A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae)

Background: Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Results: Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. Conclusions: The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological gradients in East Africa and South Africa appear to have resulted in more advanced allopatric speciation there

Genetic diversity of bitter and sweet African bush mango trees (Irvingia spp., Irvingiaceae) in West and Central Africa

Economically important food tree species in sub-Saharan Africa should be domesticated to enhance their production within agro forestry systems. The African bush mango trees (Irvingia species) are highly preserved and integrated in agro forestry systems in tropical Africa. However, the taxonomic debate related to the species or varietal status of the bitter and sweet fruited African bush mango trees hinders their domestication process and rational use. Amplified fragment length polymorphisms (AFLPs) and chloroplast simple sequence repeats (cpSSRs) were used in this study to assess the genetic diversity of African bush mango trees and to test the distinction between bitter and sweet fruited trees, sampled across Togo, Benin, Nigeria and Cameroon. Both the AFLPs and cpSSRs showed low genetic diversity for the Dahomey Gap bitter trees population. This is due to the higher fragmentation and the continuous reduction of this small sized population occurring in a limited forest ecosystem. The higher polymorphism and genetic diversity of the sweet mango tree populations in Benin and Togo showed the effects of domestication of materials of different geographical origin coupled with the frequent long distance transfer of genetic materials. When used separately, the AFLPs and cpSSRs failed to consistently discriminate the populations and type of trees. From the combined dataset, both markers differentiated geographically recognizable groups; bitter from sweet mango trees. However, Nigerian sweet mango trees clustered with the bitter ones. The suitability of AFLPs and cpSSRs to test our hypotheses within Irvingia needs to be thoroughly reassessed.Key words: AFLP, Benin, cpSSR, Togo, Dahomey Gap, Irvingia, taxonomy, domestication

Chloroplast DNA polymorphism and phylogeography of a Central African tree species widespread in mature rainforests: Greenwayodendron suaveolens (Annonaceae)

Geographic patterns of genetic variation at chloroplast markers have been successfully used to address the phylogeography and the demographic history of many plant species. Very few studies have however been conducted in important tropical centers of plant biodiversity like the African rainforests. The phylogeography of a tree species widespread in Central African mature forests, Greenwayodendron suaveolens subsp. suaveolens (Annonaceae), was investigated in the Lower Guinea phytogeographic domain (essentially Gabon and Cameroon) by sequencing an intergenic spacer of the chloroplast genome (trnC-petN1R). A total of 11 polymorphic sites, including nine single nucleotide polymorphisms (SNPs), two insertions/deletions and two inversions, defined 12 haplotypes. The taxon is represented by two sympatric varieties (var. suaveolens and var. gabonica) that carried distinct and relatively divergent haplotypes. These varieties, also well distinguishable morphologically, might therefore represent true biological species. The variety suaveolens, more common and more widespread than the variety gabonica, was represented by ten haplotypes. This taxon showed a weak but statistically significant phylogeographic structure, indicating that two sets of related haplotypes essentially occurred respectively in the northern and the southern hemispheres. These results suggest that the distribution of Greenwayodendron suaveolens subsp. suaveolens, which is currently continuous in the Lower Guinea domain, might have been more fragmented in the past, possibly in relation with Pleistocene forest fragmentation. © 2010 Springer Science+Business Media, Inc.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

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 ≥10cm 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 >50km. 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. © 2011 Blackwell Publishing Ltd