Phylogeography of the southern African vlei rat, Otomys irroratus, inferred from chromosomal and DNA sequence data
Year: 2010
Type: dissertation
Abstract: ENGLISH ABSTRACT: This study examines the phylogeography of the southern African vlei rat, Otomys \nirroratus using the mtDNA cyt b gene and chromosomal data derived using G-, and C-banding, \nAg-NOR staining and fluorescence in situ hybridization (FISH using flow sorts of Myotomys \nunisulcatus). A total of N = 102 specimens were used from the Western Cape, Eastern Cape, \nNorthern Cape, Free State, Mpumalanga and KwaZulu-Natal provinces of South Africa. Of the \nN = 102, N = 55 comprised fresh material while N = 47 comprises museum material obtained \nfrom the Durban Natural Science Museum of South Africa. \nCytogentic analysis of N = 55 specimens collected from seven localities in South Africa \nrevealed intra-specific variation resulting from two rearrangements, namely pericentric inversions \nand heterochromatin variation. Of the 55 specimens that were analyzed 47% contained \ninversions or centromeric shifts on four autosomes (OIR1, OIR4, OIR6 and OIR10) which were \npresent singly in specimens (i.e. none of the specimens contained all four inversions \nconcurrently). These inversions were present in both homozygous and heterozygous state over a \nwide geographic range suggesting that they are floating polymorphisms. Given the potential role \nof inversions in post-mating isolation (through production of aneuploid gametes), the prevalence \nof inversions as floating polymorphisms in the vlei rats suggest that they are probably retained in \nthe population through suppression of recombination in the inverted regions of the chromosomes. \nIn addition, differences between populations is due to the presence or absence of heterochromatic \narms (and not inversions), which cause variation in the NFa (40 – 49) and supernumerary B \nchromosomes, resulting in the variation in diploid number (2n = 28 – 32). Analysis of N = 55 \nspecimens revealed Ag-NORs on 7 autosomal pairs 1, 2, 5, 7, 8 and 9 proximal to the centromere \non the short arm of the chromosome. Pair 8 also displayed Ag-NOR at the distal end of the long \narm of the chromosome in individuals from the Free State province. Pair 3 showed two Ag- \nNORs occurring proximal to the centromere on the short arm and on the terminal end of the long \narm, respectively. \nI obtained 953bp of mtDNA cyt b from fresh material and 400bp from museum material. \nUsing maximum parsimony and Bayesian inference two main clades were retrieved. Clade A \nspecimens occur mainly in the Western and Eastern Cape provinces of South Africa. Clade B \nspecimens occur in the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape and \nMpumalanga provinces of South Africa. The mean sequence divergence between the main clades \n(A and B) is 7.0% and between sub-clades comprising clade B is 4.8%, while within clade A the \nsequence divergence was 1.91%. Nested clade analysis revealed allopatric fragmentation within \nO. irroratus. Chromosomal characters also support the two evolutionary lineages as clade A has \npericentric inversions which occur as floating polymorphisms which are absent in clade B. Clade \nB in turn is fixed for a complex tandem fusion rearrangement which is absent from clade A. \nDivergence date estimates indicate that the two clades separated around 1.1 MYA, which \ncoincides with climate changes since the late Pliocene/Pleistocene epochs. Cladogenesis within \nthis species complex could therefore have been influenced by habitat fragmentation. A full \ntaxonomic review of O. irroratus is therefore warranted by this study.
Author: Adriaan Engelbrecht
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W1946200713