Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes
Genís Garcia-Erill, Christian H.F. Jørgensen, Vincent B. Muwanika, Xi Wang, Malthe S. Rasmussen, Yvonne A. de Jong, Philippe Gaubert, Ayodeji Olayemi, Jordi Salmona, Thomas M. Butynski, Laura D. Bertola, Hans R. Siegismund, Anders Albrechtsen and Rasmus Heller
Molucular Biolology and Evolution 39(7):msac134
Abstract: 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.
Abstract: 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.
Butynski, T. M. & De Jong, Y. A. (2022). Conservation of Africa’s colobine monkeys (Cercopithecidae, Colobinae) with taxonomic and biogeographic considerations. In: The Colobines: Natural History, Behaviour and Ecological Diversity. I. Matsuda, C. G. Grueter & J. A. Teichroeb, eds. Cambridge University Press, Cambridge, UK. Pp. 342–393.
Can morphotaxa be assessed with photographs? Estimating the accuracy of two-dimensional cranial geometric morphometrics for the study of threatened populations of African monkeys
By Andrea Cardini, Yvonne de Jong and Tom Butynski
Abstract: The classification of most mammalian orders and families is under debate and the number of species is likely greater than currently recognized. Improving taxonomic knowledge is crucial, as biodiversity is in rapid decline. Morphology is a source of taxonomic knowledge, and geometric morphometrics applied to two dimensional (2D) photographs of anatomical structures is commonly employed for quantifying differences within and among lineages. Photographs are informative, easy to obtain, and low cost. 2D analyses, however, introduce a large source of measurement error when applied to crania and other highly three dimensional (3D) structures. To explore the potential of 2D analyses for assessing taxonomic diversity, we use patas monkeys (Erythrocebus), a genus of large, semi-terrestrial, African guenons, as a case study. By applying a range of tests to compare ventral views of adult crania measured both in 2D and 3D, we show that, despite inaccuracies accounting for up to one-fourth of individual shape differences, results in 2D almost perfectly mirror those in 3D. This apparent paradox might be explained by the small strength of covariation in the component of shape variance related to measurement error. A rigorous standardization of photographic settings and the choice of almost coplanar landmarks are likely to further improve the correspondence of 2D to 3D shapes. 2D geometric morphometrics is, thus, appropriate for taxonomic comparisons of patas ventral crania. Although it is too early to generalize, our results corroborate similar findings from previous research in mammals, and suggest that 2D shape analyses are an effective heuristic tool for morphological investigation of small differences.
Thomas M. Butynski & Yvonne A. de Jong (2021). Sympatry between desert warthog Phacochoerus aethiopicus and common warthog Phacochoerus africanus in Kenya, with particular reference to Laikipia County. Suiform Soundings 20(1): 33-44
Abstract
Desert warthog Phacochoerus aethiopicus delamerei and common warthog Phacochoerus africanus are widespread and locally common in the Horn of Africa and Kenya, east of the Eastern Rift Valley. It is of particular interest that these two taxa, the only two extant species in the genus Phacochoerus, occur in sympatry in some regions. Within Kenya, sympatry is known for the northern coast, Tsavo East National Park, Tsavo West National Park, and Meru National Park. This article presents information on a fifth region of sympatry, Laikipia County, central Kenya. Individuals that we judged to be atypical for either desert warthog or common warthog were encountered in Laikipia. New information on the distribution, abundance, population structure, ecology, and behaviour of desert warthog in Laikipia is presented. Laikipia offers considerable opportunity for comparative research on the morphology, molecular biology, ecology, and behaviour of desert warthog and common warthog.
Young adult male desert warthog Phacochoerus aethiopicus, Suyian Ranch, northern Laikipia County, central Kenya. Photo: Yvonne de Jong and Tom Butynski.
