Molecular phylogeny of Columbellidae (Gastropoda: Neogastropoda)

The neogastropod family Columbellidae is a highly successful group of small, primarily epibenthic marine snails distributed worldwide and most abundant in the tropics. The great diversity of the group makes them attractive for studying evolutionary shifts in gastropod anatomy, morphology, ecology and diversity. The existing classification of the family has been based to a large degree on the morphology of the shell and radula. Indeed, membership in the family is traditionally confirmed using the unique morphology of the radula. To reconstruct columbellid phylogeny and assess monophyly of the group, we assembled a multilocus dataset including five mitochondrial and nuclear genes, for 70 species in 31 genera. Phylogenetic analyses using Bayesian inference and maximum likelihood are not well enough resolved to support a subfamilial classification, but do support the monophyly of the family and of several well-defined genera and supra-generic groupings. Two of the most diverse nominal genera, Mitrella and Anachis, are supported as highly polyphyletic. Overall, the resulting topologies indicate that the generic and subfamilial classification is in need of extensive revision but that phylogenomic data are needed to resolve columbellid relationships.

New insights into the evolution of portunoid swimming crabs (Portunoidea, Heterotremata, Brachyura) and the brachyuran axial skeleton

Portunoidea (Heterotremata) is a morphologically disparate taxon of true crabs (Brachyura) best-known for many of its representatives being considered "swimming crabs". The term "swimming crab", however, sometimes refers to a distinct taxon (traditionally to Portunidae within Portunoidea), and sometimes to a certain morphotype in which the 5th pereiopod (P5) has a specific shape that facilitates swimming. We use the term "P5-swimming crab" or "P5-swimmer" herein, not only to restrict it to the morphotype, but also to distinguish the swimming in question from other kinds of swimming in Brachyura. The evolution of P5-swimming crabs has not yet been satisfactorily investigated. In particular, it is not known whether the morphotype evolved several times independently in different lineages of Portunoidea or whether it evolved only once and was lost in several lineages. Ours is the first approach combining molecular with morphological data to result in a new phylogenetic positioning of some members of Portunoidea. For the first time, data from the axial skeleton and extrinsic musculature are used. Morphological examinations reveal that the axial skeleton and extrinsic musculature in P5-swimming crabs are more diverse than previously thought, with the exception of the P5 anterior coxa muscle, which originates at the median plate in all P5-swimmers. Ancestral state reconstructions based on parsimony reveal that the stem species of Portunoidea already showed the morphotype of a P5-swimming crab, but with a long merus which probably resulted in less effective P5-swimming than in extant P5-swimming crab species with a short merus. Several other extant taxa represent a reversal of the P5-swimmer morphotype to varying degrees, with some extant species showing a complete reversal of unambiguous P5-swimming crab character states-one example being the well-known common shore crab Carcinus maenas. The absence of a connection between interosternite 7/8 and the sella turcica (the secondary loss of the "brachyuran sella turcica") in the stem species of Heterotremata, resulting in a junction plate which forms a cavity that offers room and attachment sites for the P5 extrinsic musculature is uncovered as preadaptation to the P5-swimmer morphotype in Heterotremata. This preadaptation is missing in Podotremata and Thoracotremata, the other two traditional main taxa of Brachyura.

Size Doesn't Matter: Integrative Taxonomy Shows Crepidula adunca and Crepidula norrisiarum Have Overlapping Shell Sizes and Broadly Concordant Distributions

AbstractThe calyptraeids Crepidula adunca and Crepidula norrisiarum, both direct developers, are abundant in the shallow waters of the northeastern Pacific. They have long been considered as two allopatric species that live on different hosts and differ in body size. In this study, we rigorously test this historical hypothesis by assessing molecular taxonomy, museum records, new morphological and host observations, and population genetic structure along the northeast Pacific coast. Results show that, contrary to previous understanding, the distributions of the two species largely overlap and that size does not effectively distinguish them, especially in the northern part of the range where the nominal "C. adunca" has been studied. Newly recognized northern occurrences of C. norrisiarum demonstrate that both species have similar, disrupted distributions that range from British Colombia through southern California. Neither species is reported to occur on the outer shores of southern Washington or Oregon, the exception being records of C. adunca at Cape Arago, Oregon. Despite this apparent geographic gap, neither species shows appreciable genetic differentiation between the northern and southern parts of its ranges. Despite body size having been used to distinguish these species, our observations do not support body size as a species-specific trait; rather, they support a new hypothesis that body size variation reflects regional differences in host use and host availability.

The complete mitogenome of the invasive Japanese mud snail Batillaria attramentaria (Gastropoda: Batillariidae) from Elkhorn Slough, California, USA

Genomic analysis of the invasive marine snail Batillaria attramentaria from Elkhorn Slough, Moss Landing, California, USA using 150 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,095 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank Accession MN557850). Gene content and organization of B. attramentaria are identical to the Turritellidae and Pachychilidae. The phylogenetic analysis of B. attramentaria resolves it in a fully supported clade with these same two families in the superfamily Cerithioidea. Nucleotide BLAST searches of the Elkhorn Slough cox1 gene of B. attramentaria yielded identical sequences from invasive populations from California and British Columbia, and native populations from northeastern and central Japan. These data show that mitogenome sequencing is a useful tool for studying the classification and phylogenetic history Cerithioidea.

DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.

Problems and Questions Posed by Cryptic Species. A Framework to Guide Future Studies

Species are the currency of biology and important units of biodiversity, thus errors in species delimitations potentially have important consequences. During the last decades, owing to the use of genetic markers, many nominal species appeared to consist of several reproductively isolated entities called cryptic species (hereafter CS). In this chapter we explain why CS are important for practical reasons related to community and ecosystem monitoring, and for biological knowledge, particularly for understanding ecological and evolutionary processes. To find solutions to practical problems and to correct biological errors, a thorough analysis of the distinct types of CS reported in the literature is necessary and some general rules have to be identified. Here we explain how to identify CS, and we propose a rational and practical classification of CS (and putative CS), based on the crossing of distinct levels of genetic isolation with distinct levels of morphological differentiation. We also explain how to identify likely explanations for a given CS (either inherent to taxonomic processes or related to taxon biology, ecology and geography) and how to build a comprehensive database aimed at answering these practical and theoretical questions. Our pilot review of the literature in marine animals established that half of the reported cases are not CS sensu stricto (i.e. where morphology cannot distinguish the entities) and just need taxonomic revision. It also revealed significant associations between CS features, such as a higher proportion of diagnostic morphological differences in sympatric than in allopatric CS and more frequent ecological differentiation between sympatric than allopatric CS, both observations supporting the competitive exclusion theory, thus suggesting that ignoring CS causes not only species diversity but also functional diversity underestimation.