Biology subjects

Boubli, J. P.

Publications and source records attributed to Boubli, J. P..

10 recordsLinked to original sources

bioRxiv2026

When suitable habitat is not enough: climate change, habitat loss, and dispersal limitation increase the vulnerability of bald-headed uakaris (Cacajao sp.) in the Amazon Rainforest

AimsSpecies geographic distribution is determined by the interplay between ecological niche and dispersal capacity, which is constrained by biogeographical barriers. Bald-headed uakaris (Cacajao spp.) are highly specialized primates often associated with seasonally flooded forests. In this study, we used ecological niche models to assess the changes in habitat suitability and geographic distribution of uakari species in future scenarios. LocationWestern Amazonia. MethodsWe integrated current deforestation data, species dispersal ability, and ecological niche models to estimate habitat suitability in future scenarios. Our models project shifts in suitable conditions for all species under two Shared Socioeconomic Pathway (SSP) scenarios: intermediate (SSP2-4.5) and very high (SSP5-8.5) greenhouse gas (GHG) emissions. ResultsThree of the five species are projected to experience substantial reductions >62% in suitable habitat conditions within their current ranges by 2050 under both climate scenarios. Our findings indicate that, across the western Amazonia, up to 219,189 km2 and 211,276 km2 of land are projected to be unsuitable within the uakari ranges under the intermediate and very high emissions scenarios, respectively. This is particularly relevant for C. calvus, C. rubicundus, and C. ucayalii, which occupy a region where substantial losses are projected. At the species level, the uakaris may lose between 343 km2 and 84,531 km2 of their ranges in the intermediate scenario and 858 km2 and 76,216 km2 in the very high scenario. In comparison to the losses, the gain of suitable areas is expected to be considerably smaller, varying from 0 to 3,638 km2 in the intermediate scenario, and from 0 to 2,856 km2 in the very high emissions scenario. These gains may occur exclusively across the ranges of C. amuna, C. novaesi, and C. ucayalii. Moreover, the uakaris are estimated to lose between 0.5% and 8% of their current ranges due to deforestation in all scenarios. Shifts in suitability due to climate change varies from 6 to 191 km in the intermediate scenario and from 5 to 168 km in the very high scenario. Main conclusionsOur findings reveal a high sensitivity of the bald-headed uakaris to the impacts of climate change, especially for species with a restricted geographic distribution. It is projected that all species may experience contractions in the suitable areas and spatial suitability within their ranges by the year 2050, underscoring climate change as a relevant threat to these taxa.

ecology↗

bioRxiv2026

The primate gut bacterial microbiome: a systematic review of research methodologies, taxonomic coverage, and conservation implications

Primates are central to both human evolutionary research and ecosystem functioning, serving as seed dispersers, predators, pollinators, and prey. Despite their value to human and ecosystem science, global primate populations continue to decline, with [~]65% of species currently threatened with extinction. Conservation biology increasingly recognises that survival depends not only on protecting habitats and populations, but also on safeguarding the microbial communities that underpin host health, nutrition, and resilience. The gut bacterial microbiome plays a critical role in digestion, immune function, and adaptation to environmental change, making it an important dimension of primate conservation. Here, we systematically and quantitatively assessed the taxonomic and geographic coverage of primate gut bacterial microbiome research to identify key knowledge gaps relevant to primate conservation. Between 2001 and 2025, 261 articles were published across 100 journals. While taxonomic coverage is high at the family level, it declines substantially at the finer taxonomic scales. Currently, [~]34.5% of species have been studied, leaving gut bacterial biodiversity undocumented for 344 species. Moreover, approximately one-third of studied species have exclusively been studied in captivity, limiting insights into natural microbiome variation and reducing the conservation relevance of these findings. Geographic biases further hinder conservation applications, with megadiverse countries such as Brazil, the Democratic Republic of Congo, and Indonesia underrepresented. In addition, study methodology and reporting standards remain inconsistent. To address these challenges, a framework for the standardised reporting of a minimum set of data for primate gut bacterial microbiome research is included in this review. Adoption of this framework will improve transparency, comparability, and data accessibility, thereby enhancing the utility of microbiome research for primate conservation. By integrating microbial ecology into conservation biology, we highlight the microbiome as a potential critical frontier for safeguarding primate health, evolutionary potential, and long-term survival.

microbiology↗

bioRxiv2025

First Comprehensive Examination of the Molecular Phylogenetics of Saki Monkeys, Genus Pithecia Desmarest, 1804, Reveals an Unexpectedly Low Taxonomic Diversity

Saki monkeys (Pithecia) are found exclusively in the Amazon, ranging from the Guiana Shield in the east to the Andean foothills in the west. The taxonomy of this genus is complex due to indeterminate type localities, numerous synonyms, sexual dichromatism and considerable geographical diversity in coat colour patterns. Previous assessments have indicated two to four species and a variable few subspecies based on morphological analyses of museum specimens. Just two species have been consistently recognised--Pithecia pithecia and Pithecia monachus. This study presents the first comprehensive molecular phylogeny of the genus, using mitochondrial cytochrome b sequences from 137 individuals across their range and a ddRADseq genomic analysis on 34 individuals. The phylogenetic results revealed three main clades: (1) Guiana Shield sakis, (2) Sedimentary Basin and Brazilian Shield sakis, and (3) a basal P. albicans south of the Rio Solimoes. The ddRADseq data further clarified species boundaries and relationships, identifying six distinct species: P. chrysocephala and P. pithecia sensu Hershkovitz (1987) on the Guiana Shield; P. albicans in central Amazonia south of the Rio Solimoes; P. monachus in western Amazonia; P. irrorata between the rios Purus, Tapajos, and Juruena; and P. vanzolinii in a limited area east of the Rio Jurua.

zoology↗

bioRxiv2025

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

BackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies. ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8 Atelidae species, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome for Ateles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are involved in central nervous system development and photorreception. ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence between Ateles and Brachyteles potentially linked to distinct environmental light levels.

genomics↗

bioRxiv2024

Assessing group size and the demographic composition of unhabituated northern muriqui (Brachyteles hypoxanthus) using non-invasive biomonitoring

Obtaining accurate population measures of endangered species is critical for effective conservation and management actions and to evaluate their success overtime. However, determining the population size and demographic composition of most canopy forest-dwelling species has proven to be challenging. Here, we apply two non-invasive biomonitoring methods, arboreal camera trap and genetic tagging of faecal samples, to estimate the population size of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus), in the Caparao National Park, Brazil. When comparing population sizes between camera trapping and genetic tagging, the genetic tagging survey estimated fewer individuals for one of the muriqui groups studied but showed slightly higher population size estimates for the other group. In terms of the cost-efficiency of both methods, arboreal camera trapping had high initial costs but was more cost-effective in the long-term. Genetic tagging on the other hand did not require expensive equipment for data collection but had higher associated expenses for laboratory consumables and data processing. We recommend the use of both methods for northern muriqui monitoring and provide suggestions for improving the implementation of these non-invasive methods for future routine monitoring. Our findings also highlight the potential of arboreal camera trapping and genetic tagging to other arboreal mammals in tropical forests.

ecology↗

bioRxiv2023

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. However, comparative samples of scanned mammal teeth suitable for analysis with DTMs remain limited in size and scope, with little or no representation of some major lineages, even within well-studied clades such as primates. In addition, current DTM protocols usually rely on proprietary software, which may be unavailable to many researchers for reasons of cost. We address these issues in the context of a DTM analysis of the primate clade Platyrrhini ("New World monkeys") by: 1) presenting a large comparative sample of scanned second lower molars (m2s) of callitrichids (marmosets and tamarins), which were previously underrepresented in publicly available platyrrhine datasets; and 2) giving full details of an entirely freeware pipeline for DTM analysis. We also present an updated discrete dietary classification scheme for extant platyrrhines, based on cluster analysis of dietary data extracted from 98 primary studies. Our freeware pipeline performs equally well in dietary classification accuracy of an existing sample of platyrrhine m2s (excluding callitrichids) as a published protocol that uses proprietary software, at least when multiple DTMs are combined. Individual DTMs however, sometimes showed very different results in classification accuracies between that of our freeware pipeline and that of the proprietary protocol, most likely due to the differences in the smoothing functions used. The addition of callitrichids still resulted in high classification accuracy in predicting diet with combined DTMs, although accuracy was considerably higher when molar size was included (90%) than excluded (73%). We conclude that our new freeware DTM pipeline is capable of accurately predicting diet in platyrrhines based on tooth shape and size, and so is suitable for inferring probable diet of taxa for which direct dietary information is unavailable, such as fossil species.

evolutionary biology↗

bioRxiv2023

Whole genome approach to the structure and dynamics of Cacajao wild populations

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

evolutionary biology↗

bioRxiv2023

The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genus Cacajao)

AimWestern Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia. LocationWestern Amazonia TaxonThe uakari monkey (genus Cacajao) MethodsWe performed a continuous phylogeographic analysis using 77 cytochrome b sequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution of Cacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in three Cacajao species that were impacted by river rearrangements. ResultsOur continuous phylogeographical reconstruction points that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River at [~]1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. The demographic analysis indicates that C. calvus, C. amuna, and C. rubicundus went through a population decline in the last 70 Kya and have a low effective population size. Main conclusionOur results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.

evolutionary biology↗

bioRxiv2023

Genomics resolves historical uncertainties on phylogenetics and accommodates the systematics of marmosets and Goeldi's monkey (Primates: Platyrrhini)

Marmosets, with a total of 24 species classified into four genera (Callithrix, Cebuella, Mico and Callibella), are the smallest of the anthropoids and one of the most diverse and widespread groups of primates in South America. In contrast, the Goeldis monkey (Callimico goeldii) is represented by a single species of black, small, fungi-eating primates, endemic to west Amazonia. The phylogenetic relationships of marmoset genera and the phylogenetic position of Goeldis monkey, and consequently their systematics, remain uncertain and subject to debate because earlier studies revealed incongruent conclusions. Here we tackle this issue by first reviewing the systematics and the history of phylogenetic studies of marmosets and Goeldis monkey. We then explore their phylogenetic relationships by reconstructing a time-calibrated phylogeny using a genome-wide sampling of all lineages of marmosets, tamarins, Goeldis monkey, lion tamarins, capuchins, and squirrel monkeys. Our results clearly demonstrate that historical disagreements on phylogenetics and systematics of marmosets are due to incomplete lineage sorting, low phylogenetic signal of morphological and ecological characters, and low sampling at the DNA level. We show that Goeldis monkey is a sister lineage to marmosets and suggest that past incongruencies between studies on its phylogenetics and systematics are due to homoplasy of morphological characters traditionally used to infer primate relationships. Accordingly, we accommodate a genus-level classification for marmosets based on a fully-resolved phylogeny and multiple biological traits, redefine the genus Mico, update the definitions of Callibella, Callithrix, and Cebuella, and sediment the family-level classification of Goeldis monkey.

zoology↗

bioRxiv2021

eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater systems

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of -diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, {beta}-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

ecology↗