Phylogenetic analysis of caprellid and corophioid amphipods (Crustacea) based on the 18S rRNA gene, with special emphasis on the phylogenetic position of Phtisicidae

Members of the amphipod suborder Caprellidea exhibit degenerated abdomens and pereopods 3 and 4. Some genera of Podoceridae (Gammaridea, Corophioidea) such as Dulichia also show reduced abdomens and pereopods and thus are generally regarded as a sister group of the Caprellidea. In addition, one of the caprellid families, the Caprogammaridae, exhibits abdominal segments that are similar to those of the podocerids, as well as rudimentary pereopods 3 and 4, which are more consistent with those of other caprellids. Therefore, an evolutionary scheme has been suggested on the basis of the gradual degeneration of the pereopods and abdomen: [Dulichia, (caprogammarids, caprellids)]. However, the Phtisicidae (Caprellidea) contradict this hypothesis because they exhibit well-developed pereopods 3 and 4, along with degenerated abdomens. Therefore, previous studies have suggested that the Phtisicidae and other caprellids may be polyphyletic. We examined the phylogenetic position of the Phtisicidae and other caprellid amphipods, using 18S rRNA gene sequence data. The results strongly indicate that the Phtisicidae and other caprellid families form a monophyletic clade. However, a close phylogenetic relationship among Dulichia (Corophioidea) and taxa belonging to the Caprellidea was not definitively supported. This study is the first to use molecular data to investigate the phylogenetic relationships among the Caprellidea.     

Embryonic development and expression analysis of Distal-less in Caprella scaura (Crustacea, Amphipoda, Caprellidea)

The Caprellidea generally possess rudimentary abdomens and degenerated third and fourth pereopods. Previous molecular phylogenetic studies support the concept that their unique body plan is derived from a gammarid-like body plan from which the abdomen or third and fourth pereopods have been lost in the Caprellidea. To understand the developmental and genetic mechanisms for the morphological evolution of the Caprellidea, we observed the embryonic development of Caprella scaura. Although in the early embryonic stage limb buds appeared in all of the pereonites, we found that elongation of the limb buds did not occur in the third and fourth pereonites; instead, only oval projections (possibly primordial gills) were observed. We next examined the gene expression of Distal-less (Dll) by in situ hybridization and found that Dll was not expressed in the third and fourth pereonites. This suggests that the suppression of Dll expression is responsible for the reduction of Caprellidea pereopods.     

A new species of Caprella (Crustacea: Amphipoda) from the Mediterranean Sea

A new caprellid amphipod, Caprella tavolarensis n. sp., is described based on specimens collected from a Posidonia oceanica seagrass meadow at the Tavolara-Punta Coda Cavallo Marine Protected Area (Sardinia, Mediterranean Sea). The species is close to Caprella liparotensis, but can be clearly distinguished by smaller size, presence of a short rostrum, body elongate and dorsally smooth, absence of serrate carina on the basis of gnathopod 2 and pereopods, mouthparts scarcely setose, absence of fine setae on peduncle of antenna 1 and absence of swimming setae on antenna 2. The number of caprellid species reported from the Mediterranean Sea has increased from 23 (1993) to 41 (2010), consequently, further taxonomical studies should be addressed to properly estimate the total amphipod diversity in the Mediterranean Sea.     

Caprellids (Crustacea: Amphipoda) from Papua New Guinea,with the description of a new species

This is the first study of caprellid amphipods from the coast of Papua New Guinea. Several collections from Madang Lagoon (north) and Bootless Bay (south) have been studied. Seven species in seven genera are recorded, of which Pseudoproto papua sp. nov. is described as new to science. The genus Pseudoproto Mayer, 1903 has consisted, so far, of only one species, Pseudoproto fallax Mayer, 1903. Although only a single male has been found of Pseudoproto papua sp. nov., differences in antennae, mouthparts, gnathopod 2 and pereopods 3 and 4 have revealed that it represents a new species of Pseudoproto. Lateral view figures of all species, together with a key to species level for the Caprellidea from Papua New Guinea are also included. Communicated by H.-D. Franke     

What lies beneath: molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea)

The crustacean family Parabathynellidae is an ancient and significant faunal component of subterranean ecosystems. Molecular data were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species diversity of this group within Australia. We also used the resultant phylogenetic framework, in combination with an ancestral state reconstruction (ASR) analysis, to explore the evolution of two key morphological characters (number of segments of the first and second antennae), previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ASR approach also allowed an assessment of whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Sequence data from the mtDNA COI and nDNA 18S rRNA genes were obtained from 32 parabathynellid species (100% of described genera and ~25% of described species) from key groundwater regions across Australia. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. Additionally, ancestral state reconstruction analysis provided evidence for multiple cases of convergent evolution for the two morphological characters evaluated, suggesting that caution needs to be shown when using these characters for elucidating phylogenetic relationships, particularly when there are few morphological characters available for reconstructing relationships. The ancestral state analysis contradicted the conventional view of parabathynellid evolution, which assumes that more simplified taxa (i.e. those with fewer-segmented appendages and setae) are derived and more complex taxa are primitive.     

Molecular phylogeny of the entomopathogenic fungi of the genus Cordyceps (Ascomycota: Clavicipitaceae) and its evolutionary implications

Abstract Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts, traditionally included in the family Clavicipitaceae of Ascomycota. Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co‐evolution of parasites and hosts in entomopathogenic ascomycetes. To this end, we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses. Based on the phylogenetic tree, we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character. The phylogenetic analyses revealed two important points. (i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps. The vertically immersed perithecia form was the ancestral state, superficial and obliquely immersed perithecia were derived characters, obliquely immersed was irreversible. Species with obliquely immersed perithecia were in a closely related group and were the derived group. (ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats. Based on the results of these analyses, host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.     

Phylogenetic relationships of freshwater bryozoans (Ectoprocta, Phylactolaemata) inferred from mitochondrial ribosomal DNA sequences

Most species of freshwater bryozoans (Ectoprocta: Phylactolaemata) have few morphological distinctions, and within phylactolaemates, the morphology of the statoblast has been used to determine evolutionary relationships. Here, two controversial phylogenies have been proposed for phylactolaemates with regard to the relationship of Lophopodidae to other families. Two plumatellid genera, Gelatinella and Hyalinella , are candidates for the ancestral type of lophopodids. In addition, the coexistence of spines on the surfaces of the statoblast has led to the suggestion that lophopodids are closely related to the family Cristatellidae. In this study, we analysed mitochondrial DNA sequences of the 12S and 16S rDNA genes of 10 phylactolaemate species. Our results suggest that plumatellids may not be a direct ancestral group of lophopodids and that cristatellids are not a sister group of lophopodids. Fredericella , which was previously thought to be an ancestral group, was revealed to be derived. In addition, our results suggest that Stephanella is the most basal phylactolaemate. Mapping morphological characteristics onto the sequence-based phylogenetic tree revealed convergent evolution of statoblast characters.     

The road to the Janiroidea: Comparative morphology and evolution of the asellote isopod crustaceans

This paper presents a new phylogenetic estimate of isopod crustaceans of the suborder Asellota with the aim of clarifying the evolution of the superfamily Janiroidea, a large and diverse group inhabiting all aqueous habitats. The phylogenetic analysis is based on a morphological evaluation of characters used in past classifications, as well as several new characters. The evolutionary polarity of the characters was determined by outgroup analysis. The characters employed were from the pleopods, the copulatory organs, the first walking legs, and the cephalon. The resulting character data set was analyzed with numerical phylogenetic computer programs to find one most parsimonious clado-gram, which is translated into a classification using the sequencing convention. The new phylogenetic estimate is significantly more parsimonious than previous trees from the literature, and several of its monophyletic groups have robust confidence limits. The superfamily Stenetrioidea belongs to the clade including the Janiroidea, not with the Aselloidea as previously suggested. The sister group of the Janiroidea is the family Pseudojaniridae, which is elevated to superfamily rank. The clade including the families Gnathostenetroididae and Protojaniridae is not the sister group of the Janiroidea, and is derived earlier in janiroidean evolution than the Stenetrioidea. Within the Janiroidea, the family Janiridae is not the most primitive taxon as previously believed. The clade including the families Munnidae and Pleurocopidae contains the earliest derived janiroideans. The data also indicate that the unusual sexual morphology of the Janiroidea did not appear suddenly but developed as a series of independent steps within the Asellota.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.     

Amphi-Atlantic distribution of the Mancocumatinae (Cumacea: Bodotriidae), with description of a new genus dwelling in marine lava caves of Tenerife (Canary Islands)

A new cumacean genus and species, Speleocuma guanche gen et sp. nov. , belonging to the subfamily Mancocumatinae Watling 1977 , is described from marine lava caves of Tenerife, Canary Islands. This genus differs from others in the subfamily in having two pairs of pleopods in males and exopods on first to third pereopods, but not on fourth pereopod, in both sexes. Correlation between phylogenetic relationships of the new genus and the geological history of the Canarian archipelago points to a probable origin of this endemism: the subfamily Mancocumatinae show a disjunct distribution on both sides of the Atlantic Ocean, a pattern which has been associated with fauna of Tethyan origin. It is suggested that present-day genera of the subfamily evolved from a common shallow water ancestor living in the late Mesozoic ( c . 120 Myr BP), when the opening of the Atlantic Ocean had begun. It survived in shallow waters off the west African coast before the emergence of the Canary Islands from the sea floor. Later on, between the late Cretaceous and the Mio-Pliocene, it was able to colonize crevicular habitats of the eastern Canary Islands through continental or land bridges. Finally, their numbers increased to occupy more recent biotops like flooded lava tube caves as well as westward islands such as Tenerife. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 134 , 453–461.     

How the worm got its pharynx: phylogeny, classification and Bayesian assessment of character evolution in Acoela

Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensive phylogenetic study of Acoela and the taxonomy of the 380 species is chaotic. Here we use two nuclear ribosomal genes and one mitochondrial gene in combination with 37 morphological characters in an analysis of 126 acoel terminals (about one-third of the described species) to estimate the phylogeny and character evolution of Acoela. We present an estimate of posterior probabilities for ancestral character states at 31 control nodes in the phylogeny. The overall reconstruction signal based on the shape of the posterior distribution of character states was computed for all morphological characters and control nodes to assess how well these were reconstructed. The body-wall musculature appears more clearly reconstructed than the reproductive organs. Posterior similarity to the root was calculated by averaging the divergence between the posterior distributions at the nodes and the root over all morphological characters. Diopisthoporidae is the sister group to all other acoels and has the highest posterior similarity to the root. Convolutidae, including several "model" acoels, is most divergent. Finally, we present a phylogenetic classification of Acoela down to the family level where six previous family level taxa are synonymized.     

The Phylogeny and Systematics of Blind Cambrian Ptychoparioid Trilobites

The paraphyletic trilobite suborder Ptychopariina includes a large proportion of Cambrian trilobite diversity and is probably ancestral to most groups of post-Cambrian trilobites. Resolution of the phylogenetic relationships within the group is therefore crucial to a better understanding of the initial radiation of trilobites. The recognition of approaches that can successfully resolve the relationships of ptychoparioid taxa is an important first step towards this aim. Cladistic analysis was used to determine relationships within the Cambrian ptychoparioid trilobite family Conocoryphidae, and to test claims that the family is polyphyletic. Ninety-seven characters were coded for 40 conocoryphid species and nine non-conocoryphids. The results indicate that the family consists of four distantly related clades. Three are recognized here as distinct families, including an extensively revised Conocoryphidae, and the families Holocephalidae and Atopidae. The fourth clade is referred to the subfamily Acontheinae (Corynexochida) as the new Tribe Hartshillini. Analysis of the disparity of these four clades shows that they are significantly less morphologically variable than the original polyphyletic taxon, demonstrating the possible effects of taxonomic error on macroevolutionary studies of morphological disparity.     

Juvenile morphology of the xanthid crab Leptodius exaratus (H. Milne-Edwards, 1834) (Decapoda: Brachyura), with notes on the appearance of sexual dimorphism

Summary

The morphometrical and meristic features of the carapace, cephalic appendages (antenna, antennule), mouthparts (maxillule, maxilla, first-third maxillipeds), sternum, pereiopods, abdomen, and pleopods of juveniles and the onset of morphological sexual dimorphism were described for the xanthid crab Leptodius exaratus (H. Milne Edwards, 1834), based on laboratory-reared and wild adult specimens collected from Tateyama Bay, Japan. First instar juveniles shared some of the features of adults (e.g. gross appearance of the carapace and cheliped propodus proportions), but differed from adults on almost all other morphological parameter examined. Morphological development was still not complete at the ninth instar; extrapolation from the rate of morphological changes between instars 1–9 suggests that L. exaratus requires about 13 ecdyses to transform into adults, including development of reproductive structures. Differences in the number and morphology of pleopods and abdomen width allowed early distinction of the sexes. Thus, males formed gonopods in the first abdominal somite and lost the paired vestigial pleopods in somites 3–5 from the fourth instar; females retained the pleopods in somites 2–5, but these became biramous and had increased setation. The abdomen grew wider in females than in males from the fifth instar. Several morphological features of juveniles have phylogenetic and taxonomic implications: carapace motifs clearly place L. exaratus in the superfamily Xanthoidea, whereas the patterns of setation in the scaphognathite and first maxilliped epipod allow separation of this (xanthid) species from crabs of other Xanthoidean families.     

Discovery of Aspidytidae,a new family of aquatic Coleoptera

The six extant aquatic families of Hydradephaga (Coleoptera) known so far represent a diverse group of beetles morphologically highly modified for life in the water. We report the discovery of a new genus with two species from South Africa and China, which differ greatly from all extant families, but resemble the Jurassic-Cretaceous dagger Liadytidae (the dagger symbol indicates that the taxa are known only as fossils). Based on a combined phylogenetic analysis of molecular and morphological data we erect a new family, Aspidytidae, which is the sister group of Dytiscidae plus Hygrobiidae. We propose a new scenario for the evolution of swimming behaviour in adephagan beetles, in which the transition into the aquatic environment is followed by complex and repeated changes in lifestyles, including the secondary complete loss of swimming ability in Aspidytidae.     

Phylogeny of Medusozoa and the evolution of cnidarian life cycles

To investigate the evolution of cnidarian life cycles, data from the small subunit of the ribosome are used to derive a phylogenetic hypothesis for Medusozoa. These data indicate that Cnidaria is monophyletic and composed of Anthozoa and Medusozoa. While Cubozoa and Hydrozoa are well supported clades, Scyphozoa appears to be paraphyletic. Stauromedusae is possibly the sister group of either Cubozoa or all other medusozoans. The phylogenetic results suggest that: the polyp probably preceded the medusa in the evolution of Cnidaria; within Hydrozoa, medusa development involving the entocodon is ancestral; within Trachylina, the polyp was lost and subsequently regained in the parasitic narcomedusans; within Siphonophorae, the float originated prior to swimming bells; stauromedusans are not likely to be descended from ancestors that produced medusae by strobilation; and cubozoan polyps are simplified from those of their ancestors, which possessed polyps with gastric septa and four mesogleal muscle bands and peristomial pits.     

The Evolution of Dental Eruption Sequence in Artiodactyls

The sequence of eruption of the second generation of teeth varies across taxa, is highly functional, and is strongly influenced by genetic effects. We assessed postcanine dental eruption sequence across artiodactyls in order to test two hypotheses: 1) dental eruption sequence is a good phylogenetic character for artiodactyls; and, 2) eruption sequence is adaptive and associated with life history variables like postnatal growth and longevity in artiodactyls (Schultz’s Rule). We examined postcanine eruption sequence in 81 genera (100 species) spanning ten families of Artiodactyla. Our ancestral state reconstruction supports the interpretation that the third molar erupted last in the ancestor of Artiodactyla, and that the fourth premolar erupted after the third molar in the ancestor of Ruminantia. Our results indicate that eruption of the third molar last evolved secondarily in the caprines, likely sometime in the Miocene. Overall, our results support the hypothesis that dental eruption sequence is phylogenetically conserved in artiodactyls. Caprines occupy high elevation habitats, and we hypothesize that evolution of their unique dental eruption sequence may be associated with limited resource availability in high elevation mountain systems and the necessity to process a wide range of vegetation types.     

A Paedomorphic parasite associated with a neotenic amphibian host: phylogenetic evidence suggests a revised systematic position for Sphyranuridae within anuran and turtle Polystomatoineans

The phylogenetic relationships of the families Polystomatidae and Sphyranuridae (subclass Polystomatoinea) within tetrapod monogenean parasites were investigated using partial 18S rDNA sequences. About 600 nucleotides of 11 species were sequenced, including 7 species of the most common subfamilies of Polystomatidae found in anurans and turtles, 1 species of the family Sphyranuridae parasitizing exclusively urodelans, and 3 species of the subclass Oligonchoinea infesting teleostean fishes. The phylogenetic analyses were performed using three reconstruction methods: neighbor-joining, maximum-parsimony, and maximum-likelihood. Polystomatoineans but not polystomatids were shown to be monophyletic. Within the polystomatoineans there are two clades: one includes the amphibian monogeneans (anuran polystomatids and urodelan sphyranurids) and the other includes the turtle polystomatids. Polystomatoineans may have coevolved with amphibian hosts, and an ancestral "polystome" dispersed at least 200 million years ago, either from the basal stem of lissamphibians or from an anuran ancestral stock, to freshwater turtles. Furthermore, the urodelan genus Sphyranura, initially assigned to the family Sphyranuridae on the basis of morphological and ontogenetic evidence, is clearly nested within polystomatids, suggesting that its systematic status must be revised. This supports recent findings which argue that species of the family Sphyranuridae may be paedomorphic parasites exclusively infesting neotenic mudpuppies.