Phylogeny of feather mite subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) inferred from combined analyses of molecular and morphological data.

Phylogenetic relationships among feather mites of the subfamily Avenzoariinae (Acari: Analgoidea: Avenzoariidae) were reconstructed by parsimony analysis of a combined data matrix. We analyzed 41 morphological characters and 246 molecular characters from a fragment of the 16S rDNA. Morphological trees were well supported at deep branches (genera and above), but showed much less support and resolution within genera. Molecular analyses produced trees with better resolution and support on terminal branches and worse support on basal branches. I(MF) index for the combined matrix pointed to the significant congruence of both data subsets with the whole of the data. The topology of the combined tree was close to the morphological tree in the deep branches and had well-resolved terminal branches as in the molecular tree. This suggests a considerable level of complimentarity between the two data sets. An analysis of association patterns of the mites and their hosts was conducted based on the results of the combined analyses for the Avenzoariinae and a phylogeny of their charadriiform hosts (compiled from various bird phylogeny hypotheses). The trees could be reconciled by the invoking of 12-13 cospeciation events, 6-7 duplications, 2 host shifts, and 26-29 sorting events. This suggests a high degree of cospeciation.     

Testing the monophyly of the New Zealand and Australian endemic family Conoesucidae Ross based on combined molecular and morphological data (Insecta: Trichoptera: Sericostomatoidea)

Conoesucidae (Trichoptera, Insecta) are restricted to SE Australia, Tasmania and New Zealand. The family includes 42 described species in 12 genera, and each genus is endemic to either New Zealand or Australia. Although monophyly has been previously assumed, no morphological characters have been proposed to represent synapomorphies for the group. We collected molecular data from two mitochondrial genes (16S and cytochrome oxidase I), one nuclear gene (elongation factor 1-α) (2237–2277 bp in total), and 12 morphological characters to produce the first phylogeny of the family. We combined the molecular and morphological characters and performed both a maximum parsimony analysis and a Bayesian analysis to test the monophyly of the family, and to hypothesize the phylogeny among its genera. The parsimony analysis revealed a single most parsimonious tree with Conoesucidae being a monophyletic taxon and sistergroup to the Calocidae. The Bayesian inference produced a distribution of trees, the consensus of which is supported with posterior probabilities of 100% for 15 out of 22 possible ingroup clades including the most basal branch of the family, indicating strong support for a monophyletic Conoesucidae. The most parsimonious tree and the tree from the Bayesian analysis were identical except that the ingroup genus Pycnocentria changed position by jumping to a neighbouring clade. Based on the assumption that the ancestral conoesucid species was present on both New Zealand and Australia, a biogeographical analysis using the dispersal-vicariance criteria demonstrated that one or two (depending on which of the two phylogenetic reconstructions were applied) sympatric speciation events took place on New Zealand prior to a single, late dispersal from New Zealand to Australia.     

Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta)

Ichneumonoid phylogeny is revised on the basis of morphological, palaeontological and molecular evidence. The only previous formal cladistic study of the phylogeny of the families of the superfamily Ichneumonoidea made many assumptions about what families lower taxa belonged to and was based on a very limited set of characters, nearly all of which were uninformative at family level. We have subdivided both Ichneumonidae and Braconidae into major groups, investigated several new character systems, reinterpreted some characters, scored several character states for extinct taxa by examining impression fossils using environment chamber scanning electron microscopy, and included data for a significant new subfamily of Braconidae from Cretaceous amber of New Jersey. Sixteen different variants of the data set were each subjected to parsimony analysis without weighting and with successive approximations weighting employing both maximum and minimum values of both the retention and rescaled consistency indices. Each analysis resulted in one of seven different strict consensus trees. Consensus trees based on subsets of these trees, selected on the basis of the optimal character compatibility index (OCCI), resulted in an eighth distinct tree. All trees had the Braconidae monophyletic with the Trachypetinae as the basal clade, and also had a clade comprising various arrangements of Apozyginae, the Rhyssalinae group, Aphidiinae and 'other cyclostomes', but relationships among the remaining braconid groups varied between trees. Only one of the consensus trees had the Ichneumonidae (including Tanychorella ) monophyletic. The Eoichneumonidae + Tanychora are the sister group the Braconidae in two of the consensus trees. Paxylommatinae were basal in the clade comprising the Eoichneumonidae + Tanychora and the Braconidae. The preferred tree, based on the highest OCCI was used for interpreting character state transitions.     

AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei)

Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.     

Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees

The molecular phylogeny of parabasalids has mainly been inferred from small subunit (SSU) rRNA sequences and has conflicted substantially with systematics based on morphological and ultrastructural characters. This raises the important question, how congruent are protein and SSU rRNA trees? New sequences from seven diverse parabasalids (six trichomonads and one hypermastigid) were added to data sets of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), enolase, alpha-tubulin and beta-tubulin and used to construct phylogenetic trees. The GAPDH tree was well resolved and identical in topology to the SSU rRNA tree. This both validates the rRNA tree and suggests that GAPDH should be a valuable tool in further phylogenetic studies of parabasalids. In particular, the GAPDH tree confirmed the polyphyly of Monocercomonadidae and Trichomonadidae and the basal position of Trichonympha agilis among parabasalids. Moreover, GAPDH strengthened the hypothesis of secondary loss of cytoskeletal structures in Monocercomonadidae such as Monocercomonas and Hypotrichomonas. In contrast to GAPDH, the enolase and both tubulin trees are poorly resolved and rather uninformative about parabasalian phylogeny, although two of these trees also identify T. agilis as representing the basal-most lineage of parabasalids. Although all four protein genes show multiple gene duplications (for 3-6 of the seven taxa examined), most duplications appear to be relatively recent (i.e., species-specific) and not a problem for phylogeny reconstruction. Only for enolase are there more ancient duplications that may confound phylogenetic interpretation.     

A phylogenetic study of the Anthozoa (phylum Cnidaria) based on morphological and molecular characters

The phylogenetic relationships within the Anthozoa were re-evaluated based on 41 morphological characters and nuclear sequences of 18S ribosomal DNA (29 anthozoans as ingroups and 3 hydrozoans as outgroups). The parsimony trees derived from the morphological data did not coincide closely with the molecular data, and the presence of several polytomies at some nodes of the trees resulted in ambiguities among the systematic relationships. On the other hand, the combined analysis using total evidence presents a more resolved and highly supported topology, as is indicated by higher bootstrap values and decay indices than either analysis alone. However, strict and semi-strict consensus trees derived from taxonomic congruence show a poorer resolution for the phylogeny of Anthozoa. The trees constructed from the molecular data, using neighbor-joining and maximum-likelihood methods, are nearly congruent with the result from the total evidence. Based on these results, Anthozoa is divided into three subclasses: Alcyonaria, Zoantharia, and Ceriantipatharia. The Ceriantipatharia now includes only one order, Ceriantharia, since the order Antipatharia is more closely related to orders within the Zoantharia. The Alcyonaria is a monophyletic group, in which the order Pennatulacea is basal, and orders Alcyonacea and Telestacea branch later. The order Gorgonacea is divided into two suborders, Holaxonia and Scleraxonia. Bellonela is more related to order Stolonifera, forming a monophyletic group. In Zoantharia, the order Zoanthinaria is basal, and the remaining taxa are divided into two clades: one includes the order Actiniaria and the other includes orders Antipatharia, Corallimorpharia, and Scleractinia. The latter two orders form a monophyletic group. This study presents a different phylogeny of actiniarians from the earlier hypothesis of scleractinian ancestry.     

Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets

The phylogenetic relationships among the loliginid squids, a species-rich group of shallowwater muscular squids, have been investigated recently using several approaches, including allozyme electrophoresis and analyses of morphological and DNA sequence data, yet no consensus has been reached. This study examines the effects of combining multiple data sets (morphology, allozymes and DNA sequence data from two mitochondrial genes) on estimates of loliginid phylogeny. Various data combinations were analysed under three maximum parsimony weighting schemes: equal weights for all characters, successive approximations and implicit weights parsimony. When feasible, support for branches within trees was assessed with nonparametric bootstrapping and decay analysis. Some ingroup relationships were consistent across all analyses, but relationships among outgroup taxa and basal ingroup taxa varied. Combining data increased bootstrap support for several nodes. Methods that downweight highly variable characters (i.e. successive approximations and implicit weights parsimony) produced very similar trees which included two major clades: a clade consisting of all species sampled from American waters (except Sepioteuthis ), and a clade of several east Atlantic species ( Loligo forbesi Steenstrup, Loligo vulgaris Lamarck and Loligo reynaudi d'Orbigny) plus several Indo-West Pacific species in the genera Uroteuthis and Loliolus. The Sepioteuthis species occupied a basal position within Loliginidae, but Sepioteuthis itself was not always monophyletic. The position of a clade of a few Lolliguncula species and Loligo (Alloteuthis) also varied across analyses. A new loliginid classification is proposed based on these findings.     

The phylogenetic relationships of lampridiform fishes (Teleostei: acanthomorpha), based on a total-evidence analysis of morphological and molecular data

We investigated the phylogenetic relationships among five species of lampridiform fishes, three basal outgroup species (two aulopiforms and one myctophiform), and two species of non-lampridiform acanthomorphs (Polymixia and Percopsis) using a combined parsimony analysis of morphological and molecular data. Morphological characters included 28 transformation series obtained from the literature. Molecular characters included 223 informative transformation series from an aligned 854-base pair fragment of 12S mtDNA and 139 informative transformation series from an aligned 561-base pair fragment of 16S mtDNA. A total-evidence analysis using the aulopiforms Synodus and Aulopus and the myctophiform Hygophum as outgroups corroborates the monophyly of Lampridiformes and unites Polymixia with Percopsis. Among the lampridiform fishes we examined, Metavelifer is basal, followed in ascending order by Lampris, Lophotus, Regalecus, and Trachipterus. This hypothesis is congruent with the most recent morphological analysis of the Lampridiformes and rejects a diphyletic origin of elongate body form within the clade. Analysis of a combined matrix of 12S and 16S mtDNA data yielded a phylogenetic hypothesis isomorphic with the total-evidence phylogeny. Analyses of partitioned DNA data sets reveals that single gene regions are poor predictors of the total-evidence phylogeny while combined analyses of both DNA data sets are good predictors of the total-evidence phylogeny.     

Re-examination and phylogeny of the genus Chondrostoma based on mitochondrial and nuclear data and the definition of 5 new genera

Previous molecular phylogenetic studies of the genus Chondrostoma (Cyprinidae: Leuciscinae) were unable to resolve the relationship among its major species groups. In this paper we present a phylogeny for this genus, based on five mitochondrial genes and the nuclear gene beta-actin, comprising a total of 4068 bp. Bayesian inference using all gene fragments yielded a fully resolved phylogeny, compatible with topologies obtained from individual fragments using maximum parsimony and minimum evolution. Mapping of morphological characters critical to the rasping feeding mode of most Chondrostoma species indicates that they evolved several times, and questions the use of these characters in the traditional definition of the genus. Our findings led us to the definition of the following new genera: Achondrostoma, Iberochondrostoma, Pseudochondrostoma, Protochondrostoma and Parachondrostoma. Our data contradict the hypothesis of a rapid radiation during Lago Mare phase, suggested by previous studies.     

Morphological Characters Are Compatible with Mitogenomic Data in Resolving the Phylogeny of Nymphalid Butterflies (Lepidoptera: Papilionoidea: Nymphalidae)

Nymphalidae is the largest family of butterflies with their phylogenetic relationships not adequately approached to date. The mitochondrial genomes (mitogenomes) of 11 new nymphalid species were reported and a comparative mitogenomic analysis was conducted together with other 22 available nymphalid mitogenomes. A phylogenetic analysis of the 33 species from all 13 currently recognized nymphalid subfamilies was done based on the mitogenomic data set with three Lycaenidae species as the outgroups. The mitogenome comparison showed that the eleven new mitogenomes were similar with those of other butterflies in gene content and order. The reconstructed phylogenetic trees reveal that the nymphalids are made up of five major clades (the nymphaline, heliconiine, satyrine, danaine and libytheine clades), with sister relationship between subfamilies Cyrestinae and Biblidinae, and most likely between subfamilies Morphinae and Satyrinae. This whole mitogenome-based phylogeny is generally congruent with those of former studies based on nuclear-gene and mitogenomic analyses, but differs considerably from the result of morphological cladistic analysis, such as the basal position of Libytheinae in morpho-phylogeny is not confirmed in molecular studies. However, we found that the mitogenomic phylogeny established herein is compatible with selected morphological characters (including developmental and adult morpho-characters).     

Advantages and Disadvantages of Molecular Phylogenetics: A Case Study of Ascaridoid Nematodes

The advantages of nucleotide sequence data for studying phylogeny have been shown to include number of potential characters available for comparison, rate independence between molecular and morphological evolution, and utility of molecular data for modeling patterns of nucleotide substitution. Potential pitfalls have also been revealed and include difficulties of inferring positional homology, incongruence between organismal and gene genealogies, and low likelihood of recovering the correct phylogeny given certain patterns in the timing of speciation events. Statistical methods for comparing phylogenetic hypotheses have been used to assess the reliability of alternative trees for ascaridoid nematodes. Based on partial ribosomal RNA sequences, tree topologies inconsistent with monophyly of the Ascaridinae were significantly worse by maximum likelihood inference. The topology of the maximum parsimony tree based on full-length sequences of 18S rRNA and 300 nucleotides of Cytochrome oxidase II for 13 ascaridoid species was generally consistent with traditional taxonomic expectations at lower ranks, but inconsistent with most proposed arrangements at higher taxonomic levels.     

Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data

A phylogeny of Iberian Aphodiini dung beetles was reconstructed based on morphological and molecular data. The data set included a total of 84 variable characters from wing venation, mouthparts, genitalia, and external morphology, as well as mitochondrial partial cytochrome c oxidase I (COI), complete tRNA-Leu (UUR), and partial cytochrome c oxidase II (COII) gene nucleotide sequences (1210 positions). Phylogenetic trees based on molecular data were relatively more resolved than those based on morphological characters. The Bayesian analysis of combined molecular and morphological data provided resolution not achieved by each data set separately. Ammoecius and Aphodius are the first lineages that branch off from the tree, followed by Acrossus, Nimbus, and Heptaulacus. The remaining studied taxa are recovered in a more derived clade that lacks internal resolution. Reconstructed trees based on molecular data showed relatively short internal nodes that were weakly supported. Such pattern may reflect a rapid radiation at the origin of the tribe Aphodiini, but also saturation of mutational changes. Several tests were conducted to discern between both competing hypotheses, as well as to assess the effect of incomplete taxon sampling.     

Molecular insights into Cumacean family relationships (Crustacea, Cumacea)

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.     

Toward a Better Understanding of the Phylogeny of the Asplanchnidae (Rotifera)

We investigated the phylogenetic relationships of Family Asplanchnidae using both morphological and molecular data. The morphological database, comprising 23 characters from 19 taxa (15 Asplanchnidae and 4 outgroups), was compiled from a survey of the literature and our own observations; the molecular data (ITS and V4 region nuclear regions and mitochondrial cox1) was sequenced from specimens that we collected. Our analysis of the morphological data set (maximum parsimony) yielded 12 most-parsimonious trees with a tree length of 27 steps. From this analysis we conclude (1) Asplanchnidae is a monophyletic group as are the three genera comprising it, (2) there is no compelling support for the argument that Asplanchna should be separated into two discrete genera, and (3) there is some support for the proposal that Asplanchnidae and Synchaetidae are sister groups. Our analysis of the molecular data set supports the first two of these conclusions while the sister group of the family varied depending on the gene region analyzed and families and genera included. Current understanding of the phylogeny of Asplanchnidae is hampered by the need for additional informative morphological characters and a lack of molecular data for the genus Harringia and several other members of the Asplanchnidae.     

Molecular Phylogeny of the Genus Paramesotriton (Caudata: Salamandridae)

To elucidate the phylogeny of the genus Paramesotriton (Caudata: Salamandridae), we investigated three mitochondrial DNA gene fragments (1207 bp in total) of cytochrome b, ND2, and ND4 for its six recognized species. The phylogenetic relationships within Paramesotriton were reconstructed by maximum parsimony (MP) and maximum likelihood (ML) methods. Phylogenetic trees (MP and ML trees) that were constructed from the combined data set of the three gene fragments indicated that all six species of Paramesotriton formed a monophyletic group, with P. caudopunctatus as basal to the other five species. This result suggests that P. fuzhongensis is a valid species in Paramesotriton.     

What can the mitochondrial genome reveal about higher‐level phylogeny of the molluscan class Cephalopoda?

We present the first analysis of cephalopod mitochondrial gene order and construct phylogenies based on gene order using Bayesian, distance, and parsimony analysis methods. Analyses included all species of cephalopod for which the whole mitochondrial genome has been sequenced. Where resolution was obtained, these analyses supported division of Neocoleoidea, in which all recent coleoid Cephalopoda can be placed, into Octopodiformes and Decapodiformes. For the same taxa, we also constructed a phylogeny in a maximum likelihood framework based on amino‐acid coded sequence data of all mitochondrial protein coding genes. As well as supporting Octopodiformes and Decapodiformes, amino‐acid analyses established support for Teuthoidea (Oegospida and Myopsida) to the exclusion of Sepiidae, and supported a monophyletic Oegopsida. Partial mitochondrial sequences of additional higher‐level taxa for which whole genome data were not available were subsequently included in the amino‐acid analysis to provide additional information on phylogeny. Spirulida was found to be basal amongst Decapodiformes. Mapping of morphological characters onto our phylogeny and consideration of palaeontological evidence suggests that our phylogeny reflects true evolutionary relationships. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 573–586.     

Mitochondrial DNA,morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae)

The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.     

The role of wood anatomy in phylogeny reconstruction of Ericales

The systematic significance of wood anatomical characters within Ericales is evaluated using separate and combined parsimony analyses including 23 wood characters and 3945 informative molecular characters. Analyses of wood features alone result in poorly resolved and conflicting topologies. However, when pedomorphic character states are coded as inapplicable, the combined bootstrap topology results in an increase of resolution and support at most deeper nodes compared with the molecular analyses. This suggests that phylogenetic information from the limited number of morphological characters is not completely swamped by an overwhelming amount of molecular data. Based on the morphology of vessels and fibers, and the distribution of axial parenchyma, two major wood types can be distinguished within Ericales: (i) a “primitive” type, nearly identical to the wood structure in the more basal outgroup Cornales, which is likely to have persisted in one major clade, and (ii) a “derived” type that must have evolved in at least two separate evolutionary lines. The occurrence of the first type is strongly correlated with shrubs to small trees growing in cold temperate or tropical montane regions, while the second type is common in tall trees of tropical lowlands. This favors the inclusion of ecologically adaptive features in phylogeny reconstruction. © The Willi Hennig Society 2006.     

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.