Thursday, April 12, 2018

[Mammalogy • 2018] Ethiopian Highlands as A Cradle of the African Fossorial Root-rats (Genus Tachyoryctes), the Genetic Evidence

Šumbera, Krásová, Lavrenchenko, et al., 2018.

• Six major genetic clades do not correspond to the expected two or 13 root-rat species.
• Ethiopian, and not Kenyan, highlands are the cradle of the genus diversity.
• Root-rat history was shaped by climatic oscillations and complex geomorphology.
• The giant root-rat is an internal lineage of the genus modified for life in the Afroalpine.
• Root-rats and mole-rats represent different specialisations for the subterranean niche.

Root-rats of the genus Tachyoryctes (Spalacidae) are subterranean herbivores occupying open humid habitats in the highlands of Eastern Africa. There is strong disagreement about species diversity of the genus, because some authors accept two species, while others more than ten. Species with relatively high surface activity, the giant root-rat Tachyoryctes macrocephalus, which is by far largest member of the genus, and the more fossorial African root-rat Tachyoryctes splendens, which eventually has been divided up to 12-13 species, represent two major morphological forms within the genus. In our study, we carried out a multilocus analysis of root-rats’ genetic diversity based on samples from 41 localities representing most of Tachyoryctes geographic distribution. Using two mitochondrial and three nuclear genes, we found six main genetic clades possibly representing separate species. These clades were organised into three basal groups whose branching is not well resolved, probably due to fast radiation in the late Pliocene and early Pleistocene. Climatic changes in that time, i.e. fast and repeated changes between extremely dry and humid conditions, which both limited root-rat dispersal, probably stimulated their initial genetic diversification. Contrary to expectation based on the largest root-rat diversity in Kenya (up to eight species by some authors), we found the highest diversity in the Ethiopian highlands, because all but one putative species occur there. All individuals outside of Ethiopia belong to a single recently diverged and expanded clade. This species should bear the name T. annectens (Thomas, 1891), and all other names of taxa described from outside of Ethiopia should be considered its junior synonyms. However, to solve taxonomic issues, future detailed morphological analyses should be conducted on all main clades together with genetic analysis of material from areas of their supposed contact. One of the most interesting findings of the study is the internal position of T. macrocephalus in T. splendens sensu lato. This demonstrates the intriguing phenomenon of accelerated morphological evolution of rodents occupying the Afroalpine zone in Ethiopia. Finally, we discuss how the distribution of Tachyoryctes is influenced by competition with another group of subterranean herbivores on the continent, the African mole-rats. We assume that both groups do not compete directly as previously expected, but specialisation to different subterranean niches is the main factor responsible for their spatial segregation.

Keywords: Tachyoryctes; fossorial rodent; Eastern Africa; Plio-Pleistocene climatic changes; Great Rift Valley; multi-species coalescent


Contrary to the expectation that root-rats have their highest species diversity in the Kenyan highlands, our results convincingly demonstrated that the Ethiopian mountains are the centre of genus diversity and the cradle of the whole group. The evolution of extant root-rats took place in the Pleistocene and was affected mainly by the interplay between climate changes and the complex geomorphology, with the presence of high mountain massifs, in Ethiopia. Root-rat genetic structure in Ethiopia suggests several cryptic species that should be explored in future taxonomic work, because it is clear that current taxonomy does not reflect the evolutionary history of the genus at all. Probably all taxa described from outside Ethiopia are descendants of a single relatively recent “out-of-Ethiopia” dispersal event and should be considered as conspecific. The fact that the largest and morphologically most deviating species, T. macrocephalus, is not a sister but an internal lineage of “splendens” is further evidence of a fast morphological evolution in response to strong selection in the Afroalpine environment in Ethiopia. We may expect that more thorough genetic surveys of unique Afroalpine taxa will reveal more such findings not only in mammals, but also in other groups of vertebrates. Finally, ecological, behavioural and physiological studies could reveal how the distribution of root-rats is influenced by competition with the African mole-rats, another group of African rodents with subterranean habits.

Radim Šumbera, Jarmila Krásová, Leonid A. Lavrenchenko, Sewnet Mengistu, Afework Bekele, Ondřej Mikula and Josef Bryja. 2018. Ethiopian Highlands as A Cradle of the African Fossorial Root-rats (Genus Tachyoryctes), the Genetic Evidence. Molecular Phylogenetics and Evolution. In Press.   DOI: 10.1016/j.ympev.2018.04.003

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