Using high-throughput sequencing to investigate the factors structuring genomic variation of a Mediterranean grasshopper of great conservation concern

Abstract

Inferring the demographic history of species is fundamental for understanding their responses to past climate/landscape alterations and improving our predictions about the future impacts of the different components of ongoing global change. Estimating the time-frame at which population fragmentation took place is also critical to determine whether such process was shaped by ancient events (e.g. past climate/geological changes) or if, conversely, it was driven by recent human activities (e.g. habitat loss). We employed genomic data (ddRAD-Seq) to determine the factors shaping contemporary patterns of genetic variation in the Iberian cross-backed grasshopper Dociostaurus crassiusculus, an endangered species with limited dispersal capacity and narrow habitat requirements. Our analyses indicate the presence of two ancient lineages and three genetic clusters resulted from historical processes of population fragmentation (~18–126 ka) that predate the Anthropocene. Landscape genetic analyses indicate that the limits of major river basins are the main geographical feature explaining large-scale patterns of genomic differentiation, with no apparent effect of human-driven habitat fragmentation. Overall, our study highlights the importance of detailed phylogeographic, demographic and spatially-explicit landscape analyses to identify evolutionary significant units and determine the relative impact of historical vs. anthropogenic factors on processes of genetic fragmentation in taxa of great conservation concern.

Topography, more than land cover, explains genetic diversity in a Neotropical savanna tree frog

“…Thus, frogs with similar habitat specializations may still present different dispersal capabilities and adaptations depending on factors such as altitude range and configuration of highlands. Our study underscores that historical natural features that preclude individual dispersal may be more critical than recent events of anthropogenic habitat modification (e.g., González‐Serna, Cordero, & Ortego, 2018). A general understanding of factors leading to diversification of stream‐breeding frogs will only become feasible when we have more comparative landscape genetic studies in tropical habitats (Torres‐Florez et al., 2018).…”

A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape

“…Our study adds to a growing list highlighting the potential for genomic data sets to detect weak, recent or otherwise subtle spatial genetic patterns (González-Serna, Cordero, & Ortego, 2018;McCartney-Melstad et al, 2018;Murphy, Jones, Price, & Weisrock, 2018;Tan et al, 2018). Considering the problems time lags present for conservation planning, the use of SNP data sets and spatially informed analyses of genetic diversity will probably become increasingly important for placing patterns of population structuring in their proper genomic, temporal and geographical contexts.…”

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)

“…Apart from these two exceptions, we did not find clear differences in spatial patterns of genetic diversity and structure between outbreak and nonoutbreak populations. Levels of genetic differentiation among Iberian populations of D. maroccanus (mean F ST = 0.067; range = 0.051–0.102) were much lower than those reported in previous SNP‐based studies on nonpest cross‐backed grasshoppers (genus Dociostaurus ) with narrower distributions such as D. crassiusculus (mean F ST = 0.129; range = 0.033–0.237; González‐Serna et al, 2018) and D. hispanicus (mean F ST = 0.189; range = 0.082–0.307; González‐Serna et al, 2019). As expected, levels of genetic differentiation among populations of the Moroccan locust were similar, albeit in some cases sensibly higher, than microsatellite‐based estimates obtained for other locusts and pest grasshoppers sampled at a similar spatial scale (Table ).…”

“…For all downstream analyses, we exported only the first SNP per RAD locus (option write_single_snp ) and retained loci with a minimum stack depth ≥ 5 ( m = 5), that were sequenced in at least 50% of the individuals of each population (parameter r = 0.5), represented in ~66% of populations, and with a minimum minor allele frequency (MAF) ≥ 0.01 to reduce the number of false polymorphic loci due to sequencing errors. As demonstrated in previous studies, the choice of different filtering thresholds affecting the proportion of missing data ( p and r in program populations ) had little impact on the obtained inferences (e.g., González‐Serna, Cordero, & Ortego, 2018; González‐Serna, Cordero, & Ortego, 2019; Ortego, Gugger, & Sork, 2018). The resulting files were used for subsequent analyses or converted into other formats using the program PGDSpider v.2.1.0.3 (Lischer & Excoffier, 2012).…”