Work Package 2:
  Climate changes and mammal evolution
10 researchers

COORDINATORS  Janice Britton-Davidian (UMR 5554 CNRS) and Conrad Matthee (Department of Botany and Zoology, University of Stellenbosch) 

Climate change during the Quaternary period has been put forward as one of the main drivers of biodiversity on the African continent.  Cyclical shifts in temperature caused major changes in vegetation and this in turn resulted in the contraction and expansion of species ranges into potential refugia.  By making use of multiple data sets derived from various sources (genetics, behaviour and ecology) and species with different life histories (predominantly rodents) the main focus of this work package is to establish multiple data sets that can be used to make general evolutionary conclusions regarding speciation of African taxa. To gain a better holistic understanding of the factors driving speciation on the African continent will have significant conservation implications.  For example, congruent geographic patters among lineages will point to vicariance and regions with high levels of genetic diversity across multiple taxa can be used to define refugia.  These data in turn can be analysed in the context of paleoclimatic modelling to place conservation networks in more optimal positions.

Project 1 : The African pygmy mouse radiation: phylogeny, chromosomes and sex determination

Participants : Frédéric Veyrunes, Janice Britton-Davidian (UMR 5554 CNRS, Montpellier), Pascale Chevret (UMR 5558 CNRS, Lyon), Terry Robinson (University of Stellenbosch).

The diversification of the savannah-dwelling African pygmy mice is accompanied by an extensive chromosomal radiation involving mostly centric fusions. In South Africa, cytogenetic and molecular analyses have so far identified two species occupying different environments, Mus indutus (semi-arid habitats) and M. minutoides (grasslands), and uncovered five different chromosomal groups within the latter differing by the number and type of centric fusions present. In addition, a new case of atypical sex determination in mammals was discovered in M. minutoides in which a high proportion of sex-reversed XY females were present.
The objectives of this project are twofold. The first is to complete the chromosomal and taxonomic survey of pygmy mice throughout South Africa. This will be achieved by implementing cytogenetic and phylogenetic approaches in newly sampled localities and in >250 previously collected museum samples. From this study, the correlation between chromosomal divergence (including the change in sex determination), taxonomic diversification and Quaternary climatic changes will be tested. The second aim involves a multidisciplinary approach on both wild and laboratory-bred animals using a variety of cytogenomic and molecular tools: (i) to identify and characterize the genetic basis of the sex-reversion (test the functionality of candidate genes), (ii) to investigate the evolutionary processes involved in the formation, fixation and persistence of this aberrant sex determining system. A breeding program will be set up in the laboratory to measure reproductive traits and perform behavioural analyses. The evolutionary impact of these parameters will be explored by a computer modelling approach.

Project 2 : The African striped mouse: A biomarker of past and present environmental changes in southern Africa

Participants: Guila Ganem (CNRS UMR 5554 Montpellier), Neville Pillay (University of Wits, Johannesburg), Nico Avenant (Museum Bloemfontein)

 Climate change and its effects on habitats are unquestionably affecting life history traits and the distribution of many living organisms. Plasticity and genetic adaptation are important mechanisms by which species can respond to changes in their environment and, in the context of recent rapid climate change, such responses could ameliorate the negative consequences of this disturbance. However, the effectiveness and generality of plasticity versus adaptive responses to rapid changes are still a matter of scientific debate and clearly deserve further investigation, which we propose to address in a successful African small mammal, the striped mouse. The striped mouse has split into two species some 2.9 million years ago during a period of marked climate oscillation, and at present its various populations occupy much diversified environments ranging from arid to humid. The striped mouse has recently benefited from many studies  resulting in a very good understanding of its biology and on which this study will build. Further we collaborate with other participants of the GDRI that address the phylogeography of this genus. The specific objectives of our project are to measure within and between populations and species variation of two behavioural characteristics that have shown to vary in the striped mouse and expected to be sensitive to environmental variations: social behaviour and odour signalling, as well as a morphological marker, mandible shape, known to be prone to plastic variations related to diet changes during ontogenesis.

Project 3 : Phylogeny of the rodent tribe Otomyini (groove-toothed rats) and phylogeography of four arid-adapted species : comparison of patterns of diversification using multiple markers

Participants: Claudine Montgelard (UMR 5175 CNRS Montpellier), Christiane Denys (MNHN, Paris), Conrad Matthee (University of Stellenbosch), Peter Taylor (University of Venda)

 Otomyini currently included 23 species in 3 genera but phylogenetic relationships among them are not yet settled. In particular monophyly of each genus is still questioned because not recovered from numerous data (morphological, chromosomal or molecular). Our first goal will be to obtain a well resolved phylogeny between the different species through sequencing of multiple nuclear genes (introns and exons).
The second objective will focus on the four arid-adapted species endemic to South Africa (Parotomys brantsii, P. littledalei, Otomys unisulcatus, and O. sloggetti) inhabiting dry and arid environments.  Phylogeographic patterns will first be compared between species using mitochondrial (cytochrome b and control region) sequences. Then we will use microsatellite markers to compare the genetic structure at the population level for the same taxa. A genomic library is currently built for Otomys unisulcatus using next-generation sequencing (pyrosequencing) that generate up to one million nucleotide data in stretches of 200-350 bp long, among which numerous microsatellites will be designed. In complement to molecules, geometric morphometrics will be performed on the same four arid taxa to analyze variations in shape of cranium and mandible and their covariations with some environmental variables. Finally, morphological variations of molars will also be analyzed on fossil specimen, allowing to investigate the past changes over the last 5 Myr (Plio-Pliocene). We will address questions such as: are the patterns of diversification congruent in space and time between markers and species or specific to each species ? Did the diverse groups appear concomitantly (paleontological and molecular dating) or not and can we identify factors (climatic or environmental) responsible for the structure (genetic and morphometric) observed?

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