Population genetics of greater cane rat (thryonomys swinderiunus) across its range areas in Africa
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Date
2023
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SOKOINE UNIVERSITY OF AGRICULTURE,
Abstract
The African Greater Cane rat (AGC) (Thryonomys Swinderiunus) is a wild rodent species
that belongs to the Family Thryonomydae and is historically endemic to Africa. The
species is widely distributed in different parts of Africa and is considered a delicacy in
some societies inhabiting the continent. Despite its food value, the rodent species is also
a pest of crops and a potential host of bacteria and worms that can impair human health.
There is a growing body of literature about cane rat species (Thronomys spp.) but most of
the published work is patchy. Currently, the spatial population distribution across suitable
habitats within its range areas in Africa, and the species' biology, particularly in the wild,
are unknown. These gaps limit broader species use for example, for commercial game
farming, for developing the potential strategies for controlling the species’ destructive
impacts on crops, and the measures to advocate for the species conservation in the wild.
This Ph.D. study was conceived to fill in these gaps and to advance knowledge on the
genetics of this species that is critical to the management and conservation of the cane rat
population in the wild. The research aimed specifically to answer four objectives; first, to
review the state of knowledge that is currently available about the cane rat species,
second; to assess the genetic diversity and population demography of the cane rat
populations inhabiting two mountains within the Eastern Arc Mountains range, third, to
assess the morphometrics of the cane rat skull to improve evolutionally knowledge of the
cane rat species and fourth, to assess the genetic relatedness of the cane rat populations
inhabiting the East and West African regions.To understand the breadth of knowledge
about the cane rat species, I conducted a systematic review of 56 years (1964 - 2020) of
cane rat research published in various outlets including theses and peer-reviewed journal
articles accessed from credible literature archives such as Web of Science, Scopus and
Google scholar. I found that the available literature on the cane rat was mostly biased
towards the West African region, and no single study published from East and Southern
Africa was available. I also found that most of the published literature was based on
captive cane rat individuals and that substantial knowledge gaps were remaining in
various topics including genetics and species biogeography, food biology, and
conservation. The knowledge generated in this systematic assessment, helped me to
focus on the identified gaps in the next chapters. Further, to answer the question of
genetic diversity and population demography of the cane rat species in the Eastern Arc
Mountains, I conducted field surveys to collect cane rat samples from traps set in four
localities in the Udzungwa south, Udzungwa north, Uluguru rural, and Uluguru urban
areas all located in the Udzungwa and Uluguru mountains respectively. I used DNA
sequencing of the D-loop region of MtDNA (515 bp) from 46 cane rat samples and various
molecular techniques to analyze these data. I found that there were high genetic
differences between than within these four populations. I also found that these four AGC
populations in Eastern Arc Mountains (EAMs) have experienced a recent population
expansion, especially among the urban population due perhaps to the influence of the
urbanization process that may have favored and/or assisted species movements across
the rural-urban landscapes. To understand the evolutionary information on the greater
cane rats in the Eastern and Southern African regions, I studied T. swinderiunus
populations in Tanzania to link molecular and geometric-morphological evidence to
characterize these populations’ diversity using tissue samples and skulls. I found that both
molecular and geomorphometric evidence were aligning T. swinderiunus into three clades
based on the location where samples were collected. This suggested that 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.Further, to assess the maternal origin of the African Greater cane
rats populations found in the spatially isolated localities in Africa, I compared mt-DNA D-
loop sequences from samples collected from two Eastern Arc Mountains, Tanzania, and
three agro-ecological zones in Ghana. I found a high genetic differentiation between AGC
populations from Tanzania and Ghana with high variation coming from between while low
variation was within the AGC populations. I also found that the populations from Tanzania
had higher haplotype diversity indicating that they are healthier demographically than
those of Ghana. I also found that the populations from Ghana do not share common
maternal lineage with those of Tanzania suggesting that the species has evolved as
distant populations that lacked connectivity.This study has important implications for the
conservation, taxonomy, farming and ranching of African Greater Canerats (AGCs) in
Tanzania. The genotype data can help to inform policy and decision-makers on
conservation priorities and potential conservation measures including the need for the
establishment of germ-plasm banks in vivo and in vitro for maintaining the genetic pool
through selection processes. Also, the results can be useful in selecting parental stocks
for establishing cane rat farming and ranching to provide farmers with viable stocks. The
study will enable the resolution of taxonomic uncertainties which is mandatory for
understanding species biology. The study has provided genetic sequences which have
been deposited in the NCBI gene bank and are available for public use. The species is
presently not endangered but if the needs arises these data can be accessed without
going back to the field and used for further research.
Keywords: African Greater Canerat (Thryonomys swinderiunus), Eastern Arc Mountains,
geometric-morphology, Genetic diversity, martenal lineage, conservation
Description
Ph.D Dissertations
Keywords
Population, genetics, greater cane, rat, thryonomydae