Molecular phylogeny of the Praomys complex (Rodentia: Murinae): a study based on DNA/DNA hybridization experiments.

Within the Murinae (Muridae: Rodentia), the African rats of the Praomys group, whose systematics has been studied through different approaches, have raised numerous taxonomic problems. Different taxa related to Praomys have successively been described, among which Mastomys, Myomys and Hylomyscus were considered either as separate genera or subgenera of Praomys. In order to clarify the relationships within the Praomys group, we conducted a series of DNA/DNA hybridization experiments involving different species of Praomys, Mastomys, Myomys and Hylomyscus plus other Murinae and a Cricetomyinae. This study indicates that the Praomys complex is a monophyletic entity clearly separated from the other African and Asian Murinae. If Mastomys and Hylomyscus appeared to be independent genera, the taxonomic situation of Praomys and Myomys is more difficult to ascertain. Indeed, Praomys tullbergi appears more closely related to Myomys daltoni than to another species of Praomys , namely P. jacksoni , suggesting paraphyly for Praomys. Furthermore, P. jacksoni is as distant from P. tullbergi as from any species of Mastomys. Additional species of Praomys and, especially, of Myomys , are needed for reaching a definitive conclusion on these latter taxa. The Praomys group is more related to Mus than to Rattus. To calibrate our molecular distances with geological time, we used a dating of 10 Myr for the Musi Rattus dichotomy. The inferred rate of molecular evolution suggests a dating of c. 8 Myr for the separation of the Praomys group from the Mus lineage.     

Estimating population structure from AFLP amplification intensity

In the last decade, amplified fragment length polymorphisms (AFLPs) have become one of the most widely used molecular markers to study the genetic structure of natural populations. Most of the statistical methods available to study the genetic structure of populations using AFLPs consider these markers as dominant and are thus unable to distinguish between individuals being heterozygous or homozygous for the dominant allele. Some attempts have been made to treat AFLPs as codominant markers by using AFLP band intensities to infer the most likely genotype of each individual. These two approaches have some drawbacks, the former discarding potentially valuable information and the latter being sometimes unable to correctly assign genotypes to individuals. In this study, we propose an alternative likelihood‐based approach, which does not attempt at inferring the genotype of each individual, but rather incorporate the uncertainty about genotypes into a Bayesian framework leading to the estimation of population‐specific F_IS and F_ST coefficients. We show with simulations that the accuracy of our method is much higher than one using AFLP as dominant markers and is generally close to what would be obtained by using the same number of Single‐Nucleotide Polymorphism (SNP) markers. The method is applied to a data set of four populations of the common vole (Microtus arvalis) from Grisons in Switzerland, for which we obtained 562 polymorphic AFLP markers. Our approach is very general and has the potential to make AFLP markers as useful as SNP data for nonmodel species.     

Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure

Although most natural populations are genetically subdivided, they are often analysed as if they were panmictic units. In particular, signals of past demographic size changes are often inferred from genetic data by assuming that the analysed sample is drawn from a population without any internal subdivision. However, it has been shown that a bottleneck signal can result from the presence of some recent immigrants in a population. It thus appears important to contrast these two alternative scenarios in a model choice procedure to prevent wrong conclusions to be made. We use here an Approximate Bayesian Computation (ABC) approach to infer whether observed patterns of genetic diversity in a given sample are more compatible with it being drawn from a panmictic population having gone through some size change, or from one or several demes belonging to a recent finite island model. Simulations show that we can correctly identify samples drawn from a subdivided population in up to 95% of the cases for a wide range of parameters. We apply our model choice procedure to the case of the chimpanzee (Pan troglodytes) and find conclusive evidence that Western and Eastern chimpanzee samples are drawn from a spatially subdivided population.     

A revision of Aceratherium blanfordi Lydekker, 1884 (Mammalia: Rhinocerotidae) from the Early Miocene of Pakistan: postcranials as a key

Rhinocerotids are particularly abundant and diversified in Neogene deposits of the Indian subcontinent, but their systematics is far from being well defined. Based on the revision of old collections and new findings from the Early Miocene of the Bugti Hills and Zinda Pir, Pakistan, ‘Aceratherium blanfordi Lydekker, 1884’ is a chimera, consisting of two dentally convergent but postcranially distinct rhinocerotid taxa: Pleuroceros blanfordi and Mesaceratherium welcommi sp. nov. Postcranial features appear to be much more diagnostic than craniodental morphology in this case. A phylogenetic analysis based on 282 morphological characters scored for 28 taxa (four outgroups and ingroup including both taxa of interest and a ‘branching group’) strengthens this statement and supports Pleuroceros and Mesaceratherium as monophyletic genera within Rhinocerotinae. Both genera are recognized for the first time outside Europe. In the Bugti Hills, P. blanfordi and M. welcommi are part of an exceptionally diversified rhinocerotid fauna, with up to nine species associated in the same locality (Kumbi 4f). This rhinocerotid assemblage confirms the earliest Miocene age (Agenian/Aquitanian) of the upper member of the Chitarwata Formation as a whole. Coeval homotaxic rhinocerotid faunas from Europe (France, Czech Republic) and East Africa (Uganda, Kenya) support broad and sustainable rhinocerotid interchanges amongst South Asia, Europe, and Africa under compatible environmental conditions throughout earliest Miocene times. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 139–194.     

A new Oligocene Ctenodactylinae (Rodentia: Mammalia) from Ulantatal (nei Mongol): new insight on the phylogenetic origins of the modern Ctenodactylidae

The four living genera of Ctenodactylidae (Rodentia) are the only survivors of a flourishing Tertiary group. In this paper, we describe a new Oligocene species from Ulantatal (Chinese Mongolia) that highlights the origins of crown ctenodactylids. This species, Helanshania deserta gen. et sp. nov. , is lophodont and displays semi‐hypsodont teeth, a dental pattern that is somewhat transitional between that of primitive Oligocene ctenodactylids and the later hypsodont genera. We perform here a cladistic assessment of the dental evidence for species produced by the successive radiations of the group. In order to get new data, to decipher homologies for the dental pattern of modern ctenodactylids, and to specify their dental replacement, we describe additional dental material of Ctenodactylus, Massoutiera, and Felovia. The phylogenetic analysis (using PAUP) considered 45 characters (mainly dental) and 31 species. The performed heuristic searches yielded 596 equally most parsimonious trees. Protataromys and Karakoromys are stem ctenodactylids and appear as the earliest offshoots of the Ctenodactylidae clade, which represents a well‐supported family rank. Within this family, the Tataromyinae appear paraphyletic, whereas the Ctenodactylinae sensu lato are a clade including the new taxon Helanshania. As such, a revision of the Tataromyinae is envisaged and a new subfamily is erected (Yindirtemyinae). Amongst the Ctenodactylinae, a tribe Ctenodactylini encompassing the crown ctenodactylines is proposed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 531–550.     

Behavioral thermoregulation in a tropical gastropod: links to climate change scenarios

Tropical species are vulnerable to global warming because they live at, or near to, their upper thermal threshold limits. Therefore, the predicted increase in the frequency of warming events in the tropics is expected to be critical for the survival of local species. This study explored the major environmental variables which were thought to be correlated with body temperatures (BTs) of the tropical snail Littoraria scabra at the niche level. A correlation between BT and substrate temperature (ST) was detected from field observations which suggests a possible causal relationship between both substrate and BTs. In contrast, there was no correlation between BT and air temperature. Field observations suggest that 33.4 °C may be L. scabra upper limit of substrate surface temperature, although further experiments are needed to assess if the upper limit of physiological tolerance is actually different. As L. scabra individuals were free to choose their substrata, the observed distribution pattern at the niche level is related to L. scabra's behavior. Additionally, substrate surface temperatures were very heterogeneous at centimeter scale (i.e. from 22.5 to 53.1 °C) and L. scabra was shown to select specific STs (i.e. between 22.5 and 33.4 °C) rather than microhabitat type. Therefore, L. scabra did not seem to behaviorally thermoregulate through microhabitat selection nor aggregation. In contrast, behavioral experiments showed that L. scabra has the ability to actively select a thermally favorable site over short temporal scale (i.e. individual average speed of 1.26 cm min^?1) following exposure to high temperatures above 33.4 °C. Hence, this study supports the crucial need to integrate intertidal invertebrate behavioral responses to thermal constraints in climate change studies.     

Effective population size estimation on Sardina pilchardus in the Bay of Biscay using a temporal genetic approach

Over three consecutive years, we surveyed the temporal variability in genetic structure of sardine populations in the Bay of Biscay and effective population size. Based on individual age, the genetic structure of year classes of the fishes was also surveyed, showing that populations of sardines have weak but significant genetic differences between sampling years and between year classes. We used two different methods to assess effective population size. The methods resulted in different values but a similar range, indicating a low effective population for Sardina pilchardus . Effective population size decreased over the 3 years, probably resulting from an abundance of fish in the Bay. Based on these results, we conclude that temporal variability in the genetic structure of the sardine population and effective size are likely related to environmental conditions in the Bay. Finally, we propose to use effective population size to estimate biomass of sardines in the Bay.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 591–602.