The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

Deck, John; Gaither, Michelle R.; Ewing, Rodney; Bird, Christopher E.; Davies, Neil; Meyer, Christopher P.; Riginos, Cynthia; Toonen, Robert J.; Crandall, Eric D.

doi:10.1371/journal.pbio.2002925

Cited by 90 publications

(84 citation statements)

References 23 publications

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“…In the analyses presented here, we removed one of these markers to avoid pseudo‐replication (see Supporting Information Text S1 for removal criteria). The raw sequence files and associated metadata can be searched and downloaded from the Genomic Observatories Metadatabase (GeOMe; https://www.geome-db.org/; Deck et al, ), an open access repository for geographic and ecological metadata associated with biosamples and genetic data. The trimmed and aligned dataset used here is available at https://github.com/DIPnet/IPDB.…”

Section: Resultsmentioning

confidence: 99%

“…The current dataset forms the core of the Genomic Observatories Metadatabase (GeOMe; Deck et al, ), which facilitates coordinated sampling strategies and metadata collection and curation. GeOMe creates a permanent link between occurrence metadata and genetic sequences (both FASTA and FASTQ formats) submitted to the International Nucleotide Sequence Database Collaboration (i.e.…”

Section: Discussionmentioning

confidence: 99%

“…Each mitochondrial dataset consisted of Sanger sequence data in FASTA format. Metadata for each sequence were assembled in a spreadsheet template generated using the Biocode Field Information Management System [Biocode FIMS; now available at GeOMe, see Deck et al ()]. Genetic data and associated metadata underwent rigorous quality control during and after submission (Supporting Information Text S1).…”

Section: Methodsmentioning

confidence: 99%

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The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns

Crandall

Riginos

Bird

et al. 2019

Global Ecol Biogeogr

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Aim To test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location The Indo‐Pacific Ocean. Time period Pliocene through the Holocene. Major taxa studied Fifty‐six marine species. Methods We tested eight biogeographic hypotheses for partitioning of the Indo‐Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance‐based redundancy analysis (dbRDA). Results We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusions Although there is support for three previously described barriers, phylogeographic discordance in the Indo‐Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo‐Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns

Crandall

Riginos

Bird

et al. 2019

Global Ecol Biogeogr

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“…Though some limitations still hinder widespread adoption of these techniques, such as cost and well‐assembled and annotated genomic resources, as technologies continue to advance we anticipate continued application and creative adaptations to meet the challenging needs of conservation researchers. If realized, this could generate capacity for large‐scale initiatives such as the creation of global genetic databases akin to those that have begun emerging recently for other taxa (e.g., Deck et al, ). This would not only expand the scope of research questions that can be investigated, but also provide traditionally resource‐limited marine turtle programmes with the ability to incorporate genetic information in their research and monitoring efforts.…”

Section: Discussionmentioning

confidence: 99%

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

Komoroske

Miller

O’Rourke

et al. 2019

Molecular Ecology Resources

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Advances in high‐throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high‐throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD‐Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large‐scale initiatives such as collaborative global marine turtle genetic databases.

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“…We used existing mitochondrial DNA (mtDNA) genetic data of nine reef species from the Diversity of Indo‐Pacific Network (DIPNet: http://diversityindopacific.net/) database (Deck et al., ) and augmented these data sets with new samples collected from the Philippines. Additional genetic data were sourced from the Barcode of Life and GenBank databases or were requested from other researchers (see Appendix S1).…”

Section: Methodsmentioning

confidence: 99%

Revisiting the “Centre Hypotheses” of the Indo‐West Pacific: Idiosyncratic genetic diversity of nine reef species offers weak support for the Coral Triangle as a centre of genetic biodiversity

Matias

Riginos

2018

Journal of Biogeography

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Aim Several biogeographic hypotheses seek to explain the extreme species diversity of the coral reefs in the Coral Triangle (CT) of the Indo‐West Pacific (IWP). Here, we investigate processes implicit to the Centre of Origin, Centre of Overlap and Centre of Survival hypotheses. We focus on intraspecific genetic data, where intraspecific diversity can provide information regarding directionality of past dispersal (gene flow) and changes in population size such as expansion from refugia. Location Indian Ocean, Coral Triangle and West Pacific Ocean. Methods We use existing mitochondrial DNA data augmented with new samples from the Philippines, thus filling in key sampling gaps from previous studies, to examine nine reef species. We first test if genetic diversity peaks in the CT. We then estimate gene flow between regions—CT vs. Indian Ocean (IO) and CT vs. Pacific Ocean (PO)—to assess concordance with predicted directions of movement (i.e. into the CT or out of the CT). Finally, we investigate the historical demography of these species and evaluate population expansions to ascertain whether genetic diversity is correlated with putative Pleistocene refugia. Results Genetic diversity in the CT was not greater than genetic diversity in the IO and PO, and we found highly variable spatial patterns of genetic diversity when species were evaluated individually. Gene flow estimates indicated very limited exchange between regions, consistent with peripheral isolation and/or signals of historical divergence. For some species, however, there were signals of movement out of the CT. While there was no significant correlation between genetic diversity and putative refugia, genetic patterns suggested that some populations have experienced population expansions. The locations of expansion were also variable across species. Overall, there was no signal of concordant processes shaping intraspecific genetic diversity. Main conclusions Genetic patterns across species were highly variable with some species lending weak support for processes aligned with each of the “Centre” of diversity hypotheses. But overall there was no compelling evidence for uniform processes underlying all species, which possibly indicate that processes underlying the different “Centre” have not strongly affected IWP species within the recent past.

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The Genomic Observatories Metadatabase (GeOMe): A new repository for field and sampling event metadata associated with genetic samples

Cited by 90 publications

References 23 publications

The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns

The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns

A versatile Rapture (RAD‐Capture) platform for genotyping marine turtles

Revisiting the “Centre Hypotheses” of the Indo‐West Pacific: Idiosyncratic genetic diversity of nine reef species offers weak support for the Coral Triangle as a centre of genetic biodiversity

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