Molecular taxonomy reveals broad trans-oceanic distributions and high species diversity of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) in chemosynthetic environments

Large vesicomyid clams are common inhabitants of sulphidic deep-sea habitats such as hydrothermal vents, hydrocarbon seeps and whale-falls. Yet, the species- and genus-level taxonomy of these diverse clams has been unstable due to insufficiencies in sampling and absence of detailed taxonomic studies that would consistently compare molecular and morphological characters. To clarify uncertainties about species-level assignments, we examined DNA sequences from mitochondrial cytochrome-c-oxidase subunit I (COI) in conjunction with morphological characters. New and published COI sequences were used to create a molecular database for 44 unique evolutionary lineages corresponding to species. Overall, the congruence between molecular and morphological characters was good. Several discrepancies due to synonymous species designations were recognized, and acceptable species names were rectified with published COI sequences in cases where morphological specimens were available. We identified seven species with trans-Pacific distributions, and two species with Indo-Pacific distributions. Presently, 27 species have only been documented from one region, which might reflect limited ranges, or insufficient geographical sampling. Vesicomyids exhibit the greatest species diversity along the northwest Pacific ridge systems and in the eastern Pacific, along the western America margin, where depth zonation typically results in segregation of closely related species. The broad distributions of several vesicomyid species suggest that their required chemosynthetic habitats might be more common than previously recognized and occur along most continental margins.     

Unravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciation

The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two‐fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly‐identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97 , 200–216.     

The smaller vesicomyid bivalves in the genus Isorropodon (Bivalvia, Vesicomyidae, Pliocardiinae) also harbour chemoautotrophic symbionts

Species of Isorropodon are vesicomyid bivalves for which little information is available regarding host phylogeny and bacterial symbioses. In this study we investigated the symbioses in three Isorropodon species from three cold seep areas: Isorropodon bigoti (Gulf of Guinea), Isorropodon megadesmus (Gulf of Cadiz) and Isorropodon perplexum (Eastern Mediterranean). Analysis of bacterial 16S ribosomal RNA gene sequences demonstrated that each vesicomyid species harbours a single symbiont phylotype, that symbionts from the three species cluster together, and that they are closely related to other known vesicomyid symbionts. These results are confirmed by other marker genes (encoding 23S rRNA and APS reductase) and by fluorescence in situ hybridization. Due to their extended depth range and transoceanic distribution Isorropodon species are interesting examples to further study evolutionary processes in bivalve hosts and their associated symbionts.     

Morphological and molecular variation in tiger beetles of the Cicindela hybrida complex: is an ‘integrative taxonomy’ possible?

Current taxon assignments at the species level are frequently discordant with DNA-based analyses. Recent studies on tiger beetles in the Cicindela hybrida complex identified discordance between mtDNA patterns and the entities currently defined by the taxonomic literature. To test the accuracy of morphologically delimited groups, five named taxa (species) from 24 representative sampling sites across Europe were scored for 41 external morphological characters. Three of the named taxa were 'diagnosable', that is, defined by between one and three characters unique to each group. Newly sequenced ITS1 and existing mitochondrial cox1 markers established 20 and 22 different haplotypes, respectively, but only cox1 produced (four) diagnosable units. Phylogenetic analysis and statistical parsimony networks showed poor congruence of character variation with the taxonomic entities (and each other). Variation in morphological characters was therefore tested directly for association with DNA-based nesting groups at various hierarchical levels using permutational contingency analysis. Significant statistical associations of 11 (of 13 variable) morphological characters were observed with nesting groups from ITS1 and mitochondrial DNA markers, predominantly at the 4-step level. The analysis demonstrates the need for formal tests of congruence with morphological variation at the level of individual characters, a step that is omitted from recent studies of 'integrative taxonomy'. In addition, statistical correlation of particular morphological characters with DNA-based nesting groups can identify the lowest hierarchical level at which various character sets show congruence, as a means to define evolutionarily separated entities supported by diverse data sources.     

Molecular phylogeny of Pholadoidea Lamarck, 1809 supports a single origin for xylotrophy (wood feeding) and xylotrophic bacterial endosymbiosis in Bivalvia

The ability to consume wood as food (xylotrophy) is unusual among animals. In terrestrial environments, termites and other xylotrophic insects are the principle wood consumers while in marine environments wood-boring bivalves fulfill this role. However, the evolutionary origin of wood feeding in bivalves has remained largely unexplored. Here we provide data indicating that xylotrophy has arisen just once in Bivalvia in a single wood-feeding bivalve lineage that subsequently diversified into distinct shallow- and deep-water branches, both of which have been broadly successful in colonizing the world’s oceans. These data also suggest that the appearance of this remarkable life habit was approximately coincident with the acquisition of bacterial endosymbionts. Here we generate a robust phylogeny for xylotrophic bivalves and related species based on sequences of small and large subunit nuclear rRNA genes. We then trace the distribution among the modern taxa of morphological characters and character states associated with xylotrophy and xylotrepesis (wood-boring) and use a parsimony-based method to infer their ancestral states. Based on these ancestral state reconstructions we propose a set of plausible hypotheses describing the evolution of symbiotic xylotrophy in Bivalvia. Within this context, we reinterpret one of the most remarkable progressions in bivalve evolution, the transformation of the “typical” myoid body plan to create a unique lineage of worm-like, tube-forming, wood-feeding clams. The well-supported phylogeny presented here is inconsistent with most taxonomic treatments for xylotrophic bivalves, indicating that the bivalve family Pholadidae and the subfamilies Teredininae and Bankiinae of the family Teredinidae are non-monophyletic, and that the principle traits used for their taxonomic diagnosis are phylogenetically misleading.     

SPECIES DISCRIMINATION AND EVOLUTIONARY MODE OF BUCHIA (BIVALVIA: BUCHIIDAE) FROM UPPER JURASSIC–LOWER CRETACEOUS STRATA OF GRASSY ISLAND, BRITISH COLUMBIA, CANADA

Abstract: Buchiid bivalves are geographically widespread in Upper Jurassic and Lower Cretaceous strata of the Northern Hemisphere. They are often abundant and their short stratigraphic ranges make them ideal biostratigraphic index fossils; these characteristics also render them useful for study of evolutionary patterns. We used multivariate methods to determine if we could discriminate between species of Buchia and examine how morphological characters change through time within the genus. Using ten morphological characters to describe shell shape and size, we tested for taxonomic differences and morphologic change in populations of buchiids collected from a single stratigraphic section on Grassy Island, located along the west coast of Vancouver Island, British Columbia. Morphometric analysis utilized traditional morphological metrics and techniques, including linear and angular measurements as well as Fourier (outline shape) analyses. Phenetic discrimination revealed considerable overlap among the recognized species in the morphospace, as well as a fairly low discriminatory power between species when compared as a group using a step‐wise canonical variate analysis. Step‐wise discriminant analyses between species pairs gave rise to much higher classification rates, suggesting that different characters are important for distinguishing between different species pairs. Our results also indicate that single individuals and small sample sizes of Buchia specimens are insufficient for biostratigraphic discrimination (unless other rarely preserved features such as the hinge and bysuss ear are available) and that a number of previously described species variants may not be taxonomically valid. A biolog using the multivariate axis that best discriminates between species (CV1) and a random walk‐based test using a Hurst estimate analysis indicate a gradualistic evolutionary mode for the Buchia species of Grassy Island. Shell shape and size of buchiids do not appear to be closely tied to lithofacies changes over the c. 10 myr time interval, suggesting that ecophenotypic variation (as it relates to substrate changes) probably had minimal influence on morphology.     

Taxonomic implication of embryo micromorphology in the genus <Emphasis Type="Italic">Vicia</Emphasis> L. (Fabaceae)

In this work, embryos of selected Vicia species were examined to reveal the micromorphological characters that could have taxonomic significance. Experimental results show that morphological characters such as cotyledons shape and colour, radicle shape, colour and position, plumule colour and stipular parts attachments are variable and could be used for taxa identification in the genus Vicia. Numerical analysis based on 38 micromorphological characters was used to build a phenogram that indicated the relationships among the studied taxa. In addition, an identification key using embryo characters was prepared for Vicia species. The variability of embryo characters were discussed in the taxonomic context. Although the embryo characters have only limited phylogenetic signal for Vicia species, they might be used for their morphological delimitation.     

Quantitative morphology and species delimitation under the general lineage concept: Optimization for Hedera (Araliaceae)

? Premise of the study: The use of continuous morphological characters in taxonomy is traditionally contingent on the existence of discrete diagnostic characters. When plant species are the result of recent divergence and gene flow and/or hybridization occur, the use of continuous morphological characters may help in species identification and delimitation. Between nine and 15 species have been recognized in the last treatments of Hedera. The recent divergence of the species and the involvement of allopolyploidization as the main force in this process may have greatly impeded the establishment of clear limits and contributed to multiple taxonomic proposals. ? Methods: A multivariate statistical decision-making procedure was applied to 56 quantitative morphological characters and 602 specimens to identify and delimit Hedera species under the general lineage concept. Species' exclusive genetic ancestry was evaluated with the genealogical sorting index from the Bayesian inference trees of 30 Hedera ITS sequences. ? Key results: The decision-making procedure allowed recognizing 12 species and two groups (stellate and scale-like trichome groups) in Hedera and provided statistical support for making decisions about long-standing taxonomic controversies. Common ancestry was detected for the populations of three species even in the absence of the species monophyly. ? Conclusions: Quantitative variation supports discrete variation and provides statistical support for the taxa recognized in some recent proposals of Hedera. The need of explicit analysis of quantitative data are claimed to reduce taxonomic subjectivity and ease decision-making when qualitative data fail.     

SPECIES CONCEPTS IN THE GENUSUSNEA(LICHENIZED ASCOMYCETES)

Practically most of the taxonomists working on vascular plants and fungi are using the so-called taxonomic species concept, relying largely on morphological criteria or other observable patterns of discontinuity and assuming that these patterns are reflecting the underlying genetic integrity of species. Such a concept is described in detail here for the genusUsnea. The typological view versus the populational view of species are discussed. The diagnostic value of characters used by previous and recent taxonomists of the genus is analysed. The fact thatUsneahas such a bad taxonomic reputation is discussed. The use by J. Motyka, author of the world monograph published in the thirties, of characters that are strongly modified by environmental factors together with a typological view of species are thought to be mainly responsible for this. More than 770 names have been published worldwide so far and it is suggested that around 50% are to be considered as synonyms.     

Integrated taxonomy of the <Emphasis Type="Italic">Asplenium normale</Emphasis> complex (Aspleniaceae) in China and adjacent areas

The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.     

Halichondrids or axinellids? Some problematic genera of sponges with descriptions of new species from the Strait of Gibraltar (southern Iberian Peninsula)

The axinellids and the halichondrids are two of the most conflictive sponge groups from a taxonomic point of view, owing to the simplicity of the morphological characters that would allow discrimination between taxa at a supraspecific level. In this sense, some of the species dealt with in this study provide an example of the controversy that exists when a species must be assigned to one of these groups. The species Axinyssa digitata is redescribed. We also propose to move the species Dictyonella madeirensis to the genus Scopalina , and the validity of the recent family Dictyonellidae Soest, Diaz & Pomponi (1990) is supported. Moreover, two new species are described: Dictyonella alonsoi , characterized by thick monactine megascleres which undergo different tip modifications, and Ciocalapata almae , characterized by the presence of anisostrongyloxeas in two size categories together with oxeas.     

Intraspecific taxonomic differentiation in ticks (Acari: Ixodidae) in the view of the morphological conception of species

The criterions for two most used intraspecific taxonomic ranks of ticks--subspecies and morphotype, have been formulated on the basis of the study of morphological variation in the distribution range of all active ontogenetic stages of 11 polymorphic species. All these species are vectors of transmissible diseases. They have vast distribution ranges and different types of host-parasite relationships. Subspecies have the complexes of visual morphological differences expressed in one or both sexes of mature ticks more limited, than those of related species. At immature stages differences of subspecies consist more often in morphometric characters and can be established by the methods of mathematical statistics only. Morphotypes, as a rule, differ at each corresponding stage by "their own" complexes of morphometric characters. All differential parameters of studied morphotypes are overlapped, but have statistically significant differences (by the Student's test). The concrete variations of differentiation by subspecies and morphotypes have been considered. The historical factors of intraspecific differentiation have been reconstructed for each species.     

Tracking the variability of phenotypic traits on a molecular phylogeny: an example from scolopendrid centipedes in peninsular India

Taxonomic studies on scolopendrid centipedes have often documented variability at the individual and population levels and applied those data to questions of species delimitation, but these investigations have mostly lacked an explicit phylogenetic framework. A molecular phylogeny and recent taxonomic revision for Indian species of the scolopendrid Digitipes Attems, 1930, permit variability of traditional taxonomic characters for Scolopendridae to be mapped onto a phylogeny. Based on their fit to the tree using maximum likelihood, reliable species-level characters include the number of glabrous antennal articles, presence of a median ridge on the tergites, and presence or absence of a tarsal spur on leg 20. Characters that are conserved within and diagnostic for particular species but labile within others (typically with geographic structure) include the first tergite with paramedian sutures, presence or absence of a lateral spine on the coxopleuron, and the number of spines in a ventromedial row on the ultimate leg prefemur. Comparisons with published accounts of variability in species of other scolopendrid genera, particularly Scolopendra and Otostigmus, show that Indian Digitipes has conserved morphology in some characters that are taxonomically useful elsewhere in the family, and most of its taxonomically informative characters have analogous patterns of variability in other genera. The approach used in this study to evaluate morphological variation in a phylogenetic framework can be applied to other taxa in which morphologically cryptic species have been reported and where species diagnosis requires a combination of characters.     

Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe

Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.     

Taxonomic revision of the Mediterranean Plakina Schulze (Porifera, Demospongiae, Homoscleromorpha)

Only three species of the sponge genus Plakina Schulze have been described from the Mediterranean since 1880, in spite of a large amount of allegedly intraspecific variability in morphological characters. However, recent genetic studies based on electrophoretic techniques have revealed extensive cryptic speciation in north-western Mediterranean Plakina , demonstrating that most of this variation was interspecific rather than intraspecific. We describe in detail the morphology and anatomy of four new species of Plakina from the Mediterranean– P. crypta, P. weinbergi, P. endoumensis and P. jani –of which the latter two were discovered through allozyme electrophoresis. Plakina monolopha Schulze and P. trilopha Schulze are redescribed, and their morphological and geographical limits are discussed along with those of P. dilopha Schulze. Accurate analysis of the internal anatomy and of the shape and ramification pattern of lophose spicules in scanning electron microscopy provides new, powerful morphological criteria for species discrimination in Plakina. More widespread use of such new taxonomic characters should provide evidence against the alleged cosmopolitanism of some Plakina species, thus generating an increase in estimates of the biodiversity of plakinids.     

INTERSPECIFIC AND INTRASPECIFIC MORPHOLOGICAL VARIATION IN MANATEES (SIRENIA: TRICHECHUS)

The three living species of Trichechus are clearly defined and well exemplify the degree of variability and taxonomic value of morphological characters in a well-understood mammalian genus. Statistical analysis of the largest sample of manatee skulls yet studied has allowed us to identify small suites of characters that effectively distinguish these species. The two subspecies of T. manatus proposed by Hatt (1934) can likewise be distinguished, and their use as taxonomic categories seems justified. This suggests that the cool winters of the northern Gulf Coast, on the one hand, and the deep water and strong currents of the Straits of Florida, on the other, are effective barriers to gene flow between Florida and Antillean manatees. Alleged taxonomic distinctions within T. senegalensis , however, have no demonstrated basis. No significant sexual dimorphism was detected in skulls of any of the species. Many interspecific differences can be correlated with feeding ecology, but others remain unexplained. Features of tooth crown morphology are among the most constant characters examined, but some osteological characters are equally good. T. manatas and T. senegalensis (which are phenetically the most similar) also seem to share a more recent common ancestor than either does with T. inunguis. However, the three species probably separated from each other at nearly the same time. T. inunguis has since become the most derived species, while T. senegalensis has changed the least.     

Colour patterns do not diagnose species: quantitative evaluation of a DNA barcoded cryptic bumblebee complex

Cryptic diversity within bumblebees (Bombus) has the potential to undermine crucial conservation efforts designed to reverse the observed decline in many bumblebee species worldwide. Central to such efforts is the ability to correctly recognise and diagnose species. The B. lucorum complex (Bombus lucorum, B. cryptarum and B. magnus) comprises one of the most abundant and important group of wild plant and crop pollinators in northern Europe. Although the workers of these species are notoriously difficult to diagnose morphologically, it has been claimed that queens are readily diagnosable from morphological characters. Here we assess the value of colour-pattern characters in species identification of DNA-barcoded queens from the B. lucorum complex. Three distinct molecular operational taxonomic units were identified each representing one species. However, no uniquely diagnostic colour-pattern character state was found for any of these three molecular units and most colour-pattern characters showed continuous variation among the units. All characters previously deemed to be unique and diagnostic for one species were displayed by specimens molecularly identified as a different species. These results presented here raise questions on the reliability of species determinations in previous studies and highlights the benefits of implementing DNA barcoding prior to ecological, taxonomic and conservation studies of these important key pollinators.     

Relationship between song characters and morphology in New World pigeons

We studied the pattern of variation in song characters among 16 New World pigeon species belonging to different taxonomic groups defined by morphological characters. Structural, temporal and frequency characters of the song were analysed. Principal components analyses showed that species belonging to the same taxonomic group were also grouped together by their song characters. In addition, individuals were correctly assigned into taxonomic groups by discriminant function analyses in more than 87.8% of cases. These analyses also showed that more than 87.5% of the individuals could be correctly classified by species when all song characters were included. Correct classification of individuals by species and taxonomic groups dropped when character types were analysed separately, thus showing that structural, as well as temporal and frequency characters are fundamental to define species- and group-specific identities of New World pigeon's songs. Correspondence between patterns of vocal and morphological variation found in this study can be a consequence of evolutionary changes in morphology affecting song production, as for example body size changes that constrain the syrinx to produce certain acoustic frequencies.