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Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma

Citation

Culshaw, Victoria et al. (2022), Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma, Dryad, Dataset, https://doi.org/10.5061/dryad.ncjsxkstw

Abstract

Premise

Genera that are widespread but have a geographically discontinuous distribution and are represented by few species are intriguing. Did they achieve their disjunct distribution recently, or is it ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale floristic pattern in which closely related species appear co-distributed in isolated regions over the edges of Africa and nearby archipelagos. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other at the ends of the African continent: C. canariense in the west, endemic to the Canary Islands; C. lyperiiflorum in the east, endemic to the Horn of Africa - Southern Arabia; and C. rotundifolia, restricted to Southern Africa.

Methods

Here, we employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae, using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian MCMC approaches. Population history was estimated with phylogeographic structured coalescent methods.

Key Results

Our results support C. rotundifolia as sister to the disjunct clade formed by C. canariense and C. lyperiiflorum. Stem divergence was dated in the Late Miocene, while the origin of extant diversification within the genus was inferred as Early Pliocene.

Conclusions

We show that the current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction/population bottlenecking events associated to historical aridification cycles, consistent with the “climatic refugia” hypothesis.

Usage Notes

For Appendix 1, please run in MrBayesv3.2.6

For Appendix 2, please run in BEASTv1.8.2

For Appendix 3, please run in RevBayesv1.0.11

For Appendix 4, please run in BEASTv1.8.2

For Appendix 5, please run in BEASTv2.4.7

Funding

Ministerio de Economía y Competitividad (MINECO), Award: BES-2013-065389

Ministerio de Economía y Competitividad (MINECO) and the European Regional Development Fund (FEDER), Award: CGL2015-67849-P, MINECO/FEDER

Ministerio de Economía y Competitividad (MINECO) and the European Regional Development Fund (FEDER), Award: CGL2015-67849-P, MINECO/FEDER