Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences [PDF]
, 2011 Methods for inferring species trees from sets of gene trees need to account for the possibility of discordance among the gene trees. Assuming that discordance is caused by incomplete lineage sorting, species tree estimates can be obtained by finding ...
Rosenberg, Noah A., Than, Cuong V.
core +1 more source
Effects of discordance between species and gene trees on phylogenetic diversity conservation
Journal of Mathematical Biology, 2022 Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into account the unique and shared evolutionary history of each species as indicated by its placement in an underlying ...
Kristina Wicke +2 more
openaire +3 more sources
Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa [PDF]
Systematic Biology, 2008 Under a coalescent model for within-species evolution, gene trees may differ from species trees to such an extent that the gene tree topology most likely to evolve along the branches of a species tree can disagree with the species tree topology. Gene tree topologies that are more likely to be produced than the topology that matches that of the species ...
Noah A, Rosenberg, Randa, Tao
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BMC Genomics, 2018 Background Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the ...
Uyen Mai, Siavash Mirarab
doaj +1 more source
Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times? [PDF]
Syst Biol, 2016 ISSN:1063 ...
Stadler T, Degnan JH, Rosenberg NA.
europepmc +6 more sources
Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence [PDF]
, 2007 Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years.
(Max) Zong-Ming Cheng +4 more
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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.
PLoS Biology, 2020 Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses ...
Dan Vanderpool +13 more
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Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics
Ecology and Evolution, 2023 Gametic isolation is thought to play an important role in the evolution of reproductive isolation in broadcast‐spawning marine invertebrates. However, it is unclear whether gametic isolation commonly evolves early in the speciation process or only ...
Matthew R. Glasenapp, Grant H. Pogson
doaj +1 more source
Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment [PDF]
, 2012 Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in ...
A Löytynoja +49 more
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Applications in Plant Sciences, 2021 Premise Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution.
Roman Ufimov +7 more
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