Spatial and temporal genetic dynamics of the grasshopper <i>Oedaleus decorus</i> revealed by museum genomics

Schmid, Sarah; Neuenschwander, Samuel; Pitteloud, Camille; Heckel, Gerald; Pajkovic, Mila; Arlettaz, Raphaël; Alvarez, Nadir

doi:10.1002/ece3.3699

Cited by 15 publications

(18 citation statements)

References 109 publications

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“…Thus, despite the small distribution range and the relatively short geographical distances separating the extant populations of D . crassiusculus , our results indicate that this species shows a remarkable genetic structure that is comparable to that reported for other Orthoptera taxa with patchy distributions and forming highly fragmented populations 27 , 28 , 51 , 52 .…”

Section: Discussionsupporting

confidence: 85%

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

González‐Serna

Ortego

2018

Sci Rep

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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.

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Section: Discussionsupporting

confidence: 85%

“…on the genetic connectivity of contemporary populations 27 , 65 . Future genomic analyses of specimens available in museum collections 3 could help to determine temporal changes in genetic diversity and study past patterns of gene flow in relation with historical landscape composition 52 .…”

Section: Discussionmentioning

confidence: 99%

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

González‐Serna

Ortego

2018

Sci Rep

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“…range retraction has triggered population differentiation in alpine chipmunks [49]). Analyses of historical DNA also evidenced reduction of diversity and/or shifts in genetic composition and structure among a wide array of other declining animals, including birds [50 -53], fishes [54] as well as insects [55,56]. In comparison to most of these regional studies however, our historical phylogeography has the advantage to analyse fine-scale genetic fluctuations using a large number of historical samples over an extended biogeographical region and constitutes one of the most exhaustive spatio-temporal survey of historical DNA to date.…”

Section: Discussionmentioning

confidence: 99%

Howling from the past: historical phylogeography and diversity losses in European grey wolves

et al. 2018

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Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf () is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.

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“…Incorporating genetic data from natural history collections representing rare/threatened species and species that are otherwise hard to access into genetic-based analyses can provide critical insights (Heckeberg et al 2016;Hundsdoerfer et al 2017;McGuire et al 2018). For example, genetic data from museum specimens has been used to track temporal and spatial changes in species distributions (Lozier & Cameron 2009), investigate population genetics (Spurgin et al 2014;Schmid et al 2018), and evaluate conservation implications (Anco et al 2018;Brandt et al 2018). Additionally, accessing molecular sequence data from natural history collections may be an invaluable resource for resolving taxonomic questions (Cappellini et al 2014), including generating genetic data from type specimens (Hawksworth 2013;Silva et al 2017;McGuire et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

Leavitt

Keuler

Newberry

et al. 2019

Plant and Fungal Systematics

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Natural history collections, including name-bearing type specimens, are an important source of genetic information. These data can be critical for appropriate taxonomic revisions in cases where the phylogenetic position of name-bearing type specimens needs to be identified, including morphologically cryptic lichen-forming fungal species. Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale data from decades-old (i.e., more than 30 years old) isotype specimens representing three vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and two subspecies. We also use data from high-throughput metagenomic shotgun sequencing to infer the phylogenetic position of an enigmatic collection, originally identified as R. haydenii, that failed to yield genetic data via Sanger sequencing. We were able to construct a 1.64 Mb alignment from over 1200 single-copy nuclear gene regions for the Rhizoplaca specimens. Phylogenomic reconstructions recovered an isotype representing Rhizoplaca haydenii subsp. arbuscula within a clade comprising other specimens identified as Rhizoplaca haydenii subsp. arbuscula, while an isotype of R. idahoensis was recovered within a clade with substantial phylogenetic substructure comprising Rhizoplaca haydenii subsp. haydenii and other specimens. Based on these data and morphological differences, Rhizoplaca haydenii subsp. arbuscula is elevated to specific rank as Rhizoplaca arbuscula. For the enigmatic collection, we were able to assemble the nearly complete nrDNA cistron and over 50 Mb of the mitochondrial genome. Using these data, we identified this specimen as a morphologically deviant form representing Xanthoparmelia aff. subcumberlandia. This study highlights the power of high-throughput metagenomic shotgun sequencing in generating larger and more comprehensive genetic data from taxonomically important herbarium specimens.

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Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics

Cited by 15 publications

References 109 publications

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

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

Howling from the past: historical phylogeography and diversity losses in European grey wolves

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

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