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The Historic Split and Merger of Gene Trees and Species Trees

from Part 2 - Commentaries

Published online by Cambridge University Press:  29 June 2018

Rasmus Grønfeldt Winther
Affiliation:
University of California
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Phylogenetic Inference, Selection Theory, and History of Science
Selected Papers of A. W. F. Edwards with Commentaries
, pp. 334 - 342
Publisher: Cambridge University Press
Print publication year: 2018

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References

Allman, E. S., Degnan, J. H., and Rhodes, J. A. 2010. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. Journal of Mathematical Biology 62, 833862.CrossRefGoogle ScholarPubMed
Avise, J. 2000. Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard University Press.CrossRefGoogle Scholar
Bradburd, G. S., Ralph, P. L., and Coop, G. M. 2013. Disentangling the effects of geographic and ecological isolation on genetic differentiation. Evolution 67, 32583273.CrossRefGoogle ScholarPubMed
Brower, A. V. Z. 2000. Evolution is not a necessary assumption of cladistics. Cladistics 16, 143154.CrossRefGoogle Scholar
Coop, G., Witonsky, D., Rienzo, A. D., and Pritchard, J. K. 2010. Using environmental correlations to identify loci underlying local adaptation. Genetics 185, 14111423.CrossRefGoogle ScholarPubMed
Edwards, S. V. and Beerli, P. 2000. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeography studies. Evolution 54, 18391854.Google Scholar
Ereshefsky, M. 2001. The Poverty of the Linnaean Hierarchy: A Philosophical Study of Biological Taxonomy. Cambridge: Cambridge University Press.Google Scholar
Farris, J. S. 1983. The logical basis of phylogenetic analysis. In Platnick, N. I. and Funk, V. A., Advances in Cladistics, New York: Columbia University Press, volume 2, 736.Google Scholar
Felsenstein, J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics 25, 471492.Google ScholarPubMed
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17, 368376.CrossRefGoogle ScholarPubMed
Felsenstein, J. 1985. Phylogenies from gene frequencies: a statistical problem. Systematic Biology 34, 300311.CrossRefGoogle Scholar
Heled, J. and Drummond, A. J. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27, 570580.CrossRefGoogle ScholarPubMed
Hudson, R. R. 1983. Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology 23, 183201.CrossRefGoogle ScholarPubMed
Kingman, J. F. C. 1982. The coalescent. Stochastic Processes and their Applications 13, 235248.Google Scholar
Lande, R. 1975. The maintenance of genetic variability of mutation in a polygenic character with linked loci. Genetical Research 26, 221235.CrossRefGoogle Scholar
Larget, B. R., Kotha, S. K., Dewey, C. N., and Ané, C. 2010. BUCKy: gene tree/species tree reconciliation with the Bayesian concordance analysis. Bioinformatics 26, 29102911.CrossRefGoogle ScholarPubMed
Liu, L., Yiu, L., Kubatko, L., Pearl, D. K., and Edwards, S. V. 2009. Coalescent methods for estimating phylogenetic trees. Molecular Phylogenetics and Evolution 53, 320328.CrossRefGoogle ScholarPubMed
Maddison, W. P. and Knowles, L. L. 2005. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55, 2130.CrossRefGoogle Scholar
Mirarab, S. Bayzid, S., Boussau, B., and Warnow, T.. 2014a. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346, doi: 10.1126/science.1250463.CrossRefGoogle ScholarPubMed
Mirarab, S., Reaz, R., Bayzid, Md. S., Zimmerman, T., Swenson, M. S., and Warnow, T.. 2014b. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541i548.CrossRefGoogle ScholarPubMed
Nielsen, R. and Beaumont, M. A.. 2009. Statistical inferences in phylogeography. Molecular Ecology 18, 10341047.CrossRefGoogle ScholarPubMed
Pamilo, P. and Nei, M. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5, 568583.Google ScholarPubMed
Pickrell, J. K. and Pritchard, J. K.. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics 8, e1002967.CrossRefGoogle ScholarPubMed
Provine, W. B. 1971. The Origins of Theoretical Population Genetics. Chicago, IL: University of Chicago Press.Google Scholar
Templeton, A. R. 2004. Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13, 789809.CrossRefGoogle ScholarPubMed
Thompson, E. A. 1975. Human Evolutionary Trees. Cambridge: Cambridge University Press.Google Scholar
Wright, S. 1968. Evolution and the Genetics of Populations, Volume 1: Genetic and Biometric Foundations. Chicago, IL: University of Chicago Press.Google Scholar

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