Otomys fortior Thomas 1906

Mizerovská, Daniela, Martynov, Aleksey A., Mikula, Ondřej, Bryjová, Anna, Meheretu, Yonas, Lavrenchenko, Leonid A. & Bryja, Josef, 2023, Genomic diversity, evolutionary history, and species limits of the endemic Ethiopian laminate-toothed rats (genus Otomys, Rodentia: Muridae), Zoological Journal of the Linnean Society 199 (4), pp. 1059-1077 : 1073

Otomys fortior Thomas 1906

Charada Vlei Rat

Otomys typus fortior : Thomas 1906:302 (type locality— Ethiopia, Kaffa, Charada Forest, 1829 m); Allen 1939:348 (listed as valid subspecies); Ellerman 1941:321 (listed as valid subspecies); Bohmann 1952:45 (taxonomic revision, retained as valid subspecies).

Otomys fortior Dollman 1915 —Kaffa, Ethiopia.

Otomys typus ( fortior ) Misonne 1974, Yalden et al. 1976 and Musser and Carleton 1993—without indication of rank.

Holotype: BMNH 6.11 .1.29.

Type locality: Ethiopia, Charada Forest, Kaffa, 1829 m a.s.l..

Taxonomic notes: Otomys fortior shares a common karyotype of 2n = 58, NFa = 58 with O. typus and O. helleri , as well as higher number of eight laminae in M3. This is the most distinct species in the TYPUS group, both genomically ( Figs 3–6 ) and ecologically (the only species living in forest clearings at relatively low elevation in south-western Ethiopia; Fig. 2 ). Morphological analysis did not show any special ecological adaptations to different environments.

Distribution: The species lives in tropical forests in south-western Ethiopia, west of the Omo River, from where we provide numerous new data [compared to Taylor et al. (2011)]. The elevational range of genetically confirmed records is 1360–2600 m a.s.l.. The specimens from the Jimma area were assigned to O. fortior based on geographic and ecological data. However, based on cranial characteristics, they are related to O. cheesmani ( Taylor et al. 2011) , which might be just an artefact of morphological analysis.

Figures

Figure 2. A, Cytb phylogeny of two groups (the TYPUS and SIMIENSIS groups) of endemic Ethiopian taxa from the O. typus complex. The numbers above the branches indicate BI posterior probability/ML bootstrap support.Maps show the distribution of the mitochondrial diversity in the Ethiopian SIMIENSIS group (B) and TYPUS group (C). Coloured circles indicate the localities with genetically characterized individuals; different colours correspond to six Ethiopian species marked by coloured bars on the right side of the phylogenetic tree.Stars of particular colours show the type localities (there are two stars for O. cheesmani; Dangila is the type locality, the paratype specimen was collected from Gojam). White dots are records of non-genotyped Otomys [based on Yalden et al. (1976, 1996) and the GBIF database; see more details in Bryja et al. (2019a)]. The shades of grey on the map indicate elevation.

Figure 3. ML tree of concatenated SNPs loci developed by ddÞD approach. Numbers above the branches indicate the bootstrap support; coloured bars correspond to six presumed Ethiopian species (for their distribution see Fig. 2B and C). The tree is based on the dataset of 5587 loci and 48 200 SNPs with a minimum 10% occupancy, but the trees from more filtered data had concordant topologies, only with progressively lower support of clades (not shown).

Figure 4. The result of sNMF analysis based on 80% occupancy dataset, i.e. 3141 biallelic SNPs (one SNP per locus).Vertical bars show individual genotypes as composed of ancestral population gene pools, whose proportional contributions are indicated by coloured segments. Horizontal lines at the boưom delimit clusters defined by the dominant ancestral contributions. The associated labels identify clusters with named species or their geographically restricted populations (B. S. = Borena Saynt, D. S. = Debre Sina).Note that specimens from the populations in Borena Saynt and Aboye Gara, identified as O. simiensis by mtDNA and concatenated ddÞD data, cluster with O. cf. yaldeni from Ankober (purple cluster).

Figure 5. Co-ancestry matrix and delimitation of gene pools by two different methods: fineSTRUCTURE (18 clusters shown by grey squares) and Infomap (three clusters shown by black squares). The intensity of the colour (from yellow to blue) indicates the level of co-ancestry among individual genomes.

Figure 6. Species trees obtained from the MSC analyses in BPP. The MCC tree from A11 analysis (A) is shown with clade PPs in its branch labels, while the tree from A00 analysis (B) shows gdi values. In circles, there are high gdi values (≥0.70) obtained for the extant or ancestral species in the original A00 analysis; in diamonds, there are high or low gdi values (white and grey background, respectively) that were obtained by the iterative merging procedure. Colour bars indicate six nominal Ethiopian species.