Phylotranscriptomics resolves ancient divergences in the Lepidoptera

Classic morphological studies of the oldest, so‐called nonditrysian lineages of Lepidoptera yielded a well‐resolved phylogeny, supported by the stepwise origin of the traits characterizing the clade Ditrysia, which contains over 98% of extant lepidopterans. Subsequent polymerase chain reaction (PCR)‐based molecular studies have robustly supported many aspects of the morphological hypothesis and strongly contradicted others, while leaving some relationships unsettled. Here we bring the greatly expanded gene sampling of RNA‐Seq to bear on nonditrysian phylogeny, especially those aspects that were not conclusively resolved by the combination of morphology and previous PCR‐based multi‐gene studies. We analysed up to 2212 genes in each of 28 species representing all 12 superfamilies and 15 of 21 families of nonditrysians, plus trichopteran outgroups and representative Ditrysia. Our maximum likelihood phylogeny estimates used both nonsynonymous changes only (degen1 coding) and all nucleotides (nt123) partitioned by codon position, recovering a novel hypothesis for early glossatan relationships that is the most strongly supported to date. We find strong support for Micropterigidae alone as the sister group to all other Lepidoptera, in agreement with morphology and early molecular evidence, but in contrast to recent PCR‐based studies. Also very strongly supported are the previously recognized clades Angiospermivora, Heteroneura, Eulepidoptera and Euheteroneura. Finally, we find strong support for paraphyly of the southern hemisphere family Palaephatidae, with the South American genus Palaephatus Butler forming the previously undetermined sister group to Ditrysia. The remaining palaephatids, Australian and South American, form the sister group to Tischeriidae.     

A new extant family of primitive moths from Kangaroo Island,Australia, and its significance for understanding early Lepidoptera evolution

We report the first discovery since the 1970s of a new extant family (Aenigmatineidae fam.n. ) of homoneurous moths, based on the small Aenigmatinea glatzella sp.n . from Kangaroo Island off southern Australia. It exhibits a combination of extraordinary anatomical characters, and, unlike most homoneurous moths, its larva is a conifer‐feeder (stem mining in Callitris, Cupressaceae). While the adult's mouthparts are strongly regressed, evidence from other morphological characters and from a Bayesian analysis of 25 genetic loci convincingly places the taxon among Glossata (‘tongue moths’). An unexpected tongue moth clade including Acanthopteroctetidae and Neopseustidae, suggested with low support in recent molecular analyses, remarkably becomes strongly supported when Aenigmatinea is included in the molecular analysis; the new taxon becomes subordinated in that clade (as sister group to Neopseustidae) and the clade itself appears as the sister group of all Heteroneura, representing the vast majority of all Lepidoptera. Including Aenigmatinea into the analysis thereby strengthens the surprising indication of non‐monophyly of Myoglossata, and the new phylogeny requires an additional number of ad hoc assumptions of convergence/character reversals in early Lepidoptera evolution. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:44393B52‐1889‐431A‐AB08‐6BBCF8F946B8 .     

Female genital configuration in the classification of Lepidoptera

In Coleoptera, Neuroptera, and Megaloptera, and the panorpoid orders Diptera, Trichoptera, and Mecoptera the common oviduct is ventral to, or opens into, the vagina or genital chamber. In Lepidoptera, in the superfamilies Micropterigoidea, Eriocranioidea, Incurvarioidea, and Nepticuloidea, the common oviduct enters the copulatory chamber ventrally; in Mnesarchaeidae, Hepialoidea, and all Ditrysia auct. the common oviduct is dorsal to the copulatory chamber, and the vagina (that region posterior to the entry of the spermatheca) opens separately from the genital ostium. Lepidoptera are unique in the complex and various arrangements of the ectodermal elements in the female genitalia.

The arrangements of, and connections between rectal and genital structures in representatives of Megaloptera, Neuroptera, and the panorpoid orders are re‐examined for comparison with the systems found in Zeugloptera, Dacnonypha, Monotrysia, and Ditrysia auct.

The Zeugloptera are here included in Lepidoptera because they have a circumcloacal chamber. Other female zeuglopteran genital structures intergrade with those of Dacnonypha, here restricted to Eriocraniidae, Agathiphagidae, Lophocoronidae, and the divergent Acanthopteroctetes. Dacnonypha have a less specialised spermathecal and vaginal structure than do most of the Monotrysia, here restricted to Incurvarioidea and Nepticuloidea (including Tischeriidae); many Monotrysia lack a cloaca, whereas it is always present in Dacnonypha.

There is no basis for retaining either Mnesarchaeidae or Hepialoidea in Monotrysia auct., as the dorsal common oviduct and the two genital openings indicate that these groups are ditrysian. They are here regarded as exoporian Ditrysia, a group characterised by the lack of a free, tubular ductus seminalis. A fixed gutter or channel between ostium and ovipore characterises the Hepialoidea, and the absence of this channel (ostium and ovipore opposable within an external genital pouch) characterises Mnesarchaeidae.

The endoporian Ditrysia all have a free, tubular ductus seminalis; where a cloaca is present it is incomplete, i.e., combines ovipore and rectum but never copulatory structures, in contrast to the complete cloaca found in Zeugloptera, Dacnonypha, and many Monotrysia. The endoporian Ditrysia comprise all other superfamilies, i.e., about 97% of species of Lepidoptera.     

The phylogeny of the superfamily Coccoidea (Hemiptera: Sternorrhyncha) based on the morphology of extant and extinct macropterous males

Currently, 49 families of scale insects are recognised, 33 of which are extant. Despite more than a decade of DNA sequence‐based phylogenetic studies of scales insects, little is known with confidence about relationships among scale insects families. Multiple lines of evidence support the monophyly of a group of 18 scale insect families informally referred to as the neococcoids. Among neococcoid families, published DNA sequence‐based estimates have supported Eriococcidae paraphyly with respect to Beesoniidae, Dactylopiidae, and Stictococcidae. No other neococcoid interfamily relationship has been strongly supported in a published study that includes exemplars of more than ten families. Likewise, no well‐supported relationships among the 15 extant scale insect families that are not neococcoids (usually referred to as ‘archaeococcoids’) have been published. We use a Bayesian approach to estimate the scale insect phylogeny from 162 adult male morphological characters, scored from 269 extant and 29 fossil species representing 43/49 families. The result is the most taxonomically comprehensive, most resolved and best supported estimate of phylogenetic relationships among scale insect families to date. Notable results include strong support for (i) Ortheziidae sister to Matsucoccidae, (ii) a clade comprising all scale insects except for Margarodidae s.s., Ortheziidae and Matsucoccidae, (iii) Coelostomidiidae paraphyletic with respect to Monophlebidae, (iv) Eriococcidae paraphyletic with respect to Stictococcidae and Beesoniidae, and (v) Aclerdidae sister to Coccidae. We recover strong support for a clade comprising Phenacoleachiidae, Pityococcidae, Putoidae, Steingeliidae and the neococcoids, along with a sister relationship between this clade and Coelostomidiidae + Monophlebidae. In addition, we recover strong support for Pityococcidae + Steingeliidae as sister to the neococcoids. Data from fossils were incomplete, and the inclusion of extinct taxa in the data matrix reduced support and phylogenetic structure. Nonetheless, these fossil data will be invaluable in DNA sequence‐based and total evidence estimates of phylogenetic divergence times.     

Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions (COI, EF-1alpha and wingless). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1alpha data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.     

A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher‐level classification

Pyraloidea, one of the largest superfamilies of Lepidoptera, comprise more than 15 684 described species worldwide, including important pests, biological control agents and experimental models. Understanding of pyraloid phylogeny, the basis for a predictive classification, is currently provisional. We present the most detailed molecular estimate of relationships to date across the subfamilies of Pyraloidea, and assess its concordance with previous morphology‐based hypotheses. We sequenced up to five nuclear genes, totalling 6633 bp, in each of 42 pyraloids spanning both families and 18 of the 21 subfamilies, plus up to 14 additional genes, for a total of 14 826 bp, in 21 of those pyraloids plus all 24 outgroups. Maximum likelihood analyses yield trees that, within Pyraloidea, differ little among datasets and character treatments and are strongly supported at all levels of divergence (83% of nodes with bootstrap ≥80%). Subfamily relationships within Pyralidae, all very strongly supported (>90% bootstrap), differ only slightly from a previous morphological analysis, and can be summarized as Galleriinae + Chrysauginae (Phycitinae (Pyralinae + Epipaschiinae)). The main remaining uncertainty involves Chrysauginae, of which the poorly studied Australian genera may constitute the basal elements of Galleriinae + Chrysauginae or even of Pyralidae. In Crambidae the molecular phylogeny is also strongly supported, but conflicts with most previous hypotheses. Among the newly proposed groupings are a ‘wet‐habitat clade’ comprising Acentropinae + Schoenobiinae + Midilinae, and a provisional ‘mustard oil clade’ containing Glaphyriinae, Evergestinae and Noordinae, in which the majority of described larvae feed on Brassicales. Within this clade a previous synonymy of Dichogaminae with the Glaphyriinae is supported. Evergestinae syn. n. and Noordinae syn. n. are here newly synonymized with Glaphyriinae, which appear to be paraphyletic with respect to both. Pyraustinae and Spilomelinae as sampled here are each monophyletic but form a sister group pair. Wurthiinae n. syn. , comprising the single genus Niphopyralis Hampson, which lives in ant nests, are closely related to, apparently subordinate within, and here newly synonymized with, Spilomelinae syn. n.     

Phylogeny,divergence times and biogeography of window flies (Scenopinidae) and the therevoid clade (Diptera: Asiloidea)

The evolution of the ‘therevoid’ clade, with an emphasis on window flies (Scenopinidae), is presented by combining DNA sequence data with morphological characters for living and fossil species. The therevoid clade represents a group of four families (Apsilocephalidae, Evocoidae, Scenopinidae and Therevidae) of lower brachyceran Diptera in the superfamily Asiloidea. A comprehensive phylogenetic analysis using parsimony and likelihood methods was undertaken using extensive taxon sampling from all families and subfamilies, and compared with outgroup taxa sampled from the related families Asilidae, Mydidae, Apioceridae and Empididae. Fifty‐nine morphological characters (adult, larval and pupal) were combined with 6.4 kb of DNA sequences for two ribosomal genes (16S and 18S ribosomal DNA) and three protein‐encoding genes [cytochrome oxidase I (COI), triose phosphate isomerase (TPI) and the CPSase region of carbamoyl‐phosphate synthase‐aspartate transcarbamoylase‐dihydroorotase (CAD)]. Results from combined analyses of morphological and molecular data for 78 taxa representing all families of the therevoid clade are presented. Specific hypotheses of the relationship between respective families and subfamilies were tested statistically using four‐cluster likelihood mapping. The therevoid clade is a well‐supported monophyletic group within Asiloidea, with Evocoidae sister to Apsilocephalidae and Therevidae sister to Scenopinidae. Temporal and zoogeographical aspects of therevoid clade evolution were investigated using Bayesian divergence time estimates and Lagrange ancestral range scenarios. The effect of inclusion of fossils as terminal taxa on phylogenetic and divergence time estimation was investigated, with morphological scoring for fossil representatives included in the analyses rather than used simply as minimum age constraints. In each analysis there was either improvement in estimation, or only marginal and localized loss in tree resolution, and with younger estimates of divergence time across the tree. The historical biogeography of the therevoid clade was examined with multiple trans‐Antarctic vicariance events between Australasia and South America evident during the Late Cretaceous to early Palaeogene. Scenopininae is newly subdivided into two tribes, Metatrichini trib.n. and Scenopinini Fallén stat.r. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:4974EBF8‐3117‐4189‐B6DE‐7D5BF9B23E53 .     

The wing vestiture of the non-ditrysian Lepidoptera (Insecta). Comparative morphology and phylogenetic implications

The ultrastructure of the dorsal forewing vestiture in exemplars of all family group taxa of non‐ditrysian Lepidoptera is examined, and the evolutionary implications at family level and above are discussed. Wing‐scale terminology is reviewed. Three different types of bilayer wing‐scale covering are recognized; only a few groups have a single‐layer wing‐scale covering. The general scale arrangement is random, but a few taxa have clustered scale arrangements and scattered heteroneurans have scales arranged in transverse rows. Cross ribs are present in all taxa, but only as vestiges in eriocraniid cover scales. Ridge dimorphism is widespread in Neolepidoptera. Surprisingly, ridges and cross ribs on the adwing scale surface are of general occurrence in Neopseustidae and Hepialidae, and are even found on parts of the ground scales of many other Neolepidoptera. Morphological evidence strongly indicates that the fused wing‐scale types found in non‐Coelolepidan Lepidoptera and Neolepidoptera are independently evolved, as evidenced from the presence of vestigial perforations. Absence of perforations is not infallible evidence that a scale is solid. Microtrichia are independently reduced in a number of taxa and probably re‐evolved in at least higher nepticulids. Wing vestiture and scale characters indicate that Tischerioidea may be the sister group of Ditrysia.     

Phylogeny of a new supertribe Cephenniitae with generic review of Eutheiini and description of a new tribe Marcepaniini (Coleoptera: Staphylinidae: Scydmaeninae)

Genera of Eutheiini are reviewed and Eutheimorphus is removed from this tribe of ant‐like stone beetles (Scydmaeninae) and transferred to Cephenniini. A monogeneric Marcepaniini trib.n. is described to accommodate Marcepania gen.n. from Malaysia, with five species: M. semengohensis sp.n. (the type species of Marcepania), M. tuberculata sp.n. , M. seramaensis sp.n. , M. minutissima sp.n. and M. elongata sp.n. A phylogenetic analysis of all genera of Cephenniini, Eutheiini and Marcepaniini based on adult morphological characters resulted in recovering a well‐supported monophyletic clade Eutheiini + (Marcepaniini + Cephenniini) and these tribes are included in Cephenniitae stat.n. (Eutheiini and Cephenniini are therefore removed from Scydmaenitae). Only a weak support for monophyly of Eutheiini was found, but morphological characters allow for maintaining this presumably relic group as a separate tribe. Previously proposed monophyletic groups within Cephenniini were recovered as such, but after inclusion of Eutheimorphus, a sister taxon to the ‘Cephennomicrus group’, the latter lineage gained weak statistical support. The evolutionary history of Cephenniitae is discussed, with focus on known northern hemisphere fossils classified in Scydmaenitae and Hapsomelitae, but possibly closely allied to Cephenniitae. Establishing the supertribe Cephenniitae is the first step toward a profound reclassification of Scydmaeninae on a robust phylogenetic basis. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:B0E1B12D-9587-4C4F-A908-A12A0C424A8C .     

Sex chromatin and sex chromosome systems in nonditrysian Lepidoptera (Insecta)

Eleven representatives of the superorder Amphiesmenoptera (Trichoptera + Lepidoptera) were examined for sex chromatin status. Three species represent stenopsychoid, limnephiloid and leptoceroid branches of the Trichoptera; eight species belong to the primitive, so-called nonditrysian Lepidoptera and represent the infra-orders Zeugloptera, Dacnonypha, Exoporia, Incurvariina, Nepticulina and Tischeriina. The female-specific sex chromatin body was found in the interphase somatic nuclei of Tischeria ekebladella (Bjerkander 1795) (Lepidoptera, Tischeriina). The sex chromatin was absent in all investigated Trichoptera species as well as in all representatives of the nonditrysian Lepidoptera except Tischeria ekebladella . The sex chromosome mechanism of Limnephilus lunatus Curtis 1834 (Trichoptera, Limnephilidae) is Z/ZZ. The sex chromosome mechanism of Tischeria ekebladella (Lepidoptera, Tischeriina) is ZW/ZZ including the W chromosome as the largest element in the chromosome set. The data obtained support the hypothesis that the Z/ZZ sex chromosome system, the female heterogamety and the absence of the sex chromatin body in interphase nuclei are ancestral traits in the superorder Amphiesmenoptera. These ancestral characters are probably kept constant in all the Trichoptera and in the most primitive Lepidoptera. The W sex chromosome and the sex chromatin evolved later in the nonditrysian grade of the Lepidoptera. It is proposed that the sex chromatin is a synapomorphy of Tischeriina and Ditrysia.     

A Large-Scale,Higher-Level,Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

Background

Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.

Methodology / Principal Findings

483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity.

Conclusions / Significance

Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.     

Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide

Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.     

Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data

The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.     

Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?

This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.     

Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

Comprehensive phylogeny of the Cleroidea (Coleoptera: Cucujiformia)

The first thorough molecular phylogeny of the superfamily Cleroidea, represented by 377 taxa, and the first with an emphasis on Trogossitidae, was undertaken. Maximum likelihood and Bayesian analyses were performed on a four‐gene dataset (18S, 28S, cox1, cytb) of 395 taxa (along with 18 outgroups), including all 16 currently recognized families of Cleroidea and all current and formerly recognized tribes of Trogossitidae. The superfamily as a whole received strong support in Bayesian analyses. On the basis of phylogenetic results, 18 families in Cleroidea are recognized, including three taxa elevated to family for the first time and two reinstated families. The former tribe Rentoniini (Trogossitidae: Peltinae) was strongly supported as a monophyletic group apart from the remainder of Trogossitidae, and is herein elevated to family status, Rentoniidae stat.n. Protopeltis was also found to be an isolated lineage and becomes Protopeltidae stat.n. Peltini + Larinotini were recovered as a weakly supported sister grouping; Peltini (including only Peltis) becomes Peltidae stat.rest. The trogossitid subfamily Lophocaterinae, to the exclusion of Decamerini, formed a clade which is here designated Lophocateridae stat.rest. and sensu n. The Trogossitinae tribes Calityini, Egoliini (represented by Egolia) and Larinotini were recovered apart from core Trogossitidae but showed no strong affinities to other taxa or congruence between analyses; they are here conservatively retained in Trogossitidae as Calityinae stat.rest. , Egoliinae stat.rest. and Larinotinae stat.rest. The genus Thymalus of the peltine tribe Thymalini was indicated with moderate to strong support as the sister group of the Decamerini (Trogossitidae: Lophocaterinae); together these represent Thymalidae stat.n. and sensu n. with subfamilies Decamerinae stat.rest. ( new placement ) and Thymalinae stat.n. The remainder of Trogossitinae, the tribes Trogossitini and Gymnochilini, formed a well‐supported clade which comprises the Trogossitidae: Trogossitinae sensu n. The tribe Gymnochilini syn.n. is synonymized with Trogossitini. The monotypic family Phloiophilidae was recovered, contradicting a recent placement within Trogossitidae. The melyrid lineage was recovered with moderate (maximum likelihood) to strong (Bayesian analyses) support and includes the families Phycosecidae, Rhadalidae, Mauroniscidae, Prionoceridae and Melyridae (including Dasytidae and Malachiidae). The genus Dasyrhadus is tentatively transferred from Rhadalidae to Mauroniscidae. The genus Gietella, once proposed as a distinct family but recently placed within Dasytidae, was recovered as strongly sister to Rhadalidae sensu n. , and we transfer it to that family as Gietellinae new placement . Attalomiminae (formerly Attalomimidae) syn.n. is synonymized with Melyridae: Malachiinae: Lemphini sensu n. Melyridae sensu n. includes only Dasytinae, Malachiinae and Melyrinae. Metaxina is returned to the Chaetosomatidae sensu n. , of which Metaxinidae syn.n. becomes a junior synonym. Resolution within Cleridae was generally poor, but a broadly defined Korynetinae stat rest. + Epiclininae received high support (Bayesian analyses). Outside of Trogossitidae, the main focus of this study, major rearrangements of the classification of Cleroidea were not undertaken, despite evidence indicating such changes are needed.     

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.     

A new genus and species of hypodermatine bot flies (Diptera: Oestridae)

The bot fly Gruninomyia mira Szpila & Pape, gen.n. , sp.n. is described from Iran, North Khorasan, based on a single adult male and with no larval or host data. The monotypic genus shows a mixture of features otherwise found in either the rodent/lagomorph‐parasitizing oestromyine clade (Oestroderma + Oestromyia) or the artiodactyl‐parasitizing hypodermatine clade (Hypoderma + Pallasiomyia + Pavlovskiata + Przhevalskiana + Strobiloestrus) of subfamily Hypodermatinae. A morphology‐based phylogenetic analysis is marginally in favour of a position of Gruninomyia Szpila & Pape, gen.n. as sister taxon of (Oestroderma + Oestromyia). The COI barcode sequence is provided for the new species, and a phylogenetic analysis based on this marker for Oestridae retrieved from GenBank is in agreement with the conclusions based on morphological data. This published work has been registered in ZooBank: http://zoobank.org/urn:lsid:zoobank.org:pub:8F0CBE07‐4E74‐4186‐B690‐2C97D7ED7DA7 .