Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene

Mussmann, Steven M.; Douglas, Michael E.; Anthonysamy, Whitney J. B.; Davis, Mark A.; Simpson, Scott A.; Louis, Wade

doi:10.1098/rsos.160736

Cited by 31 publications

(28 citation statements)

References 71 publications

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“…Contemporary and predicted climatic pressures in the midwest include higher temperatures and more intense precipitation interspersed by extended drought, with forested habitat being the most severely affected (Pryor et al 2014). Alternatively, agricultural expansion has already fragmented the native prairie grassland habitat on which some endemic species depend (Samson et al 2004; Mussmann et al 2017), potentially reducing biodiversity and eroding species boundaries by reintroducing ecologically divergent species (Haddad et al 2015; Grabenstein & Taylor 2018). The midwest may thus be subject to a bi-directional assault on both forested and prairie-grassland habitat.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, T. ornata and T. carolina are separated by greater genetic distances than are the southeastern taxa (Martin et al 2013), and accordingly the lack of hybrids beyond F 1 may reflect intrinsic genetic incompatibilities (Barton 2001; Abbott et al 2013). The low frequency of F 1 hybrids in the Illinois ONxEA population may be facilitated by recent degradation of the prairie grassland habitat (Manning 2001; Mussmann et al 2017) that, in turn, initiated increased heterospecific contact. However, this hypothesis cannot be explicitly tested herein.…”

Section: Discussionmentioning

confidence: 99%

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Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

Martin

Douglas

Chafin

et al. 2019

Preprint

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22Hybridization is differentially manifested across the genome, with observed introgression 23 representing a balance between selection and migration. The capacity to quantify introgression 24 and subsequently pinpoint the constituent genetic elements governing cross-species exchange has 25 been promoted by the unprecedented resolution of contemporary sequencing technologies. 26Furthermore, the availability of annotated reference genomes has allowed genomic patterns to be 27 associated with ecologically relevant phenotypes. We followed this pattern herein by harnessing 28 genomic resources to decipher the role of selection in shaping hybrid zones at the interface of 29 species-boundaries in North American box turtles (Terrapene). By so doing, we identified 30 adaptive divergence in genes related to immune system function and intrinsic thermal 31 adaptations. These, in turn, impact temperature-dependent sex determination and hypoxia 32 tolerance. Their patterns were then contrasted among inter-and intra-specific hybrid zones that 33 differed in a temporal and biogeographic context. Our results demonstrate that hybridization is 34 broadly apparent in Terrapene, but with varying levels of divergence at loci that impinge upon 35 thermal adaptation. These loci displayed signatures of adaptive introgression across intraspecific 36 boundaries, and do so despite a genome-wide selective trend against intergrades. By contrast, 37 interspecific comparisons at the same loci retained evidence of divergence. Importantly, 38 adaptations that shape species-boundaries in Terrapene not only underscore climatic boundaries 39 for these terrestrial ectotherms, but also bookmark their vulnerability to anthropogenic pressures. 40

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

Martin

Douglas

Chafin

et al. 2019

Preprint

Self Cite

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“…The field of conservation genetics, borne of these molecular developments over the last several decades, is increasingly empowered by access to large‐scale data through advances in DNA sequencing technology . Molecular approaches can answer many questions, which would be intractable for “boots‐on‐the‐ground” conservation methods such as: defining conservation units as a function of both historical geomorphic processes and contemporary climate change; how human habitat modification affects integrity of biodiversity “units”; and evaluating the success of prior management action …”

Section: Demonstrations Of Utilitymentioning

confidence: 99%

“…34,35 Molecular approaches can answer many questions, which would be intractable for "boots-on-the-ground" conservation methods such as: defining conservation units as a function of both historical geomorphic processes 36 and contemporary climate change 37 ; how human habitat modification affects integrity of biodiversity "units" 38 ; and evaluating the success of prior management action. 39 The emergence of conservation genetics into the era of "biological big data" exposes a critical limitation in that our ability to generate data often out-paces our bioinformatic and computational capabilities. Conservation geneticists (and indeed most biologists using genomic data) face unique constraints such as dataset size (sometimes at the terabyte scale) and limited scalability of analytical methods, restricting applicability of most XSEDE systems.…”

Section: Science Impactsmentioning

confidence: 99%

Jetstream—Early operations performance, adoption, and impacts

Hancock

Stewart

Vaughn³

et al. 2018

Concurrency and Computation

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Summary Jetstream is a first of its kind system for the NSF — a distributed production cloud resource. We review the purpose for creating Jetstream, discuss Jetstream's key characteristics, describe our experiences from the first year of maintaining an OpenStack‐based cloud environment, and share some of the early scientific impacts achieved by Jetstream users. Jetstream offers a unique capability within the XSEDE‐supported US national cyberinfrastructure, delivering interactive virtual machines (VMs) via the Atmosphere interface. As a multi‐region deployment that operates as an integrated system, Jetstream is proving effective in supporting modes and disciplines of research traditionally underrepresented on larger XSEDE‐supported clusters and supercomputers. Already, Jetstream has been used to perform research and education in biology, biochemistry, atmospheric science, earth science, and computer science.

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“…Such data are often used to distinguish populations and to gauge levels of differentiation at very fine spatial scales (e.g. Hopken, Douglas, & Douglas, ; Mussmann et al, ). They can also provide a deep historical perspective by deriving genetic patterns that differentiate species (e.g.…”

Section: Introductionmentioning

confidence: 99%

BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data

2019

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Quantifying “demographic independence” is a vital step in establishing potential conservation units for a species in that it effectively distinguishes migration from within‐population reproduction. This is an important aspect because it allows for an accurate estimate of recruitment. For example, populations may be designated as 'management units' (=MUs) if indeed population growth results from local demography rather than immigration. Of additional interest is the calculation of immigrant ancestry and ascertainment of the temporal context over which immigration occurred. This is because MUs depend largely upon local (self‐sustaining) birth and death rates, and the quantification of ancestry is necessary to validate demographic independence. Dispersal rate is also of immediate interest to conservation biologists, and can be assessed by quantifying genetic divergence among populations. The capacity with which to gauge these benchmarks has now been extended herein to genome‐wide molecular data, in an attempt to adjust an analytical tool that was until now intractable for the next generation sequencing data. In this study, a popular legacy program for migrant detection (i.e. BayesAss3) has been modified to accept SNP (single nucleotide polymorphism) data. We validated BA3‐SNPs using empirical data to demonstrate its suitability for both high‐performance and desktop computing environments. We also facilitate high analytical throughput by presenting a binary search algorithm that automates MCMC (Markov chain Monte Carlo) parameter tuning. Our BA3‐SNPs‐autotune program required five or fewer rounds of optimization for 99% of input files, with acceptable mixing parameters derived in 100% of our test cases. Runtime for BA3‐SNPs is a function of the number of loci analysed. Benchmarking yielded an average runtime <32 hr (10 million MCMC generations) for datasets containing thousands of SNPs. The BA3 algorithm remains a viable option for analysing modern SNP datasets. Source code (C++ and Python) is released publicly under the GNU General Public License v3.0, and is available for download (Linux and Mac OSX) from the following URL: .

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Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene

Cited by 31 publications

References 71 publications

Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

Jetstream—Early operations performance, adoption, and impacts

BA3‐SNPs: Contemporary migration reconfigured in BayesAss for next‐generation sequence data

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