Species delimitation in poorly known and diverse taxa is usually performed based on monolocus, DNA-­barcoding-­like approaches, while multilocus data are often used to test alternative species hypotheses in well-­studied groups. We combined both approaches to delimit species in the Xenuroturris/Iotyrris complex, a group of venomous marine gastropods from the Indo-P­ acific. First, COI sequences were analysed using three methods of species delimitation to propose primary species hypotheses. Second, RAD sequencing data were also obtained and a maximum-l­ikelihood phylogenetic tree produced. We tested the impact of the level of missing data on the robustness of the phylogenetic tree obtained with the RAD-­seq data. Alternative species partitions revealed with the COI data set were also tested using the RAD-­seq data and the Bayes factor species delimitation method. The congruence between the species hypotheses proposed with the mitochondrial nuclear data sets, together with the morphological variability of the shell and the radula and the distribution pattern, was used to turn the primary species hypotheses into secondary species hypotheses. Allopatric primary species hypotheses defined with the COI gene were interpreted to correspond to intraspecific structure. Most of the species are found sympatrically in the Philippines, and only one is confidently identified as a new species and described as Iotyrris conotaxis n. sp. The results obtained demonstrate the efficiency of the combined monolocus/multilocus approach to delimit species.

ATIMO VATAE, INHACA 2011, MAINBAZA, Restricted, PAPUA NIUGINI, SANTO 2006, TERRASSES

Transcriptome-based exon capture methods provide an approach to recover several hundred markers from genomic DNA, allowing for robust phylogenetic estimation at deep timescales. We applied this method to a highly diverse group of venomous marine snails, Conoidea, for which published phylogenetic trees remain mostly unresolved for the deeper nodes. We targeted 850 protein coding genes (678,322 bp) in ca. 120 samples, spanning all (except one) known families of Conoidea and a broad selection of non-Conoidea neogastropods. The capture was successful for most samples, although capture efficiency decreased when DNA libraries were of insufficient quality and/or quantity (dried samples or low starting DNA concentration) and when targeting the most divergent lineages. An average of 75.4% of proteins was recovered, and the resulting tree, reconstructed using both supermatrix (IQ-tree) and supertree (Astral-II, combined with the Weighted Statistical Binning method) approaches, are almost fully supported. A reconstructed fossil-calibrated tree dates the origin of Conoidea to the Lower Cretaceous. We provide descriptions for two new families. The phylogeny revealed in this study provides a robust framework to reinterpret changes in Conoidea anatomy through time. Finally, we used the phylogeny to test the impact of the venom gland and radular type on diversification rates. Our analyses revealed that repeated losses of the venom gland had no effect on diversification rates, while families with a breadth of radula types showed increases in diversification rates, thus suggesting that trophic ecology may have an impact on the evolution of Conoidea.

ATIMO VATAE, AURORA 2007, BIOPAPUA, CEAMARC-AA, CONCALIS, Restricted, DongSha 2014, EXBODI, GUYANE 2014, ILES DU SALUT, INHACA 2011, KARUBENTHOS 2012, KAVIENG 2014, MAINBAZA, NORFOLK 2, NanHai 2014, PANGLAO 2005, PAPUA NIUGINI, Restricted, SALOMONBOA 3, TAIWAN 2013, TERRASSES, Restricted

Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also a significant percentage of other putative venom components such as chymotrypsin and L-rhamnose-binding lectin. The large majority of conotoxins appeared to be from new gene superfamilies, three of which are highly different from previously reported venom peptide toxins. Their low conotoxin diversity and the type of insulin found suggested that these species, for which no ecological information are available, have a worm or molluscan diet associated with a narrow dietary breadth. Our results indicate that Profundiconus venom is highly distinct from that of other cone snails, and therefore important for examining venom evolution in the Conidae family.

KANACONO

AURORA 2007, INHACA 2011, KAVIENG 2014, PANGLAO 2004, PAPUA NIUGINI, SANTO 2006

For over a decade now, High Throughput sequencing (HTS) approaches have revolutionized phylogenetics, both in terms of data production and methodology. While transcriptomes and (reduced) genomes are increasingly used, generating and analyzing HTS datasets remain expensive, time consuming and complex for most nonmodel taxa. Indeed, a literature survey revealed that 74% of the molecular phylogenetics trees published in 2018 are based on data obtained through Sanger sequencing. In this context, our goal was to identify the strategy that would represent the best compromise among costs, time and robustness of the resulting tree. We sequenced and assembled 32 transcriptomes of the marine mollusk family Turridae, considered as a typical non-model animal taxon. From these data, we extracted the loci most commonly used in gastropod phylogenies (cox1, 12S, 16S, 28S, h3 and 18S), full mitogenomes, and a reduced nuclear transcriptome representation. With each dataset, we reconstructed phylogenies and compared their robustness and accuracy. We discuss the impact of missing data and the use of statistical tests, tree metrics, and supertree and supermatrix methods to further improve phylogenetic data acquisition pipelines. We evaluated the overall costs (time and money) in order to identify the best compromise for phylogenetic data sampling in non-model animal taxa. Although sequencing full mitogenomes seems to constitute the best compromise both in terms of costs and node support, they are known to induce biases in phylogenetic reconstructions. Rather, we recommend to systematically include loci commonly used for phylogenetics and taxonomy (i.e. DNA barcodes, rRNA genes, full mitogenomes, etc.) among the other loci when designing baits for capture.

KANACONO, KAVIENG 2014

Abstract The practice of species delimitation using molecular data commonly leads to the revealing of species complexes and an increase in the number of delimited species. In a few instances, however, DNA-based taxonomy has led to lumping together of previously described species. Here, we delimit species in the genus Cryptogemma (Gastropoda: Conoidea: Turridae), a group of deep-sea snails with a wide geographical distribution, primarily by using the mitochondrial COI gene. Three approaches of species delimitation (ABGD, mPTP and GMYC) were applied to define species partitions. All approaches resulted in eight species. According to previous taxonomic studies and shell morphology, 23 available names potentially apply to the eight Cryptogemma species that were recognized herein. Shell morphometrics, radular characters and geographical and bathymetric distributions were used to link type specimens to these delimited species. In all, 23 of these available names are here attributed to seven species, resulting in 16 synonymizations, and one species is described as new: Cryptogemma powelli sp. nov. We discuss the possible reasons underlying the apparent overdescription of species within Cryptogemma, which is shown here to constitute a rare case of DNA-based species lumping in the hyper-diversified superfamily Conoidea.

ATIMO VATAE, AURORA 2007, BIOMAGLO, BIOPAPUA, CONCALIS, DongSha 2014, EBISCO, EXBODI, GUYANE 2014, KANACONO, KANADEEP, KAVIENG 2014, MADEEP, MAINBAZA, MIRIKY, NORFOLK 2, NanHai 2014, PANGLAO 2004, PAPUA NIUGINI, SALOMON 2, SALOMONBOA 3, TAIWAN 2013, TARASOC, TERRASSES, ZhongSha 2015