ORCID Profile
0000-0001-8580-3651
Current Organisation
Pennsylvania State University
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Publisher: Public Library of Science (PLoS)
Date: 03-08-2017
Publisher: Proceedings of the National Academy of Sciences
Date: 17-08-2021
Abstract: Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic ersity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world’s largest genomic data repository, we found that most archived genomic datasets (87%) lacked the spatiotemporal metadata necessary for genetic bio ersity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 39% (51% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today’s genetic bio ersity and to plug the growing metadata gap.
Publisher: Wiley
Date: 11-10-2012
DOI: 10.1111/MEC.12031
Abstract: Marine species in the Indo-Pacific have ranges that can span thousands of kilometres, yet studies increasingly suggest that mean larval dispersal distances are less than historically assumed. Gene flow across these ranges must therefore rely to some extent on larval dispersal among intermediate 'stepping-stone' populations in combination with long-distance dispersal far beyond the mean of the dispersal kernel. We evaluate the strength of stepping-stone dynamics by employing a spatially explicit biophysical model of larval dispersal in the tropical Pacific to construct hypotheses for dispersal pathways. We evaluate these hypotheses with coalescent models of gene flow among high-island archipelagos in four neritid gastropod species. Two of the species live in the marine intertidal, while the other two are hidromous, living in fresh water but retaining pelagic dispersal. Dispersal pathways predicted by the biophysical model were strongly favoured in 16 of 18 tests against alternate hypotheses. In regions where connectivity among high-island archipelagos was predicted as direct, there was no difference in gene flow between marine and hidromous species. In regions where connectivity was predicted through stepping-stone atolls only accessible to marine species, gene flow estimates between high-island archipelagos were significantly higher in marine species. Moreover, one of the marine species showed a significant pattern of isolation by distance consistent with stepping-stone dynamics. While our results support stepping-stone dynamics in Indo-Pacific species, we also see evidence for nonequilibrium processes such as range expansions or rare long-distance dispersal events. This study couples population genetic and biophysical models to help to shed light on larval dispersal pathways.
Publisher: Bulletin of Marine Science
Date: 2014
Publisher: Bulletin of Marine Science
Date: 2014
Publisher: Bulletin of Marine Science
Date: 2014
Publisher: Wiley
Date: 27-10-2020
Publisher: Bulletin of Marine Science
Date: 2014
Publisher: Cold Spring Harbor Laboratory
Date: 15-09-2022
DOI: 10.1101/2022.09.12.507034
Abstract: Genetic ersity within species represents a fundamental yet underappreciated level of bio ersity. Because genetic ersity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic ersity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained s les from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 in iduals or BioS les from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the s les were taken was the most easily found information about s ling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.
Publisher: Oxford University Press (OUP)
Date: 06-07-2016
DOI: 10.1093/CZ/ZOW067
Publisher: Wiley
Date: 22-04-2019
DOI: 10.1111/GEB.12905
Publisher: Bulletin of Marine Science
Date: 2014
Publisher: Wiley
Date: 10-03-2023
DOI: 10.1111/COBI.14061
Abstract: Genetic ersity within species represents a fundamental yet underappreciated level of bio ersity. Because genetic ersity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic ersity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly s les from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets ( n = 440 data sets with data on 45,105 in iduals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data‐sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.
Publisher: Wiley
Date: 27-04-2022
DOI: 10.1111/GCB.16192
Abstract: The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for ex le hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km
Location: United States of America
Location: United States of America
No related grants have been discovered for Eric Crandall.