Nuclear gene sequences confirm an ancient link between New Zealand's short-tailed bat and South American noctilionoid bats

Molecular and morphological hypotheses disagree on the phylogenetic position of New Zealand's short-tailed bat Mystacina tuberculata. Most morphological analyses place Mystacina in the superfamily Vespertilionoidea, whereas molecular studies unite Mystacina with the Neotropical noctilionoids and imply a shared Gondwanan history. To date, competing hypotheses for the placement of Mystacina have not been addressed with a large concatenation of nuclear protein sequences. We investigated this problem using 7.1kb of nuclear sequence data that included segments from five nuclear protein-coding genes for representatives of 14 bat families and six laurasiatherian outgroups. We employed the Thorne/Kishino method of molecular dating, allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution on different branches on the phylogenetic tree, to estimate basal divergence times within key chiropteran clades. Maximum likelihood, minimum evolution, maximum parsimony, and Bayesian posterior probabilities all provide robust support for the association of Mystacina with the South American noctilionoids. The basal divergence within Chiroptera was estimated at 67mya and the mystacinid/noctilionoid split was calculated at 47mya. Although the mystacinid lineage is too young to have originated in New Zealand before it split from the other Gondwanan landmasses (80mya), the exact geographic origin of these lineages is still uncertain and will not be answered until more fossils are found. It is most probable that Mystacina dispersed from Australia to New Zealand while other noctilionoid bats either remained in or dispersed to South America.     

Phylogenetic relationships of the Cochliopinae (Rissooidea: Hydrobiidae): an enigmatic group of aquatic gastropods

Phylogenetic analysis based on a partial sequence of the mitochondrial cytochrome c oxidase subunit I gene was performed for 26 representatives of the aquatic gastropod subfamily Cochliopinae, 6 additional members of the family Hydrobiidae, and outgroup species of the families Rissoidae and Pomatiopsidae. Maximum-parsimony analysis yielded a single shortest tree which resolved two monophyletic groups: (1) a clade containing all cochliopine taxa with the exception of Antroselates and (2) a clade composed of Antroselates and the hydrobiid genus Amnicola. The clade containing both of these monophyletic groups was depicted as more closely related to members of the family Pomatiopsidae than to other hydrobiid snails which were basally positioned in our topology. New anatomical evidence supports recognition of the cochliopine and Antroselates-Amnicola clades, and structure within the monophyletic group of cochliopines is largely congruent with genitalic characters. However, the close relationship between the Pomatiopsidae and these clades is in conflict with commonly accepted classifications and suggests that a widely accepted scenario for genitalic evolution in these snails is in need of further study.     

Limb myology and phylogenetic relationships in the superfamily Dipodoidea (birch mice, jumping mice, and jerboas)

Limb muscles were dissected in seven genera, representing all six superfamilies, of dipodoid rodents and myoloic characters were used to construct a phylogenetic hpothesis of relationships within this cfade. Mologic differences among genera suported tie monophyly of the superfamily Dipodoidea reLtive to the outrou taxon and reveaEd thatSicista is the sister group to all other zapodid and dipodid enera. Tkis picement of Sicista differs markedly from its position in previous classifications where it has been regarded merely as a primitive zapodid genus. The phlograrn based on rnyologic characters also indicated that Cardiocranius is not a rimitive dipodid genus; it is the sister group to the subfamily Dipodinae. Although myologic differences among taxa were not sufficient to warrant the continued separation of zaodids and dipodids into two families, a new classification that places Sicista in its own family, ficistidae, and places the remaining zaodids and dipodids in the family Dipodidae, is proposed. Differences in karyology, genitaP morholoy, and postcranial osteological characters among dipodoid rodents are discussed in light or this pjylogeny.     

Clustering of protein domains in the human genome

We present a systematic study of the clustering of genes within the human genome based on homology inferred from both sequence and structural similarity. The 3D-Genomics automated proteome annotation pipeline () was utilised to infer homology for each protein domain in the genome, for the 26 superfamilies most highly represented in the Structural Classification Of Proteins (SCOP) database. This approach enabled us to identify homologues that could not be detected by sequence-based methods alone. For each superfamily, we investigated the distribution, both within and among chromosomes, of genes encoding at least one domain within the superfamily. The results indicate a diversity of clustering behaviours: some superfamilies showed no evidence of any clustering, and others displayed significant clustering either within or among chromosomes, or both. Removal of tandem repeats reduced the levels of clustering observed, but some superfamilies still displayed highly significant clustering. Thus, our study suggests that either the process of gene duplication, or the evolution of the resulting clusters, differs between structural superfamilies.     

Polycladida phylogeny and evolution: integrating evidence from 28S rDNA and morphology

Polyclad flatworms have a troubled classification history, with two contradicting systems in use. They both rely on a ventral adhesive structure to define the suborders Acotylea and Cotylea, but superfamilies were defined according to eyespot arrangement (Prudhoe’s system) or prostatic vesicle characters (Faubel’s system). Molecular data available cover a very limited part of the known polyclad family diversity and have not allowed testing morphology-based classification systems on Polycladida yet. We thus sampled a suitable marker, partial 28S ribosomal DNA (rDNA), from Polycladida (19 families and 32 genera), generating 136 new sequences and the first comprehensive genetic dataset on polyclads. Our maximum likelihood (ML) analyses recovered Polycladida, but the traditional suborders were not monophyletic, as the supposedly acotyleans Cestoplana and Theama were nested within Cotylea; we suggest that these genera should be included in Cotylea. The partial 28S rDNA trees were generally well supported and robust but in conflict with both Faubel’s and Prudhoe’s superfamilies. Therefore, we compiled morphological and anatomical characters for all taxa used and examined their distribution on our molecular tree. Combining morphological and molecular evidence, we redefined polyclad superfamilies. Acotylea contain tentaculated and atentaculated groups and is now divided in three superfamilies. The suborder Cotylea can be divided in five superfamilies. In general, there is a trait of anteriorization of sensory structures, from the plesiomorphic acotylean body plan to the cotylean gross morphology. Traditionally used characters, such as prostatic vesicle, eyespot distribution, and type of pharynx, are all homoplastic and likely have misled polyclad systematics so far.     

A new large philisid (Mammalia,Chiroptera, Vespertilionoidea) from the late Early Eocene of Chambi,Tunisia

Abstract: Among the new dental remains from the late Early Eocene of Chambi (Kasserine area, Tunisia) is a large‐sized upper molar of a new bat species, Witwatia sigei nov. sp. (Chiroptera, Vespertilionoidea, Philisidae), described herein. The locality of Chambi has revealed evidence for an early appearance of two modern microchiropteran superfamilies in Africa: Dizzya exsultans, a Philisidae, which is considered to be an archaic Vespertilionoidea, and an indeterminate Rhinolophoidea. In addition to D. exsultans, the new species, W. sigei, is the second representative of the Philisidae in this locality. W. sigei extends back to the late Early Eocene the occurrence of the genus Witwatia, which was previously only reported from the early Late Eocene of the Fayum (BQ‐2, Egypt). By analogy with the largest extant microbats, the large size of Witwatia suggests a tendency to the opportunistic diet of this taxon, thereby contrasting with the strict insectivory characterizing primitive bats found in other continents in the same epoch.     

AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings

MOTIVATION: The sequence patterns contained in the available motif and hidden Markov model (HMM) databases are a valuable source of information for protein sequence annotation. For structure prediction and fold recognition purposes, we computed mappings from such pattern databases to the protein domain hierarchy given by the ASTRAL compendium and applied them to the prediction of SCOP classifications. Our aim is to make highly confident predictions also for non-trivial cases if possible and abstain from a prediction otherwise, and thus to provide a method that can be used as a first step in a pipeline of prediction methods. We describe two successful examples for such pipelines. With the AutoSCOP approach, it is possible to make predictions in a large-scale manner for many domains of the available sequences in the well-known protein sequence databases. RESULTS: AutoSCOP computes unique sequence patterns and pattern combinations for SCOP classifications. For instance, we assign a SCOP superfamily to a pattern found in its members whenever the pattern does not occur in any other SCOP superfamily. Especially on the fold and superfamily level, our method achieves both high sensitivity (above 93%) and high specificity (above 98%) on the difference set between two ASTRAL versions, due to being able to abstain from unreliable predictions. Further, on a harder test set filtered at low sequence identity, the combination with profile-profile alignments improves accuracy and performs comparably even to structure alignment methods. Integrating our method with structure alignment, we are able to achieve an accuracy of 99% on SCOP fold classifications on this set. In an analysis of false assignments of domains from new folds/superfamilies/families to existing SCOP classifications, AutoSCOP correctly abstains for more than 70% of the domains belonging to new folds and superfamilies, and more than 80% of the domains belonging to new families. These findings show that our approach is a useful additional filter for SCOP classification prediction of protein domains in combination with well-known methods such as profile-profile alignment. AVAILABILITY: A web server where users can input their domain sequences is available at http://www.bio.ifi.lmu.de/autoscop.     

Molecular systematics of caridean shrimps based on five nuclear genes: Implications for superfamily classification

Caridean shrimps are the second most diverse group of Decapoda. Over the years, several different systematic classifications, exclusively based on morphology, have been proposed, but the classification of the infraorder Caridea remains unresolved. In this study, five nuclear genes, 18S rRNA, enolase, histone 3, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α-subunit, were used to examine the systematic status of caridean families and superfamilies. We constructed gene trees based on a combined dataset of 3819 bp, containing 35 caridean species from 19 families in 11 superfamilies. At the family level, and based on our restricted representation, our molecular data support monophyly of the families Glyphocrangonidae, Crangonidae, Pandalidae, Alpheidae, Rhynchocinetidae, Nematocarcinidae, Pasiphaeidae, Atyidae and Stylodactylidae. In contrast, both the Hippolytidae and Palaemonidae are polyphyletic in our analysis. Two major clades are revealed. The Alpheidae, Hippolytidae, Crangonidae, Glyphocrangonidae, Barbouriidae, Pandalidae, Hymenoceridae, Gnathophyllidae and Palaemonidae make up the first clade, while the second clade comprises the Rhynchocinetidae, Oplophoridae, Nematocarcinidae, Alvinocarididae, Campylonotidae, Pasiphaeidae and Eugonatonotidae. Two families, Bathypalaemonellidae and Stylodactylidae, are shown to be basal groups in our tree. At the superfamily level, our results do not support the currently accepted superfamily classification, although there is support for a superfamily Palaemonoidea, though only three out of its eight families are included. The results suggest that the currently accepted superfamily classification of the Caridea does not reflect their evolutionary relationships. A major revision of the higher systematics of Caridea appears thus to be vital, ideally incorporating both molecular and morphological evidence.     

New gammaroid family, genera and species from subterranean waters of Japan, and their phylogenetic relationships (Crustacea: Amphipoda)

Luciobliviidae, a new family in the superfamily Gammaroidea (Amphipoda: Crustacea), is described on the basis of species in the genus Lucioblivio gen. nov. from subterranean waters of Japan. Mesogammaridae Bousfield, 1977 is rediagnosed; Octopupilla gen. nov. from subterranean waters of Japan is described and Eoniphargus (Uéno, 1955) from subterranean waters of Japan and Korea is included. The members of Lucioblivio , Octopupilla and Eoniphargus share several characters, including reduced eyes, a setose body, reduced coxae, feeble appendages and pedunculate coxal gills. To elucidate the phylogeny of the three genera among others, a sequence analysis of the 28S rRNA gene was conducted for 14 species in six families, including the three genera, from the superfamilies, Gammaroidea, Crangonyctoidea and Hadzioidea. The tree from a neighbour-joining analysis and the strict consensus tree from a maximum-parsimony analysis indicate monophyly of Mesogammaridae. Luciobliviidae is embedded within a clade of taxa belonging to the superfamily Gammaroidea. These results and the occurrence of gammarid-type calceoli in species of the new family indicate that Luciobliviidae should be placed within the superfamily Gammaroidea. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 643–670.     

Phylogenetic balance and ecological evenness

The frequency distribution of numbers of species in taxonomic groups, where many species belong to a few very diverse higher taxa, is mirrored by that of species in most communities, where many individuals belong to a few very abundant species. Various hypotheses mechanistically link a species' community abundance with the diversity of the higher level taxon (genus, family, order) to which it belongs, but empirical data are equivocal about general trends in the relation between rank-taxon diversity and mean abundance. One reason for this inconclusive result may be the effect of the semisubjective nature of rank-based classification. We assessed the relationship between clade diversity and mean species abundance for two diverse tropical tree communities, using both traditional rank-based analysis and two new phylogenetic analyses (based on the ratio of individuals to taxa at each node in the phylogeny). Both rank-based and phylogenetic analyses using taxonomic ranks above the species level as terminal taxa detected a trend associating common species with species-rich families. In contrast, phylogenetic analyses using species as terminal taxa could not distinguish the observed distribution of species abundances from a random distribution with respect to clade diversity. The difference between these results might be due to (1) the absence of a real phylogeny-wide relationship between clade abundance and diversity, (2) the influence of poor phylogenetic resolution within families in our phylogenies, or (3) insufficient sensitivity of our metrics to subtle tree-wide effects. Further development and application of phylogeny-based methods for testing abundance-diversity relationships is needed.     

Plumage based classification of the bowerbird genus Sericulus evaluated using a multi-gene, multi-genome analysis

Past classifications of taxa within the bowerbird genus Sericulus (family: Ptilonorhynchidae) conflict since the discovery of hybrids identified though male plumage characteristics. We use molecular data to help define species within this genus, and by estimating a phylogeny, test for lability in the evolution of male plumage patterns. Because this genus includes the most brightly colored bowerbird species, and is hypothesized to be the basal genus of the avenue building bowerbird clade, the organization of the four taxa within this genus is especially important in understanding how bowerbird plumage coloration evolved. Analyses of two mitochondrial and six nuclear gene regions confirm the basal placement of Sericulus in the avenue building bowerbirds and Sericulus monophyly, and suggests the Australian S. chrysocephalus is the basal Sericulus species. Our analysis additionally supports the existence of three New Guinea Sericulus species, contrary to some previous plumage based classifications, as they are genetically equidistant from each other. Molecular and geographic data of New Guinea are consistent suggesting a series of speciation events starting approximately 3.7-4.3MYA leading to four extant Sericulus species. The absence of resolution within the New Guinea species precludes any statements of trait lability, but does suggest that traits under high selection pressures may not accurately indicate species level distinctions within this genus.     

Taxonomic surrogacy in biodiversity assessments,and the meaning of Linnaean ranks

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

Phylogenetic relationships of the Clavelinidae and Pycnoclavellidae (Ascidiacea) inferred from mtDNA data

Abstract. The phylogenetic relationships within the Order Aplousobranchiata (Ascidiacea) are largely unexplored. In this work, we study the phylogenetic status of the genera Clavelina and Pycnoclavella. Traditionally, both genera had been included in the family Clavelinidae, until the new family Pycnoclavellidae was defined, removing the genus Pycnoclavella from Clavelinidae. Not all authors accept the validity of Clavelina and Pycnoclavella as distinct genera, let alone their belonging to different families. In addition, the assignment of species to these genera, as well as to the genus Archidistoma , has been controversial. We analyzed sequences of the mitochondrial gene cytochrome c oxidase subunit I belonging to ten species of Pycnoclavella (including several formerly assigned to Archidistoma and Clavelina ), 11 species of Clavelinidae, and ten species of other aplousobranch genera belonging to seven families, plus two outgroups. Two different tree construction methods (maximum likelihood and Bayesian inference) showed similar results. Pycnoclavella and Clavelina appeared in distinct clades but formed a monophyletic group relative to representatives of the main families of the order Aplousobranchiata. Our phylogenetic results indicate that both genera are valid but should be included within a single family, with the name Clavelinidae having precedence. The monotypic clavelinid genus Nephtheis branches in our trees within the clade of the genus Clavelina. Our results also confirm that some forms assigned to Archidistoma and Clavelina have been misplaced and belong to the genus Pycnoclavella. Pycnoclavella martae n.sp. is described.     

Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions

ABSTRACT: BACKGROUND: Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescence-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. RESULTS: We found that divergence estimates, from both concatenated gene tree and coalescence-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. CONCLUSIONS: Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

Camping in a Different Tree: Results of Molecular Systematic Studies of Bats Using DNA–DNA Hybridization

We examined taxa from 13 of the 17 chiropteran families, using single-copy DNA hybridization. Five taxa that either represented points of controversy in systematics or were members of problematic families were included in the experiment. The resulting data were used to build phylogenetic trees of 14 and 19 taxa, and by combining this study's data with those from two previous studies, a supertree of 36 taxa was constructed. The trees based on the three different matrices are compared and contrasted, and a phylogenetic hypothesis supporting the association of the rhinolophoid and the pteropodid groups of bats is presented. On the basis of this study, we conclude that the phylogenetically correct placement of the family Nycteridae is in a clade that does not include their putative relatives, the Rhinolophoidea. Our results suggest that the Emballonuridae, while a monophyletic group, are well embedded within the Yangochiroptera, and do not comprise the sister taxon to all other microbats. This study supports earlier DNA-hybridization results with respect to the placement of Mystacinidae within the Noctilionoidea, replicating those earlier findings. Finally, we determine that Miniopterus may well warrant recognition as a family distinct from the Vespertilionidae in which it is usually placed.     

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish.     

Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology

Higher‐level phylogenetics of Pycnogonida has been discussed for many decades but scarcely studied from a cladistic perspective. Traditional taxonomic classifications are yet to be tested and affinities among families and genera are not well understood. Pycnogonida includes more than 1300 species described, but no systematic revisions at any level are available. Previous attempts to propose a phylogeny of the sea spiders were limited in characters and taxon sampling, therefore not allowing a robust test of relationships among lineages. Herein, we present the first comprehensive phylogenetic analysis of the Pycnogonida based on a total evidence approach and Direct Optimization. Sixty‐three pycnogonid species representing all families including fossil taxa were included. For most of the extant taxa more than 6 kb of nuclear and mitochondrial DNA and 78 morphological characters were scored. The most parsimonious hypotheses obtained in equally weighted total evidence analyses show the two most diverse families Ammotheidae and Callipallenidae to be non‐monophyletic. Austrodecidae + Colossendeidae + Pycnogonidae are in the basal most clade, these are morphologically diverse groups of species mostly found in cold waters. The raising of the family Pallenopsidae is supported, while Eurycyde and Ascorhynchus are definitely separated from Ammotheidae. The four fossil taxa are grouped within living Pycnogonida, instead of being an early derived clade. This phylogeny represents a solid framework to work towards the understanding of pycnogonid systematics, providing a data set and a testable hypothesis that indicate those clades that need severe testing, especially some of the deep nodes of the pycnogonid tree and the relationships of ammotheid and callipallenid forms. The inclusion of more rare taxa and additional sources of evidence are necessary for a phylogenetic classification of the Pycnogonida. © The Willi Hennig Society 2006.