A region of suppressed recombination misleads neoavian phylogenomics

• 成果类型: Article
• 署名作者: Mirarab, Siavash; Rivas-Gonzalez, Iker; Feng, Shaohong; Stiller, Josefin; Fang, Qi; Mai, Uyen; Hickey, Glenn; Chen, Guangji; Brajuka, Nadolina; Fedrigo, Olivier; Formenti, Giulio; Wolf, Jochen B. W.; Howe, Kerstin; Antunes, Agostinho; Schierup, Mikkel H.; Paten, Benedict; Jarvis, Erich D.; Zhang, Guojie; Braun, Edward L.
• 署名单位: University of California System; University of California San Diego; Aarhus University; Zhejiang University; Liangzhu Laboratory; Zhejiang University; University of Copenhagen; University of California System; University of California Santa Cruz; Rockefeller University; University of Munich; Wellcome Trust Sanger Institute; Universidade do Porto; Universidade do Porto; State University System of Florida; University of Florida
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8869
• DOI: 10.1073/pnas.2319506121
• 发表日期: 2024-04-09
• 关键词: gene trees; avian tree; data sets; selection; introgression; speciation; landscape; reveals; package; LIFE

摘要

Genomes are typically mosaics of regions with different evolutionary histories. When speciation events are closely spaced in time, recombination makes the regions sharing the same history small, and the evolutionary history changes rapidly as we move along the genome. When examining rapid radiations such as the early diversification of Neoaves 66 Mya, typically no consistent history is observed across segments exceeding kilobases of the genome. Here, we report an exception. We found that a 21-Mb region in avian genomes, mapped to chicken chromosome 4, shows an extremely strong and discordance-free signal for a history different from that of the inferred species tree. Such a strong discordance-free signal, indicative of suppressed recombination across many millions of base pairs, is not observed elsewhere in the genome for any deep avian relationships. Although long regions with suppressed recombination have been documented in recently diverged species, our results pertain to relationships dating circa 65 Mya. We provide evidence that this strong signal may be due to an ancient rearrangement that blocked recombination and remained polymorphic for several million years prior to fixation. We show that the presence of this region has misled previous phylogenomic efforts with lower taxon sampling, showing the interplay between taxon and locus sampling. We predict that similar ancient rearrangements may confound phylogenetic analyses in other clades, pointing to a need for new analytical models that incorporate the possibility of such events.