Abstract
AbstractAimMost of the fundamental questions in conservation biogeography require the description of species geographic boundaries and the identification of discrete biological units within these boundaries. International conservation efforts and institutions rely mainly on traditional taxonomic approaches for defining these boundaries, resulting in significant cryptic diversity going undetected and often extinct. Here, we combine high‐throughput genomic data with publicly available environmental data to identify cryptic diversity in the threatened bird's‐eye primrose (Primula farinosa). We aim to characterize evolutionary lineages and test whether they co‐occur with changes in environmental conditions. These lineages can be used as intraspecific units for conservation to enhance assessments regarding the status of threatened species.LocationEurope and temperate Asia (latitude, 40–65°N; longitude, 10°E–115°W).MethodsWe genotyped 93 individuals from 71 populations at 1,220 loci (4,089 SNPs) across the Eurasian distribution of P. farinosa. We used phylogenomic and population structure approaches to identify intraspecific lineages. We further extracted statistically derived and remotely sensed environmental information, that is land cover, climate and soil characteristics, to define the biotic and abiotic environment inhabited by each lineage and test for niche similarities among lineages. Additionally, we tested for isolation by distance among populations and applied linear and polynomial regressions to identify lineage‐environment associations.ResultsAnalyses of genomic data revealed six major lineages within P. farinosa corresponding to distinct geographic areas. Niche similarity tests indicated that lineages occupy distinct abiotic and biotic space. Isolation by distance indicated that geography alone cannot explain genetic divergence within P. farinosa, while lineage‐environment associations suggested potential adaptation to different abiotic conditions across lineages. However, relationships with the land cover classes, a proxy for habitat, were weaker.Main conclusionOur results highlight the need for incorporating intraspecific diversity in global assessments of species conservation status and the utility of genomic and publicly available environmental data in conservation biogeography.
Highlights
Most of the fundamental questions in conservation biogeography require knowledge of the geographic distributions and ecologi‐ cal niches of individual species (Riddle, Ladle, Lourie, & Whittaker, 2011; Whittaker et al, 2005)
To assess intraspecific genetic structure and phylogenetic relation‐ ships in P. farinosa, we used the Variant Call Format (VCF) file ex‐ ported by stacks and filtered it using Gonospy to exclude SNPs (a) that were represented by ≤5% of the total reads for the correspond‐ ing locus within each individual, (b) with a frequency ≤0.05 across all individuals and (c) absent in more than 30% of the sampled individu‐ als
We subsequently reduced the dimensions of the dataset by performing principal components analysis (PCA) implemented in the package Matplotlib (Hunter, 2007) in Python
Summary
Most of the fundamental questions in conservation biogeography require knowledge of the geographic distributions and ecologi‐ cal niches of individual species (Riddle, Ladle, Lourie, & Whittaker, 2011; Whittaker et al, 2005). Wide‐range species, those with limited vagility or dispersal potential, often show strong phylogeographic structure across their distributions (Avise, 2009) This structure has been mostly shaped by past geological, ecological and evolutionary pro‐ cesses, and the resulting intraspecific units (i.e., historically isolated groups of populations; hereafter referred to as “lineages”) frequently display distinct ecological characteristics (Allendorf, Luikart, & Aitken, 2013). Responding to recent and ongoing destructive impacts of global cli‐ mate change and human activities on intraspecific diversity (Miraldo et al, 2016; Pauls, Nowak, Balint, & Pfenninger, 2013), and to ecosystems (Des Roches et al, 2018), requires the integration of genetic and environmental data Conservation studies integrating both biodiversity aspects are still scarce but are expected to in‐ crease as more genetic and environmental data are becoming avail‐ able (Jenkins, Yannic, Schaefer, Conolly, & Lecomte, 2018; Wilting et al, 2015; Yannic et al, 2017)
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