Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations

Near, Thomas J.; MacGuigan, Daniel J.; Parker, E. Davis; Struthers, Carl D.; Jones, Christopher D.; Dornburg, Alex

doi:10.1016/j.ympev.2018.09.001

Cited by 77 publications

(92 citation statements)

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“…On average, this results in more polymorphic loci, that are each more informative. In a de novo context, these results will benefit any study focused on species with low diversity, and in particular phylogenetics studies, where sparse genotype matrices are being constructed across many species (Near et al, ). When RAD loci are ordered onto chromosomes (i.e., using a native reference genome, or if de novo‐assembled loci have been mapped to an external reference genome), a higher information density along the genome results, which should help resolve linkage patterns at a finer scale and identify evolutionary events that may have been missed with a sparser sampling of the genome (McKinney et al, ).…”

Section: Discussionmentioning

confidence: 98%

“…The union of genome sampling protocols with massively parallel, short-read sequencing has produced an immensely successful research programme in population (Bassham, Catchen, Lescak, von Hippel, & Cresko, 2018), conservation (Dierickx, Shultz, Sato, Hiraoka, & Edwards, 2015) and landscape genomics (Bay et al, 2018), phylogenetics (Spriggs et al, 2019), and epigenetics (Trucchi et al, 2016), creating new experimental space for non-model organisms, and allowing, for example, ambitious sampling regimes in large geographical surveys (Dudaniec, Yong, Lancaster, Svensson, & Hansson, 2018), as well as wide-ranging taxon breadth in phylogenetic studies (Near et al, 2018). Regardless of the analytical approach, and in addition to any challenges of the experimental design, all RADseq strategies present two fundamental issues.…”

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confidence: 99%

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Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

2019

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For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from the natural world. Here, we describe the first software natively capable of using paired‐end sequencing to derive short contigs from de novo RAD data. Stacks version 2 employs a de Bruijn graph assembler to build and connect contigs from forward and reverse reads for each de novo RAD locus, which it then uses as a reference for read alignments. The new architecture allows all the individuals in a metapopulation to be considered at the same time as each RAD locus is processed. This enables a Bayesian genotype caller to provide precise SNPs, and a robust algorithm to phase those SNPs into long haplotypes, generating RAD loci that are 400–800 bp in length. To prove its recall and precision, we tested the software with simulated data and compared reference‐aligned and de novo analyses of three empirical data sets. Our study shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired‐end de novo data sets.

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Section: Discussionmentioning

confidence: 98%

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confidence: 99%

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

2019

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“…A scenario of rapid cladogenesis-such as that hypothesised to have occurred during post-K-Pg extinction recovery -provides a logical explanation for the distinctive combination of extremely short phylogenetic internodes and incomplete lineage sorting that may be responsible for the lack of a clear branching pattern for this portion of the bird tree of life. The combination of a deep timescale and short times between phylogenetic divergences render this scenario among the most challenging of phylogenetic problems for molecular evidence to disentangle (Townsend et al 2012;Dornburg et al 2017aDornburg et al , 2017bDornburg et al , 2018. Additionally, expectations based on other rapid evolutionary radiations suggest the possibility of high levels of gene-flow among early diverging lineages (Meier et al 2017).…”

Section: Rapid Post-cretaceous Radiation As An Explanation For the 'Nmentioning

confidence: 99%

“…Advocates of this approach have long argued that investigators use predictive frameworks for selecting loci of high utility for specific phylogenetic problems (Townsend 2007;Townsend et al 2012;Chen et al 2015;Prum et al 2015;Dornburg et al 2016Dornburg et al , 2017bBleidorn 2017;Duchêne et al 2017a). The use and development of these approaches has largely been restricted to tackling issues arising when character states converge due to either substitution saturation (Dornburg et al 2014;Theriot et al 2015;Gilbert et al 2018;Near et al 2018) or biased patterns of nucleotide change (Borowiec et al 2015;Romiguier et al 2016;Dornburg et al 2017a). However, selecting loci that do not depict a signature of directional change in molecular rates as a consequence of life history shifts is also an experimental design problem.…”

Section: The Way Forwardmentioning

confidence: 99%

Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation

Field

Berv

Hsiang

et al. 2019

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Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic—in line with a model of rapid post-extinction niche filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. This uncertainty has often been ascribed to a patchy avian fossil record, but the possibility of model misspecification in molecular divergence time analyses represents an important and relatively underexplored alternative hypothesis. Here, we highlight the necessity of further developing and using models that account for coordinated variation in rates of molecular evolution across a phylogeny (e.g. molecular early bursts) as a means of assessing support for a rapid post-Cretaceous radiation of crown birds. We discuss how relationships between life-history and substitution rates can mislead divergence time studies that do not account for directional changes in substitution rates over time, and suggest that these effects might have caused some of the variation in existing molecular date estimates for birds. We suggest multiple paths forward that could help resolve this and similar conflicts within other major eukaryotic clades.

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“…The genotyping-by-sequencing (GBS) technique can rapidly generate considerable numbers of genome-wide genetic markers, which has revolutionized the field of ecological and evolutionary genomics (Elshire et al, 2012;Andrews et al, 2016;Hume et al, 2018). Using the GBS technique, increasing numbers of studies have revealed fine-scale population genetic structure (Near et al, 2018;Palaiokostas et al, 2018;Robledo et al, 2018;Zhao et al, 2018). Most cryptic species have been distinguished by DNA-barcoding and other genetic methods, while few have been verified to be reproductively isolated or incompatible using interbreeding experiments (Kress et al, 2015;Lehnert et al, 2016;Paterson et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

et al. 2020

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The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.

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Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations

Cited by 77 publications

References 92 publications

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

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