The historical distribution of the central gelada, Theropithecus gelada obscurus, an Ethiopian endemic primate, is generally considered to be bounded on the west by the Blue Nile Gorge. However, a small number of museum specimens reported as being collected in the areas of Gojjam and Ambo Mineral Springs (west of Lake Tana) have long represented the only physical evidence suggesting a former occurrence of geladas west of this barrier. In this short communication, we reassessed the provenance of all T. gelada specimens collected during the 1926–1927 Abyssinian Expedition of the Field Museum of Chicago by integrating archival field diaries, expedition reports, original specimen tags, catalog records, photographs, and illustrations. Our analysis demonstrates that three specimens historically attributed to Gojjam and Ambo Mineral Springs (FHMN 27038, FHMN 27039, and FHMN 27040) were in fact collected at the Muger River Canyon in Shewa in October 1926 and were subsequently mislabeled due to cataloging errors. No verified gelada specimens from Gojjam or west of Lake Tana are therefore currently housed in the Field Museum. These findings remove the only physical evidence supporting the historical presence of T. gelada west of the Blue Nile Gorge and leave as the sole remaining record of geladas in Gojjam an unconfirmed indirect report by Rüppell. This reassessment has important implications for reconstructing the historical biogeography and range limits of T. gelada and highlights the value of the “extended specimen” approach for museum collections.

Genomic data are increasingly used in primatology to understand how landscape features, dispersal patterns, and historical processes shape population structure and conservation-relevant diversity. The gelada (Theropithecus gelada), an endemic primate of the Ethiopian highlands, is currently divided into three subspecies; yet little is known about the extent of genomic variation within these groups. This gap is most pronounced for the Central gelada (T. gelada obscurus), the most widespread subspecies, for which genomic data have until now been available from only three individuals from a single site. To broaden this representation, we generated whole-genome sequence data from ten Central gelada individuals sampled across four central Ethiopian sites and two Southern geladas (T. gelada arsi), doubling the number of available genomes for this recently Endangered subspecies. Combining these new data with previously published genomes, we assessed patterns of genomic diversity across the species and tested how major geophysical features of the Ethiopian highlands influence population connectivity. Models incorporating preferred altitudinal ranges for geladas provided a substantially better fit to observed genomic distances than models based only on straight-line geographic distance, indicating that elevational structure strongly constrains movement. Using this framework, we inferred the affinities of unsampled Northern populations, finding stronger support for an east-west than a north-south division between the Northern gelada (T. gelada gelada) and Central gelada. These results highlight the importance of highland topography in shaping gelada population structure and inform future research and conservation planning for Ethiopian primates.

OBJECTIVES:Baboons possess sophisticated physical and social cognitive abilities; hence, the lack of evidence to date of large-scale behavioral variation in these primates is puzzling. Here we studied a candidate for such variation-the stripping of bark from Acacia robusta trees for consumption of the sap and soft tissue underneath-in Gorongosa National Park, Mozambique. MATERIALS AND METHODS:We surveyed an area inhabited by ~60 troops of chacma baboons, recording the availability and characteristics of the target trees, as well as the presence or absence of bark-stripping at 45 habitat plots distributed across a grid covering an area of ~300 km2. RESULTS:Camera traps confirmed the presence of baboons at all habitat plots, and we identified regional clumping in the distribution of the behavior, a pattern consistent across two consecutive years. Proportion and mean height/width of A. robusta did not predict whether bark-stripping behavior was present at a given site, nor did broader ecological variables such as habitat type and distance to the nearest water source. However, stripping sites had significantly higher numbers of A. robusta than non-stripping sites, and within a given bark-stripping site, baboons preferred to strip taller and wider trees among those available. DISCUSSION:The prominent geographical clustering we uncovered may have been driven by opportunity (i.e., the prevalence of A. robusta at a given site), but is also consistent with a possible (non-mutually exclusive) cultural interpretation. We propose avenues for future research on Gorongosa's baboons to better quantify the relative contributions of ecology, genetics, and social learning to the prevalence of bark stripping. We also briefly consider the potential relevance of baboon bark stripping to elucidating early hominin foraging strategies.

Dispersal behavior influences gene flow and the spatial distribution of genetic diversity, which is crucial for a species' evolutionary trajectory and population persistence under environmental changes. We used gene flow as a proxy to investigate dispersal patterns in the grayfoot chacma baboon (Papio ursinus griseipes) in Gorongosa National Park (GNP), central Mozambique. The baboons inhabit a mosaic landscape with a seasonally variable environment. Thirty-two years ago, GNP was the epicenter of a major war that severely reduced apex predators, resulting in limited mammalian predation on baboons. We aimed to characterize genetic diversity, examine the extent and direction of sex-biased gene flow at different time frames and investigate changes in population size and recent migration events. We collected 121 non-invasive DNA samples and analyzed uni- and bi-parentally inherited markers, comprising mitochondrial DNA, autosomal and Y-linked microsatellites, at two geographic locations (GNP and Catapú Forest Reserve) 150 km apart. We observed high genetic diversity and no evidence of a recent population decline. We identified six mitochondrial haplotypes, including a genetically distinct one in Catapu Forest Reserve. We found molecular evidence for historical and current male-mediated gene flow and female philopatry. Our results highlight the resilience of dispersal patterns in Papio sp. in diverse and seasonally variable ecosystems which have been disturbed by anthropogenic activities.

The Southwest National Primate Research Center of San Antonio, Texas, hosts one of the largest captive colonies of baboons used for biomedical research. Pedigreed animals can be traced back to the second part of the last century from individuals of two Papio species: P. anubis and P. cynocephalus. We leveraged recently published genomic data from more than 800 baboons to investigate the ancestry profile of the colony members. By combining phylogenetic analysis of mitochondrial DNA and nuclear genomic ancestry estimations, we confirmed P. anubis and P. cynocephalus as the main sources of the colony genetic variation. Previously unreported contributions from additional Papio species were also detected in almost 5% of the colony samples, of which P. hamadryas was the most notable, while others occurred sporadically across the data set. This extensive ancestry characterisation will be of help in biomedical investigations making use of baboons from the Southwest National Primate Research Center.

The true lemurs (genus Eulemur) are a genetically diverse and spatially widespread group of species inhabiting most of Madagascar's forests. Including 12 recognized species, the genus can be divided into four major evolutionary groups: E. rubriventer, E. mongoz, the Brown Lemur Species Complex (BLSC), and the coronatus-macaco-flavifrons complex (CMFC), although monophyly for the CMFC is not always supported. Recent genome-based studies highlighted topological and chronological differences between nuclear and mitochondrial phylogenies of true lemurs, which could be explained by events of hybridisation. In order to reconstruct the evolutionary history of the genus, we test for gene-flow between Eulemur clades using a set of whole genome sequences representative of the diversity of the genus. Events of hybridization among true lemurs clades were identified, explaining discordances between mitochondrial and nuclear phylogenies and providing the context for mito-nuclear co-evolution, which we detected for E. rubriventer. Overall, by directly testing for hybridization among Eulemur species, we developed an evolutionary model that deepens our understanding of the unique and complex history of the genus Eulemur, and sets it as a starting point for future research.

OBJECTIVES:Hybridisation plays a critical role in species evolution and is widespread among primates, particularly in the genus Papio. Several baboon hybridisation zones have been identified in Africa, with Gorongosa National Park in Mozambique being notable for chacma baboons exhibiting phenotypic and genomic traits of both chacma and yellow baboons. This study builds on earlier research by leveraging new genomic data to refine our understanding of the relationships between Central Mozambique baboons and other baboon populations, focusing on chacma, yellow, and kinda baboons. MATERIALS AND METHODS:We analyzed uniparental genetic markers alongside autosomal and X chromosome variants, incorporating unpublished low-coverage genomes from fecal samples collected in Central Mozambique. These data were compared with the broader genomic landscape of Papio baboons based on recent surveys. RESULTS:The analysis of uniparental markers suggests a time to the most recent common ancestor of less than 200kya for chacma baboons in Zambia and Gorongosa, with both lineages sharing a node with yellow baboons from Tanzania less than 1 Mya. Genomic analyses indicate introgression in Central Mozambique and Zambia chacmas likely originated from populations closer to eastern rather than western Tanzanian yellow baboons. DISCUSSION:Our findings reveal yellow baboon introgression in Central Mozambique chacmas, confirming this being a region hosting baboons with complex ancestry composition. Broader genomic surveys across Mozambique are necessary to uncover the population structure and evolutionary history of chacmas in this area, as well as the role of this region as a biodiversity crossroads for primates.

IntroductionSexual dimorphism in cranial morphology is a significant aspect of primate evolution, providing insights into evolutionary pressures and mating systems in different species. This study focuses on cranial sexual dimorphism in Papio and Theropithecus, two closely related genera within the tribe Papionini. MethodsUsing geometric morphometric techniques, we analyzed 570 cranial specimens from both genera, with data sourced from various studies and repositories. Thirty craniofacial landmarks were defined and analyzed through Geometric Morphometrics tools to evaluate shape variation. ResultsOur findings reveal distinct morphological clusters for each genus and sex, with Papio and Theropithecus exhibiting significant sexual dimorphism. The results distinguish genera and sex-based groups, indicating differential impacts of size on shape across groups. The findings suggest that while sexual dimorphism is stable in magnitude within each genus, the specific morphological manifestations differ. DiscussionThis research advances our understanding of the evolutionary mechanisms driving sexual dimorphism and emphasizes the need for further studies to explore the genetic and environmental factors influencing these differences. The innovative approach and comprehensive dataset provide a robust framework for future investigations into primate cranial morphology and its evolutionary implications.

Substance Use Disorders (SUDs) are a significant public health concern with complex etiologies involving genetic, environmental, and psychological factors. Here, we present BioSUD, a biobank that, by integrating genomic data with comprehensive phenotypic assessments, including sociodemographic, psychosocial, and addiction-related variables, was designed to investigate the etiology of SUDs within the Southern Italian population. We assessed a cohort of 1,806 participants (1,508 controls and 298 individuals with SUD diagnosis). Genomic analyses of the newly generated genotypes showed a predominantly Southern Italian ancestry for the BioSUD cohort. Admixture analysis reveals a complex history of genetic admixture in Southern Italian populations, exhibiting Southern European, African, and other ancestries. This results in significant genetic variation, potentially limiting the applicability of translational studies primarily based on Northern European ancestries. From a social and psychological perspective, individuals with SUDs exhibited lower socioeconomic status, increased exposure to adverse experiences, and compromised familial and peer relationships relative to controls. These results show that the BioSUD cohort is valuable for studying SUD-associated complex behavioral traits.

Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.

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.

1Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy *Correspondence: [email protected]

Investigating primates’ behavioral variation at the inter-population level is important for the understanding of the evolutionary processes leading to species-specific patterns. The study of behavioral diversity among populations also contributes to improving’ primate conservation efforts. Dispersal patterns tend to be similar among close phylogenetic lineages but may vary in response to individual-based responses. Here, we investigate dispersal patterns of chacma baboons (Papio ursinus griseipes) living in Gorongosa National Park (GNP) and the Catapu Forest Reserve (CFR) in central Mozambique. The park consists of a mosaic landscape, located in a seasonally variable area. GNP was the epicenter of a major war, which severely reduced most apex predators resulting in limited mammalian predation on baboons and a steep increase in number of groups and/or group’s fission. We used a genetic dataset of 121 non-invasive DNA samples analyzed for uni- and bi-parentally inherited markers aiming to characterize the spatial distribution of genetic variation and investigate the extent and direction of sex-mediated gene flow at different time scales. We found high levels of genetic diversity as estimated using autosomal microsatellite loci data and no evidence for a significant contraction of the population size in the last generations. A very distinct mitochondrial DNA haplotype was sampled in CFR. We found evidence for historical and instantaneous male-biased dispersal and female philopatry, estimated among localities and at short distances in GNP, respectively. Our study highlights the strong conservation of sex-biased dispersal patterns and philopatry in chacma baboons and suggests that dispersal behaviors in chacma baboons are resilient to environmental changes and seasonality.

STR loci localized on the X chromosome provide information additional to the autosomal markers routinely analyzed in forensic genetics, integrating genetic systems as Y-STRs and mitochondrial DNA in the investigation of complex kinship scenarios and mass disaster cases.In this study we genotyped 12 X-STR loci in 251 male samples from four populations of Namibia in southern Africa using the Investigator Argus X-12 kit (Qiagen, Hilden, Germany). Forensic efficiency parameters indicated high power of discrimination in the considered populations. As part of our investigation, we highlighted partial linkage associations between loci within known linkage groups (LGs) and identified several occurrences of previously unreported out-of-ladder (OL) alleles.Genetic distances between the Namibian populations here investigated and other African (Eritrea, Ethiopia, Somalia, Guinea, Cape Verde) and non-African (Germany, China, Philippines) populations using loci grouped in LGs mirrored their biogeographical distribution differently for each linkage group. Haplotype sharing within each LG revealed a high degree of population-specific types, hinting to the potential of these markers for ancestry applications.These results highlight the importance to produce specific and freely available population databases especially for multi-ethnic countries. This novel dataset is expected to be of interest for population studies that need an accessible reference dataset of African regions not currently well represented, as well as possible relevance for forensic applications focusing on the biogeographic origin of samples.

Geography is a well-known factor shaping genetic variation in human populations. However, the potential role played by cultural variables remains much understudied. This study investigates the impact of socio-cultural variables on genomic similarity and the saliva microbiome, using data from populations in Lesotho and Namibia. Geographic distance within Lesotho increases genetic differentiation, while shared clan affiliation surprisingly increases it. In Namibia, ethnicity is the predominant factor influencing genetic affinity. Saliva metagenomic data shows a negative correlation between age and alpha diversity, with notable differences in host-interacting taxa and viral load. These findings highlight the role of geography in shaping genetic affinity even at small scales and the complex influences of cultural factors. The saliva microbiome appears primarily affected by unrecorded individual behaviors rather than geographic or cultural variables. At population-level these oral microbiomes reveal insights into some dietary habits, oral health, and also the communal viral load, which appears to have greater incidence in Lesotho possibly related to the long-term effects of the HIV epidemic in the country.

Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.

Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.

In this repo you will find three samples mapped to the Y chromosome (NC_044997.1) of Panubis1.0 reference: 2 P. papio samples, T14 and 70K, and 1 P. ursinus sample. The short reads were mapped and filtered according to Materials and Methods in Mutti et al, 2023. The files are in BAM format.

Post‐release monitoring is important to improve translocation success because it provides an opportunity to identify factors relevant to the survival of local populations. We studied a population of the endangered collared brown lemur ( Eulemur collaris ) translocated from a degraded forest fragment to a nearby littoral forest within the Mandena Conservation Area in southeast Madagascar from 2000–2011. We compared genetic surveys of mitochondrial and nuclear markers with the genetic profile of nearby populations to examine the dispersal capacity of the collared brown lemur. We also performed a landscape analysis to assess changes in connectivity between forest fragments. There was a fluctuating trend characterized by a phase of demographic and genetic stability shortly after translocation, followed by an increase in genetic diversity coinciding with a population decrease and a gradual recovery of initial conditions. These results demonstrated the ability of the collared brown lemur to disperse through unfavorable landscapes and to recover after translocation. Our study revealed the importance of monitoring translocated populations over time using a multidisciplinary approach.