The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Molecular evolution and diversification of the moss family Daltoniaceae (Hookeriales,Bryophyta) with emphasis on the unravelling of the phylogeny of Distichophyllum and its allies

Phylogenetic relationships in Daltoniaceae (～200 species in 14 genera) are inferred from nucleotide sequences from five genes, representing all genomic compartments, using parsimony, likelihood and Bayesian methods. Alternative classifications for Daltoniaceae have favoured traits from either sporophytes or gametophytes; phylogenetic transitions in gametophytic leaf limbidia and sporophytic exostome ornamentation were evaluated using ancestral state reconstruction to assess the levels of conflict between these generations. Elimbate leaves and the cross‐striate exostome are reconstructed as plesiomorphic states. Limbate leaves and papillose exostomes evolved at least two and six times, respectively, without reversals. The evolution of leaf limbidia is relatively conserved, but exostome ornamentation is highly homoplasious, indicating that superficial similarity in peristomes gives unreliable approximations of phylogenetic relatedness. Our phylogenetic analyses show that Achrophyllum and Calyptrochaeta are reciprocally monophyletic. Within core Daltoniaceae, relationships among taxa with elimbate leaves are generally well understood. However, taxa with limbate leaves form a monophyletic group, but resolved subclades correspond to biogeographical entities, rather than to traditional concepts of genera. Daltonia (～21 species), Distichophyllum (～100 species) and Leskeodon (～20 species) are polyphyletic. Seven nomenclatural changes are proposed here. As the current taxonomy of Daltoniaceae lacks phylogenetic consistency, critical generic revisions are needed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses

Lebedev, V.S., Bannikova, A.A., Pagès, M., Pisano, J., Michaux, J.R. & Shenbrot, G.I. (2012). Molecular phylogeny and systematics of Dipodoidea: a test of morphology‐based hypotheses. —Zoologica Scripta, 42, 231–249. The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid‐dwelling jerboas (Dipodinae – three‐toed jerboas, Allactaginae – five‐toed jerboas, Cardiocraniinae – pygmy jerboas and Euchoreutinae – long‐eared jerboas), the other two are represented by more generalized quadrupedal taxa (Zapodinae – jumping mice and Sminthinae – birch mice). Despite considerable effort from morphologists, the taxonomy as well as the phylogeny of the Dipodoidea remains controversial. Strikingly, molecular approach has never been envisaged to investigate these questions. In this study, the phylogenetic relationships among the main dipodoid lineages were reconstructed for the first time using DNA sequence data from four nuclear genes (IRBP, GHR, BRCA1, RAG1). No evidence of conflict among genes was revealed. The same robustly supported tree topology was inferred from the concatenated alignment whatever the phylogenetic methods used (maximum parsimony, maximum‐likelihood and Bayesian phylogenetic methods). Sminthinae branches basally within the dipodoids followed by Zapodinae. Monophyletic Cardiocraniinae is sister to all other jerboas. Within the latter, the monophyly of both Dipodinae and Allactaginae is highly supported. The relationships between Dipodinae, Allactaginae and Euchoreutinae should be regarded as unresolved trichotomy. Morphological hypotheses were confronted to findings based on the presented molecular data. As a result, previously proposed sister group relationships between Euchoreutes and Sicista, Paradipus and Cardiocraniinae as well as the monophyly of Cardiocaniinae + Dipodinae were rejected. However, the latter association is consistently supported by most morphological analyses. The basis of the obvious conflict between genes and morphology remains unclear. Suggested modifications to the taxonomy of Dipodoidea imply recognition of three families: Sminthidae, Zapodidae and Dipodidae, the latter including Cardiocraniinae, Euchoreutinae, Allactaginae and Dipodinae as subfamilies.     

Comparative demography of commercially important parrotfish species from Micronesia

Fishery‐independent sampling was used to determine growth patterns, life span, mortality rates and timing of maturation and sex change in 12 common parrotfishes (Labridae: tribe Scarinae) from five genera (Calotomus, Cetoscarus, Chlorurus, Hipposcarus and Scarus) in Micronesia. Interspecific variation in life‐history traits was explored using multivariate analysis. All species displayed strong sex‐specific patterns of length‐at‐age among which males reached larger asymptotic lengths. There was a high level of correlation among life‐history traits across species. Relationships between length‐based and age‐based variables were weakest, with a tenuous link between maximum body size and life span. Cluster analysis based on similarities among life‐history traits demonstrated that species were significantly grouped at two major levels. The first grouping was driven by length‐based variables (lengths at maturity and sex change and maximum length) and separated the small‐ and large‐bodied species. Within these, species were grouped by age‐based variables (age at maturity, mortality and life span). Groupings based on demographic and life‐history features were independent of phylogenetic relationships at the given taxonomic level. The results reiterate that body size is an important characteristic differentiating species, but interspecific variation in age‐based traits complicates its use as a life‐history proxy. Detailed life‐history metrics should facilitate future quantitative assessments of vulnerability to overexploitation in multispecies fisheries.     

SEQUENTIAL RADIATIONS AND PATTERNS OF SPECIATION IN THE HAWAIIAN CRICKET GENUS LAUPALA INFERRED FROM DNA SEQUENCES

The tremendous diversity of endemic Hawaiian crickets is thought to have originated primarily through intraisland radiations, in contrast to an interisland mode of diversification in the native Hawaiian Drosophila. The Hawaiian cricket genus Laupala (family Gryllidae) is one of several native genera of flightless crickets found in rain-forest habitat across the Hawaiian archipelago. I examined the phylogenetic relationships among mitochondrial DNA (mtDNA) sequences sampled from 17 species of Laupala, including the 12S ribosomal RNA (rRNA), transfer RNA (RNA)^val and 16S rRNA regions. The distribution of mtDNA variants suggests that species within Laupala are endemic to single islands. The phylogenetic estimate produced from both maximum likelihood and maximum parsimony supports the hypothesis that speciation in Laupala occurred mainly within islands. The inferred biogeographical history suggests that diversification in Laupala began on Kauai, the oldest rain-forested Hawaiian island. Subsequently, colonization to younger islands in the archipelago resulted in a radiation of considerable phylogenetic diversity. Phylogenetic patterns in mtDNA are not congruent with prior systematic or taxonomic hypotheses. Hypotheses that may explain the conflict between the phylogenetic patterns of mtDNA variation and the species taxonomy are discussed.     

Old views and new insights: taxonomic revision of the Bukovina blind mole rat,Spalax graecus (Rodentia: Spalacinae)

As a result of their rather uniform external appearance and gross cranial morphology, the systematics of blind mole rats has been hotly debated over the last century; however, the separation of the large‐bodied and small‐bodied blind mole rats at the genus level (Spalax and Nannospalax, respectively), suggested earlier on morphological grounds, is strongly supported by recent molecular biological evidence. The species of Spalax have so far been distinguished from each other by cranial traits only, especially the outline of sutures of the cranium, and the shape and relative size of the nasal and parietal bones. Based on mitochondrial DNA sequences (with the widest taxonomic and geographic coverage so far) and detailed anatomical comparisons of museum specimens, we herewith provide a revision of the taxonomic and phylogenetic status of the westernmost representative of the genus, Spalax graecus s.l. We clarify that antiquus and istricus – presently regarded as synonyms of graecus – are well‐defined species, and they together form a separate clade within Spalax. The robustness of our conclusions is supported by the combined evidence of morphology, multilocus phylogeny, species distribution, and taxon history (species congruence with past tectonic and climate events). © 2013 The Linnean Society of London     

Adults of European ant‐like stone beetles (Coleoptera: Staphylinidae: Scydmaeninae) Scydmaenus tarsatus Müller & Kunze and Scydmaenus hellwigii (Herbst) prey on soft‐bodied arthropods

Scydmaenine beetles are commonly described as predators specialized in capturing and feeding on armored mites of the order Oribatida, and documented cases of feeding on other live arthropods have not been known. Based on laboratory observations and a broad choice of Acari (armored and soft‐bodied) and other soil arthropods, food preferences and associated behavior of two scydmaenine species are clarified and described. Adults of Scydmaenus tarsatus ignored oribatid and mesostigmatan mites, but readily attacked and fed on a soft‐bodied Rhizoglyphus sp. (Acaridae), and on small springtails, especially on Ceratophysella denticulata (Hypogastruridae). A water drinking behavior was observed for this species, not reported previously in any Staphylinidae. Scydmaenus hellwigii ignored all tested Acari (including Rhizoglyphus) and scavenged on dead neanurine collembolans or freshly cut pieces of large springtails; a long term culture was maintained by feeding beetles with isotomid springtails. Previously reported strict specialization of Scydmaenus as a predator on Oribatida was not confirmed and it is concluded that the studied species feed on live soft‐bodied organisms and scavenge on dead arthropods.     

Genetic barcoding of marine leeches (Ozobranchus spp.) from Florida sea turtles and their divergence in host specificity

Ozobranchus margoi and Ozobranchus branchiatus are the only two species of marine turtle leeches (Ozobranchus spp.) known to inhabit the Atlantic coast of the United States and the Gulf of Mexico. In early reports of fibropapillomatosis (FP) in green turtles (Chelonia mydas), O. branchiatus was implicated as a vector in the transmission of Fibropapilloma‐associated turtle herpesvirus (FPTHV). It is imperative that the leech species be identified to elucidate the role Ozobranchus spp. may play in disease transmission. In this study, Ozobranchus branchiatus has been identified for the first time on a loggerhead (Caretta caretta) turtle, and the molecular data for this species is now available for the first time in GenBank. Both species of leeches were also found infecting a single C. mydas. Using morphological taxonomy combined with distance‐ and character‐based genetic sequence analyses, this study has established a DNA barcode for both species of Ozobranchus spp. leech and has shown it can be applied successfully to the identification of leeches at earlier stages of development when morphological taxonomy cannot be employed. The results suggest a different haplotype may exist for O. branchiatus leeches found on C. caretta versus C. mydas. Leech cocoon residue collected from a C. mydas was identified using the new method.     

Comparative morphology,biology and phylogeny of terminal‐instar larvae of the European species of Toryminae (Hym., Chalcidoidea,Torymidae) parasitoids of gall wasps (Hym. Cynipidae)

We present a phylogenetic and taxonomic study of the morphology and biology of the terminal‐instar larval stage of 19 species representing all the genera of Torymidae parasitoids of gall wasps in Europe, with the single exception of Megastigmus. The genera studied include Adontomerus Nikol'skaya, Idiomacromerus Crawford, Chalcimerus Steffan & Andriescu, Glyphomerus Förster, Pseudotorymus Masi and Torymus Dalman. We primarily used chaetotaxy and some head structures. The terminal‐instar larvae of all studied species are thoroughly described for the first time and illustrated with SEM images. We provide diagnostic characters for the family and the genera studied, and keys to genera and species for the identification of torymid larvae associated with cynipid galls. The majority of the torymid larvae studied are solitary monophagous parasitoids. Finally, to assess the potential use of larval characters in systematic studies of the family, a phylogenetic analysis of the studied taxa based on 42 larval morphological characters is proposed and compared with the current taxonomy of Torymidae. Our results suggest that body chaetotaxy, and characters of the head and mouthparts could be used for genera and species discrimination. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 676–721.     

The role of phylogeny and ecology in shaping morphology in 21 genera and 127 species of Australo‐Papuan myobatrachid frogs

Body shape is predicted to differ among species for functional reasons and in relation to environmental niche and phylogenetic history. We quantified morphological differences in shape and size among 98.5% of the 129 species and all 21 genera of the Australo‐Papuan endemic myobatrachid frogs to test the hypothesis that habitat type predicts body shape in this radiation. We tested this hypothesis in a phylogenetic context at two taxonomic levels: across the entire radiation and within the four largest genera. Thirty‐four external measurements were taken on 623 museum specimens representing 127 species. Data for seven key environmental variables relevant to anurans were assembled for all Australian‐distributed species based on species' distributions and 131,306 locality records. The Australo‐Papuan myobatrachid radiation showed high diversity in adult body size, ranging from minute (15 mm snout–vent length) to very large species (92 mm), and shape, particularly sin relative limb length. Five main morphological and environmental summary variables displayed strong phylogenetic signal. There was no clear relationship between body size and environmental niche, and this result persisted following phylogenetic correction. For most species, there was a better match between environment/habitat and body shape, but this relationship did not persist following phylogenetic correction. At a broad level, species fell into three broad groups based on environmental niche and body shape: 1) species in wet habitats with relatively long limbs, 2) species in arid environments with relatively short limbs (many of which are forward or backward burrowers) and 3) habitat generalist species with a conservative body shape. However, these patterns were not repeated within the four largest genera ? Crinia, Limnodynastes, Pseudophryne and Uperoleia. Each of these genera displayed a highly conservative anuran body shape, yet individual species were distributed across the full spectrum of Australian environments. Our results suggest that phylogenetic legacy is important in the evolution of body size and shape in Australian anurans, but also that the conservative body plan of many frogs works well in a wide variety of habitats.     

Taxonomic classification of the reef coral families Merulinidae,Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia)

Modern coral taxonomy has begun to resolve many long‐standing problems in traditional systematics stemming from its reliance on skeletal macromorphology. By integrating examinations of colony, corallite, and subcorallite morphology with the molecular sequence data that have proliferated in the last decade, many taxa spread across the scleractinian tree of life have been incorporated into a rigorous classification underpinned by greater phylogenetic understanding. This monograph focuses on one of the most challenging clades recovered to date – its disarray epitomized by the informal name ‘Bigmessidae’. This group of predominantly Indo‐Pacific species previously comprised families Merulinidae, Faviidae, Pectiniidae, and Trachyphylliidae, but in a recent study these have been incorporated within Merulinidae. We studied 84 living merulinid species by examining morphological traits at three different scales of coral skeletal structure ? macromorphology, micromorphology, and microstructure ? to construct a morphological matrix comprising 44 characters. Data were analysed via maximum parsimony and also transformed onto a robust molecular phylogeny under the parsimony and maximum likelihood criteria. Comparisons amongst morphological character types suggest that although many characters at every scale are homoplastic, some to a greater extent than others, several can aid in distinguishing genus‐level clades. Our resulting trees and character analyses form the basis of a revised classification that spans a total of 139 species contained within 24 genera. The tree topologies necessitate the synonymization of Barabattoia as Dipsastraea, and Phymastrea as Favites. Furthermore, Astrea and Coelastrea are resurrected, and one new genus, P aramontastraea Huang & Budd gen. nov. , is described. All the genera in Merulinidae, along with the monotypic Montastraeidae and Diploastraeidae, are diagnosed based on the characters examined. The integrative classification system proposed here will form the framework for more accurate biodiversity estimates and guide the taxonomic placement of extinct species. © 2014 The Linnean Society of London     

Molecular and morphometric systematics of Diapterus (Perciformes,Gerreidae)

The fish belonging to Gerreidae are common representatives of the coastal ichthyofauna of the tropics and subtropics of the world. The genus Diapterus has a neotropical distribution and currently includes four species: two in the Atlantic Ocean [Irish mojarra D. auratus Ranzani 1842 and rhombic mojarra D. rhombeus (Cuvier 1829)] and two in the Pacific Ocean [short‐beaked mojarra D. brevirostris (Sauvage 1879) and golden mojarra D. aureolus (Jordan & Gilbert 1882)]. This genus has uncertain taxonomy based on the remarkable and dissimilar morphology of D. aureolus. We evaluated the taxonomy and phylogeny of Diapterus with statistical (canonical discriminant analysis) and phylogenetic analyses (maximum parsimony, maximum likelihood and Bayesian inference) of geometric morphometric data (relative warps) and molecular data (12Sr RNA, 16Sr RNA, COI and RAG1 sequences). Our results indicate that the genus Diapterus as we currently conceive it is a polyphyletic group: [(Gerres cinereus – Eucinostomus spp. (D. aureolus – (Eugerres spp. (D. auratus – (D. brevirostris – D. rhombeus)))))]. Therefore, a taxonomic rearrangement is needed. To preserve the monophyly of the group, our proposal is to remove D. aureolus and place it in a new monotypic genus. A neotype is designated for D. aureolus as well as an artificial identification key for the genera and the species treated in this article.     

New fossils from China elucidating the phylogeny of Praesiricidae (Insecta: Hymenoptera)

A new subfamily of Praesiricidae (Pamphilioidea), Decorisiricinae subfam.n. , is erected based on three new genera: Decorisiricius gen.n. , Limbisiricius gen.n. and Brevisiricius gen.n. Two new species – Decorisiricius patulus gen. et sp.n. and D. longus sp.n. – from the Lower Cretaceous Yixian Formation and three species –Limbisiricius aequalis gen. et sp.n. , Limbisiricius complanatus sp.n. and Brevisiricius partialis gen. et sp.n. – from the Middle Jurassic Jiulongshan Formation, are described. Based on these well‐preserved new fossil specimens and previously published data, the nonmonophyly of Praesiricidae is confirmed and the phylogenetic relationships of species of Praesiricidae are analysed for the first time. Two main clades within Praesiricidae are recognized from the cladistic analysis: Decorisiricinae subfam.n. forms a monophyletic lineage, with the remaining members of Praesiricidae plus Megalodontes (Megalodontesidae) forming its sister group. The two subfamilies Archoxyelydinae and Praesiricinae are discarded with no strong supported synapomorphic characters based on phylogenetic research. A key to all genera of Praesiricidae is provided. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:38D703ED‐127A‐4DB0‐8153‐8D78AF4AC212 .     

Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies

The globally distributed avian family Motacillidae consists of five to seven genera (Anthus, Dendronanthus, Tmetothylacus, Macronyx and Motacilla, and depending on the taxonomy followed, Amaurocichla and Madanga) and 66–68 recognized species, of which 32 species in four genera occur in sub‐Saharan Africa. The taxonomy of the Motacillidae has been contentious, with variable numbers of genera, species and subspecies proposed and some studies suggesting greater taxonomic diversity than currently recognized (five genera and 67 species). Using one nuclear (Mb) and two mitochondrial (cyt b and CO1) gene regions amplified from DNA extracted from contemporary and museum specimens, we investigated the taxonomic status of 56 of the currently recognized motacillid species and present the most taxonomically complete and expanded phylogeny of this family to date. Our results suggest that the family comprises six clades broadly reflecting continental distributions: sub‐Saharan Africa (two clades), the New World (one clade), Palaearctic (one clade), a widespread large‐bodied Anthus clade, and a sixth widespread genus, Motacilla. Within the Afrotropical region, our phylogeny further supports recognition of Wood Pipit Anthus nyassae as a valid species, and the treatment of Long‐tailed Pipit Anthus longicaudatus and Kimberley Pipit Anthus pseudosimilis as junior subjective synonyms of Buffy Pipit Anthus vaalensis and African Pipit Anthus cinnamomeus, respectively. As the disjunct populations of Long‐billed Pipit Anthus similis in southern and East Africa are genetically distinct and geographically separated, we propose a specific status for the southern African population under the earliest available name, Nicholson's Pipit Anthus nicholsoni. Further, as our analyses indicate that Yellow‐breasted Pipit Anthus chloris and Golden Pipit Tmetothylacus tenellus are both nested within the Macronyx longclaws, we propose transferring these species to the latter genus.     

Phylogenomic relationships of bioluminescent elateroids define the ‘lampyroid’ clade with clicking Sinopyrophoridae as its earliest member

Bioluminescence has been hypothesized as aposematic signalling, intersexual communication and a predatory strategy, but origins and relationships among bioluminescent beetles have been contentious. We reconstruct the phylogeny of the bioluminescent elateroid beetles (i.e. Elateridae, Lampyridae, Phengodidae and Rhagophthalmidae), analysing genomic data of Sinopyrophorus Bi & Li, and in light of our phylogenetic results, we erect Sinopyrophoridae Bi & Li, stat.n . as a clicking elaterid‐like sister group of the soft‐bodied bioluminescent elateroid beetles, that is, Lampyridae, Phengodidae and Rhagophthalmidae. We suggest a single origin of bioluminescence for these four families, designated as the ‘lampyroid clade’, and examine the origins of bioluminescence in the terminal lineages of click beetles (Elateridae). The soft‐bodied bioluminescent lineages originated from the fully sclerotized elateroids as a derived clade with clicking Sinopyrophorus and Elateridae as their serial sister groups. This relationship indicates that the bioluminescent soft‐bodied elateroids are modified click beetles. We assume that bioluminescence was not present in the most recent common ancestor of Elateridae and the lampyroid clade and it evolved among this group with some delay, at the latest in the mid‐Cretaceous period, presumably in eastern Laurasia. The delimitation and internal structure of the elaterid‐lampyroid clade provides a phylogenetic framework for further studies on the genomic variation underlying the evolution of bioluminescence.     

Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification

The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT‐psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long‐held assumption that morphology may render spurious or low‐quality results in this taxonomic group is challenged. The morphological trends previously proposed are re‐evaluated in light of the new phylogenetic scheme.     

Phylogenetic signal in the evolution of body colour and spicule skeleton in calcareous sponges

Some of the morphological characters used in Porifera taxonomy have often been shown to be inconsistent. In the present study, we tested the phylogenetic coherence of currently used taxonomic characters of the calcarean genus Clathrina. For this, 20 species of Clathrina and three other calcinean genera (Ascandra, Guancha, and Leucetta) were sequenced for the ITS and D2 region of the 28S ribosomal DNA. Maximum‐likelihood and maximum‐parsimony algorithms were used to reconstruct phylogenetic trees. Deep divergences were observed in our tree and Clathrina was shown to be paraphyletic. The major split in our topology showed a clear‐cut distinction between sponges with and without tetractine spicules. Moreover, a group of yellow‐coloured Clathrina was clearly separated from the remaining white‐coloured species. Our results show that the presence of diactines, water‐collecting tubes, the degree of cormus anastomosis, and actine shapes do not correlate with the major clades of the calcinean phylogeny. On the other hand, the presence of tripods, the absence of tetractines, and the presence of spines in the apical actine of tetractines seem to be good synapomorphies for clades in our tree. Our results demonstrate that skeleton characters can be reliably used in higher level taxonomy in Clathrinida. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1026–1034.