Phylogenomic analyses provide insights into primate evolution

Shao, Yong; Zhou, Long; Fang, Li; Zhao, Lan; Zhang, Baolin; Shao, Feng; Chen, Jiawei; Chen, Chun-Yan; Bi, Xupeng; Zhuang, Xiao-Lin; Zhu, Haoxiang; Hu, Jinqiang; Sun, Zongyi; Li, Xin; Wang, Depeng; Rivas-González, Iker; Wang, Sheng; Wang, Yun-Mei; Chen, Wu; Luo, Gang; Lu, Hui‐Meng; Liu, Yang; Kuderna, Lukas F. K.; Farh, Kyle Kai‐How; Fan, Peng‐Fei; Yu, Li; Li, Ming; Liu, Zhijin; Tiley, George P.; Yoder, Anne D.; Roos, Christian; Hayakawa, Takashi; Marquès‐Bonet, Tomàs; Rogers, Jeffrey; Stenson, Peter D.; Cooper, David Neil; Schierup, Mikkel H.; Yao, Yong‐Gang; Zhang, Ya‐Ping; Wang, Wen; Qi, Xiao-Guang; Wu, Dong‐Dong

doi:10.1126/science.abn6919

Cited by 65 publications

(42 citation statements)

References 242 publications

(142 reference statements)

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“…Using SNPeff v5.1 (Cingolani et al, 2012), we built a database with the reference genome for the golden-handed tamarin (Shao et al, 2023). SNPeff was then used to calculate the genetic load of the samples using the golden-handed tamarin database with the filtered VCF file not allowing for missingness and only variable positions in the cotton-top tamarins without minor allele frequency filtering and with minimum read depth of 5, maximum read depth of 50 and minimum genotype quality of 30.…”

Section: Population Demographymentioning

confidence: 99%

Assessing the genetic composition of cotton‐top tamarins (Saguinus oedipus) before sweeping anthropogenic impact

Rasmussen,

Fontsere,

Soto‐Calderón

et al. 2023

Molecular Ecology

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During the last century, the critically endangered cotton‐top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low‐medium coverage, to unravel how the cotton‐top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome‐wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton‐top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision‐making for the species.

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Section: Population Demographymentioning

confidence: 99%

Assessing the genetic composition of cotton‐top tamarins (Saguinus oedipus) before sweeping anthropogenic impact

Rasmussen,

Fontsere,

Soto‐Calderón

et al. 2023

Molecular Ecology

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“…Similar to the enrichment seen in the human-specific SNCs, we found significant enrichment of HARs in HGARs among the three reported HAR sets identified by different methods (fig. S14A) (26,39,40). In total, there are 359 HAR-overlapping HGARs (fig.…”

Section: Genetic Basis and Neuropsychiatric Relevance Of The Human Re...mentioning

confidence: 99%

“…The human-fixed SNC position file was downloaded from http://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/. The HAR position file was sourced from previous studies (26,39,40). The density of the human-fixed SNC or HAR with ARs was calculated as the average number of SNCs or HARs overlapping with ARs per kilobase.…”

Section: Human-fixed Snc and Har Enrichment Analysismentioning

confidence: 99%

Comparative single-cell regulome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis

Liu,

Luo,

Sun

et al. 2023

Preprint

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The cellular and genetic mechanism underlying the human-specific features of cortex development remains unclear. We generated a cell-type resolved atlas of transcriptome and regulome of the developing macaque and mouse prefrontal cortex, and conducted evolutionary analyses with the published complementary human data. We discovered a primate-specific expansion of two neural progenitor subclasses, glia-committed radial glia (RG) and truncated RG. Specifically, the human neural progenitors show extensive transcriptional rewiring in the growth factor and extracellular matrix pathways. Expression of the human-specific progenitor marker ITGA2 in the cortex of fetal mouse promotes progenitor proliferation and an increased upper-layer neuron proportion. We demonstrate that these transcriptional divergences are primarily driven by the activity changes of the distal regulatory elements in the genome. Markedly, the chromatin regions with human-gained accessibility enrich the human-fixed sequence changes, as well as sequence polymorphisms associated with intelligence and neuropsychiatric disorders. Our results uncover evolutionary innovations in neural progenitors and gene regulatory mechanism during primate cortex evolution.

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“…The close genetic relationship and physiological similarities shared by humans and macaques make them ideal NHP biomedical models 11,[27][28][29][30][31] . In addition, the critical phylogenetic position of macaques (basal group of Catarrhini) in primate phylogeny makes them indispensable for evolutionary comparisons to shed light on lineage-specific genetic changes related to primate adaptation and human disease susceptibility 11,[32][33][34][35] .…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of macaques and integrated insights into genetic variation and population history

Zhang,

Xu,

et al. 2024

Preprint

Self Cite

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The crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g.,CYP2C76andEHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g.,PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g.,FOLH1andPIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g.,STAB1,SEMA3F, andHOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

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Phylogenomic analyses provide insights into primate evolution

Cited by 65 publications

References 242 publications

Assessing the genetic composition of cotton‐top tamarins (Saguinus oedipus) before sweeping anthropogenic impact

Assessing the genetic composition of cotton‐top tamarins (Saguinus oedipus) before sweeping anthropogenic impact

Comparative single-cell regulome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis

Comparative genomics of macaques and integrated insights into genetic variation and population history

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