Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda

2018 ◽  
Vol 31 (11) ◽  
pp. 1623-1631 ◽  
Author(s):  
Lucas Freitas ◽  
Beatriz Mello ◽  
Carlos G. Schrago
Keyword(s):  
Coalescent Analysis ◽  
Multispecies Coalescent

scholarly journals Multispecies Coalescent Analysis of the Early Diversification of Neotropical Primates: Phylogenetic Inference under Strong Gene Trees/Species Tree Conflict

2014 ◽  
Vol 6 (11) ◽  
pp. 3105-3114 ◽  
Author(s):  
C. G. Schrago ◽  
A. N. Menezes ◽  
C. Furtado ◽  
C. R. Bonvicino ◽  
H. N. Seuanez
Keyword(s):  
Phylogenetic Inference ◽  
Species Tree ◽  
Gene Trees ◽  
Neotropical Primates ◽  
Coalescent Analysis ◽  
Multispecies Coalescent ◽  
Early Diversification

scholarly journals Impact of long-term chromosomal shuffling on the multispecies coalescent analysis of two anthropoid primate lineages

2017 ◽  
Vol 8 (2) ◽  
pp. 1206-1216 ◽  
Author(s):  
Carlos G. Schrago ◽  
Beatriz Mello ◽  
Anieli G. Pereira ◽  
Carolina Furtado ◽  
Hector N. Seuánez
Keyword(s):  
Coalescent Analysis ◽  
Anthropoid Primate ◽  
Multispecies Coalescent

scholarly journals Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

Cladistics ◽  
2017 ◽  
Vol 34 (1) ◽  
pp. 57-77 ◽  
Author(s):  
Limin Lu ◽  
Cymon J. Cox ◽  
Sarah Mathews ◽  
Wei Wang ◽  
Jun Wen ◽  
...  
Keyword(s):  
Data Partitioning ◽  
Multispecies Coalescent

Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data

AIDS ◽  
2011 ◽  
Vol 25 (16) ◽  
pp. 2019-2026 ◽  
Author(s):  
Art F.Y. Poon ◽  
Rachel A. McGovern ◽  
Theresa Mo ◽  
David J.H.F. Knapp ◽  
Bluma Brenner ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hiv Infection ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Coalescent Analysis ◽  
Generation Sequencing

scholarly journals Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

2016 ◽  
Vol 94 ◽  
pp. 447-462 ◽  
Author(s):  
Scott V. Edwards ◽  
Zhenxiang Xi ◽  
Axel Janke ◽  
Brant C. Faircloth ◽  
John E. McCormack ◽  
...  
Keyword(s):  
Coalescent Model ◽  
Multispecies Coalescent

scholarly journals Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

2020 ◽  
Vol 44 (1) ◽  
pp. 161-205
Author(s):  
J.C. Zamora ◽  
S. Ekman
Keyword(s):  
Species Level ◽  
Single Locus ◽  
Phenotypic Characters ◽  
New Family ◽  
Multispecies Coalescent ◽  
Morphometric Analyses ◽  
Methodological Approaches ◽  
First Time ◽  
A New Species ◽  
Multilocus Phylogeny

We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted with in the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

scholarly journals A novel coalescent method insensitive to population structure

2020 ◽  
Author(s):  
Zeqi Yao ◽  
Kehui Liu ◽  
Shanjun Deng ◽  
Xionglei He
Keyword(s):  
Population Structure ◽  
Phylogenetic Tree ◽  
Simulated Data ◽  
Structured Populations ◽  
Population History ◽  
Cell Populations ◽  
Developmental History ◽  
Coalescent Analysis ◽  
History Of ◽  
Larger Sample

AbstractConventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation (one generation back) is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. i-coalescent analysis computes the instantaneous coalescent rate (iCR) by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.

scholarly journals Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

2022 ◽  
Author(s):  
XiaoXu Pang ◽  
Da-Yong Zhang
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Tree Methods ◽  
The Impact

The species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

scholarly journals Bayesian Coalescent Analysis Reveals a High Rate of Molecular Evolution in GB Virus C

2008 ◽  
Vol 66 (3) ◽  
pp. 292-297 ◽  
Author(s):  
Camila M. Romano ◽  
Paolo M. de A. Zanotto ◽  
Edward C. Holmes
Keyword(s):  
Molecular Evolution ◽  
High Rate ◽  
Gb Virus C ◽  
Coalescent Analysis ◽  
Rate Of Molecular Evolution ◽  
Virus C
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