{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:41:17Z","timestamp":1775979677890,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,9,9]],"date-time":"2018-09-09T00:00:00Z","timestamp":1536451200000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1355998"],"award-info":[{"award-number":["DBI-1355998"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CCF-1302179"],"award-info":[{"award-number":["CCF-1302179"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CCF-1514177"],"award-info":[{"award-number":["CCF-1514177"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1547433"],"award-info":[{"award-number":["DMS-1547433"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Species and gene trees represent how species and individual loci within their genomes evolve from their most recent common ancestors. These trees are central to addressing several questions in biology relating to, among other issues, species conservation, trait evolution and gene function. Consequently, their accurate inference from genomic data is a major endeavor. One approach to their inference is to co-estimate species and gene trees from genome-wide data. Indeed, Bayesian methods based on this approach already exist. However, these methods are very slow, limiting their applicability to datasets with small numbers of taxa. The more commonly used approach is to first infer gene trees individually, and then use gene tree estimates to infer the species tree. Methods in this category rely significantly on the accuracy of the gene trees which is often not high when the dataset includes closely related species.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we introduce a simple, yet effective, iterative method for co-estimating gene and species trees from sequence data of multiple, unlinked loci. In every iteration, the method estimates a species tree, uses it as a generative process to simulate a collection of gene trees, and then selects gene trees for the individual loci from among the simulated gene trees by making use of the sequence data. We demonstrate the accuracy and efficiency of our method on simulated as well as biological data, and compare them to those of existing competing methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The method has been implemented in PhyloNet, which is publicly available at http:\/\/bioinfocs.rice.edu\/phylonet.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty599","type":"journal-article","created":{"date-parts":[[2018,7,7]],"date-time":"2018-07-07T06:00:37Z","timestamp":1530943237000},"page":"i697-i705","source":"Crossref","is-referenced-by-count":12,"title":["Towards an accurate and efficient heuristic for species\/gene tree co-estimation"],"prefix":"10.1093","volume":"34","author":[{"given":"Yaxuan","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Computer Science, Rice University, Houston, TX, USA"},{"name":"Department of Computer Science, Rice University, Houston, TX, USA"}]},{"given":"Luay","family":"Nakhleh","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Rice University, Houston, TX, USA"},{"name":"Department of BioSciences, Rice University, Houston, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,9,8]]},"reference":[{"key":"2023061402421948500_bty599-B1","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.1093\/molbev\/mss086","article-title":"Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis","volume":"29","author":"Bryant","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"2023061402421948500_bty599-B2","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.tree.2009.01.009","article-title":"Gene tree discordance, phylogenetic inference and the multispecies coalescent","volume":"24","author":"Degnan","year":"2009","journal-title":"Trends Ecol. Evol."},{"key":"2023061402421948500_bty599-B3","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"Drummond","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"2023061402421948500_bty599-B4","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1146\/annurev.ge.22.120188.002513","article-title":"Phylogenies from molecular sequences: inference and reliability","volume":"22","author":"Felsenstein","year":"1988","journal-title":"Annu. Rev. Genet."},{"key":"2023061402421948500_bty599-B5","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1093\/molbev\/msp274","article-title":"Bayesian inference of species trees from multilocus data","volume":"27","author":"Heled","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"2023061402421948500_bty599-B6","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","article-title":"Generating samples under a wright\u2013fisher neutral model of genetic variation","volume":"18","author":"Hudson","year":"2002","journal-title":"Bioinformatics"},{"key":"2023061402421948500_bty599-B7","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1093\/bioinformatics\/btp079","article-title":"Stem: species tree estimation using maximum likelihood for gene trees under coalescence","volume":"25","author":"Kubatko","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061402421948500_bty599-B8","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1093\/sysbio\/syr011","article-title":"Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in sistrurus rattlesnakes","volume":"60","author":"Kubatko","year":"2011","journal-title":"Syst. Biol."},{"key":"2023061402421948500_bty599-B9","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1093\/sysbio\/syp031","article-title":"Estimating species phylogenies using coalescence times among sequences","volume":"58","author":"Liu","year":"2009","journal-title":"Syst. Biol."},{"key":"2023061402421948500_bty599-B10","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/sysbio\/46.3.523","article-title":"Gene trees in species trees","volume":"46","author":"Maddison","year":"1997","journal-title":"Syst. Biol."},{"key":"2023061402421948500_bty599-B11","doi-asserted-by":"crossref","first-page":"i541","DOI":"10.1093\/bioinformatics\/btu462","article-title":"Astral: genome-scale coalescent-based species tree estimation","volume":"30","author":"Mirarab","year":"2014","journal-title":"Bioinformatics"},{"key":"2023061402421948500_bty599-B12","doi-asserted-by":"crossref","first-page":"i44","DOI":"10.1093\/bioinformatics\/btv234","article-title":"Astral-ii: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes","volume":"31","author":"Mirarab","year":"2015","journal-title":"Bioinformatics"},{"key":"2023061402421948500_bty599-B13","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1109\/TCBB.2008.66","article-title":"Incomplete lineage sorting: consistent phylogeny estimation from multiple loci","volume":"7","author":"Mossel","year":"2010","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf. (TCBB)"},{"key":"2023061402421948500_bty599-B14","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.tree.2013.09.004","article-title":"Computational approaches to species phylogeny inference and gene tree reconciliation","volume":"28","author":"Nakhleh","year":"2013","journal-title":"Trends Ecol. Evol."},{"key":"2023061402421948500_bty599-B15","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"Fasttree 2\u2013approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"2023061402421948500_bty599-B16","first-page":"235","article-title":"Seq-gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees","volume":"13","author":"Rambaut","year":"1997","journal-title":"Comput. Appl. Biosci."},{"key":"2023061402421948500_bty599-B17","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1093\/sysbio\/syw119","article-title":"Efficient bayesian species tree inference under the multispecies coalescent","volume":"66","author":"Rannala","year":"2017","journal-title":"Syst. Biol."},{"key":"2023061402421948500_bty599-B18","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","article-title":"Comparison of phylogenetic trees","volume":"53","author":"Robinson","year":"1981","journal-title":"Math. Biosci."},{"key":"2023061402421948500_bty599-B19","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"2023061402421948500_bty599-B20","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2023061402421948500_bty599-B21","doi-asserted-by":"crossref","first-page":"e1000501","DOI":"10.1371\/journal.pcbi.1000501","article-title":"Species tree inference by minimizing deep coalescences","volume":"5","author":"Than","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023061402421948500_bty599-B22","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1186\/1471-2105-9-322","article-title":"PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships","volume":"9","author":"Than","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023061402421948500_bty599-B23","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1093\/sysbio\/syy015","article-title":"Inferring phylogenetic networks using PhyloNet","volume":"67","author":"Wen","year":"2018","journal-title":"Syst. Biol."},{"key":"2023061402421948500_bty599-B24","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1111\/j.1558-5646.2011.01476.x","article-title":"Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood","volume":"66","author":"Wu","year":"2012","journal-title":"Evolution"},{"key":"2023061402421948500_bty599-B25","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1093\/sysbio\/sys076","article-title":"Treefix: statistically informed gene tree error correction using species trees","volume":"62","author":"Wu","year":"2013","journal-title":"Syst. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/i697\/50582741\/bioinformatics_34_17_i697.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/i697\/50582741\/bioinformatics_34_17_i697.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T02:43:11Z","timestamp":1686710591000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/17\/i697\/5093212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,9,1]]},"references-count":25,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2018,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty599","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,1]]},"published":{"date-parts":[[2018,9,1]]}}}