Afro-alpine flagships revisited: Parallel adaptation, intermountain admixture and shallow genetic structuring in the giant senecios (Dendrosenecio)

Recent parallel speciation in Antirrhinum involved complex haplotypes and multiple adaptive characters

A role of ecological adaptation in speciation can be obscured by stochastic processes and differences that species accumulate after genetic isolation. One way to identify adaptive characters and their underlying genes is to study cases of speciation involving parallel adaptations. Recently resolved phylogenies reveal that alpine morphology has evolved in parallel in the genus Antirrhinum (snapdragons): first in an early split of an alpine from a lowland lineage and, more recently, from within the lowland lineage to produce closely related sympatric species with contrasting alpine and lowland forms. Here, we find that two of these later diverged sympatric species are differentiated by only around 2% of nuclear loci. Though showing evidence of recent gene flow, the species remain distinct for a suite of morphological characters typical of earlier-diverged alpine or lowland lineages and their morphologies correlate with features of the local landscape, as expected of ecological adaptations. Morphological differences between the two species involve multiple, unlinked genes so that parental character combinations are readily broken up by recombination in hybrids. We detect little evidence for post-pollination barriers to gene flow or recombination, suggesting that genetic isolation related to ecological adaptation is important in maintaining character combinations and might have contributed to parallel speciation. We also find evidence that genes involved in the earlier alpine-lowland split were reused in parallel evolution of alpine species, consistent with introgressive hybridisation, and speculate that many non-ecological barriers to gene flow might have been purged during the process.

Repeatedly Northwards and Upwards: Southern African Grasslands Fuel the Colonization of the African Sky Islands in Helichrysum (Compositae)

The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene-Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.

Climate-driven convergent evolution in riparian ecosystems on sky islands

Climate-induced evolution will determine population persistence in a changing world. However, finding natural systems in which to study these responses has been a barrier to estimating the impact of global change on a broad scale. We propose that isolated sky islands (SI) and adjacent mountain chains (MC) are natural laboratories for studying long-term and contemporary climatic pressures on natural populations. We used greenhouse common garden trees to test whether populations on SI exposed to hot and dry climates since the end of the Pleistocene have phenotypically diverged from populations on MC, and if SI populations have converged in these traits. We show: (1) populations of Populus angustifolia from SI have diverged from MC, and converged across SI, in reproductive and productivity traits, (2) these traits (cloning and aboveground biomass, respectively) are significantly correlated, suggesting a genetic linkage between them, and (3) the trait variation is driven by both natural selection and genetic drift. These shifts represent potentially beneficial phenotypes for population persistence in a changing world. These results suggest that the SI-MC comparison is a natural laboratory, as well as a predictive framework, for studying long-term responses to climate change across the globe.

Plastid phylogenomics and insights into the inter-mountain dispersal of the Eastern African giant senecios (Dendrosenecio, Asteraceae)

Giant senecios (Dendrosenecio, Asteraceae), endemic to the tropical mountains of Eastern Africa, are one of the most conspicuous alpine plant groups in the world. Although the group has received substantial attention from researchers, its infrageneric relationships are contentious, and the speciation history remains poorly understood. In this study, whole chloroplast genome sequences of 46 individuals were used to reconstruct the phylogeny of giant senecios using Maximum Likelihood and Bayesian Inference methods. The divergence times of this emblematic group were estimated using fossil-based calibrations. Additionally, the ancestral areas were inferred, and ecological niche modeling was used to predict their suitable habitats. Phylogenetic analyses yielded two robustly supported clades. One clade included taxa sampled from Tanzania, while the other clade included species from other regions. Giant senecios likely originated from the North of Tanzania approximately 2.3 million years ago (highest posterior density 95%; 0.77-4.40), then rapidly radiated into the Kenyan and Ugandan mountains within the last one million years. The potential routes of dispersal have been proposed based on the inferred ancestral areas, estimated time, and predicted past suitable niches. Plio-Pleistocene climate oscillations and orogeny instigated early divergence of the genus. Whereas in situ radiation of giant senecios was chiefly driven by multiple long-distance dispersal events followed by episodes of vicariance, and allopatric speciation (geographic and/or altitudinal).