Complete mitochondrial genome of the giant root-rat (<i>Tachyoryctes macrocephalus</i>)

Reuber, Victoria; Rey‐Iglesia, Alba; Westbury, Michael V.; Cabrera, Andrea A.; Farwig, Nina; Skovrind, Mikkel; Šumbera, Radim; Wube, Tilaye; Opgenoorth, Lars; Schabo, Dana G.; Lorenzen, Eline D.

doi:10.1080/23802359.2021.1944388

Cited by 2 publications

(2 citation statements)

References 18 publications

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“…We merged overlapping paired‐end reads using FLASHv1.2.11 (Magoč & Salzberg, 2011) with default parameters. We mapped both merged and unmerged reads to the hoary bamboo rat ( Rhizomys pruinosus ) nuclear genome (Genbank accession: VZQC00000000.1; Guo et al., 2021) which is the nearest relative of the giant root‐rat with an available genome, combined with the giant root‐rat mitogenome (Genbank accession: MW751806; Reuber et al., 2021). The divergence time between the hoary bamboo rat and the giant root‐rat is ~14 million years (median time estimate based on 4 studies from http://www.timetree.org), and mapping to a divergent reference may lead to the recovery of more conserved regions in the genome.…”

Section: Methodsmentioning

confidence: 99%

Topographic barriers drive the pronounced genetic subdivision of a range‐limited fossorial rodent

Reuber,

Westbury,

Rey‐Iglesia

et al. 2024

Molecular Ecology

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Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high‐elevation systems in Africa, we studied the giant root‐rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro‐alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low‐coverage nuclear genomes, we investigated 77 giant root‐rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000–16,000 years ago). Despite this landscape‐scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local‐scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

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Section: Methodsmentioning

confidence: 99%

Topographic barriers drive the pronounced genetic subdivision of a range‐limited fossorial rodent

Reuber,

Westbury,

Rey‐Iglesia

et al. 2024

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

show abstract

“…We merged overlapping paired-end reads using FLASHv1.2v11 (Magoč & Salzberg, 2011) with default parameters. We mapped both merged and unmerged reads to the hoary bamboo rat (Rhizomys pruinosus) nuclear genome (Genbank accession: VZQC00000000.1; Guo et al, 2021) which is the nearest relative of the giant root-rat with an available genome, combined with the giant root-rat mitogenome (Genbank accession: MW751806; Reuber et al, 2021). We used BWA v0.7.15 utilising the mem algorithm and default parameters.…”

Section: Data Generation Of Mitochondrial and Nuclear Dnamentioning

confidence: 99%

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent

Reuber¹,

Westbury

Rey‐Iglesia

et al. 2023

Preprint

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Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species susceptible to environmental change. The giant root-rat (Tachyoryctes macrocephalus) is a highly fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its whole ~1,000 km2 range. Our data revealed a distinct division into northern and southern subpopulations, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial genomes indicated that population subdivision was driven by steep slopes and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000 to 16,000 years ago). Despite the pronounced subdivision observed at the range-wide scale, weak geographic structuring of sampling localities within subpopulations indicated gene flow across distances of at least 16 km, suggesting aboveground dispersal and high mobility for relatively long distances. Our study highlights how topographic barriers can lead to the genetic subdivision of fossorial species, despite their potential to maintain gene flow at the local scale. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

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Complete mitochondrial genome of the giant root-rat (Tachyoryctes macrocephalus)

Cited by 2 publications

References 18 publications

Topographic barriers drive the pronounced genetic subdivision of a range‐limited fossorial rodent

Topographic barriers drive the pronounced genetic subdivision of a range‐limited fossorial rodent

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent

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