Frogs and tuns and tritons - A molecular phylogeny and revised family classification of the predatory gastropod superfamily Tonnoidea (Caenogastropoda).

The Tonnoidea is a moderately diverse group of large, predatory gastropods with ∼360 valid species. Known for their ability to secrete sulfuric acid, they use it to prey on a diversity of invertebrates, primarily echinoderms. Tonnoideans currently are classified in seven accepted families: the comparatively well known, shallow water Bursidae, Cassidae, Personidae, Ranellidae, and Tonnidae, and the lesser-known, deep water Laubierinidae and Pisanianuridae. We assembled a mitochondrial and nuclear gene (COI, 16S, 12S, 28S) dataset for ∼80 species and 38 genera currently recognized as valid. Bayesian analysis of the concatenated dataset recovered a monophyletic Tonnoidea, with Ficus as its sister group. Unexpectedly, Thalassocyon, currently classified in the Ficidae, was nested within the ingroup as the sister group to Distorsionella. Among currently recognized families, Tonnidae, Cassidae, Bursidae and Personidae were supported as monophyletic but the Ranellidae and Ranellinae were not, with Cymatiinae, Ranella and Charonia supported as three unrelated clades. The Laubierinidae and Pisanianuridae together form a monophyletic group. Although not all currently accepted genera have been included in the analysis, the new phylogeny is sufficiently robust and stable to the inclusion/exclusion of nonconserved regions to establish a revised family-level classification with nine families: Bursidae, Cassidae, Charoniidae, Cymatiidae, Laubierinidae, Personidae, Ranellidae, Thalassocyonidae and Tonnidae. The results reveal that many genera as presently circumscribed are para- or polyphyletic and, in some cases support the rescue of several genus-group names from synonymy (Austrosassia, Austrotriton, Laminilabrum, Lampadopsis, Personella, Proxicharonia, Tritonoranella) or conversely, support their synonymization (Biplex with Gyrineum). Several species complexes are also revealed that merit further investigation (e.g., Personidae: Distorsio decipiens, D. reticularis; Bursidae: Bursa tuberosissima; Cassidae: Echinophoria wyvillei, Galeodea bituminata, and Semicassis bisulcata). Consequently, despite their teleplanic larvae, the apparently circumglobal distribution of some tonnoidean species is the result of excessive synonymy. The superfamily is estimated to have diverged during the early Jurassic (∼186 Ma), with most families originating during a narrow ∼20 My window in Albian-Aptian times as part of the Mesozoic Marine Revolution.

Species are hypotheses: avoid connectivity assessments based on pillars of sand.

Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.

New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: insights on systematics and ancestral areas.

The Sicydiinae subfamily (Teleostei: Gobioidei) is the biggest contributor to the diversity of fish communities in river systems of tropical islands. These species are found in the Indo-Pacific area, the Caribbean region and West Africa. They spawn in freshwater, their planktotrophic larvae drift downstream to the sea where they develop, before returning to the rivers to grow and reproduce. Hence, they are called amphidromous. Their phylogeny has been explored using a total of 3545 sites from 5 molecular markers (mitochondrial DNA: 16S rDNA, cytochrome oxidase I, cytochrome b; nuclear DNA: rhodopsin gene and a nuclear marker specially developed for this study, the interferon regulatory factor 2 binding protein 1-IRF2PB1). Sequences were obtained for 59 Sicydiinae specimens of 9 known genera. The Bayesian and maximum likelihood analyses support the monophyly of the subfamily as well as the monophylyof all genera except Sicydium, which is paraphyletic. Five major clades were identified within this subfamily. One clade contained the genus Stiphodon. Another clade contained Sicyopterus, Sicydium and Parasicydium with Sicyopterus as sister genus of Sicydium. The non-monophyly of Sicydium subclade, because it includes the monotypic genus Parasicydium, challenged the validity of Parasicydium genus. Ancestral area reconstruction showed that the subfamily emerged in the Central West Pacific region implying that previous hypotheses proposing a dispersal route for Sicydiinae into the Atlantic Ocean are unsupported by the present analysis. Our results suggest that the hypotheses for the dispersal route of the genus Sicydium should be reconsidered.

Evolution of diadromy in fish: insights from a tropical genus (Kuhlia species).

Diadromous species undergo regular migration between fresh and marine waters. This behavior is found in many species, including fish, mollusks, and crustaceans, some of which are commercially valuable species. Several attempts to trace the evolution of this behavior have been made in Salmonidae and Galaxiidae, but ambiguous phylogenies and multiple character state changes prevented unequivocal conclusions. The Kuhliidae family consists of 12 fish species that inhabit tropical islands in the Indo-Pacific region. The species have marine, partially catadromous, or fully catadromous life histories (i.e., they migrate from rivers to the sea to reproduce). The evolution of migratory behavior was traced on a well-resolved phylogeny. Catadromous Kuhlia species were basal, and partially catadromous and marine species formed derived monophyletic groups. This is, to our knowledge, the first time that a clear origin and polarity for the diadromous character has been demonstrated. We propose that the relative lack of resources in tropical, inshore, marine habitats and the ephemeral and isolated nature of freshwater environments of tropical islands, combined with phenotypic plasticity of migratory traits, play key roles in driving the evolution of diadromy in the Kuhliidae and probably in other groups. This work is an important starting point to understand the role of diadromy in speciation and adaptation in unstable habitats.

Elephantis, a new genus for Caridina natalensis Bouvier, 1925 from eastern rivers of Madagascar.

Elephantis, new genus, is established for Caridina natalensis Bouvier, 1925 hitherto known only from South Africa with one male specimen. Recently, three surveys by electric fishing (2004, 2008 and 2010) of some eastern rivers from Madagascar have permitted to discover numerous specimens of this species. Caridina natalensis is different from all other known species of Caridina by its remarkably broad endopod of the male first pleopod, a long clubbed appendix masculina on the male second pleopod reaching beyond distal end of endopod and strong third pereiopods. Therefore a new genus name is proposed for this species. In addition to detailed description of diagnostic morphological characters, molecular sequences obtained from mitochondrial 16S gene are provided for six specimens of this species. These DNA sequences are integrated to the 16S molecular phylogeny of atyid freshwater shrimps recently published by von Rintelen et al. (2012). Elephantis natalensis comb. nov. sequences formed a divergent group supported in maximum likelihood analysis. The availability of DNA samples could be used as reference and integrated in further phylogenetic studies on atyid freshwater shrimps.

Deep-sea benthic communities in the largest oceanic desert are structured by the presence of polymetallic crust.

Based on the specimens collected during three deep-sea cruises, and deposited at the Muséum National d'Histoire Naturelle (MNHN) in Paris, we analysed the diversity of benthic communities within the EEZ of French Polynesia. The literature and the MNHN database allowed us to inventory 471 species of invertebrates, among which 169 were newly described. We mainly found data for Mollusca, Crustacea, Brachiopoda and Crinoidea. We also found samples from other taxa, which still remain unidentified within the collections of the MNHN. Although this inventory is incomplete, we demonstrate that the deep waters of French Polynesia host unique benthic communities and endemic species. Using diversity and multivariate analyses, we show that the deep-sea benthic communities are structured by depth, habitats, geography and also by the presence of polymetallic crust. Furthermore, by focusing on the molluscs of the central area of French Polynesia, we show that the spectrum of shell size differs among deep-sea habitats. Specifically, shells tend to be smaller on encrusted seamounts than on island slopes. Together with the size range of organisms, low abundance, rarity and endemism designate these habitats as sensitive. These results should thus be taken into account in the evaluation of the expected impact of mining activities on biological communities.

Revalidation of Caridina natalensis De Man, 1908 (Crustacea: Decapoda: Atyidae) in the South Western Indian Ocean.

Numerous specimens of a freshwater shrimp with small eggs belonging to the Caridina nilotica complex collected in the South Western Indian Ocean were studied and compared with recent and old collection specimens genetically (16S mitochondrial analysis for recent and type specimens) and morphologically. The results revealed that, in the Indian Ocean, what has been identified by several authors under various species names of the complex C. nilotica, was in fact C. natalensis De Man, 1908. This valid species is re-described and compared with closely related species, often confused with it in this area: C. brachydactyla De Man, 1908, C. brevidactyla Roux, 1920, C. gracilipes De Man, 1892 and C. longirostris H. Milne Edwards, 1837.

Phylogenetic species delimitation for crayfishes of the genus Pacifastacus.

Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genus Pacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly, Pacifastacus includes both the widely invasive signal crayfish Pacifastacus leniusculus, as well as several species of conservation concern like the Shasta crayfish Pacifastacus fortis. Our analysis used 83 individuals sampled across the four extant Pacifastacus species (omitting the extinct Pacifastacus nigrescens), representing the known taxonomic diversity and geographic distributions within this genus as comprehensively as possible. We reconstructed phylogenetic trees from mitochondrial (16S, COI) and nuclear genes (GAPDH), both separately and using a combined or concatenated dataset, and performed several species delimitation analyses (PTP, ABGD, GMYC) on the COI phylogeny to propose Primary Species Hypotheses (PSHs) within the genus. All phylogenies recovered the genus Pacifastacus as monophyletic, within which we identified a range of six to 21 PSHs; more abundant PSHs delimitations from GMYC and ABGD were always nested within PSHs delimited by the more conservative PTP method. Pacifastacus leniusculus included the majority of PSHs and was not monophyletic relative to the other Pacifastacus species considered. Several of these highly distinct P. leniusculus PSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities for Pacifastacus crayfishes in western North America, and may inform better understanding and management of P. leniusculus in regions where it is invasive, such as Europe and Japan.

New primers for DNA barcoding of digeneans and cestodes (Platyhelminthes).

Digeneans and cestodes are species-rich taxa and can seriously impact human health, fisheries, aqua- and agriculture, and wildlife conservation and management. DNA barcoding using the COI Folmer region could be applied for species detection and identification, but both 'universal' and taxon-specific COI primers fail to amplify in many flatworm taxa. We found that high levels of nucleotide variation at priming sites made it unrealistic to design primers targeting all flatworms. We developed new degenerate primers that enabled acquisition of the COI barcode region from 100% of specimens tested (n = 46), representing 23 families of digeneans and 6 orders of cestodes. This high success rate represents an improvement over existing methods. Primers and methods provided here are critical pieces towards redressing the current paucity of COI barcodes for these taxa in public databases.

A good compromise: rapid and robust species proxies for inventorying biodiversity hotspots using the Terebridae (Gastropoda: Conoidea).

Devising a reproducible approach for species delimitation of hyperdiverse groups is an ongoing challenge in evolutionary biology. Speciation processes combine modes of passive and adaptive trait divergence requiring an integrative taxonomy approach to accurately generate robust species hypotheses. However, in light of the rapid decline of diversity on Earth, complete integrative approaches may not be practical in certain species-rich environments. As an alternative, we applied a two-step strategy combining ABGD (Automated Barcode Gap Discovery) and Klee diagrams, to balance speed and accuracy in producing primary species hypotheses (PSHs). Specifically, an ABGD/Klee approach was used for species delimitation in the Terebridae, a neurotoxin-producing marine snail family included in the Conoidea. Delimitation of species boundaries is problematic in the Conoidea, as traditional taxonomic approaches are hampered by the high levels of variation, convergence and morphological plasticity of shell characters. We used ABGD to analyze gaps in the distribution of pairwise distances of 454 COI sequences attributed to 87 morphospecies and obtained 98 to 125 Primary Species Hypotheses (PSHs). The PSH partitions were subsequently visualized as a Klee diagram color map, allowing easy detection of the incongruences that were further evaluated individually with two other species delimitation models, General Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP). GMYC and PTP results confirmed the presence of 17 putative cryptic terebrid species in our dataset. The consensus of GMYC, PTP, and ABGD/Klee findings suggest the combination of ABGD and Klee diagrams is an effective approach for rapidly proposing primary species proxies in hyperdiverse groups and a reliable first step for macroscopic biodiversity assessment.

Contrasting genetic structure among populations of two amphidromous fish species (Sicydiinae) in the Central West Pacific.

Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9-0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79-625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion.