Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses.

Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses.

Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations.

Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.

Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay.

Rodents of the Praomys daltoni complex are typical inhabitants of the Sudanian savanna ecosystem in western Africa and represent a suitable model for testing the effects of Quaternary climatic oscillations on extant genetic variation patterns. Phylogeographical analyses of mitochondrial DNA sequences (cytochrome b) across the distribution range of the complex revealed several well-defined clades that do not support the division of the clade into the two species currently recognized on the basis of morphology, i.e. P. daltoni (Thomas, 1892) and Praomys derooi (Van der Straeten & Verheyen 1978). The observed genetic structure fits the refuge hypothesis, suggesting that only a small number of populations repeatedly survived in distinct forest-savanna mosaic blocks during the arid phases of the Pleistocene, and then expanded again during moister periods. West African rivers may also have contributed to genetic differentiation, especially by forming barriers after secondary contact of expanding populations. The combination of three types of genetic markers (mtDNA sequences, microsatellite loci, cytogenetic data) provides evidence for the presence of up to three lineages, which most probably represent distinct biological species. Furthermore, incongruence between nuclear and mtDNA markers in some individuals unambiguously points towards a past introgression event. Our results highlight the importance of combining different molecular markers for an accurate interpretation of genetic data.

Comparative phylogeography of two sibling species of forest-dwelling rodent (Praomys rostratus and P. tullbergi) in West Africa: different reactions to past forest fragmentation.

Two sibling species of the rodent genus Praomys occur in West African forests: P. tullbergi and P. rostratus. By sampling across their geographical ranges (459 individuals from 77 localities), we test the hypothesis that climatic oscillations during the Quaternary made an impact on the observed pattern of cytochrome b sequence variation. We show that, although these two species have parapatric geographical distributions, their phylogeographical histories are dissimilar, which could be related to their distinct ecological requirements. Since the arid phases of the Pleistocene were characterized by isolated forest patches, and intervening wetter periods by forest expansion, these changes in forest cover may be the common mechanism responsible for the observed phylogeographical patterns in both of these species. For example, in both species, most clades had either allopatric or parapatric geographical distributions; however, genetic diversity was much lower in P. tullbergi than in P. rostratus. The genetic pattern of P. tullbergi fits the refuge hypothesis, indicating that a very small number of populations survived in distinct forest blocks during the arid phases, then expanded again with forest recovery. In contrast, a number of populations of P. rostratus appear to have survived during the dry periods in more fragmented forest habitats, with varying levels of gene flow between these patches depending on climatic conditions and forest extent. In addition, historical variations of the West African hydrographic network could also have contributed to the pattern of genetic differentiation observed in both species.

Mitochondrial phylogeny of African wood mice, genus Hylomyscus (Rodentia, Muridae): implications for their taxonomy and biogeography.

This paper investigates the usefulness of two mitochondrial genes (16S rRNA and cytochrome b) to solve taxonomical difficulties within the genus Hylomyscus and to infer its evolutionary history. Both genes proved to be suitable molecular markers for diagnosis of Hylomyscus species. Nevertheless the resolving powers of these two genes differ, and with both markers (either analyzed singly or in combination), some nodes remain unresolved. This is probably related to the fact that the species emerged during a rapid diversification event that occurred 2-6 Myr ago (4-5 Myr ago for most divergence events). Our molecular data support the recognition of an "aeta" group, while the "alleni" and "parvus" groups are not fully supported. Based on tree topology and genetic divergence, two taxa generally recognized as subspecies should be elevated at the species level (H. simus and H. cf kaimosae). H. stella populations exhibit ancient haplotype segregation that may represent currently unrecognized allopatric species. The existence of cryptic species within H. parvus is questioned. Finally, three potentially new species may occur in West Central Africa. The Congo and Oubangui Rivers, as well as the Volta and Niger Rivers and/or the Dahomey gap could have formed effective barriers to Hylomyscus species dispersal, favoring their speciation in allopatry. The pronounced shifts in African climate during the late Pliocene and Miocene, which resulted in major changes in the distribution and composition of the vegetation, could have promoted speciation within the genus (refuge theory). Future reports should focus on the geographic distribution of Hylomyscus species in order to get a better understanding of the evolutionary history of the genus.

[A new flea species of the genus Allopsylla Beaucournu et Fain, 1982 (Siphonaptera: Ischnopsyllidae) from Central African Republic, found on a little known molossid bat]. / Une nouvelle puce du genre Allopsylla Beaucournu et Fain, 1982 (Siphonaptera: Ischnopsyllidae) en Republique Centrafricaine, sur un chiroptère Molossidae méconnu.

A pair of Allopsylla lobayensis Beaucournu & Barrière, new species were collected the first of November 1999 in Ngotto forest, in the south-western part of the Lobaye basin, Central African Republic (CAR). The host specimen, a little known molossid bat (Myopterus whitleyi), constitutes the first record of this species in CAR. The new flea species appears taxonomically close to A. hetera Beaucournu & Fain, 1982, one of the two other Allopsylla species, previously know from other faunal regions (A. alloides in Nigeria and A. hetera in Democratic Republic of the Congo). The parasitism of three distinctly different hosts by the three known Allopsylla species raises questions regarding the host-parasite specificity of this group.

Phylogeny and evolution of African shrews (Mammalia: Soricidae) inferred from 16s rRNA sequences.

Current phylogenetic hypotheses on the African Crocidurinae (Soricidae) are based upon morpho-anatomical, karyological, and allozyme studies. The present study attempts to resolve the interrelationships among African Crocidurinae and their relationships to Eurasian Crocidurinae and to the subfamily Soricinae, on the basis of partial mitochondrial 16s rRNA sequences (549 bp). This is the first molecular study to include all but one of the nine currently recognized African shrew genera. In agreement with current views, two major lineages emerge. The first lineage includes Myosorex and Congosorex and supports the existence of a myosoricine taxon. The second lineage includes the six remaining genera. The genus Sylvisorex appears to be polyphyletic, whereas species of the controversial genus Crocidura are monophyletic. The genus Suncus presumably originated in Africa. The monospecific genera Ruwenzorisorex and Scutisorex and the two representatives of Paracrocidura cluster with species of other genera. Grouping patterns of species from different continents suggest that there have been multiple exchanges between Africa and Eurasia. The time estimates of these exchanges, inferred from two independent fossil-based calibrations of a molecular clock, coincide with the time estimates for migration events in other mammalian taxa.

[Forest ecosystems and Ebola virus]. / Ecosystèmes forestiers et virus Ebola.

Despite data collected since the emergence of the Ebola virus in 1976, its natural transmission cycle and especially the nature of its reservoirs and means of transmission are still an enigma. This means that effective epidemiological surveillance and prevention are difficult to implement. The location of outbreak areas has suggested that the reservoir and the transmission cycle of the Ebola virus are closely linked to the rainforest ecosystem. The fact that outbreaks seldom occur suggests the presence of a rare animal reservoir having few contacts with man. Paradoxically, various serological investigations have shown a high prevalence in human beings, especially in forest areas of the Central African Republic (CAR), with no pathology associated. This would appear to suggest a circulation of both pathogenic and non-pathogenic strains as well as frequent contacts with man. The ecological changes resulting from human activity (agriculture and logging) account for the modification of the fauna (movement of rainforest fauna, introduction of savannah species) and could explain a multiplication of contacts. Likewise, it is interesting to note that the centre of outbreaks has always been in areas bordering on forests (ecotone foreset-savannah in the Democratic Republic of Congo, savannah in Sudan). All these considerations have led us to establish a permanent "watch" in areas bordering on forests in the CAR, involving a multidisciplinary approach to the virological study (strain isolation, molecular biology) of the biodiversity of small terrestrial mammals. The results of a study conducted on 947 small mammals has shown for the first time the presence of the Ebola virus genome in two species of rodents and one species of shrew living in forest border areas. These animals must be considered as intermediary hosts and research should now focus on reservoirs in the ecosystem of forest border areas where contacts with man are likely to be more frequent.

Identification of Ebola virus sequences present as RNA or DNA in organs of terrestrial small mammals of the Central African Republic.

The life cycle of the Ebola (EBO) virus remains enigmatic. We tested for EBO virus in the organs of 242 small mammals captured during ecological studies in the Central African Republic. EBO virus glycoprotein or polymerase gene sequences were detected by reverse transcription PCR in RNA extracts of the organs of seven animals and by PCR in DNA extract of one animal. Neither live virus nor virus antigen was detected in any organ sample. Direct sequencing of amplicons identified the virus as being of the Zaire/Gabon subtype. Virus-like nucleocapsids were observed by electron microscopy in the cytoplasm of the spleen cells of one animal. The animals belonged to two genera of rodents (Muridae; Mus setulosus, Praomys sp1 and P. sp2) and one species of shrew (Soricidae; Sylvisorex ollula). These preliminary results provide evidence that common terrestrial small mammals living in peripheral forest areas have been in contact with the EBO virus and demonstrate the persistence of EBO virus RNA and DNA in the organs of the animals. Our findings should lead to better targeting of research into the life cycle of the EBO virus.