Scientific Reports, Год журнала: 2025, Номер 15(1)
Опубликована: Апрель 28, 2025
Язык: Английский
Опубликована: Янв. 8, 2025
Classical genes within the Major Histocompatibility Complex (MHC) are responsible for peptide presentation to T cells, thus playing a central role in immune defense against pathogens. These subject strong selective pressures including both balancing and directional selection, resulting exceptional genetic diversity—thousands of alleles per gene humans. Moreover, some appear be shared between primate species, phenomenon known as trans-species polymorphism (TSP) or incomplete lineage sorting, which is rare genome overall. However, despite clinical evolutionary importance MHC diversity, we currently lack full picture evolution. To start addressing this gap, explore variation across species our companion paper (Fortier Pritchard, 2024) here individual genes. We used Bayesian phylogenetic methods determine extent TSP at 17 genes, classical non-classical Class I II find support deep 7 10 including—remarkably—between humans old-world monkeys MHC-DQB1. Despite long-term persistence ancient lineages, additionally observe rapid evolution nucleotides encoding proteins’ peptide-binding domains. The most rapidly-evolving amino acid positions extremely enriched autoimmune infectious disease associations. Together, these results suggest complex forces—arising from differential binding—that drive short-term allelic turnover lineages while also maintaining deeply divergent least 31 million years.
Язык: Английский
Процитировано
2
Science, Год журнала: 2025, Номер unknown
Опубликована: Янв. 23, 2025
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference tree life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, current practice leaves out large chunks genomes. As more high-quality genomes become available, we urgently need methods infer directly from a multiple genome alignment. Here, introduce CASTER, theoretically justified site-based method that eliminates predefine recombination-free loci. CASTER is scalable hundreds mammalian whole We demonstrate accuracy in simulations include recombination apply several biological datasets, showing its per-site scores can reveal both artefactual patterns discordance across genome.
Язык: Английский
Процитировано
2
Science, Год журнала: 2024, Номер 383(6690)
Опубликована: Фев. 29, 2024
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (
Язык: Английский
Процитировано
14
Biology Letters, Год журнала: 2024, Номер 20(1)
Опубликована: Янв. 1, 2024
The Picrodontidae from the middle Palaeocene of North America are enigmatic placental mammals that were allied with various mammalian groups but generally now considered to have close affinities paromomyid and palaechthonid plesiadapiforms based on proposed dental synapomorphies. picrodontid fossil record consists entirely gnathic remains except for one partial cranium Zanycteris paleocenus (AMNH 17180). Here, we use µCT technology unveil previously undocumented morphology in AMNH 17180, describe compare basicranial a first time, incorporate these new data into cladistic analyses. Z. is distinct shares similarities Palaeogene Apatemyidae Nyctitheriidae. Results analyses incorporating novel suggest picrodontids not stem primates nor euarchontan synapomorphies uniting and, by extension, evolved independently. highlight need scrutinize highly autapomorphic taxa limited records.
Язык: Английский
Процитировано
7
Molecular Biology and Evolution, Год журнала: 2023, Номер 40(5)
Опубликована: Апрель 18, 2023
Abstract Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown experience horizontal TEs at what appears be a high rate compared with other mammals. We investigated the occurrence horizontally transferred (HT) DNA transposons involving bats. found over 200 putative HT within bats; 16 were shared across distantly related mammalian clades, 2 fish two lizard species. Our results indicate that bats are hotspot for transposons. These events broadly coincide diversification several bat supporting hypothesis transposon invasions contributed
Язык: Английский
Процитировано
12
Current Biology, Год журнала: 2023, Номер 33(15), С. 3073 - 3082.e3
Опубликована: Июнь 27, 2023
The timing of the placental mammal radiation has been focus debate over efficacy competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that mammals originated before Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from Late Cretaceous to Jurassic. However, absence definitive fossils placentals K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur it can be manifest phenotypically in descendent lineages. This, combined non-uniformity rock and fossil records, requires record interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model estimates age origination and, where applicable, extinction through probabilistic interpretation record. Cretaceous, ordinal crown groups originating at or after boundary. results reduce plausible interval younger range molecular estimates. Our findings support both Long Fuse Soft Explosive models diversification, indicating shortly prior extinction. many modern lineages overlapped followed
Язык: Английский
Процитировано
11
Integrative Zoology, Год журнала: 2023, Номер 19(5), С. 989 - 998
Опубликована: Окт. 18, 2023
Bats, members of the Chiroptera order, rank as second most diverse group among mammals. Recent molecular systematic studies on bats have successfully classified 21 families within two suborders: Yinpterochiroptera and Yangochiroptera. Nevertheless, phylogeny these has remained a subject controversy. In this study, we employed balanced approach to establish robust family-level phylogenetic hypothesis for bats, utilizing more comprehensive dataset. This dataset includes representative species from all bat families, resulting in reduced level missing genetic information. The tree comprises lineages that are strongly supported, each corresponding one families. Our findings support place Emballonuroidea superfamily basal lineage Yangochiroptera, Myzopodidae should be situated Emballonuroidea, forming sister relationship with clade consisting Nycteridae Emballonuridae. Finally, conducted dating analyses newly resolved tree, providing divergence times family. Collectively, our study relatively encompassing improved framework will significantly contribute understanding evolutionary processes, ecological roles, disease dynamics, biodiversity conservation realm bats.
Язык: Английский
Процитировано
11
Science, Год журнала: 2024, Номер 384(6699), С. 1007 - 1012
Опубликована: Май 30, 2024
The evolutionary histories of major clades, including mammals, often comprise changes in their diversification dynamics, but how these occur remains debated. We combined comprehensive phylogenetic and fossil information a new "birth-death diffusion" model that provides detailed characterization variation rates mammals. found an early rising sustained scenario, wherein speciation increased before during the Cretaceous-Paleogene (K-Pg) boundary. K-Pg mass extinction event filtered out more slowly speciating lineages was followed by subsequent slowing rather than rebounds. These dynamics arose from imbalanced process, with separate giving rise to many, less speciation-prone descendants. Diversity seems have been brought about isolated, fast-speciating lineages, few punctuated innovations.
Язык: Английский
Процитировано
4
Опубликована: Янв. 13, 2025
Gene families are groups of evolutionarily-related genes. One large gene family that has experienced rapid evolution is the Major Histocompatibility Complex (MHC), whose proteins serve critical roles in innate and adaptive immunity. Across ∼60 million year history primates, some MHC genes have turned over completely, changed function, converged others remained essentially unchanged. Past work typically focused on identifying alleles within particular species or comparing content, but more needed to understand overall across species. Thus, despite immunologic importance its peculiar evolutionary history, we lack a complete picture primates. We readdress this question using sequences from dozens pseudogenes spanning entire primate order, building comprehensive set allele trees with modern methods. Overall, find Class I subfamily evolving much quickly than II subfamily, exception MHC-DRB also pay special attention often-ignored pseudogenes, which use reconstruct different events region. shared function species, employ genes, haplotypes, patterns variation achieve successful immune response. Our extensive literature review represent most look into date.
Язык: Английский
Процитировано
0
Опубликована: Янв. 13, 2025
Gene families are groups of evolutionarily-related genes. One large gene family that has experienced rapid evolution is the Major Histocompatibility Complex (MHC), whose proteins serve critical roles in innate and adaptive immunity. Across ∼60 million year history primates, some MHC genes have turned over completely, changed function, converged others remained essentially unchanged. Past work typically focused on identifying alleles within particular species or comparing content, but more needed to understand overall across species. Thus, despite immunologic importance its peculiar evolutionary history, we lack a complete picture primates. We readdress this question using sequences from dozens pseudogenes spanning entire primate order, building comprehensive set allele trees with modern methods. Overall, find Class I subfamily evolving much quickly than II subfamily, exception MHC-DRB also pay special attention often-ignored pseudogenes, which use reconstruct different events region. shared function species, employ genes, haplotypes, patterns variation achieve successful immune response. Our extensive literature review represent most look into date.
Язык: Английский
Процитировано
0