Biodiversity Data in the Information Age: Do 21st Century Floras Make the Grade?

Palmer, Michael W.; Richardson, J. Channing

doi:10.2179/11-035

Cited by 25 publications

(17 citation statements)

References 89 publications

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“…The low quality of biodiversity datasets and the lack of standards in publication and data management limit their usefulness (Palmer and Richardson 2012). There is a growing interest in standards for taxonomic information (e.g., Taxonomic Databases Working Group 2007) and hopefully the quality of datasets will improve in the near future.…”

Section: Discussionmentioning

confidence: 99%

Diversity and distribution of amphibians in Romania

Cogălniceanu¹,

Székely²,

Samoilă³

et al. 2013

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Nineteen species of amphibians inhabit Romania, 9 of which reach their range limit on this territory. Based on published occurrence reports, museum collections and our own data we compiled a national database of amphibian occurrences. We georeferenced 26779 amphibian species occurrences, and performed an analysis of their spatial patterns, checking for hotspots and patterns of species richness. The results of spatial statistic analyses supported the idea of a biased sampling for Romania, with clear hotspots of increased sampling efforts. The sampling effort is biased towards species with high detectability, protected areas, and large cities. Future sampling efforts should be focused mostly on species with a high rarity score in order to accurately map their range. Our results are an important step in achieving the long-term goals of increasing the efficiency of conservation efforts and evaluating the species range shifts under climate change scenarios.

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Section: Discussionmentioning

confidence: 99%

Diversity and distribution of amphibians in Romania

Cogălniceanu¹,

Székely²,

Samoilă³

et al. 2013

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“…Regional Floras and checklists are a rich source of information on species distributions that often also contain detailed descriptions of species traits and other information such as conservation status and human uses (Palmer & Richardson, 2012). In the past, botanical knowledge was recorded primarily in printed books (Frodin, 2001), which are labour-intensive to convert into structured data.…”

Section: Content and S Truc Ture Of G If T 21 | Overviewmentioning

confidence: 99%

GIFT – A Global Inventory of Floras and Traits for macroecology and biogeography

Weigelt

König

Kreft

2019

Journal of Biogeography

157

189

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Aim:To understand how functional traits and evolutionary history shape the geographic distribution of plant life on Earth, we need to integrate high-quality and global-scale distribution data with functional and phylogenetic information. Largescale distribution data for plants are, however, often restricted to either certain taxonomic groups or geographic regions. Range maps only exist for a small subset of all plant species and digitally available point-occurrence information is biased both geographically and taxonomically. Floras and checklists represent an alternative, yet rarely used potential source of information. They contain highly curated information about the species composition of a clearly defined area, and together virtually cover the entire global land surface. Here, we report on our recent efforts to mobilize this information for macroecological and biogeographical analyses in the GIFT database, the Global Inventory of Floras and Traits. Location: Global. Taxon: Land plants (Embryophyta).Methods: GIFT integrates plant distributions from regional Floras and checklists with functional traits, phylogenetic information, and region-level geographic, environmental and socio-economic data. It contains information about the floristic status (native, endemic, alien and naturalized) and takes advantage of the wealth of trait information in the regional Floras, complemented by data from global trait databases.Results: GIFT 1.0 holds species lists for 2,893 regions across the whole globe including ~315,000 taxonomically standardized species names (i.e. c. 80% of all known land plant species) and ~3 million species-by-region occurrences. Based on a hierarchical and taxonomical derivation scheme, GIFT contains information for 83 functional traits and more than 2.3 million trait-by-species combinations and achieves unprecedented coverage in categorical traits such as woodiness (~233,000 spp.) or growth form (~213,000 spp.). Main conclusions:Here, we present the structure, content and automated workflows of GIFT and a corresponding web-interface (http://gift.uni-goett ingen.de) as proof of concept for the feasibility and potential of mobilizing aggregated biodiversity data for global macroecological and biogeographical research.

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“…On the other hand, floristic studies are an essential tool for any evolutionary study (Funk 2006), being sometimes the only updated repository where morphological descriptions and identification keys can be found. Such studies support the correct application of names to samples in an evolutionary study (Palmer & Richardson 2012). For this reason, a complete descriptive Flora can influence the results and quality of the phylogenetic hypotheses.…”

Section: Discussionmentioning

confidence: 66%

Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study

et al. 2019

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Background: GenBank is a public repository that houses millions of nucleotide sequences. Several software have been developed to extract information stored in GenBank. However, none of them are useful to extract and organize GenBank accession based on metadata. We developed a new script called Datataxa, which works to mine GenBank information. The checklist of the Flora del Bajío y de Regiones Adyacentes (FBRA) was used as a case study to apply our script.Questions: How many species occurring in the FBRA have records in GenBank? What percentage of those records have been used for phylogenetic, phylogeographic, phylogenomic, barcoding, genetic diversity, and biogeographic studies?Methods: Datataxa was written in AutoIt Scripting Language in order to facilitate the extraction of information from GenBank. This information was classified in six study categories. A checklist of species published fascicles of FBRA was used as study case to apply our new script, and the previous categories were applied to the FBRA species list.Results: The script allowed us to search for meta information, like publication titles, for 2,558 species that were included in the FBRA. Of these, 1,575 had a least one record in GenBank. A total of 1,322 species were used in phylogenetic studies, followed by barcoding studies (326) and biogeographic studies (298). Phylogenomic (41), phylogeographic (34), and diversity studies (34) were the least represented.Conclusions: Datataxa was useful for mining metadata sequence information from GenBank and can be used with any list of species to get the GenBank accessions’ metadata.

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Biodiversity Data in the Information Age: Do 21st Century Floras Make the Grade?

Cited by 25 publications

References 89 publications

Diversity and distribution of amphibians in Romania

Diversity and distribution of amphibians in Romania

GIFT – A Global Inventory of Floras and Traits for macroecology and biogeography

Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study

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