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Fernando Villanea Works Cited

Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, and Kruglyak L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2(10):e286.

Alter SE, Newsome SD, and Palumbi SR. 2012. Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes. PLoS ONE 7(5):e35039.

Ammerman AJ, and Cavalli-Sforza LL. 1984. The Neolithic Transition and the Genetics of Populations in Europe. Princeton, New Jersey: Princeton University Press. 200 p.

Anderson CNK, Ramakrishnan U, Chan YL, and Hadly EA. 2005. Serial SimCoal: A population genetics model for data from multiple populations and points in time. Bioinformatics 21(8):1733-1734.

Atkinson QD, Gray RD, and Drummond AJ. 2008. mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory. Molecular Biology and Evolution 25(2):468-474.

Atkinson QD, Gray RD, and Drummond AJ. 2009. Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. Proceedings of the Royal Society of London B: Biological Sciences 276(1655):367-373.

Barta JL, Monroe C, and Kemp BM. 2013. Further Evaluation of the Efficacy of Contamination Removal From Bone Surfaces. Forensic Sci Int 231:340-348.

Barta JL, Monroe C, Teisberg JE, Winters M, Flanigan K, and Kemp BM. 2014. One of the Key Characteristics of Ancient and Forensic DNA, Low Copy Number, May be a Product of its Extraction. Journal of Archaeological Science 46:281-289.

Beaumont MA. 1999. Detecting Population Expansion and Decline Using Microsatellites. Genetics 153(4):2013-2029.

Berniell-Lee G, Calafell F, Bosch E, Heyer E, Sica L, Mouguiama-Daouda P, van der Veen L, Hombert J-M, Quintana-Murci L, and Comas D. 2009. Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages. Molecular Biology and Evolution 26(7):1581-1589.

Bertorelle G, Benazzo A, and Mona S. 2010. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Molecular Ecology 19(13):2609-2625.

Bonatto SL, and Salzano FM. 1997a. Diversity and Age of the Four Major mtDNA Haplogroups, and Their Implications for the Peopling of the New World. The American Journal of Human Genetics 61(6):1413-1423.

Bonatto SL, and Salzano FM. 1997b. A single and early migration for the peopling of the Americas supported by mitochondrial DNA sequence data. Proc Natl Acad Sci 94:1866-1871.

Box GEP, and Draper NR. 1987. Empirical Model Building and Response Surfaces. New York, NY: John Wiley & Sons. 688 p.

Buzbas E. 2015. ABC: resources on approximate Bayesian computational methods. In: Buzbas E, editor. Moscow, Idaho.

Buzbas EO, and Rosenberg NA. 2015. AABC: Approximate approximate Bayesian computation for inference in population-genetic models. Theoretical Population Biology 99(0):31-42.

Casella G. 2008. Bayesians and Frequentists: Models, Assumptions, and Inference. ACCP 37th Annual Meeting. Philadelphia, PA.

Chan YL, Anderson CNK, and Hadly EA. 2006. Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA. PLoS Genet 2(4):e59.

Cooper A, and Poinar HN. 2000. Ancient DNA: do it right or not at all. Science 289(5482):1139.

Cornuet J-M, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois Rl, Marin J-M, and Estoup A. 2014. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics 30(8):1187-1189.

Csillery K, Blum M, Gaggiotti O, and Francois O. 2010. Approximate Bayesian Computation (ABC) in practice. Trends in Ecology & Evolution 25(7):410-418.

Csilléry K, François O, and Blum MGB. 2012. abc: an R package for approximate Bayesian computation (ABC). Methods in Ecology and Evolution 3(3):475-479.

Der Sarkissian C, Allentoft ME, Avila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernandez R, da Fonseca R, Ginolhac A and others. 2014. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 370(1660).

Donnelly P, and Tavare S. 1995. Coalescents and Genealogical Structure Under Neutrality. Annual Review of Genetics 29(1):401-421.

Drummond A, and Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7(1):214.

Drummond AJ, Rambaut A, Shapiro B, and Pybus OG. 2005. Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. Molecular Biology and Evolution 22(5):1185-1192.

Drummond AJ, Suchard MA, Xie D, and Rambaut A. 2012. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29(8):1969-1973.

Edwards AWF. 1970. Estimation of the Branch Points of a Branching Diffusion Process. Journal of the Royal Statistical Society Series B (Methodological) 32(2):155-174.

Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, and Foll M. 2013. Robust demographic inference from genomic and SNP data. PLoS Genet 9(10):e1003905.

Excoffier L, and Foll M. 2011. Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27(9):1332-1334.

Excoffier L, Novembre J, and Schneider S. 2000. SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J Hered 91(6):506-509.

Fagundes NJR, Kanitz R, and Bonatto SL. 2008a. A Reevaluation of the Native American MtDNA Genome Diversity and Its Bearing on the Models of Early Colonization of Beringia. PLOS One 3(9):e3157.

Fagundes NJR, Kanitz R, Eckert R, Valls ACS, Bogo MR, Salzano FM, Smith DG, Silva Jr WA, Zago MA, Ribeiro-dos-Santos AK and others. 2008b. Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas. The American Journal of Human Genetics 82(3):583-592.

Foote AD, Kaschner K, Schultze SE, Garilao C, Ho SY, Post K, Higham TF, Stokowska C, van der Es H, and Embling CB. 2013. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts. Nature communications 4:1677.

Fu YX, and Li WH. 1999. Coalescing into the 21st century: An overview and prospects of coalescent theory. Theor Popul Biol 56(1):1-10.

Gignoux CR, Henn BM, and Mountain JL. 2011. Rapid, global demographic expansions after the origins of agriculture. Proceedings of the National Academy of Sciences 108(15):6044-6049.

Gilbert MTP. 2006. Postmortem Damage of Mitochondrial DNA. In: Bandelt H-J, Macaulay V, and Richards M, editors. Human Mitochondrial DNA and the Evolution of Homo sapiens. Berlin: Springer-Verlag p91-115.

Gilbert MTP, Bandelt H-J, Hofreiter M, and Barnes I. 2005. Assessing ancient DNA studies. TRENDS in Ecology and Evolution 20(10):541-544.

Grayson DK, and Meltzer DJ. 2003. A requiem for North American overkill. Journal of Archaeological Science 30(5):585-593.

Griffiths RC, and Tavare S. 1994. Sampling Theory for Neutral Alleles in a Varying Environment. Philosophical Transactions of the Royal Society of London B: Biological Sciences 344(1310):403-410.

Hartl DL, and Clark AG. 2006. Principles of Population Genetics. Sunderland, MA: Sinauer Associates, Inc. 545 p.

Heled J, and Drummond AJ. 2008. Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology 8(289).

Hey J. 2005. On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biol 3(e193).

Hey J, and Nielsen R. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A 104(8):2785-2790.

Ho SYW, and Shapiro B. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Molecular Ecology Resources 11(3):423-434.

Hudson R, Futuyma DJ, and Antonovics J. 1990. Gene Genealogies and the Coalescent. Oxford Surveys in Evolutionary Biology: Oxford Univ. Press, Oxford.

Kass RE, and Raftery AE. 1995. Bayes Factors. Journal of the American Statistical Association 90(430):773-795.

Kemp BM, Monroe C, Judd KG, Reams E, and Grier C. 2014a. Evaluation of Methods that Subdue the Effects of Polymerase Chain Reaction Inhibitors in the Study of Ancient and Degraded DNA. Journal of Archaeological Science 42:373-380.

Kemp BM, Winters M, Monroe C, and Barta JL. 2014b. How Much DNA is Lost? Measuring DNA Loss of Short-Tandem-Repeat Length Fragments Targeted by the PowerPlex 16® System Using the Qiagen MinElute Purification Kit. Human Biology 86:313-329.

Kingman JFC. 1982a. The coalescent. Stochastic Processes and their Applications 13(3):235-248.

Kingman JFC. 1982b. On the Genealogy of Large Populations. Journal of Applied Probability 19:27-43.

Kitchen A, Miyamoto MM, and Mulligan CJ. 2008. A Three-Stage Colonization Model for the Peopling of the Americas. PLoS ONE 3(2):e1596.

Konigsberg LW, and Frankenberg SR. 2013. Bayes in biological anthropology. American Journal of Physical Anthropology 152:153-184.

Krzywinski M, and Altman N. 2013a. Points of Significance: Error bars. Nat Meth 10(10):921-922.

Krzywinski M, and Altman N. 2013b. Points of significance: Importance of being uncertain. Nat Meth 10(9):809-810.

Krzywinski M, and Altman N. 2013c. Points of significance: Significance, P values and t-tests. Nat Meth 10(11):1041-1042.

Kuhner MK. 2009. Coalescent genealogy samplers: windows into population history. Trends in Ecology and Evolution 24(2):86-93.

Lorenzen ED, Nogues-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R and others. 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479(7373):359-364.

Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F and others. 2005. Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes. Science 308(5724):1034-1036.

Minin VN, Bloomquist EW, and Suchard MA. 2008. Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics. Molecular Biology and Evolution 25(7):1459-1471.

Mulligan CJ, Kitchen A, and Miyamoto MM. 2008. Updated Three-Stage Model for the Peopling of the Americas. PLoS ONE 3(9):e3199.

Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G, Krause J, Detter JC, Paabo S, and Rubin EM. 2005. Genomic sequencing of Pleistocene cave bears. Science 309(5734):597-599.

Pääbo S. 1989. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci U S A 86:1939-1943.

Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, and Hofreiter M. 2004. Genetic analyses from ancient DNA. Annu Rev Genet 38:645-679.

Pinsky ML, Newsome SD, Dickerson BR, Fang Y, Van Tuinen M, Kennett DJ, Ream RR, and Hadly EA. 2010. Dispersal provided resilience to range collapse in a marine mammal: insights from the past to inform conservation biology. Molecular Ecology 19(12):2418-2429.

Prost S, Smirnov N, Fedorov VB, Sommer RS, Stiller M, Nagel D, Knapp M, and Hofreiter M. 2010. Influence of Climate Warming on Arctic Mammals? New Insights from Ancient DNA Studies of the Collared Lemming Dicrostonyx torquatus. PLoS ONE 5(5):e10447.

Puga JL, Krzywinski M, and Altman N. 2015a. Points of Significance: Bayes’ theorem. Nat Meth 12(4):277-278.

Puga JL, Krzywinski M, and Altman N. 2015b. Points of significance: Bayesian statistics. Nat Meth 12(5):377-378.

Pybus OG, and Rambaut A. 2002. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18(10):1404-1405.

Pybus OG, Rambaut A, and Harvey PH. 2000. An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies. Genetics 155(3):1429-1437.

Ramakrishnan UMA, and Hadly EA. 2009. Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Molecular Ecology 18(7):1310-1330.

Ray N, Wegmann D, Fagundes NJR, Wang S, Ruiz-Linares A, and Excoffier L. 2010. A Statistical Evaluation of Models for the Initial Settlement of the American Continent Emphasizes the Importance of Gene Flow with Asia. Mol Biol Evol 27(2):337-345.

Rice S. 2004. Evolutionary Theory: Mathematical and Conceptial Foundations. Sunderland, MA: Sinauer. 370 p.

Sandoval-Castellanos E, Palkopoulou E, and Dalen L. 2014. Back to BaySICS: A User-Friendly Program for Bayesian Statistical Inference from Coalescent Simulations. PLoS ONE 9(5):e98011.

Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M, Possnert G, and Paabo S. 2004. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2(3):E57.

Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MTP, Barnes I, Binladen J and others. 2004. Rise and Fall of the Beringian Steppe Bison. Science 306(5701):1561-1565.

Strimmer K, and Pybus OG. 2001. Exploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot. Molecular Biology and Evolution 18(12):2298-2305.

Tajima F. 1989. Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123(3):585-595.

Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK and others. 2007. Beringian Standstill and Spread of Native American Founders. PLOS One 9:e829 (821-826).

Toups MA, Kitchen A, Light JE, and Reed DL. 2011. Origin of Clothing Lice Indicates Early Clothing Use by Anatomically Modern Humans in Africa. Molecular Biology and Evolution 28(1):29-32.

Wakeley J. 2009. Coalescent Theory: An introduction. Greenwood Village, CO: Roberts and Company Publishers. 326 p.

Wilson IJ, and Balding DJ. 1998. Genealogical Inference From Microsatellite Data. Genetics 150(1):499-510.