While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org).

The superfamily Buccinoidea is distributed across the oceans of the world from the Arctic Ocean to the Antarctic and from intertidal to abyssal depths. It encompasses 3351 recent species in 337 genera. The latest taxonomic account recognized eight full families. For the first time, the monophyly of the superfamily and the relationships among the families are tested with molecular data supplemented by anatomical and radula data. Five genetic markers were used: fragments of mitochondrial COI, 16S rRNA, 12S rRNA and nuclear Histone 3 (H3) and 28S rRNA genes (for 225 species of 117 genera). Our analysis recovered Buccinoidea monophyletic in Bayesian analyses. The relationships between the formerly recognized families and subfamilies are drastically revised and a new classification of the superfamily is here proposed, now including 20 taxa of family rank and 23 subfamilies. Five new families (Chauvetiidae, Dolicholatiridae, Eosiphonidae, Prodotiidae and Retimohniidae) and one subfamily of Nassariidae (Tomliniinae) are described. Austrosiphonidae and Tudiclidae are resurrected from synonymy and employed in a new taxonomical extension. All but 40 recent genera are reclassified. Our results demonstrate that anatomy is rather uniform within the superfamily. With exceptions, the rather uniform radular morphology alone does not allow the allocation of genera to a particular family without additional molecular data.

With about 800 Recent species, ‘miters’ are a widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West P

The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in the early stages of diversification, generating a “bush” at the base of their evolutionary tree, which has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, 3 prove problematic: First, the uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major “core Neogastropoda” grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analyzed phylogenetic signal of targeted loci in relation to potential biases, and we propose the most probable resolutions in the latter 2 recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.