A Decade of GigaScience: Milestones in Open Science.

Open Science has gained momentum over the past decade, and embracing that, GigaScience, from its launch a decade ago has aimed at pushing scientific publishing beyond just making articles open access toward making the entire research process open and available as an embedded part of the publishing process. Before the journal's launch in July 2012, the editors aimed to make publishing more than a narrative presentation of work already done into a fully open process. Major milestones include creating our own data repository, embracing FAIR principles, promoting and integrating preprints, and working with other platforms to contribute to a 21st century publishing infrastructure. Almost 10 years after GigaScience's launch, UNESCO published its Open Science Recommendations. With these in mind, looking back, we are happy to have contributed in various ways to UNESCO's aim to "foster a culture of Open Science and aligning incentives for Open Science" from the very beginning, and, more, to use those recommendations to guide our path into the future: to truly embrace the full spectrum of information, tools, and access to Open Science for all participants in scientific endeavours.

Editorial: We need to talk about authorship.

In our day-to-day editorial work at GigaScience, time and again we see issues cropping up that make us worry whether everyone understands good scientific practice when it comes to listing author names on the title page. There are many issues that underlie inappropriate authorship designations, but there are also guidelines to help potential authors determine when and how a researcher should be included with a manuscript. Here, we help clarify this and also provide a clear statement of our expectations around how authors are assigned to manuscripts submitted to GigaScience.

Looking back: forward looking.

GigaScience is now 5 years old, having been launched at the 2012 Intelligent Systems for Molecular Biology conference. Anyone who has attended what is the largest computational biology conference since then has had the opportunity to join us for each birthday celebration-and receive 1 of our fun T-shirts as a party prize. Since launching, we have pushed our agenda of openness, transparency, reproducibility, and reusability. Here, we look back at our first 5 years and what we have done to forward our open science goals in scientific publishing. Our mainstay has been to create a process that allows the availability and publication of as many "research objects" as possible to create a more complete way of communicating how the research process is done.

Evolution of robustness in the signaling network of Pristionchus vulva development.

Robustness to environmental or genetic perturbation, like any other trait, is affected by evolutionary change. However, direct studies on the interplay of robustness and evolvability are limited and require experimental microevolutionary studies of developmental processes. One system in which such microevolutionary studies can be performed is vulva development in the nematode Pristionchus pacificus. Three vulval precursor cells respond to redundant cell-cell interactions, including signals from the gonad and the epidermal cell P8.p. Interestingly, P. pacificus P8.p is involved in cell fate specification of the future vulva cells by lateral inhibition but is incompetent to respond to the inductive signal from the gonad itself. These functional properties of P8.p are unknown from other nematodes, such as Caenorhabditis elegans. We began an experimental and genetic analysis of the microevolution of P8.p function. We show that vulva misspecification events differ between Pristionchus strains and species. Similarly, lateral inhibition and developmental competence of P8.p evolved within the genus Pristionchus and between natural isolates of P. pacificus. Surprisingly, in some recombinant inbred lines of two distinct P. pacificus isolates, P8.p gained competence to form vulva tissue, a trait that was never observed in P. pacificus isolates. Our results suggest differences in developmental stability between natural isolates, and we hypothesize that the remarkable evolvability of redundant cell-cell interactions allows for adaptive evolution of robustness to developmental noise.

Distinct patterns of genetic variation in Pristionchus pacificus and Caenorhabditis elegans, two partially selfing nematodes with cosmopolitan distribution.

Hermaphroditism has evolved several times independently in nematodes. The model organism Caenorhabditis elegans and Pristionchus pacificus are self-fertile hermaphrodites with rare facultative males. Both species are members of different families: C. elegans belongs to the Rhabditidae and P. pacificus to the Diplogastridae. Also, both species differ in their ecology: C. elegans is a soil-dwelling nematode that is often found in compost heaps. In contrast, field studies in Europe and North America indicate that Pristionchus nematodes are closely associated with scarab beetles. In C. elegans, several recent studies have found low genetic diversity and rare out-crossing events. Little is known about diversity levels and population structure in free-living hermaphroditic nematodes outside the genus Caenorhabditis. Taking a comparative approach, we analyse patterns of molecular diversity and linkage disequilibrium in 18 strains of P. pacificus from eight countries and four continents. Mitochondrial sequence data of P. pacificus isolates reveal a substantially higher genetic diversity on a global scale when compared to C. elegans. A mitochondrial-derived hermaphrodite phylogeny shows little geographic structuring, indicating several worldwide dispersal events. Amplified fragment length polymorphism and single strand conformation polymorphism analyses demonstrate a high degree of genome-wide linkage disequilibrium, which also extends to the mitochondrial genome. Together, these findings indicate distinct patterns of genetic variation of the two species. The low level of genetic diversity observed in C. elegans might reflect a recent human-associated dispersal, whereas the P. pacificus diversity might reflect a long-lasting and ongoing insect association. Thus, despite similar lifestyle characteristics in the laboratory, the reproductive mode of hermaphroditism with rare facultative males can result in distinct genetic variability patterns in different ecological settings.

Differential regulation of msx genes in the development of the gonopodium, an intromittent organ, and of the "sword," a sexually selected trait of swordtail fishes (Xiphophorus).

The possession of a conspicuous extension of colored ventral rays of the caudal fin in male fish of swordtails (genus Xiphophorus) is a prominent example for a trait that evolved by sexual selection. To understand the evolutionary history of this so-called sword molecularly, it is of interest to unravel the developmental pathways responsible for extended growth of sword rays during development of swordtail males. We isolated two msx genes and showed that they are differentially regulated during sword outgrowth. During sword growth in juvenile males, as well as during testosterone-induced sword development and fin ray regeneration in the sword after amputation, expression of msxC is markedly up-regulated in the sword forming fin rays. In contrast, msxE/1 is not differentially expressed in ventral and dorsal male fin rays, suggesting a link between the development of male secondary sexual characters in fins and up-regulation of msxC expression. In addition, we showed that msx gene expression patterns differ significantly between Xiphophorus and zebrafish. We also included in our study the gonopodium, a testosterone-dependent anal fin modification that serves as a fertilization organ in males of live-bearing fishes. Our finding that increased levels of msxC expression are associated with the testosterone-induced outgrowth of the gonopodium might suggest either that at least parts of the signaling pathways that pattern the evolutionary older gonopodium have been coopted to evolve a sexually selected innovation such as the sword or that increased msxC expression may be inherent to the growth process of long fin rays in general.