Lost branches on the tree of life.

摘要: Given that reproducibility is a pillar of scientific research, the preservation knowledge (underlying data) paramount importance. The standard can be evaluated based on criteria methodological rigor and legitimacy, which sometimes used to distinguish “hard” from “soft” sciences. In phylogenetics, discipline routinely uses DNA sequences build trees reflecting organismal relationships, scale data collection complexity analytical software have both increased dramatically during past decade. Consequently, ability navigate publications reproduce analyses more challenging than ever. When sequencing was initially employed in systematics late 1980s, there some reluctance deposit nucleotide open repositories such as GenBank [1]. This ultimately changed when high-impact journals (e.g., Proceedings National Academy Sciences, Nature, Science) began requiring submission prerequisite for publication [1],[2]; now virtually every evolutionary biology journal observes this requirement (but see [3]). Until recently, uploading (or EMBL) generally considered sufficient ensure phylogenetic studies using sequence data. Increasingly, however, community realizing archiving raw not adequate, underlying alignments well resulting are pivotal reproducibility, comparative purposes, meta-analyses, synthesis. Indeed, has been growing clamor adopt enforce rigorous practices across diverse disciplines [4]–[8]. As result, about 35 [5],[9] adopted policies encourage or require authors upload alignments, trees, other files requisite study [5] TreeBASE (http://treebase.org/) and/or public Dryad (http://datadryad.org). Unfortunately, enforcement deposition lax, most evolution still do alignment tree deposition. published papers systematics/phylogenetics remain inaccessible at large [8],[10].