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.     

Molecular systematics of the order anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI)

Fragments from three mitochondrial genes (12S, 16S, and COI) were sequenced to reconstruct a molecular phylogeny of the opisthobranch order Anaspidea. The molecular phylogeny supports the placement of the genus Akera, a taxon previously regarded by some authors as a cephalaspidean, within the Anaspidea. Incongruence between the molecular data and the classifications based on morphology suggests that some of the taxonomic characters (i.e., shell, parapodia fusion) traditionally used for the classification of sea hares must be reevaluated, since they may be homoplastic. The ancestral nature of Notarchus based on the molecular evidence suggests that homoplasy may be an explanation for the morphological resemblance of this species to the more derived sea hares with highly fused parapodia and concentrated nerve ganglia. Finally, examples are given of how comparative studies of the evolution of learning mechanisms in the anaspidean clade will benefit from the phylogenetic hypothesis presented in this paper.     

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

Background  

Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

Relationships within the family Actiniidae (Cnidaria,Actiniaria) based on molecular characters

Current sea anemone systematics is based on relatively few morphological characters, and potentially could benefit from the use of molecular characters. In this paper, the phylogenetic relationships of 12 species from 6 genera in the family Actiniidae have been investigated using electrophoretically separated isozymes. A numerical cladistic analysis has produced an estimated phylogeny. The implications of this phylogeny for the taxonomic use of certain morphological characters are discussed.     

Phylogenetic relationships of woodcreepers (Aves: Dendrocolaptinae) – incongruence between molecular and morphological data

The woodcreepers is a highly specialized lineage within the New World suboscine radiation. Most systematic studies of higher level relationships of this group rely on morphological characters, and few studies utilizing molecular data exist. In this paper, we present a molecular phylogeny of the major lineages of woodcreepers (Aves: Dendrocolaptinae), based on nucleotide sequence data from a nuclear non-coding gene region (myoglobin intron II) and a protein-coding mitochondrial gene (cytochrome b ). A good topological agreement between the individual gene trees suggests that the resulting phylogeny reflects the true evolutionary history of woodcreepers well. However, the DNA-based phylogeny conflicts with the results of a parsimony analysis of morphological characters. The topological differences mainly concern the basal branches of the trees. The morphological data places the genus Drymornis in a basal position (mainly supported by characters in the hindlimb), while our data suggests it to be derived among woodcreepers. Unlike most other woodcreepers, Drymornis is ground-adapted, as are the ovenbirds. The observed morphological similarities between Drymornis and the ovenbird outgroup may thus be explained with convergence or with reversal to an ancestral state. This observation raises the question of the use of characters associated with locomotion and feeding in phylogenetic reconstruction based on parsimony.     

Understanding phylogenetic incongruence: lessons from phyllostomid bats

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar‐feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species‐rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar‐feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well‐studied organisms such as phyllostomid bats.     

The utility of morphological characters in gastropod phylogenetics: an example from the Calyptraeidae

Organismal taxonomy is often based on a single or a small number of morphological characters. When they are morphologically simple or known to be plastic, we may not have great confidence in the taxonomic conclusions of analyses based on these characters. For example, calyptraeid gastropod shells are well known for their simplicity and plasticity, and appear to be subject to frequent evolutionary convergences, but are nevertheless the basis for calyptraeid taxonomy. In a case like this, knowing how the pattern of relationships inferred from morphological features used in traditional taxonomy compares to the patterns of relationships inferred from other morphological characters or DNA sequence data would be useful. In this paper, I examine the relative utility of traditional taxonomic characters (shell characters), anatomical characters and molecular characters for reconstructing the phylogeny of calyptraeid gastropods. The results of an ILD test and comparisons of the recovered tree topologies suggest that there is conflict between the DNA sequence data and the morphological data. Very few of the nodes recovered by the morphological data were recovered by any other dataset. Despite this conflict, the inclusion of morphological data increased the resolution and support of nodes in the topology recovered from a combined dataset. The RIs and CIs of the morphological data on the best estimate topology were not any worse than these indices for the other datasets. This analysis demonstrates that although analyses can be misled by these convergences if morphological characters are used alone, these characters contribute significantly to the combined dataset.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 541–593.     

Conflict and congruence in a combined DNA–morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae)

The phylogeny of megabats (Mammalia: Chiroptera: Megachiroptera) has been addressed only on molecular grounds, as little effort has previously been made to describe the impressive morphological variation of the group in terms of phylogenetically informative characters. Here we provide a morphological matrix of 236 characters from the integument, dentition, cranial and post‐cranial skeleton, digestive apparatus and urogenital system. This data set covers most characters discussed previously in more restricted taxonomic contexts, as well a large number of new characters. Our aim was to generate a phylogenetic hypothesis for megabats based on a combined analysis of morphological characters and available gene sequence data from four mitochondrial and one nuclear loci. We used direct optimization under conventional equal costs, as well as under a cost ratio that maximizes homology when inapplicables (gaps) are present. Our results contradict the allegedly high level of conflict between the molecular and morphological partitions. We found that, although morphology alone recovered trees different and to some extent incompatible with those from previous molecular analyses, the combination of the two sources of evidence easily accommodated the morphological and molecular signals, yielding a resolved and relatively well‐supported phylogeny of Megachiroptera that is in reasonable agreement with the current morphology‐based taxonomy of the group. Overall congruence favored the maximization of homology by a narrow margin. In addition, partial analyses showed that implied weighting of morphology performed slightly better than equal weighting with respect to the combined analyses. © The Willi Hennig Society 2005.     

Do orthologous gene phylogenies really support tree-thinking?

Background  

Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.     

Lophotrochozoan mitochondrial genomes

Progress in both molecular techniques and phylogenetic methodshas challenged many of the interpretations of traditional taxonomy.One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships withinthis group and the inclusion of some phyla remain uncertain.While much of this progress in phylogenetic reconstruction hasbeen based on comparing single gene sequences, there are alsohigher order features of genomes, such as the relative orderof genes, that have contributed, and this seems likely to beeven more fruitful in the future. Even though tremendous progressis being made on the sequence determination of whole nucleargenomes, the dataset of choice for genome-level characters formany animals across a broad taxonomic range remains mitochondrialgenomes. We review here what is known about mitochondrial genomesof the lophotrochozoans and how comparisons of some of thesefeatures may be useful in discerning the phylogeny of this group.     

Phylogeny of Antarctic dragonfishes (Bathydraconidae,Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes

Although Antarctic teleosts of the suborder Notothenioidei are well studied, the status of some families remains unclear because of limited taxonomic sampling and sometimes poor statistical support from molecular phylogenies. It is true for the Bathydraconidae, the sister-family of the famous haemoglobin-less icefishes, the Channichthyidae. The present study is aimed at clarifying bathydraconid phylogeny and the interrelationships of higher notothenioid families, taking nototheniids as the outgroup. For this purpose, about 300 positions in the mitochondrial control region, 750 positions in the cytochrome b, and a matrix of morphological characters were employed for separate and simultaneous phylogenetic analyses. We conclude that (1) molecular data strongly support the split of bathydraconids into three clades, here called the Bathydraconinae (Bathydraco, Prionodraco, Racovitzia), the Gymnodraconinae (Gymnodraco, Psilodraco, Acanthodraco), and the Cygnodraconinae (Cygnodraco, Gerlachea, Parachaenichthys). Interrelationships between these three and the Channichthyidae remain unclear. Molecular data support neither paraphyly nor monophyly of the bathydraconids, while morphology leads to the monophyly of the family based on the synapomorphic loss of the spinous dorsal fin; (2) The Channichthyidae, the Harpagiferidae, and the Artedidraconidae are monophyletic families; (3) the phylogeny of the haemoglobin-less channichthyids is completely resolved and congruent with the conclusions of based on anatomical characters; (4) The present molecular results as well as other molecular studies favour the hypothesis that harpagiferids are the sister-group of artedidraconids, though our morphological matrix puts harpagiferids as the sister-group of all other families on the basis of a single character. With regard to harpagiferid relationships, it is interesting to notice that, when analysed simultaneously, morphological characters are not automatically "swamped" within molecular ones: in the tree based on the simultaneous analysis of all available data, morphological characters impose their topology on molecules.     

Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA

The Blastocladiomycota is a recently described phylum of ecologically diverse zoosporic fungi whose species have not been thoroughly sampled and placed within a molecular phylogeny. In this study, we investigated the phylogeny of the Blastocladiomycota based on ribosomal DNA sequences from strains identified by traditional morphological and ultrastructural characters. Our results support the monophyly of the Coelomomycetaceae and Physodermataceae but the Blastocladiaceae and Catenariaceae are paraphyletic or polyphyletic. The data support two clades within Allomyces with strains identified as Allomyces arbusculus in both clades, suggesting that species concepts in Allomyces are in need of revision. A clade of Catenaria species isolated from midge larvae group separately from other Catenaria species, suggesting that this genus may need revision. In the Physodermataceae, Urophlyctis species cluster with a clade of Physoderma species. The algal parasite Paraphysoderma sedebokerensis nom. prov. clusters sister to other taxa in the Physodermataceae. Catenomyces persicinus, which has been classified in the Catenariaceae, groups with the Chytridiomycota rather than Blastocladiomycota. The rDNA operon seems to be suitable for classification within the Blastocladiomycota and distinguishes among genera; however, this region alone is not suitable to determine the position of the Blastocladiomycota among other basal fungal phyla with statistical support. A focused effort to find and isolate, or directly amplify DNA from additional taxa will be necessary to evaluate diversity in this phylum. We provide this rDNA phylogeny as a preliminary framework to guide further taxon and gene sampling and to facilitate future ecological, morphological, and systematic studies.     

178 Molecular Systematics of the Ulvellaceae (Ulvales, Ulvophyceae) Inferred from Nuclear and Chloroplast DNA Sequences

The traditional use of thallus morphology to define lineages within the Ulvophyceae proved problematic because parallelism and convergence obscured natural relationships. The advent of transmission electron microscopy led to a re-evaluation of groups on the basis of zoid characters. Within TEM-defined lineages, the Ulotrichales and Ulvales were considered closely related orders, and molecular evidence has substantiated this hypothesis. In our molecular systematic studies of ulvophyceous green algae, we have broadened taxon sampling among these two orders. We show that the Ulvales and Ulotrichales are indeed monophyletic orders. However, the phylogenetic placement of species in the genera Bolbocoleon, Ctenocladus, Phaeophila, Pseudendoclonium and Acroblaste indicates that one or more additional lineages, placed between Ulvales and Ulotrichales in gene sequence trees, must be recognized. These species may constitute a separate order (Ctenocladales) consisting of multiple families. Our findings will be compared with taxonomic concepts based on morphological criteria.     

Phylogenetic relationships of Ruteae (Rutaceae): new evidence from the chloroplast genome and comparisons with non-molecular data

Phylogenetic analyses of three cpDNA markers (matK, rpl16, and trnL–trnF) were performed to evaluate previous treatments of Ruteae based on morphology and phytochemistry that contradicted each other, especially regarding the taxonomic status of Haplophyllum and Dictamnus. Trees derived from morphological, phytochemical, and molecular datasets of Ruteae were then compared to look for possible patterns of agreement among them. Furthermore, non-molecular characters were mapped on the molecular phylogeny to identify uniquely derived states and patterns of homoplasy in the morphological and phytochemical datasets. The phylogenetic analyses determined that Haplophyllum and Ruta form reciprocally exclusive monophyletic groups and that Dictamnus is not closely related to the other genera of Ruteae. The different types of datasets were partly incongruent with each other. The discordant phylogenetic patterns between the phytochemical and molecular trees might be best explained in terms of convergence in secondary chemical compounds. Finally, only a few non-molecular synapomorphies provided support for the clades of the molecular tree, while most of the morphological characters traditionally used for taxonomic purposes were found to be homoplasious. Within the context of the phylogenetic relationships supported by molecular data, Ruta, the type genus for the family, can only be diagnosed by using a combination of plesiomorphic, homoplasious, and autapomorphic morphological character states.     

Molecular phylogeny and morphological homoplasy in fruitbats.

The present study evaluates the evolutionary framework of the Old World fruitbats based on the cytochrome b and 16S rRNA mitochondrial gene sequences from a wide range of taxa. Phylogenetic analyses indicated that morphology-based subfamilies and most suprageneric groups are nonnatural assemblages. They also support the existence of an endemic African clade of fruitbats. The discrepancy between the evolutionary relationships yielded by molecular and morphological data sets may be, at least in part, explained by the recurrent retention of primitive morphology (Rousettus-like) across different lineages. The maintenance of primitive characters in different groups of flying foxes, as well as morphological convergence in nectar-feeding bats and possibly also in short-muzzle bats, may have led to high levels of homoplasy, resulting in misleading taxonomic arrangements. This may be particularly so with respect to high taxonomic levels based on morphological characters.