BMC Bioinformatics, 2007 Background Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate the gene tree and population/species
Takebayashi Naoki +2 more
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A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree [PDF]
, 2012 In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of
Degnan, James H., Stadler, Tanja
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Geographic variation in the calling songs and genetics of Bartram’s round-winged katydid Amblycorypha bartrami (Tettigoniidae, Phaneropterinae) reveal new species [PDF]
Journal of Orthoptera Research, 2023 Previous work on Bartram’s round-winged katydid, Amblycorypha bartrami Walker, found inconsistencies in song variation across the species’ range. Individuals of purported populations of A. bartrami from sandhills across the southeastern US were collected,
Timothy G. Forrest +4 more
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European Journal of Taxonomy, 2022 Gloydius is a widespread pitviper group occurring from Eastern Europe to Korea and Siberia, with only one known species, G. himalayanus (Günther, 1864), found south of the Himalayas. We provide combined genetic and morphological data for G.
Sourish Kuttalam +10 more
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Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae) [PDF]
, 2019 A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns ...
Aparicio Martínez, Abelardo +7 more
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New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. [PDF]
PLoS ONE, 2013 Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the ...
Aurélien Miralles, Miguel Vences
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Stochastic Safety Radius on UPGMA
Algorithms, 2022 Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences.
Ruriko Yoshida +2 more
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Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data [PDF]
, 2014 1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity.
Barraclough, Timothy G +4 more
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Analysis of DNA sequence variation within marine species using Beta-coalescents [PDF]
, 2011 We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme
Birkner, Matthias +2 more
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The performance of coalescent-based species tree estimation methods under models of missing data
BMC Genomics, 2018 Background Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ from each other and from the species
Michael Nute +3 more
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