Phylogeny and biogeography of the African Bathyergidae : a review of patterns and processes

BACKGROUND : We review genealogical relationships, biogeographic patterns and broad historical drivers of speciation within the Bathyergidae, a group of endemic African rodents, as well as identify key taxa which need further research. METHODS : We sourced comparable cytochrome b sequence data (comparable data available for all members for the Family) and geographic information for all six genera of the African subterranean rodent. This information was combined into the most comprehensive and geographically representative evolutionary study for the Bathyergidae to date. RESULTS : Species richness within the Bathyergidae appears to be underestimated, with undescribed taxa in five of the six genera. Biogeographic patterns suggest large historical distributions, which were repeatedly fragmented by major landscape changes (especially rifting, uplift and drainage evolution) since the Miocene. Aside from vicariant events, other factors (ecological specialization, population-level responses and climatic change) may have been instrumental in driving divergences in the Bathyergidae. As such, adaptive differences may exist among both populations and species across their discrete ranges, driving independent evolutionary trajectories among taxa. In addition, highly fragmented distributions of divergent (and often relict) lineages indicates the possibility of narrow endemics restricted to diminishing suitable habitats. From this, it is clear that a systematic revision of the Bathyergidae is necessary; such a revision should include comprehensive sampling of all putative taxa, the addition of genomic information to assess adaptive differences, as well as ecological information.Supplement 1: Phylogeny of the Bathyergidae based on cytochrome b sequence data. Phylogeny of the Bathyergidae constructed through Bayesian analysis (in BEAST) and based on the cytochrome b sequence data for all the available sample haplotypes listed in Table S1. The various mole-rat species included and identified within each genus are indicated. Values above nodes represent posterior probability values derived from the Bayesian analysis in BEAST and MrBayes respectively, while values below nodes indicate bootstrap values derived after Maximum Likelihood analysis in RAxML.Supplement 2: Specimen/sequence information of the bathyergids included in this study. Accession numbers of the cytochrome b haplotypes used in this study, also indicating the species (as designated on the public database), reference to the original study in which the sequence was generated, the species designation in the original study, the species designation in the current study and geographic information and coordinates of the sampling locality from where the species originates.Supplement 3: Species authorities on the bathyergid species included in this study.Supplement 4: Uncorrected sequence divergences among the six bathyergid genera. Pairwise estimates of uncorrected sequence divergence among the six bathyergid genera.Supplement 5: Uncorrected sequence divergences among the species within Heliophobius. Pairwise estimates of uncorrected sequence divergence among the various species included and identified within the genus Heliophobius.Supplement 6: Uncorrected sequence divergences among the species within Georychus. Pairwise estimates of uncorrected sequence divergence among the various species included and identified within the genus Georychus.Supplement 7: Uncorrected sequence divergences among the species within Bathyergus. Pairwise estimates of uncorrected sequence divergence among the various species included and identified within the genus Bathyergus.Supplement 8: Uncorrected sequence divergences among the species within Cryptomys. Pairwise estimates of uncorrected sequence divergence among the various species (subspecies) included and identified within the genus Cryptomys.Supplement 9: Uncorrected sequence divergences among the species within Fukomys. Pairwise estimates of uncorrected sequence divergence among the various species included and identified within the genus Fukomys.https://peerj.comam2020Zoology and Entomolog

Assessing introgressive hybridization in roan antelope (Hippotragus equinus):Lessons from South Africa

Biological diversity is being lost at unprecedented rates, with genetic admixture and introgression presenting major threats to biodiversity. Our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Biological Diversity. The current study concerns roan antelope, the second largest antelope in Africa. Despite their large size, these antelope are sensitive to habitat disturbance and interspecific competition, leading to the species being listed as Least Concern but with decreasing population trends, and as extinct over parts of its range. Molecular research identified the presence of two evolutionary significant units across their sub-Saharan range, corresponding to a West African lineage and a second larger group which includes animals from East, Central and Southern Africa. Within South Africa, one of the remaining bastions with increasing population sizes, there are a number of West African roan antelope populations on private farms, and concerns are that these animals hybridize with roan that naturally occur in the southern African region. We used a suite of 27 microsatellite markers to conduct admixture analysis. Our results indicate evidence of hybridization, with our developed tests using a simulated dataset being able to accurately identify F1, F2 and non-admixed individuals at threshold values of qi > 0.80 and qi > 0.85. However, further backcrosses were not always detectable with backcrossed-Western roan individuals (46.7-60%), backcrossed-East, Central and Southern African roan individuals (28.3-45%) and double backcrossed (83.3-98.3%) being incorrectly classified as non-admixed. Our study is the first to confirm ongoing hybridization in this within this iconic African antelope, and we provide recommendations for the future conservation and management of this species