Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion

Abstract

Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (h T(cpSSR) ¼ 0.903-0.948) and population differentiation (G ST(RFLP) ¼ 0.700-0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (G ST(cpSSR) ¼ 0.392; R ST ¼ 0.673; R ST 4R ST (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.

Population genomics of the widespread African savannah treesAfzelia africanaandAfzelia quanzensisreveals no significant past fragmentation of their distribution ranges

“…However, our data were not powerful enough to identify whether these signatures reflect range expansions (and from which source) or only a demographic expansion without change of distribution range. In any case, populations of both savannah species apparently did not experience major disturbances leading to their fragmentation and/or demographic decline in the latest hundreds to thousands of generations, as has been suggested for some other savannah species (Bryja et al, 2010;Odee et al, 2012;Sexton et al, 2015). Fig.…”

“…The absence of clear‐cut genetic discontinuities over large distances for A. africana and A. quanzensis is consistent with results reported in the savannah tree species Adansonia digitata and Khaya senegalensis , which showed no geographic discontinuities of the genetic variation (Tsy et al., ; Sexton et al., ). Acacia senegal displays strong differentiation between Sudanian and Zambezian populations, but low diversity and structure at a nuclear ribosomal marker across the Sudanian savannahs suggest a recent range expansion (Odee et al., , but see Lyam et al., ). These results suggest that the African savannahs have not experienced major upheavals that led to their fragmentation (Salzmann et al., ; Vincens et al., ; Watrin et al., ), in contrast to the major fluctuations of the rainforest cover over time (Maley, ).…”

“…Three of the species occur in the Sudanian savannah (northern hemisphere): the shea tree (Vitellaria paradoxa; Allal et al, 2011;Logossa et al, 2011), the African mahogany (Khaya senegalensis; Sexton et al, 2015), and the locust bean (Parkia biglobosa; Lompo et al, 2018). The other two species have a Sudano-Zambezian distribution (northern and southern hemispheres): the baobab (Adansonia digitata; Tsy et al, 2009;Kyndt et al, 2009) and Arabic gum (Acacia senegal; Odee et al, 2012;Lyam et al, 2018). Within the Sudanian savannah, weak genetic structure was detected in K. senegalensis and A. digitata, while moderate differentiation was found in A. senegal, mostly in chloroplast markers.…”

Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

“…Hence, species delimitation requires to integrate data from molecular phylogeny, classical taxonomy (morphology-based), ecology, historical and contemporaneous biogeography in a way that permits the reconstruction of the evolutionary history of the target taxon (see, for example, Datwyler and Weiblen, 2004;Odee et al, 2012;Scotti-Saintagne et al, 2012). We adopted a pluralistic approach to infer biogeographical history and delimit significant evolutionary units in the African genus Milicia Sim.…”

Population genomics of the widespread African savannah treesAfzelia africanaandAfzelia quanzensis(Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges

“…Three of the species occur in the Sudanian savannah (Northern Hemisphere): the shea tree Vitellaria paradoxa (Allal et al, 2011; Logossa et al, 2011), the African Mahogany Khaya senegalensis (Sexton et al, 2015), and the Locust Bean Parkia biglobosa (Lompo et al, 2018). The other two species exhibit a Sudano-Zambezian distribution (Northern and Southern Hemispheres): the baobab, Adansonia digitata (Tsy et al, 2009; Kyndt et al, 2009) and the Arabic gum species Acacia senegal (Odee et al, 2012; Lyam et al, 2018). Within the Sudanian savannah, weak genetic structure was detected in K. senegalensis and A. digitata , while moderate differentiation was found in A. senegal .…”