François Michonneau

Ten Simple Rules for Digital Data Storage

Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institutional support for large sensor networks, and sky surveys with large-format digital cameras have created massive quantities of data. At the same time, the combination of increasingly diverse research teams and data aggregation in portals (e.g. for biodiversity data, GBIF or iDigBio) necessitates increased coordination among data collectors and institutions. As a consequence, “data” can now mean anything from petabytes of information stored in professionally-maintained databases, through spreadsheets on a single computer, to hand-written tables in lab notebooks on shelves. All remain important, but data curation practices must continue to keep pace with the changes brought about by new forms and practices of data collection and storage.

Cryptic and not-so-cryptic species in the complex Holothuria (Thymiosycia) impatiens (Forssk&aringl, 1775) (Echinodermata: Holothuroidea)

Identifying accurately species is critical for our understanding of patterns of diversity and speciation. However, for many organisms with simple and variable morphological traits, the characters traditionally used by taxonomists to identify species might lead to a considerable under appreciation of their diversity. Recent advances in molecular-data based computational methods have considerably improved our ability to identify and test species limits. Here, we use an integrative approach to delineate species in a complex of sea cucumbers. We used a three-step approach to show that “Holothuria impatiens”, a common, shallow-water species, occurring across the Indo-Pacific, the Western Atlantic and the Mediterranean Sea, targeted locally by fisheries, is a complex of at least 13 species. (1) We used the Generalized Mixed Yule Coalescent (GMYC) model to identify putative species without a priori hypotheses. In the process, we also show that the number of putative species estimated with GMYC can be affected considerably by the priors used to build the input tree. (2) We assessed based on coloration patterns and distributional information, the most relevant hypothesis. This approach allowed us to identify unambiguously 9 species. However, some of the lineages consistently assigned to belong to different species using GMYC, are occurring in sympatry and are not differentiated morphologically. (3) We used Bayes factors to compare competing models of species assignment using the multispecies coalescent as implemented in *BEAST. This approach allowed us to validate that the species identified using GMYC were likely reproductively isolated. Estimates of the timing of diversification also showed that these species diverged less than 2 Ma, which is the fastest case of closely related species occurring in sympatry for a marine metazoan. Our study demonstrates how clarifying species limits contribute to refining our understanding of speciation.

More than meets the eye: diversity and geographic patterns in sea cucumbers

Estimates for the number of species in the sea vary by orders of magnitude. Molecular taxonomy can greatly speed up screening for diversity and evaluating species boundaries, while gaining insights into the biology of the species. DNA barcoding with a region of cytochrome oxidase 1 (COI) is now widely used as a first pass for molecular evaluation of diversity, as it has good potential for identifying cryptic species and improving our understanding of marine biodiversity. We present the results of a large scale barcoding effort for holothuroids (sea cucumbers). We sequenced 3048 individuals from numerous localities spanning the diversity of habitats in which the group occurs, with a particular focus in the shallow tropics (Indo-Pacific and Caribbean) and the Antarctic region. The number of cryptic species is much higher than currently recognized. The vast majority of sister species have allopatric distributions, with species showing genetic differentiation between ocean basins, and some are even differentiated among archipelagos. However, many closely related and sympatric forms, that exhibit distinct color patterns and/or ecology, show little differentiation in, and cannotbe separatedby, COI sequence data. This pattern is much more common among echinoderms than among molluscs or arthropods, and suggests that echinoderms acquire reproductive isolation at a much faster pace than other marine phyla. Understanding the causes behind such patterns will refine our understanding of diversification and biodiversity in the sea.