Biogeography and conservation of desert warthog Phacochoerus aethiopicus and common warthog Phacochoerus africanus (Artiodactyla: Suidae) in the Horn of Africa

Two species of warthog are currently widely recognised, the poorly known desert warthog Phacochoerus aethiopicus and the widely distributed common warthog Phacochoerus africanus. Spatial data for both species were collected during field surveys and from the literature, museums, colleagues, naturalists, local experts, and online resources to assess their biogeography in the Horn of Africa (HoA). Their distributions were overlaid with ArcGIS datasets for altitude, rainfall, temperature, and ecoregions. Phacochoerus aethiopicus appears to be restricted to Ethiopia, Kenya, and Somalia, with no records west of the Eastern Rift Valley (ERV). The estimated current geographic distribution of P. aethiopicus is 1,109,000 km2. Phacochoerus africanus occurs in all five countries of the HoA and has an estimated current geographic distribution in the HoA of 1,213,000 km2. Phacochoerus africanus appears to be the more adaptable species although P. aethiopicus is able to live where mean annual rainfall is more variable. Although both species are allopatric over vast regions, they are sympatric in central east Ethiopia, north Somalia, central Kenya, north coast of Kenya, and southeast Kenya. Both suids remain locally common, their populations are, however, in decline due to the negative impacts on the environment by the rapidly growing human populations in all five countries.

Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes

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.

On the true nature of the sphenoidal “pits” in the common warthog, Phacochoerus africanus (Artiodactyla, Suidae), and a description of the cranial sinuses

The peculiar sphenoidal “pits” of the common warthog (Phacochoerus africanus) long have been recognized as a feature that distinguishes that species from the closely related desert warthog (P. aethiopicus). Authors seem to regard these structures as blind pockets that do not extend beyond the basicranium. However, these structures actually are openings that lead into a complex system of sinuses (the sphenoidal sinuses) located in the sphenoid and squamosal, and occasionally extending into the occipital and parietal bones. The openings appear to serve as a drain into the nasopharynx. The sphenoidal “pits” of P. africanus as currently defined by most authors are, therefore, not homologous with the sphenoidal pits of P. aethiopicus. We suggest that the term “sphenoidal apertures” be applied to these openings. The true homologue of the sphenoidal pits of P. aethiopicus is the bone that surrounds the sphenoidal apertures in P. africanus. This would include the thin bony sheet that forms the floor of the opening and that bears a shallow fossa. We recommend the term “sphenoidal shelf” be employed to describe this part of the true sphenoidal pit of P. africanus. In addition to the sphenoidal sinuses, the maxillary and frontal sinuses of P. africanus also are described. We report the possibility of mammalian cranial sinuses arising from nasopharyngeal diverticula rather than from diverticula originating from the nasal cavity proper. Previously, such nasopharyngeal pneumatization only has been known to occur in Reptilia. Possible sinus functions are discussed including shock absorption, lightening of the skull, improvement of olfaction, and enhancement of the immune system. In addition to P. africanus, sphenoidal apertures also occur in Babyrousa, and in an extinct perissodactyl, a brontothere (= titanothere).

The case of the grass-eating suids in the Plio-Pleistocene Turkana Basin: 3D dental topography in relation to diet in extant and fossil pigs

Two separate subfamilies of Plio-Pleistocene African pigs (suids) consecutively evolved hypsodont and horizodont molars with flat occlusal surfaces, commonly interpreted as an adaptive trait to a grazing diet, similar to that of the present warthogs (Phacochoerus spp.). To investigate this in detail, we studied the 3D-dental topography of fossil specimens from the Turkana Basin, using geographic information systems-based methods. To establish baselines for interpretation of the Turkana Basin suids, topography of third molars of extant suids with known diets were analyzed: grazing warthog (Phacochoerus africanus), herbivorous mixed-feeder forest hog (Hylochoerus meinertzhageni), omnivorous generalist wild boar (Sus scrofa), omnivorous fruit and tuber eater bush pig (Potamochoerus spp.), and omnivorous fruit eater babirusa (Babyrousa spp.) In addition, we analyzed supposedly browsing Miocene suids, Listriodon spp. The same topographic measures were applied to Plio-Pleistocene specimens from the Turkana Basin, Kenya: Notochoerus euilus, Notochoerus scotti, Kolpochoerus heseloni, and Metridiochoerus andrewsi. With some differences between techniques, 3D-dental topography analysis of extant suid molars mostly predicts the dietary differences between the species correctly. The grazing P. africanus differs from both the omnivorous suids and the herbivorous mixed-feeder H. meinertzhageni in all except one metrics. The omnivorous mostly tropical suids, Potamochoerus and Babyrousa, primarily differ from the generalist, S. scrofa, in the orientation patch count analysis, showing higher occlusal complexity in the latter. Although, there might be significant gaps between the morphological changes and the ecological changes, we conclude that based on comparison of dental topography with the present-day suids, N. scotti and M. andrewsi were most likely highly specialized grazers, while N. euilus and K. heseloni retained more of their ancestral, omnivorous heritage, but consumed grasses more than the extant omnivorous suids. RESEARCH HIGHLIGHTS: Dental topography can predict different diets in present-day wild pigs. The Plio-Pleistocene pigs in the Turkana Basin had dental topography mostly similar to extant grazing warthog, although some species also had resemblances to omnivorous forest pigs.

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Background

Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept.

Results

The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia.

Conclusions

The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.

Comparative molecular cytogenetics in Cetartiodactyla

Cetartiodactyla comprises Artiodactyla (even-toed ungulates) and Cetacea (whales, dolphins and porpoises). Artiodactyla is a large taxon represented by about 200 living species ranked in 10 families. Cetacea are classified into 13 families with almost 80 species. Many publications concerning karyotypic relationships in Cetartiodactyla have been published in previous decades. Formerly, the karyotypes of closely related species were compared by chromosome banding. Introduction of molecular cytogenetic methods facilitated comparative mapping between species with highly rearranged karyotypes and distantly related species. Such information is a prerequisite for the understanding of karyotypic phylogeny and the reconstruction of the karyotypes of common ancestors. This study summarizes the data on chromosome evolution in Cetartiodactyla, mainly derived from molecular cytogenetic studies. Traditionally, phylogenetic relationships of most groups have been estimated using morphological data. However, the results of some molecular studies of mammalian phylogeny are discordant with traditional conceptions of phylogeny. Cetartiodactyls provide several examples of incongruence between traditional morphological and molecular data. Such cases of conflict include the relationships of the major clades of artiodactyls, the relationships among the extant families of the suborder Ruminantia or the phylogeny of the family Bovidae. The most unexpected aspect of the molecular phylogeny was the recognition that Cetacea is a deeply nested member of Artiodactyla. The largest living order of terrestrial hoofed mammals is the even-toed hoofed mammals, or Artiodactyla. The artiodactyls are composed of over 190 living species including pigs, peccaries, hippos, camels, llamas, deer, pronghorns, giraffes, sheep, goats, cattle and antelopes. Cetacea is an order of wholly aquatic mammals, which include whales, dolphins and porpoises. Cetartiodactyla has become the generally accepted name for the clade containing both of these orders.

Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable?

The European wild boar is an important game species, subjected to local extinctions and translocations in the past, and currently enormously and worryingly expanding in some areas where management is urgently required. Understanding the relative roles of ancient and recent events in shaping the genetic structure of this species is therefore not only an interesting scientific issue, but it represents also the basis for addressing future management strategies. In addition, several pig breeds descend from the European wild boar, but the geographical location of the domestication area(s) and the possible introgression of pig genomes into wild populations are still open questions. Here, we analysed the genetic variation in different wild boar populations in Europe. Ten polymorphic microsatellites were typed in 252 wild boars and the mtDNA control region was sequenced in a subset of 145 individuals. Some samples from different pig breeds were also analysed. Our results, which were obtained considering also 612 published mtDNA sequences, suggest that (i) most populations are similarly differentiated, but the major discontinuity is found along the Alps; (ii) except for the Italian populations, European wild boars show the signature of a postglacial demographic expansion; (iii) Italian populations seem to preserve a high proportion of preglaciation diversity; (iv) the demographic decline which occurred in some areas in the last few centuries did not produce a noticeable reduction of genetic variation; (v) signs of human-mediated gene flow among populations are weak, although in some regions the effects of translocations are detectable and a low degree of pig introgression can be identified; (vi) the hypothesis of an independent domestication centre in Italy is not supported by our data, which in turn confirm that Central European wild boar might have represented an important source for domestic breeds. We can therefore conclude that recent human activities had a limited effect on the wild boar genetic structure. It follows that areas with high variation and differentiation represent natural reservoirs of genetic diversity to be protected avoiding translocations. In this context controlling some populations by hunting is not expected to affect significantly genetic variation in this species.

The pygmy hog is a unique genus: 19th century taxonomists got it right first time round

The pygmy hog, Sus salvanius, the smallest and rarest extant suid was first described as the only member of the genus Porcula. It is currently regarded as member of the genus Sus and a sister taxon of the domestic pig/Eurasian wild boar (Sus scrofa). Phylogenetic analyses of 2316 bp from three mtDNA loci (control-region, cytochrome b, 16S) by Bayesian inference and statistical testing of alternative phylogenetic hypotheses all support the original classification of the pygmy hog as a unique genus. Thus, we propose that the species name Porcula salvania should be resurrected. The reclassification will heighten awareness of the need for the future protection and survival of this unique species.

Faecal steroid metabolites for non-invasive assessment of reproduction in common warthogs (Phacochoerus africanus), red river hogs (Potamochoerus porcus) and babirusa (Babyrousa babyrussa)

The objectives of this study were to analyse faecal steroid metabolites in African and South East Asian pig species kept in European zoos. Species studied were the warthog (Phacochoerus africanus), the red river hog (Potamochoerus porcus) and the babirusa (Babyrousa babyrussa). Faecal samples were collected 1-3 times per week from non-pregnant and pregnant captive female warthogs (n = 9), red river hogs (n = 7) and babirusas (n = 5). Enzyme-immunoassays for faecal progesterone, androgen, and oestrogen metabolites, were tested for their ability to determine follicular and luteal phases. In all three species, oestrous cycles could be monitored with 20alpha-OH- and 20-oxo-pregnane assays. In contrast, oestrogens and androgens were not useful in characterising follicular activity during the oestrous cycle in any species. Faecal 20alpha-OH- and 20-oxo-pregnane values were significantly correlated. Faecal pregnane concentrations revealed species-specific differences. Luteal phase values of 20alpha-OH-pregnanes were considerably higher than 20-oxo-pregnanes; 20alpha-OH-pregnanes were in the range of 3-10 microg/g in warthogs and red river hogs, whereas concentrations were 30-200 microg/g faeces in the babirusa. Regular oestrus cycles had a length of about 35 days in all three species studied. Results indicated a seasonal influence on the occurrence of reproductive cycles in the warthog with anoestrous periods in the European summer. The red river hog was found to be a seasonal and poly oestrous breeder; oestrus cycles started by January and continued until summer. In contrast, the babirusa showed non-seasonal ovarian cyclicity. In pregnant red river hogs, progesterone metabolites were comparable to luteal phase values of the oestrous cycle during the first 3 months of gestation, but did further increase during the last month of pregnancy. Oestrogens and 17-oxo-androstanes were significantly elevated during the second half of gestation. In summary, the reproductive biology of three exotic pig species was studied using non-invasive faecal steroid analysis and these methods were used for comparative investigations of oestrous cycles, pregnancy and seasonality.

A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)

Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains controversial. Using the supertree approach of matrix representation with parsimony, we present the first phylogeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However, due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus, Muntiacus, Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.