publisher={The Royal Society}
}


@article {Allendorf:09,
	author = {Allendorf, Fred W. and Hard, Jeffrey J.},
	title = {Human-induced evolution caused by unnatural selection through harvest of wild animals},
	volume = {106},
	number = {Supplement 1},
	pages = {9987--9994},
	year = {2009},
	doi = {10.1073/pnas.0901069106},
	publisher = {National Academy of Sciences},
	issn = {0027-8424},
	URL = {http://www.pnas.org/content/106/Supplement_1/9987},
	eprint = {http://www.pnas.org/content/106/Supplement_1/9987.full.pdf},
	journal = {Proceedings of the National Academy of Sciences}
}



@article{haldane:42,
  title={The selective elimination of silver foxes in eastern Canada},
  author={Haldane, JBS},
  journal={Journal of Genetics},
  volume={44},
  number={2-3},
  pages={296--304},
  year={1942},
  publisher={Springer}
}


%%%%foxes data from Haldane 1942
@Book{elton:42,
  author = 	 {Elton, Charles},
  OPTeditor = 	 {},
  title = 	 {Voles, mice and lemmings. Problems in population dynamics.},
  publisher = 	 {Oxford: Clarendon Press},
  year = 	 {1942},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{tajima:89,
  title={Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.},
  author={Tajima, Fumio},
  journal={Genetics},
  volume={123},
  number={3},
  pages={585--595},
  year={1989},
  publisher={Genetics Soc America}
}


@article{nelson:12,
  title={An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people},
  author={Nelson, Matthew R and Wegmann, Daniel and Ehm, Margaret G and Kessner, Darren and Jean, Pamela St and Verzilli, Claudio and Shen, Judong and Tang, Zhengzheng and Bacanu, Silviu-Alin and Fraser, Dana and others},
  journal={Science},
  pages={1217876},
  year={2012},
  publisher={American Association for the Advancement of Science}
}


@article{brandvain:14,
  title={Speciation and introgression between Mimulus nasutus and Mimulus guttatus},
  author={Brandvain, Yaniv and Kenney, Amanda M and Flagel, Lex and Coop, Graham and Sweigart, Andrea L},
  journal={PLoS Genetics},
  volume={10},
  number={6},
  pages={e1004410},
  year={2014},
  publisher={Public Library of Science}
}



@article{leffler:12,
  title={Revisiting an old riddle: what determines genetic diversity levels within species?},
  author={Leffler, Ellen M and Bullaughey, Kevin and Matute, Daniel R and Meyer, Wynn K and Segurel, Laure and Venkat, Aarti and Andolfatto, Peter and Przeworski, Molly},
  journal={PLoS biology},
  volume={10},
  number={9},
  pages={e1001388},
  year={2012},
  publisher={Public Library of Science}
}



@article{wilkinson:93,
  title={Artificial sexual selection alters allometry in the stalk-eyed fly Cyrtodiopsis dalmanni (Diptera: Diopsidae)},
  author={Wilkinson, Gerald S},
  journal={Genetics Research},
  volume={62},
  number={3},
  pages={213--222},
  year={1993},
  publisher={Cambridge University Press}
}


@article{Messier:97,
  title={Episodic adaptive evolution of primate lysozymes},
  author={Messier, Walter and Stewart, Caro-Beth},
  journal={Nature},
  volume={385},
  number={6612},
  pages={151},
  year={1997},
  publisher={Nature Publishing Group}
}


@article{Yang:98,
author = {Yang, Z},
title = {Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.},
journal = {Molecular Biology and Evolution},
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