The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses.

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

Researchers join forces to conserve red colobus (Piliocolobus badius temminckii) in West Africa.

The recent development of the Red Colobus Conservation Action Plan has spurred momentum to promote site-based conservation of red colobus while forging partnerships among researchers and building local capacity. Communities for Red Colobus (C4RC) is a community-centered conservation organization in The Gambia, West Africa, that aims to protect Temminck's red colobus (Piliocolobus badius temminckii) while advancing opportunities for local people. We highlight the inception and initial development of C4RC with its educational and ranger teams and describe how local and international collaborations have positively impacted the organization through training and mentoring programs. This conservation program has the potential to become sustainable with plans for continued ecological monitoring, reforestation efforts, use of alternative methods of cooking, and the expansion of ecotourism. We hope that the dissemination of project information through Gambian broadcast and social media channels and wider community outreach activities will improve perceptions and conservation of primates and inspire the development of other red colobus initiatives at suitable forest sites based on the C4RC model of community-based conservation.

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia.

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2 - characterized by strains that cause human extraintestinal infections - and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes - indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.

UNLABELLED: Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens. IMPORTANCE: The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.

The coevolution of circumperineal color and terrestriality.

Old World monkeys (Cercopithecoidea) are unusual among primates for the high percentage of species exhibiting circumperineal coloration, as well as the large percentage of highly terrestrial species. Kingdon [1974, 1980] suggested that circumperineal skin coloration is functionally related to terrestriality, but this hypothesis has not been tested. From the literature, we collected data on habitat use (terrestrial/arboreal) and circumperineal coloration (present/absent) for 78 species. Indeed, among the 78 species surveyed here, 75% of them fall into either the category of colored circumperineals with terrestrial lifestyle, or of uncolored circumperineals with arboreal lifestyle (Χ(2)(1) = 19.550, P < 0.001). However, conventional statistical procedures assume all taxa are equally related-which is not usually the case in multispecies analyses-leading to higher rates of both type I and II statistical errors. We performed Bayesian trait coevolution analyses that show that models of dependent trait evolution are not significantly better than models assuming independent evolution of the two traits (log-likelihood ratio test P = 0.396, Bayes Factor = 1). Bayesian nodal reconstructions of the cercopithecoid phylogeny indicate that relatively few trait transitions are needed to account for the distributions of the two traits. Further, chi-squared distributional tests show that sub-family affiliation (i.e., Cercopithecinae, Colobinae) is an accurate predictor of trait status. The discordance of the analyses may represent the results of a few different evolutionary scenarios, but ultimately circumperineal coloration seems weakly linked to terrestrial ecology.