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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., (© 2024. The Author(s).) more...

Estimating population densities and their trends over time is essential for understanding primate ecology and for guiding conservation efforts. From 2011 through to 2019, we counted two guenon species during seasonal road transect surveys in Lake Manyara National Park: the Tanzania-endemic Manyara monkey Cercopithecus mitis manyaraensis (International Union for Conservation of Nature and Natural Resources, IUCN, Red List category of "endangered") and the vervet monkey Chlorocebus pygerythrus (Red List category of "least concern"). To account for imperfect detectability, we analysed the data in a line distance sampling framework, fitted species-specific detection functions, and subsequently estimated seasonal densities. To test for seasonal differences and yearly trends in the species-specific density estimates, we fitted generalized additive models. Seasonal point density estimates fluctuated considerably during the 9 years (2011-2019) of our study, ranging from 3 to 29 individuals km - 2 for Manyara monkeys and from 19 to 83 individuals km - 2 for vervet monkeys. Densities of both taxa did not differ seasonally, and we did not detect marked directional population trends. Our study illustrates the utility and limitations of line distance sampling for long-term primate monitoring. Beyond informing primate ecology and management, our results highlight the conservation importance of Lake Manyara National Park for primate conservation., Competing Interests: At least one of the (co-)authors is a member of the editorial board of . The peer-review process was guided by an independent editor, and the authors also have no other competing interests to declare., (Copyright: © 2022 Christian Kiffner et al.) more...

African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000-1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region's importance in African biogeography. We found that immune system-related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.) more...

In 2020, a new subspecies was described in the Cercopithecus mitis complex, the Manyara monkey C. m. manyaraensis , Butynski & De Jong, 2020. The internal taxonomy of this species complex is still debated, and the phylogenetic relationships among the taxa are unclear. Here we provide the first mitochondrial sequence data for C. m. manyaraensis to determine its position within the mitochondrial phylogeny of C. mitis . This subspecies clusters within the youngest (internal divergences between 1.01 and 0.42 Ma) of three main taxonomic clades of C. mitis . Its sister lineages are C. m. boutourlinii (Ethiopia), C. m. albotorquatus (Kenya and Somalia), C. m. albogularis (Kenya and Tanzania), and C. m. monoides (Tanzania and Mozambique). In general, the phylogenetic tree of C. mitis based on mitochondrial sequence data indicates several paraphyletic relationships within the C. mitis complex. As in other African cercopithecines (e.g. Papio and Chlorocebus ), these data are suitable for reconstructing historic biogeographical patterns, but they are only of limited value for delimitating taxa., Competing Interests: At least one of the (co-)authors is a member of the editorial board of . The peer-review process was guided by an independent editor, and the authors also have no other competing interests to declare., (Copyright: © 2022 Dietmar Zinner et al.) more...

The common chimpanzee Pan troglodytes is the closest extant relative of modern humans and is often used as a model organism to help understand prehistoric human behavior and ecology. Originally presumed herbivorous, chimpanzees have been observed hunting 24 species of birds, ungulates, rodents, and other primates, using an array of techniques from tools to group cooperation. Using the literature on chimpanzee hunting behavior and diet from 13 studies, we aimed to determine the prey preferences of chimpanzees. We extracted data on prey-specific variables such as targeted species, their body weight, and their abundance within the prey community, and hunter-specific variables such as hunting method, and chimpanzee group size and sex ratio. We used these data in a generalized linear model to determine what factors drive chimpanzee prey preference. We calculated a Jacobs' index value for each prey species killed at two sites in Uganda and two sites in Tanzania. Chimpanzees prefer prey with a body weight of 7.6 ± 0.4 kg or less, which corresponds to animals such as juvenile bushbuck ( Tragelaphus scriptus ) and adult ashy red colobus monkeys ( Piliocolobus tephrosceles ). Sex ratio in chimpanzee groups is a main driver in developing these preferences, where chimpanzees increasingly prefer prey when in proportionally male-dominated groups. Prey preference information from chimpanzee research can assist conservation management programs by identifying key prey species to manage, as well as contribute to a better understanding of the evolution of human hunting behavior., Competing Interests: To the best of our knowledge, there is no conflict of interest., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.) more...

Kenya has a rich mammalian fauna. We reviewed recently published books and papers including the six volumes of Mammals of Africa to develop an up-to-date annotated checklist of all mammals recorded from Kenya. A total of 390 species have been identified in the country, including 106 species of rodents, 104 species of bats, 63 species of even-toed ungulates (including whales and dolphins), 36 species of insectivores and carnivores, 19 species of primates, five species of elephant shrews, four species of hyraxes and odd-toed ungulates, three species of afrosoricids, pangolins, and hares, and one species of aardvark, elephant, sirenian and hedgehog. The number of species in this checklist is expected to increase with additional surveys and as the taxonomic status of small mammals (e.g., bats, shrews and rodents) becomes better understood. more...

Background: Aggressive behaviors are an integral part of competitive interactions. There is considerable variation in aggressiveness among individuals both within and among species. Aggressiveness is a quantitative trait that is highly heritable. In modern humans and macaques (Macaca spp.), variation in aggressiveness among individuals is associated with polymorphisms in the serotonergic (5-HT) neurotransmitter system. To further investigate the genetics underlying interspecific variation in aggressiveness, 123 wild individuals from five baboon species (Papio papio, P. hamadryas, P. anubis, P. cynocephalus, and P. ursinus) were screened for two polymorphisms in promoter regions of genes relevant for the 5-HT system (5-HTTLPR and MAOALPR)., Results: Surprisingly, despite considerable interspecific variation in aggressiveness, baboons are monomorphic in 5-HTTLPR, except for P. hamadryas, which carries one additional allele. Accordingly, this locus cannot be linked to behavioral variation among species. A comparison among 19 papionin species, including nine species of macaques, shows that the most common baboon allele is similar to the one described for Barbary macaques (Macaca sylvanus), probably representing the ancestral allele in this tribe. It should be noted that (almost) all baboons live in Africa, but within Macaca only M. sylvanus lives on this continent. Baboons are, however, highly polymorphic in the so-called 'warrior gene' MAOALPR, carrying three alleles. Due to considerable variation in allele frequencies among populations of the same species, this genotype cannot be invoked to explain variation in aggressiveness at the species level., Conclusions: This study provides another indication that 5-HTTLPR is not related to aggressiveness in primates per se, but may have been under differential selective pressures among taxa and potentially among populations in different geographic regions. The results on MAOALPR alleles in Papio indicate that variation in the metabolism of monoamine neurotransmitters and associated behaviors is more important among populations than among species. We, therefore, propose to compile behavioral data from additional populations of Papio to obtain further insight into the genetics underlying behavioral differences among primate species. more...

Many species of Arabian mammals are considered to be of Afrotropical origin and for most of them the Red Sea has constituted an obstacle for dispersal since the Miocene-Pliocene transition. There are two possible routes, the 'northern' and the 'southern', for terrestrial mammals (including humans) to move between Africa and Arabia. The 'northern route', crossing the Sinai Peninsula, is confirmed for several taxa by an extensive fossil record, especially from northern Egypt and the Levant, whereas the 'southern route', across the Bab-el-Mandab Strait, which links the Red Sea with the Gulf of Aden, is more controversial, although post-Pliocene terrestrial crossings of the Red Sea might have been possible during glacial maxima when sea levels were low. Hamadryas baboons (Papio hamadryas) are the only baboon taxon to disperse out of Africa and still inhabit Arabia. In this study, we investigate the origin of Arabian hamadryas baboons using mitochondrial sequence data from 294 samples collected in Arabia and Northeast Africa. Through the analysis of the geographic distribution of genetic diversity, the timing of population expansions, and divergence time estimates combined with palaeoecological data, we test: (i) if Arabian and African hamadryas baboons are genetically distinct; (ii) if Arabian baboons exhibit population substructure; and (iii) when, and via which route, baboons colonized Arabia. Our results suggest that hamadryas baboons colonized Arabia during the Late Pleistocene (130-12 kya [thousands of years ago]) and also moved back to Africa. We reject the hypothesis that hamadryas baboons were introduced to Arabia by humans, because the initial colonization considerably predates the earliest records of human seafaring in this region. Our results strongly suggest that the 'southern route' from Africa to Arabia could have been used by hamadryas baboons during the same time period as proposed for modern humans., (Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.) more...

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action. more...

A distinct species of mangabey was independently found at two sites 370 kilometers apart in southern Tanzania (Mount Rungwe and Livingstone in the Southern Highlands and Ndundulu in the Udzungwa Mountains). This new species is described here and given the name "highland mangabey" Lophocebus kipunji sp. nov. We place this monkey in Lophocebus, because it possesses noncontrasting black eyelids and is arboreal. L. kipunji is distinguished from other mangabeys by the color of its pelage; long, upright crest; off-white tail and ventrum; and loud call. This find has implications for primate evolution, African biogeography, and forest conservation. more...