Putting GenBank Data on the Map

Marques, Antônio Carlos; Maronna, Maximiliano M.; Collins, Allen G.

doi:10.1126/science.341.6152.1341-a

Cited by 26 publications

(23 citation statements)

References 1 publication

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We also urge data collectors to upload metadata such as collection year and spatial coordinates when depositing sequences in databases-a remarkably large number of sequences in GenBank do not have a collection year (e.g. 95% of amphibian sequences, hence their exclusion from this analysis; Marques et al 2013;Pope et al 2015). Global monitoring of genetic diversity would improve our ability to detect change and attribute the causes of worldwide patterns of spatial and temporal variation in genetic diversity we report here.…”

Section: Discussionmentioning

confidence: 99%

Worldwide impacts of humans on animal genetic diversity

Millette

Fugère

Debyser

et al. 2019

Preprint

View full text Add to dashboard Cite

SummaryHuman impacts on genetic diversity are poorly understood yet critical to understanding the evolutionary capacity of the world’s biodiversity. We used global maps of land use and human density to assess human impacts on the intraspecific genetic diversity of 15,946 species of birds, fishes, insects, and mammals over time and across four spatial scales worldwide. We analyzed 164,518 mitochondrial cytochrome c oxidase subunit I (COI) sequences to quantify changes in genetic diversity between 1980-2016. We found temporal change in genetic diversity, with both increasing and decreasing trends observed. The magnitude and sign of human impacts on genetic diversity depended on scale and taxon. In contrast, latitude was a strong predictor of diversity in fish, insects, and mammals. Our analyses provide a first worldwide picture of human impacts on animal genetic diversity. A global effort to systematically monitor genetic diversity is needed to fill the gaps in taxonomic and geographic coverage in this dataset.

show abstract

Section: Discussionmentioning

confidence: 99%

Worldwide impacts of humans on animal genetic diversity

Millette

Fugère

Debyser

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Our findings are made possible by repurposing existing georeferenced genetic data (e.g., Sidlauskas et al., ), Such data contain immense potential for insight (Dawson, ; Soltis & Soltis, ) because thousands of studies investigating the geographical distribution of genetic variation have been published to date, each collecting data from hundreds of samples (Garrick et al., ). Unfortunately, only 7% of GenBank accessions of barcoding genes, such as COI, include latitude and longitude, and only 18% list museum catalogue information that can be used to link the sequence to a particular specimen (Marques, Maronna, & Collins, ). The disassociation of genetic and geographical accessions limits the utility of open source databases and must be addressed if biodiversity scientists are to leverage the information contained within existing data to meet the challenges associated with conservation of species and understanding patterns in evolution on a global scale (Pope, Liggins, Keyse, Carvalho, & Riginos, ).…”

Section: Discussionmentioning

confidence: 99%

A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation

Carstens

Morales

Field

et al. 2018

Journal of Biogeography

View full text Add to dashboard Cite

Aim Our work seeks to understand the global demographical response of bat species to the climate change that occurred at the Last Glacial Maximum (LGM). Location All continents except Antarctica. Methods Mitochondrial DNA sequences were sampled from bat species throughout the planet where we could associate a georeferenced sample with a given DNA sequence. Our investigation estimates the historical demographical response using over 12,000 samples from >300 nominal species of bats. Custom Python and R scripts were written to aggregate sequence data from GenBank, locality information from GBIF, and to associate these records to individual samples. We conducted approximate Bayesian computation to calculate the posterior probability of demographical bottleneck and expansion responses to the end of the Pleistocene, and then collected organismal trait data to identify traits that were associated with either demographical response. We also used R to estimate current and end‐Pleistocene species distribution models (SDM) for species where >10 georeferenced samples were available. Results Analysis of the genetic data indicate that some temperate insectivores responded to the end of the Pleistocene by undergoing a demographical expansion. However, the neotropical family Phyllostomidae experienced the most dramatic response, with many of its species undergoing demographical bottlenecks. Larger bats, and those with shorter forewings, were more likely to undergo a demographical bottleneck. In contrast with the results of the genetic data analysis, the automated SDMs all predicted range expansion since the LGM. Main conclusions Historical populations of Neotropical bats that rely on Angiosperms for resources (i.e., pollen, nectar, fruit) were negatively influenced by the climate change that occurred at the end of the Pleistocene. Our work highlights the utility of incorporating exploratory trait‐based analyses in phylogeography. It serves as an example of automated big data phylogeography, and suggests that repurposed data can lead to new insights about global biodiversity.

show abstract

“…Without this, however, these databases risk becoming holding houses for occurrence data of highly questionable utility, as GenBank has become for DNA sequences (e.g. Marques et al 2013;Lindsay et al 2015). In response to these problems with GenBank, initiatives such as the Cnidarian Barcoding Initiative (2016) and the Sponge Barcoding Project (2016) have been established where databases only contain sequence data for which identifications have been vetted by a taxonomist (named in the metadata) and for which a voucher specimen exists.…”

Section: Discussionmentioning

confidence: 99%

The perils of online biogeographic databases: a case study with the ‘monospecific’ genus Aegina (Cnidaria, Hydrozoa, Narcomedusae)

Lindsay

Grossmann

Bentlage

et al. 2017

Marine Biology Research

View full text Add to dashboard Cite

Online biogeographic databases are increasingly being used as data sources for scientific papers and reports, for example, to characterize global patterns and predictors of marine biodiversity and to identify areas of ecological significance in the open oceans and deep seas. However, the utility of such databases is entirely dependent on the quality of the data they contain. We present a case study that evaluated online biogeographic information available for a hydrozoan narcomedusan jellyfish, Aegina citrea. This medusa is considered one of the easiest to identify because it is one of very few species with only four large tentacles protruding from midway up the exumbrella and it is the only recognized species in its genus. Online resources such as the Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS) suggest that A. citrea is broadly distributed throughout the world's oceans. However, lack of traceability to information from original providers made it impossible to validate the great majority of records in online resources, casting doubt on species identification. Thus, we conducted a new systematic investigation of A. citrea, integrating morphological and genetic observations of specimens obtained from a variety of different localities. Contrary to the status quo, our molecular phylogenetic analysis shows that the genus Aegina and the family Aeginidae are polyphyletic. In conjunction with our phylogenetic framework, we clarify the morphological characters distinguishing different clades of 'Aegina'. To accommodate for the previously unrecognized diversity in this group, we describe two new families, three new genera, and one new species. In addition, we clarify the identities of found species by providing updated descriptions. Specifically, we redescribe A. citrea, and resurrect and redescribe A. rosea, A. brunnea (as Aeginona brunnea gen. nov.), A. rhodina and A. pentanema, erecting a new family and genus for the latter two species (Pseudaeginidae, Pseudaegina). A new genus and species, Solmundaegina nematophora, is also described, with the erection of a new family Solmundaeginidae to contain it and the genera Solmundella, Aeginopsis and Solmundus. In light of our integrative systematic study, we find that many past conclusions about the biology of 'Aegina citrea', from life history to ecology to distributions, are compromised because observations of more than one species were applied to a single name, highlighting how systematics and taxonomy provide the foundation upon which all other biological science is built.http://zoobank.org/urn:lsid:zoobank.org:pub:AF6B533C-8110-44A0-A7E5-B71F878DAC4A ARTICLE HISTORY

show abstract

Putting GenBank Data on the Map

Cited by 26 publications

References 1 publication

Worldwide impacts of humans on animal genetic diversity

Worldwide impacts of humans on animal genetic diversity

A global analysis of bats using automated comparative phylogeography uncovers a surprising impact of Pleistocene glaciation

The perils of online biogeographic databases: a case study with the ‘monospecific’ genus Aegina (Cnidaria, Hydrozoa, Narcomedusae)

Contact Info

Product

Resources

About