A global catalog of whole-genome diversity from 233 primate species

Decoding human brain evolution: Insights from genomics

The human brain has undergone remarkable structural and functional specializations compared to that of nonhuman primates (NHPs), underlying the advanced cognitive abilities unique to humans. However, the cellular and genetic basis driving these specializations remains largely unknown. Comparing humans to our closest living relatives, chimpanzee and other great apes, is essential for identifying truly human-specific features. Recent comparative studies with closely related NHPs at the single-cell resolution using multimodal genomic profiling, assisted with high-throughput functional screening have provided unprecedented insights into human-specific brain features and their genetic underpinnings. In this review, we synthesize the current knowledge of human brain evolution at cellular and molecular levels, emphasizing how genetic changes have shaped these adaptations. We also discuss the emerging opportunities presented by new technologies and comprehensive atlases for advancing our understanding of human brain evolution.

Population genetics of captive spider monkeys in Japan for ex situ conservation

Spider monkeys (Ateles sp.) are among the most endangered primates in tropical forests, ranging from Central to South America. The current consensus on their classification is split into 7 species. However, species identification of Ateles individuals is challenging because their intraspecific and interspecific morphological traits gradually change and diversify among species, especially in pelage color and patterning. This problem makes it challenging to perform conservation in both wild (in situ) and captive (ex situ) populations. Currently, there are approximately 150 captive spider monkeys in around 30 Japanese zoos, reflecting more than 120 years of generational changes. To understand the genetic structure of the Ateles population in Japan and promote its ex situ conservation, we performed a population genetic analysis. Genomic DNA was extracted from 127 individuals using their fresh hair follicles. We determined the nucleotide sequences of three mitochondrial DNA regions and the nucleotide lengths of nine nuclear microsatellite loci in all individuals. Our analysis revealed the maternal lineages of four species (A. chamek, A. fusciceps, A. geoffroyi, and A. hybridus) from mitochondrial DNA analysis, and we identified novel haplotypes not previously reported. By comparing the maternal lineages of each individual with zoos' breeding records, we discovered at least 29 hybrid individuals, comprising about 20% of the current Japanese population. The results of the nuclear microsatellite analysis confirmed the genetic structure of hybrid individuals and suggested the presence of additional hybrids that could not be identified based on maternal lineage analysis and zoos' breeding records alone. These findings can contribute to the more appropriate management of spider monkeys toward ex situ conservation.

Unveiling the Evolutionary History of cis-Andean Alouatta (Atelidae, Alouattinae) Through Mitochondrial Genomes

Alouatta, a genus widely distributed throughout South and Central America, displays remarkable species diversity across various morphoclimatic domains. To clarify the ancestral distribution and its role in the radiation of Alouatta, our study employed time-tree phylogenetic analyses to better understand the current distribution patterns of the cis-Andean species. We generated 36 mitogenomes, including a species and representatives of populations not previously analyzed, to reconstruct a molecular-dated tree, estimate genetic distance-based analyses, and infer the ancestral distribution range of Alouatta. Our study suggests an initial split within the Alouatta during the Miocene, leading to the separation of the cis-Andean and trans-Andean clades. Through ancestral range reconstruction, we found that the most recent common ancestor of Alouatta was broadly distributed across South America. Within the cis-Andean clade, two major splits were identified. One split revealed a close relationship between the Amazonia-endemic species A. seniculus and A. caraya, a species adapted to open-dry domains, with ancestral range in the Amazonia and dry-open domains. In contrast, for the A. guariba and A. belzebul groups, which occur in Amazonia and the Atlantic Forest, the ancestral range included both domains. The diversification of the Alouatta was driven by two cladogenesis events. The formation of the extant species was primarily driven by founder events during the Pleistocene and involved long-distance dispersal events with posterior population isolation. These events played a crucial role in the formation of new populations that underwent rapid divergence, resulting in distinct phylogenetic lineages. Our findings shed new light on the origins of cis-Andean lineages of Alouatta across a broad geographic range, as well as the emergence of more recent taxa during the Pleistocene. This provides insights into their relationships, highlighting the crucial role of Pleistocene climatic changes and founder events in shaping the diversification and geographic distribution of extant species.

De novo whole-genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides)

The southern muriqui (Brachyteles arachnoides) is one of the 2 species of muriquis (genus Brachyteles), the largest body-sized nonhuman primate from the Neotropics. Deforestation and illegal hunting have led to a continuing decline in the muriqui population, leading to their current classification as critically endangered. The lack of a reference genome for the genus Brachyteles prevents scientists from taking full advantage of genomic tools to improve their conservation status. This study reports the first whole-genome assemblies of the genus Brachyteles, using DNA from 2 zoo-housed southern muriqui females. We performed sequencing with Oxford Nanopore Technologies' PromethION 2 Solo using a native DNA library preparation to preserve DNA modifications. We used Flye to assemble genomes for each individual. The best final assembly was 2.6 Gb, in 319 contigs, with an N50 of 58.8 Mb and an L50 of 17. BUSCO completeness score for this assembly was 99.5%. The assembly of the second individual had similar quality, with a length of 2.6 Gb, 759 contigs, an N50 of 47.9 Mb, an L50 of 18, and a BUSCO completeness score of 99.04%. Both assemblies had <1% duplicates, missing, or fragments. Gene model mapper detected 24,353 protein-coding genes, and repetitive elements accounted for 46% of the genome. We also reported the mitogenome, which had 16,562 bp over 37 genes, and global methylation of CpG sites, which revealed a mean of 80% methylation. Our study provides a high-quality reference genome assembly for the southern muriqui, expanding the tools that can be used to aid in their conservation efforts.

Comparative functional analyses of the prostate-specific KLK3 enzyme in primates reveal the impact of sexual selection

Male reproductive proteins frequently evolve rapidly in animals, potentially due to adaptive evolution driven by sperm competition, polyspermy avoidance, or pathogen defense. Alternatively, elevated rates of protein change may be due to relaxed constraint. The prostate-specific protease KLK3 has experienced dynamic evolution since its origin stemming from a gene duplication in the ancestor of all Old World primates, with instances of rapid evolution, stasis, and pseudogenization. As we demonstrate with functional assays using recombinant proteins, these changes have resulted in a chimpanzee KLK3 ortholog with greater enzyme velocity and higher efficiency than other apes, including humans. Reduced enzyme efficiency was observed in gorillas and gibbons who both possess a chimeric KLK2/KLK3 enzyme resulting from independent genomic deletions. The relative efficiency of KLK3 homologs among these species correlates well with their presumed levels of sperm competition. Furthermore, the reconstructed protein of the human-chimpanzee last common ancestor has enzyme kinetics identical to modern humans, suggesting that the observed functional differences between humans and chimpanzees are derived in the latter and allowing us to tentatively speculate that their common ancestor did not possess a polygynandrous mating system similar to modern chimpanzees.

Salt-driven dynamic folding of halophile-origin enzymes: Insights into evolution and protein exploitation

Many years ago, life transitioned from the ocean to land, evolving from halophilic to non-halophilic organisms. Our research indicates that some enzymes from halophiles require salt for soluble expression in E. coli and retain activity within certain salt concentration ranges in the growth medium. The cytoplasmic electrical resistance varies in accordance with the salt concentration in the medium. Further experiments and simulations reveal that the protein structure undergoes dynamic and sophisticated changes under different salt concentrations, affecting soluble expression, surface charge and enzyme activity. This suggests that salt concentrations affect enzyme functionality and potentially influence overall metabolic processes, pointing to a sophisticated adaptive system that operates independently of genetic molecules. Our findings propose insights into a type of environmental cue induced evolution of halophilic microorganisms from the perspective of protein structure. Ultimately, given our extensive marine and other saline resources, our research lays a foundational basis for the development and utilization of halophile-origin enzymes.

Characterizing the Rates and Patterns of De Novo Germline Mutations in the Aye-Aye (Daubentonia madagascariensis)

Given the many levels of biological variation in mutation rates observed to date in primates-spanning from species to individuals to genomic regions-future steps in our understanding of mutation rate evolution will not only be aided by a greater breadth of species coverage across the primate clade but also by a greater depth as afforded by an evaluation of multiple trios within individual species. In order to help bridge these gaps, we here present an analysis of a species representing one of the most basal splits on the primate tree (aye-ayes), combining whole-genome sequencing of seven parent-offspring trios from a three-generation pedigree with a novel computational pipeline that takes advantage of recently developed pan-genome graphs, thereby circumventing the application of (highly subjective) quality metrics that has previously been shown to result in notable differences in the detection of de novo mutations and ultimately estimates of mutation rates. This deep sampling has enabled both a detailed picture of parental age effects and sex dependency in mutation rates, which we here compare with previously studied primates, but has also provided unique insights into the nature of genetic variation in one of the most endangered primates on the planet.

Mitochondrial DNA for Phylogeny Building: Assessing Individual and Grouped mtGenes as Proxies for the mtGenome in Platyrrhines

Phylogenetic trees are analytic tools used in primate studies to elucidate evolutionary relationships. Because of its relative ease to sequence and rapid evolution compared to nuclear genomes, mitochondrial DNA is frequently used for phylogeny building. This project evaluated the effectiveness of using individual or grouped mitochondrial genes (mtGenes) as a proxy for the mitochondrial genome (mtGenome) in phylogeny building within two nested primate datasets, Cebidae and Platyrrhini, with differing divergence dates. mtGene utility rankings were determined based on congruence values to the mtGenome tree. mtGenes trees were also assessed on tree resolution and ability to sort nested clades. We found that most individual mtGenes, including ribosomal genes (12S and 16S), COX genes, most ND genes, and d-Loop are not appropriate for use as proxies for the mtGenome when tree building in either the Cebidae or Platyrrhini set. On average, grouped mtGenes outperformed individual mtGenes in both sets, and mtGene and grouped mtGene rankings varied between sets. Pairing CYB and COX3 together or pairing ND2 and CYB worked well in both the Cebidae set and the Platyrrhini set. We also found that nucleotide diversity is not a predictor of mtGene performance. Instead, it may be that unique mtGene or mtGene system evolutionary history impacts mtGene performance.

Reanalysis of Samburupithecus reveals similarities to nyanzapithecines

Samburupithecus kiptalami is an ape found in Late Miocene deposits (ca. 9.5 Ma) of northern Kenya. Initial assessments of the holotype specimen (KNM-SH 8531), a female-gorilla-sized maxillary fragment preserving the postcanine tooth row, noted similarities to gorillas or to African apes more broadly. More recently, primitive features of the maxilla and dentition have been used to propose a stem hominoid position for Samburupithecus. In particular, Samburupithecus shares some dental features with orepithecids (nyanzapithecines and Oreopithecus). To evaluate these competing hypotheses, and investigate possible affinities to oreopithecids, we reanalyzed the dentition of Samburupithecus quantitatively and assessed qualitative dental and maxillary features shared by oreopithecids and Samburupithecus. Based on the results of our analyses, we suggest that Samburupithecus is a late-occurring African oreopithecid, which we regard as a long-lived family of stem hominoids. The inclusion of Samburupithecus within Oreopithecidae highlights that stem hominoids and oreopithecids, in particular, spanned a large range of body sizes, similar to the range of size variation seen among all extant apes. Finally, the presence of oreopithecids in Africa on either side of a notable gap in the Late Miocene African fossil record of apes (from ∼13 to 10 Ma) demonstrates that the rarity of fossil African apes (i.e., nonhominin hominines) during this period is likely due to sampling biases rather than a recent immigration back into Africa from Eurasia.

Avoidable false PSMC population size peaks occur across numerous studies

Inferring historical population sizes is key to identifying drivers of ecological and evolutionary change and crucial to predicting the future of species on our rapidly changing planet. The pairwise sequentially Markovian coalescent (PSMC) method provided a revolutionary framework to reconstruct species' demographic histories over millions of years based on the genome sequence of a single individual. Here, we detected and solved a common artifact in PSMC and related methods: recent population peaks followed by population collapses. Combining real and simulated genomes, we show that these peaks do not represent true population dynamics. Instead, ill-set default parameters cause false peaks in our own and published data, which can be avoided by adjusting parameter settings. Furthermore, we show that certain changes in population structure can cause similar patterns. Newer methods, like Beta-PSMC, perform better but do not always avoid this artifact. Our results suggest testing multiple parameters that split the first time window before interpreting recent population peaks followed by collapses and call for the development of robust methods.

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

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 to overcome PCR bias, we assemble the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem. This raises the question as to whether the enamelome alone provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments for each protein and estimated the evolutionary rate for each site. We examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1 to 2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We tested phylogenetic analysis on combinations of different enamel proteins and found that the composition of the proteome can influence deep splits in the phylogeny. With our methods, we provide guidance for researchers on how to evaluate the potential of paleoproteomics for phylogenetic studies before sampling valuable ancient specimens.

Evolutionary and Functional Analysis of Monoamine Oxidase F: A Novel Member of the Monoamine Oxidase Gene Family

The monoamine oxidase (MAO) gene family encodes for enzymes that perform the oxidative deamination of monoamines, a process required to degrade norepinephrine, serotonin, dopamine, and other amines. While mammalian MAO enzymes, MAO A and MAO B, have been extensively studied, the molecular properties of the other family members are only partly uncovered. This study aims to explore the evolution of MAOs, emphasizing understanding of the MAO gene repertoire among vertebrates. Our analyses show that the duplication that gave rise to MAO A and MAO B occurred in the ancestor of tetrapods, between 408 and 352 million years ago. Nontetrapod jawed vertebrates possess the ancestral preduplicative condition of MAO A/B. Our results also identified a new family member, MAO F, in nontetrapod jawed vertebrates. Thus, most jawed vertebrates possess a repertoire of two MAO genes, MAO A and MAO B in tetrapods and MAO A/B and MAO F in nontetrapod jawed vertebrates, representing different MAO gene lineages. Jawless vertebrates possess the ancestral condition of a single copy gene, MAO A/B/F. Enzymatic assays conducted on the MAO recombinant enzymes of the Indo-Pacific tarpon show that both proteins, MAO A/B and MAO F, have enzymatic and molecular properties more similar to human MAO A, with the former featuring a strikingly higher activity rate when compared with all other MAO enzymes. Our analyses underscore the importance of scanning the tree of life for new gene lineages to understand phenotypic diversity and gain detailed insights into their function.

Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations

The time of integration of germline-targeting Long Terminal Repeat (LTR) retroposons, such as endogenous retroviruses (ERVs), can be estimated by assessing the nucleotide divergence between the LTR sequences flanking the viral genes. Due to the viral replication mechanism, both LTRs are identical at the moment of integration, when the provirus becomes part of the host genome. After that time, proviral sequences evolve within the host DNA. When the mutation rate is known, nucleotide divergence between the LTRs would then be a measure of time elapsed since integration. Though frequently used, the approach has been complicated by the choice of host mutation rate and, to a lesser extent, by the method selected to estimate nucleotide divergence. As a result, outcomes can be incompatible with, for instance, speciation events identified from the fossil record. The review will give an overview of research reporting LTR-retroposon dating, and a summary of important factors to consider, including the quality, assembly, and alignment of sequences, the mutation rate of foreign DNA in host genomes, and the choice of a distance estimation method. Primates will here be the focus of the analysis because their genomes, ERVs, and fossil record have been extensively studied. However, most of the factors discussed have a wide applicability in the vertebrate field.

Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science.

Tile by tile: capturing the evolutionary mosaic of human conditions

The collection of Homo sapiens anatomical hallmarks hypothesized to support the 'human condition' did not appear at one specific time and place, but gradually, creating a reticulate evolutionary trajectory. The recent reconstruction of migration patterns and gene flows across different hominin species and populations draws a mosaic that we contend can be illuminated by genomic comparisons and specific experiments. Here, we first review key discoveries that could allow this experimental endeavor by describing recent advances in a variety of fields, stressing the importance of charting the current human neurodiversity as an interpretive substrate for evolutionary changes. Then, we identify key cellular and molecular observables. Finally, given the vast amount of possible variants, we focus the discussion on technologies that could allow their interrogation in a way that is compatible with the staggering amount of contemporary genomic and phenotypic characterization.

Additional analyses of stem catarrhine and hominoid dental morphology support Kapi ramnagarensis as a stem hylobatid

Fossil gibbons are exceedingly rare, with much of the hylobatid fossil record and, consequently, hylobatid evolutionary history remaining unknown. Kapi ramnagarensis was described as a stem hylobatid on the basis of an isolated lower right M3 from ∼13.0-12.5 Ma deposits surrounding Ramnagar (J&K), India. This interpretation was recently challenged, with alternative hypotheses suggesting that it is instead a stem catarrhine or a strangely derived pliopithecoid that has converged on hylobatid morphology. A series of morphological features were said to distinguish Kapi from fossil and extant hylobatids; notably, however, none of these features were examined or compared using quantitative analyses. Here, we further examine the dental morphology of Kapi, providing quantitative analyses to critically evaluate the hypothesis that Kapi represents a stem catarrhine or pliopithecoid rather than a stem hylobatid. Results demonstrate that none of the claimed differences between Kapi and hylobatids hold up under closer scrutiny, and multivariate discriminant analyses taking size and shape into account strongly support Kapi as a hylobatid with high posterior probabilities. Although only represented by a single lower molar, Kapi remains the most compelling candidate for the earliest known hylobatid in the fossil record and thus likely documents the simultaneous arrival of lesser and great apes to Asia during the Middle Miocene.

Historical Demography and Species Distribution Models Shed Light on Speciation in Primates of Northeast India

Past climate change is one of the important factors influencing primate speciation. Populations of various species could have risen or declined in response to these climatic fluctuations. Northeast India harbors a rich diversity of primates, where such fluctuations can be implicated. Recent advances in climate modeling as well as genomic data analysis has paved the way for understanding how species accumulate at a particular geographic region. We utilized these methods to explore the primate diversity in this unique region in relation to past climate change. To ascertain the population level changes, we inferred the demographic history of nine species of primates found in Northeast India and compared it with species distribution models of Pliocene and Pleistocene period. Through this study, we are able to provide a detailed picture of how past climatic changes have resulted in the present species diversity and this mixture of species have either originated in the region or have dispersed from mainland Southeast Asia. We observe that effective population size has decreased for all the species, but distributions are different for all the four genera: Macaca, Trachypithecus, Hoolock and Nycticebus. It also gives an idea about how each species is affected differently by climate change, and why it should be given emphasis in framing species-wise conservation models for future climate change.

Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar

Every mammal studied to date has been found to have a male mutation bias: male parents transmit more de novo mutations to offspring than female parents, contributing increasingly more mutations with age. Although male-biased mutation has been studied for more than 75 years, its causes are still debated. One obstacle to understanding this pattern is its near universality-without variation in mutation bias, it is difficult to find an underlying cause. Here, we present new data on multiple pedigrees from two primate species: aye-ayes (Daubentonia madagascariensis), a member of the strepsirrhine primates, and olive baboons (Papio anubis). In stark contrast to the pattern found across mammals, we find a much larger effect of maternal age than paternal age on mutation rates in the aye-aye. In addition, older aye-aye mothers transmit substantially more mutations than older fathers. We carry out both computational and experimental validation of our results, contrasting them with results from baboons and other primates using the same methodologies. Further, we analyze a set of DNA repair and replication genes to identify candidate mutations that may be responsible for the change in mutation bias observed in aye-ayes. Our results demonstrate that mutation bias is not an immutable trait, but rather one that can evolve between closely related species. Further work on aye-ayes (and possibly other lemuriform primates) should help to explain the molecular basis for sex-biased mutation.

Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of identical-by-descent DNA segments (IBD) yield the most precise relatedness estimates. Here, we leverage different methods for estimating IBD segments from low-depth whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4 to 6× depth data from a rhesus macaque (Macaca mulatta) population with long-term pedigree data, we show that we can infer the number and length of IBD segments across the genome with high accuracy even at 0.5× sequencing depth. In line with expectations based on simulation, the resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. By comparing the IBD-based estimates with pedigree and short tandem repeat-based methods, we show that IBD estimates are more reliable and provide more detailed information on kinship. The inferred IBD segments also identify cryptic genetic relatives not represented in the pedigree and reveal elevated recombination rates in females relative to males, which enables the majority of close maternal and paternal kin to be distinguished with genotype data alone. Our findings represent a breakthrough in the ability to study the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

Successful Traceability of Wildlife Samples Contributes to Wildlife Conservation: A Case Study of Tracing the Snub-Nosed Monkey (Rhinopithecus spp.)

Rapid and effective methods for tracing the geographic origin of wildlife samples are essential for tackling the illegal wildlife trade. Traditional morphological categorization methods are often inadequate as relying on the mitochondrial COXI barcode is insufficient for determining geographic populations. To address these limitations, we developed a bioinformatics-based pipeline for the rapid identification of traceable nuclear genome loci. This pipeline has been applied to the whole-genome sequence (WGS) data of China's flagship species, the snub-nosed monkey (Rhinopithecus spp.). These species are known for sex-biased dispersal and hybrid speciation, which complicates genealogy tracing. Using phylogenetic principles, we employed the Robinson and Foulds (RF) distance and scanned over 1,850,726 population-specific loci, identifying five pairs that can trace genealogy origins rapidly and cost-effectively using PCR. Additionally, we found that relying only on mitochondrial genetic information is insufficient for rapid and accurate traceability to subspecies-level geographic populations. Our pipeline efficiently identifies loci and traces the geographic origin of snub-nosed monkey individuals, providing a valuable tool for species preservation and combating the wildlife trade. This approach can be extended to other species, aiding in the conservation of endangered wildlife and tracing criminal evidence.

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

The influence of long-term climatic changes such as glacial cycles on the history of living organisms has been a subject of research for decades, but the detailed population dynamics during the environmental fluctuations and their effects on genetic diversity and genetic load are not well understood on a genome-wide scale. The Japanese macaque (Macaca fuscata) is a unique primate adapted to the cold environments of the Japanese archipelago. Despite the past intensive research for the Japanese macaque population genetics, the genetic background of Japanese macaques at the whole-genome level has been limited to a few individuals, and the comprehensive demographic history and genetic differentiation of Japanese macaques have been underexplored. We conducted whole-genome sequencing of 64 Japanese macaque individuals from 5 different regions, revealing significant genetic differentiation and functional variant diversity across populations. In particular, Japanese macaques have low genetic diversity and harbor many shared and population-specific gene loss, which might contribute to population-specific phenotypes. Our estimation of population demography using phased haplotypes suggested that, after the strong population bottleneck shared among all populations around 400 to 500 kya, the divergence among populations initiated around 150 to 200 kya, but there has been the time with strong gene flow between some populations after the split, indicating multiple population split and merge events probably due to habitat fragmentation and fusion during glacial cycles. These findings not only present a complex population history of Japanese macaques but also enhance their value as research models, particularly in neuroscience and behavioral studies. This comprehensive genomic analysis sheds light on the adaptation and evolution of Japanese macaques, contributing valuable insights to both evolutionary biology and biomedical research.

Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar

Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.

Landscape and conservation genetics of western black crested gibbons (Nomascus concolor) in China

Despite decades of field study, very little is known about the molecular ecology of gibbons, particularly as it relates to their ability to disperse across degraded and fragmentary landscapes. The critically endangered western black crested gibbon (Nomascus concolor) has been reduced to a small, fragmented population with about 1300 individuals. In the largest population genetic study of free-ranging gibbons to date, we sampled 47 of these gibbons from 13 sites in China and generated 15 polymorphic autosomal microsatellite markers. We identify three population clusters of N. concolor in Yunnan centered in 1) the Wuliang and Ailao Mountains, 2) the Yongde Daxueshan Mountains, and 3) an isolated remnant near the border with Vietnam. Within the Wuliang Mountains, we identified four subclusters, three of which are bounded by high-altitude rhododendron forest, and one that is isolated from the main population by ~2 km of degraded forest and pasture. Least-cost path analysis and isolation by resistance modeling demonstrates that the population genetic distances among gibbons in Wuliangshan National Nature Reserve are significantly correlated with geographic paths that avoid use of high-altitude rhododendron forest in favor of evergreen broadleaf forest. Although these gibbons have likely undergone reductions in heterozygosity from recent consanguineous mating, we suggest that their active avoidance of inbreeding on the population level maintains higher than expected levels of genetic diversity. This research provides new insights into how gibbons interact with heterogeneous environments and expands our understanding of their molecular ecology and conservation genetics.

Nonhuman primate models of pediatric viral diseases

Infectious diseases are the leading cause of death in infants and children under 5 years of age. In utero exposure to viruses can lead to spontaneous abortion, preterm birth, congenital abnormalities or other developmental defects, often resulting in lifelong health sequalae. The underlying biological mechanisms are difficult to study in humans due to ethical concerns and limited sample access. Nonhuman primates (NHP) are closely related to humans, and pregnancy and immune ontogeny in infants are very similar to humans. Therefore, NHP are a highly relevant model for understanding fetal and postnatal virus-host interactions and to define immune mechanisms associated with increased morbidity and mortality in infants. We will discuss NHP models of viruses causing congenital infections, respiratory diseases in early life, and HIV. Cytomegalovirus (CMV) remains the most common cause of congenital defects worldwide. Measles is a vaccine-preventable disease, yet measles cases are resurging. Zika is an example of an emerging arbovirus with devastating consequences for the developing fetus and the surviving infant. Among the respiratory viruses, we will discuss influenza and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We will finish with HIV as an example of a lifelong infection without a cure or vaccine. The review will highlight (i) the impact of viral infections on fetal and infant immune development, (ii) how differences in infant and adult immune responses to infection alter disease outcome, and emphasize the invaluable contribution of pediatric NHP infection models to the design of effective treatment and prevention strategies, including vaccines, for human infants.

Detecting diversifying selection for a trait from within and between-species genotypes and phenotypes

To quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, methods using within-species variation do not integrate the changes at the macro-evolutionary scale. Conversely, current methods using between-species variation usually discard within-species variation, thus not accounting for processes at the micro-evolutionary scale. The main goal of this study is to define a neutrality index for a quantitative trait, by combining within- and between-species variation. This neutrality index integrates nucleotide polymorphism and divergence for normalizing trait variation. As such, it does not require estimation of population size nor of time of speciation for normalization. Our index can be used to seek deviation from the null model of neutral evolution, and test for diversifying selection. Applied to brain mass and body mass at the mammalian scale, we show that brain mass is under diversifying selection. Finally, we show that our test is not sensitive to the assumption that population sizes, mutation rates and generation time are constant across the phylogeny, and automatically adjust for it.

Y chromosome introgression between deeply divergent primate species

Hybridization and introgression are widespread in nature, with important implications for adaptation and speciation. Since heterogametic hybrids often have lower fitness than homogametic individuals, a phenomenon known as Haldane's rule, loci inherited strictly through the heterogametic sex rarely introgress. We focus on the Y-chromosomal history of guenons, African primates that hybridized extensively in the past. Although our inferences suggest that Haldane's rule generally applies, we uncover a Y chromosome introgression event between two species ca. six million years after their initial divergence. Using simulations, we show that selection likely drove the introgressing Y chromosome to fixation from a low initial frequency. We identify non-synonymous substitutions on the novel Y chromosome as candidate targets of selection, and explore meiotic drive as an alternative mechanism. Our results provide a rare example of Y chromosome introgression, showing that the ability to produce fertile heterogametic hybrids likely persisted for six million years in guenons.

Characterizing the rates and patterns of de novo germline mutations in the aye-aye (Daubentonia madagascariensis)

Given the many levels of biological variation in mutation rates observed to date in primates - spanning from species to individuals to genomic regions - future steps in our understanding of mutation rate evolution will be aided by both a greater breadth of species coverage across the primate clade, but also by a greater depth as afforded by an evaluation of multiple trios within individual species. In order to help bridge these gaps, we here present an analysis of a species representing one of the most basal splits on the primate tree (aye-ayes), combining whole-genome sequencing of seven parent-offspring trios from a three-generation pedigree with a novel computational pipeline that takes advantage of recently developed pan-genome graphs, thereby circumventing the application of (highly subjective) quality metrics that has previously been shown to result in notable differences in the detection of de novo mutations, and ultimately estimates of mutation rates. This deep sampling has enabled both a detailed picture of parental age effects as well as sex dependency in mutation rates which we here compare with previously studied primates, but has also provided unique insights into the nature of genetic variation in one of the most endangered primates on the planet.

A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model

The aye-aye (Daubentonia madagascariensis) is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation within aye-aye populations, and the relative influences of neutral and selective processes in shaping that variation, is thus important for future conservation efforts. In this study, we performed the first whole-genome scans for recent positive and balancing selection in the species, utilizing high-coverage population genomic data from newly sequenced individuals. We generated null thresholds for our genomic scans by creating an evolutionarily appropriate baseline model that incorporates the demographic history of this aye-aye population, and identified a small number of candidate genes. Most notably, a suite of genes involved in olfaction - a key trait in these nocturnal primates - were identified as experiencing long-term balancing selection. We also conducted analyses to quantify the expected statistical power to detect positive and balancing selection in this population using site frequency spectrum-based inference methods, once accounting for the potentially confounding contributions of population history, recombination and mutation rate variation, and purifying and background selection. This work, presenting the first high-quality, genome-wide polymorphism data across the functional regions of the aye-aye genome, thus provides important insights into the landscape of episodic selective forces in this highly endangered species.

Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys

Background/Objective: The Bale monkey (Chlorocebus djamdjamensis) is a threatened primate species endemic to Ethiopia and, in contrast to other members of the genus Chlorocebus, lives at high altitudes and feeds mainly on bamboo. Two populations of the species are present, one in continuous bamboo forest (CF) in the eastern part of the species' range, and the other in fragmented forest (FF) in the western part. Based on mitochondrial DNA and phenotypic characteristics, previous studies have suggested introgression by parapatric congeners into the FF population but not into the CF population. The objective of this study was to gain insights into the evolutionary history of Bale monkeys and their potential genetic adaptations to high altitudes and for bamboo consumption. Methods: We sequenced the whole genomes of individuals from both populations and compared their genomes with those of the other five Chlorocebus species. We applied phylogenetic methods and conducted population demographic simulations to elucidate their evolutionary history. A genome-wide analysis was conducted to assess gene flow and identify mutations potentially associated with adaptations to high altitudes and for bamboo metabolism. Results: Our analyses revealed Bale monkeys as the sister clade to Chlorocebus aethiops and showed that gene flow occurred between C. aethiops and FF but not between C. aethiops and CF. In addition, we detected non-synonymous mutations in genes potentially associated with the adaptation to high altitudes (EPAS1) in both populations and with the adaptation for bamboo metabolism (TAS2R16, MPST, and TST) mainly in the CF population. Conclusions: Our study provides insights into the evolutionary history of a threatened primate species and reveals the genetic basis for its adaptions to unique environments and for diet specialization.

Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.

Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.

Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts

Evolutionary innovations can be driven by changes in the rates of RNA translation and the emergence of new genes and small open reading frames (sORFs). In this study, we characterized the transcriptional and translational landscape of the hearts of four primate and two rodent species through integrative ribosome and transcriptomic profiling, including adult left ventricle tissues and induced pluripotent stem cell-derived cardiomyocyte cell cultures. We show here that the translational efficiencies of subunits of the mitochondrial oxidative phosphorylation chain complexes IV and V evolved rapidly across mammalian evolution. Moreover, we discovered hundreds of species-specific and lineage-specific genomic innovations that emerged during primate evolution in the heart, including 551 genes, 504 sORFs and 76 evolutionarily conserved genes displaying human-specific cardiac-enriched expression. Overall, our work describes the evolutionary processes and mechanisms that have shaped cardiac transcription and translation in recent primate evolution and sheds light on how these can contribute to cardiac development and disease.

Molecular determinants of cross-species transmission in emerging viral infections

SUMMARYSeveral examples of high-impact cross-species transmission of newly emerging or re-emerging bat-borne viruses, such as Sudan virus, Nipah virus, and severe acute respiratory syndrome coronavirus 2, have occurred in the past decades. Recent advancements in next-generation sequencing have strengthened ongoing efforts to catalog the global virome, in particular from the multitude of different bat species. However, functional characterization of these novel viruses and virus sequences is typically limited with regard to assessment of their cross-species potential. Our understanding of the intricate interplay between virus and host underlying successful cross-species transmission has focused on the basic mechanisms of entry and replication, as well as the importance of host innate immune responses. In this review, we discuss the various roles of the respective molecular mechanisms underlying cross-species transmission using different recent bat-borne viruses as examples. To delineate the crucial cellular and molecular steps underlying cross-species transmission, we propose a framework of overall characterization to improve our capacity to characterize viruses as benign, of interest, or of concern.

The Primate Major Histocompatibility Complex: An Illustrative Example of Gene Family Evolution

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 the ~60 million year history of the primates, some MHC genes have turned over completely, some have changed function, some have converged in function, and others have remained essentially unchanged. Past work has typically focused on identifying MHC alleles within particular species or comparing gene content, but more work is needed to understand the overall evolution of the gene family across species. Thus, despite the immunologic importance of the MHC and its peculiar evolutionary history, we lack a complete picture of MHC evolution in the primates. We readdress this question using sequences from dozens of MHC genes and pseudogenes spanning the entire primate order, building a comprehensive set of gene and allele trees with modern methods. Overall, we find that the Class I gene subfamily is evolving much more quickly than the Class II gene subfamily, with the exception of the Class II MHC-DRB genes. We also pay special attention to the often-ignored pseudogenes, which we use to reconstruct different events in the evolution of the Class I region. We find that despite the shared function of the MHC across species, different species employ different genes, haplotypes, and patterns of variation to achieve a successful immune response. Our trees and extensive literature review represent the most comprehensive look into MHC evolution to date.

Genomic diversity and demographic history of the endangered Sichuan hill-partridge (Arborophila rufipectus)

Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum, possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.

Inbreeding avoidance, competition and natal dispersal in a pair-living, genetically monogamous mammal, Azara's owl monkey (Aotus azarae)

Natal dispersal is an important life-history stage influencing individual fitness, social dynamics of groups and population structure. Understanding factors influencing dispersal is essential for evaluating explanations for the evolution and maintenance of social organization, including parental care and mating systems. The social and mating systems of Azara's owl monkeys (Aotus azarae) are infrequent among mammals; these primates are pair-living, serially and genetically monogamous and both sexes directly care for offspring. To evaluate the role that competition and inbreeding avoidance play in shaping dispersal patterns, we used 25 years of demographic and genetic data to examine how variation in timing of natal dispersal is related to social (adult replacements, step-parents, births and group size) and ecological factors (seasonal abundance of resources) in a wild population of A. azarae in Formosa, Argentina. We found that all males and females dispersed from their natal groups, but subadults delayed dispersal when a step-parent of the opposite sex joined the group, indicating that they may perceive these step-parents as potential mates. Dispersal was more probable when resource conditions were better, regardless of age. Overall, agonistic conflict over food and potential mates with adults in the natal group, as well as inbreeding avoidance, contribute to regulating dispersal.

From molecular variations to behavioral adaptations: Unveiling adaptive epistasis in primate oxytocin system

OBJECTIVE

Our primary objective was to investigate the variability of oxytocin (OT) and the GAMEN binding motif within the LNPEP oxytocinase in primates.

MATERIALS AND METHODS

We sequenced the LNPEP segment encompassing the GAMEN motif in 34 Platyrrhini species, with 21 of them also sequenced for the OT gene. Our dataset was supplemented with primate sequences of LNPEP, OT, and the oxytocin receptor (OTR) sourced from public databases. Evolutionary analysis and coevolution predictions were made followed by the macroevolution analysis of relevant amino acids associated with phenotypic traits, such as mating systems, parental care, and litter size. To account for phylogenetic structure, we utilized two distinct statistical tests. Additionally, we calculated binding energies focusing on the interaction between Callithtrix jacchus VAMEN and Pro8OT.

RESULTS

We identified two novel motifs (AAMEN and VAMEN), challenging the current knowledge of motif conservation in placental mammals. Coevolution analysis demonstrated a correlation between GAMEN, AAMEN, and VAMEN and their corresponding OTs and OTRs. Callithrix jacchus exhibited a higher binding energy between VAMEN and Pro8OT than orthologous molecules found in humans (GAMEN and Leu8OT).

DISCUSSION

The coevolution of AAMEN and VAMEN with their corresponding OTs and OTRs suggests a functional relationship that could have contributed to specific reproductive and adaptive behaviors, including paternal care, social monogamy, and twin births, prominent traits in Cebidae species, such as marmosets and tamarins. Our findings underscore the coevolution of taxon-specific amino acids among the three studied molecules, shedding light on the oxytocinergic system as an adaptive epistatic repertoire in primates.

Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics

Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding of inter- and intra-species SV has been historically hampered by the quality of draft primate genomes and the absence of genome resources for key taxa. Recently, advances in long-read sequencing and genome assembly have begun to radically reshape our understanding of SVs. Two landmark achievements include the publication of a human telomere-to-telomere (T2T) genome as well as the development of the first human pangenome reference. In this review, we first look back to the major works laying the foundation for these projects. We then examine the ways in which T2T genome assemblies and pangenomes are transforming our understanding of and approach to primate SV. Finally, we discuss what the future of primate SV research may look like in the era of T2T genomes and pangenomics.

Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models

Understanding and treating human diseases require valid animal models. Leveraging the genetic diversity in rhesus macaque populations across eight primate centers in the United States, we conduct targeted-sequencing on 1845 individuals for 374 genes linked to inherited human retinal and neurodevelopmental diseases. We identify over 47,000 single nucleotide variants, a substantial proportion of which are shared with human populations. By combining rhesus and human allele frequencies with established variant prediction methods, we develop a machine learning-based score that outperforms established methods in predicting missense variant pathogenicity. Remarkably, we find a marked number of loss-of-function variants and putative deleterious variants, which may lead to the development of rhesus disease models. Through phenotyping of macaques carrying a pathogenic OPA1:p.A8S variant, we identify a genetic model of autosomal dominant optic atrophy. Finally, we present a public website housing variant and genotype data from over two thousand rhesus macaques.

Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates

Bitter taste perception is important in preventing animals from ingesting potentially toxic compounds. Whole-genome assembly (WGA) data have revealed that bitter taste receptor genes (TAS2Rs) comprise a multigene family with dozens of intact and disrupted genes in primates. However, publicly available WGA data are often incomplete, especially for multigene families. In this study, we employed a targeted capture (TC) approach specifically probing TAS2Rs for ten species of cercopithecid primates with diverse diets, including eight omnivorous cercopithecine species and two folivorous colobine species. We designed RNA probes for all TAS2Rs that we modeled to be intact in the common ancestor of cercopithecids ("ancestral-cercopithecid TAS2R gene set"). The TC was followed by short-read and high-depth massive-parallel sequencing. TC retrieved more intact TAS2R genes than found in WGA databases. We confirmed a large number of gene "births" at the common ancestor of cercopithecids and found that the colobine common ancestor and the cercopithecine common ancestor had contrasting trajectories: four gene "deaths" and three gene births, respectively. The number of intact TAS2R genes was markedly reduced in colobines (25-28 detected via TC and 20-26 detected via WGA analysis) as compared with cercopithecines (27-36 via TC and 19-30 via WGA). Birth or death events occurred at almost every phylogenetic-tree branch, making the composition of intact genes variable among species. These results show that evolutionary change in intact TAS2R genes is a complex process, refute a simple general prediction that herbivory favors more TAS2R genes, and have implications for understanding dietary adaptations and the evolution of detoxification abilities.

Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi

Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution, and single-cell RNA-seq CRISPR interference (CRISPRi) screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla, and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct at the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPRi screen. Hence, we provide valuable resources for performing and further extending CRISPRi in human and non-human primates.

New mitogenomes of Runcinidae and Facelinidae: two understudied heterobranch families (Mollusca: Gastropoda)

Here, we present the mitochondrial sequences of two sea slugs (Heterobranchia): Runcina aurata and Facelina auriculata, the latter being the type species of the family. The mitochondrial genomes are 14,282 and 14,171bp in length, respectively, with a complete set of 13 PCGs, 2 rRNAs, and 22 tRNAs. None of the mitogenomes show gene reorganization, keeping the standard mitogenomic structure of Heterobranchia. Nucleotide composition differs significantly between them, with R. aurata showing the most AT-rich mitogenome (25.7% GC content) reported to date in Heterobranchia, and F. auriculata showing a rich GC content (35%) compared with other heterobranch mitochondrial genomes.

Homorepeat variability within the human population

Genetic variation within populations plays a crucial role in driving evolution. Unlike the average protein sequence, the evolution of homorepeats can be influenced by DNA replication slippage, when DNA polymerases either add or skip repeats of nucleotides. While there are some diseases known to be caused by abnormal changes in the length of amino acid homorepeats, naturally occurring variations in homorepeat length remain relatively unexplored. In our study, we examined the variation in amino acid homorepeat length of human individuals by analyzing 125 748 exomes, as well as 15 708 whole genomes. Our analyses revealed significant variability in homorepeat length across the human population, indicating that these motifs are prone to mutations at higher rates than non repeat sequences. We focused our study on glutamine homorepeats, also known as polyQ sequences, and found that shorter polyQ sequences tend to exhibit greater length variation, while longer ones primarily undergo deletions. Notably, polyQ sequencesthat are more conserved across primates tend to show less variation within the human population, indicating stronger selective pressure to maintain their length. Overall, our results demonstrate that there is large natural variation in the length of homorepeats within the human population, with no apparent impact on observable traits.

Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates

SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane. Cells expressing great ape SLC22A10 orthologs exhibit significant accumulation of estradiol-17β-glucuronide, unlike those expressing human SLC22A10. Sequence alignments reveal a proline at position 220 in humans, which is a leucine in great apes. Replacing proline with leucine in SLC22A10-P220L restores plasma membrane localization and uptake function. Neanderthal and Denisovan genomes show proline at position 220, akin to modern humans, indicating functional loss during hominin evolution. Human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220, while in great apes, its orthologs transport sex steroid conjugates. Characterizing SLC22A10 across species sheds light on its biological role, influencing organism development and steroid homeostasis.

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

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., CYP2C76 and EHBP1L1 ). 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., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). 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.

A multi-million-year natural experiment: Comparative genomics on a massive scale and its implications for human health

Improving the diversity and quality of genome assemblies for non-human mammals has been a long-standing goal of comparative genomics. The last year saw substantial progress towards this goal, including the release of genome alignments for 240 mammals and nearly half the primate order. These resources have increased our ability to identify evolutionarily constrained regions of the genome, and together strongly support the importance of these regions to biomedically relevant trait variation in humans. They also provide new strategies for identifying the genetic basis of changes unique to individual lineages, illustrating the value of evolutionary comparative approaches for understanding human health.

Species-aware DNA language models capture regulatory elements and their evolution

BACKGROUND

The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution.

RESULTS

Here, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA language models capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA language models reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery.

CONCLUSIONS

Collectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.

Review: Wildlife forensic genetics-Biological evidence, DNA markers, analytical approaches, and challenges

Wildlife-related crimes are the second most prevalent lawbreaking offense globally. This illicit trade encompasses hunting, breeding and trafficking. Besides diminishing many species and their habitats and ecosystems, hindering the economic development of local communities that depend on them, undermining the rule of law and financing terrorism, various cross-species transmissions (zoonoses) of pathogens, including COVID-19, can be attributed to wildlife crimes. Wildlife forensics applies interdisciplinary scientific analyses to support law enforcement in investigating wildlife crimes. Its main objectives are to identify the taxonomic species in question, determine if a crime has been committed, link a suspect to the crime and support the conviction and prosecution of the perpetrator. This article reviews wildlife crime and its implications, wildlife forensic science investigation, common forms of wildlife biological evidence, including DNA, wildlife DNA techniques and challenges in wildlife forensic genetics. The article also reviews the contributions of genetic markers such as short tandem repeat (STR) and mitochondrial DNA (mtDNA) markers, which provide the probative genetic data representing the bulk of DNA evidence for solving wildlife crime. This review provides an overview of wildlife DNA databases, which are critical for searching and matching forensic DNA profiles and sequences and establishing how frequent forensic DNA profiles and sequences are in a particular population or geographic region. As such, this review will contain an in-depth analysis of the current status of wildlife forensic genetics, and it will be of general interest to wildlife and conservation biologists, law enforcement officers, and academics interested in combating crimes against wildlife using animal forensic DNA methods.