Mitochondrial genetic diversity of the Greater Cane rat (Thryonomys swinderianus) populations from the Eastern Arc Mountains ecosystem, Tanzania

Kilwanila, Shadia I.; Lyimo, Charles Moses; Rija, Alfan A.

doi:10.1007/s11033-022-07823-1

Cited by 3 publications

(8 citation statements)

References 35 publications

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“…In Tanzania, all the fecal samples were from wild AGC trapped from two mountain blocks (Uluguru and Udzungwa) of the Eastern Arc (Figure 1). Details of the field sampling, DNA extraction, PCR and sequencing have been provided elsewhere (Kilwanila et al, 2022). The genetic sequences (D-loop region) of the AGC from Tanzania were compared with genetic sequences from Western and Southern Africa retrieved from NCBI GenBank: Ghana with accession nos.…”

Section: Source Of Datamentioning

confidence: 99%

“…However, to date, there is a scarcity of information on these populations' demographic history and genetic variation. This knowledge gap limits a broader understanding of the potential speciation process that may exist and is an impediment to the development of management strategies and conservation efforts where the species is considered a pest, or a game species across its range in Africa (Kilwanila et al 2022). Further, species utilization as wild meat through either hunting or ranching requires a deeper understanding of the conservation efforts required across these regions (Kilwanila et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Kilwanila,

Lyimo,

Rija

et al. 2023

Tropical Conservation Science

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Background and aim: African Greater Cane (ACG) rat populations are widely distributed across Africa but the ancestral origin of populations inhabiting different geographical regions is unknown. There is currently no information available on the genetic differentiation of these populations resulting from long-time geographical isolation, environmental and anthropogenic pressures they face in each region. This limits our ability to understand potential speciation processes in AGC and their implications for their conservation and of other small wild mammals exposed to similar ecological conditions in the savannah biomes in Africa. Methods: We analyzed mitochondrial genes targeting the D-loop region of AGC samples from two blocks of the Eastern Arc Mountains in Tanzania (eastern), three agro-ecological zones in Ghana (western) and four sites in South Africa (southern) to characterize the phylogeographical patterns of the species. Results: AGC populations from Tanzania revealed higher haplotype diversity than those from the two other régions. Analysis of variance (AMOVA) revealed higher genetic variations within than between populations in all geographic regions. Demographic history analysis revealed a negative and significant Tajima’s D for a single southern African population as well as close relatedness with the Eastern Africa populations, suggesting a common ancestral origin. Conclusion: This is the first study to compare maternal lineages of AGC populations from eastern, western and southern Africa and provides a basis for future genetic studies of the species, its evolutionary ecology and the conservation of these populations across their range. Conservation implications: Evidence of recent population size expansion underpinned by high genetic diversity observed in the Uluguru urban (Tanzania) Guinea savannah (Ghana) and Kwazulu Natal (South Africa) populations suggest that the AGC populations are not currently threatened, consistent with the current IUCN status. Also, the distinct haplotypes observed in each region suggest that the populations can be managed as meta-populations, thus providing opportunities for potential local game-farming programs.

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Section: Source Of Datamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Kilwanila,

Lyimo,

Rija

et al. 2023

Tropical Conservation Science

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“…using the most appropriate substitution model as described in [43]. Furthermore, to assess the relative amount of shape variation (representing biological variation) among individuals, we ran a Procrustes analysis of variance (ANOVA) using location and age as classifiers.…”

Section: Data Analysis 221 Geometric Morphometric Assessmentmentioning

confidence: 99%

“…The Mantel test was then performed in R using the "vegan" package [40,41] with Procrustes distance and genetic distance matrices. The genetic distance matrix was generated in MEGA software version 6.0 [42] using the most appropriate substitution model as described in [43]. Furthermore, to assess the relative amount of shape variation (representing biological variation) among individuals, we ran a Procrustes analysis of variance (ANOVA) using location and age as classifiers.…”

Section: Data Analysis 221 Geometric Morphometric Assessmentmentioning

confidence: 99%

“…Following quality control procedures, 46 sequences were retained for analysis and were deposited in the NCBI gene bank with accession numbers OM475549-OM475594. Using MEGA program version 6.0, aligned sequences were used to infer the evolutionary history of T. swinderianus by constructing a neighbor-oining phylogenetic tree as explained in [43]. The nodes' robustness was tested using 100,000 bootstraps.…”

Section: Molecular Analysismentioning

confidence: 99%

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Isolating Greater Cane Rat Populations (Thryonomys swinderianus) from Eastern Arc Mountains, Tanzania: Linking Diversity to Morphometric and Molecular Characteristics

et al. 2023

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Evolutionary information on the greater cane rat (Thryonomys swinderianus) in the Eastern and Southern African regions is scarce, making population management and conservation of the species challenging. We studied T. swinderianus populations from two spatially isolated Eastern Arc Mountains in Tanzania to link molecular and geometric–morphological evidence to characterize these populations’ diversity. Fecal samples (n = 50) and skulls (n = 99) of T. swinderianus were collected from Udzungwa (north and south) and Uluguru mountains (urban and rural sites) and analyzed using molecular and geomorphometry techniques. Molecular analysis grouped the population into three distinct clades based on the location where the samples were collected, while the morphometric method was not able to distinctively separate the populations. Both methods revealed that the population obeyed the isolation by distance model with higher genetic distance between the Udzungwa and Uluguru populations and lower distance between Uluguru urban and rural populations. Both Mahalanobis and Procrustes distances in skull landmarks between the Udzungwa and Uluguru populations were significantly higher across the dorsal, ventral, and lateral views of the skulls, suggesting strongly that molecular and morphometric methods applied together can be useful in characterizing the population traits of the least known species. Our study suggests genetic and morphometric methods could complement each other in understanding the evolutionary biology and within-species diversity of vertebrate species that do not exhibit strong intra-species differentiation.

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Pattern and composition of wildlife roadkill across urban-rural gradient in an African expanding city

Mariki,

Kessy,

Byamungu

et al. 2024

Eur J Wildl Res

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Mitochondrial genetic diversity of the Greater Cane rat (Thryonomys swinderianus) populations from the Eastern Arc Mountains ecosystem, Tanzania

Cited by 3 publications

References 35 publications

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Isolating Greater Cane Rat Populations (Thryonomys swinderianus) from Eastern Arc Mountains, Tanzania: Linking Diversity to Morphometric and Molecular Characteristics

Pattern and composition of wildlife roadkill across urban-rural gradient in an African expanding city

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