ArticleProceedings of the National Academy of Sciences of the United States of America2016
The probability of monophyly of a sample of gene lineages on a species tree.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Ages, sizes and (trees within) trees of taxa and of urns, from Yule to today.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
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- All galls are divided into three or more parts: recursive enumeration of labeled histories for galled trees.Algorithms for molecular biology : AMB · 2023Article
- The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns.PloS one · 2020Article
- Fungal species boundaries in the genomics era.Fungal genetics and biology : FG & B · 2019Review
- The probability of reciprocal monophyly of gene lineages in three and four species.Theoretical population biology · 2019Article
- An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees.BMC bioinformatics · 2016Article
- In the light of evolution X: Comparative phylogeography.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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3 authors.
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Abstract
Monophyletic groups-groups that consist of all of the descendants of a most recent common ancestor-arise naturally as a consequence of descent processes that result in meaningful distinctions between organisms. Aspects of monophyly are therefore central to fields that examine and use genealogical descent. In particular, studies in conservation genetics, phylogeography, population genetics, species delimitation, and systematics can all make use of mathematical predictions under evolutionary models about features of monophyly. One important calculation, the probability that a set of gene lineages is monophyletic under a two-species neutral coalescent model, has been used in many studies. Here, we extend this calculation for a species tree model that contains arbitrarily many species. We study the effects of species tree topology and branch lengths on the monophyly probability. These analyses reveal new behavior, including the maintenance of nontrivial monophyly probabilities for gene lineage samples that span multiple species and even for lineages that do not derive from a monophyletic species group. We illustrate the mathematical results using an example application to data from maize and teosinte.
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