Accurate and efficient reconstruction of deep phylogenies from structured RNAs

Molecular phylogeny of mega-diverse Carabus attests late Miocene evolution of alpine environments in the Himalayan-Tibetan Orogen

The timing, sequence, and scale of uplift of the Himalayan-Tibetan Orogen (HTO) are controversially debated. Many geoscientific studies assume paleoelevations close to present-day elevations and the existence of alpine environments across the HTO already in the late Paleogene, contradicting fossil data. Using molecular genetic data of ground beetles, we aim to reconstruct the paleoenvironmental history of the HTO, focusing on its southern margin (Himalayas, South Tibet). Based on a comprehensive sampling of extratropical Carabus, and ~ 10,000 bp of mitochondrial and nuclear DNA we applied Bayesian and Maximum likelihood methods to infer the phylogenetic relationships. We show that Carabus arrived in the HTO at the Oligocene-Miocene boundary. During the early Miocene, five lineages diversified in different parts of the HTO, initially in its southern center and on its eastern margin. Evolution of alpine taxa occurred during the late Miocene. There were apparently no habitats for Carabus before the late Oligocene. Until the Late Oligocene elevations must have been low throughout the HTO. Temperate forests emerged in South Tibet in the late Oligocene at the earliest. Alpine environments developed in the HTO from the late Miocene and, in large scale, during the Pliocene-Quaternary. Findings are consistent with fossil records but contrast with uplift models recovered from stable isotope paleoaltimetry.

Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea)

The SSU nrDNA, a small subunit of the nuclear ribosomal DNA (coding 18S rRNA), is one of the most frequently sequenced genes in molecular studies in Hexapoda. In insects, including true bugs (Hemiptera: Heteroptera), only its primary structures (i.e., aligned sequences) are predominantly used in phylogenetic reconstructions. It is known that including RNA secondary structures in the alignment procedure is essential for improving accuracy and robustness in phylogenetic tree reconstruction. Moreover, local plasticity in rRNAs might impact their tertiary structures and corresponding functions. To determine the systematic position of Thaumastellidae within the superfamily Pentatomoidea, the secondary and-for the first time among all Hexapoda-tertiary structures of 18S rRNAs in twelve pentatomoid families were compared and analysed. Results indicate that the shapes of the secondary and tertiary structures of the length-variable regions (LVRs) in the 18S rRNA are phylogenetically highly informative. Based on these results, it is suggested that the Thaumastellidae is maintained as an independent family within the superfamily Pentatomoidea, rather than as a part of the family Cydnidae. Moreover, the analyses indicate a close relationship between Sehirinae and Parastrachiidae, expressed in morpho-molecular synapomorphies in the predicted secondary and tertiary structures of the length-variable region L (LVR L).

Phylogenomic Analyses of the Tenthredinoidea Support the Familial Rank of Athaliidae (Insecta, Tenthredinoidea)

The systematic status of the genus Athalia and related genera is a perennial controversy in sawfly taxonomy. Several authors have hypothesized that the placement of Athalia within the Tenthredinidae is artificial, but no studies have focused on this topic. If the hypothesis that Athalia does not belong to Tenthredinidae can be supported, the taxonomic framework of Tenthredinoidea needs revision. We present a comprehensive phylogenomic study of Tenthredinoidae, focusing on the positions of Athalia and related genera by sampling 80 representatives mainly of the Tenthredinoidea, including Heptamelinae and Blasticotomidae. Our phylogenetic reconstructions based on nuclear genes and mitochondrial (mt) sequences support Athalia and related genera as a distinct clade sister to Tenthredinidae + (Cimbicidae + Diprionidae). A comparison of symphytan mitochondrial genomes reveals an innovative gene rearrangement pattern in Athaliidae, in which Dentathalia demonstrates a more ancestral pattern than Athalia and Hypsathalia. The lineage specificity of mt rRNA secondary structures also provides sufficient support to consider Athaliidae as a separate family. In summary, the phylogeny and genomic structural changes unanimously support the taxonomic treatment of Athaliidae as a family and the re-establishment of Dentathalia as a valid genus.

On the edge of the Shivaliks: An insight into the origin and taxonomic position of Pakistani toads from the Duttaphrynus melanostictus complex (Amphibia, Bufonidae)

The common Asian toad Duttaphrynus melanostictus (Schneider, 1799) complex has a wide distribution ranging from western foothills of the Himalaya to the easternmost range of the Wallacea, with the evidence of human-mediated introductions to some other areas. In the entire distribution range, the complex is formed by several evolutionary clades, distributed mostly in South-East Asia with unresolved taxonomy. In the northwestern edge of its distribution (Pakistan), the name D. melanostictus hazarensis (Khan, 2001) has been assigned to local populations but its biological basis remained, so far, understudied and unvalidated. Therefore, we re-evaluated the available genetic data (mitochondrial and nuclear) to show the relationships between Pakistani populations (including the type locality of D. m. hazarensis) and others from across the range. Our results showed that Pakistani populations are associated with one, deeply diverged, well-supported and widely distributed clade (so-called Duttaphrynus sp. 1 according to 16S, or clade B based on tRNAGly-ND3), that has already been detected in previous studies. This clade is further distributed in India, Nepal, Bangladesh, Malaysia, Singapore, and Indonesia and is characterized by a low level of genetic variability. This further suggests that both natural, as well as potential human-mediated dispersal, might have played an important role in setting up the current phylogeographic and distribution pattern of this clade. The clade is deeply divergent from other clades of the complex and represents a taxonomically unresolved entity. We here argue that the clade Duttaphrynus sp. 1/B represents a distinct species for which the name Duttaphrynus bengalensis (Daudin, 1802) comb. nov. is applicable, while the description of D. m. hazarensis does not satisfy the rules of the International Code of Zoological Nomenclature.

Global diversification and evolutionary history of onchidiid slugs (Gastropoda, Pulmonata)

Many marine species are specialized to specific parts of a habitat. In a mangrove forest, for instance, species may be restricted to the mud surface, the roots and trunks of mangrove trees, or rotting logs, which can be regarded as distinct microhabitats. Shifts to new microhabitats may be an important driver of sympatric speciation. However, the evolutionary history of these shifts is still poorly understood in most groups of marine organisms, because it requires a well-supported phylogeny with relatively complete taxon sampling. Onchidiid slugs are an ideal case study for the evolutionary history of habitat and microhabitat shifts because onchidiid species are specialized to different tidal zones and microhabitats in mangrove forests and rocky shores, and the taxonomy of the family in the Indo-West Pacific has been recently revised in a series of monographs. Here, DNA sequences for onchidiid species from the North and East Pacific, the Caribbean, and the Atlantic are used to reconstruct phylogenetic relationships among Onchidella species, and are combined with new data for Indo-West Pacific species to reconstruct a global phylogeny of the family. The phylogenetic relationships of onchidiid slugs are reconstructed based on three mitochondrial markers (COI, 12S, 16S) and three nuclear markers (28S, ITS2, H3) and nearly complete taxon sampling (all 13 genera and 62 of the 67 species). The highly-supported phylogeny presented here suggests that ancestral onchidiids most likely lived in the rocky intertidal, and that a lineage restricted to the tropical Indo-West Pacific colonized new habitats, including mudflats, mangrove forests, and high-elevation rainforests. Many onchidiid species in the Indo-West Pacific diverged during the Miocene, around the same time that a high diversity of mangrove plants appears in the fossil record, while divergence among Onchidella species occurred earlier, likely beginning in the Eocene. It is demonstrated that ecological specialization to microhabitats underlies the divergence between onchidiid genera, as well as the diversification through sympatric speciation in the genera Wallaconchis and Platevindex. The geographic distributions of onchidiid species also indicate that allopatric speciation played a key role in the diversification of several genera, especially Onchidella and Peronia. The evolutionary history of several morphological traits (penial gland, rectal gland, dorsal eyes, intestinal loops) is examined in relation to habitat and microhabitat evolutionary transitions and that the rectal gland of onchidiids is an adaptation to high intertidal and terrestrial habitats.

Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

BACKGROUND

The Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet.

METHODS

We obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests.

RESULTS

Consistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau.

18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera

BACKGROUND

18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an important phylogenetic marker for many groups, often to the point of being the only marker available for some. A core structure across eukaryotes exists for this molecule that can help to inform about its evolution in different groups. Using an alignment of 18S rDNA for Rotifera as traditionally recognized (=Bdelloidea, Monogononta, and Seisonacea, but not Acanthocephala), I fitted sequences for three exemplar species (Adineta vaga, Brachionus plicatilis, and Seison nebaliae, respectively) to the core structure and used these maps to reveal patterns of evolution for the remainder of this diverse group of microscopic animals.

RESULTS

The obtained variability maps of the 18S rRNA molecule revealed a pattern of high diversity among the three major rotifer clades coupled with strong conservation within each of bdelloids and monogononts. A majority of individual sites (ca. 60%) were constant even across rotifers as a whole with variable sites showing only intermediate rates of evolution. Although the three structural maps each showed good agreement with the inferred core structure for eukaryotic 18S rRNA and so were highly similar to one another at the secondary and tertiary levels, the overall pattern is of three highly distinct, but conserved motifs within the group at the primary sequence level. A novel finding was that of a variably expressed deletion at the 3' end of the V3 hypervariable region among some bdelloid species that occasionally extended into and included the pseudoknot structure following this region as well as the central "square" of the 18S rRNA molecule. Compared to other groups, levels of variation and rates of evolution for 18S rRNA in Rotifera roughly matched those for Gastropoda and Acanthocephala, despite increasing evidence for the latter being a clade within Rotifera.

CONCLUSIONS

The lack of comparative data for comparable groups makes interpretation of the results (i.e., very low variation within each of the three major rotifer clades, but high variation between them) and their potential novelty difficult. However, these findings in combination with the high morphological diversity within rotifers potentially help to explain why no clear consensus has been reached to date with regard to the phylogenetic relationships among the major groups.

Revisited Molecular Phylogeny of the Genus Sphaerotheca (Anura: Dicroglossidae): The Biogeographic Status of Northernmost Populations and Further Taxonomic Changes

Heretofore, the populations of the genus Sphaerotheca Günther, 1859 (Dicroglossidae) in their northern and western borders laying in Pakistan have been assigned to two species, S. breviceps (Schneider, 1799) and S. strachani (Murray, 1884). The genus originated in the Oriental zoogeographic region and comes to close geographic proximity with the Palearctic region in Pakistan. The recent molecular studies have on one hand restricted the distribution range of S. breviceps to the eastern coastal plains of India and, on the other hand, revealed the northern- and westernmost population in India as a separate species, S. pashchima Padhye et al., 2017. This species has recently been synonymized with S. maskeyi (Schleich and Anders, 1998). These taxonomic changes, however, warranted the need for validation of Pakistani Sphaerotheca based on genetic data. We sequenced and analyzed 16S rRNA mitochondrial gene from specimens originating from the Himalayan foothills of Pakistan and compared these with all available GenBank sequences of the genus. Based on this data, we conclude that the Himalayan foothills of Pakistan are occupied by S. maskeyi. Simultaneously, we bring the first record of this species for the Palearctic region. We further suggest that more genetic material from across Pakistan is required to ascertain the validity of S. strachani and for the phylogeographic evaluation of western and northern border populations of the genus. Our geographically wide and revisited molecular phylogeny shows that the genus exhibits genetic diversity suggesting further taxonomic changes. The low level of genetic divergences between S. breviceps and S. magadha Prasad et al., 2019 compared to other species of the genus, indicates that the taxonomic status of S. magadha is questionable. Moreover, we found that S. magadha and S. swani (Mayers and Leviton, 1956) are genetically conspecific with S. breviceps and both should be thus considered its junior synonyms. On the other hand, S. dobsonii and populations from Myanmar need further detailed investigations.

Phylogenomics of the Hyalella amphipod species-flock of the Andean Altiplano

Species diversification in ancient lakes has enabled essential insights into evolutionary theory as they embody an evolutionary microcosm compared to continental terrestrial habitats. We have studied the high-altitude amphipods of the Andes Altiplano using mitogenomic, nuclear ribosomal and single-copy nuclear gene sequences obtained from 36 Hyalella genomic libraries, focusing on species of the Lake Titicaca and other water bodies of the Altiplano northern plateau. Results show that early Miocene South American lineages have recently (late Pliocene or early Pleistocene) diversified in the Andes with a striking morphological convergence among lineages. This pattern is consistent with the ecological opportunities (access to unoccupied resources, initial relaxed selection on ecologically-significant traits and low competition) offered by the lacustrine habitats established after the Andean uplift.

Phylogeny and biogeography of Astraea with new insights into the evolutionary history of Crotoneae (Euphorbiaceae)

We investigated species relationships in Astraea, a primarily Neotropical genus of tribe Crotoneae centered in Brazil, using data from the nuclear ribosomal ITS, and the plastid trnL-trnF and psbA-trnH spacers. With all species of Astraea sampled, along with representatives from across Crotoneae, the evolutionary history of Astraea was interpreted in a broader framework, as well as divergence time estimates and reconstructions of ancestral areas and morphological character states for Crotoneae. Our results show that Astraea is monophyletic, consisting of three main clades, and that most of its diversification took place from the Oligocene to the Pliocene, coincident with the formation of the South American "dry diagonal". As for Crotoneae, our data show incongruent phylogenetic positions between the nuclear and chloroplast data for most of its genera, and that the ancestor of the tribe was probably arborescent and might have occupied the Amazon Basin, most likely in moist forest, from which it spread throughout South America in the early Eocene. Ancestral state reconstruction recovered deeply lobed leaves and staminate petals bearing moniliform trichomes as putative synapomorphies for Astraea, whereas the absence or strong reduction of pistillate petals is widespread in Crotoneae and may be a synapomorphy for the tribe.

Characteristic and variability of five complete aphid mitochondrial genomes: Aphis fabae mordvilkoi, Aphis craccivora, Myzus persicae, Therioaphis tenera and Appendiseta robiniae (Hemiptera; Sternorrhyncha; Aphididae)

The complete mitochondrial genomes of aphids Aphis fabae mordvilkoi, A. craccivora, Myzus persicae from Aphidinae as well as Therioaphis tenera and Appendiseta robiniae from Calaphidinae were sequenced and compared with the genomes of other aphid species. A. fabae mordvilkoi, Th. tenera and A. robiniae mitogenomes were sequenced and analyzed for the first time. The annotation of A. craccivora and M. persicae were corrected compared to what was previously published. According to our data there is no translocation of tRNA-Tyr gene in A. craccivora mitogenome and this aphid species has an ancestral type of mitochondrial gene order. A + T content in all 5 mitogenomes was higher than 80%. A + T content in the Th. tenera CR was 59.5% which is untypically low. CRs of all 5 studied mitogenomes had 2 conserved motifs at their ends and extended G + C rich region. A. craccivora, M. persicae and Th. tenera had large tandem repeats inside the CRs. Detailed molecular analysis of all 5 aphid mitochondrial genomes showed the importance of a deep understanding of the molecular organization of all the functional regions of the mitochondrial DNA, which helps to avoid mistakes during genome annotation.

Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group

Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.

Polyclad phylogeny persists to be problematic

Two conflicting morphological approaches to polyclad systematics highlight the relevance of molecular data for resolving the interrelationships of Polycladida. In the present study, phylogenetic trees were reconstructed based on a short alignment of the 28S rDNA marker gene with 118 polyclad terminals (24 new) including 100 different polyclad species from 44 genera and 22 families, as well as on a combined dataset using 18S and 28S rDNA genes with 27 polyclad terminals (19 new) covering 26 different polyclad species. In both approaches, Theamatidae and Cestoplanidae were included, two families that have previously been shown to switch from Acotylea to Cotylea. Three different alignment methods were used, both with and without alignment curation by Gblocks, and all alignments were subjected to Bayesian inference and maximum likelihood tree calculations. Over all trees of the combined dataset, an extended majority-rule consensus tree had weak support for Theamatidae and Cestoplanidae as acotyleans, and also the cotylean genera Boninia, Chromyella and Pericelis appeared as acotyleans. With the most inclusive short 28S dataset, on the other hand, there is good support for the aforementioned taxa as cotyleans. Especially with the short 28S matrix, taxon sampling, outgroup selection, alignment method and curation, as well as model choice were all decisive for tree topology. Well-supported parts of the phylogeny over all trees include Pseudocerotoidea, Prosthiostomoidea, Stylochoidea, Leptoplanoidea and Cryptoceloidea, the latter three with new definitions. Unstable positions in the tree were found not only for Theamatidae, Cestoplanidae, Boninia, Chromyella and Pericelis, but also for Anonymus, Chromoplana and Cycloporus.

Molecular phylogeny and evolution of world Tachinidae (Diptera)

We reconstructed phylogenetic relationships within the diverse parasitoid fly family Tachinidae using four nuclear loci (7800 bp) and including an exceptionally large sample of more than 500 taxa from around the world. The position of the earthworm-parasitizing Polleniinae (Calliphoridae s.l.) as sister to Tachinidae is strongly supported. Our analyses recovered each of the four tachinid subfamilies and most recognized tribes, with some important exceptions in the Dexiinae and Tachininae. Most notably, the tachinine tribes Macquartiini and Myiophasiini form a clade sister to all other Tachinidae, and a clade of Palpostomatini is reconstructed as sister to Dexiinae + Phasiinae. Although most nodes are well-supported, relationships within several lineages that appear to have undergone rapid episodes of diversification (basal Dexiinae and Tachininae, Blondeliini) were poorly resolved. Reconstructions of host use evolution are equivocal, but generally support the hypothesis that the ancestral host of tachinids was a beetle and that subsequent host shifts to caterpillars may coincide with accelerated diversification. Evolutionary reconstructions of reproductive strategy using alternative methods were incongruent, however it is most likely that ancestral tachinids possessed unincubated, thick shelled eggs from which incubated eggs evolved repeatedly, potentially expanding available host niches. These results provide a broad foundation for understanding the phylogeny and evolution of this important family of parasitoid insects. We hope it will serve as a framework to be used in concert with morphology and other sources of evidence to revise the higher taxonomic classification of Tachinidae and further explore their evolutionary history and diversification.

The phylogeny of Ryocalanoidea (Copepoda, Calanoida) based on morphology and a multi-gene analysis with a description of new ryocalanoidean species

Two new species of ryocalanoid copepods (Crustacea: Calanoida), Ryocalanus squamatus sp. nov. and Yrocalanus kurilensis sp. nov. are described together with a female of Ryocalanus infelix Tanaka, 1956, type species for the genus Ryocalanus Tanaka, 1956, from abyssal depths in the Kurile-Kamchatka trench. The new species can be assigned to the superfamily Ryocalanoidea based on the segmentation and armature of the swimming legs and the modification of the male right antennule. A new interpretation of the fusions of segments in the male right antennule of Ryocalanus shows the marked differences between the ryocalanoidean genera. The status of Ryocalanoidea within the Calanoida is discussed based on morphology and a first molecular multi-gene analysis with cytochrome oxidase subunit I, cytochrome b, nuclear ribosomal 18S and 28S rDNA and internal transcribed spacer 2. This analysis supports the close interrelationship between Ryocalanoidea and Spinocalanoidea. The monophyletic status of Ryocalanoidea could not be retrieved in the phylogenetic analysis, as specimens of Yrocalanus formed a clade within Spinocalanoidea. The inconclusive results between morphological and molecular analyses are discussed with a proposition to keep the current system until more males of taxa belonging to the Spinocalanoidea are discovered, as the male antennule plays a crucial role in the interpretation of relationships between Ryocalanoidea and Spinocalanoidea.

Climate and host-plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ∼53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (∼34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (∼26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (∼14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.

Clarifying the phylogenetic relationships and taxonomy of Stenonema, Stenacron and Maccaffertium, three common eastern North American mayfly genera

Stenonema, Stenacron, and Maccaffertium are three closely related genera of mayflies (Ephemeroptera:Heptageniidae) commonly found across North America. Due to their primarily aquatic life history and sensitivity to aquatic pollutants, these mayflies are often used as water quality indicators. However, there is little morphological variation within these genera, leading to difficulties in identification and rampant taxonomic confusion, limiting their utility as bioindicators. In an attempt to resolve the phylogenetic relationships of Stenonema, Stenacron, and Maccaffertium, and to clarify their higher-level classifications, we sequenced regions of two mitochondrial genes (cytochrome oxidase subunit 1 (cox1) and 16S ribosomal RNA (rrnl)) and two nuclear genes (Wingless (Wg) and histone H3) from 60 individuals representing most of the described species in these genera and included data from representatives of three heptageniid genera (Kageronia, Macdunnoa and Pseudiron) proposed in previous studies to be closely related to our focal taxa as well as two more distantly related heptageniid genera (Epeorus and Heptagenia) to root the phylogenies. Maximum likelihood and Bayesian analysis were conducted on single-gene and concatenated multi-gene data sets and species tree methods were utilized to resolve relationships. These analyses resolved Stenacron as a monophyletic group sister to a clade comprising Macdunnoa, Maccaffertium and Stenonema. Maccaffertium was found to be paraphyletic, with Stenonema femoratum resolved within Maccaffertium as sister to M. mexicanum. Many relationships remained unresolved or varied across analyses, making revision of the classification based on phylogenetic considerations challenging. To minimize confusion while naming clades and acknowledging uncertainty in our phylogenetic conclusions, we redefine Stenonema to include Maccaffertium and propose three subgenera-Stenonema, Maccaffertium and Lewisa- for key well-supported clades.

A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic

We investigate mitochondrial (COI, 16S rDNA) and nuclear (ITS2, 28S rDNA) genetic structure of North East Atlantic lineages of Terebellides, a genus of sedentary annelids mainly inhabiting continental shelf and slope sediments. We demonstrate the presence of more than 25 species of which only seven are formally described. Species boundaries are determined with molecular data using a broad range of analytical methods. Many of the new species are common and wide spread, and the majority of the species are found in sympatry with several other species in the complex. Being one of the most regularly encountered annelid taxa in the North East Atlantic, it is more likely to find an undescribed species of Terebellides than a described one.

The role of progenesis in the diversification of the interstitial annelid lineage Psammodrilidae

Psammodrilidae constitutes a family of understudied, nearly completely ciliated, small-sized annelids, whose systematic position in Annelida remains unsettled and whose internal phylogeny is here investigated for the first time. Psammodrilids possess hooked chaetae typical of macroscopic tube-dwelling semi-sessile annelids, such as Arenicolidae. Yet, several minute members resemble, with their conspicuous gliding by ciliary motion and vagile lifestyle, interstitial fauna, adapted to move between sand grains. Moreover, psammodrilids exhibit a range of unique features, for example, bendable aciculae, a collar region with polygonal unciliated cells, and a muscular pumping pharynx. We here present a combined phylogeny of Psammodrilidae including molecular and morphological data of all eight described species (two described herein as Psammodrilus didomenicoi, sp. nov. and P. norenburgi, sp. nov.) as well as four undescribed species. Ancestral character state reconstruction suggests the ancestor of Psammodrilidae was a semi-sessile larger form. Miniaturisation seems to have occurred multiple times independently within Psammodrilidae, possibly through progenesis, yielding small species with resemblance to a juvenile stage of the larger species. We find several new cryptic species and generally reveal an unexpected diversity and distribution of this small family. This success may be favoured by their adaptive morphology, here indicated to be genetically susceptible to progenesis.

A new species of Malenchus (Nematoda: Tylenchomorpha) with an updated phylogeny of the Tylenchidae

The family Tylenchidae is one of most abundant and diverse nematode groups found in soil habitats. In this study, a new species named Malenchus cylindricus sp. n. is described based on light and scanning electron microscopy and molecular data. The new species is characterised by elongate-cylindrical vulva-anus body shape and a narrow annulation. We updated the phylogeny of Tylenchidae by including molecular data for the rare genera Miculenchus and Tenunemellus and by improving the morphological characterisation of the genus Lelenchus. Additionally, we compared the effect of alignment methods on the tree topologies and branch support values. The results suggest that the position of subfamily Ecphyadophorinae within Tylenchidae needs to be further revised. Phylogenies inferred from different sequence-based alignments were relatively more similar (i.e., tree topology and branch support) to one another than to secondary structure-aided methods. Finally, conflicting branch support values can be reconciled by properly selecting the alignment method.

Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA)

Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI). Phylogenetic analyses based on these two genomic regions validated the sisterhood of the genera Triconia and the Oncaea sensu stricto. ITS1 and ITS2 phylogenies produced incongruent results about the position of Oncaea curta, calling for further investigations on this species. We also characterised the ITS2 region by secondary structure predictions and found that all the sequences analysed presented the distinct eukaryotic hallmarks. A Compensatory Base Change search corroborated the close relationship between O. venusta and O. curta and between O. media and O. venusta already identified by ITS phylogenies. The present results, which stem from the integration of molecular and morphological taxonomy, represent an encouraging step towards an improved knowledge of copepod biodiversity: The two complementary approaches, when applied to long-term copepod monitoring, will also help to better understanding their genetic variations and ecological niches of co-occurring species.

Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes

The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.

Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils

This study presents the use of relaxed molecular clock methods to infer the dates of divergence between Panagrolaimus species. Autocorrelated relaxed tree methods, combined with well characterised fossil calibration dates, yield estimates of nematode divergence dates in accordance with the palaeontological age of fossil ascarid eggs and with the previously estimated date of 18 Ma (range 11.6 to 29.9 Ma) for the divergence of the Caenorhabditis lineage. Our data indicate that Panagrolaimus davidi from Antarctica separated ca 21.98 Ma from its currently known, most closely related strain. Thus, P. davidi may have existed in Antarctica prior to the Last Glacial Maximum, although this seems unlikely as it shares physiological and life history traits with closely related nematodes from temperate climates. These traits may have facilitated colonisation of Antarctica by P. davidi after the quaternary glaciation, analogous to the colonisation of Surtsey Island, Iceland, by P. superbus after its volcanic formation. This study demonstrates that autocorrelated relaxed tree methods combined with well characterised fossil calibration dates may be used as a method to estimate the divergence dates within nematodes in order to gain insight into their evolutionary history.

Arthonia parietinaria - A common but frequently misunderstood lichenicolous fungus on species of the Xanthoria parietina-group

Arthonia parietinaria is described as new to science. Host of the type and at the same time the only confirmed host species is the foliose macrolichen Xanthoria parietina. Sequence data of nucLSU rRNA genes reveal a close relationship to Arthonia molendoi. A. parietinaria is recorded for many countries in Europe, western Asia, and northern Africa.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

Vector soup: high-throughput identification of Neotropical phlebotomine sand flies using metabarcoding

Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.

Five new cryptic freshwater gastropod species from New Caledonia (Caenogastropoda, Truncatelloidea, Tateidae)

During the course of a project aiming at the reconstruction of the colonization of the South Pacific islands by tateid gastropods based on molecular data we discovered five new species on New Caledonia belonging to the genera Hemistomia and Leiorhagium, respectively. We describe these species based on morphological, anatomical and genetic data. All five species are morphologically cryptic as they closely resemble or are even indistinguishable from known species stressing the importance of a comprehensive taxonomic approach integrating several methods. As a consequence of their small and fragmented geographic ranges and the rapidly progressing anthropogenic land cover changes on New Caledonia, all five species qualify as critically endangered according to the criteria of the IUCN.

Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment

BACKGROUND

Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites.

RESULTS

Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98-100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona.

CONCLUSIONS

Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.

Molecular phylogeny and a modified approach of character-based barcoding refining the taxonomy of New Caledonian freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae)

The islands of New Caledonia represent one of the world's biodiversity hotspots with many endemic species including freshwater gastropods of the family Tateidae. A phylogenetic analysis based on the mitochondrial COI and 16S rRNA and the nuclear ITS2 genes revealed two cryptic genera, Crosseana gen. n. and Novacaledonia gen. n. In order to provide character-based diagnoses we modified a DNA barcoding approach identifying strings of pairwise diagnostic characters, i.e. alignment positions, at which two genera are alternatively fixed for different nucleotides. The combination or string of all pairwise diagnostic characters was unique for each genus. Inconsistent mitochondrial and nuclear topologies suggest that Hemistomia cockerelli Haase and Bouchet, 1998 and H. fabrorum Haase and Bouchet, 1998, two morphologically well-defined species, hybridize. The age of the most recent common ancestor of the New Caledonian radiation of Tateidae was estimated at 24.6±9.5 MY. These findings are in line with the notion that New Caledonia is rather a Darwinian island that was colonized after an extended phase of submergence - in case of the tateids probably from Australia - despite being a fragment of Gondwanaland.

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

BACKGROUND

Phylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines. Currently no stand-alone or pipeline compatible program exists that offers a broad range of manipulation and processing steps for multiple sequence alignments in a single process run.

RESULTS

Here we present FASconCAT-G, a system independent editor, which offers various processing options for multiple sequence alignments. The software provides a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation between nucleotide and amino acid states, consensus generation of specific sequence blocks, sequence concatenation, model selection of amino acid replacement with ProtTest, two types of RY coding as well as site exclusions and extraction of parsimony informative sites. Convieniently, most options can be invoked in combination and performed during a single process run. Additionally, FASconCAT-G prints useful information regarding alignment characteristics and editing processes such as base compositions of single in- and outfiles, sequence areas in a concatenated supermatrix, as well as paired stem and loop regions in secondary structure sequence strings.

CONCLUSIONS

FASconCAT-G is a command-line driven Perl program that delivers computationally fast and user-friendly processing of multiple sequence alignments for phylogenetic and population genetic applications and is well suited for incorporation into analysis pipelines.

Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea)

Background

Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012).

Results

We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure.

Conclusions

Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.

Stereopsidales--a new order of mushroom-forming fungi

One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked lineage, but both species harbor cryptic diversity. In addition, a third species, C. macounii, appears as a plausible sister to the new lineage, but there is conflict in the data. All specimens of S. radicans and S. globosa analysed here are from the South and Central Americas; several records of S. radicans have been made also from tropical Asia. We expect the true diversity in this group to be a lot higher than presented in this paper. Stereopsis radicans was formerly included in Polyporales, but a placement within that order is rejected by our data through SH tests. The dataset consisted of four nuclear markers: rpb2, tef1, LSU and SSU, each of which was analysed separately using maximum likelihood and Bayesian inference. Recombination detection tests indicate no plausible recombinations. The potential of S. radicans, S. globosa and C. macounii being amphitallic is briefly discussed.

Shallow-water northern hemisphere Jaera (Crustacea, Isopoda, Janiridae) found on whale bones in the southern ocean deep sea: ecology and description of Jaera tyleri sp. nov

The skeleton of a natural whale fall discovered in the Southern Ocean at 1,445 m was densely covered by one small, janirid isopod. Jaera tyleri sp. nov. is the first of its genus found in the southern hemisphere and in the deep sea and is described herein. Morphological and molecular investigations revealed the systematic position of this species new to science. Phylogenetic analysis of the 18S locus confirms that this species falls in a strongly supported monophyletic clade of Jaera species. The whale bone habitat of J. tyleri sp. nov. is quite different from those of other species of the genus Jaera. The analysis of bathymetric and distribution patterns of the Janiridae in general and Jaera specifically confirm the unusualness of the habitat for this isopod species. The abundance of J. tyleri sp. nov. on the whale bones and its absence from other nearby habitats suggests it to be a whale-fall specialist. The analysis of the size-frequency distributions of J. tyleri sp. nov. suggests multimodal population structure with continuous breeding activity throughout the year. The fecundity of the species is low but in line with reduced fecundity observed in polar and small-sized isopods.

Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly?

The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic "orders" within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of other Anthozoa and Medusozoa groups. In addition, nuclear markers were used to check the relative phylogenetic position of Ceriantharia in relation to other Cnidaria members. The results demonstrated a pattern of divergence of mitochondrial DNA completely different from those estimated for other anthozoans, and phylogenetic analyses indicate that Ceriantharia is not included within hexacorallians in most performed analyses. Thus, we propose that the Ceriantharia should be addressed as a separate clade.

Prosogynopora riseri, gen. et sp. nov., a phylogenetically problematic lithophoran proseriate (Platyhelminthes : Rhabditophora) with inverted genital pores from the New England coast

A new lithophoran proseriate flatworm, Prosogynopora riseri, gen. et sp. nov. (Platyhelminthes: Rhabditophora: Proseriata), is described from the New England coast (USA). The species shares characters with members of the families Calviriidae and Coelogynoporidae, e.g. the presence of paracnida, the short common female duct, a septum and diaphragm at the base of the pharynx. However, the inverted topology of the genital system, presenting an anterior female pore shortly behind the mouth and a male pore opening nearly on the caudal terminus, is unique within the Proseriata, and permits inclusion into neither family on morphological grounds. We investigated the phylogenetic position of the new species within the available diversity of proseriate 18S and 28S rRNA sequences. However, an exploration of diverse homology schemes, alignment conditions and optimality criteria proved the position of P. riseri, gen. et sp. nov. to be remarkably unstable, particularly with respect to the method of alignment, variously suggesting sister-group relationships with (or within) Coelogynoporidae, with Calviriidae, or with a clade composed of all other Lithophora. Despite its unique morphology and the absence of molecular phylogenetic evidence for its inclusion within any family as currently defined, we refrain from assigning a higher taxonomic rank to the new lineage, pending critical re-assessment of homology in several character systems and the availability of further taxon- and gene-rich enquiries into the phylogeny of Proseriata. Apingospermata, new taxon and Dolichogynoducta, new taxon are proposed as two rankless taxonomic names of Lithophora, corresponding to well-supported clades in our molecular phylogenetic hypothesis.