The phylogeny of Iberian Aphodiini species (Coleoptera, Scarabaeoidea, Scarabaeidae, Aphodiinae) based on morphology

Abstract.  The phylogeny of Iberian Aphodiini species was reconstructed based on morphology. Wing venation, mouthparts, male and female genitalia, and external morphology provided ninety-four characters scored for ninety-three Aphodiini species. Phylogenetic analyses were based on maximum parsimony and Bayesian inference criteria. Maximum parsimony consensus trees recovered Acrossus species as a sister group of the remaining Aphodiini, followed by two other branches, one including Neagolius , Plagiogonus , Ahermodontus and Ammoecius species, and the other including Oxyomus , Nimbus , Heptaulacus and Euheptaulacus species. The remaining studied taxa clustered in an unresolved group. Bayesian inference trees recovered Acrossus as the sister group of the remaining Iberian Aphodiini, followed by Colobopterus erraticus and the rest of the Iberian Aphodiini, but this latter branch was unresolved. The general lack of statistical support for the inferred phylogenetic relationships at terminal nodes using both maximum parsimony and Bayesian inference suggests that variation in morphological characters useful for phylogenetic inference in the present study is small, perhaps as a consequence of a radiation event occurring at the origin of the tribe. A probable evolutionary pattern for Aphodiini is proposed which infers six groups, namely Acrossian, Ammoecian, Oxyomian, Aphodian s.str., Colobopteran and Aphodian s.l. clades.     

Phylogenetic and systematic study of Korean <Emphasis Type="Italic">Orius</Emphasis> species (Heteroptera: Anthocoridae) on the basis of molecular and morphological data

A phylogenetic and systematic study of Orius species (Heteroptera: Anthocoridae) from Korea has been conducted using both morphological and molecular characters. Thirty morphological character states were coded for 10 strains of 9 species. Five molecular markers, partial cytochrome c oxidase I (COI), cytochrome b (CytB), 16S rRNA (16S), 18S rRNA (18S), and 28S rRNA (28S), from mitochondrial and nuclear genes, were tested. Phylogenetic analyses based on molecular data were conducted by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic (BP) analyses. Analysis of morphological data was performed using the parsimony programs NONA, and the combined dataset of morphological and molecular data was analyzed using BP analyses. The results of this study indicate that use of COI and CytB enabled relatively effective identification of species, whereas the sequences of 16S, 18S and 28S did not enable identification of closely related species such as Orius minutus and O. strigicollis. We discuss the usefulness of the five molecular markers for determining phylogenetic relationships and identifying the species.     

Systematics and phylogeny of the tribe Paragini (Diptera: Syrphidae) based on molecular and morphological characters

We studied the phylogeny and systematics of the tribe Paragini (Diptera: Syrphidae) using morphological and molecular data. The paper presents separate parsimony analyses of both adult morphological characters and partial DNA sequence data from mitochondrial cytochrome c oxidase I and nuclear ribosomal 28S rRNA gene, as well as a combined analysis of all the data. The data set of morphological characters included some features of the male terminalia (i.e. shape of the ejaculatory apodeme; relative position of elements of the aedeagal complex; shape of surstylar apodeme; shape of the aedeagal apodeme) not previously used in the systematics of the Paragini. The trees obtained from separate parsimony analyses of molecular and morphological data produced almost identical topologies. Four lineages are supported by the combined data set, and we establish two new subgenera, i.e. Serratoparagus Vujić et Radenković subgen. nov., and Afroparagus Vujić et Radenković subgen. nov., and redefine Pandasyopthalmus Stuckenberg, 1954 stat. rev. and Paragus Latreille, 1804, stat. rev. The monophyly of the Pandasyopthalmus clade, including the species fitting neither of the current species groups ( jozanus -group) of Paragini, is established. Diagnoses of all known species groups are presented, including a new arrangement of almost all valid species of Paragini.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 507–536.     

Molecular identification of three Ompok species using mitochondrial COI gene

A DNA-based barcode identification system that is applicable to all animal species will provide a simple, universal tool for the identification of fish species. The barcode system is based on sequence diversity in subunit 1 cytochrome c oxidase (COI) gene. Identification and characterization of fish species based on morphological characters are sometimes found to be erroneous and environmentally affected. There are no studies on the genus Ompok in India at molecular level and species identification of the Ompok is usually carried out through morphological features. A total of 106 samples from three species Ompok pabda, O. pabo and O. bimaculatus were collected from eight sampling sites of seven Indian rivers. One hundred and six sequences were generated from COI region of three Ompok species and 21 haplotypes were observed. The sequence analysis of COI gene revealed three genetically distinct Ompok species and exhibited identical phylogenetic resolution among them. The partial COI gene sequence can be used as a diagnostic molecular marker for identification and resolution of taxonomic ambiguity of Ompok species.     

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.     

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.     

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.     

Examining monophyly in a large radiation of Madagascan butterflies (Lepidoptera: Satyrinae: Mycalesina) based on mitochondrial DNA data

The satyrine butterfly subtribe Mycalesina has undergone one of the more spectacular evolutionary radiations of butterflies in the Old World tropics. Perhaps the most phenotypically pronounced diversification of the group has occurred in the Malagasy region, where 68 currently recognized species are divided among five genera. Here, we report the results of phylogenetic analyses of sequence data from the cytochrome c oxidase II and cytochrome b mitochondrial genes, for a total of 54 mycalesine taxa, mostly from Madagascar. These molecular data complement an existing data set based on male morphological characters. The molecular results support the suggestion from morphology that three of the five Malagasy genera are paraphyletic and support the monophyly of at least three major morphological clades. Novel hypotheses of terminal taxon pairs are generated by the molecular data. Dense taxon sampling appears to be crucial for elucidating phylogenetic relationships within this large radiation. A potentially complex scenario for the origin of Malagasy mycalesines is proposed.     

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.     

Phylogenetic analysis of six species of pacific abalone (Haliotidae) based on DNA sequences of 16s rRNA and cytochrome c oxidase subunit I mitochondrial genes

Six species of abalones (Haliotidae) are found on the Korean coasts. Identification and characterization of these abalones are usually based on morphologic characters. In this research we compared the partial sequences of the mitochondrial 16S ribosomal RNA and cytochrome c oxidase subunit I genes to identify species using molecular data and to determine their phylogenetic relationships. Sequence alignments and phylogenetic analysis revealed that the 6 species fell into 2 distinct groups which were genetically distant from each other and exhibited little internal phylogenetic resolution. One group included Haliotis discus hannai, H. discus discus, H. madaka, and H. gigantea, while the other group contained H. diversicolor supertexta and H. diversicolor diversicolor. The 16S rRNA sequences were relatively more conserved than to the COI sequences, but both gene sequences provided sufficient phylogenetic information to distinguish among the 6 species of Pacific abalone, and thus could be valuable molecular characters for species identification.     

Cryptic species within the Chydorus sphaericus species complex (Crustacea: Cladocera) revealed by molecular markers and sexual stage morphology

The cosmopolitanism paradigm in the biogeography of freshwater invertebrates is currently being replaced by non-cosmopolitanism or continental endemism. Benthic water fleas (Cladocera) from the family Chydoridae were the first group of freshwater invertebrates for which non-cosmopolitanism and cryptic diversity was substantiated by morphological studies. Yet, little is known about genetic differentiation and evolutionary history of chydorid species complexes. Here we present the first analysis of the genetic versus morphological differentiation in a benthic cladoceran species complex—Chydorus sphaericus s. str. using sequence variation in a nuclear (ribosomal internal transcribed spacer 2, ITS-2) and a mitochondrial (cytochrome c oxidase subunit I, COI) genes in 50 Holarctic localities. We tested for continental endemism and cryptic diversity predicted by previous morphological studies. We found evidence for the presence of at least seven putative regional species in the Holarctic, at least three of them being distributed beyond a single continent. While the molecular and sexual stage characters showed general concordance on species lineages, parthenogenetic female characters lacked resolution or were unassociated with molecular lineages. We conclude that cryptic regional lineages of benthic cladocerans are apparent and that the sexual stages represent the most informative morphological source of species characters for this environmental indicator group.     

Molecular phylogeny of the fungus gnat tribe Exechiini (Mycetophilidae, Diptera)

The phylogenetic relationships within the fungus gnat tribe Exechiini have been left unattended for many years. Recent studies have not shed much light on the intergeneric relationship within the tribe. Here the first attempt to resolve the phylogeny of the tribe Exechiini using molecular markers is presented. The nuclear 18S and the mitochondrial 16S, and cytochrome oxidase subunit I (COI) genes were successfully sequenced for 20 species representing 15 Exechiini genera and five outgroup genera. Bayesian, maximum parsimony and maximum likelihood analyses revealed basically congruent tree topologies and the monophyly of Exechiini, including the genus Cordyla , is confirmed. The molecular data corroborate previous morphological studies in several aspects. Cordyla is found in a basal clade together with Brachypeza , Pseudorymosia and Stigmatomeria . The splitting of the genera Allodiopsis s.l. and Brevicornu s.l. as well as the sistergroup relationship of Exechia and Exechiopsis is also supported. The limited phylogenetic information provided by morphological characters is mirrored in the limited resolution of the molecular markers used in this study. Short internal and long-terminal branches obtained may indicate a rapid radiation of the Exechiini genera during a short evolutionary period.     

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.     

Phylogenetic relationships of Nembrothinae (Mollusca: Doridacea: Polyceridae) inferred from morphology and mitochondrial DNA

Within the Polyceridae, Nembrothinae includes some of the most striking and conspicuous sea slugs known, although several features of their biology and phylogenetic relationships remain unknown. This paper reports a phylogenetic analysis based on partial sequences of two mitochondrial genes (cytochrome c oxidase subunit I and 16S rRNA) and morphology for most species included in Nembrothinae. Our phylogenetic reconstructions using both molecular and combined morphological and molecular data support the taxonomic splitting of Nembrothinae into several taxa. Excluding one species (Tambja tentaculata), the monophyly of Roboastra was supported by all the phylogenetic analyses of the combined molecular data. Nembrotha was monophyletic both in the morphological and molecular analyses, always with high support. However, Tambja was recovered as para- or polyphyletic, depending on the analysis performed. Our study also rejects the monophyly of "phanerobranch" dorids based on molecular data.     

Molecular systematics of the genus Megoura (Hemiptera: Aphididae) using mitochondrial and nuclear DNA sequences

To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identifi-cation was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha (EF1 alpha), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, EF1 alpha, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and EF1alpha gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for EF1 alpha). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.     

Phylogenetic analysis of Macrobiotidae (Eutardigrada, Parachela): a combined morphological and molecular approach

Combined analyses of morphological and molecular data were used to resolve phylogenetic relationships within Macrobiotidae (Eutardigrada). Morphological data were analysed using a cladistic approach with a matrix comprising 15 taxa with 17 characters to obtain a phylogenetic reconstruction. Molecular data were obtained by sequencing the cytochrome c oxidase subunit I gene in seven species of Macrobiotidae and one of Eohypsibiidae (used as outgroup). The morphological character defining the family, symmetrical claw on each leg, turns out to be plesiomorphic. Moreover, neither morphological nor molecular analyses supports a monophyletic clade for the subfamily Macrobiotinae, whereas both support a well defined evolutionary line (Murrayinae) within the family. We propose elevating the latter to family level (Murrayidae) while temporarily retaining as valid the family Macrobiotidae (amending its diagnosis, including within it only Macrobiotinae). Murrayidae opens an interesting evolutionary prospective, because the entire line has differentiated without sexual reproduction, constituting an example of evolution of asexual lineages.     

Taking phylogenetics beyond pattern analysis: can models of genome dynamics guide predictions about homoplasy in morphological and behavioral data sets?

Despite the considerable amount of interest in phylogeny reconstruction, patterns of homoplasy in morphological and behavioral data have received only limited attention to date, whereas the patterns of homoplasy in molecular data are relatively well understood. First, because the number of alternative molecular character states is strictly limited (particularly for nucleotide sequence data), higher rates of substitution generate higher levels of homoplasy. Second, depending on the relative proportions of constrained and unconstrained sites, each molecular data set has a time frame of applicability outside of which resolution becomes ambiguous. There is good evidence to suggest that numbers of alternative character states for morphological and even behavioral data may be similarly limited and that higher rates of evolution are often linked to higher rates of homoplasy. Like molecular data sets, morphological and behavioral data sets contain rapidly evolving characters as well as more conservative elements. Morphologies and behaviors related to sexual recognition and reproduction show low levels of intraspecific variation, but high levels of lability between species, making them crucial for species identification but often poor as markers of relationship at greater time depths. The organization theory of speciation derived by Carson is a model based on genome dynamics, and it predicts exactly this window of applicability for characters related to sexual reproduction. Nonsexual characters related to environmental adaptation should be applicable at greater phylogenetic depths. A better understanding of patterns of homoplasy enables a more sophisticated approach to the assessment of the relative reliabilities of alternative tree topologies.     

Cryptic species of mites (Uropodoidea: Uroobovella spp.) associated with burying beetles (Silphidae: Nicrophorus): The collapse of a host generalist revealed by molecular and morphological analyses

Uroobovella (Mesostigmata: Uropodoidea: Urodinychidae) species are among the most common mites associated with carrion-feeding Nicrophorus (Silphidae) beetles. Previous taxonomic understanding suggests that a single host generalist, U. nova, disperses and lives with Nicrophorus species worldwide (reported from at least seven host species). Using morphometrics and morphological characteristics, as well as partial cytochrome oxidase I (COI) and the entire internal transcribed spacer 2 (ITS2) markers, we tested whether this apparent generalist is truly a generalist or rather a complex of cryptic species with narrower host ranges. Based on deutonymph mites collected from 14 host species across six countries and 17 provinces or states, we show that U. nova represents at least five morphologically similar species with relatively restricted host ranges. Except for one species which yielded no molecular data (but did exhibit morphological differences), both molecular and morphological datasets were congruent in delimiting species boundaries. Moreover, comparing the mite phylogeny with the known ecology and phylogenetic relationships of their host species suggests that these mites are coevolving with their silphid hosts rather than tracking ecologically similar species.     

DNA Barcoding for Identification of Sugarcane Borers in China

Sugarcane borers are economically damaging insects with species that vary in distribution patterns both geographically and temporally, and vary based on ecological niche. Currently, identification of sugarcane borers is mostly based on morphological characters. However, morphological identification requires taxonomic expertise. An alternative method to identify sugarcane borers is the use of molecular data. DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has proven to be a useful tool for rapid and accurate species determination in many insect taxa. This study was conducted to test the effectiveness of DNA barcodes to discriminate among sugarcane borer species in China. Partial sequences of the COI gene (709 bp) were obtained from six species collected from different geographic areas. Results showed that the pairwise intraspecies genetic distance was < 0.02, whereas the interspecies genetic distance ranged from 0.117 to 0.182. Results from a neighbor-joining tree showed that the six sugarcane borer species were certainly separated. These results suggested that the partial COI sequences had high barcoding resolution in discriminating among sugarcane borer species. Our study emphasized the use of DNA barcodes for identification of the analyzed sugarcane borer species and represents an important step for building a comprehensive barcode library for sugarcane borers in China.