Unlocking the vault: next‐generation museum population genomics

Bi, Ke; Linderoth, Tyler; Vanderpool, Dan; Good, Jeffrey M.; Nielsen, Rasmus; Moritz, Craig

doi:10.1111/mec.12516

Cited by 346 publications

(446 citation statements)

References 85 publications

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“…using museum specimens), then it could be possible to observe evolutionary shifts in: key functional traits (or their proxies) that confer adaptation; underlying genetic markers linked to those traits and frequency and biogeographic patterns of hybridization that are concordant with a range expansion (sensu [53,80]). As the impacts of invasive species and global change become more evident, such data might be obtainable [81,82]. In the absence of such data, indirect assessments of hybridization's role in range expansion require an integrated approach that combines ecological surveys, trait assays, fitness measures, and population and genetic analyses.…”

Section: Testing the Hypothesis That Hybridization Facilitates Speciementioning

confidence: 99%

Hybridization as a facilitator of species range expansion

Pfennig¹,

Kelly²,

Pierce³

2016

Proc. R. Soc. B.

142

152

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Explaining the evolution of species geographical ranges is fundamental to understanding how biodiversity is distributed and maintained. The solution to this classic problem in ecology and evolution remains elusive: we still do not fully know how species geographical ranges evolve and what factors fuel range expansions. Resolving this problem is now more crucial than ever with increasing biodiversity loss, global change and movement of species by humans. Here, we describe and evaluate the hypothesis that hybridization between species can contribute to species range expansion. We discuss how such a process can occur and the empirical data that are needed to test this hypothesis. We also examine how species can expand into new environments via hybridization with a resident species, and yet remain distinct species. Generally, hybridization may play an underappreciated role in influencing the evolution of species ranges. Whether-and to what extent-hybridization has such an effect requires further study across more diverse taxa.

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Section: Testing the Hypothesis That Hybridization Facilitates Speciementioning

confidence: 99%

Hybridization as a facilitator of species range expansion

Pfennig¹,

Kelly²,

Pierce³

2016

Proc. R. Soc. B.

142

152

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“…Genomic analysis of ancient samples -considered anything from a museum specimen to archaeological specimens [84] -can establish baseline levels of genetic parameters in ancestral populations prior to demographic declines [85]. This concerns both the amount of genetic variation that might have been lost over time and the origin of contemporary population structure.…”

Section: Box 1 -An Emerging Area Stemming From Ancient Dna Technologymentioning

confidence: 99%

“…scat, hair, scales) 390 of poor quality. Utilizing genomic techniques often employed for ancient DNA studies (e.g., [85,87]), holds potential not only to recover genetic information from the species of interest, but additionally reveal aspects of pathogens (e.g., [88]) that might prove relevant for conservation and management.…”

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confidence: 99%

Genomics and the challenging translation into conservation practice

Shafer¹,

Wolf²,

Alves³

et al. 2015

Trends in Ecology & Evolution

460

470

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The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subsequent analyses and interpretations are still challenging and largely confined to academic research in ecology and 20evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners. 3 Conservation biology and genomicsLike most of the life sciences, conservation biology is being confronted with the challenge of how to integrate the collection and analysis of large-scale genomic data into its toolbox. Conservation biologists pull from a wide array of disciplines in an effort to preserve biodiversity and ecosystem services [1]. Genetic data have helped in this regard by 30 detecting, for example, population substructure, measuring genetic connectivity, and identifying potential risks associated with demographic change and inbreeding [2]. Traditionally, conservation genetics (see Glossary) has relied on a handful of molecular markers ranging from a few allozymes to dozens of microsatellites [3]. But for close to a decade [4], genomics -broadly defined high-throughput sampling of nucleic acids [5] -has been touted as an important advancement to the field, a panacea of sorts for the unresolved conservation problems typically addressed 35 with genetic data [6,7]. This transition has led to much promise, but also hyperbole, where concrete empirical examples of genomic data having a conservation impact remain rare.Under the premise that assisting conservation of the world's biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution towards this goal. While there 40are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvest [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.Maintaining genetic diversity has largely been an afterthought when it comes to national biodiversity policies [11,12], and attempts to identify areas that might prove to be essential for conserving biological diversity rarely mention 45 genomics (e.g. [13,14]). An obvious reason for this disconnect is that many of the pressing conservation issues (e.g., [15,16]) simply do not need genomics, but instead need political will.The traditional use of gene...

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“…Additionally, we hope more researchers will explore the connections between vegetation change and other biological signals of change such as isotopic signatures derived from spatially coincident animal specimens (e.g. Rubidge et al 2011;Bi et al 2013).…”

Section: Discussionmentioning

confidence: 99%

“…There is great potential in these data synergies to further expand the scope and scale of VTM analysis. For example, first, synergies between genome sequencing of biological specimens with historical and future vegetation allow us to move beyond single species vegetation type analysis and understand the dynamic nature of ecological communities (Rubidge et al 2011;Preston et al 2012;Bi et al 2013). Second, more can be done using historical vegetation data with current and future climates using new species distribution models.…”

Section: New Developments In Data Synthesismentioning

confidence: 99%

Rescuing and Sharing Historical Vegetation Data for Ecological Analysis: The California Vegetation Type Mapping Project

Kelly¹

2016

Biodiv. Inf.

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Abstract.-Research efforts that synthesize historical and contemporary ecological data with modeling approaches improve our understanding of the complex response of species, communities, and landscapes to changing biophysical conditions through time and in space. Historical ecological data are particularly important in this respect. There are remaining barriers that limit such data synthesis, and technological improvements that make multiple diverse datasets more readily available for integration and synthesis are needed. This paper presents one case study of the Wieslander Vegetation Type Mapping project in California and highlights the importance of rescuing, digitizing and sharing historical datasets. We review the varied ecological uses of the historical collection: the vegetation maps have been used to understand legacies of land use change and plan for the future; the plot data have been used to examine changes to chaparral and forest communities around the state and to predict community structure and shifts under a changing climate; the photographs have been used to understand changing vegetation structure; and the voucher specimens in combination with other specimen collections have been used for large scale distribution modeling efforts. The digitization and sharing of the data via the web has broadened the scope and scale of the types of analysis performed. Yet, additional research avenues can be pursued using multiple types of VTM data, and by linking VTM data with contemporary data. The digital VTM collection is an example of a data infrastructure that expands the potential of large scale research through the integration and synthesis of data drawn from numerous data sources; its journey from analog to digital is a cautionary tale of the importance of finding historical data, digitizing it with best practices, linking it with other datasets, and sharing it with the research community.

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Unlocking the vault: next‐generation museum population genomics

Cited by 346 publications

References 85 publications

Hybridization as a facilitator of species range expansion

Hybridization as a facilitator of species range expansion

Genomics and the challenging translation into conservation practice

Rescuing and Sharing Historical Vegetation Data for Ecological Analysis: The California Vegetation Type Mapping Project

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