Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)
Published: April 28, 2025
Language: Английский
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half have no functional annotations Encyclopedia of DNA Elements (ENCODE) resource. Changes genes regulatory associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast imperiled biodiversity offers distinctive power identifying genetic variants function organismal phenotypes.
Language: Английский
Citations
140
Science, Journal Year: 2023, Volume and Issue: 382(6667)
Published: Oct. 12, 2023
The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates poorly understood. We used comparative single-nucleus transcriptomics to analyze samples the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, common marmosets understand human-specific features neocortex. Human, chimpanzee, gorilla MTG showed highly similar cell-type composition laminar organization as well a large shift in proportions deep-layer intratelencephalic-projecting neurons compared with macaque marmoset MTG. Microglia, astrocytes, oligodendrocytes had more-divergent expression across species or oligodendrocyte precursor cells, neuronal diverged more rapidly on human lineage. Only few hundred genes patterning, suggesting that relatively changes distinctively define cortical structure.
Language: Английский
Citations
88
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal relationships exhibit relatively low rates conflict diverse datasets analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades radiated during the Cenozoic. Genomic time trees reveal accumulation cladogenic before immediately after Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance K-Pg extinction in radiation.
Language: Английский
Citations
82
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. found that although mammals resemble one another total and diversity, they show substantial differences with regard recent accumulation. This includes multiple expansion quiescence events across mammalian tree. Young TEs, particularly long interspersed elements, drive increases size, whereas DNA transposons are associated smaller genomes. Mammals tend accumulate only a few types TEs at any given time, type dominating. also association between dietary habit presence transposon invasions. These detailed annotations will serve as benchmark for future comparative analyses among mammals.
Language: Английский
Citations
66
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (
Language: Английский
Citations
58
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent functionally conserved despite low sequence conservation. We developed Tissue-Aware Conservation Inference Toolkit (TACIT) associate candidate with species' using predictions from machine learning models trained on specific tissues. Applying TACIT motor cortex parvalbumin-positive interneuron neurological revealed dozens enhancer-phenotype associations, including brain size-associated interact genes implicated in microcephaly or macrocephaly. provides a foundation for identifying associated evolution any convergently evolved phenotype large group aligned genomes.
Language: Английский
Citations
43
Trends in Ecology & Evolution, Journal Year: 2024, Volume and Issue: 39(7), P. 677 - 688
Published: March 19, 2024
Language: Английский
Citations
27
Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(8)
Published: Feb. 12, 2024
The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed genomes 124 species across all orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, 2,384 intergenic segments. conducted a comprehensive sensitivity analysis to account for heterogeneity different leading an optimal tree Neoaves with high resolution. This features novel dichotomy comprising two monophyletic clades: previously recognized Telluraves (land birds) newly circumscribed Aquaterraves (waterbirds relatives). Molecular dating analyses 20 fossil calibrations indicate that diversification modern birds began in Late Cretaceous underwent constant steady KPg boundary, concurrent rise angiosperms as well other major Cenozoic animal groups placental multituberculate mammals. catastrophe had limited impact on avian evolution compared Paleocene–Eocene Thermal Maximum, which triggered rapid seabirds. Our findings suggest followed slow process gradualism rather than punctuated equilibrium, interruption by catastrophe. study places bird into new context within vertebrates, ramifications Earth’s biota.
Language: Английский
Citations
24
Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(7), P. 1353 - 1364
Published: June 10, 2024
Language: Английский
Citations
20
Science Immunology, Journal Year: 2025, Volume and Issue: 10(103)
Published: Jan. 3, 2025
Mechanistic understanding of the inhibitory immunoreceptor PD-1 is largely based on mouse models, but human and share only 59.6% amino acid identity. Here, we found that more than PD-1, owing to stronger interactions with ligands PD-L1 PD-L2 efficient recruitment effector phosphatase Shp2. In a melanoma model adoptively transferred T cells, humanization intracellular domain disrupted antitumor activity CD8
Language: Английский
Citations
6