Repositories for Taxonomic Data: Where We Are and What is Missing

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].

Data storage and data re-use in taxonomy—the need for improved storage and accessibility of heterogeneous data

The ability to rapidly generate and share molecular, visual, and acoustic data, and to compare them with existing information, and thereby to detect and name biological entities is fundamentally changing our understanding of evolutionary relationships among organisms and is also impacting taxonomy. Harnessing taxonomic data for rapid, automated species identification by machine learning tools or DNA metabarcoding techniques has great potential but will require their review, accessible storage, comprehensive comparison, and integration with prior knowledge and information. Currently, data production, management, and sharing in taxonomic studies are not keeping pace with these needs. Indeed, a survey of recent taxonomic publications provides evidence that few species descriptions in zoology and botany incorporate DNA sequence data. The use of modern high-throughput (-omics) data is so far the exception in alpha-taxonomy, although they are easily stored in GenBank and similar databases. By contrast, for the more routinely used image data, the problem is that they are rarely made available in openly accessible repositories. Improved sharing and re-using of both types of data requires institutions that maintain long-term data storage and capacity with workable, user-friendly but highly automated pipelines. Top priority should be given to standardization and pipeline development for the easy submission and storage of machine-readable data (e.g., images, audio files, videos, tables of measurements). The taxonomic community in Germany and the German Federation for Biological Data are researching options for a higher level of automation, improved linking among data submission and storage platforms, and for making existing taxonomic information more readily accessible.

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.

Expressed sequence tag-derived polymorphic SSR markers for Fucus serratus and amplification in other species of Fucus

The seaweed genus Fucus is a dominant component of intertidal shores throughout the North Atlantic and North Pacific and has been the focus of considerable developmental, ecological, and evolutionary research for the past century. Here, we present details of 21 expressed sequence tag-derived simple sequence repeat markers (microsatellites). All 21 were polymorphic for F. serratus, which also display considerable cross-reactivity with the sister species F. distichus (18) and the more distantly related F. vesiculosus (13), and F. spiralis (5).

Polyphasic typing of Cryptosporidium baileyi: a suggested model for characterization of cryptosporidia

The present study was undertaken to characterize the oocyst morphology, host specificity, organ location, virulence, and sequences of the small subunit ribosomal RNA, 70-kDa heat shock protein, and oocyst wall protein genes of Cryptosporidium baileyi, and to compare this strain with other Cryptosporidium species. This study also aims to serve as a model for polyphasic (phenetic and genetic) characterization of Cryptosporidium species and strains. On the basis of these results, further genetic and phenetic characterization of an avian isolate is needed if the difference between the length or width, or both, of oocysts of an isolate and of C. baileyi is > or = 10% or if the difference between the oocyst shape index of the isolate and of C. baileyi is > or = 3% (or both). The isolate is infectious for mammals or lower vertebrates, or the host range is narrow, i.e., infectious only for some bird species; after oral or intratracheal inoculation, the parasites are not located in the cloaca and in the bursa of Fabricius or the respiratory tract; clinical disease or weight gain reduction can be observed after oral inoculation; the genetic distance for the examined gene between C. baileyi and the isolate is similar in magnitude to that observed between most closely related Cryptosporidium species.

Morphologic and genetic characterization of Onchocerca lupi infecting dogs

In the past decades, sporadic cases of ocular Onchocerca infection have been reported in canids in US and Europe. The present study was undertaken to provide a detailed description of the morphologic characteristics of adults and microfilariae and to characterize the 5S ribosomal rRNA gene (5S rDNA) spacer sequences of Onchocerca lupi causing canine onchocercosis. The morphology of O. lupi is unique within the genus, and morphology based cluster analysis indicates that O. lupi is not closely related to the members of domestic cattle or horse clades occurring in North America and Europe. Similarly, the signature of the 5S rDNA spacer sequences of O. lupi does not resemble any other Onchocerca 5S rDNA spacer sequences including those of the members of domestic cattle or horse clades. The adult and microfilarial morphology and sequence signature supports the biological arguments that a distinct species, O. lupi and not O. lienalis, is responsible for canine ocular onchocercosis.

Phylogeny of six naviculoid diatoms based on 18S rDNA sequences

18S rDNA sequences of six Naviculaceae species [Amphora montana, Gomphonema parvulum, Eolimna minima (syn. Navicula minima), Eolimna subminuscula (syn. Navicula subminuscula), Navicula veneta and Phaeodactylum tricornutum] were determined in order to assess the monophyly of this important group of diatoms, to date not included in 18S rDNA databases, and also that of the recently described genus Eolimna. Phylogenetic trees were constructed using other known diatom 18S rDNA sequences, and best tree topologies obtained were tested against alternative trees for their reliability. The analyses do not reject the monophyly of Naviculaceae and strongly support the separation of the genus Eolimna from Navicula sensu lato. The two species of Eolimna, however, do not appear to be each other's closest relatives among the species investigated: rather, E. subminuscula shows affinities to A. montana, and E. minima to P. tricornutum. A. montana, a species which it has been proposed should be transferred into a separate taxon from the other five species, was found to have grouped well within them in all analyses.