Abstract
Habitat fragmentation due to anthropogenic activities is the major cause of biodiversity loss. Endemic and narrowly distributed species are the most susceptible to habitat degradation. Penstemon scariosus is one of many species whose natural habitat is vulnerable to industrialization. All varieties of P. scariosus (P. scariosus var. albifluvis, P. scariosus var. cyanomontanus, P. scariosus var. garrettii, P. scariosus var. scariosus) have small distribution ranges, but only P. scariosus var. albifluvis is being considered for listing under the Endangered Species Act. We used eight microsatellites or simple sequence repeats (SSRs) loci and two amplified fragment length polymorphism (AFLP) primer combinations to investigate the population genetic structure and diversity of P. scariosus varieties. Moreover, we compared the utility of the two marker systems in conservation genetics and estimated an appropriate sample size in population genetic studies. Genetic differentiation among populations based on Fst ranged from low to moderate (Fst = 0.056–0.157) and from moderate to high when estimated with Des (Des = 0.15–0.32). Also, AMOVA analysis shows that most of the genetic variation is within populations. Inbreeding coefficients (Fis) were high in all varieties (0.20–0.56). The Bayesian analysis, STRUCTURE, identified three clusters from SSR data and four clusters from AFLPs. Clusters were not consistent between marker systems and did not represent the current taxonomy. MEMGENE revealed that a high proportion of the genetic variation is due to geographic distance (R2 = 0.38, P = 0.001). Comparing the genetic measurements from AFLPs and SSRs, we found that AFLP results were more accurate than SSR results across sample size when populations were larger than 25 individuals. As sample size decreases, the estimates become less stable in both AFLP and SSR datasets. Finally, this study provides insight into the population genetic structure of these varieties, which could be used in conservation efforts.
Highlights
Anthropogenic activities are the main cause of biodiversity loss today (Pimm and Raven 2000; Ceballos et al 2015)
Using the Delta-K method, as implemented in STRUCTURE HARVESTER, we found that K = 2 (Online Resource 1, Figure S2) was the most likely value followed by K = 3 (Online Resource 1, Figure S3)
For the amplified fragment length polymorphism (AFLP) data subsets, we found that the larger the sample size, the closest the estimates were to those calculated from the full dataset (Online Resource 1, Figures S5 and S6)
Summary
Anthropogenic activities are the main cause of biodiversity loss today (Pimm and Raven 2000; Ceballos et al 2015). In the United States, most endangered plants (81%) are threatened by habitat loss and degradation. The expansion of agricultural boundaries (excluding pasturing) is the leading cause of habitat destruction in the United States (Wilcove et al 1998). 33% of endangered plants are affected by livestock grazing. 133 species in the United States are threatened due to activities linked to mining for oil and gas (Wilcove et al 1998). The state of Utah has the largest mining excavation in the world with the second largest copper producer in the United States (Lee 2016). There are 42 Utah species listed under the Endangered
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