Identifiability and Reconstructibility of Species Phylogenies Under a Modified Coalescent

2017/01/24 by Colby Long, Laura Kubatko, Long, Colby +1
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE)

paper · pdf · doi:10.48550/arxiv.1701.06871

openalex publication_date 2017/01/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees. It has been shown that the unrooted topology of the species tree parameter of the multispecies coalescent is generically identifiable. Moreover, a statistically consistent reconstruction method called SVDQuartets has been developed to recover this parameter. In this paper, we describe a modified multispecies coalescent model that allows for varying effective population size and violations of the molecular clock. We show that the unrooted topology of the species tree for these models is generically identifiable and that SVDQuartets is still a statistically consistent method for inferring this parameter.

Citations

• Evolutionary trees from DNA sequences: A maximum likelihood approach
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
• On the genealogy of large populations

Related

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• Identifying the Rooted Species Tree from the Distribution of Unrooted Gene Trees under the Coalescent
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• Macro-evolutionary models and coalescent point processes: The shape and probability of reconstructed phylogenies