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

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.