Patterns and processes of rodent and shrew assemblages in the Savanna Biome of KwaZulu-Natal, South Africa.

Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.The identification of non-random species composition patterns predicted by assembly rules is a central theme in community ecology. Based on life history characteristics, species composition patterns of rodents and shrews should be consistent with predictions from nestedness rather than competition hypotheses. This study investigated the seasonal changes in rodent and shrew assemblages in eleven savanna vegetation types in a protected reserve in South Africa. Rodents and shrews were sampled between 2009 and 2010 at Phinda Private Game Reserve (PPGR), KwaZulu-Natal. Sample-based rarefaction curves showed that rodent and shrew abundance and richness varied among seasons and vegetation types. Species richness estimators indicated that inventories for rodents (80%) and shrews (100%) were fairly complete. Null-model analyses found no evidence that species co-occurrence patterns in the reserve were non-random with respect to predictions from Diamond’s Assembly rules, niche limitation hypothesis and nestedness hypothesis. I also investigated seasonal changes in species richness and abundance of rodent and shrew assemblages on cattle, pineapple and former cattle farms surrounding PPGR, and used cluster analyses to compare the species composition of rodents and shrews at farm and PPGR study sites. Small mammal assemblages exhibited a heterogeneous distribution and species composition patterns changed between seasons. Sample-based rarefaction curves showed that rodent and shrew abundance and richness varied among seasons and study sites. Species richness estimators indicated that inventories for the rodents (91%) and shrews (100%) on the farms were essentially complete. Rodent and shrew species composition patterns did not group study sites according to land use, nor could species composition patterns be explained by vegetation characteristics. My results suggest that complex biotic and abiotic processes other than competition, nestedness, land use and vegetation characteristics operate at different spatial and temporal scales to structure rodent and shrew assemblages

Cryptic speciation and chromosomal repatterning in the South African climbing mice Dendromus (Rodentia, Nesomyidae)

We evaluate the intra- and interspecific diversity in the four South African rodent species of the genus Dendromus. The molecular phylogenetic analysis on twenty-three individuals have been conducted on a combined dataset of nuclear and mitochondrial markers. Moreover, the extent and processes underlying chromosomal variation, have been investigated on three species by mean of G-, C-bands, NORs and Zoo-FISH analysis. The molecular analysis shows the presence of six monophyletic lineages corresponding to D. mesomelas, D. mystacalis and four lineages within D. cfr. melanotis with high divergence values (ranges: 10.6% – 18.3%) that raises the question of the possible presence of cryptic species. The first description of the karyotype for D. mesomelas and D. mystacalis and C- and G- banding for one lineage of D. cfr. melanotis are reported highlighting an extended karyotype reorganization in the genus. Furthermore, the G-banding and Zoo-FISH evidenced an autosome-sex chromosome translocation characterizing all the species and our timing estimates this mutation date back 7.4 mya (Late Miocene). Finally, the molecular clock suggests that cladogenesis took place since the end of Miocene to Plio-Pleistocene, probably due to ecological factors, isolation in refugia followed by differential adaptation to the mesic or dry habitat

G Banding of South African <i>Dendromus</i>.

<p>G-banded karyotypes of (a) a female of <i>D. melanotis</i> (b) a male of <i>D. mesomelas</i> (c) a female of <i>D. mystacalis</i>.</p

Pairwise genetic distances.

<p>The pairwise genetic divergence (net between-group mean distances) among the four lineages of the clade C1 (lineages L1-L4) and the clades C2 and C3 based on cyt <i>b</i> (lower triangle) and Fib I7 (upper triangle).</p

Phylogenetic tree and divergence times for South African <i>Dendromus</i>.

<p>Bayesian 50% majority rule consensus tree performed on the combined dataset (cyt <i>b</i> and Fib I7). The values at nodes indicate the posterior probability of the combined dataset (above the node) and the posterior probability of the corresponding node in the cyt <i>b</i> (on left, below the node) and Fib I7 (on right, below the node) trees. The asterisks (*) indicate incongruence at node; the double dash (–) indicate a node with a posterior probability less than 0,50. On the tree is also reported a time scale with the dating of the principal nodes (dots a – f) from relaxed molecular clock analysis.</p

Autosome-sex chromosome translocation.

<p>Zoo FISH results of the <i>Mus musculus</i> chromosome 15 probe hybridization on the sex chromosomes in <i>D. melanotis</i> (a) and <i>D. mesomelas</i> (b).</p

A common variant mapping to CACNA1A is associated with susceptibility to exfoliation syndrome

Exfoliation syndrome (XFS) is the most common recognizable cause of open-angle glaucoma worldwide. To better understand the etiology of XFS, we conducted a genome-wide association study (GWAS) of 1,484 cases and 1,188 controls from Japan and followed up the most significant findings in a further 6,901 cases and 20,727 controls from 17 countries across 6 continents. We discovered a genome-wide significant association between a new locus (CACNA1A rs4926244) and increased susceptibility to XFS (odds ratio (OR) = 1.16, P = 3.36 × 10(-11)). Although we also confirmed overwhelming association at the LOXL1 locus, the key SNP marker (LOXL1 rs4886776) demonstrated allelic reversal depending on the ancestry group (Japanese: OR(A allele) = 9.87, P = 2.13 × 10(-217); non-Japanese: OR(A allele) = 0.49, P = 2.35 × 10(-31)). Our findings represent the first genetic locus outside of LOXL1 surpassing genome-wide significance for XFS and provide insight into the biology and pathogenesis of the disease

A common variant mapping to <i>CACNA1A </i>is associated with susceptibility to exfoliation syndrome

Author manuscript available from PMC http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4605818/Exfoliation syndrome (XFS) is the most common recognizable cause of open-angle glaucoma worldwide. To better understand the etiology of XFS, we conducted a genome-wide association study (GWAS) of 1,484 cases and 1,188 controls from Japan and followed up the most significant findings in a further 6,901 cases and 20,727 controls from 17 countries across 6 continents. We discovered a genome-wide significant association between a new locus (CACNA1A rs4926244) and increased susceptibility to XFS (odds ratio (OR) = 1.16, P = 3.36 × 10−11). Although we also confirmed overwhelming association at the LOXL1 locus, the key SNP marker (LOXL1 rs4886776) demonstrated allelic reversal depending on the ancestry group (Japanese: ORA allele = 9.87, P = 2.13 × 10−217; non-Japanese: ORA allele = 0.49, P = 2.35 × 10−31). Our findings represent the first genetic locus outside of LOXL1 surpassing genome-wide significance for XFS and provide insight into the biology and pathogenesis of the disease