Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group)

Abstract

Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. Conclusion The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Patterns and Predictors of Small Mammal Phylogenetic and Functional Diversity in Contrasting Elevational Gradients in Kenya

“…The clades sampled at the highest elevations in Mt. Kenya, besides the locally abundant ones such as clades in the genera Lophuromys and Crocidura (Musila et al, 2019a;Onditi et al, 2021), included Dendromus, Otomys, Dasymys, and Rhabdomys clades that were overall rarer at transects in lower elevations (Supplementary Materials 1, 4) and noted to have evolved to prefer the moist highland forests (Carleton and Musser, 2013;Denys et al, 2017). In Chyulu, such specialists included clades in the genera Grammomys, Otomys, Praomys, and Zelotomys, which were not recorded below the 1,800-and 2,000-m transects that had patches of Afromontane rainforests.…”

Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals

“…The genera Rhabdomys and Montemys do not occur in the ARM at all (the latter is replaced there by its ecological equivalent Praomys jacksoni; Mizerovská et al, 2019). The SRM species in the genera Hylomyscus and Lophuromys are replaced in the ARM by phylogenetically distant congeneric species (Kerbis Peterhans et al, 2020;Onditi et al, 2021). In other taxa, the phylogenetic affinities probably also depend on the level of specialization to montane forests.…”

“…There is a growing database of rodent and shrew mtDNA sequences for the cytochrome b gene (CYTB), enabling comparative analyses of genetic structure. Even though CYTB is only one non-recombining locus, which might introgress into other evolutionary lineages (e.g., between rodent taxa in geomorphologically complex Ethiopian Highlands; Bryja et al, 2018b;Komarova et al, 2021), it is an informative marker to explore genetic structure in the studied area, as demonstrated by comparison of mtDNA structure with that obtained by nuclear markers (Bryja et al, 2014b(Bryja et al, , 2017Krásová et al, 2019;Onditi et al, 2021) or even genomic approaches (our unpublished data). Therefore, we performed comparative analysis of phylogeographic structure using CYTB as a main marker.…”

“…The robustness of the nodes was evaluated by the default bootstrap procedure with 1,000 replicates and new sequences were considered as part of previously defined taxa/clades if the bootstrap support was > 95%. Specifically, we compared the new sequences with relevant data in recent phylogenetic studies (Castiglia et al, 2012;Colangelo et al, 2013;Bryja et al, 2014a,b;Stanley et al, 2015;Bryja et al, 2017Bryja et al, , 2018aMazoch et al, 2018;Petružela et al, 2018;Sabuni et al, 2018;Krásová et al, 2019Krásová et al, , 2021Hánová et al, 2021a,b;Onditi et al, 2021;Dianat et al, unpublished data) and/or with unpublished sequences obtained by our teams in East Africa in the last decade. The distribution maps of genetic…”

Species of the cyprinid genus Garra in Mount Kenya, East Africa: Species delineation, taxonomy and historical biogeography

“…More attention has recently been focused on hidden biodiversity, phylogeography, speciation and multiple genetically divergent, but morphologically cryptic lineages for various taxa within the EAR (Bannikova et al, 2021;Demos et al, 2014;Hughes et al, 2018;Mairal et al, 2017;Onditi et al, 2021). Integrative approaches have proven extremely valuable in the detection of unrecognized diversity for rheophilic fishes of the region, particularly widespread taxa (Bart et al, 2019;Chakona et al, 2018;Moritz et al, 2019;Schmidt et al, 2014Schmidt et al, , 2015Schmidt et al, , 2017Schmidt et al, , 2018.…”