The biodiversity hotspot as evolutionary hot-bed : spectacular radiation of Erica in the Cape Floristic Region

CITATION: Pirie, M. D., et al. 2016. The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region.BMC Evolutionary Biology, 16:190, doi:10.1186/s12862-016-0764-3.The original publication is available at https://bmcevolbiol.biomedcentral.comBackground: The disproportionate species richness of the world’s biodiversity hotspots could be explained by low extinction (the evolutionary “museum”) and/or high speciation (the “hot-bed”) models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the genus Erica L. We generate a novel phylogenetic hypothesis informed by nuclear and plastid DNA sequences of c. 60 % of the c. 800 Erica species (of which 690 are endemic to the CFR), and use this to estimate clade ages (using RELTIME; BEAST), net diversification rates (GEIGER), and shifts in rates of diversification in different areas (BAMM; MuSSE). Results: The diversity of Erica species in the CFR is the result of a single radiation within the last c. 15 million years. Compared to ancestral lineages in the Palearctic, the rate of speciation accelerated across Africa and Madagascar, with a further burst of speciation within the CFR that also exceeds the net diversification rates of other Cape clades. Conclusions: Erica exemplifies the “hotbed” model of assemblage through recent speciation, implying that with the advent of the modern Cape a multitude of new niches opened and were successively occupied through local species diversification.https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0764-3Publisher's versio

Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

Whilst most of the immense species richness of heathers (Calluna, Daboecia and Erica: Ericeae; Ericaceae) is endemic to Africa, particularly the Cape Floristic Region, the oldest lineages are found in the Northern Hemisphere. We present phylogenetic hypotheses for the major clades of Ericeae represented by multiple accessions of all northern Erica species and placeholder taxa for the large nested African/Madagascan clade. We identified consistent, strongly supported conflict between gene trees inferred from ITS and chloroplast DNA sequences with regard to the position of Erica lusitanica. We used coalescent simulations to test whether this conflict could be explained by coalescent stochasticity, as opposed to reticulation (e.g. hybridisation), given estimates of clade ages, generation time and effective population sizes (Ne). A standard approach, comparing overall differences between real and simulated trees, could not clearly reject coalescence. However, additional simulations showed that at the (higher) Ne necessary to explain conflict in E. lusitanica, further topological conflict would also be expected. Ancient hybridisation between ancestors of northern species is therefore a plausible scenario to explain the origin of E. lusitanica, and its morphological similarities to E. arborea. Assuming either process influences the results of species tree and further evolutionary inference. The coalescence scenario is equivocal with regard the standing hypothesis of stepping stone dispersal of Erica from Europe into Africa; whereas reticulate evolution in E. lusitanica would imply that the colonisation of Tropical East Africa by E. arborea instead occurred independently of dispersals within the rest of the African/Madagascan clade

The biodiversity hotspot as evolutionary hot-bed : spectacular radiation of Erica in the Cape Floristic Region

CITATION: Pirie, M. D., et al. 2016. The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region.BMC Evolutionary Biology, 16:190, doi:10.1186/s12862-016-0764-3.The original publication is available at https://bmcevolbiol.biomedcentral.comBackground: The disproportionate species richness of the world’s biodiversity hotspots could be explained by low extinction (the evolutionary “museum”) and/or high speciation (the “hot-bed”) models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the genus Erica L. We generate a novel phylogenetic hypothesis informed by nuclear and plastid DNA sequences of c. 60 % of the c. 800 Erica species (of which 690 are endemic to the CFR), and use this to estimate clade ages (using RELTIME; BEAST), net diversification rates (GEIGER), and shifts in rates of diversification in different areas (BAMM; MuSSE). Results: The diversity of Erica species in the CFR is the result of a single radiation within the last c. 15 million years. Compared to ancestral lineages in the Palearctic, the rate of speciation accelerated across Africa and Madagascar, with a further burst of speciation within the CFR that also exceeds the net diversification rates of other Cape clades. Conclusions: Erica exemplifies the “hotbed” model of assemblage through recent speciation, implying that with the advent of the modern Cape a multitude of new niches opened and were successively occupied through local species diversification.https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0764-3Publisher's versio

Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

Accepted version of:<br><br>Mugrabi de Kuppler AL, Fagúndez J, Bellstedt DU, Oliver EGH, Léon J, Pirie MD (2015) Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae). Molecular Phylogenetics and Evolution 88:121–131. http://dx.doi.org/10.1016/j.ympev.2015.04.005<br

Additional file 3: Figure S2. of The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region

Relaxed clock molecular dating results: a) age estimates for clades within Erica inferred using RELTIME [24] with the best tree from RAxML (Additional file 2: Figure S1c); b) and c) phylogeny and relaxed clock molecular dating age estimates for clades within Erica inferred using BEAST [23] on a reduced matrix of 62 taxa b) with and c) without additional constraint based on microfossil evidence (error bars represent 95 % Posterior Probability (PP) intervals; PP clade support is indicated at nodes). (ZIP 11562 kb

Additional file 6: Table S3. of The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region

Summary of BAMM results based on 25 rate-smoothed RAxML bootstrap trees. (DOCX 12 kb

Additional file 5: Figures S3. of The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region

BAMM diversification rate results: a) BAMM tree as presented in Fig. 1, including labels for tips and nodes referred to in the text; branches subtending Erica, Calluna and Daboecia are not to scale. b) Probabilities of overall numbers of diversification shifts inferred using BAMM. (ZIP 2444 kb

Additional file 2: Figure S1. of The biodiversity hotspot as evolutionary hot-bed: spectacular radiation of Erica in the Cape Floristic Region

Phylogenetic hypotheses: best trees with bootstrap support values from RAxML analyses of a) concatenated plastid data and b) from nuclear ribosomal ITS (with taxa showing conflicting positions according to the two gene trees highlighted in yellow); and c) and d) of the combined data (excluding conflicting taxa): c) with and d) without Erica pauciovulata (exclusion of which leads to increased support for the Cape clade from 70 % to 89 %). (ZIP 8409 kb