Primate taxonomy: species and conservation

Parasites and Viruses in Callithrix in Brazil

PURPOSE

As a result of environmental imbalances of anthropogenic origin, the potential for transmission of parasites and viruses between different primates, including humans, might increase. Thus, parasitic studies have great relevance to primatology, which motivated us to conduct a literature review to synthesize the information available in American primates of the Callithrix genus.

METHODS

We carried out the bibliographic search on the main groups of parasites (protozoa, helminths, arthropods, ectoparasites) and viruses found in Callithrix in Brazil in search platforms and consider all manuscript that appeared in search engines, published between the years 1910 and December 2022. In each selected article, the following information was recorded: the host species; parasite taxa; scientific classification of the parasite; host habitat (free-living, captive); diagnostic technique; state; and bibliographic reference. Data were tabulated and arranged in a parasite-host table.

RESULTS

Some endemic genera, such as Callithrix, are widely distributed geographically across Brazil and have characteristics of adaptation to different habitats due to their flexibility in diet and behavior. These factors can make them subject to a greater diversity of parasites and viruses in the country. Here, we identified 68 parasitic taxa, belonging to the clades protozoa (n = 22), helminths (n = 34), ectoparasites (n = 7), and viruses (n = 5). Out of this total, 19 have zoonotic potential. Of the six existing marmoset species, Callithrix jacchus was the most frequent in studies, and Callithrix flaviceps did not have reports. All regions of the country had occurrences, mainly the Southeast, where 54% of the cases were reported. In 46% of the reported parasites and viruses, it was not possible to identify the corresponding species.

CONCLUSION

We conclude that in part of the works the identification methods are not being specific, which makes it difficult to identify the species that affects Callithrix spp. Furthermore, the studies present geographic disparities, being concentrated in the southeast of the country, making it impossible to have a more uniform analysis of the findings. Thus, it is observed that information about parasites and viruses is incipient in the genus Callithrix in Brazil.

J, Roos C, Farias IP, Hrbek T. A dataset of new occurrence records of primates from the arc of deforestation, Brazil

​​​​​​​The so-called arc of deforestation is a major agricultural and industrial frontier in southern Amazonia and northern Cerrado of Brazil. As arboreal mammals, the primates in this region are therefore threatened by forest loss and fragmentation. At the same time, knowledge about the taxonomic diversity and distribution ranges of these taxa is incomplete, which might hamper efficient conservation measurements. New species have been recently discovered in this region, and their ranges remain imprecise because only a few occurrence records are available for each species. Here we present 192 new records of 22 species and subspecies of Alouatta, Aotus, Ateles, Cebus, Chiropotes, Lagothrix, Leontocebus, Pithecia, Plecturocebus, Saimiri, and Sapajus, collected in 56 different localities during 10 field expeditions across the arc of deforestation between 2015 and 2018. Based on these new records, we extend the ranges of Alouatta puruensis, Ateles chamek, and Saimiri collinsi; identify potential hybridization zones between A. puruensis and A. discolor, and between At. chamek and At. marginatus; redefine the range of Plecturocebus moloch; and clarify the ranges of P. baptista and P. hoffmannsi. Moreover, these results and the dataset are valuable for further research on, for example, species distribution and habitat use modeling, for assessing species extinction risks, and for supporting efforts for the conservation of species increasingly threatened on a global deforestation frontier.

Interspecies Papillomavirus Type Infection and a Novel Papillomavirus Type in Red Ruffed Lemurs (Varecia rubra)

The Papillomaviridae are a family of vertebrate-infecting viruses of oncogenic potential generally thought to be host species- and tissue-specific. Despite their phylogenetic relatedness to humans, there is a scarcity of data on papillomaviruses (PVs) in speciose non-human primate lineages, particularly the lemuriform primates. Varecia variegata (black-and-white ruffed lemurs) and Varecia rubra (red ruffed lemurs), two closely related species comprising the Varecia genus, are critically endangered with large global captive populations. Varecia variegata papillomavirus (VavPV) types -1 and -2, the first PVs in lemurs with a fully identified genome, were previously characterized from captive V. variegata saliva. To build upon this discovery, saliva samples were collected from captive V. rubra with the following aims: (1) to identify PVs shared between V. variegata and V. rubra and (2) to characterize novel PVs in V. rubra to better understand PV diversity in the lemuriform primates. Three complete PV genomes were determined from V. rubra samples. Two of these PV genomes share 98% L1 nucleotide identity with VavPV2, denoting interspecies infection of V. rubra by VavPV2. This work represents the first reported case of interspecies PV infection amongst the strepsirrhine primates. The third PV genome shares <68% L1 nucleotide identity with that of all PVs. Thus, it represents a new PV species and has been named Varecia rubra papillomavirus 1 (VarPV1). VavPV1, VavPV2, and VarPV1 form a new clade within the Papillomaviridae family, likely representing a novel genus. Future work diversifying sample collection (i.e., lemur host species from multiple genera, sample type, geographic location, and wild populations) is likely to uncover a world of diverse lemur PVs.

Explaining the primate extinction crisis: predictors of extinction risk and active threats

Explaining why some species are disproportionately impacted by the extinction crisis is of critical importance for conservation biology as a science and for proactively protecting species that are likely to become threatened in the future. Using the most current data on threat status, population trends, and threat types for 446 primate species, we advance previous research on the determinants of extinction risk by including a wider array of phenotypic traits as predictors, filling gaps in these trait data using multiple imputation, and investigating the mechanisms that connect organismal traits to extinction risk. Our Bayesian phylogenetically controlled analyses reveal that insular species exhibit higher threat status, while those that are more omnivorous and live in larger groups have lower threat status. The same traits are not linked to risk when repeating our analyses with older IUCN data, which may suggest that the traits influencing species risk are changing as anthropogenic effects continue to transform natural landscapes. We also show that non-insular, larger-bodied, and arboreal species are more susceptible to key threats responsible for primate population declines. Collectively, these results provide new insights to the determinants of primate extinction and identify the mechanisms (i.e. threats) that link traits to extinction risk.

Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea)

The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.

Variation in macroevolutionary dynamics among extant primates

Objectives

This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity.

Materials and methods

Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification.

Results

Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages.

Conclusions

Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.

Primate conservation in the Arc of Deforestation: a case study of Vieira's titi monkey Plecturocebus vieirai

Fifty years of deforestation in the Arc of Deforestation have put at risk species survival, ecosystem services and the stability of biogeochemical cycles in Amazonia, with global repercussions. In response, we need to understand the diversity, distribution and abundance of flagship species groups, such as primates, which can serve as umbrella species for broad biodiversity conservation strategies and help mitigate climate change. Here we identify the range, suitable habitat areas and population size of Vieira's titi monkey Plecturocebus vieirai and use it as an emblematic example to discuss biodiversity conservation and climate change mitigation in one of the largest deforestation frontiers. Our findings show that deforestation for agriculture and cattle-ranching expansion is the major threat to P. vieirai and is responsible for present (56%) and projected (14%) reductions in habitat area and population size. We also found that human-driven climate change affects the P. vieirai niche negatively, triggering habitat degradation and further population decline even inside protected areas. Primate watching can be a profitable alternative to forest exploitation on private, public or Indigenous lands in the Arc of Deforestation and is a way to shift the traditional, predatory extraction of natural resources from Amazonia towards sustainable land use based on biodiversity conservation at local, regional and global scales, local people's welfare and climate change mitigation. New models of land use and income generation are required to protect the unique natural and human heritages of the Arc of Deforestation and the life-supporting ecosystem services and products provided by Amazonia.

Distribution and diversity of primates and threats to their survival in the Awi Zone, northwestern Ethiopia

Habitat loss and fragmentation affect the diversity and distribution of primates in a human-modified landscape. Ethiopia has a high diversity of primates, but increasing human pressure has negatively impacted their distribution and abundance across the country, primarily due to deforestation. To date, the diversity and distribution of primate species are poorly known in northwestern Ethiopia. From October 2020 until September 2021, we assessed the diversity and distribution of primate species in 26 forest patches in the Awi Zone, Northwestern Ethiopia using line transect surveys, and we examined the potential conservation threats to the survival of these taxa. Across transects, we encountered 459 groups of four primate taxa: olive baboons (Papio anubis), grivet monkeys (Chlorocebus aethiops), Boutourlini's blue monkeys (Cercopithecus mitis boutourlinii), and black-and-white colobus monkeys (Colobus guereza spp. guereza). The latter two are endemic to Ethiopia. We observed black-and-white colobus monkeys in all surveyed forest patches, while we observed Boutourlini's blue monkeys in 18 patches. Black-and-white colobus monkeys were the most frequently observed (n = 325 sighting; relative encounter frequency = 70.8%), while grivet monkeys (Chlorocebus aethiops) were the least (n = 34 sighting; relative encounter frequency = 7.4%) in the region. Similarly, the relative encounter frequency of olive baboons was 9.2% (n = 42 sighting). The overall mean group size for each species was: Boutourlini's blue monkeys (26.1 individuals), black-and-white colobus monkeys (8.8 individuals), grivet monkeys (34.1 individuals), and olive baboons (41.4 individuals). We identified agricultural expansions, exotic tree plantations, deforestations, firewood collections, livestock grazing, and killings over their crop-feeding behaviors as the main threats to primates and their habitats in the region. This study provides crucial information on an area likely to support primate species that we know very little about. Assigning protected connecting forest patches should be an urgent priority for the conservation of the primates in this region.

Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing

Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.

An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation

Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena-Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.

The ultimate database to (re)set the evolutionary history of primate genital bones

Scientific literature concerning genital bones in primates consists of both ancient works (dating back to the nineteenth century) and more recent revisions/meta-analyses, which, however, are not always so detailed or exhaustive. Based on a thorough analysis, several conflicting data, inaccurate references, and questionable claims have emerged. We generated a binary matrix of genital bone occurrence data, considering only data at the species level, based on (1) a rigorous literature search protocol, (2) raw data (collected exclusively from primary literature), (3) an updated taxonomy (often tracing back to the species taxonomic history) and (4) new occurrence data from scanned genitals of fresh and museum specimens (using micro-computed tomography-micro-CT). Thanks to this methodological approach, we almost doubled available occurrence data so far, avoiding any arbitrary extension of generic data to conspecific species. This practice, in fact, has been recently responsible for an overestimation of the occurrence data, definitively flattening the interspecific variability. We performed the ancestral state reconstruction analysis of genital bone occurrence and results were mapped onto the most updated phylogeny of primates. As for baculum, we definitively demonstrated its simplesiomorphy for the entire order. As for baubellum, we interpreted all scattered absences as losses, actually proposing (for the first time) a simplesiomorphic state for the clitoral bone as well. The occurrence data obtained, while indirectly confirming the baculum/baubellum homology (i.e., for each baubellum a baculum was invariably present), could also directly demonstrate an intra-specific variability affecting ossa genitalia occurrence. With our results, we established a radically improved and updated database about the occurrence of genital bones in primates, available for further comparative analyses.

Occurrence and conservation of the Vulnerable titi monkey Callicebus melanochir in fragmented landscapes of the Atlantic Forest hotspot

Tropical forest hotspots have a high diversity of species but have lost > 70% of their original vegetation cover and are characterized by a multitude of small and isolated fragments. Paradoxically, conservation actions in these areas are still mainly focused on protection of large tracts of forests, a strategy now infeasible because of the small area of forest remnants. Here we use the Vulnerable black-handed titi monkey Callicebus melanochir as a model to study the effects of habitat loss, fragmentation and degradation on arboreal mammals and to provide insights for science-driven conservation in fragmented landscapes in tropical forest hotspots. We surveyed 38 Atlantic Forest fragments in Bahia State, Brazil and assessed the effects of patch area, quality and visibility, and landscape connectivity on the occurrence of our model species. Patch area was the single best model explaining species occurrence. Nonetheless, patch quality and visibility, and landscape connectivity, positively affect occurrence. In addition to patch area, patch quality, patch visibility and landscape connectivity are useful for predicting the occurrence of arboreal mammals in the fragments of tropical forest hotspots. We encourage the assessment of habitat quality (based on remotely sensed vegetation indices) and habitat visibility (based on digital elevation models) to improve discoverability of arboreal mammal populations and selection of fragments for conservation purposes across fragmented landscapes of tropical forest hotspots. Large remnants of tropical forest hotspots are scarce and therefore we require baseline data to support conservation actions and management in small forest fragments.

Insights from macroevolutionary modelling and ancestral state reconstruction into the radiation and historical dietary ecology of Lemuriformes (Primates, Mammalia)

Background

Lemurs once rivalled the diversity of rest of the primate order despite thier confinement to the island of Madagascar. We test the adaptive radiation model of Malagasy lemur diversity using a novel combination of phylogenetic comparative methods and geometric methods for quantifying tooth shape.

Results

We apply macroevolutionary model fitting approaches and disparity through time analysis to dental topography metrics associated with dietary adaptation, an aspect of mammalian ecology which appears to be closely related to diversification in many clades. Metrics were also reconstructed at internal nodes of the lemur tree and these reconstructions were combined to generate dietary classification probabilities at internal nodes using discriminant function analysis. We used these reconstructions to calculate rates of transition toward folivory per million-year intervals. Finally, lower second molar shape was reconstructed at internal nodes by modelling the change in shape of 3D meshes using squared change parsimony along the branches of the lemur tree. Our analyses of dental topography metrics do not recover an early burst in rates of change or a pattern of early partitioning of subclade disparity. However, rates of change in adaptations for folivory were highest during the Oligocene, an interval of possible forest expansion on the island.

Conclusions

There was no clear phylogenetic signal of bursts of morphological evolution early in lemur history. Reconstruction of the molar morphologies corresponding to the ancestral nodes of the lemur tree suggest that this may have been driven by a shift toward defended plant resources, however. This suggests a response to the ecological opportunity offered by expanding forests, but not necessarily a classic adaptive radiation initiated by dispersal to Madagascar.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01793-x.

Phylogeographic evidence for two species of muriqui (genus Brachyteles)

The taxonomy of muriquis, the largest extant primates in the New World, is controversial. While some specialists argue for a monotypic genus (Brachyteles arachnoides), others favor a two-species classification, splitting northern muriquis (Brachyteles hypoxanthus) from southern muriquis (B. arachnoides). This uncertainty affects how we study the differences between these highly endangered and charismatic primates, as well as the design of more effective conservation programs. To address this issue, between 2003 and 2017 we collected over 230 muriqui fecal samples across the genus' distribution in the Brazilian Atlantic Forest, extracted DNA from these samples, and sequenced 423 base pairs of the mitochondrial DNA (mtDNA) control region. Phylogenetic and species delimitation analyses of our sequence dataset robustly support two reciprocally monophyletic groups corresponding to northern and southern muriquis separated by an average 12.7% genetic distance. The phylogeographic break between these lineages seems to be associated with the Paraíba do Sul River and coincides with the transition between the north and south Atlantic Forest biogeographic zones. Published divergence estimates from whole mitochondrial genomes and nuclear loci date the split between northern and southern muriquis to the Early Pleistocene (ca. 2.0 mya), and our new mtDNA dataset places the coalescence time for each of these two clades near the last interglacial (ca. 120-80 kya). Our results, together with both phenotypic and ecological differences, support recognizing northern and southern muriquis as sister species that should be managed as distinct evolutionarily significant units. Given that only a few thousand muriquis remain in nature, it is imperative that conservation strategies are tailored to protect both species from extinction.

Morphological integration affects the evolution of midline cranial base, lateral basicranium, and face across primates

OBJECTIVES

The basicranium and face are two integrated bony structures displaying great morphological diversity across primates. Previous studies in hominids determined that the basicranium is composed of two independent modules: the midline basicranium, mostly influenced by brain size, and the lateral basicranium, predominantly associated with facial shape. To better assess how morphological integration impacts the evolution of primate cranial shape diversity, we test to determine whether the relationships found in hominids are retained across the order.

MATERIALS AND METHODS

Three-dimensional landmarks (29) were placed on 143 computed tomography scans of six major clades of extant primate crania. We assessed the covariation between midline basicranium, lateral basicranium, face, and endocranial volume using phylogenetically informed partial least squares analyses and phylogenetic generalized least squares models.

RESULTS

We found significant integration between lateral basicranium and face and between midline basicranium and face. We also described a significant correlation between midline basicranium and endocranial volume but not between lateral basicranium and endocranial volume.

DISCUSSION

Our findings demonstrate a significant and pervasive integration in the craniofacial structures across primates, differing from previous results in hominids. The uniqueness of module organization in hominids may explain this distinction. We found that endocranial volume is significantly integrated to the midline basicranium but not to the lateral basicranium. This finding underlines the significant effect of brain size on the shape of the midline structures of the cranial base in primates. With the covariations linking the studied features defined here, we suggest that future studies should focus on determining the causal links between them.

Macroevolutionary effects on primate trophic evolution and their implications for reconstructing primate origins

The visual-predation hypothesis proposes that certain derived features shared by crown primates reflect an insectivorous ancestry. Critics of this idea have argued that because insectivory is uncommon among extant primates it is unlikely to have been a major influence on early primate evolution. According to this perspective, the low frequency of insectivory indicates that it is an apomorphic deviation from the mostly conserved primate ecological pattern of herbivory. The present study tests two alternative hypotheses that are compatible with an insectivorous ancestor: (1) that trophic evolution was biased, such that herbivory evolved repeatedly with few shifts back to insectivory, and (2) that insectivorous lineages have diversified at a lower rate than herbivorous lineages owing to differential trophic effects on speciation and extinction probabilities. Model-based analysis conducted using trait data for 307 extant primate species indicates that rates of transition into and out of insectivory are similar, rejecting the hypothesis of biased trophic evolution. On the other hand, the hypothesis of asymmetric diversification is supported, with insectivorous lineages having a lower rate of diversification than herbivorous lineages. This correlation is mediated by activity pattern: insectivory occurs mostly in nocturnal lineages, which have a lower diversification rate than diurnal lineages. The frequency of insectivory also appears to have been shaped by repeated transitions into ecological contexts in which insectivory is absent (large body size) or rare (diurnality). These findings suggest that the current distribution of trophic strategies among extant primates is the result of macroevolutionary processes that have favored the proliferation and persistence of herbivory relative to insectivory. This conclusion implies that the low frequency of insectivory is not necessarily evidence against the visual-predation hypothesis.

Emerging and Enduring Issues in Primate Conservation Genetics

Conservation genetics is a branch of conservation biology that uses molecular data to assist in the conservation and management of imperiled populations, subspecies, and species. In this review, I examine conservation action plans (CAPs)—instrumental documents designed to influence conservation policy—for selected primate species. I use the information contained in CAPs as a means to guide this review. The primary genetics-based topics that are mentioned in CAPs are genetic connectivity, inbreeding, and subspecies/species delimitation. I discuss these topics as well as historical demographic inference and hybridization using examples from wild primate species to illustrate the myriad ways in which genetics can assist in conservation efforts. I also discuss some recent technological advances such as genomic capture techniques and the potential to do molecular work in remote locations.

A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America

Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.

To increase trust, change the social design behind aggregated biodiversity data

Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors 'at the source.' We show that this strategy falls systematically short of a full diagnosis of the underlying causes of distrust. In particular, trust in an aggregator is not just a feature of the data signal quality provided by the sources to the aggregator, but also a consequence of the social design of the aggregation process and the resulting power balance between individual data contributors and aggregators. The latter have created an accountability gap by downplaying the authorship and significance of the taxonomic hierarchies-frequently called 'backbones'-they generate, and which are in effect novel classification theories that operate at the core of data-structuring process. The Darwin Core standard for sharing occurrence records plays an under-appreciated role in maintaining the accountability gap, because this standard lacks the syntactic structure needed to preserve the taxonomic coherence of data packages submitted for aggregation, potentially leading to inferences that no individual source would support. Since high-quality data packages can mirror competing and conflicting classifications, i.e. unsettled systematic research, this plurality must be accommodated in the design of biodiversity data integration. Looking forward, a key directive is to develop new technical pathways and social incentives for experts to contribute directly to the validation of taxonomically coherent data packages as part of a greater, trustworthy aggregation process.

Primate diversification inferred from phylogenies and fossils

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.

What does variation in primate behavior mean?

Interest in intraspecific behavioral variation has grown with concerns about the ability of primates to adapt to the rapidly changing ecological and demographic conditions that threaten their survival. Now, in addition to identifying the causes and phylogenetic distribution of normative, species-specific behavior patterns for interspecific comparisons, there is widespread recognition of the need to incorporate intraspecific variation. This variation is evident across groups and populations of the same species as well over the long histories of single groups of long-lived, socially complex animals with overlapping generations. Yet, analyses of both cross-sectional and longitudinal data require explicit criteria about how to classify and interpret behavioral variation, and must be sensitive to the limitations of space-for-time substitutions in these comparisons. Current approaches have made great advances, but there remains an urgent challenge of understanding intraspecific variation in a way that will facilitate the development of new predictive models to assess population resilience and extinction risks in the face of climate change and other anthropogenic influences.

Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview

We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.

Impending extinction crisis of the world's primates: Why primates matter

Nonhuman primates, our closest biological relatives, play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases. They are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Current information shows the existence of 504 species in 79 genera distributed in the Neotropics, mainland Africa, Madagascar, and Asia. Alarmingly, ~60% of primate species are now threatened with extinction and ~75% have declining populations. This situation is the result of escalating anthropogenic pressures on primates and their habitats-mainly global and local market demands, leading to extensive habitat loss through the expansion of industrial agriculture, large-scale cattle ranching, logging, oil and gas drilling, mining, dam building, and the construction of new road networks in primate range regions. Other important drivers are increased bushmeat hunting and the illegal trade of primates as pets and primate body parts, along with emerging threats, such as climate change and anthroponotic diseases. Often, these pressures act in synergy, exacerbating primate population declines. Given that primate range regions overlap extensively with a large, and rapidly growing, human population characterized by high levels of poverty, global attention is needed immediately to reverse the looming risk of primate extinctions and to attend to local human needs in sustainable ways. Raising global scientific and public awareness of the plight of the world's primates and the costs of their loss to ecosystem health and human society is imperative.

Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal

Overview. Taxonomic names are imperfect identifiers of specific and sometimes conflicting taxonomic perspectives in aggregated biodiversity data environments. The inherent ambiguities of names can be mitigated using syntactic and semantic conventions developed under the taxonomic concept approach. These include: (1) representation of taxonomic concept labels (TCLs: name sec. source) to precisely identify name usages and meanings, (2) use of parent/child relationships to assemble separate taxonomic perspectives, and (3) expert provision of Region Connection Calculus articulations (RCC–5: congruence, [inverse] inclusion, overlap, exclusion) that specify how data identified to different-sourced TCLs can be integrated. Application of these conventions greatly increases trust in biodiversity data networks, most of which promote unitary taxonomic 'syntheses' that obscure the actual diversity of expert-held views. Better design solutions allow users to control the taxonomic variable and thereby assess the robustness of their biological inferences under different perspectives. A unique constellation of prior efforts – including the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts and more than 75,000 RCC–5 articulations – provides the opportunity to build a first full-scale concept resolution service for SERNEC, the SouthEast Regional Network of Expertise and Collections, currently with 60 member herbaria and 2 million occurrence records.

Intellectual merit. We have developed a multi-dimensional, step-wise plan to transition SERNEC's data culture from name- to concept-based practices. (1) We will engage SERNEC experts through annual, regional workshops and follow-up interactions that will foster buy-in and ultimately the completion of 12 community-identified use cases. (2). We will leverage RCC–5 data from the Weakley Flora and further development of the Euler/X logic reasoning toolkit to provide comprehensive genus- to variety-level concept alignments for at least 10 major flora treatments with highest relevance to SERNEC. The visualizations and estimated &gt; 1 billion inferred concept-to-concept relations will effectively drive specimen data integration in the transformed portal. (3) We will expand Symbiota's taxonomy and occurrence schemas and related user interfaces to support the new concept data, including novel batch and map-based specimen determination modules, with easy output options in Darwin Core Archive format. (4) Through combinations of the new technology, enlisted taxonomic expertise, and SERNEC's large image resources, we will upgrade minimally 80% of all SERNEC specimen identifications from names to the narrowest suitable TCLs, or add "uncertainty" flags to specimens needing further study. (5) We will utilize the novel tools and data to demonstrate how controlling for the taxonomic variable in 12 use cases variously drives the outcomes of evolutionary, ecological, and conservation-based research hypotheses.

Broader impacts. Our project is focused on just one herbarium network, but the potential impact is as wide as Darwin Core or even comparative biology. We believe that trust in networked biodiversity data depends on open and dynamic system designs, allowing expert access and resolution of multiple conflicting views that reflect the complex realities of ongoing taxonomic research. Taking well over 1 million SERNEC records from name- to TCL-resolution will show that "big" specimen data can pass the credibility threshold needed to validate the substantive data mobilization investment. We will mentor one postdoctoral researcher (UNC), two Ph.D. students (ASU, UIUC), and at least 15 undergraduate students (ASU). Each of our workshops will capacitate 10-15 SERNEC experts, who in turn can recruit colleagues and students at their home collections. We will incorporate the project theme and use cases into undergraduate courses taught at six institutions and reaching an estimated 300-500 students annually (10-40% minority students). At each institution, project members will make a systematic effort to recruit new students from underrepresented groups. Our group's leadership of Symbiota (with close ties to iDigBio), SERNEC, and local biodiversity projects and centers will further promote the new data culture. We will create a feature story "Where do plant species occur?" for ASU's popular "Ask A Biologist" website, and a series of undergraduate student-led "How-To" videos that illustrate the use case workflows, including the creation of multi-taxonomy alignments.

Two Influential Primate Classifications Logically Aligned

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms.

Primate Taxonomy: Inflation or Real?

This article reviews changes in primate taxonomy, especially those pertaining to the meaning of the term species, since its inception two and a half centuries ago. Despite continuing discoveries and the involvement of competent practitioners, the adoption of the polytypic species concept, especially underpinned by the biological species concept, ensured that primate taxonomy was in a sorry state by the middle of the twentieth century. In the latter half of the twentieth century, a gradual rethinking of the nature of species took place, and many different species concepts were proposed. The phylogenetic species concept has been widely adopted over the past ∼20 years, sustained by a gradual realization that species are evolutionary lineages. This review provides examples of how the old way of thinking about species hampered our understanding of primate biodiversity and of how the phylogenetic species concept (or the diagnosability criterion under the general lineage concept) has clarified matters, opening them up for discussion. The adoption of this evolutionary view of species has implications for conservation, particularly because it increases recognition of biodiversity.