The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

Abstract

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

“…Population genetics studies of Isoëtes species around the world have been reported different levels of genetic diversity in Isoëtes species, applying other genetic markers (Caplen & Werth, 2000;Chen et al, 2005;Kang et al, 2005;Kim et al, 2008;Gentili et al, 2010;Li et al, 2013;Stelt et al, 2017;Ma et al, 2019;Zheng et al, 2020). Santos et al (2020) also found a high genetic diversity using ISSR markers but the presence of a genetically differentiated on the North of the Amendoim Lake was not corroborated by our results. Genetic diversity metrics at the individual level showed that the expected heterozygosity is significantly different in each area but the observed heterozygosity is higher and significantly different in the west sampling area, indicating that this area holds more genetic diversity.…”

“…We collected leaf samples of 55 specimens of I. cangae distributed along the whole area of the Amendoim Lake (Table S1) in five sampling areas, four of them representing similar areas used by Santos et al (2020): north (n = 13), south (n = 10), east…”

“…We employed the N e value-and confidence interval-found in the complete dataset with all neutral SNPs for MVP estimates. N c indicates the census size of the species (representing the total number of individuals) and was estimated through a survey according to Santos et al (2020) by free-diving in the perimeter of the Amendoim Lake up to the 4 m isobath in October 2018-in deeper areas I. cangae was not observed. We sampled 190 points randomly distributed, but in order to understand the entire perimeter of the lake.…”

“…Fragment Length Polymorphism (AFLP; Jung et al, 2014;Kang et al, 2005), Inter-Simple Single Repeat (ISSR; Gentili et al, 2010;Ma et al, 2019;Santos et al, 2020), microsatellites (Li et al, 2013;Stelt et al, 2017;Zheng et al, 2020), chloroplast DNA (Jung et al, 2014;Nunes et al, 2018;Zheng et al, 2020), or Random Amplified Polymorphic DNA (RAPD; Chen et al, 2007;Kim et al, 2008;Gentili et al, 2010). These studies have shown that some Isoëtes species are marked by low genetic diversity (Kang et al, 2005;Kim et al, 2008) and others by moderate and higher diversity (Gentili et al, 2010;Chen et al, 2012;Stelt et al, 2017).…”

“…We also estimated effective population size (N e ) using genomic data to provide information about minimum viable population (MVP), a primordial data for species long-term survival. Furthermore, with thousands of SNPs, we evaluated whether I. cangae is a Neotropical NES with low genetic diversity as classical studies supposed or, according to Santos et al (2020) using ISSR markers, whether the species is a NES with high genetic diversity.…”