Опубликована: Март 31, 2025
Язык: Английский
Nature Ecology & Evolution, Год журнала: 2025, Номер unknown
Опубликована: Фев. 28, 2025
Язык: Английский
Процитировано
1
Science Advances, Год журнала: 2023, Номер 9(22)
Опубликована: Июнь 1, 2023
Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque and show that the fascicularis group originated an ancient hybridization between sinica silenus groups ~3.45 to 3.56 million years ago. The X chromosomes low-recombination regions exhibited equal contributions each parental lineage, suggesting they were less affected by subsequent backcrossing hence could have played important role maintaining integrity. We identified many reproduction-associated genes contributed development of mixed sexual phenotypes characteristic group. phylogeny within was also resolved, functional experimentation confirmed all extant Western are susceptible HIV-1 infection. Our study provides novel insights into evolution reveals a event occurred very primates.
Язык: Английский
Процитировано
19
Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(16)
Опубликована: Апрель 10, 2024
In primates, high-acuity vision is mediated by the fovea, a small specialized central region of retina. The unique to anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, extent cellular similarity across foveas and molecular underpinnings foveal maturation remain unclear. Here, we used high-throughput single-cell RNA sequencing profile retinal cells common marmoset (
Язык: Английский
Процитировано
7
American Journal of Primatology, Год журнала: 2025, Номер 87(3)
Опубликована: Март 1, 2025
Phylogenetic trees are analytic tools used in primate studies to elucidate evolutionary relationships. Because of its relative ease sequence and rapid evolution compared nuclear genomes, mitochondrial DNA is frequently for phylogeny building. This project evaluated the effectiveness using individual or grouped genes (mtGenes) as a proxy genome (mtGenome) building within two nested datasets, Cebidae Platyrrhini, with differing divergence dates. mtGene utility rankings were determined based on congruence values mtGenome tree. mtGenes also assessed tree resolution ability sort clades. We found that most mtGenes, including ribosomal (12S 16S), COX genes, ND d-Loop not appropriate use proxies when either Platyrrhini set. On average, outperformed both sets, varied between sets. Pairing CYB COX3 together pairing ND2 worked well set nucleotide diversity predictor performance. Instead, it may be unique system history impacts
Язык: Английский
Процитировано
0
Frontiers in Cell and Developmental Biology, Год журнала: 2025, Номер 13
Опубликована: Март 19, 2025
Small apes (family Hylobatidae), encompassing gibbons and siamangs, occupy a pivotal evolutionary position within the hominoid lineage, bridging gap between great catarrhine monkeys. Although they possess distinctive genomic phenotypic features-such as rapid chromosomal rearrangements adaptations for brachiation-functional studies on small have been hindered by limited availability of biological samples developmental models. Here, we address this successfully reprogramming primary skin fibroblasts from three ape species: lar (Hylobates lar), Abbott's gray abbotti), siamangs (Symphalangus syndactylus). Using Sendai virus-based stealth RNA vectors, generated 31 reprogrammed cell lines, five which were developed into transgene-free induced pluripotent stem cells. These iPSCs displayed canonical features primed pluripotency, both morphologically molecularly, consistent with other primate iPSCs. Directed differentiation experiments confirmed capacity to generate cells representing all germ layers. In particular, their successful limb bud mesoderm underscores utility in investigating molecular mechanisms unique forelimb evolution. Transcriptomic profiling revealed significant upregulation pluripotency-associated genes, alongside elevated expression transposable elements. Remarkably, LAVA retrotransposons-a class elements specific apes-exhibited particularly high levels these Comparative transcriptomic analyses humans, apes, macaques identified trends clade-specific gene signatures. signatures highlighted processes linked stability death, providing insights ape-specific adaptations. This study positions transformative tool advancing functional genomics biology. By facilitating detailed investigations genome evolution diversification, system bridges critical gaps comparative research, enabling deeper exploration genetic cellular underpinnings traits.
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Март 7, 2024
Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase overcome PCR bias, assembled the 3.1 Gb maned sloth genome, surpassing previous 500 Mb protocol size limit. Our also improves assemblies other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting as valuable sample resources facilitating assembly tiny challenging organisms, our study advances efforts obtain reference genomes all eukaryotes.
Язык: Английский
Процитировано
4
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Апрель 8, 2024
ABSTRACT The crab-eating macaques ( Macaca fascicularis ) and rhesus M. mulatta are widely studied nonhuman primates in biomedical evolutionary research. Despite their significance, the current understanding of complex genomic structure differences between species requires substantial improvement. Here, we present a complete genome assembly macaque 20 haplotype-resolved assemblies to investigate regions major species. Segmental duplication is ∼42% lower, while centromeres ∼3.7 times longer than those humans. characterization ∼2 Mbp fixed genetic variants ∼240 loci highlights potential associations with metabolic two (e.g., CYP2C76 EHBP1L1 ). Additionally, hundreds alternative splicing show post-transcriptional regulation divergence these PNPO We also characterize 91 large-scale humans at single-base-pair resolution highlight impact on gene primate evolution FOLH1 PIEZO2 Finally, population genetics recapitulates speciation selective sweeps, highlighting basis reproduction tail phenotype STAB1 , SEMA3F HOXD13 In summary, integrated analysis variation greatly enhances our comprehension lineage-specific phenotypes, adaptation, evolution, thereby improving applications human diseases.
Язык: Английский
Процитировано
4
Current Opinion in Genetics & Development, Год журнала: 2024, Номер 87, С. 102233 - 102233
Опубликована: Июль 23, 2024
Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding inter- intra-species SV has been historically hampered by quality draft genomes absence genome resources key taxa. Recently, advances in long-read sequencing assembly have begun to radically reshape SVs. Two landmark achievements include publication a human telomere-to-telomere (T2T) as well development first pangenome reference. In this review, we look back major works laying foundation these projects. We then examine ways which T2T assemblies pangenomes are transforming approach SV. Finally, discuss what future research may like era pangenomics.
Язык: Английский
Процитировано
4
Forensic Science International, Год журнала: 2025, Номер 367, С. 112370 - 112370
Опубликована: Янв. 12, 2025
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown
Опубликована: Янв. 24, 2025
The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree life, yet achieving a complete species-level phylogeny remains distant goal due to significant costs and computational demands. Traditional species inference methods, though effective, are hampered by need for high-coverage sequencing, high-quality genomic alignments, extensive resources. To address these challenges, this study introduces WASTER, novel de novo tool trees directly from short-read sequences. WASTER employs k-mer based approach identifying variable sites, circumventing genome assembly alignment. Using simulations, we demonstrate that achieves accuracy comparable traditional alignment-based even low depth, substantially higher than other alignment-free methods. We validate WASTER's efficacy on real data, where it accurately reconstructs phylogenies eukaryotic with as depth 1.5X. provides fast efficient solution estimation in cases and/or alignment may bias analyses or is challenging, example depth. It also method generating guide tree-based algorithms. ability estimate low-coverage data without relying will lead reduced phylogenomic projects.
Язык: Английский
Процитировано
0