Data partitioning in Bayesian analysis: molecular phylogenetics of metalmark moths (Lepidoptera: Choreutidae)

In this study a multilocus phylogenetic analysis of metalmark moths (Lepidoptera: Choreutidae) focused on resolving the higher‐level phylogeny of this group is presented. Through the analysis of this dataset, I explore different data‐partitioning strategies in Bayesian phylogenetic inference, and find that a partitioning strategy can have a large influence on the results of phylogenetic analysis. Depending on how the data are partitioned, there can be significant differences in branch support. I also test for the existence of the Bayesian star tree paradox, and its importance in this dataset, and find that it appears to inflate support for the clade including Rhobonda gaurisana, Hemerophila houttuinialis, H. diva and H. felis, but plays no role in other cases where the differences between maximum‐likelihood bootstraps and Bayesian posterior probabilities are large. The results of all the phylogenetic analyses strongly suggest that including Millieriinae in Choreutidae renders the family polyphyletic. The monophyly of the other two subfamilies, Brenthiinae and Choreutinae, as well as their sister‐group relationship, is strongly supported. Similarly, the monophyly of all the genera examined except Hemerophila is also well supported. To bring the classification of Choreutidae in line with our current understanding of the phylogenetic relationships in the family, I propose to exclude Millieriinae from Choreutidae, elevate it to Millieriidae Heppner, and place it as incertae sedis within Ditrysia.     

Phylogeny of the subfamily Larentiinae (Lepidoptera: Geometridae): integrating molecular data and traditional classifications

Larentiinae are the second largest subfamily of Geometridae, with more than 6200 described species. Despite recent advances in molecular systematics of geometrid moths, phylogenetic relationships between the numerous subgroups of Larentiinae are poorly known. In this study we present the most comprehensive attempt to date to resolve the phylogeny of Larentiinae, having sampled at least one species from all currently recognized 23 tribes. Fragments of one mitochondrial (COI) and eight nuclear (EF‐1α, WGL, GAPDH, RPS5, IDH, MDH, CAD and 28S) genes were sequenced, for a total of 6939 bp. Maximum likelihood and Bayesian analyses resulted in identical well‐resolved phylogenetic trees, which had maximum or near‐maximum support values at most nodes. Almost all conventionally recognized tribes represented by more than one genus were found to be monophyletic. Close to the root of Larentiinae, six tribes branch off the main lineage one after another, with Dyspteridini being sister to all other members of the subfamily. The rest of larentiines are divided into two very diverse lineages, comprising eight and at least ten tribes, respectively. There were just three findings incongruent with the conventional tribal subdivision of the subfamily. First, the genera Collix Guenée and Anticollix Prout formed a separate, previously unrecognized but well‐supported clade at the tribe level. Second, the Palaearctic genus Pelurga Hübner was placed apart from Larentia Treitschke and Mesoleuca Hübner, which were the other members of Larentiini in this analysis. Third, Cataclysmini appeared together with genera belonging to Xanthorhoini, leaving the latter paraphyletic. The Neotropic genus Oligopleura Herrich‐Schäffer is shown to belong to the tribe Euphyiini ( comb.n. ) according to both molecular data and male genital morphology. The results and the tribal classification of Larentiinae are discussed with reference to the principal publications since the end of the 19th Century. We conclude that the current tribal classification of Larentiinae is not controversial from the phylogenetic point of view and that its increasing complexity has merely reflected the accumulation of information, mainly through different methods of biosystematic study having become available for researchers. Our results indicate that diurnal lifestyle, accompanied by conspicuous coloration, has evolved independently in several subgroups of Larentiinae.     

12 Phylogeny of the euglenoid loricate genera trachelomonas and strombomonas based on morphological and molecular data

Since the separation of the Trachelomonas subgroup “Saccatae” into a new genus, Strombomonas Deflandre (1930), there has been some question as to its validity. Deflandre's separation was based on morphological characteristics such as the shape of the lorica, lack of a distinctive collar, possession of a tailpiece, lack of ornamentation, and ability to aggregate particles on the lorica. Recent molecular analyses indicated that the loricate taxa were monophyletic, but few species have been sampled. The LSU rDNA from eleven Strombomonas and thirty‐eight Trachelomonas species was sequenced to evaluate the monophyly of the two genera. Bayesian and maximum‐likelihood analyses found one monophyletic clade for each genus. The Trachelomonas clade was weakly supported, but had five strongly supported subclades. Morphological characters, such as lorica development and pellicle strip reduction, also supported separation of the genera. Lorica development in Strombomonas occurred from the anterior of the cell to the posterior, forming a shroud over the protoplast whereas in Trachelomonas, a layer of mucilage was excreted over the entire protoplast, followed by creation of the collar at the anterior end. Taxa from both genera underwent exponential strip reduction at the anterior and posterior poles. In Strombomonas, only one reduction was visible in the anterior pole, while in most Trachelomonas species, two reductions were visible. Likewise, Strombomonas species possessed two whorls of strip reduction in their posterior end compared to a single whorl of strip reduction in Trachelomonas species. The combined morphological and molecular data support the retention of Trachelomonas and Strombomonas as separate genera.     

Phylogeny of New Zealand hepialid moths (Lepidoptera: Hepialidae) inferred from a cladistic analysis of morphological data

The phylogeny of the New Zealand hepialid moths was estimated from a cladistic analysis of sixty‐three morphological characters, from all life cycle stages. One hundred and sixteen maximum parsimony trees were produced. The phylogenetic reconstruction indicated that the currently recognized generic concepts, and the four informal lineages hypothesized in a previous morphological taxonomic revision, were monophyletic. The relationships of species within genus Wiseana were not fully resolved. Analysis of a data set of thirty‐nine adult male characters from the New Zealand taxa and the Australian genera Jeana, Oxycanus and Trictena supported the monophyly of the New Zealand ‘Oxycanus’ s.s lineage.     

Phylogeny of the Pantomorus–Naupactus complex based on morphological and molecular data (Coleoptera: Curculionidae)

The Pantomorus–Naupactus complex is a Neotropical group of broad‐nosed weevils (Coleoptera: Curculionidae) including several parthenogenetic species usually assigned to the genera Naupactus Dejean, Pantomorus Schoenherr, Asynonychus Crotch, Aramigus Horn, Eurymetopus Schoenherr and Graphognathus Buchanan. Sixteen species were studied to test hypotheses on the monophyly of these genera, and on the origin of the parthenogenetic lineages. A matrix of 30 morphological characters and 999 positions of the Cytochrome Oxidase I gene, was analyzed with separate partitions and simultaneously, under equal and implied weights, and with different transversion/transitions costs. The ILD test indicates that the incongruence between the molecular and morphological data is not significant. Under equal weights, the molecular data resulted in a single tree and morphology in 34 trees; under implied weights morphology gave a different tree, and under TV:TS ≥ 4:1 molecular and combined analyses resulted in the same optimal tree. According to the latter, Naupactus includes Graphognathus, and is thus paraphyletic and basal regarding remaining genera, Pantomorus is polyphyletic and includes Aramigus and Asynonychus, and Eurymetopus is monophyletic. The species in which apomictic parthenogenesis has been verified (Aramigus tessellatus, Asynonychus cervinus and Graphognathus lecuoloma), belong to different clades of the Pantomorus‐Naupactus complex, with basal sexual relatives. © The Willi Hennig Society 2005.     

Reconsideration of systematic relationships within the order Euplotida (Protista, Ciliophora) using new sequences of the gene coding for small-subunit rRNA and testing the use of combined data sets to construct phylogenies of the Diophrys-complex

Comprehensive molecular analyses of phylogenetic relationships within euplotid ciliates are relatively rare, and the relationships among some families remain questionable. We performed phylogenetic analyses of the order Euplotida based on new sequences of the gene coding for small-subunit RNA (SSrRNA) from a variety of taxa across the entire order as well as sequences from some of these taxa of other genes (ITS1-5.8S-ITS2 region and histone H4) that have not been included in previous analyses. Phylogenetic trees based on SSrRNA gene sequences constructed with four different methods had a consistent branching pattern that included the following features: (1) the “typical” euplotids comprised a paraphyletic assemblage composed of two divergent clades (family Uronychiidae and families Euplotidae–Certesiidae–Aspidiscidae–Gastrocirrhidae), (2) in the family Uronychiidae, the genera Uronychia and Paradiophrys formed a clearly outlined, well-supported clade that seemed to be rather divergent from Diophrys and Diophryopsis, suggesting that the Diophrys-complex may have had a longer and more separate evolutionary history than previously supposed, (3) inclusion of 12 new SSrRNA sequences in analyses of Euplotidae revealed two new clades of species within the family and cast additional doubt on the present classification of genera within the family, and (4) the intraspecific divergence among five species of Aspidisca was far greater than those of closely related genera. The ITS1-5.8S-ITS2 coding regions and partial histone H4 genes of six morphospecies in the Diophrys-complex were sequenced along with their SSrRNA genes and used to compare phylogenies constructed from single data sets to those constructed from combined sets. Results indicated that combined analyses could be used to construct more reliable, less ambiguous phylogenies of complex groups like the order Euplotida, because they provide a greater amount and diversity of information.     

Phylogeny and classification of the tribe Hydaticini (Coleoptera: Dytiscidae): partition choice for Bayesian analysis with multiple nuclear and mitochondrial protein-coding genes

A phylogenetic analysis of the diving beetle tribe Hydaticini Sharp (Coleoptera: Dytiscidae: Dytiscinae) is presented based on data from adult morphology, two nuclear (histone III and wingless) and two mitochondrial (cytochrome c oxidase I and II) protein‐coding genes. We explore how to best partition a data set of multiple nuclear and mitochondrial protein‐coding genes by using Bayes factor and a penalized modification of Bayes Factor. Ten biologically relevant partitioning strategies were identified ranging from all DNA analysed under a single model to each codon position of each gene treated with a separate model. Model selection criteria AIC, AICc, BIC and four ways of traversing parameter space in a hierarchical likelihood ratio test were applied to each partition. All unique partitioning and model combinations were analysed with Bayesian methods. Results show that partitioning by codon position and genome source (nuclear vs. mitochondrial) is strongly favoured over partitioning by gene. We also find evidence that Bayes Factor can penalize overparameterization even when comparing nested models. Species groups showing a strong geographical pattern were generally highly supported, however, the sister group relationship of an isolated Madagascan and Australian species were shown to be artefactual with a long‐branch extraction test. The following conclusions were supported in both the selected method of partitioning the Bayesian analysis and combined parsimony analyses: (i) the tribe Hydaticini is monophyletic (ii) the genus Hydaticus Leach is paraphyletic with respect to Prodaticus Sharp (iii) the subgenus Hydaticus (Hydaticus) is monophyletic, and (iv) the subgenus H. (Guignotites) Brinck is paraphyletic with respect to Prodaticus and the subgenera H. (Pleurodytes) Régimbart and H. (Hydaticinus) Guignot. Based on these results, Hydaticus and Prodaticus are each recognized as valid genera and Guignotites, Hydaticinus and Pleurodytes are each placed as junior synonyms of Prodaticus (new synonymies).     

Phylogenetic analysis of RAD‐seq data: examining the influence of gene genealogy conflict on analysis of concatenated data

One of the major issues in phylogenetic analysis is that gene genealogies from different gene regions may not reflect the true species tree or history of speciation. This has led to considerable debate about whether concatenation of loci is the best approach for phylogenetic analysis. The application of Next‐generation sequencing techniques such as RAD‐seq generates thousands of relatively short sequence reads from across the genomes of the sampled taxa. These data sets are typically concatenated for phylogenetic analysis leading to data sets that contain millions of base pairs per taxon. The influence of gene region conflict among so many loci in determining the phylogenetic relationships among taxa is unclear. We simulated RAD‐seq data by sampling 100 and 500 base pairs from alignments of over 6000 coding regions that each produce one of three highly supported alternative phylogenies of seven species of Drosophila. We conducted phylogenetic analyses on different sets of these regions to vary the sampling of loci with alternative gene trees to examine the effect on detecting the species tree. Irrespective of sequence length sampled per region and which subset of regions was used, phylogenetic analyses of the concatenated data always recovered the species tree. The results suggest that concatenated alignments of Next‐generation data that consist of many short sequences are robust to gene tree/species tree conflict when the goal is to determine the phylogenetic relationships among taxa.     

PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN. NOV. (EUGLENOPHYTA)1

A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid‐containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well‐supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well‐supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well‐supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well‐supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage.     

Partitioning the variation in a plot‐by‐species data matrix that is related to n sets of explanatory variables

Abstract. Variation partitioning by (partial) constrained ordination is a popular method for exploratory data analysis, but applications are mostly restricted to simple ecological questions only involving two or three sets of explanatory variables, such as climate and soil, this because of the rapid increase in complexity of calculations and results with an increasing number of explanatory variable sets. The existence is demonstrated of a unique algorithm for partitioning the variation in a set of response variables on n sets of explanatory variables; it is shown how the 2n– 1 non‐overlapping components of variation can be calculated. Methods for evaluation and presentation of variation partitioning results are reviewed, and a recursive algorithm is proposed for distributing the many small components of variation over simpler components. Several issues related to the use and usefulness of variation partitioning with n sets of explanatory variables are discussed with reference to a worked example.     

Phylogenetics of Escallonia (Escalloniaceae) based on plastid DNA sequence data

Escallonia (Escalloniaceae) is a New World genus of c. 39 species distributed mainly in the South American highlands. Plastid DNA sequence data from the intergenic spacers trnS‐trnG and 3′ trnV‐ndhC and the ndhF gene for 32 species were used to examine the relationships among species and related genera and to analyse the relationship between phylogeny and the geographical distribution of the species. Maximum parsimony and Bayesian inference were employed to analyse the data. The sister relationship of Escallonia to Forgesia and Valdivia was corroborated. We recovered five strongly supported clades that are geographically structured, suggesting that the evolutionary history of the genus may be linked to historical processes, including the uplift of mountainous systems in South America. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 442–451.     

Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data

The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We used molecular data from eight gene regions (one mitochondrial and seven nuclear protein‐coding genes) comprising a total of ~6700 bp from 96 taxa to infer a well‐supported phylogenetic hypothesis for the family. Based on this hypothesis, we revise the higher classification for all pierid genera. We resurrect the tribe Teracolini stat. rev. in the subfamily Pierinae to include the genera Teracolus, Pinacopteryx, Gideona, Ixias, Eronia, Colotis and most likely Calopieris. We transfer Hebomoia to the tribe Anthocharidini and assign the previously unplaced genera Belenois and Dixeia to the subtribe Aporiina. Three lineages near the base of Pierinae (Leptosia, Elodina and Nepheronia + Pareronia) remain unplaced. For each of these, we describe and delineate new tribes: Elodinini Braby tribus nova, Leptosiaini Braby tribus nova and Nepheroniini Braby tribus nova. The proposed higher classification is based on well‐supported monophyletic groups and is likely to remain stable even with the addition of more data.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

Unweaving hippolytoid systematics (Crustacea,Decapoda, Hippolytidae): resurrection of several families

The Hippolytidae is the fourth largest family within the Caridea, currently containing over 330 described species in 37 genera, and the classification of this family has been rather controversial. In this study, sequences of two nuclear protein‐coding genes, enolase and sodium‐potassium ATPase α‐subunit, and the mitochondrial 16S rRNA gene (totalling 1405 bp) from 29 hippolytid species in 20 genera plus 17 species from eight other caridean families were used to examine the phylogenetic status of Hippolytidae sensu lato. Our results clearly reject the monophyly of Hippolytidae and support the recognition of the Lysmatidae Dana, 1852, Thoridae Kingsley, 1879, Bythocarididae Christoffersen 1987 and Merguiidae Christoffersen 1990 .     

A global molecular phylogeny of 147 periwinkle species (Gastropoda,Littorininae)

Reid, D. G., Dyal, P. & Williams, S.T. (2012) A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). —Zoologica Scripta, 41, 125–136. Complete species‐level molecular phylogenies have been published for several genera of Littorinidae (e.g. Echinolittorina, Littoraria). Here we add new sequence data from three genes (28S rRNA, 12S rRNA, cytochrome oxidase c subunit I) for single specimens of an additional 24 species, to make a data set of 147 (97%) of the 152 recognized species of the subfamily Littorininae. This three‐gene data set is analysed to produce a phylogenetic hypothesis for the subfamily, which includes the first complete species‐level phylogeny of the genus Peasiella and the first three‐gene phylogeny of all Littorina species. The non‐planktotrophic species of Littorina have previously been classified together (as subgenus Neritrema), implying a single origin of this developmental mode. Tests of this hypothesis with the new data are inconclusive, and resolution is not improved in a tree constructed from five genes (adding previously published sequences of 16S rRNA and cytochrome b). Using available fossils for calibration we generate a BEAST chronogram, which emphasizes that the radiation of Littorina is more recent than that of other littorinine genera. A database is provided, listing all known species of Littorininae, with their distributions, development, ecology and gene sequences, as a tool for future evolutionary studies of this model group.     

Morphology agrees with molecular data: phylogenetic affinities of Euptychiina butterflies (Nymphalidae: Satyrinae)

Euptychiina is the most species‐rich subtribe of Neotropical Satyrinae, with over 450 known species in 47 genera (14 monotypic). Here, we use morphological characters to examine the phylogenetic relationships within Euptychiina. Taxonomic sampling included 105 species representing the majority of the genera, as well as five outgroups. A total of 103 characters were obtained: 45 from wing pattern, 48 from genitalia and 10 from wing venation. The data matrix was analysed using maximum parsimony under both equal and extended implied weights. Euptychiina was recovered as monophyletic with ten monophyletic genera, contrasting previous DNA sequence‐based phylogenies that did not recover the monophyly of the group. In agreement with sequence‐based hypotheses, however, three main clades were recognized: the ‘Megisto clade’ with six monophyletic and three polyphyletic genera, the ‘Taygetis clade’ with nine genera of which three were monophyletic, and the ‘Pareuptyhia clade’ with four monophyletic and two polyphyletic genera. This is the first morphology‐based phylogenetic hypothesis for Euptychiina and the results will be used to complement molecular data in a combined analysis and to provide critical synapomorphies for clades and genera in this taxonomically confused group.     

Local outbreaks of Operophtera brumata and Operophtera fagata cannot be explained by low vulnerability to pupal predation

• 1 One of the unresolved questions in studies on population dynamics of forest Lepidoptera is why some populations at times reach outbreak densities, whereas others never do. Resolving this question is especially challenging if populations of the same species in different areas or of closely‐related species in the same area are considered.
• 2 The present study focused on three closely‐related geometrid moth species, autumnal Epirrita autumnata, winter Operophtera brumata and northern winter moths Operophtera fagata, in southern Finland. There, winter and northern winter moth populations can reach outbreak densities, whereas autumnal moth densities stay relatively low.
• 3 We tested the hypothesis that a lower vulnerability to pupal predation may explain the observed differences in population dynamics. The results obtained do not support this hypothesis because pupal predation probabilities were not significantly different between the two genera within or without the Operophtera outbreak area or in years with or without a current Operophtera outbreak.
• 4 Overall, pupal predation was even higher in winter and northern winter moths than in autumnal moths. Differences in larval predation and parasitism, as well as in the reproductive capacities of the species, might be other candidates.

     

New data on the family Caucasinidae N. Bykova (late Cretaceous-Miocene Foraminifers)

Caucasina oligocenica Chalilov (type species) and C. schischkinskayae (Samoilova) are shown to be separate species. The diagnoses of the genera Caucasina, Caucasinella, and Tergrigorjanzaella of the family Caucasinidae are revised and emended. Based on the structure of the test, aperture with the toothplate, and the radially crystalline wall, this family is assigned to the order Buliminida. The data on the species composition, geographical and stratigraphic distribution of the family Caucasinidae are expanded; the paleoecology of this group is revised. The diagnoses of the listed genera are emended and new species, Caucasina robusta, C. bogdanoviczi, C. maryensis, and Caucasinella bykovae are established.