Morphological and genetic characterization of Mount Kenya brush-furred rats (Lophuromys Peters 1874); relevance to taxonomy and ecology

Onditi, Kenneth Otieno; Peterhans, Julian Kerbis; Demos, Terrence C.; Musila, Simon; Chen, Zhongzheng; Jiang, Xue‐Long

doi:10.1007/s13364-019-00470-1

Cited by 5 publications

(8 citation statements)

References 63 publications

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“…The distribution of L. zena overlaps with L. stanleyi and L. ansorgei in the Kakamega Forest and with L. ansorgei in Yala Swamp. This distribution supports the conclusions of Onditi et al [72] that L. zena could have been much more widespread in Kenya than previously known [12,14]. The range of L. stanleyi is also much more extensive than previously described.…”

Section: Taxonomic Assessment Of the Non-ethiopian Avopunctatus Memberssupporting

confidence: 91%

“…L. margarettae was described by Heller [82] from the Mount Gargues (Mathews range), north-central Kenya, with Verheyen et al [12], Verheyen et al [14] con rming its presence on the lower elevations of the Kenya highlands. However, Onditi et al [72] did not record L. margarettae in the entire elevation gradient of Mount Kenya (ca. 1,700 -4,000 meters).…”

Section: Makundiimentioning

confidence: 98%

“…We performed a regression analysis with CS as an independent variable and the Procrustes coordinates as a dependent variable and used the resulting regression residuals as shape variables, free of CS variation, for consequent analyses. For the linear craniodental variation analysis, we used the same measurements and extraction techniques as in Onditi et al [72].…”

Section: Morphometric Datamentioning

confidence: 99%

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Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

Onditi

Peterhans

Chen

et al. 2021

Preprint

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Background: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) has been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity. 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 agreed 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 conform to demonstrated hypotheses surrounding the paleoclimatic and ecosystem refugium impacts on the evolutionary radiation of rodents dependent on stably humid conditions in the East Africa region. 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.

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Section: Taxonomic Assessment Of the Non-ethiopian Avopunctatus Memberssupporting

confidence: 91%

Section: Makundiimentioning

confidence: 98%

Section: Morphometric Datamentioning

confidence: 99%

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Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

Onditi

Peterhans

Chen

et al. 2021

Preprint

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“…This distribution agrees with Onditi et al . [ 72 ] who noted that L. zena was more widespread in Kenya than previously known [ 12 , 14 ]. The range of L. stanleyi is also much more extensive than previously described.…”

Section: Discussionmentioning

confidence: 99%

“…However, Onditi et al . [ 72 ] did not record L. margarettae in the entire elevation gradient of Mount Kenya (ca. 1700–4000 m).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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.

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Species of the cyprinid genusGarrain Mount Kenya, East Africa: Species delineation, taxonomy and historical biogeography

et al. 2023

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The cyprinid genus Garra is so far represented in Mount Kenya streams by a single species, but which species it should be referred to as remains yet to be determined. Molecular phylogenetic analysis of Garra species from the mountain is still lacking. Here, an integrative analysis, based on morphological and molecular data, unravelled the hidden species diversity of Garra from Mount Kenya. In mitochondrial genes‐based trees, samples formerly identified as Garra dembeensis from the mountain nested into three distinct lineages that were distantly allied to the lineage constituted by topotypical samples of the species; the three lineages are morphologically distinguishable, and thus represent three distinct species: Garra hindii and two undescribed species, herein named as Garra alticauda sp. nov. and Garra minibarbata sp. nov., respectively, from the Mara River and the Ragati River of the mid‐upper Tana River basin. The phylogeographic pattern of the three species is incongruent with the present‐day basin pattern of Mount Kenya. The allopatry of the paired species G. alticauda and G. hindii points to river piracy ever incurring between the upper Ewaso Ngiro River and the middle Tana River basin in Mount Kenya. Besides, the molecular phylogenetic analysis of sampled African Garra species in this study, based on a broad set of sequences, provides evidence in support for the existing hypothesis of Asia‐to‐Africa biodispersal via the Arabian Peninsula to the Horn of Africa.

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Morphological and genetic characterization of Mount Kenya brush-furred rats (Lophuromys Peters 1874); relevance to taxonomy and ecology

Cited by 5 publications

References 63 publications

Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

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

Species of the cyprinid genusGarrain Mount Kenya, East Africa: Species delineation, taxonomy and historical biogeography

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