{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T06:09:51Z","timestamp":1792649391948,"version":"4.5.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,9,12]],"date-time":"2023-09-12T00:00:00Z","timestamp":1694476800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1902892"],"award-info":[{"award-number":["DMS-1902892"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2023239"],"award-info":[{"award-number":["2023239"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The evolutionary implications and frequency of hybridization and introgression are increasingly being recognized across the tree of life. To detect hybridization from multi-locus and genome-wide sequence data, a popular class of methods are based on summary statistics from subsets of 3 or 4 taxa. However, these methods often carry the assumption of a constant substitution rate across lineages and genes, which is commonly violated in many groups. In this work, we quantify the effects of rate variation on the D test (also known as ABBA\u2013BABA test), the D3 test, and HyDe. All 3 tests are used widely across a range of taxonomic groups, in part because they are very fast to compute. We consider rate variation across species lineages, across genes, their lineage-by-gene interaction, and rate variation across gene-tree edges. We simulated species networks according to a birth\u2013death-hybridization process, so as to capture a range of realistic species phylogenies. For all 3 methods tested, we found a marked increase in the false discovery of reticulation (type-1 error rate) when there is rate variation across species lineages. The D3 test was the most sensitive, with around 80% type-1 error, such that D3 appears to more sensitive to a departure from the clock than to the presence of reticulation. For all 3 tests, the power to detect hybridization events decreased as the number of hybridization events increased, indicating that multiple hybridization events can obscure one another if they occur within a small subset of taxa. Our study highlights the need to consider rate variation when using site-based summary statistics, and points to the advantages of methods that do not require assumptions on evolutionary rates across lineages or across genes.<\/jats:p>","DOI":"10.1093\/sysbio\/syad056","type":"journal-article","created":{"date-parts":[[2023,9,8]],"date-time":"2023-09-08T16:02:39Z","timestamp":1694188959000},"page":"1357-1369","source":"Crossref","is-referenced-by-count":50,"title":["Summary Tests of Introgression Are Highly Sensitive to Rate Variation Across Lineages"],"prefix":"10.1093","volume":"72","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3002-6784","authenticated-orcid":false,"given":"Lauren E","family":"Frankel","sequence":"first","affiliation":[{"name":"Department of Botany, University of Wisconsin\u2013Madison , Madison, WI 53706 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4702-8217","authenticated-orcid":false,"given":"C\u00e9cile","family":"An\u00e9","sequence":"additional","affiliation":[{"name":"Department of Botany, University of Wisconsin\u2013Madison , Madison, WI 53706 , USA"},{"name":"Department of Statistics, University of Wisconsin\u2013Madison , Madison, WI 53706 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,9,12]]},"reference":[{"issue":"11","key":"2024091208322813800_CIT0001","doi-asserted-by":"crossref","first-page":"2762","DOI":"10.1093\/molbev\/msx197","article-title":"Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker","volume":"34","author":"Allio","year":"2017","journal-title":"Mol. 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