Statistical inconsistency of the unrooted minimize deep coalescence criterion
| Autor: | Ayed A. R. Alanzi, James H. Degnan |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Leaves Social Sciences Variation (game tree) Plant Science 01 natural sciences Biochemistry Coalescent theory Trees Nucleic Acids Quantitative Biology::Populations and Evolution Psychology Coalescence (chemistry) Phylogeny Mathematics Data Management Caterpillars Multidisciplinary Animal Behavior Plant Anatomy Gene tree Eukaryota Phylogenetic Analysis Plants Quantitative Biology::Genomics Biological Evolution Phylogenetics Insects Moths and Butterflies Medicine Imitation Algorithms Research Article Computer and Information Sciences Arthropoda Genetic Speciation Science 010603 evolutionary biology Statistics Nonparametric 03 medical and health sciences Genetics Animals Humans Evolutionary Systematics Computer Simulation Taxonomy Evolutionary Biology Behavior Models Statistical Models Genetic Organisms Biology and Life Sciences Correction Statistical model DNA Invertebrates 030104 developmental biology Taxon Evolutionary biology Genetic Loci Tree (set theory) Zoology Entomology Software |
| Zdroj: | PLoS ONE PLoS ONE, Vol 16, Iss 5, p e0251107 (2021) |
| ISSN: | 1932-6203 |
| Popis: | Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa. |
| Databáze: | OpenAIRE |
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