Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices

Abstract

Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

Genetic Diversity and DNA Barcoding of Yam Accessions from Southern Nigeria

“…Phylogenetic reconstruction of the generated Dioscorea species using rbcL marker resolved them into ten groups and this indicates different existing isolated groups inherent in the accessions. The existence of these different accessions among the collections could be attributable to lack of exchange of yam tubers by farmers among villages thereby resulting in a stronger heterozygosity among species compared to wild ones as reported by Ngo Ngwe et al [24]. A contribution of evolutionary biology regarding conservation is the knowledge of diverse phylogenetic diversities, defined by the sums of branch lengths of the evolutionary trees connecting a set of taxa or individuals [55].…”

“…diversification for resistance to drastic changes in climate, introgression, cross hybridization and conservation processes to reduce genetic erosion [18]- [24]. To have adequate knowledge of these yam accessions, characterization to the species level, genetic richness and assessment of phylogenetic diversity (PD) are of utmost importance following the genetic resource preservation roles of PD in crop extinction [25], functionality in ecosystems [26] [27] and abiotic variability [28] and these can be achievable with accurate, sensitive and reliable methods.…”

Guinea yam (Dioscorea spp., Dioscoreaceae) wild relatives identified using whole plastome phylogenetic analyses

“…The origin of cultivated yam remains uncertain. -Previous phylogenetic studies conducted on Dioscorea were based on short plastid sequence data and resulted in generally poorly supported molecular phylogenies (Caddick & al., 2002;Chaïr & al., 2005Chaïr & al., , 2016Wilkin & al., 2005;Gao & al., 2008;Hsu & al., 2013;Mukherjee & Bhat, 2013;Ngo Ngwe & al., 2015;Maurin & al., 2016;. Here, for the first time, we used whole plastome sequence data, which led to an overall highly supported phylogeny of West African Dioscorea species.…”

“…Previous studies reported difficulty in separating D. abyssinica, D. praehensilis, D. rotundata and D. cayenensis (Terauchi & al., 1992;Ramser & al., 1997;Chaïr & al., 2005;Ngo Ngwe & al., 2015). Despite the use of whole chloroplast information, we still only obtained poor resolution among the wild species D. abyssinica, D. praehensilis and D. sagittifolia and the cultivated species D. rotundata and D. cayenensis.…”

High contiguityde novogenome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

“…sect. Lasiophyton ) in phylogenetic analyses [10,11]. They also differ in chromosome number [8,12,13] making it unlikely that genetic maps can be directly transferred to D. dumetorum .…”