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.     

Predicting alpha diversity of African rain forests: models based on climate and satellite‐derived data do not perform better than a purely spatial model

Aim Our aim was to evaluate the extent to which we can predict and map tree alpha diversity across broad spatial scales either by using climate and remote sensing data or by exploiting spatial autocorrelation patterns. Location Tropical rain forest, West Africa and Atlantic Central Africa. Methods Alpha diversity estimates were compiled for trees with diameter at breast height ≥ 10 cm in 573 inventory plots. Linear regression (ordinary least squares, OLS) and random forest (RF) statistical techniques were used to project alpha diversity estimates at unsampled locations using climate data and remote sensing data [Moderate Resolution Imaging Spectroradiometer (MODIS), normalized difference vegetation index (NDVI), Quick Scatterometer (QSCAT), tree cover, elevation]. The prediction reliabilities of OLS and RF models were evaluated using a novel approach and compared to that of a kriging model based on geographic location alone. Results The predictive power of the kriging model was comparable to that of OLS and RF models based on climatic and remote sensing data. The three models provided congruent predictions of alpha diversity in well‐sampled areas but not in poorly inventoried locations. The reliability of the predictions of all three models declined markedly with distance from points with inventory data, becoming very low at distances > 50 km. According to inventory data, Atlantic Central African forests display a higher mean alpha diversity than do West African forests. Main conclusions The lower tree alpha diversity in West Africa than in Atlantic Central Africa may reflect a richer regional species pool in the latter. Our results emphasize and illustrate the need to test model predictions in a spatially explicit manner. Good OLS or RF model predictions from inventory data at short distance largely result from the strong spatial autocorrelation displayed by both the alpha diversity and the predictive variables rather than necessarily from causal relationships. Our results suggest that alpha diversity is driven by history rather than by the contemporary environment. Given the low predictive power of models, we call for a major effort to broaden the geographical extent and intensity of forest assessments to expand our knowledge of African rain forest diversity.     

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling

Background and Aims A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia.Methods Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM).Key Results A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction.Conclusions Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had contracted at the LGM. This signature of contraction from lower rainfall areas is consistent with current observations of decline on the semi-arid margin of the range, and indicates low capacity to tolerate forecast climatic change. Identification of a paleo-historical context for current tree decline enables conservation interventions to focus on maintaining genetic diversity, which provides the evolutionary potential for adaptation to climate change.     

The Branchiopoda (Crustacea: Anomopoda, Ctenopoda and Cyclestherida) of the rain forests of Cameroon, West Africa: low abundances, few endemics and a boreal–tropical disjunction

Aim We provide the first in‐depth study of the Branchiopoda of the rain forests of Cameroon and also of the African continent. Location Surface water environments, Cameroon. Methods Qualitative plankton samples were collected in all types of surface water environments present, ranging from big lakes to water collected in rock crevices or fallen fruit cavities. A tow or hand‐held plankton net of mesh size 100 μm was used, and water volumes filtered were at least several m³ in large water bodies, or half to whole water volume in small water bodies. Results We recorded 61 species (53 first records for the country), based on 700+ samples collected between September 1998 and March 2002. Anomopoda (92%) was the dominant order, followed by Ctenopoda (6.5%) and Cyclestherida (1.5%). Chydoridae (67%) was the most speciose family followed by Macrothricidae (6.5%) and Daphniidae (5%). Alona (11%) was the dominant genus followed by Chydorus (10%) and Pleuroxus (8%). Several species of Chydorinae, especially of the genus Pleuroxus, are shared with continental Eurasia–North America, but are absent from the Mediterranean and desert–steppe–savanna zones of Africa (boreal–tropical disjunction). Daphnia was absent, as in most tropical lowlands. No single species was really abundant, and a majority were rare to very rare, and of restricted occurrence within the rain forest patches. Comparing Africa, South America and Southeast Asia, we found a current total of 196 species for the combined rain forest areas, out of a world total of 500+ species. Systematic trends in richness at three taxonomic levels were the same for all continents: Anomopoda–Ctenopoda–Cyclestherida at ordinal level, Chydoridae–Daphniidae–Macrothricidae–Sididae at family level and Alona–Chydorus–Macrothrix–Diaphanosoma at genus level. Southeast Asia was richest (111 species, 14 endemics) with South America a close second (110 species, 27 endemics). Africa was the most species‐poor (95 species, of which only 5 are endemics). Main conclusions We hypothesize that the post‐Miocene cooling and aridization of the world climate hit the freshwater biota of Africa particularly hard, with more extinction here than elsewhere, and little recolonization. Most extinction occurred in the savanna‐desert belt, and eight disjunct boreal species (four Pleuroxus, Picripleuroxus laevis, Kurzia latissima, Alonella exigua, and Monospilus dispar) survive morphologically unchanged since pre‐Pleistocene times in the Cameroon rain forest. Slow evolution thus appears typical of these cyclic parthenogenetic branchiopods in which sexual recombination occurs only at intervals. Illustrative of the same slow evolution is the fact that the two endemic cladocerans of Cameroon (Nicsmirnovius camerounensis and Bryospilus africanus) belong to tropicopolitan genera of Gondwanan age.     

Tests of species‐specific models reveal the importance of drought in postglacial range shifts of a Mediterranean‐climate tree: insights from integrative distributional,demographic and coalescent modelling and ABC model selection

Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species‐specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade‐offs in functional traits, and local‐scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade‐off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a generic ENM, in which the variables found to make the most important contribution to the ENM have strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common.