Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)

Escudero, Marcial; Eaton, Deren A. R.; Hahn, Marlene; Hipp, Andrew L.

doi:10.1016/j.ympev.2014.06.026

Cited by 107 publications

(93 citation statements)

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“…Challenges for taxonomic resolution at low taxonomic levels mainly arise due to biological events such as gene flow by hybridization and introgression [41], gene duplication [42], horizontal gene transfer [43], and incomplete lineage sorting [44]. To address the challenge of resolving the phylogenetic relationships among very closely related species, large genome-scale data sets can be used [45]. Reduced-representation methods provide powerful and cost-effective tools, producing abundant large-scale genomic data [46] and have been used in many phylogenetic studies [45, 47–51].…”

Section: Introductionmentioning

confidence: 99%

“…To address the challenge of resolving the phylogenetic relationships among very closely related species, large genome-scale data sets can be used [45]. Reduced-representation methods provide powerful and cost-effective tools, producing abundant large-scale genomic data [46] and have been used in many phylogenetic studies [45, 47–51]. …”

Section: Introductionmentioning

confidence: 99%

“…A large number of variants are generated by GBS [53] and have been applied to a wide range of crops such as barley [54], lentils [51], maize [55], potato [56], reed canarygrass [57], rice [58], soybean [59], switchgrass [60], and wheat [61]. GBS has been used to infer the classification of wild species like chickpea [62], lentils [51], sedges [45], and tomatoes [63]. …”

Section: Introductionmentioning

confidence: 99%

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Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

et al. 2016

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BackgroundThe majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex.ResultsWe used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic.ConclusionsOur study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0806-x) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

et al. 2016

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“…One of these methodologies is restriction-site-associated DNA sequencing (RAD-seq), which combines enzymatic fragmentation of genomic DNA with high-throughput sequencing for the generation of large numbers of markers . RAD-seq has shown great promise to resolve difficult phylogenetic, phylogeographic, and species delimitation questions in diverse groups of eukaryotes Nadeau et al 2012;Jones et al 2013;Cruaud et al 2014;Escudero et al 2014;Hipp et al 2014;Leache et al 2014;Herrera et al Chapter 3), including cnidarians ) and most recently deep-sea octocorals (Pante et al 2014). The number of orthologous restriction sites that can be retained across taxa, which decreases as divergence increases, limits the usefulness of RAD-seq for these kinds of studies.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary and ecological genomics in deep-sea organisms

Monroy¹

2015

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Hydrothermal vents and coral ecosystems are conspicuous biological hot spots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, genetic diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomic tools and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. Using these tools I find that the predictability of restriction site frequencies in eukaryotic genomes is chiefly determined by the phylogenetic position of the target species and the recognition sequence of the selected restriction enzyme. These tools are then applied to test global-scale historical biogeographic hypotheses of vent fauna using barnacles as model. Phylogeographic inferences suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastward along the southern hemisphere during the Neogene. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa in addition to barnacles. Regional-scale analyses indicate that vent barnacle populations are well connected within basins and ridge systems, and that their diversity patterns do not conform to the predictions from the hypothesis that seamounts are centers of endemism. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa, by unambiguously resolving evolutionary relationships and objectively inferring species boundaries. Finally, I explore the adaptive potential of deep-sea coral species to environmental changes by examining a case of adaptation to shallow water from the deep sea. Candidate positive-selection markers shared between pairs of shallow and deep populations are identified as likely makers for genomic regions involved in adaptation. Overall, the results from this thesis constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems. AKNOWLEDGEMENTSThis degree is the fulfillment of a lifelong dream. I am infinitely grateful to Tim Shank, for taking a chance with me, for challenging me constantly, for honest advising, for providing limitless opportunities to pursue my interests and develop my skills, for unconditional support and trust, and for making me feel more like a colleague than a student since the first day. I could not imagine a better place to have done my PhD. I look forward to many more ventures to come. I am extremely grateful to my committee ...

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“…The GBS approach has gained momentum in a range of biological fields including reconstructions of the phylogenetic histories across species (e.g., Leache et al, 2015;Manthey et al, 2016;Hamon et al, 2017) and identifying genomic regions influencing: hybridization (Escudero et al, 2014), speciation (Jones et al, 2013) and adaptive processes (Keller et al, 2013). GBS can provide large numbers (10 5 "s) of homologous loci that are: suitable for phylogenetic inference among closely related taxa, amenable to a broader set of questions about evolutionary history, and are highly efficient at documenting evolutionary history from shallow timescales to divergences dating back to 50-60 MYA, unambiguously (Leache et al, 2015;Pyron 2015;Manthey et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

Lifat¹

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Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)

Cited by 107 publications

References 67 publications

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Evolutionary and ecological genomics in deep-sea organisms

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

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