{"title":"SPECIES TREE INFERENCE FROM GENOMIC SEQUENCES USING THE LOG-DET DISTANCE.","authors":"Elizabeth S Allman, Colby Long, John A Rhodes","doi":"10.1137/18m1194134","DOIUrl":null,"url":null,"abstract":"<p><p>The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled with a distance-based tree construction method, also permits consistent inference of species trees under mixture models appropriate to aligned genomic-scale sequences data. Data may include sites from many genetic loci, which evolved on different gene trees due to incomplete lineage sorting on an ultrametric species tree, with different time-reversible substitution processes. The simplicity and speed of distance-based inference suggests log-det based methods should serve as benchmarks for judging more elaborate and computationally-intensive species trees inference methods.</p>","PeriodicalId":48489,"journal":{"name":"SIAM Journal on Applied Algebra and Geometry","volume":null,"pages":null},"PeriodicalIF":1.6000,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643864/pdf/nihms-1554294.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"SIAM Journal on Applied Algebra and Geometry","FirstCategoryId":"100","ListUrlMain":"https://doi.org/10.1137/18m1194134","RegionNum":2,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2019/3/14 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"MATHEMATICS, APPLIED","Score":null,"Total":0}
引用次数: 0
Abstract
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled with a distance-based tree construction method, also permits consistent inference of species trees under mixture models appropriate to aligned genomic-scale sequences data. Data may include sites from many genetic loci, which evolved on different gene trees due to incomplete lineage sorting on an ultrametric species tree, with different time-reversible substitution processes. The simplicity and speed of distance-based inference suggests log-det based methods should serve as benchmarks for judging more elaborate and computationally-intensive species trees inference methods.