Wikipedia as an encyclopaedia of life

In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision

Taxonomic diversity and identification problems of oncaeid microcopepods in the Mediterranean Sea

The species diversity of the pelagic microcopepod family Oncaeidae collected with nets of 0.1-mm mesh size was studied at 6 stations along a west-to-east transect in the Mediterranean Sea down to a maximum depth of 1,000 m. A total of 27 species and two form variants have been identified, including three new records for the Mediterranean. In addition, about 20, as yet undescribed, new morphospecies were found (mainly from the genera Epicalymma and Triconia) which need to be examined further. The total number of identified oncaeid species was similar in the Western and Eastern Basins, but for some cooccurring sibling species, the estimated numerical dominance changed. The deep-sea fauna of Oncaeidae, studied at selected depth layers between 400 m and the near-bottom layer at >4,200 m depth in the eastern Mediterranean (Levantine Sea), showed rather constant species numbers down to ∼3,000 m depth. In the near-bottom layers, the diversity of oncaeids declined and species of Epicalymma strongly increased in numerical importance. The taxonomic status of all oncaeid species recorded earlier in the Mediterranean Sea is evaluated: 19 out of the 46 known valid oncaeid species are insufficiently described, and most of the taxonomically unresolved species (13 species) have originally been described from this area (type locality). The deficiencies in the species identification of oncaeids cast into doubt the allegedly cosmopolitan distribution of some species, in particular those of Mediterranean origin. The existing identification problems even of well-described oncaeid species are exemplified for the Oncaea mediacomplex, including O. media Giesbrecht, O. scottodicarloi Heron & Bradford-Grieve, and O. waldemari Bersano & Boxshall, which are often erroneously identified as a single species (O. media). The inadequacy in the species identification of Oncaeidae, in particular those from the Atlantic and Mediterranean, is mainly due to the lack of reliable identification keys for Oncaeidae in warm-temperate and/or tropical seas. Future efforts should be directed to the construction of identification keys that can be updated according to the latest taxonomic findings, which can be used by the non-expert as well as by the specialist. The adequate consideration of the numerous, as yet undescribed, microcopepod species in the world oceans, in particular the Oncaeidae, is a challenge for the study of the structure and function of plankton communities as well as for global biodiversity estimates

Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca)

Background: Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. Methodology/Principal Findings: We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. Conclusions/Significance: Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.FCT - SFRH/BD/25568/ 2006EC FP6 - GOCE-CT-2005-511234 HERMESFCT - PTDC/MAR/69892/2006 LusomarBo

Genetic Isolation between the Western and Eastern Pacific Populations of Pronghorn Spiny Lobster Panulirus penicillatus

The pronghorn spiny lobster, Panulirus penicillatus, is a circumtropical species which has the widest global distribution among all the species of spiny lobster, ranging throughout the entire Indo-Pacific region. Partial nucleotide sequences of mitochondrial DNA COI (1,142–1,207 bp) and 16S rDNA (535–546 bp) regions were determined for adult and phyllosoma larval samples collected from the Eastern Pacific (EP)(Galápagos Islands and its adjacent water), Central Pacific (CP)(Hawaii and Tuamotu) and the Western Pacific (WP)(Japan, Indonesia, Fiji, New Caledonia and Australia). Phylogenetic analyses revealed two distinct large clades corresponding to the geographic origin of samples (EP and CP+WP). No haplotype was shared between the two regional samples, and average nucleotide sequence divergence (Kimura's two parameter distance) between EP and CP+WP samples was 3.8±0.5% for COI and 1.0±0.4% for 16S rDNA, both of which were much larger than those within samples. The present results indicate that the Pacific population of the pronghorn spiny lobster is subdivided into two distinct populations (Eastern Pacific and Central to Western Pacific), with no gene flow between them. Although the pronghorn spiny lobster have long-lived teleplanic larvae, the vast expanse of Pacific Ocean with no islands and no shallow substrate which is known as the East Pacific Barrier appears to have isolated these two populations for a long time (c.a. 1MY)

Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library

Background: The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. Description: A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article locating service is exposed as a standard OpenURL resolver on the BioStor web site http://biostor.org/openurl/. This resolver can be used on the web, or called by bibliographic tools that support OpenURL. Conclusions: BioStor provides tools for extracting, annotating, and visualising articles from the Biodiversity Heritage Library. BioStor is available from http://biostor.org

Ocurrence of male morphotypes of Macrobrachium amazonicum (Caridea, Palaemonidae) in a population with an entirely freshwater life cycle

This study records, for the first time, the occurrence of all four male morphotypes in a population of Macrobrachium amazonicum from a continental environment, with an entirely freshwater life cycle. The specimens studied came from the Tietê River, state of São Paulo, Brazil, and were collected in a lotic environment downstream from Ibitinga Dam. This population was compared with other continental populations, including a population from the dam itself, collected in a previous study. Four samples of 30 minutes were taken monthly, using a trap, from January to April 2011. Each male specimen was measured with respect to seven body dimensions as follows: carapace length (CL), right cheliped length (RCL), dactyl length (DCL), propodus length (PPL), carpus length (CRL), merus length (ML) and ischium length (IL). The relative growth was analyzed based on the change in growth patterns of certain body parts in relation to the independent variable CL. The four male morphotypes proposed for the species were found using morphological and morphometric analyses. Different biological characteristics were found between the populations studied. The male population of the lake of Ibitinga and from Pantanal presented mean sizes and number of morphotypes lower than the population studied here. These differences seem to be closely related to ecological characteristics of the environments inhabited by these populations. Our results supported the hypothesis that coastal and continental populations of M. amazonicum belong to the same species.Este estudo registra, pela primeira vez, a ocorrência dos quatro morfotipos de Macrobrachium amazonicum em uma população continental com ciclo de vida totalmente dulcícola. Os camarões são provenientes do Rio Tietê, estado de São Paulo, Brasil, e foram coletados em um ambiente lótico abaixo da Barragem de Ibitinga. Essa população foi comparada com outras populações provenientes de ambientes continentais, incluindo a de um estudo anterior na represa da barragem de Ibitinga. Quatro amostras de 30 minutos foram realizadas mensalmente, utilizando armadilhas, de janeiro a abril de 2011. Cada indivíduo macho foi mensurado em relação a sete dimensões corporais, sendo elas: comprimento da carapaça (CL), comprimento total do quelípodo direito (RCL), comprimento do dáctilo (DCL), comprimento do própodo (PPL), comprimento do carpo (CRL), comprimento do mero (ML) e comprimento do ísquio (IL). O crescimento relativo foi analisado de acordo com as mudanças nas taxas de crescimento de determinadas partes do corpo em relação à variável independente CL. Os quatro morfotipos descritos para a espécie foram encontrados, utilizando análises morfológicas e morfométricas. Diferentes características biológicas foram encontradas entre a população estudada e as demais, incluindo a proveniente do reservatório. A população de machos da represa de Ibitinga e do Pantanal apresentaram tamanhos médios e número de morfotipos inferiores aos da população estudada aqui. Essas diferenças parecem estar intimamente relacionadas às características ecológicas dos ambientes onde estas populações estão inseridas. A hipótese de que populações costeiras e continentais de M. amazonicum pertençam à mesma espécie é suportada por nossos resultados.Universidade Estadual Paulista “Júlio de Mesquita Filho” – UNESP Faculdade de Ciências Departamento de Ciências BiológicasUniversidade Federal de Sergipe – UFS Centro de Ciências Biológicas e da Saúde – CCBS Laboratório de CarcinologiaUniversidade Estadual Paulista “Júlio de Mesquita Filho” – UNESP Faculdade de Ciências Departamento de Ciências Biológica