Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

Abstract

BackgroundSpecies delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure.ResultsWest African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance.ConclusionsOur genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.

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

“…As a caveat, it is questionable whether the low number of SSR loci used in this study (six) was not too limited to detect such parapatric genetic clusters. However, this is not supported by studies of other African trees: five SSR loci were sufficient to recover four genetic clusters in Symphonia globulifera (Budde et al., ), and seven SSR loci detected six genetic clusters in Milicia excelsa , where the same clusters were retrieved using SNP data (Dainou et al., ). In addition, our six SSR loci were sufficient to characterize IBD patterns in our Afzelia species and showed perfect congruence with the IBD pattern derived from our GBS data in A. africana .…”

“…In the last few years, population genetic data have accumulated for a number of African rainforest trees and revealed well-differentiated parapatric genetic clusters in Central and West African rainforests for most species (e.g., Budde et al, 2013;Hardy et al, 2013;Daïnou et al, 2014Daïnou et al, , 2016Heuertz et al, 2014;Piñeiro et al, 2017;Demenou et al, 2018;Migliore et al, 2018). In general, this genetic structuring cannot be explained by current geographic barriers such as the main mountain chains (Cameroonian Volcanic Line, Cristal Mountains, and Chaillu massif) or major rivers in the region (Sanaga, Dja, and Oougué Rivers).…”

“…Studies on the population genetic structure of African trees have largely focused on rainforest species (e.g., Hardy et al., ; Daïnou et al., , ; Duminil et al., ; Ikabanga et al., ; Demenou et al., ; Monthe et al., ). In contrast, the evolutionary history of trees from the drier Sudanian and Zambezian regions, situated respectively north and south of the Guineo‐Congolian rainforest (Fig.…”

The hitchhiker's guide to single‐locus species delimitation

“…However, ribosomal DNA markers such as intervening spacer sequences (ITSs) are also characterized by small effective population sizes due to their concerted mode of evolution, and their fast mutation rates make them ideal candidate markers for single‐locus species delimitation. Although they remain rare, studies using single diploid sequence markers to delineate species are presently on the rise, either alone (Adjeroud et al., ; Daïnou et al., ) or in conjunction with an organellar marker such as COI (Copilaş‐Ciocianu et al., ; Flot, Dahl, & André, ; Papakostas et al., ). Our take‐home message may therefore be: if you sequence a single marker to delineate species, make it a nuclear one; and if you sequence two markers, include at least one nuclear marker (instead of piling up two mitochondrial or chloroplastic DNA regions, which behave as a single marker because they are linked together on the same molecule).…”

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.)

“…Given the genetic closeness, it can be difficult to identify genetic diversity unless comprehensive approaches are utilized. A recent study in tree genus Milica , where population structure was analyzed using nuclear SNPs, SSRs and DNA sequences, revealed hidden species diversity in closely related species [23]. In sweet cherry, a previous study compared and evaluated the utility of 7 simple sequence repeat (SSR) molecular markers versus 40 single nucleotide polymorphism (SNP) molecular markers to determine the genetic diversity and relatedness in 99 cultivated genotypes of sweet cherry [24].…”