Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice.

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

DNA-based taxonomy of larval stages reveals huge unknown species diversity in neotropical seed weevils (genus Conotrachelus): relevance to evolutionary ecology.

High diversity in tropical phytophagous insects may be linked to narrow host specificity and host shifts, but tests are complicated by incomplete taxonomy and difficulties in food source identification. Specimens of the highly diverse New World genus Conotrachelus (Coleoptera: Curculionoidea) were reared from >17,500 fruits (seeds) at six Central American rain forests. Interception traps were used for comparison with assemblages flying in the forest. Mitochondrial cox1 and the nuclear 28S genes were sequenced for 483 larval and adult specimens. A Yule-Coalescent technique was used to group cox1 sequences into putative species (17 from traps, 48 from rearing). Cox1 sequences of 24 species from museum collections provided matches for three species from traps and no match for the reared species. Inga (Fabaceae) was the predominant host among 15 other genera and 67% of the weevils were monophagous. A three gene tree (cox1, rrnL, 28S) recovered four well-supported clades feeding on Inga confirmed by phylogenetic community analyzes that showed phylogenetic conservation of host plant utilization. This suggests that host shifts are not directly involved in speciation, while the broad taxonomic host range and the evolutionary repeated shifts still contribute to the high species richness in Conotrachelus. The DNA-based approach combining species delimitation and phylogenetic analysis elucidated the evolutionary diversification of this lineage, despite insufficient taxonomic knowledge. Conotrachelus is an example of the diverse tropical groups that require DNA-based taxonomy to study their evolutionary ecology.

Digitising legacy zoological taxonomic literature: Processes, products and using the output.

By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original - the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people's ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. A means to do this is through marking up content into XML, and the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. We now need to automate this process as far as possible. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying in its production the requirements of the Code, is fit for purpose in the future.

The rectal valve in Curculionoidea (Insecta: Coleoptera).

A rectal valve is known from Bostrichiformia (e.g. Dermestidae, Bostrichidae, Ptinidae), Cucujiformia (e.g. Chrysmeloidea, Cleridae, Curculionoidea, Endomychidae, Tenebrionidae) and Buprestidae, associated with the cryptonephridial system for water recovery from fecal matter. The valve is probably homologous in at least the Bostrichiformia and Cucujiformia although the form it takes may not be. It comprises a sclerotized band lying in the wall of the rectum where this meets the perinephric membrane. The valve is plesiomorphically a narrow crimped ring, probably acting as a sphincter to retain fecal matter for water extraction. Apomorphically it extends longitudinally along the rectum and supports the perinephric chamber; this state has probably arisen independently several times. Larval and adult morphology may be similar or different. Within the Curculionoidea different apomorphic forms suggest monophyly of groups within the Anthribidae and Dryophthoridae, and within the curculionid subfamilies Entiminae, Mesoptiliinae, Molytinae and Cossoninae + Scolytinae, although limited weight should be placed on a single character. No support is provided for a relationship between the Platypodinae and Scolytinae. The genera Cylindrotypetes Zimmerman 1942 and Edaphotrypetes Morimoto 1995 are transferred from Molytinae: Phoenicobatini to Cossoninae: Pentrarthini.

Impacts of logging on density-dependent predation of dipterocarp seeds in a South East Asian rainforest.

Much of the forest remaining in South East Asia has been selectively logged. The processes promoting species coexistence may be the key to the recovery and maintenance of diversity in these forests. One such process is the Janzen-Connell mechanism, where specialized natural enemies such as seed predators maintain diversity by inhibiting regeneration near conspecifics. In Neotropical forests, anthropogenic disturbance can disrupt the Janzen-Connell mechanism, but similar data are unavailable for South East Asia. We investigated the effects of conspecific density (two spatial scales) and distance from fruiting trees on seed and seedling survival of the canopy tree Parashorea malaanonan in unlogged and logged forests in Sabah, Malaysia. The production of mature seeds was higher in unlogged forest, perhaps because high adult densities facilitate pollination or satiate pre-dispersal predators. In both forest types, post-dispersal survival was reduced by small-scale (1 m(2)) conspecific density, but not by proximity to the nearest fruiting tree. Large-scale conspecific density (seeds per fruiting tree) reduced predation, probably by satiating predators. Higher seed production in unlogged forest, in combination with slightly higher survival, meant that recruitment was almost entirely limited to unlogged forest. Thus, while logging might not affect the Janzen-Connell mechanism at this site, it may influence the recruitment of particular species.