RAD Capture (Rapture): Flexible and efficient sequence-based genotyping

Ali, Omar A.; O’Rourke, Sean; Amish, Stephen J.; Meek, Mariah H.; Luikart, Gordon; Jeffres, Carson A.; Miller, Michael R.

doi:10.1101/028837

Cited by 49 publications

(61 citation statements)

References 36 publications

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“…In this study, we used a new RAD sequencing protocol (Ali et al 2016) to generate a high-quality genomic data set capable of identifying many polymorphisms in DHP. Using our data set, we were able to successfully characterize genetic variation within DHP and build a SNP panel to be used as a genetic monitoring resource.…”

Section: Discussionmentioning

confidence: 99%

“…In total, we sequenced 32 pupfish individuals: 24 DHP, four AMP and four OWP (sampling details given in Appendix S1, Supporting information). DNA was extracted from fin clips using an Ampure bead-based protocol, and RAD libraries were constructed using the PstI restriction enzyme and a new RAD protocol described in Ali et al (2016). De novo loci discovery and contig extension were carried out via custom PERL scripts (Miller et al 2012), the alignment program Novoalign and the genome assembler PRICE (Ruby et al 2013) (Appendix S1, Supporting information).…”

Section: Sampling Sequence Generation and Rad Loci Discoverymentioning

confidence: 99%

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Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

et al. 2016

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The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m(2) pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an evolutionary and conservation perspective has been questioned. Here we present a high-resolution genomic analysis of DHP and two closely related species, with the goal of thoroughly examining the temporal divergence of DHP. To this end, we inferred the evolutionary history of DHP from multiple random genomic subsets and evaluated four historical scenarios using the multispecies coalescent. Our results provide substantial information regarding the evolutionary history of DHP. Genomic patterns of secondary contact present strong evidence that DHP were isolated in Devils Hole prior to 20-10 ka and the model best supported by geological history and known mutation rates predicts DHP diverged around 60 ka, approximately the same time Devils Hole opened to the surface. We make the novel prediction that DHP colonized and have survived in Devils Hole since the cavern opened, and the two events (colonization and collapse of the cavern's roof) were caused by a common geologic event. Our results emphasize the power of evolutionary theory as a predictive framework and reaffirm DHP as an important evolutionary novelty, worthy of continued conservation and exploration.

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Section: Discussionmentioning

confidence: 99%

Section: Sampling Sequence Generation and Rad Loci Discoverymentioning

confidence: 99%

Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

et al. 2016

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“…Genome scans on 219 individuals were conducted following the BestRAD library preparation protocol with some modifications (Ali et al 2016). 100 ng of DNA was digested using the SbfI restriction enzyme (New England Biolabs, USA) and fragments were ligated with SbfI adapters prepared with biotinylated ends.…”

Section: Snp Discovery and Snp Filteringmentioning

confidence: 99%

Ecological genomics predicts climate vulnerability in an endangered southwestern songbird

et al. 2018

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Few regions have been more severely impacted by climate change in the USA than the Desert Southwest. Here, we use ecological genomics to assess the potential for adaptation to rising global temperatures in a widespread songbird, the willow flycatcher (Empidonax traillii), and find the endangered desert southwestern subspecies (E. t. extimus) most vulnerable to future climate change. Highly significant correlations between present abundance and estimates of genomic vulnerability - the mismatch between current and predicted future genotype-environment relationships - indicate small, fragmented populations of the southwestern willow flycatcher will have to adapt most to keep pace with climate change. Links between climate-associated genotypes and genes important to thermal tolerance in birds provide a potential mechanism for adaptation to temperature extremes. Our results demonstrate that the incorporation of genotype-environment relationships into landscape-scale models of climate vulnerability can facilitate more precise predictions of climate impacts and help guide conservation in threatened and endangered groups.

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“…We extracted DNA from tissue samples (total n = 3149 individuals) and genotyped individuals as described in . In short, we conducted restriction site-associated DNA (RAD) capture (Ali et al 2016) and sequenced libraries using HiSeq (Illumina, San Diego, California, USA). We randomly sampled one read at each single nucleotide polymorphism (SNP) per individual.…”

Section: Summarizing Variation In Migratory Vs Resident Allele Frequmentioning

confidence: 99%

Partial migration alters population ecology and food chain length: evidence from a salmonid fish

et al. 2020

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Many migratory species, from monarch butterflies to wildebeest, express partial migration, where only a subset of a population migrates. This intraspecific variation is likely to have large ecological consequences. We studied the ecological consequences of partial migration in a salmonid fish, Oncorhynchus mykiss, in coastal streams in California, USA. One ecotype, steelhead trout, migrates to the ocean, whereas the other, rainbow trout, completes its lifecycle in freshwater. Migration has a strong genetic basis in O. mykiss. In one stream, we found differences in the frequency of migration‐linked genotypes below and above a waterfall barrier (migratory allele frequency of 60% below vs. 31% above). Below the waterfall, in the migratory‐dominated region, the density of young fish (<1 yr old) was approximately twice that in the resident‐dominated region above the waterfall (0.46 vs. 0.26 individuals/m2, respectively), presumably reflecting the higher fecundity of migratory females. Additionally, there were half as many older fish (>1 yr old) in pools downstream of the waterfall (0.05 vs. 0.13 individuals/m2). In a second stream, between‐year variation in the dominance of migratory vs. resident fish allowed us to explore differences in fish density and size structure through time, and we found a consistent pattern. In brief, when migratory genotypes dominated, we found higher densities of young fish and lower densities of older fish, resulting in a simpler size structure, compared to when resident genotypes dominated. Moreover, large resident trout had a slightly higher trophic position than young fish (3.92 vs. 3.42 in one creek and 3.77 vs. 3.17 in the other), quantified with stable isotope data. The difference in fish size structure did not generate trophic cascades. Partial migration is widespread among migratory populations, as is phenotypic divergence between resident and migratory forms, suggesting the potential for widespread ecological effects arising from this common form of intraspecific variation.

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RAD Capture (Rapture): Flexible and efficient sequence-based genotyping

Cited by 49 publications

References 36 publications

Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

Ecological genomics predicts climate vulnerability in an endangered southwestern songbird

Partial migration alters population ecology and food chain length: evidence from a salmonid fish

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