Phylogeny of the water strider genus Gerris Fabricius (Heteroptera: Gerridae) based on COI mtDNA, EF-1α nuclear DNA and morphology

Phylogenetic relationships between water striders (Heteroptera: Gerridae) of genus Gerris Fabricius were examined using molecular and morphological characters. The molecular dataset was 820 bp DNA from the 3′ half of the mitochondrial gene encoding cytochrome oxidase subunit I and 515 bp DNA from the nuclear gene encoding elongation factor 1 alpha. The morphological dataset was a slightly modified version of a previously published dataset. Representatives from all eight recognized species groups of Gerris, as well as six species from three related genera, including Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Aquarius najas, A. conformis and A. paludum, were included. Unweighted parsimony analyses of the COI sequences gave a topology with strong support for only those nodes that were already recognized as closely related based on morphological characters. Similar analyses of EF‐1α gave a cladogram with a topology quite different from that based on morphology and COI. Unweighted parsimony analyses of the ‘total evidence’ dataset largely supports the traditional view of Gerris phylogeny. Finally, the implications of the reconstructed phylogeny in relation to biogeography and ecological phylogenetics of Gerris is discussed.     

The evolution of marine insects: phylogenetic, ecological and geographical aspects of species diversity in marine water striders

No other group of insects have been more successful in colonizing marine habitats than water striders and their allies (Heteroptera, Gerromorpha). More than 10% of the 1700 species of gerromorphan bugs are marine. Water striders have colonized the marine environment at least 14 times. The fossil records suggest that marine habitats were invaded by members of the families Veliidae and Gerridae earlier than 20-30 and 45 million years before present, respectively. Estuaries and mangrove swamps are undoubtedly the ancestral type of habitat, but water striders have diversified further in marine habitats including the surface of the open ocean (sea skaters. Halobates). Except for being obligatorily flightless, marine water striders are structurally very similar to their non-marine relatives. Physiological and behavioral rather than morphological specializations are likely to have been key innovations in the transition from limnic to marine habitats. The oldest and most species-rich clades originated in the Indo-West Pacific region. There are 3.5 times as many species of marine water striders in the Indo-West Pacific region than in the Atlantic/Caribbean/East Pacific region. This "diversity anomaly" is explained historically by region-specific differences in the origin and proliferation of clades, in paleoclimate and paleogeography, and in the propensity for dispersal between regions.     

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.     

Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.

The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and compared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The molecular sequence chosen is demonstrably far from saturation and sister groups have divergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point mutations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a moderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearman's rank correlation test, which requires only relative magnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the number of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approximate to a clocklike model within restricted echinoid clades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.     

Marine insects: genital morphology, phylogeny and evolution of sea skaters, genus Halobates (Hemiptera: Gerridae)

Five species of sea skaters, genus Halobates Eschscholtz, are the only insects to have successfully colonized the open ocean. In addition, 36 species are found in sheltered coastal waters throughout tropical Indo-Pacific. The taxonomy of the genus is relatively well known, but reliable hypotheses about phylogenetic relationships are required if the biogeography and evolution of sea skaters is to be discussed in a meaningful way. This work presents the results of a study of new characters from the genital segments, especially those of the male phallus and the female gynatrial complex, and a reinterpretation for several other characters. In total 64 characters were scored for 26 species of Halobates , two species ofAsclepios and one species of Metrocoris. With Asclepios and Metrocoris species as outgroups, the character state sets were analysed cladistically using the computer program Hennig86. After critical evaluations of both characters and clades, a phylogeny for Halobates is presented and its taxonomic implications are discussed. A number of monophyletic species groups are delimited. One genus-level synonymy and three species-level synonymies are suggested. The evolution of Halobates is discussed in the light of the reconstructed phylogeny and present knowledge of the ecology and behaviour of sea skaters. A hypothesis of ecological evolution in halobatine water striders is proposed and tested.     

Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)

The series Staphyliniformia is one of the mega‐diverse groups of Coleoptera, but the relationships among the main families are still poorly understood. In this paper we address the interrelationships of staphyliniform groups, with special emphasis on Hydrophiloidea and Hydraenidae, based on partial sequences of the ribosomal genes 18S rDNA and 28S rDNA. Sequence data were analysed with parsimony and Bayesian posterior probabilities, in an attempt to overcome the likely effect of some branches longer than the 95% cumulative probability of the estimated normal distribution of the path lengths of the species. The inter‐family relationships in the trees obtained with both methods were in general poorly supported, although most of the results based on the sequence data are in good agreement with morphological studies. In none of our analyses a close relationship between Hydraenidae and Hydrophiloidea was supported, contrary to the traditional view but in agreement with recent morphological investigations. Hydraenidae form a clade with Ptiliidae and Scydmaenidae in the tree obtained with Bayesian probabilities, but are placed as basal group of Staphyliniformia (with Silphidae as subordinate group) in the parsimony tree. Based on the analysed data with a limited set of outgroups Scarabaeoidea are nested within Staphyliniformia. However, this needs further support. Hydrophiloidea s.str., Sphaeridiinae, Histeroidea (Histeridae + Sphaeritidae), and all staphylinoid families included are confirmed as monophyletic, with the exception of Hydraenidae in the parsimony tree. Spercheidae are not a basal group within Hydrophiloidea, as has been previously suggested, but included in a polytomy with other Hydrophilidae in the Bayesian analyses, or its sistergroup (with the inclusion of Epimetopidae) in the parsimony tree. Helophorus is placed at the base of Hydrophiloidea in the parsimony tree. The monophyly of Hydrophiloidea s.l. (including the histeroid families) and Staphylinoidea could not be confirmed by the analysed data. Some results, such as a placement of Silphidae as subordinate group of Hydraenidae (parsimony tree), or a sistergroup relationship between Ptiliidae and Scydmaenidae, appear unlikely from a morphological point of view.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes

Extant gars represent the remaining members of a formerly diverse assemblage of ancient ray-finned fishes and have been the subject of multiple phylogenetic analyses using morphological data. Here, we present the first hypothesis of phylogenetic relationships among living gar species based on molecular data, through the examination of gene tree heterogeneity and coalescent species tree analyses of a portion of one mitochondrial (COI) and seven nuclear (ENC1, myh6, plagl2, S7 ribosomal protein intron 1, sreb2, tbr1, and zic1) genes. Individual gene trees displayed varying degrees of resolution with regards to species-level relationships, and the gene trees inferred from COI and the S7 intron were the only two that were completely resolved. Coalescent species tree analyses of nuclear genes resulted in a well-resolved and strongly supported phylogenetic tree of living gar species, for which Bayesian posterior node support was further improved by the inclusion of the mitochondrial gene. Species-level relationships among gars inferred from our molecular data set were highly congruent with previously published morphological phylogenies, with the exception of the placement of two species, Lepisosteus osseus and L. platostomus. Re-examination of the character coding used by previous authors provided partial resolution of this topological discordance, resulting in broad concordance in the phylogenies inferred from individual genes, the coalescent species tree analysis, and morphology. The completely resolved phylogeny inferred from the molecular data set with strong Bayesian posterior support at all nodes provided insights into the potential for introgressive hybridization and patterns of allopatric speciation in the evolutionary history of living gars, as well as a solid foundation for future examinations of functional diversification and evolutionary stasis in a "living fossil" lineage.     

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca ), some Australian species of Melaleuca , a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea , and Regelia , and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus , and Phymatocarpus . All molecular analyses sup port the monophyly of Conothamnus and of Regelia , genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia . The findings have implications for both taxonomy and biogeography.     

True and false gharials: a nuclear gene phylogeny of crocodylia

The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.     

Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants

A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate that hornworts are the earliest land plants. To help resolve this conflict, we used parsimony and likelihood methods to analyze a 6, 095-character data set composed of four genes (chloroplast rbcL and small-subunit rDNA from all three plant genomes) from all major land plant lineages. In all analyses, significant support was obtained for the monophyly of vascular plants, lycophytes, ferns (including PSILOTUM: and EQUISETUM:), seed plants, and angiosperms. Relationships among the three bryophyte lineages were unresolved in parsimony analyses in which all positions were included and weighted equally. However, in parsimony and likelihood analyses in which rbcL third-codon-position transitions were either excluded or downweighted (due to apparent saturation), hornworts were placed as sister to all other land plants, with mosses and liverworts jointly forming the second deepest lineage. Decay analyses and Kishino-Hasegawa tests of the third-position-excluded data set showed significant support for the hornwort-basal topology over several alternative topologies, including the commonly cited liverwort-basal topology. Among the four genes used, mitochondrial small-subunit rDNA showed the lowest homoplasy and alone recovered essentially the same topology as the multigene tree. This molecular phylogeny presents new opportunities to assess paleontological evidence and morphological innovations that occurred during the early evolution of terrestrial plants.     

Sources of character conflict in a clade of water striders (Heteroptera: Gerridae)

Incongruence among trees reconstructed with different data may stem from historical (gene tree‐species tree conflict) or process (character change biases) phenomena. Regardless of the source, incongruent data, as determined with “global” measures of homoplasy, have often been excluded from parsimony analysis of the combined data. Recent studies suggest that these homoplasy measures do not predict the contribution of each character to overall tree structure. Branch support measures identify, on a character to node basis, sources of support and conflict resulting from a simultaneous analysis of the data. We implement these branch support measures to identify sources of character conflict in a clade of water striders consisting of Gerris Fabricius, Aquarius Schellenberg, and Limnoporus Stål species. Separate analyses of morphology, mitochondrial cytochrome oxidase I (COI), large mitochondrial ribosomal subunit (16SrRNA), and elongation factor‐1α (EF‐1α) data resulted in cladograms that varied in resolution and topological concordance. Simultaneous analysis of the data resulted in two trees that were unresolved for one node in a strict consensus. The topology agreed with current classification except for the placements of Aquarius chilensis and the Aquarius remigis species group closer to Gerris than to congeneric species. Branch support measures indicated that support derived from each data set varied among nodes, but COI had an overall negative effect on branch support. However, Spearman rank correlation of partitioned branch support values indicated no negative associations of branch support between any data sets and a positive association between EF‐1α and 16SrRNA. Thus incongruence among data sets was not drastic and the gene‐tree versus species tree phenomenon was not implicated. Biases in character change were a more likely reason for incongruence, although saturation curves and incongruence length difference for COI indicated little potential for homoplasy. However, a posteriori inspection of COI nucleotide change with reference to the simultaneous analysis tree revealed AT and codon biases. These biases were not associated with branch support measures. Therefore, it is difficult to predict incongruence or identify its cause. Exclusion of data is ill advised because every character is potentially parsimony informative.     

Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence

The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.     

Phylogeny of Mysis (Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data

We studied the phylogenetic history of opossum shrimps of the genus Mysis Latreille, 1802 (Crustacea: Mysida) using parsimony analyses of morphological characters, DNA sequence data from mitochondrial (16S, COI and CytB) and nuclear genes (ITS2, 18S), and eight allozyme loci. With these data we aimed to resolve a long‐debated question of the origin of the non‐marine (continental) taxa in the genus, i.e., “glacial relicts” in circumpolar postglacial lakes and “arctic immigrants” in the Caspian Sea. A simultaneous analysis of the data sets gave a single tree supporting monophyly of all continental species, as well as monophyly of the taxa from circumpolar lakes and from the Caspian Sea. A clade of three circumarctic marine species was sister group to the continental taxa, whereas Atlantic species had more distant relationships to the others. Small molecular differentiation among the morphologically diverse endemic species from the Caspian Sea suggested their recent speciation, while the phenotypically more uniform “glacial relict” species from circumpolar lakes (Mysis relicta group) showed deep molecular divergences. For the length‐variable ITS2 region both direct optimization and a priori alignment procedures gave similar topologies, although the former approach provided a better overall resolution. In terms of partitioned Bremer support (PBS), mitochondrial protein coding genes provided the largest contribution (83%) to the total tree resolution. This estimate however, appears to be partly spurious, due to the concerted inheritance of mitochondrial characters and probable cases of introgression or ancestral polymorphism. © The Willi Hennig Society 2005.     

The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: the problem of incomplete data

We considered the contribution of two mitochondrial and two nuclear data sets for the phylogenetic reconstruction of 22 species of seed beetles in the genus Curculio (Coleoptera: Cuculionidae). A phylogenetic tree from representatives found on various hosts was inferred from a combined data set of mitochondrial DNA cytochrome oxidase subunit I, mitochondrial cytochrome b, nuclear elongation factor 1alpha, and nuclear phosphoglycerate mutase, used for the first time as a molecular marker. Separate parsimony analyses of each data set showed that individual gene trees were mainly congruent and often complementary in the support of clades but the analysis was complicated by failure of PCR amplification of nuclear genes for many taxa and hence missing data entries. When the four gene partitions were combined in a simultaneous analysis despite the missing data, this increased the resolution and taxonomic coverage compared to the individual source trees. Alternative approaches of combining the information via supertree methodology produced a comparatively less resolved tree, and hence seem inferior to combining data matrices even in cases where numerous taxa are missing. The molecular data suggest a classification of the European species into two species groups that are in accordance with morphological characteristics but the data do no support any of the previously recognised American species groups.     

Analysis of the systematic relationships among ticks of the genera Rhipicephalus and Boophilus (Acari: Ixodidae) based on mitochondrial 12S ribosomal DNA gene sequences and morphological characters

A portion of mitochondrial 12S rDNA sequences (337-355 base pairs) and 63 morphological characters of 36 hard-tick species belonging to 7 genera were analyzed to determine the phylogenetic relationships among groups and species of Rhipicephalus and between the genera Rhipicephalus and Boophilus. Molecular and morphological data sets were first examined separately. The molecular data were analyzed by maximum parsimony (MP), maximum likelihood, and neighbor-joining distance methods; the morphological data were analyzed by MP After their level of congruence was evaluated by a partition homogeneity test, all characters were combined and analyzed by MP. The branches of the tree obtained by combining the data sets were better resolved than those of the trees inferred from the separate analyses. Boophilus is monophyletic and arose within Rhipicephalus. Boophilus species clustered with species of the Rhipicephalus evertsi group. Most of the clustering within Rhipicephalus was, however, consistent with previous classifications based on morphological data. Morphological characters were traced on the molecular reconstruction in order to identify characters diagnostic for monophyletic clades. Within the Rhipicephalus sanguineus complex, the sequences of specimens morphologically identified as Rhipicephalus turanicus were characterized by a high level of variability, indicating that R. turanicus-like morphology may cover a spectrum of distinct species.     

Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae).

Estimations of phylogenies from morphological and molecular data often show contrasting results. We compared morphological and molecular phylogenies in an ancient family of woody dicots, the Betulaceae (birch family). The phylogeny of the family was estimated from parsimony analysis of morphological characters in the genera Alnus, Betula, Carpinus, Corylus, Ostrya, and Ostryopsis and from parsimony and distance-matrix analyses of DNA sequences of the chloroplast gene encoding the large subunit of ribulose-1,5-biphosphate carboxylase (rbcL) in the genera Alnus, Betula, Carpinus, Corylus, and Ostrya and in two outgroups, Quercus and Liquidambar. The topologies obtained by the different methods were completely congruent, and bootstrapping strongly supported the division of the family Betulaceae into two major clades, Betuleae (Alnus and Betula) and Coryleae (other members). Only slightly more homoplasy was present in the rbcL sequence data set than in the morphological set. Relative-rate tests indicated that the Coryleae clade had a faster rate of rbcL evolution than did the Betuleae clade. Heterogeneity of rates of morphological evolution also paralleled those for rbcL.     

COMBINED AND SEPARATE ANALYSES OF MORPHOLOGICAL AND MOLECULAR DATA IN THE PLANT FAMILY RUBIACEAE

Abstract— The Rubiaceae are one of the largest of the families of angiosperms, with over 10000 species. The tribal and subfamilial classification is provisional due to the lack of phylogenetic hypotheses. The present study of the Rubiaceae is based on 33 genera and three data sets, one morphological and two molecular from chloroplast DNA, restriction sites andrbcL sequences. There is much congruence between the morphological and the molecular data sets, but also conflict. For parsimony reasons, the best phylogenetic hypothesis is a tree based on an analysis of the combined data sets. The so-called “total evidence” criterion for the combined analysis is simply a reiteration of the principle of parsimony. In this particular study, the classification would be almost the same even if based on the separate analyses instead of the combined. Despite the inapplicability of consensus trees or trees from separate analyses for phylogenetic hypotheses and classification, separate analyses may provide important information. It is the best way to reveal conflicts between different data sets. Knowledge of the conflicts can promote further detailed investigation in order to improve understanding of characters and phylogenetic hypotheses. In this study, the tribe Vanguerieae provides such an example; morphological data support a position in the subfamily Cinchonoideae, but DNA and a tree based on the combined data support a position in subfamily Ixoroideae. The tribe's position in the morphological tree is probably due to missing information concerning the correct pollen presentation system. Bootstrap fractions and K. Bremer's branch support values are used to evaluate the stability of particular nodes in the trees. Interestingly these values are not always correlated, e.g. in the morphological tree, the node with the highest branch support value has very low bootstrap fraction. The reasons for these differences are unclear, but large differences are presumably more likely to occur on short branches.     

Gene tree parsimony of multilocus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss

The proliferation of gene data from multiple loci of large multigene families has been greatly facilitated by considerable recent advances in sequence generation. The evolution of such gene families, which often undergo complex histories and different rates of change, combined with increases in sequence data, pose complex problems for traditional phylogenetic analyses, and in particular, those that aim to successfully recover species relationships from gene trees. Here, we implement gene tree parsimony analyses on multicopy gene family data sets of snake venom proteins for two separate groups of taxa, incorporating Bayesian posterior distributions as a rigorous strategy to account for the uncertainty present in gene trees. Gene tree parsimony largely failed to infer species trees congruent with each other or with species phylogenies derived from mitochondrial and single-copy nuclear sequences. Analysis of four toxin gene families from a large expressed sequence tag data set from the viper genus Echis failed to produce a consistent topology, and reanalysis of a previously published gene tree parsimony data set, from the family Elapidae, suggested that species tree topologies were predominantly unsupported. We suggest that gene tree parsimony failure in the family Elapidae is likely the result of unequal and/or incomplete sampling of paralogous genes and demonstrate that multiple parallel gene losses are likely responsible for the significant species tree conflict observed in the genus Echis. These results highlight the potential for gene tree parsimony analyses to be undermined by rapidly evolving multilocus gene families under strong natural selection.     

Phylogeny of Tunicata inferred from molecular and morphological characters

The phylogeny of the Tunicata was reconstructed using molecular and morphological characters. Mitochondrial cytochrome oxidase I (cox1) and 18S rDNA sequences were obtained for 14 and 4 tunicate species, respectively. 18S rDNA sequences were aligned with gene sequences obtained from GenBank of 57 tunicates, a cephalochordate, and a selachian craniate. Cox1 sequences were aligned with the sequence of two ascidians and a cephalochordate obtained from GenBank. Traditional, morphological, life history, and biochemical characters of larval and adult stages were compiled from the literature and analyzed cladistically. Separate and simultaneous parsimony analyses of molecular and morphological data were carried out. Aplousobranch ascidians from three different families were included in a molecular phylogenetic analysis for the first time. Analysis of the morphological, life history, and biochemical characters results in a highly unresolved tree. Aplousobranchiata form a strongly supported monophylum in the analysis of the 18S rDNA data, the morphological data, and the combined data set. Cionidae is not included in the Aplousobranchiata but nests within the Phlebobranchiata. Appendicularia (=Larvacea) nest within the 'Ascidiacea' as the sister taxon of Aplousobranchiata in the parsimony analysis of the 18S rDNA data and the combined analysis. A potential morphological synapomorphy of Aplousobranchiata plus Appendicularia is the horizontal orientation of the larval tail. In the 18S rDNA and the combined analysis, Thaliacea is included in the 'Ascidiacea' as the sister group to Phlebobranchiata. Pyrosomatida is found to be the sister taxon to the Salpidae in analyses of 18S rDNA and combined data, whereas the analysis of the morphological data recovers a sister group relationship between Doliolidae and Salpidae. Results of cox1 analyses are incongruent with both the 18S rDNA and the morphological phylogenies. Cox1 sequences may evolve too rapidly to resolve relationships of higher tunicate taxa. However, the cox1 data may be useful at lower taxonomic levels.