A molecular phylogeny of living primates

Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses

Simian immunodeficiency viruses (SIVs) comprise a large group of primate lentiviruses that endemically infect African monkeys. HIV-1 spilled over to humans from this viral reservoir, but the spillover did not occur directly from monkeys to humans. Instead, a key event was the introduction of SIVs into great apes, which then set the stage for infection of humans. Here, we investigate the role of the lentiviral entry receptor, CD4, in this key and fateful event in the history of SIV/HIV emergence. First, we reconstructed and tested ancient forms of CD4 at two important nodes in ape speciation, both prior to the infection of chimpanzees and gorillas with these viruses. These ancestral CD4s fully supported entry of diverse SIV isolates related to the viruses that made this initial jump to apes. In stark contrast, modern chimpanzee and gorilla CD4 orthologs are more resistant to these viruses. To investigate how this resistance in CD4 was gained, we acquired CD4 gene sequences from 32 gorilla individuals of two species and identified alleles that encode 8 unique CD4 protein variants. Functional testing of these identified variant-specific differences in susceptibility to virus entry. By engineering single-point mutations from resistant gorilla CD4 variants into the permissive human CD4 receptor, we demonstrate that acquired substitutions in gorilla CD4 did convey resistance to virus entry. We provide a population genetic analysis to support the theory that selection is acting in favor of more and more resistant CD4 alleles in ape species harboring SIV endemically (gorillas and chimpanzees), but not in other ape species that lack SIV infections (bonobos and orangutans). Taken together, our results show that SIV has placed intense selective pressure on ape CD4, acting to propagate SIV-resistant alleles in chimpanzee and gorilla populations.

The Earliest Known Radiation of Pitheciine Primates

Two of the more interesting and controversial platyrrhine primate taxa from the Miocene of Patagonia are Soriacebus and Mazzonicebus. Although they are known basically from isolated teeth and partial mandibles and maxillae, their morphology is highly distinctive. Opinions about their phylogenetic relationships differ widely. We interpret these fossils as belonging to the lineage of the anatomically derived, living pitheciine seed-predators; others hold the view that they are stem platyrrhines with convergent adaptations with pitheciines (with the single exception of Proteropithecia among the Patagonian forms), somewhat distant relatives converging coincidently with pitheciines. Here we tested these hypotheses in two ways: (1) by summarizing a character analysis of taxonomically informative traits; (2) we implemented "blind" parsimony analyses using the software package TNT, including a combined matrix of both morphological and molecular data, and replication studies of other matrices. We make some criticisms on the applied methodology of Parsimony in our analysis. Soriacebus and Mazzonicebus resulted sister-taxa nested deeply within the pitheciid clade; thus, and according to our inferences, they are not stem platyrrhines. Most of the differences separating them from the younger and uniformly recognized pitheciine fossils Proteropithecia, Nuciruptor and Cebupithecia are explained as being of more primitive character states; the vast majority of resemblances and their broader functional patterns are definitively pitheciine, as typified by the living pitheciines (sakis and uakaris). We therefore found that none of the Miocene Patagonian genera treated here can be reliably interpreted as stem platyrrhines. Rather, they tend to ratify the Long Lineage Hypothesis.

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.

Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments

With the increasing availability of genomic data, biologists aim to find more accurate descriptions of evolutionary histories influenced by secondary contact, where diverging lineages reconnect before diverging again. Such reticulate evolutionary events can be more accurately represented in phylogenetic networks than in phylogenetic trees. Since the root location of phylogenetic networks cannot be inferred from biological data under several evolutionary models, we consider semi-directed (phylogenetic) networks: partially directed graphs without a root in which the directed edges represent reticulate evolutionary events. By specifying a known outgroup, the rooted topology can be recovered from such networks. We introduce the algorithm Squirrel (Semi-directed Quarnet-based Inference to Reconstruct Level-1 Networks) which constructs a semi-directed level-1 network from a full set of quarnets (four-leaf semi-directed networks). Our method also includes a heuristic to construct such a quarnet set directly from sequence alignments. We demonstrate Squirrel's performance through simulations and on real sequence data sets, the largest of which contains 29 aligned sequences close to 1.7 Mb long. The resulting networks are obtained on a standard laptop within a few minutes. Lastly, we prove that Squirrel is combinatorially consistent: given a full set of quarnets coming from a triangle-free semi-directed level-1 network, it is guaranteed to reconstruct the original network. Squirrel is implemented in Python, has an easy-to-use graphical user interface that takes sequence alignments or quarnets as input, and is freely available at https://github.com/nholtgrefe/squirrel.

DR5 is a restriction factor for human herpesviruses

Restriction factors are dominant proteins that target different essential steps of the viral life cycle; thus, these proteins provide an early line of defense against viruses. Here, we found that the internalization of DR5, an important receptor of the extrinsic apoptotic pathway, initiates apoptosis to inhibit Kaposi sarcoma-associated herpesvirus (KSHV) lytic replication. An evolutionary analysis of the DR5 sequence demonstrated that three amino acids underwent positive selection in primates. Notably, one of these positive selection sites, A62, is essential for the antiviral function of DR5 and is important for the binding of DR5 to its ligand, TNF-related apoptosis-inducing ligand. Moreover, DR5 exhibits broad antiviral activity against and inhibits various herpesviruses, including Epstein-Barr virus, herpes simplex virus type 1, and herpes simplex virus type 2. As a countermeasure, the KSHV K5 protein interacts with DR5 and promotes DR5 degradation through the lysosomal and proteasomal degradation pathways; lysine 245 of DR5 is essential for K5-induced DR5 degradation. These findings demonstrate that DR5 is a restriction factor for human herpesviruses.

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.

Assessing the Sociodemographic Factors Associated With Mycobacterium tuberculosis Complex Infection Among Free-Ranging Long-Tailed Macaques (Macaca fascicularis) in Thailand

The threat of disease transmission at the intersection of human-wildlife interfaces underscores the urgent need for detailed studies on the transmission of human-borne pathogens across species, especially among nonhuman primates in urban areas. This research focuses on the social and demographic determinants of Mycobacterium tuberculosis complex (MTBC) infection in free-ranging long-tailed macaques (Macaca fascicularis) in Thailand. Behavioral observations and noninvasive biological specimens (freshly defecated feces and rope-baited oral samples) were collected from 98 long-tailed macaques living in Wat Khao Thamon, southern Thailand, between August 2021 and February 2022. We detected the MTBC antigen using IS6110 nested-PCR method in 11 out of 98 monkeys (11.22%). Logistic GLMs revealed that the risk of MTBC acquisition was higher among macaques with frequent human-macaque interactions, whereas increased social grooming of conspecifics showed a nonsignificant trend toward reducing the risk. Our findings suggest that anthropogenic exposure increases the risk of MTBC infection among macaques, but this risk may be mitigated (socially buffered) by increased within-group affiliative interactions. More generally, the potential for increased disease prevalence in wildlife with frequent human interactions or reduced social buffering highlights the need to consider animal socio-demography when developing strategies to understand and prevent the transmission of diseases between humans and wildlife.

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.

getphylo: rapid and automatic generation of multi-locus phylogenetic trees

BACKGROUND

The increasing amount of genomic data calls for tools that can create genome-scale phylogenies quickly and efficiently. Existing tools rely on large reference databases or require lengthy de novo calculations to identify orthologues, meaning that they have long run times and are limited in their taxonomic scope. To address this, we created getphylo, a python tool for the rapid generation of phylogenetic trees de novo from annotated sequences.

RESULTS

We present getphylo (Genbank to Phylogeny), a tool that automatically builds phylogenetic trees from annotated genomes alone. Orthologues are identified heuristically by searching for singletons (single copy genes) across all input genomes and the phylogeny is inferred from a concatenated alignment of all coding sequences by maximum likelihood. We performed a thorough benchmarking of getphylo against two existing tools, autoMLST and GTDB-tk, to show that it can produce trees of comparable quality in a fraction of the time. We also demonstrate the flexibility of getphylo across four case studies including bacterial and eukaryotic genomes, and biosynthetic gene clusters.

CONCLUSIONS

getphylo is a quick and reliable tool for the automated generation of genome-scale phylogenetic trees. getphylo can produce phylogenies comparable to other software in a fraction of the time, without the need large local databases or intense computation. getphylo can rapidly identify orthologues from a wide variety of datasets regardless of taxonomic or genomic scope. The usability, speed, flexibility of getphylo makes it a valuable addition to the phylogenetics toolkit.

Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data

The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of population size using traditional census methods. Therefore, alternative estimates provided by population genetic inference are essential for yielding much needed information for conservation measures and for enabling ecological and evolutionary studies of this species. Here, we utilize genomic data from 17 individuals-including 5 newly sequenced, high-coverage genomes-to estimate this history. Essential to this estimation are recently published annotations of the aye-aye genome which allow for variation at putatively neutral genomic regions to be included in the estimation procedures, and regions subject to selective constraints, or in linkage to such sites, to be excluded owing to the biasing effects of selection on demographic inference. By comparing a variety of demographic estimation tools to develop a well-supported model of population history, we find strong support for two demes, separating northern Madagascar from the rest of the island. Additionally, we find that the aye-aye has experienced two severe reductions in population size. The first occurred rapidly, ∼3,000 to 5,000 years ago, and likely corresponded with the arrival of humans to Madagascar. The second occurred over the past few decades and is likely related to substantial habitat loss, suggesting that the species is still undergoing population decline and remains at great risk for extinction.

"Ontogenetic Scaling of the Primate Middle Ear"

The study of primate auditory morphology is a significant area of interest for comparative anatomists, given the phylogenetic relationships that link primate hearing and the morphology of these auditory structures. Extensive literature addresses the form-to-function relationship of the auditory system (outer, middle, and inner ear) in primates and, by extension, provides insight into the auditory system of extinct primates and even modern humans. We add to this literature by describing the ontogenetic trajectory of the middle ear cavity and ossicular chain (malleus, incus, and stapes) due to their critical role in relaying auditory stimuli for interpretation. We examined middle ear morphology in neonatal primates and adult primates using a taxonomically broad sample. We focused primarily on nocturnal primate taxa (Daubentonia, Loris, Galago, Aotus, and Tarsier), which are underrepresented in the literature. However, we also included three diurnal taxa (Macaca, Lemur, and Saguinus). Using 3D Slicer, we visualized middle ear structures in three dimensions using conventional micro CT data informed by diffusible iodine-based contrast-enhanced CT (diceCT) data. We illustrated how spatial relationships between otic elements, such as the various epitympanic sinuses of the middle ear and the auditory ossicles, vary throughout ontogeny. Our major findings include that the central tympanic cavity scaled with negative allometry in all taxa and that the accessory cavities scaled with isometry or positive allometry in most taxa. Despite these changes in chamber size, the size of the ear ossicles remained relatively consistent through ontogeny in most taxa. We confirmed our expectation that anthropoids exhibit an increase in the complexity of accessory cavities throughout ontogeny, mirroring the exponential pneumatization of the face in anthropoids. These findings provide an ontogenetic perspective and reveal further functional complexities of the middle ear as a conduit for sound proliferation and as a pressure regulator.

Primate conservation: A public issue?

Nonhuman primates (primates) are one of the most endangered mammalian taxa in the world. In the Global North, primates are considered exotic species and, as such, humans' impact on primate conservation and responsibility to protect primates is often ignored. This view differs from the spectrum of relations and attitudes of humans that live in connection to primates, which can include viewing these animals as culturally/religiously significant, cohabitors of forests, nuisances, or sources of protein. While conservationists argue that primates deserve our protection, the conservation crisis facing primates is rarely framed as a public issue, in contrast to other global crises, such as climate change. However, over half of the world's human population lives within 100 km of primate habitat. Thus, humans and primates share the same environments. We suggest leveraging a holistic approach, such as One Health, that considers the interconnectedness of primates, humans, and their shared environments, through the lens of public anthropology. By approaching primate conservation as an intersectional issue that affects and is affected by humans, researchers and conservationists can identify strategies that simultaneously protect primates and address global inequities that frequently affect people in primate range countries. Reflexive research practices further allow academics to consider the broader impact of their ecological research through means such as publicly accessible dissemination of results, equitable capacity-building of high-quality personnel in primate range countries, and social activism. The use of inter-, multi-, and transdisciplinary concepts and methodology can address the intersectional challenges associated with implementing ethical and sustainable primate conservation measures.

Translational Insights From Cell Type Variation Across Amygdala Subnuclei in Rhesus Monkeys and Humans

OBJECTIVE

Theories of amygdala function are central to our understanding of psychiatric and neurodevelopmental disorders. However, limited knowledge of the molecular and cellular composition of the amygdala impedes translational research aimed at developing new treatments and interventions. The aim of this study was to characterize and compare the composition of amygdala cells to help bridge the gap between preclinical models and human psychiatric and neurodevelopmental disorders.

METHODS

Tissue was dissected from multiple amygdala subnuclei in both humans (N=3, male) and rhesus macaques (N=3, male). Single-nucleus RNA sequencing was performed to characterize the transcriptomes of individual nuclei.

RESULTS

The results reveal substantial heterogeneity between regions, even when restricted to inhibitory or excitatory neurons. Consistent with previous work, the data highlight the complexities of individual marker genes for uniquely targeting specific cell types. Cross-species analyses suggest that the rhesus monkey model is well-suited to understanding the human amygdala, but also identify limitations. For example, a cell cluster in the ventral lateral nucleus of the amygdala (vLa) is enriched in humans relative to rhesus macaques. Additionally, the data describe specific cell clusters with relative enrichment of disorder-related genes. These analyses point to the human-enriched vLa cell cluster as relevant to autism spectrum disorder, potentially highlighting a vulnerability to neurodevelopmental disorders that has emerged in recent primate evolution. Further, a cluster of cells expressing markers for intercalated cells is enriched for genes reported in human genome-wide association studies of neuroticism, anxiety disorders, and depressive disorders.

CONCLUSIONS

Together, these findings shed light on the composition of the amygdala and identify specific cell types that can be prioritized in basic science research to better understand human psychopathology and guide the development of potential treatments.

Variation in Molar Size and Proportions in the Hominid Lineage: An Inter- and Intraspecific Approach

The implications of the inhibitory cascade (IC) model in dental diversification have been primarily studied at an interspecific or higher level. In contrast, the study of organisms with recent evolutionary divergence or at an interpopulational scale is still very limited. Here, we assess the effect of changes in molar size and the ratio of local activators to inhibitors on molar proportions based on a compilation of data of crown diameters of the first, second, and third lower and upper molars of extinct and extant hominids and modern human populations. The analysis of allometric changes between the size of each tooth and the size of the molar row shows a negative allometry in first molars (M1), isometric changes in second molars (M2), and a positive allometry in third molars (M3) in both hominin phylogeny and modern human populations. On the other hand, the proportions of lower and upper molars of several hominid species fall outside the morphospace defined by the IC model, while most of the modern human populations fall within the morphospace defined by the model as M1 > M2 > M3. We conclude that there is a phylogenetic structuring for molar size, particularly in the maxilla, with a trend toward mesial-to-distal reduction in the molar row area accompanied by allometric changes. Our findings also show the limitations of the IC model for explaining molar proportions in primates, particularly the variation in the relative size at the interspecific scale in the hominid lineage.

Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data

The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of population size using traditional census methods. Therefore, alternative estimates provided by population genetic inference are essential for yielding much needed information for conservation measures and for enabling ecological and evolutionary studies of this species. Here, we utilize genomic data from 17 unrelated individuals - including 5 newly sequenced, high-coverage genomes - to estimate this history. Essential to this estimation are recently published annotations of the aye-aye genome which allow for variation at putatively neutral genomic regions to be included in the estimation procedures, and regions subject to selective constraints, or in linkage to such sites, to be excluded owing to the biasing effects of selection on demographic inference. By comparing a variety of demographic estimation tools to develop a well-supported model of population history, we find strong support for the species to consist of two demes, separating northern Madagascar from the rest of the island. Additionally, we find that the aye-aye has experienced two severe reductions in population size. The first occurred rapidly, approximately 3,000 to 5,000 years ago, and likely corresponded with the arrival of humans to Madagascar. The second occurred over the past few decades and is likely related to substantial habitat loss, suggesting that the species is still undergoing population decline and remains at great risk for extinction.

Contagious yawning and scratching in captive lemurs

Behavioral contagion is thought to play a significant role in social synchronization and coordination across animal taxa. While there is extensive evidence of behavioral contagion in Haplorrhines (i.e. monkeys and apes), limited research exists in Strepsirrhines (i.e. lemurs). Here, we aimed to investigate the presence of contagious yawning and scratching in two captive groups of black-and-white ruffed lemurs (Varecia variegata) (N = 4) and red ruffed lemurs (Varecia rubra) (N = 4), and further test whether behavioral contagion is modulated by the model's social integration in the group. We conducted all occurrence sampling to examine whether individuals observing a yawning or scratching event (i.e. trigger event) were more likely to yawn or scratch in the following 2 min, as compared to individuals who did not observe it. We ran generalized linear mixed models and found that the likelihood of yawning and scratching was higher for subjects observing the trigger event than for subjects who did not observe the event, although the model's social integration had no modulating effect on the probability of showing behavioral contagion. Our findings represent the first evidence of behavioral contagion in this genus and contribute to shed light on the distribution and the possible adaptive function of this phenomenon in primates.

Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213

Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition receptors to detect cognate pathogens while ignoring others. How the E3 ubiquitin ligase RNF213 can respond to phylogenetically distant pathogens, including Gram-negative Salmonella, Gram-positive Listeria, and eukaryotic Toxoplasma, remains unknown. Here we report that the evolutionary history of RNF213 is indicative of repeated adaptation to diverse pathogen target structures, especially in and around its newly identified CBM20 carbohydrate-binding domain, which we have resolved by cryo-EM. We find that RNF213 forms coats on phylogenetically distant pathogens. ATP hydrolysis by RNF213's dynein-like domain is essential for coat formation on all three pathogens studied as is RZ finger-mediated E3 ligase activity for bacteria. Coat formation is not diffusion-limited but instead relies on rate-limiting initiation events and subsequent cooperative incorporation of further RNF213 molecules. We conclude that RNF213 responds to evolutionarily distant pathogens through enzymatically amplified cooperative recruitment.

Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics

Biological sex is key information for archeological and forensic studies, which can be determined by proteomics. However, the lack of a standardized approach for fast and accurate sex identification currently limits the reach of proteomics applications. Here, we introduce a streamlined mass spectrometry (MS)-based workflow for the determination of biological sex using human dental enamel. Our approach builds on a minimally invasive sampling strategy by acid etching, a rapid online liquid chromatography (LC) gradient coupled to a high-resolution parallel reaction monitoring (PRM) assay allowing for a throughput of 200 samples per day (SPD) with high quantitative performance enabling confident identification of both males and females. Additionally, we developed a streamlined data analysis pipeline and integrated it into a Shiny interface for ease of use. The method was first developed and optimized using modern teeth and then validated in an independent set of deciduous teeth of known sex. Finally, the assay was successfully applied to archeological material, enabling the analysis of over 300 individuals. We demonstrate unprecedented performance and scalability, speeding up MS analysis by 10-fold compared to conventional proteomics-based sex identification methods. This work paves the way for large-scale archeological or forensic studies enabling the investigation of entire populations rather than focusing on individual high-profile specimens. Data are available via ProteomeXchange with the identifier PXD049326.

A transposable element prevents severe hemophilia B and provides insights into the evolution of new- and old world primates

Alu-elements comprise a large part of the human genome and some insertions have been shown to cause diseases. Here, we illuminate the protective role of an Alu-element in the 3'UTR of the human Factor 9 gene and its ability to ameliorate a poly(A) site mutation in a hemophilia B patient, preventing him from developing a severe disease. Using a minigene, we examined the disease-causing mutation and the modifying effect of the transposon in cellulo. Further, we simulated evolutionary scenarios regarding alternative polyadenylation before and after Alu insertion. A sequence analysis revealed that Old World monkeys displayed a highly conserved polyadenylation sites in this Alu-element, whereas New World monkeys lacked this motif, indicating a selective pressure. We conclude that this transposon has inserted shortly before the separation of Old and New World monkeys and thus also serves as a molecular landmark in primate evolution.

Systematic review and meta-analysis on seroprevalence of leptospirosis in non-human primates worldwide

Leptospirosis is a zoonotic disease whose transmission is linked to multiple factors involving the interface between animals, humans, and the environment. This disease is of great importance for public health, as it profoundly affects the health aspects of the population and animals. Considering the importance of non-human primates in this epidemiological chain, the objective of this research was to conduct a systematic literature review with meta-analysis, providing information on leptospirosis in non-human primates (NHPs) and an update on the infection situation in Brazil and other countries. Thus, a search was performed in five databases, initially finding 3332 studies, of which 32 met the eligibility criteria and were used for the systematic review. According to them, the most prevalent serogroup in non-human primates was Icterohaemorrhagiae, which is adapted to rodents as primary hosts. A wide distribution of the infection was found in the regions of both wild and captive animals. Through meta-analysis, the seroprevalence rate of leptospirosis in non-human primates was 27.21% (CI 17.97-38.95%). Cochran's Q test (p < 0.01) identified heterogeneity between studies, classified as high by the Higgins and Thompson test (I2 = 92.4%). Therefore, seroepidemiological and Leptospira isolation studies in non-human primates are important to investigate and monitor the suspected impact of these species as maintainers or transmitters of the pathogen to humans and other wild and domestic animals, in addition to demonstrating the need for standardization related to control and prevention measures.

Gelada genomes highlight events of gene flow, hybridisation and local adaptation that track past climatic changes

Theropithecus gelada, the last surviving species of this genus, occupy a unique and highly specialised ecological niche in the Ethiopian highlands. A subdivision into three geographically defined populations (Northern, Central and Southern) has been tentatively proposed for this species on the basis of genetic analyses, but genomic data have been investigated only for two of these groups (Northern and Central). Here we combined newly generated whole genome sequences of individuals sampled from the population living south of the East Africa Great Rift Valley with available data from the other two gelada populations to reconstruct the evolutionary history of the species. Integrating genomic and paleoclimatic data we found that gene-flow across populations and with Papio species tracked past climate changes. The isolation and climatic conditions experienced by Southern geladas during the Holocene shaped local diversity and generated diet-related genomic signatures.

The evolution of gestation length in eutherian mammals

Eutherian mammals exhibit considerable variation in their gestation lengths, which has traditionally been linked to variation in other traits, including body mass and lifespan. To understand how gestation length variation, including its association with body mass and lifespan variation, changed over mammalian evolution, we conducted phylogeny-informed analyses of 845 representative extant species. We found that gestation length substantially differed in both whether and how strongly it was associated with body mass and lifespan across mammals. For example, gestation length was not associated with lifespan or body mass in Chiroptera and Cetacea but was strongly associated only with body mass in Carnivora. We also identified 52 evolutionary shifts in gestation length variation across the mammal phylogeny and 14 shifts when we jointly considered variation of all three traits; six shifts were shared. Notably, two of these shifts, both positive, occurred at the roots of Cetacea and Pinnipedia, respectively, coinciding with the transition of these clades to the marine environment, whereas a negative shift occurred at the root of Chiroptera, coinciding with the evolution of flight in this clade. These results suggest that the relationship between gestation length and the two other traits has varied substantially across mammalian phylogeny.

The Quest for an Integrated Set of Neural Mechanisms Underlying Object Recognition in Primates

Inferences made about objects via vision, such as rapid and accurate categorization, are core to primate cognition despite the algorithmic challenge posed by varying viewpoints and scenes. Until recently, the brain mechanisms that support these capabilities were deeply mysterious. However, over the past decade, this scientific mystery has been illuminated by the discovery and development of brain-inspired, image-computable, artificial neural network (ANN) systems that rival primates in these behavioral feats. Apart from fundamentally changing the landscape of artificial intelligence, modified versions of these ANN systems are the current leading scientific hypotheses of an integrated set of mechanisms in the primate ventral visual stream that support core object recognition. What separates brain-mapped versions of these systems from prior conceptual models is that they are sensory computable, mechanistic, anatomically referenced, and testable (SMART). In this article, we review and provide perspective on the brain mechanisms addressed by the current leading SMART models. We review their empirical brain and behavioral alignment successes and failures, discuss the next frontiers for an even more accurate mechanistic understanding, and outline the likely applications.

Low-cost, portable, easy-to-use kiosks to facilitate home-cage testing of nonhuman primates during vision-based behavioral tasks

Nonhuman primates (NHPs), especially rhesus macaques, have significantly contributed to our understanding of the neural computations underlying human vision. Besides the established homologies in the visual brain areas between these species and our ability to probe detailed neural mechanisms in monkeys at multiple scales, NHPs' ability to perform human-like visual behavior makes them an extremely appealing animal model of human vision. Traditionally, such behavioral studies have been conducted in controlled laboratory settings, offering experimenters tight control over variables like luminance, eye movements, and auditory interference. However, in-lab experiments have several constraints, including limited experimental time, the need for dedicated human experimenters, additional lab space requirements, invasive surgeries for headpost implants, and extra time and training for chairing and head restraints. To overcome these limitations, we propose adopting home-cage behavioral training and testing of NHPs, enabling the administration of many vision-based behavioral tasks simultaneously across multiple monkeys with reduced human personnel requirements, no NHP head restraint, and monkeys' unrestricted access to experiments. In this article, we present a portable, low-cost, easy-to-use kiosk system developed to conduct home-cage vision-based behavioral tasks in NHPs. We provide details of its operation and build to enable more open-source development of this technology. Furthermore, we present validation results using behavioral measurements performed in the lab and in NHP home cages, demonstrating the system's reliability and potential to enhance the efficiency and flexibility of NHP behavioral research.NEW & NOTEWORTHY Training nonhuman primates (NHPs) for vision-based behavioral tasks in a laboratory setting is a time-consuming process and comes with many limitations. To overcome these challenges, we have developed an affordable, open-source, wireless, touchscreen training system that can be placed in the NHPs' housing environment. This system enables NHPs to work at their own pace. It provides a platform to implement continuous behavioral training protocols without major experimenter intervention and eliminates the need for other standard practices like NHP chair training, collar placement, and head restraints. Hence, these kiosks ultimately contribute to animal welfare and therefore better-quality neuroscience in the long run. In addition, NHPs quickly learn complex behavioral tasks using this system, making it a promising tool for wireless electrophysiological research in naturalistic, unrestricted environments to probe the relation between brain and behavior.

The Risk of Virus Emergence in South America: A Subtle Balance Between Increasingly Favorable Conditions and a Protective Environment

South American ecosystems host astonishing biodiversity, with potentially great richness in viruses. However, these ecosystems have not yet been the source of any widespread, epidemic viruses. Here we explore a set of putative causes that may explain this apparent paradox. We discuss that human presence in South America is recent, beginning around 14,000 years ago; that few domestications of native species have occurred; and that successive immigration events associated with Old World virus introductions reduced the likelihood of spillovers and adaptation of local viruses into humans. Also, the diversity and ecological characteristics of vertebrate hosts might serve as protective factors. Moreover, although forest areas remained well preserved until recently, current brutal, sudden, and large-scale clear cuts through the forest have resulted in nearly no ecotones, which are essential for creating an adaptive gradient of microbes, hosts, and vectors. This may be temporarily preventing virus emergence. Nevertheless, the mid-term effect of such drastic changes in habitats and landscapes, coupled with explosive urbanization and climate changes, must not be overlooked by health authorities.

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.

Evolution of threat response-related polymorphisms at the SLC6A4 locus in callitrichid primates

Variation in an upstream repetitive region at the SLC6A4 locus, which encodes the serotonin transporter, is associated with anxiety-related behaviour in a few primate species, including humans and rhesus macaques, and has been suggested to be related to ecological adaptability among macaques. In this study, we investigate evolution of SLC6A4 polymorphisms associated with anxiety-related behaviour in common marmosets (Callithrix jacchus). Assaying variation in the SLC6A4 repeat region across 14 species in eight genera of callitrichid primates (marmosets and tamarins), we find large interspecific variation in the number of repeats present (24-43). The black tufted-ear marmoset (C. penicillata) has sequence polymorphisms similar to those found in the common marmoset, which is its sister species, and no other species has intraspecific variation at these sites. We conclude that, similar to humans and macaques, the functional polymorphism at SLC6A4 in common marmosets has a recent evolutionary origin, and that the anxiety-related allele is evolutionarily derived. Common/black tufted-ear marmosets and rhesus/bonnet macaques share high ecological adaptability and behavioural flexibility that we propose may be related to the maintenance of the polymorphism.

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.

Examining infantile facial features and their influence on caretaking behaviors in free-ranging Japanese macaques (Macaca fuscata)

Facial features of immature individuals play a pivotal role in eliciting caretaking behaviors in humans. It has been posited that non-human animals share particular infantile facial features with humans, which can elicit caregivers' attention and caretaking behaviors. Nevertheless, the empirical examination of this hypothesis is extremely limited. In this study, we investigated infantile facial features in Japanese macaques (Macaca fuscata), their developmental processes, and their correlation with caretaking and infant behaviors, based on 470 facial photographs from one free-ranging group. We measured the size of facial parts and evaluated these features using non-contact procedures with the animals. The results indicated that, although some partial species differences were observed, the infantile facial features in Japanese macaques were broadly consistent with those previously observed in humans and great apes. Furthermore, half of the infant subjects displayed non-linear developmental trajectories of infantile faces, similar to those suggested in humans. However, unlike previous studies in humans, infantile faces were not significantly associated with maternal or non-maternal caretaking behaviors, nor were their developmental changes correlated with infant behavioral development. These findings indicate that while many aspects of infantile facial features are shared among particular primates, humans may have evolved a uniquely elevated preference for selecting such features among the primate lineage.

Cold-induced expression of a truncated adenylyl cyclase 3 acts as rheostat to brown fat function

Promoting brown adipose tissue (BAT) activity innovatively targets obesity and metabolic disease. While thermogenic activation of BAT is well understood, the rheostatic regulation of BAT to avoid excessive energy dissipation remains ill-defined. Here, we demonstrate that adenylyl cyclase 3 (AC3) is key for BAT function. We identified a cold-inducible promoter that generates a 5' truncated AC3 mRNA isoform (Adcy3-at), whose expression is driven by a cold-induced, truncated isoform of PPARGC1A (PPARGC1A-AT). Male mice lacking Adcy3-at display increased energy expenditure and are resistant to obesity and ensuing metabolic imbalances. Mouse and human AC3-AT are retained in the endoplasmic reticulum, unable to translocate to the plasma membrane and lack enzymatic activity. AC3-AT interacts with AC3 and sequesters it in the endoplasmic reticulum, reducing the pool of adenylyl cyclases available for G-protein-mediated cAMP synthesis. Thus, AC3-AT acts as a cold-induced rheostat in BAT, limiting adverse consequences of cAMP activity during chronic BAT activation.

Relationships between Bitter Taste Receptor Gene Evolution, Diet, and Gene Repertoire in Primates

Bitter taste perception plays a critical role in deterring animals from consuming harmful and toxic substances. To characterize the evolution of primate Tas2r, test the generality of Tas2r duplication in Cercopithecidae species, and examine whether dietary preferences have shaped the Tas2r repertoire of primate species, we identified Tas2r in the genomes of 35 primate species, including 16 Cercopithecidae, 6 Hominidae, 4 Cebidae, 3 Lemuridae, and 6 other species. The results showed that the total number of primate Tas2r ranged from 27 to 51, concentrating on 2 to 4 scaffolds of each species. Closely related genes were tandemly duplicated in the same scaffold. Phylogenetic construction revealed that Tas2r can be divided into 21 clades, including anthropoid-, Strepsirrhini-, and Cercopithecidae-specific Tas2r duplications. Phylogenetically independent contrast analysis revealed that the number of intact Tas2r significantly correlated with feeding preferences. Altogether, our data support diet as a driver of primate Tas2r evolution, and Cercopithecidae species have developed some specific Tas2r duplication during evolution. These results are probably because most Cercopithecidae species feed on plants containing many toxins, and it is necessary to develop specialized Tas2r to protect them from poisoning.

Description and taxonomic assessment of fossil Cercopithecidae from the Pliocene Galili Formation (Ethiopia)

The Mount Galili Formation in the Afar region, Ethiopia, samples a critical time in hominin evolution, 4.4 to 3.8 Ma, documenting the last appearance of Ardipithecus and the origin of Australopithecus. This period is also important in the evolution of cercopithecids, especially the origin of Theropithecus in general and Theropithecus oswaldi lineage in particular. Galili has provided a total of 655 cercopithecid specimens that include crania, mandibles, isolated teeth and postcrania. All the fossils were recovered from the Lasdanan (5.3-4.43 Ma), Dhidinley (4.43-3.9 Ma) and Shabeley Laag (∼3.92-3.8 Ma) Members. Here, we described and analyzed 362 fossils employing both qualitative and quantitative methods. Descriptions of the material were supplemented with dental metrics and cranial shape analysis using three-dimensional geometric morphometrics. Results indicate the presence of at least six cercopithecid taxa: Theropithecus oswaldi serengetensis (n = 28), Theropithecus sp. (n = 2), three non-Theropithecus papionin groups (n = 134) and one colobine-size group (n = 58). The T. o. serengetensis represents the earliest form of the lineage, documented from ∼3.9 Ma Galili sediments. The three Galili papionins include a smaller taxon, a medium-sized taxon comparable to Pliopapio alemui and a large papionin overlapping in size with Soromandrillus, Gorgopithecus and Dinopithecus. The majority of Galili colobines have closest affinities to Kuseracolobus aramisi and some overlap with other taxa. Papionins dominate the Galili cercopithecid collection, although colobines are still fairly common (approximately 25% of the sample). Thus, Galili sample is like Kanapoi (4.2-4.1 Ma) and Gona (5.2-3.9 Ma) localities but distinct from Aramis, suggesting paleoecological similarity to the former sites. On the other hand, Theropithecus is less abundant at Galili than geologically younger Hadar (3.4-3.2 Ma) and Woranso-Mille (3.8-3.6 Ma) sites. Whether this difference is due to sampling, time or landscape variation requires further investigation.

An evolutionary timeline of the oxytocin signaling pathway

Oxytocin is a neuropeptide associated with both psychological and somatic processes like parturition and social bonding. Although oxytocin homologs have been identified in many species, the evolutionary timeline of the entire oxytocin signaling gene pathway has yet to be described. Using protein sequence similarity searches, microsynteny, and phylostratigraphy, we assigned the genes supporting the oxytocin pathway to different phylostrata based on when we found they likely arose in evolution. We show that the majority (64%) of genes in the pathway are 'modern'. Most of the modern genes evolved around the emergence of vertebrates or jawed vertebrates (540 - 530 million years ago, 'mya'), including OXTR, OXT and CD38. Of those, 45% were under positive selection at some point during vertebrate evolution. We also found that 18% of the genes in the oxytocin pathway are 'ancient', meaning their emergence dates back to cellular organisms and opisthokonta (3500-1100 mya). The remaining genes (18%) that evolved after ancient and before modern genes were classified as 'medium-aged'. Functional analyses revealed that, in humans, medium-aged oxytocin pathway genes are highly expressed in contractile organs, while modern genes in the oxytocin pathway are primarily expressed in the brain and muscle tissue.

Viral-based animal models in polyglutamine disorders

Polyglutamine disorders are a complex group of incurable neurodegenerative disorders caused by an abnormal expansion in the trinucleotide cytosine-adenine-guanine tract of the affected gene. To better understand these disorders, our dependence on animal models persists, primarily relying on transgenic models. In an effort to complement and deepen our knowledge, researchers have also developed animal models of polyglutamine disorders employing viral vectors. Viral vectors have been extensively used to deliver genes to the brain, not only for therapeutic purposes but also for the development of animal models, given their remarkable flexibility. In a time- and cost-effective manner, it is possible to use different transgenes, at varying doses, in diverse targeted tissues, at different ages, and in different species, to recreate polyglutamine pathology. This paper aims to showcase the utility of viral vectors in disease modelling, share essential considerations for developing animal models with viral vectors, and provide a comprehensive review of existing viral-based animal models for polyglutamine disorders.

A conserved NR5A1-responsive enhancer regulates SRY in testis-determination

The Y-linked SRY gene initiates mammalian testis-determination. However, how the expression of SRY is regulated remains elusive. Here, we demonstrate that a conserved steroidogenic factor-1 (SF-1)/NR5A1 binding enhancer is required for appropriate SRY expression to initiate testis-determination in humans. Comparative sequence analysis of SRY 5' regions in mammals identified an evolutionary conserved SF-1/NR5A1-binding motif within a 250 bp region of open chromatin located 5 kilobases upstream of the SRY transcription start site. Genomic analysis of 46,XY individuals with disrupted testis-determination, including a large multigenerational family, identified unique single-base substitutions of highly conserved residues within the SF-1/NR5A1-binding element. In silico modelling and in vitro assays demonstrate the enhancer properties of the NR5A1 motif. Deletion of this hemizygous element by genome-editing, in a novel in vitro cellular model recapitulating human Sertoli cell formation, resulted in a significant reduction in expression of SRY. Therefore, human NR5A1 acts as a regulatory switch between testis and ovary development by upregulating SRY expression, a role that may predate the eutherian radiation. We show that disruption of an enhancer can phenocopy variants in the coding regions of SRY that cause human testis dysgenesis. Since disease causing variants in enhancers are currently rare, the regulation of gene expression in testis-determination offers a paradigm to define enhancer activity in a key developmental process.

Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses

Simian immunodeficiency viruses (SIVs) comprise a large group of primate lentiviruses that endemically infect African monkeys. HIV-1 spilled over to humans from this viral reservoir, but the spillover did not occur directly from monkeys to humans. Instead, a key event was the introduction of SIVs into great apes, which then set the stage for infection of humans. Here, we investigate the role of the lentiviral entry receptor, CD4, in this key and fateful event in the history of SIV/HIV emergence. First, we reconstructed and tested ancient forms of CD4 at two important nodes in ape speciation, both prior to the infection of chimpanzees and gorillas with these viruses. These ancestral CD4s fully supported entry of diverse SIV isolates related to the viruses that made this initial jump to apes. In stark contrast, modern chimpanzee and gorilla CD4 orthologs are more resistant to these viruses. To investigate how this resistance in CD4 was gained, we acquired CD4 gene sequences from 32 gorilla individuals of two species, and identified alleles that encode 8 unique CD4 protein variants. Functional testing of these identified variant-specific differences in susceptibility to virus entry. By engineering single point mutations from resistant gorilla CD4 variants into the permissive human CD4 receptor, we demonstrate that acquired substitutions in gorilla CD4 did convey resistance to virus entry. We provide a population genetic analysis to support the theory that selection is acting in favor of more and more resistant CD4 alleles in ape species harboring SIV endemically (gorillas and chimpanzees), but not in other ape species that lack SIV infections (bonobos and orangutans). Taken together, our results show that SIV has placed intense selective pressure on ape CD4, acting to propagate SIV-resistant alleles in chimpanzee and gorilla populations.

Attention-sensitive signalling by 7- to 20-month-old infants in a comparative perspective

Attention-sensitive signalling is the pragmatic skill of signallers who adjust the modality of their communicative signals to their recipient's attention state. This study provides the first comprehensive evidence for its onset and development in 7-to 20-month-olds human infants, and underlines its significance for language acquisition and evolutionary history. Mother-infant dyads (N = 30) were studied in naturalistic settings, sampled according to three developmental periods (in months); [7-10], [11-14], and [15-20]. Infant's signals were classified by dominant perceptible sensory modality and proportions compared according to their mother's visual attention, infant-directed speech and tactile contact. Maternal visual attention and infant-directed speech were influential on the onset and steepness of infants' communicative adjustments. The ability to inhibit silent-visual signals towards visually inattentive mothers (unimodal adjustment) predated the ability to deploy audible-or-contact signals in this case (cross-modal adjustment). Maternal scaffolding of infant's early pragmatic skills through her infant-directed speech operates on the facilitation of infant's unimodal adjustment, the preference for oral over gestural signals, and the audio-visual combinations of signals. Additionally, breakdowns in maternal visual attention are associated with increased use of the audible-oral modality/channel. The evolutionary role of the sharing of attentional resources between parents and infants into the emergence of modern language is discussed.

Structurally divergent and recurrently mutated regions of primate genomes

We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.

Diverse cytomegalovirus US11 antagonism and MHC-A evasion strategies reveal a tit-for-tat coevolutionary arms race in hominids

Recurrent, ancient arms races between viruses and hosts have shaped both host immunological defense strategies as well as viral countermeasures. One such battle is waged by the glycoprotein US11 encoded by the persisting human cytomegalovirus. US11 mediates degradation of major histocompatibility class I (MHC-I) molecules to prevent CD8+ T-cell activation. Here, we studied the consequences of the arms race between US11 and primate MHC-A proteins, leading us to uncover a tit-for-tat coevolution and its impact on MHC-A diversification. We found that US11 spurred MHC-A adaptation to evade viral antagonism: In an ancestor of great apes, the MHC-A A2 lineage acquired a Pro184Ala mutation, which confers resistance against the ancestral US11 targeting strategy. In response, US11 deployed a unique low-complexity region (LCR), which exploits the MHC-I peptide loading complex to target the MHC-A2 peptide-binding groove. In addition, the global spread of the human HLA-A*02 allelic family prompted US11 to employ a superior LCR strategy with an optimally fitting peptide mimetic that specifically antagonizes HLA-A*02. Thus, despite cytomegaloviruses low pathogenic potential, the increasing commitment of US11 to MHC-A has significantly promoted diversification of MHC-A in hominids.

DNA methylation and transcriptome analysis reveal epigenomic differences among three macaque species

Macaques (genus Macaca) are the most widely distributed non-human primates, and their evolutionary history, gene expression profiles, and genetic differences have been extensively studied. However, the DNA methylomes of macaque species are not available in public databases, which hampers understanding of epigenetic differences among macaque species. Epigenetic modifications can potentially affect development, physiology, behavior, and evolution. Here, we investigated the methylation patterns of the Tibetan macaque (M. thibetana; TM), Chinese rhesus macaque (M. mulatta lasiota; CR), and crab-eating macaque (M. fascicularis; CE) through whole-genome bisulfite sequencing from peripheral blood. We compared genome-wide methylation site information for the three species. We identified 12,128 (CR vs. CE), 59,165 (CR vs. TM), and 39,751 (CE vs. TM) differentially methylated regions (DMRs) in the three macaques. Furthermore, we obtained the differentially expressed genes (DEGs) among the three macaque species. The differences between CR and CE were smaller at both the methylome and transcriptome levels than compared with TM (CR vs. TM and CE vs. TM). We also found a change in the density of single nucleotide mutations in DMRs relative to their flanking regions, indicating a potential mechanism through which genomic alterations may modulate methylation landscapes, thereby influencing the transcriptome. Functional enrichment analyses showed the DMR-related genes were enriched in developmental processes and neurological functions, such as the growth hormone-related pathway, insulin secretion pathway, thyroid hormone synthesis pathway, morphine addiction, and GABAergic synapses. These differences may be associated with variations in physiology and habitat among the macaques. Our study provides one of the first genome-wide comparisons of genetic, gene expression, and epigenetic variations across different macaques. Our results should facilitate further research on comparative genomic and genetic differences in macaque species.

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites

Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.

Tempo and mode of gene expression evolution in the brain across primates

Primate evolution has led to a remarkable diversity of behavioral specializations and pronounced brain size variation among species (Barton, 2012; DeCasien and Higham, 2019; Powell et al., 2017). Gene expression provides a promising opportunity for studying the molecular basis of brain evolution, but it has been explored in very few primate species to date (e.g. Khaitovich et al., 2005; Khrameeva et al., 2020; Ma et al., 2022; Somel et al., 2009). To understand the landscape of gene expression evolution across the primate lineage, we generated and analyzed RNA-seq data from four brain regions in an unprecedented eighteen species. Here, we show a remarkable level of variation in gene expression among hominid species, including humans and chimpanzees, despite their relatively recent divergence time from other primates. We found that individual genes display a wide range of expression dynamics across evolutionary time reflective of the diverse selection pressures acting on genes within primate brain tissue. Using our samples that represent a 190-fold difference in primate brain size, we identified genes with variation in expression most correlated with brain size. Our study extensively broadens the phylogenetic context of what is known about the molecular evolution of the brain across primates and identifies novel candidate genes for the study of genetic regulation of brain evolution.

Strongyloides in non-human primates: significance for public health control

Primates are an important source of infectious disease in humans. Strongyloidiasis affects an estimated 600 million people worldwide, with a global distribution and hotspots of infection in tropical and subtropical regions. Recently added to the list of neglected tropical diseases, global attention has been demanded in the drive for its control. Through a literature review of Strongyloides in humans and non-human primates (NHP), we analysed the most common identification methods and gaps in knowledge about this nematode genus. The rise of molecular-based methods for Strongyloides detection is evident in both humans and NHP and provides an opportunity to analyse all data available from primates. Dogs were also included as an important host species of Strongyloides and a potential bridge host between humans and NHP. This review highlights the lack of molecular data across all hosts-humans, NHP and dogs-with the latter highly underrepresented in the database. Despite the cosmopolitan nature of Strongyloides, there are still large gaps in our knowledge for certain species when considering transmission and pathogenicity. We suggest that a unified approach to Strongyloides detection be taken, with an optimized, repeatable molecular-based method to improve our understanding of this parasitic infection. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Intrageneric taxonomic distinction based on morphological variation in the macaque (Macaca) skeleton

Taxonomic classification is important for understanding the natural world, yet current methods for species assessment often focus on craniodental morphology rather than the entire skeleton. Moreover, it is currently unknown how much variation could, or should, exist intragenerically. Here, we tested whether taxonomy can be accurately predicted based on patterns of morphological variation in macaques (H1 ) and whether postcranial bones reflect subgeneric macaque taxonomy similarly, or better, than the cranium (H2 ). Data included 3D scans of cranial and postcranial bones for eight macaque species (Macaca arctoides, Macaca fascicularis, Macaca fuscata, Macaca mulatta, Macaca nemestrina, Macaca nigra, Macaca radiata, and Macaca sylvanus). Fixed anatomical and semilandmarks were applied to scans of eight skeletal elements (crania = 45; mandible = 31; scapula = 66; humerus = 38; radius = 33; os coxa = 28; femur = 40; tibia = 40). For each skeletal element, regression analyses were performed to minimize the effects of sexual dimorphism. Between-groups principal components analysis was used to visualize the major patterns of among-species morphological variation, while the strength of correct taxon classification was measured with discriminant function analysis. Results suggested accepting the alternate hypothesis that different macaque species can be distinguished morphologically. Both cranial and many postcranial elements appeared to possess a taxonomic signal, and the limb bones-especially the upper limb-are reported to be more useful for taxonomic assessment than previously realized. Theoretically, certain behaviors and/or ecogeographical factors, as well as phylogeny, influenced skeletal morphology in macaques, likely contributing to taxonomic distinctions among different species.

Fetal head-down posture may explain the rapid brain evolution in humans and other primates: An interpretative review

Evolutionary cerebrovascular consequences of upside-down postural verticality of the anthropoid fetus have been largely overlooked in the literature. This working hypothesis-based report provides a literature interpretation from an aspect that the rapid evolution of the human brain has been promoted by fetal head-down position due to maternal upright and semi-upright posture. Habitual vertical torso posture is a feature not only of humans, but also of monkeys and non-human apes that spend considerable time in a sitting position. Consequently, the head-down position of the fetus may have caused physiological craniovascular hypertension that stimulated expansion of the intracranial vessels and acted as an epigenetic physiological stress, which enhanced neurogenesis and eventually, along with other selective pressures, led to the progressive growth of the anthropoid brain and its organization. This article collaterally opens a new insight into the conundrum of high cephalopelvic proportions (i.e., the tight fit between the pelvic birth canal and fetal head) in phylogenetically distant lineages of monkeys, lesser apes, and humans. Low cephalopelvic proportions in non-human great apes could be accounted for by their energetically efficient horizontal nest-sleeping and consequently by their larger body mass compared to monkeys and lesser apes that sleep upright. One can further hypothesize that brain size varies in anthropoids according to the degree of exposure of the fetus to postural verticality. The supporting evidence for this postulation includes a finding that in fossil hominins cerebral blood flow rate increased faster than brain volume. This testable hypothesis opens a perspective for research on fetal postural cerebral hemodynamics.

A Comparative Perspective on the Cerebello-Cerebral System and Its Link to Cognition

The longstanding idea that the cerebral cortex is the main neural correlate of human cognition can be elaborated by comparative analyses along the vertebrate phylogenetic tree that support the view that the cerebello-cerebral system is suited to support non-motor functions more generally. In humans, diverse accounts have illustrated cerebellar involvement in cognitive functions. Although the neocortex, and its transmodal association cortices such as the prefrontal cortex, have become disproportionately large over primate evolution specifically, human neocortical volume does not appear to be exceptional relative to the variability within primates. Rather, several lines of evidence indicate that the exceptional volumetric increase of the lateral cerebellum in conjunction with its connectivity with the cerebral cortical system may be linked to non-motor functions and mental operation in primates. This idea is supported by diverging cerebello-cerebral adaptations that potentially coevolve with cognitive abilities across other vertebrates such as dolphins, parrots, and elephants. Modular adaptations upon the vertebrate cerebello-cerebral system may thus help better understand the neuroevolutionary trajectory of the primate brain and its relation to cognition in humans. Lateral cerebellar lobules crura I-II and their reciprocal connections to the cerebral cortical association areas appear to have substantially expanded in great apes, and humans. This, along with the notable increase in the ventral portions of the dentate nucleus and a shift to increased relative prefrontal-cerebellar connectivity, suggests that modular cerebellar adaptations support cognitive functions in humans. In sum, we show how comparative neuroscience provides new avenues to broaden our understanding of cerebellar and cerebello-cerebral functions in the context of cognition.

Auditory thresholds compatible with optimal speech reception likely evolved before the human-chimpanzee split

The anatomy of the auditory region of fossil hominins may shed light on the emergence of human spoken language. Humans differ from other great apes in several features of the external, middle and inner ear (e.g., short external ear canal, small tympanic membrane, large oval window). However, the functional implications of these differences remain poorly understood as comparative audiometric data from great apes are scarce and conflicting. Here, we measure the sound transfer function of the external and middle ears of humans, chimpanzees and bonobos, using laser-Doppler vibrometry and finite element analysis. This sound transfer function affects auditory thresholds, which relate to speech reception thresholds in humans. Unexpectedly we find that external and middle ears of chimpanzees and bonobos transfer sound better than human ones in the frequency range of spoken language. Our results suggest that auditory thresholds of the last common ancestor of Homo and Pan were already compatible with speech reception as observed in humans. Therefore, it seems unlikely that the morphological evolution observed in the bony auditory region of fossil hominins was driven by the emergence of spoken language. Instead, the peculiar human configuration may be a by-product of morpho-functional constraints linked to brain expansion.

Evolutionary Insight into the Association between New Jersey Polyomavirus and Humans

Advances in viral discovery techniques have led to the identification of numerous novel viruses in human samples. However, the low prevalence of certain viruses in humans raises doubts about their association with our species. To ascertain the authenticity of a virus as a genuine human-infecting agent, it can be useful to investigate the diversification of its lineage within hominines, the group encompassing humans and African great apes. Building upon this rationale, we examined the case of the New Jersey polyomavirus (NJPyV; Alphapolyomavirus terdecihominis), which has only been detected in a single patient thus far. In this study, we obtained and analyzed sequences from closely related viruses infecting all African great ape species. We show that NJPyV nests within the diversity of these viruses and that its lineage placement is compatible with an ancient origin in humans, despite its apparent rarity in human populations.

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

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

Frontal mechanisms underlying primate calls recognition by humans

Introduction

The ability to process verbal language seems unique to humans and relies not only on semantics but on other forms of communication such as affective vocalizations, that we share with other primate species-particularly great apes (Hominidae).

Methods

To better understand these processes at the behavioral and brain level, we asked human participants to categorize vocalizations of four primate species including human, great apes (chimpanzee and bonobo), and monkey (rhesus macaque) during MRI acquisition.

Results

Classification was above chance level for all species but bonobo vocalizations. Imaging analyses were computed using a participant-specific, trial-by-trial fitted probability categorization value in a model-based style of data analysis. Model-based analyses revealed the implication of the bilateral orbitofrontal cortex and inferior frontal gyrus pars triangularis (IFGtri) respectively correlating and anti-correlating with the fitted probability of accurate species classification. Further conjunction analyses revealed enhanced activity in a sub-area of the left IFGtri specifically for the accurate classification of chimpanzee calls compared to human voices.

Discussion

Our data-that are controlled for acoustic variability between species-therefore reveal distinct frontal mechanisms that shed light on how the human brain evolved to process vocal signals.