A region of suppressed recombination misleads neoavian phylogenomics

TitelA region of suppressed recombination misleads neoavian phylogenomics
MedientypJournal Article
Jahr der Veröffentlichung2024
AutorenMirarab, S., I. Rivas-González, S. Feng, J. Stiller, Q. Fang, U. Mai, G. Hickey, G. Chen, N. Brajuka, O. Fedrigo, G. Formenti, J. B. W. Wolf, K. Howe, A. Antunes, M. H. Schierup, B. Paten, E. D. Jarvis, G. Zhang, and E. L. Braun
JournalProceedings of the National Academy of SciencesProceedings of the National Academy of Sciences
Volume121
Problem15
Seitennummerierunge2319506121
Veröffentlichungsdatum2024
Zusammenfassung

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.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.

URLhttps://doi.org/10.1073/pnas.2319506121



'Es spielt keine Rolle, wie schön deine Theorie ist. Es spielt keine Rolle, wie klug du bist. Passt sie nicht zu den experimentellen Ergebnissen/Beobachtungen, dann ist sie falsch!'. {nach Richard Feynman, Nobelpreis für Physik 1965}