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

Background: Species 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. Results: West 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. Conclusions: Our 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

Large Scale_Khaya

Differentiation among species of African Mahogany (Khaya sp.) based on a large SNP arra

Impact of Gene Flow and Introgression on the Range Wide Genetic Structure of Quercus robur (L.) in Europe

As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction

Bayern_Families

Bayern_Familie

Inbreeding_Prunusavium_ReadMe

Inbreeding_Prunusavium_ReadM

Limited pollen dispersal and biparental inbreeding in Symphonia globulifera in French Guiana

In this paper, we report a study of the mating system and gene flow of Symphonia globulifera, a hermaphroditic, mainly bird-pollinated tree species with a large geographic distribution in the tropical Americas and Africa.Using three microsatellites, we analysed 534 seeds of 28 open pollinated families and 164 adults at the experimental site 'Paracou' in French Guiana. We observed, compared to other tropical tree species, relatively high values for the effective number of alleles. Significant spatial genetic structure was detected, with trees at distances up to 150 m more genetically similar than expected at random. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, tm, was 0.920. A significant level of biparental inbreeding and a high proportion of full-sibs were estimated for the 28 seed arrays. We estimated mean pollen dispersal distances between 27 and 53 m according to the dispersal models used. Although the adult population density of S. globulifera in Paracou was relatively high, the joint estimation of pollen dispersal and density of reproductive trees gave effective density estimates of 1.6 and 1.3trees/ha. The parameters of the mating system and gene flow are discussed in the context of spatial genetic and demographic structures, flowering phenology and pollinator composition and behaviour