Detecting a hierarchical genetic population structure: the case study of the Fire Salamander (Salamandra salamandra) in Northern Italy

Abstract

The multistep method here applied in studying the genetic structure of a low dispersal and philopatric species, such as the Fire Salamander Salamandra salamandra, was proved to be effective in identifying the hierarchical structure of populations living in broad-leaved forest ecosystems in Northern Italy. In this study, 477 salamander larvae, collected in 28 sampling populations (SPs) in the Prealpine and in the foothill areas of Northern Italy, were genotyped at 16 specie-specific microsatellites. SPs showed a significant overall genetic variation (Global FST = 0.032, P < 0.001). The genetic population structure was assessed by using STRUCTURE 2.3.4. We found two main genetic groups, one represented by SPs inhabiting the Prealpine belt, which maintain connections with those of the Eastern foothill lowland (PEF), and a second group with the SPs of the Western foothill lowland (WF). The two groups were significantly distinct with a Global FST of 0.010 (P < 0.001). While the first group showed a moderate structure, with only one divergent SP (Global FST = 0.006, P < 0.001), the second group proved more structured being divided in four clusters (Global FST = 0.017, P = 0.058). This genetic population structure should be due to the large conurbations and main roads that separate the WF group from the Prealpine belt and the Eastern foothill lowland. The adopted methods allowed the analysis of the genetic population structure of Fire Salamander from wide to local scale, identifying different degrees of genetic divergence of their populations derived from forest fragmentation induced by urban and infrastructure sprawl.

Effects of landscape features on gene flow among urban frog populations

“…While results from a single species cannot be generalized for other taxonomic groups, R. ornativentris data are illustrative for other pond-breeding amphibians such as bufonid toads and small salamanders that inhabit secondary forests surrounded by urbanized areas, because they share many life history traits Maeda & Matsui, 1999). Our study also indicates that even widespread species persisting in small habitat patches with high gene flow (Sumida & Nishioka, 1996) suffer from genetic drift and loss of genetic diversity due to habitat fragmentation (Bani et al, 2017;Ortego et al, 2015;Pisa et al, 2015). Information on pervasive species, generally disregarded in most conservation genetic studies (Ortego et al, 2015; but see Lange et al, 2010), may greatly contribute to elucidating the genetic impacts of habitat fragmentation.…”

Diversity among peripheral populations: genetic and evolutionary differentiation ofSalamandra atraat the southern edge of the Alps

“…This pattern of genetic differentiation between southern periphery and northern core range is particularly clear in our dataset and confirms previous analyses on the geographic variation of S. atra, including an AFLP analysis of few samples from the Orobian mountains and the Sette Comuni plateau(Rib eron et al, 2004), and a preliminary analysis of the mitochondrial variation in samples from the Orobian mountains(Helfer et al, 2011).The genetic differentiation among populations of S. atra within the core range is still largely unknown. Moreover, the among-population differentiation of S. atra across the southern Prealps is higher than that found in the related species S. salamandra among populations inhabiting the foothills of the southern Prealps and fragmented during recent human landscape modifications (F st < 0.08;Pisa et al, 2015), and between insular and mainland Iberian populations separated about 9 kya (F st < 0.27; Velo-Ant on, Zamudio, & Cordero-Rivera, 2012). The peripheral populations of the southern Prealps are also more differentiated than the fragmented populations of the Dinarides (F st < 0.57;Razpet et al, 2016).…”

“…. salamandra among populations inhabiting the foothills of the southern Prealps and fragmented during recent human landscape modifications (F st < 0.08;Pisa et al, 2015), and between insular andmainland Iberian populations separated about 9 kya (F st < 0.27; Velo-Ant on, Zamudio, & Cordero-Rivera, 2012). In general, in terrestrial organisms with narrow climatic tolerance and low dispersal ability, adjacent isolated populations are expected to accumulate genetic divergence even in the absence of eco-morphological adaptive differentiation.…”

Application of network methods for understanding evolutionary dynamics in discrete habitats

“…; Viricel & Rosel ; Pisa et al . ). Such hierarchical structures are often difficult to observe, especially when the underlying migration patterns are complex.…”

“…Many discrete habitats in nature are also modular, and gene-flow patterns in such habitats often have hierarchical and modular genetic structures (e.g. McCauley & Eanes 1987;Fletcher et al 2013;Viricel & Rosel 2014;Pisa et al 2015). Such hierarchical structures are often difficult to observe, especially when the underlying migration patterns are complex.…”