A computational method for quantifying morphological variation in scleractinian corals

Morphological variation in marine sessile organisms is frequently related to environmental factors. Quantifying such variation is relevant in a range of ecological studies. For example, analyzing the growth form of fossil organisms may indicate the state of the physical environment in which the organism lived. A quantitative morphological comparison is important in studies where marine sessile organisms are transplanted from one environment to another. This study presents a method for the quantitative analysis of three-dimensional (3D) images of scleractinian corals obtained with X-ray Computed Tomography scanning techniques. The advantage of Computed Tomography scanning is that a full 3D image of a complex branching object, including internal structures, can be obtained with a very high precision. There are several complications in the analysis of this data set. In the analysis of a complex branching object, landmark-based methods usually do not work and different approaches are required where various artifacts (for example cavities, holes in the skeleton, scanning artifacts, etc.) in the data set have to be removed before the analysis. A method is presented, which is based on the construction of a medial axis and a combination of image-processing techniques for the analysis of a 3D image of a complex branching object where the complications mentioned above can be overcome. The method is tested on a range of 3D images of samples of the branching scleractinian coral Madracis mirabilis collected at different depths. It is demonstrated that the morphological variation of these samples can be quantified, and that biologically relevant morphological characteristics, like branch-spacing and surface/volume ratios, can be computed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Histological data in a combined phylogenetic analysis of scleractinian reef corals

Scleractinian systematics have undergone rapid changes due to increased use of molecular phylogenetics and new perspectives on skeletal morphology from micromorphology and microstructure. Despite this increase in characters there are still unresolved clades in the phylogeny, indicating that more characters are needed. This study investigates a new source of morphological data within the soft tissue of Indo‐Pacific scleractinian corals. Features of tissue layers, especially cnidocytes, are described in hematoxylin and eosin stained thin sections. Based on this new histological data source, a combined analysis with mitochondrial DNA and skeletal data is performed using parsimony and Bayesian analysis. Parsimony analysis yields three most‐parsimonious trees similar to trees based on Bayesian analysis. Character maps are also produced that show origination of histomorphological traits at deep nodes within the phylogeny. In general, both analyses retain the previously designated families Lobophylliidae and Merulinidae, but some genera are found to be paraphyletic. Nonetheless, the combined analysis produces a highly resolved and well‐supported phylogeny, which could lead to more effective use of biological conservation metrics based on evolutionary distinctiveness. These results show for the first time that inclusion of histomorphological characters improves the resolution of phylogenetic analyses of reef corals. J. Morphol. 277:494–511, 2016. © 2016 Wiley Periodicals, Inc.     

A modern approach to rotiferan phylogeny: combining morphological and molecular data

The phylogeny of selected members of the phylum Rotifera is examined based on analyses under parsimony direct optimization and Bayesian inference of phylogeny. Species of the higher metazoan lineages Acanthocephala, Micrognathozoa, Cycliophora, and potential outgroups are included to test rotiferan monophyly. The data include 74 morphological characters combined with DNA sequence data from four molecular loci, including the nuclear 18S rRNA, 28S rRNA, histone H3, and the mitochondrial cytochrome c oxidase subunit I. The combined molecular and total evidence analyses support the inclusion of Acanthocephala as a rotiferan ingroup, but do not support the inclusion of Micrognathozoa and Cycliophora. Within Rotifera, the monophyletic Monogononta is sister group to a clade consisting of Acanthocephala, Seisonidea, and Bdelloidea-for which we propose the name Hemirotifera. We also formally propose the inclusion of Acanthocephala within Rotifera, but maintaining the name Rotifera for the new expanded phylum. Within Monogononta, Gnesiotrocha and Ploima are also supported by the data. The relationships within Ploima remain unstable to parameter variation or to the method of phylogeny reconstruction and poorly supported, and the analyses showed that monophyly was questionable for the families Dicranophoridae, Notommatidae, and Brachionidae, and for the genus Proales. Otherwise, monophyly was generally supported for the represented ploimid families and genera.     

Total evidence phylogeny of Gasterosteidae: combining molecular, morphological and behavioral data

Genealogical relationships among Gasterosteidae (Teleostei: Gasterosteiformes) were tested with 84 morphological, 48 behavioral, and 2879 molecular characters. Phylogenetic analysis of the combined data set identified a single (CI = 0.735) best‐supported hypothesis (Spinachia (Apeltes ((Pungitius + Culaea)(Gasterosteus aculeatus + G. wheatlandi)))). This hypothesis is identical to previous phylogenetic propositions proposed on the basis of behavioral, and behavioral plus morphological data. Our hypothesis, however, differed from a molecular‐based phylogeny in the placement of Apeltes. This analysis highlights the importance of combining all available evidence in order to produce the best‐supported proposition of genealogical relationships.     

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

Coral taxonomy and systematics continue to be plagued by a host of problems. Due to high phenotypic variability within species, morphological approaches have often failed to recognize natural taxa, and molecular techniques have yet to be applied to many groups. Here, we summarize the levels of paraphyly found for scleractinian corals and test, based on new data, whether paraphyly is also a significant problem in Faviidae, the second-most speciose hermatypic scleractinian family. Using both DNA sequence and morphological data we find that, regardless of analysis technique (maximum parsimony, maximum likelihood and Bayesian likelihood), many conventional taxonomic groups are not monophyletic. Based on two mitochondrial markers (COI and a noncoding region) that we amplified for 81 samples representing 41 faviid species and 13 genera, five genera that are represented by more than one species are paraphyletic, as is the family Faviidae. The morphological characters currently used to identify these corals similarly fail to recover many genera. Furthermore, trees based on both data types are incongruent, and total evidence analysis does little to salvage conventional taxonomic groupings. Morphological convergence, phenotypic variability in response to the environment, and recent speciation are likely causes for these conflicts, which suggest that the present classification of corals is in need of a major overhaul. We propose more detailed studies of problematic faviid taxa using standardized morphological, mitochondrial, and nuclear genetic markers to facilitate combining of data.     

Mammalian phylogeny: comparison of morphological and molecular results

In an attempt to resolve the "bushy" part at the root of the eutherian tree, 182 nondental morphological characters from 100 species (79 extant and 21 extinct; 98 mammalian and 2 nonmammalian) were analyzed using two maximum-parsimony tree-building algorithms. Parallel analyses of 2,258 pairwise immunodiffusion comparisons with chicken antisera on 101 mammalian species and of amino acid sequence data of alpha and beta hemoglobins and other published protein sequences were also carried out. The morphological and molecular phylogenies agree in depicting the infraclass Eutheria as consisting of five major clades (thus resolving part of the "bush"). Rates of evolution were also found to be similar in the two types of phylogenies.     

The phylogeny of the Trypanosomatidae: the molecular and morphological approaches

The results of comparative analysis of two phylogenetic trees of the trypanosomatids based on morphological and molecular characters are discussed. The morphological dendrogram was based on 33 ultrastructural characters, 6 light microscope characteristics and 8 biological characters. Molecular UPGMA dendrogram depicting differences (Dice distance) between examined trypanosomatids is based on the universally primed PCR polymorphisms. The general topology of both dendrograms are similar, with the Trypanosoma at the base. The genus Wallaceina appears to be monophyletic. In a contrary, the genera Leptomonas, Crithidia and Herpetomonas look like artificial groups according to both methods used. The cyst-forming homoxenous trypanosomatids from insects represent a monophyletic clade, which seems to be a separate genus. Two species of within genus Wallaceina are arranged as a separate subgenus.     

Hormones and reproduction in scleractinian corals

Most broadcast spawning scleractinian corals synchronously release gametes during a brief annual spawning period. In southern Taiwan, the mass spawning of scleractinians occurs in lunar mid-March. The exact cues triggering this annual phenomenon remain unclear. A scleractinian coral, Euphyllia ancora has been selected as a model for the hormones and reproduction studies. Testosterone (T) and estradiol (E2) in free and glucuronided forms were identified and consistently detected in coral polyps throughout the year. Peak levels of free E2, glucuronided E2 and T were obtained in the coral tissue just prior to spawning. The presence of specific aromatase activity was demonstrated in coral tissue. Higher concentrations of free E2 than glucuronided E2 were detected in the coral tissue throughout the year. In contrast, higher levels of glucuronided E2 than free E2 and glucuronided T were found in seawater during mass coral spawning. Furthermore, immunoreactivity and biological activity of immunoreactive gonadotropin-releasing hormone (irGnRH) was detected and quantified in coral tissue. Coral extracts (irGnRH) and mammalian (m)GnRH agonist had a similar dose-dependent effect on luteinizing hormone (LH) release in black porgy fish pituitary cells (in vitro). Peak levels of irGnRH were detected during the spawning period. In in vivo experiments, mGnRH agonist time- and dose-dependently stimulated aromatase activity, as well as the levels of T and E2 in free and glucuronided forms in coral. In conclusion, our data suggest that irGnRH and glucuronided E2 may play important roles in the control of reproduction and mass spawning in corals.     

Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data

This study represents the first formal morphological and combined (morphological and molecular) phylogenetic analyses of the order Ephemeroptera. Taxonomic sampling comprised 112 species in 107 genera, including 42 recognized families (all major lineages of Ephemeroptera). Morphological data consisted of 101 morphological characters. Molecular data were acquired from DNA sequences of the 12S, 16S, 18S, 28S and H3 genes. The Asian genus Siphluriscus (Siphluriscidae) was supported as sister to all other mayflies. The lineages Carapacea, Furcatergalia, Fossoriae, Pannota, Caenoidea and Ephemerelloidea were supported as monophyletic, as were many of the families. However, some recognized families (for example, Ameletopsidae and Coloburiscidae) and major lineages (such as Setisura, Pisciforma and Ephemeroidea among others) were not supported as monophyletic, mainly due to convergences within nymphal characters. Clade robustness was evaluated by multiple methods and approaches.     

Reassessing evolutionary relationships of scleractinian corals

The widely accepted family tree of Scleractinia published by Wells, based on a combination of morphological coral taxonomy and the fossil record, has recently been revised by Veron. It is now possible to test the validity of some of the conclusions reached by these and other authors by the use of molecular techniques. This paper reviews the results to date. Studies of ribosomal DNA have shown that the Scleractinia are monophyletic, i.e. derived from the same ancestral taxon. Extensions of this same data set now indicate that the Poritidae and Dendrophylliidae, with their fossil antecedents, may each warrant separate suborder status. They further suggest (a) that the Suborder Faviina (faviids, mussids and their allies) should probably be retained as a monophyletic group and (b) that Wells' original account of the isolated position of the Pocilloporidae and Astrocoeniidae is correct. These conclusions all accord with Veron's family tree. However, the Fungiina, even after removal of the Poritidae, are unlikely to be a monophyletic group at suborder level. The molecular data further show that externally observable morphological characters used in the taxonomy of extant corals distinguish families more reliably than do internal micro-skeletal characters frequently used in coral palaeontology.     

Lack of congruence between morphological and molecular data in reconstructing the phylogeny of the galagonidae.

Published cladistic reconstructions of galagonid phylogeny based on morphological, behavioral, and genetic data have had few elements in common. A recent molecular study indicated that 2 of the 3 generic groupings derived from morphological data were not consistent with tree topologies constructed from the analysis of mitochondrial DNA sequences. In this study, we compiled and analyzed a data set based on craniodental morphology in 13 galagonid and 8 outgroup taxa, comprising 3 dwarf-lemur and 5 loris species, and subjected it to cladistic analysis. Our aim was not only to generate a new phylogenetic hypothesis based on these data, but also to investigate the conditions under which congruence could be achieved between these results and those obtained previously. The data set was found to be highly sensitive to the choice of outgroup, with the lorises showing high interspecific variability in cranial structure. Congruence between the craniodental and molecular trees could be achieved only if Arctocebus was used as the outgroup and two characters were preferentially weighted. Further progress in the reconstruction of galagonid phylogeny will require seeking consensus in a variety of other data sets, including postcranial morphology, behavior, and additional gene sequences. The effect of different outgroups on molecular analysis needs attention.     

Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions (COI, EF-1alpha and wingless). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1alpha data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.     

Physiology and taxonomy of scleractinian corals: a case study in the genus Stylophora

The morphology and skeletal characteristics of colonies of the coral genus Stylophora living on the reef edge at 1 m depth on the Jordanian coast of the Gulf of Aqaba (Red Sea) are those of S. mordax (Dana 1846) which has not been reported previously from that area. These colonies were considered earlier as ecomorphs of S. pistillata (Esper 1797) which lives down to at least 67 m on the reef slopes. Growth, organic content and metabolism were compared in colonies living at different depths (1,5,10 and 30 m). The trends of twelve parameters between 1 and 5 m were different from the variation observed between 5 and 30 m. Colonies living at 1 m have a higher chlorophyll content but a lower metabolic activity and growth rate than colonies living at 5 m. Most of these pecularities cannot be explained by the influence of environmental factors. It is therefore suggested that S. mordax is a valid taxon.     

Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

Deuterostomes are a monophyletic group of animals that include the vertebrates, invertebrate chordates, ambulacrarians and xenoturbellids. Fossil representatives from most major deuterostome groups, including some phylum-level crown groups, are found in the Lower Cambrian, suggesting that evolutionary divergence occurred in the Late Precambrian, in agreement with some molecular clock estimates. Molecular phylogenies, larval morphology and the adult heart/kidney complex all support echinoderms and hemichordates as a sister grouping (Ambulacraria). Xenoturbellids are a relatively newly discovered phylum of worm-like deuterostomes that lacks a fossil record, but molecular evidence suggests that these animals are a sister group to the Ambulacraria. Within the chordates, cephalochordates share large stretches of chromosomal synteny with the vertebrates, have a complete Hox complex and are sister group to the vertebrates based on ribosomal and mitochondrial gene evidence. In contrast, tunicates have a highly derived adult body plan and are sister group to the vertebrates based on the analyses of concatenated genomic sequences. Cephalochordates and hemichordates share gill slits and an acellular cartilage, suggesting that the ancestral deuterostome also shared these features. Gene network data suggest that the deuterostome ancestor had an anterior-posterior body axis specified by Hox and Wnt genes, a dorsoventral axis specified by a BMP/chordin gradient, and was bilaterally symmetrical with left-right asymmetry determined by expression of nodal.     

Corallite wall and septal microstructure in scleractinian reef corals: Comparison of molecular clades within the family Faviidae

Recent molecular phylogenies conflict with traditional scleractinian classification at ranks ranging from suborder to genus, challenging morphologists to discover new characters that better agree with molecular data. Such characters are essential for including fossils in analyses and tracing evolutionary patterns through geologic time. We examine the skeletal morphology of 36 species belonging to the traditional families Faviidae, Merulinidae, Pectiniidae, and Trachyphylliidae (3 Atlantic, 14 Indo‐Pacific, 2 cosmopolitan genera) at the macromorphological, micromorphological, and microstructural levels. Molecular analyses indicate that the families are not monophyletic groups, but consist of six family‐level clades, four of which are examined [clade XV = Diploastrea heliopora; clade XVI = Montastraea cavernosa; clade XVII (“Pacific faviids”) = Pacific faviids (part) + merulinids (part) + pectiniids (part) + M. annularis complex; clade XXI (“Atlantic faviids”) = Atlantic faviids (part) + Atlantic mussids]. Comparisons among molecular clades indicate that micromorphological and microstructural characters (singly and in combination) are clade diagnostic, but with two exceptions, macromorphologic characters are not. The septal teeth of “Atlantic faviids” are paddle‐shaped (strong secondary calcification axes) or blocky, whereas the septal teeth of “Pacific faviids” are spine‐shaped or multidirectional. Corallite walls in “Atlantic faviids” are usually septothecal, with occasional trabeculothecal elements; whereas corallite walls in “Pacific faviids” are usually trabeculothecal or parathecal or they contain abortive septa. Exceptions include subclades of “Pacific faviids” consisting of a) Caulastraea and Oulophyllia (strong secondary axes) and b) Cyphastrea (septothecal walls). Diploastrea has a diagnostic synapticulothecal wall and thick triangular teeth; Montastraea cavernosa is also distinct, possessing both “Pacific faviid” (abortive septa) and “Atlantic faviid” (paddle‐shaped teeth) attributes. The development of secondary axes is similar in traditional Atlantic faviids and mussids, supporting molecular results placing them in the same clade. Subclades of “Pacific faviids” reveal differences in wall structure and the arrangement and distinctiveness of centers of rapid accretion. J. Morphol. 272:66–88, 2011. © 2010 Wiley‐Liss, Inc.     

Dinoflagellate phylogeny revisited: reconciling morphological and molecular based phylogenies

Ultrastructural and molecular phylogenetic data suggest that dinoflagellates diverged as a lineage possibly as early as the Precambrian. However, the fossil record is problematic before the Mesozoic. From the mid Triassic, though, the fossil record of dinoflagellates is a rich source of information on Mesozoic-Cenozoic dinoflagellates, especially the gonyaulacoids and peridinioids. From the sequence of appearance of species and tabulation types and the impression of early morphological experimentation and later stabilization, the early Mesozoic radiation of dinoflagellates appears to be a real evolutionary event: indeed, dinoflagellate morphology as we know it today may originate in that event. This would explain why it is so difficult to interpret earlier fossils as dinoflagellates. However, that the dinoflagellate lineage existed in some form in the pre-Mesozoic is supported by biogeochemical data, early results of which indicate that certain early Paleozoic acanthomorph acritarchs may belong to the lineage.

A surprising degree of consistency is observed between ultrastructural (including tabulational), coarse biochemical and molecular sequence data. For example, sequence data provided by small subunit (SSU) rRNA support the hypothesis of progressive loss of histones within the dinoflagellates. Gymnodinioids have long been considered to be polyphyletic but are thought of generally as forerunners to the strongly thecate groups such as gonyaulacoids and peridinioids. In molecular trees they appear in both early-derived and late-derived positions, but mostly the latter. SSU data clearly support the gonyaulacoid/peridinioid ordinal separation, as does the fossil record. Prorocentroids are now thought to be the among the most derived dinoflagellates (and presumably the morphologically similar dinophysoids), but SSU sequences have so far failed to resolve the relationships of most gymnodinioids, peridinioids and prorocentroids (the so-called GPP complex) to one another. However, they do suggest the origin of prorocentroids from peridinioids rather than gonyaulacoids and that gymnodinioids probably had several origins.