Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa

Abstract

While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano-Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within-population diversity: allelic richness ranged from R(nuc) = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (F(STnuc) = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub-set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (R(cp) = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (G(STcp) = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10,000 bp) have probably enhanced gene flow and population expansion.

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

“…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, ). Nevertheless, Vitellaria paradoxa (Allal et al., ; Logossa et al., ) and Parkia biglobosa (Lompo et al., ) show clear genetic discontinuities in the Sudanian region (but include genetically homogenous clusters extending over large distances in central west Africa). Whether their genetic structures have been influenced by human activities remains an open question because these species of high socioeconomic importance in agroforestry systems produce seeds that are marketed and widely used for human consumption.…”

“…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. For V. paradoxa and P. biglobosa , genetic discontinuities in the form of parapatric genetic clusters were detected in the Sudanian savannah, although in both cases widespread genetically homogeneous clusters were observed in central West Africa (Logossa et al., ; Lompo et al., ). Within the Zambezian domain, significant population genetic structure was detected for A. senegal , but not for A. digitata .…”

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

“…The strong genetic structure in these populations was probably caused by a combination of the greater geographic distances separating them [16], [67] and the presence of geographic barriers such as discontinuous mountain ridges [68]–[69] and large plains and valleys [25] (Fig. 1).…”

“…Further, the focus must be on preserving the overall genetic diversity and natural evolutionary processes in metapopulations rather than the diversity within separate subpopulations [11]. Thus, large-scale genetic structure analysis covering species’ ranges has been applied to numerous forest tree species, especially species that are economically, ecologically, and/or genetically important for a specific region [5]–[6], [8], [11]–[16].…”

Genetic effects of forest management practices: Global synthesis and perspectives

“…Parkland management has favored gene flow at local and regional levels and has created the conditions to support high genetic diversity within the species and good adaptation to local environment (Allal et al, 2011;Logossa et al, 2005;Sanou et al, 2005). Parkland management has not reduced the variability of economical important traits such as lipid seed constituents in this species (Davrieux et al, 2010).…”