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As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was \u226510. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6\/15 phylogenomic datasets. Finally, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.<\/jats:p>","DOI":"10.1093\/sysbio\/syae031","type":"journal-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T05:09:14Z","timestamp":1719551354000},"page":"807-822","source":"Crossref","is-referenced-by-count":15,"title":["The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics"],"prefix":"10.1093","volume":"73","author":[{"given":"Chao","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Plant Protection, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University , Hangzhou 310058 ,","place":["China"]},{"name":"Centre for Evolutionary & Organismal Biology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2879-6317","authenticated-orcid":false,"given":"Xiaofan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University , Guangzhou 510642 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2206-5804","authenticated-orcid":false,"given":"Yuanning","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Marine Science and Technology, Shandong University , Qingdao 266237 ,","place":["China"]},{"name":"Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University , Nashville, TN 37235 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5088-7461","authenticated-orcid":false,"given":"Chris Todd","family":"Hittinger","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, J. 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Crow Institute for the Study of Evolution, University of Wisconsin-Madison , Madison, WI 53706 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronghui","family":"Pan","sequence":"additional","affiliation":[{"name":"ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou , 310027 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyan","family":"Huang","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Pancreatic Disease, Zhejiang University School of Medicine First Affiliated Hospital , Hangzhou 310003 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9109-8853","authenticated-orcid":false,"given":"Xue-xin","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7248-6551","authenticated-orcid":false,"given":"Antonis","family":"Rokas","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University , Nashville, TN 37235 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5663-2352","authenticated-orcid":false,"given":"Yun","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5765-1419","authenticated-orcid":false,"given":"Xing-Xing","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University , Hangzhou 310058 ,","place":["China"]},{"name":"Centre for Evolutionary & Organismal Biology, Zhejiang University , Hangzhou 310058 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,6,28]]},"reference":[{"key":"2025062720020135400_CIT0001","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/s41559-018-0494-6","article-title":"Explosive diversification of marine fishes at the Cretaceous\u2013Palaeogene boundary","volume":"2","author":"Alfaro","year":"2018","journal-title":"Nat. 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