Journal ArticleDOI
The performance of phylogenetic algorithms in estimating haplotype genealogies with migration.
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TLDR
In this article, the performance of traditional phylogenetic algorithms, neighbour-joining, maximum parsimony and maximum likelihood in estimating genealogies from nonrecombining haplotypic genetic data is evaluated.Abstract:
Genealogies estimated from haplotypic genetic data play a prominent role in various biological disciplines in general and in phylogenetics, population genetics and phylogeography in particular. Several software packages have specifically been developed for the purpose of reconstructing genealogies from closely related, and hence, highly similar haplotype sequence data. Here, we use simulated data sets to test the performance of traditional phylogenetic algorithms, neighbour-joining, maximum parsimony and maximum likelihood in estimating genealogies from nonrecombining haplotypic genetic data. We demonstrate that these methods are suitable for constructing genealogies from sets of closely related DNA sequences with or without migration. As genealogies based on phylogenetic reconstructions are fully resolved, but not necessarily bifurcating, and without reticulations, these approaches outperform widespread 'network' constructing methods. In our simulations of coalescent scenarios involving panmictic, symmetric and asymmetric migration, we found that phylogenetic reconstruction methods performed well, while the statistical parsimony approach as implemented in TCS performed poorly. Overall, parsimony as implemented in the PHYLIP package performed slightly better than other methods. We further point out that we are not making the case that widespread 'network' constructing methods are bad, but that traditional phylogenetic tree finding methods are applicable to haplotypic data and exhibit reasonable performance with respect to accuracy and robustness. We also discuss some of the problems of converting a tree to a haplotype genealogy, in particular that it is nonunique.read more
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Journal ArticleDOI
Circulation of four Anaplasma phagocytophilum ecotypes in Europe
Setareh Jahfari,E. Claudia Coipan,Manoj Fonville,Arieke Docters van Leeuwen,Paul Hengeveld,Dieter Heylen,Paul Heyman,Cees van Maanen,C M Butler,Gábor Földvári,Sándor Szekeres,Gilian van Duijvendijk,Wesley Tack,Jolianne M. Rijks,Joke van der Giessen,Willem Takken,Sipke E. van Wieren,Katsuhisa Takumi,Hein Sprong +18 more
TL;DR: Four ecotypes of A. phagocytophilum with differential enzootic cycles were identified, and based on population genetic parameters, the potentially zoonotic ecotype showed significant expansion, indicating a recent increase of the acarological risk of exposure of humans and animals.
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A road map for molecular ecology.
Rose L. Andrew,Louis Bernatchez,Aurélie Bonin,C. Alex Buerkle,Bryan C. Carstens,Brent C. Emerson,Dany Garant,Tatiana Giraud,Nolan C. Kane,Sean M. Rogers,Jon Slate,Harry Smith,Victoria L. Sork,Graham N. Stone,Timothy H. Vines,Lisette P. Waits,Alex Widmer,Loren H. Rieseberg,Loren H. Rieseberg +18 more
TL;DR: The discipline of molecular ecology has undergone enormous changes since the journal bearing its name was launched approximately two decades ago as discussed by the authors, and the field has seen great strides in analytical methods development, made groundbreaking discoveries and experienced a revolution in genotyping technology.
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Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation
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Diana M. Percy,George W. Argus,Quentin C. B. Cronk,Aron J. Fazekas,Prasad Kesanakurti,Kevin S. Burgess,Brian C. Husband,Steven G. Newmaster,Spencer C. H. Barrett,Sean W. Graham +9 more
TL;DR: The most likely explanation for the patterns the authors observed involves recent repeated plastid capture events, aided by widespread hybridization and long‐range seed dispersal, but primarily propelled by one or more trans‐species selective sweeps.
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Glacial history of a modern invader: phylogeography and species distribution modelling of the Asian tiger mosquito Aedes albopictus.
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References
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Journal ArticleDOI
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Journal ArticleDOI
Arlequin (version 3.0): An integrated software package for population genetics data analysis
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Journal ArticleDOI
Evolutionary trees from DNA sequences: A maximum likelihood approach
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.