DdRAD sequencing of the endangered species Primula Palinuri Petagna reveals high levels of inter-population diversity

Abstract

Population genetics studies provide information regarding genetic diversity and genetic structure of populations. This information can in turn be used to inform conservation strategies. In view of programmed conservation efforts, we aimed at investigating the genetic composition of Primula palinuri Petagna, an endemic vulnerable species in Southern Italy. Ninety-one individuals of P. palinuri from seven populations were investigated using double digest Restriction Associated DNA sequencing (ddRAD-seq) and a total of 99,014 Single nucleotide polymorphisms (SNPs) were identified. Low levels of heterozygosity (0.08-0.12) and high levels of kinship (0.20-0.30) and inbreeding (0.34-0.49) were detected in all study populations. Kinship computed irrespective of population was low, suggesting that the level of inter-population relatedness is low. Analysis of the genetic structure showed that the populations were differentiated from each other and formed three major clusters, broadly corresponding to the geographic sampling locations. We identified the SNPs mostly contributing to the separation in population clusters, and we identified a reduced set of 40 SNPs that can successfully discriminate between the three population clusters. In conclusion, our study shows that the sampled P. palinuri populations have low heterozygosity, low intra-population variability and high inter-population variability.

Keywords: Admixture; Endemic species; Genotyping; Population genetics; Population structure.

Fig. 1

Geographic location of the studied samples. Geographic locations correspond to LAM (Lambro river), FIU (Fiuzzi), ID (Dino’ Island), PC (Punta Caina), SGP (San Giovanni a Piro), CIM (Vaccuta) and PPA (Palinuro Cape). The 10 × 10 km grid regions represent the official distribution of P. palinuri according to the Habitat Directive Report (2013–2018) https://reportingdirettivahabitat.isprambiente.it/downloads.

Fig. 2

Boxplots of population genetics parameters. (a) Observed heterozygosity for different populations. (b) Kinship coefficient and (c) Inbreeding coefficient. Population names are listed in Table 1. “ALL” denote statistics computed considering the whole dataset as a single population. Populations with the same letter are not significantly different from each other (Wilcoxon’s test). Geographic locations correspond to LAM (Lambro river), FIU (Fiuzzi), ID (Dino’ Island), PC (Punta Caina), SGP (San Giovanni a Piro), CIM (Vaccuta) and PPA (Palinuro Cape). “n” denotes the number of sequenced individuals per population.

Fig. 3

PCA, admixture analysis and phylogenetic tree. (a) Principal component analysis (PCA) with colors representing each population and each individual depicted with a square. (b) Admixture analysis in the studied individuals of Primula palinuri. Each barplot represents an individual. The elevation of each colored bar represents the probability of assignment to the corresponding population when assuming the presence of three ancestral populations (K = 3). (c) Phylogenetic neighbor-joining unrooted tree based on Nei’s distance and bootstrap = 100. Geographic locations correspond to LAM (Lambro river), FIU (Fiuzzi), ID (Dino’ Island), PC (Punta Caina), SGP (San Giovanni a Piro), CIM (Vaccuta) and PPA (Palinuro Cape).

Fig. 4

Biplot with a subset of 40 SNPs. Subset of the 40 SNPs more contributing to the separation of population clusters. Colors correspond to different populations and SNPs are represented with red arrows. Geographic locations correspond to LAM (Lambro river), FIU (Fiuzzi), ID (Dino’ Island), PC (Punta Caina), SGP (San Giovanni a Piro), CIM (Vaccuta) and PPA (Palinuro Cape).