Abstract
Medemia argun is a wild, dioecious palm, adapted to the harsh arid environment of the Nubian Desert in Sudan and southern Egypt. There is a concern about its conservation status, since little is known about its distribution, abundance, and genetic variation. M. argun grows on the floodplains of seasonal rivers (wadis). The continuing loss of suitable habitats in the Nubian Desert is threatening the survival of this species. We analyzed the genetic diversity, population genetic structure, and occurrence of M. argun populations to foster the development of conservation strategies for M. argun. Genotyping-by-sequencing (GBS) analyses were performed using a whole-genome profiling service. We found an overall low genetic diversity and moderate genetic structuring based on 40 single-nucleotide polymorphisms (SNPs) and 9,866 SilicoDArT markers. The expected heterozygosity of the total population (HT) equaled 0.036 and 0.127, and genetic differentiation among populations/groups (FST) was 0.052 and 0.092, based on SNP and SilicoDArT markers, respectively. Bayesian clustering analyses defined five genetic clusters that did not display any ancestral gene flow among each other. Based on SilicoDArT markers, the results of the analysis of molecular variance (AMOVA) confirmed the previously observed genetic differentiation among generation groups (23%; p < 0.01). Pairwise FST values indicated a genetic gap between old and young individuals. The observed low genetic diversity and its loss among generation groups, even under the detected high gene flow, show genetically vulnerable M. argun populations in the Nubian Desert in Sudan. To enrich and maintain genetic variability in these populations, conservation plans are required, including collection of seed material from genetically diverse populations and development of ex situ gene banks.
Highlights
The open-habitat palm (Medemia argun) is a dioecious species native to Sudan (Broun and Massey, 1929; Andrews, 1956) and adapted to harsh arid environments
We estimated the relative levels of gene flow contributions from seed and pollen migration by comparing nuclear DNA (SNP/SilicoDArT markers) differentiation detected in this study with chloroplast DNA differentiation previously analyzed by us (Elshibli and Korpelainen, 2018) for the same set of M. argun samples
Lower diversities were observed for single-nucleotide polymorphisms (SNPs) markers compared to SilicoDArT markers, the overall diversity shows comparable trends for both marker types, as elucidated by the moderate positive correlation revealed by the Mantel test
Summary
The open-habitat palm (Medemia argun) is a dioecious species native to Sudan (Broun and Massey, 1929; Andrews, 1956) and adapted to harsh arid environments. Little is known on the distribution, abundance, and genetic variation of M. argun, which has previously been listed by the International Union for Conservation of Nature’s (IUCN) Red List as a critically endangered (IUCN, 1998), and very recently as a vulnerable species. The latter assessment was proposed by Cosiaux et al (2020) based on the number of individuals deduced from satellite imagery (Google Earth and Bing Maps; Figure 1B). In Sudan, M. argun has been reported to exist only in the Nubian Desert (Ali and Idris, 2016)
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