Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Апрель 25, 2024

Abstract Asian mock vipers of the genus Psammodynastes and African forest snakes Buhoma are two genera belonging to snake superfamily Elapoidea. The phylogenetic placements within Elapoidea has been extremely unstable which resulted in their uncertain debated taxonomy. We used ultraconserved elements traditional nuclear mitochondrial markers infer relationships these with other elapoids. , for a reference genome sequenced, were found, strong branch support, be relatively early diverging split that is sister clade consisting Elapidae, Micrelapidae Lamprophiidae. Hence, we allocate its own family, Psammodynastidae new family . However, position could not resolved high degree confidence. Attempts identify possible sources conflict rapid radiation elapoid suggest both hybridisation/introgression during diversification, including ghost introgression, as well incomplete lineage sorting likely have had confounding role. usual practice combining loci genomic data appears mislead phylogeny reconstructions scenarios, especially absence scale data.

Язык: Английский

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Population Genomics of Japanese Macaques (Macaca fuscata): Insights into Deep Population Divergence and Multiple Merging Histories

Genome Biology and Evolution, Год журнала: 2025, Номер 17(1)

Опубликована: Янв. 1, 2025

The influence of long-term climatic changes such as glacial cycles on the history living organisms has been a subject research for decades, but detailed population dynamics during environmental fluctuations and their effects genetic diversity load are not well understood genome-wide scale. Japanese macaque (Macaca fuscata) is unique primate adapted to cold environments archipelago. Despite past intensive genetics, background macaques at whole-genome level limited few individuals, comprehensive demographic differentiation have underexplored. We conducted sequencing 64 individuals from five different regions, revealing significant functional variant across populations. In particular, low harbor many shared population-specific gene loss, which might contribute phenotypes. Our estimation demography using phased haplotypes suggested that, after strong bottleneck among all populations around 400-500 kya, divergence initiated 150-200 there time with flow between some split, indicating multiple split merge events probably due habitat fragmentation fusion cycles. These findings only present complex also enhance value models, particularly in neuroscience behavioral studies. This genomic analysis sheds light adaptation evolution macaques, contributing valuable insights both evolutionary biology biomedical research.

Язык: Английский

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Genomic basis of non-human-primate diversity and adaptation

Опубликована: Март 31, 2025

Язык: Английский

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Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(12)

Опубликована: Ноя. 21, 2023

Abstract Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important force. Using whole-genome sequencing data from 22 species guenons (tribe Cercopithecini), one world's largest primate radiations, we show that rampant gene flow characterizes their history identify ancient across deeply divergent lineages differ ecology, morphology, karyotypes. Some events resulted mitochondrial introgression between distant lineages, likely facilitated by cointrogression coadapted nuclear variants. Although genomic landscapes were largely lineage specific, found genes with immune functions overrepresented introgressing regions, line adaptive introgression, whereas involved pigmentation morphology may contribute to reproductive isolation. In reports other systems might facilitate diversification, find some most species-rich guenon clades are admixed origin. This study provides insights into prevalence, role, outcomes ancestral a large mammalian radiation.

Язык: Английский

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Comparative transcriptome analysis between rhesus macaques (<i>Macaca mulatta</i>) and crab-eating macaques (<i>M. fascicularis</i>)

动物学研究, Год журнала: 2023, Номер 45(2), С. 299 - 310

Опубликована: Дек. 28, 2023

Understanding the variations in gene expression between species is pivotal for deciphering evolutionary diversity phenotypes. Rhesus macaques and crab-eating serve as crucial nonhuman primate biomedical models with different phenotypes, but large-scale of comparative transcriptome research these two has yet to be fully elucidated. Here, we conduct systematic comparisons utilizing newly sequenced RNA-seq data from 84 samples (41 Mfa 43 Mmu samples) encompassing 14 common tissues. Our findings reveal that a small fraction genes (~3.7%) show differential macaque species, while ~36.5% tissue-specific both macaques. We also compare humans ~22.6 % orthologous at least 2 Moreover, ~19.41% overlapped macaque-specific structural variants are more likely Of these, FAM220A shows elevated compared because lineage-specific duplication. In summary, our study presents analysis transcriptomes within humans. These insights into will enhance utility contributing broader realm genomic studies.

Язык: Английский

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Documenting homoploid hybrid speciation

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Май 23, 2024

Abstract Homoploid hybrid speciation is challenging to document because hybridization can lead outcomes other than speciation. Thus, some authors have argued that establishment of homoploid should include evidence reproductive barriers isolating the neo‐species from its parental species were derived hybridization. While this criterion difficult satisfy, several recent papers successfully employed a common pipeline identify candidate genes underlying such and (in one case) validate their function. We describe pipeline, application plant animal what we learned about as consequence. argue – given ubiquity admixture polygenic basis isolation could be much more protracted suggested by earlier conceptual arguments theoretical studies.

Язык: Английский

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Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation

Molecular Biology and Evolution, Год журнала: 2023, Номер 40(11)

Опубликована: Окт. 12, 2023

Abstract The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents most successful example of adaptive radiation nonhuman primates. However, intrageneric phylogenetic relationships among remain controversial have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated 8 published macaque genomes. We found strong evidence supporting division Incomplete lineage sorting (ILS) was primary factor contributing discordance observed gene trees; however, also hybridization events, specifically between ancestral arctoides/sinica silenus/nigra lineages that resulted in hybrid formation fascicularis/mulatta group. Combined with fossil data, our data were used establish scenario for radiation. These findings provide insights ILS potential ancient introgression events involved macaques, which will lead better understanding rapid speciation occurring

Язык: Английский

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Harvesting the fruits of the first stage of the Primate Genome Project

动物学研究, Год журнала: 2023, Номер 44(4), С. 725 - 728

Опубликована: Янв. 1, 2023

Язык: Английский

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Next-generation primate genomics: New genome assemblies unlock new questions

Cell, Год журнала: 2023, Номер 186(25), С. 5433 - 5437

Опубликована: Дек. 1, 2023

Язык: Английский

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Incomplete lineage sorting and gene flow within Allium (Amayllidaceae)

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 195, С. 108054 - 108054

Опубликована: Март 11, 2024

Язык: Английский

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