Higher level phylogeny for the passion-vine butterflies (Nymphalidae, Heliconiinae) based on early stage and adult morphology

A higher level phylogeny for the passion-vine butterflies (Nymphalidae, Heliconiinae) was generated by cladistic analysis of 146 morphological characters from all life stages. The 24 species studied were selected representatives of the ten currently accepted genera of the sub-tribe Heliconiiti. Analyses of only characters from larvae and pupae did not produce well resolved trees. However, some characters of the immature stages provided critical support for the monophyly of two clades. Analysis of only adult characters yielded a tree that closely resembled that obtained from all data combined. The phylogeny here derived from the combined analysis of early stage and adult characters differed in topology from all previously proposed hypotheses, and supported the monophyly of all currently recognized genera. Characters supporting each clade are described and illustrated, and various hypotheses of phylogenetic relatedness of passion-vine butterfly taxa are discussed.     

The phylogeny of the social Anelosimus spiders (Araneae: Theridiidae) inferred from six molecular loci and morphology

We use fragments of three nuclear genes (Histone 3, 18SrDNA, and 28SrDNA) and three mitochondrial genes (16SrDNA, ND1, and COI) totalling approximately 4.5kb, in addition to morphological data, to estimate the phylogenetic relationships among Anelosimus spiders, well known for their sociality. The analysis includes 67 individuals representing 23 of the 53 currently recognized Anelosimus species and all species groups previously recognized by morphological evidence. We analyse the data using Bayesian, maximum likelihood, and parsimony methods, considering the genes individually as well as combined (mitochondrial, nuclear, and both combined) in addition to a 'total evidence' analysis including morphology. Most of the data partitions are congruent in agreeing on several fundamental aspects of the phylogeny, and the combined molecular data yield a tree broadly similar to an existing morphological hypothesis. We argue that such congruence among data partitions is an important indicator of support that may go undetected by standard robustness estimators. Our results strongly support Anelosimus monophyly, and the monophyly of the recently revised American 'eximius lineage', although slightly altered by excluding A. pacificus. There was consistent support for the scattering of American Anelosimus species in three clades suggesting intercontinental dispersal. Several recently described species are reconstructed as monophyletic, supporting taxonomic decisions based on morphology and behaviour in this taxonomically difficult group. Corroborating previous results from morphology, the molecular data suggest that social species are scattered across the genus and thus that sociality has evolved multiple times, a significant finding for exploring the causes and consequences of social evolution in this group of organisms.     

Phylogenetic relationships among families of the Scaphopoda (Mollusca)

Phylogenetic relationships among families in the molluscan class Scaphopoda were analysed using morphological characters and cladistic parsimony methods. A maximum parsimony analysis of 34 discrete characters, treated as unordered and equally weighted, from nine ingroup terminal taxa produced a single most parsimonious tree; supplementary analyses of tree length frequency distribution and Bremer support indices indicate a strong phylogenetic signal from the data and moderate to minimally supported clades. The traditional major division of the class, the orders Dentaliida and Gadilida, is supported as both taxa are confirmed as monophyletic clades. Within the Dentaliida, two clades are recognized, the first comprised of the families Dentaliidae and Fustiariidae, the second of the Rhabdidae and Calliodentaliidae; together, these groups comprise a third clade, which has the Gadilinidae as sister. Within the Gadilida, a nested series of relationships is found among [Entalinidae, [Pulsellidae, [Wemersoniellidae, Gadilidae]]]. These results lend cladistic support to earlier hypotheses of shared common ancestry for some families, but are at variance with other previous hypotheses of evolution in the Scaphopoda. Furthermore, analysis of constituent Gadilinidae representatives provide evidence for paraphyly of this family. The relationships supported here provide a working hypothesis that the development of new characters and greater breadth of taxonomic sampling can test, with a suggested primary goal of establishing monophyly at the family level.     

Phylogeny and biogeography of the extant species of triplespine fishes (Triacanthidae, Tetraodontiformes)

A new phylogenetic hypothesis for the living species of triplespine fishes of the Indo-Western Pacific family Triacanthidae (Tetraodontiformes, Teleostei) is proposed. A data set of 55 morphological characters (34 osteological and 21 morphometric) was constructed. A cladistic analysis of the osteological data set yielded a single most-parsimonious tree. This cladogram does not support the monophyly of one of the four genera, Tripodichthys , but Bremer values for this analysis are low. The osteological data set was then combined with a data set of 21 morphometric characters that had previously been used to diagnose the four genera. The analysis of the combined data set produced the same phylogenetic hypothesis, but with greater nodal support. The biogeographical distribution of the living species is then interpreted with the use of this new phylogenetic information.     

槭树科植物广义形态学性状分支分析

通过45个广义的形态学性状对槭树科(Aceraceae)尤其是槭属(Acer L.)的主要类群做了分支分析,结果显示：1)槭属内由于各类群分布着较多的同塑性状状态,而难以为属下组间关系的解决提供更多有价值的信息;通过对具体的性状状态分布分析显示,对于象槭属这样在形态上分化较大的类群,由于多数分类性状在不同类群间经历了平行和逆转演化,因而在较低分类阶元水平很难选择合适的性状来通过分支分析构建其系统发育;2)鸡爪槭组(section Palmata)作为整个槭属的基部类群,虽然支持率较低,但与其它类群相比在槭属内维持了较多的原始性状;3)金钱槭属(Dipteronia Oliv.)的两个种作为单系得到了100％的靴带支持,且和槭属作为姐妹群也得到了较好的支持。     

Phylogenetic relationships within the Eurasian cattish family Siluridae (Pisces: Siluriformes), with comments on generic validities and biogeography

A numerical cladistic analysis, based on 23 terminal groups and 63 morphological characters, was done to infer phylogenetic relationships within the Eurasian catfish family Siluridae. Nine hundred and forty-five equally most parsimonious trees (134 steps, consistency index 0.634) were found that differ in their resolutions of four polychotomies. Strict consensus of these trees includes ten internal nodes, does not support monophyly of Silurus, Ompok and Kryptopterus , as usually defined, and offers ambiguous support for monophyly of Wallago. Silurus and Kryptopterus are each composed of two non-sister group clades, and Ompok is composed of at least two such clades. Heuristic searches constrained by monophyly of Silurus, Ompok or Kryptopterus yielded trees five or six steps longer than the shortest trees free of constraints. The strict consensus also infers a basal dichotomy that separates the Siluridae into a temperate Eurasian clade with about 20 nominal species and a subtropical/tropical south and southeast Asian clade with about 75 nominal species. The distributions of these clades overlap in a relatively narrow region of east Asia. A heuristic search for trees 1 step longer than the shortest trees yielded 253890 trees. A strict consensus of these trees also infers a basal dichotomy between the above-mentioned clades. This analysis revealed four additional putative synapomorphies of the Siluridae, pending further resolution of the family's outgroup relationships.     

Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences

The conifers, which traditionally comprise seven families, are the largest and most diverse group of living gymnosperms. Efforts to systematize this diversity without a cladistic phylogenetic framework have often resulted in the segregation of certain genera and/or families from the conifers. In order to understand better the relationships between the families, we performed cladistic analyses using a new data set obtained from 28S rRNA gene sequences. These analyses strongly support the monophyly of conifers including Taxaceae. Within the conifers, the Pinaceae are the first to diverge, being the sister group of the rest of conifers. A recently discovered Australian genus Wollemia is confirmed to be a natural member of the Araucariaceae. The Taxaceae are nested within the conifer clade, being the most closely related to the Cephalotaxaceae. The Taxodiaceae and Cupressaceae together form a monophyletic group. Sciadopitys should be considered as constituting a separate family. These relationships are consistent with previous cladistic analyses of morphological and molecular (18S rRNA, rbcL) data. Furthermore, the well-supported clade linking the Araucariaceae and Podocarpaceae, which has not been previously reported, suggests that the common ancestor of these families, both having the greatest diversity in the Southern Hemisphere, inhabited Gondwanaland.     

Phylogeny of the Apodan Holothurians (Echinodermata) inferred from morphology

The Apodida is an order of littoral to deep-sea, largely infaunal sea cucumbers with about 270 extant species in 32 genera and three families, Synaptidae, Chiridotidae and Myriotrochidae. In this study, I perform the first phylogenetic test of the taxonomic and palaeontological hypotheses about evolutionary relationships within Apodida by using cladistic analyses of 34 morphological characters. I introduce several previously unconsidered synapomorphic characters, examine the relationships between all recognized suprageneric taxonomic groups and assess the assumptions of monophyly for each family. Maximum-parsimony analyses of type species from 14 genera and use of three rooting methods recovered identical topologies at the subordinal level and subfamily level within Synaptidae. Overall, the current higher-level classification of Apodida was well corroborated. Within Synaptidae, the relationships (Synaptinae, (Leptosynaptinae, Rynkatorpinae)) are well supported. The monophyly of Chiridotidae was not supported and appears paraphyletic at the subfamily level. Calibrating the phylogenetic hypothesis of Apodida against the fossil record indicated that most higher-level divergences occurred within the Palaeozoic, unlike that of extant non-holothuroid echinoderms, which radiated in the early Mesozoic. Synaptidae appears to have radiated during the Lower Cretaceous. Alternatively, and if one discounts the considerable ghost lineage duration that this hypothesis requires, they may have radiated during the Eocene.     

Phylogenetic study of heliconiine butterflies based on morphology and restriction analysis of ribosomal RNA genes

Relationships of ten heliconiine butterflies (genera Dryas and Heliconius , family Nymphalidae) were elucidated by phylogenetic analysis of characters based on ribosomal DNA restriction site variation and morphology. Agraulis vanillae , also a heliconiine, was used as the outgroup species. Although neither the morphological nor the molecular data unambiguously resolve relationships among the heliconiines, a combined analysis of both data sets results in a tree that is similar to traditional systematic arrangements and previous views of radiation in the group. Both pupal-mating and nonpupal-mating species group as clades in the combined analysis. However, the restriction site data alone do not support the monophyly of the pupal-mating clade, and the morphological data alone do not support the monophyly of the non-pupal-mating clade. Furthermore, relationships of H. melpomene, H. cydno and the silvaniform species depart from traditional arrangements based on morphology and reproductive compatibility experiments. All trees support the independent evolution of similar wing patterns of species previously suggested to be members of mimicry complexes. Several mimicry complexes appear to have a member in each of the two major monophyletic groups (pupal-mating and non-pupal-mating clades).     

Molecular analysis of the biting midges (Diptera: Ceratopogonidae), based on mitochondrial cytochrome oxidase subunit 2

Sequences from the mitochondrial cytochrome oxidase subunit 2 gene (cox2) were determined for 14 species from the family Ceratopogonidae, representing 12 genera and all five subfamilies, along with six representatives of other nematoceran families. The purpose was to develop a molecular phylogeny of the Ceratopogonidae, and interpret the phylogenetic position of the family within the infraorder Culicomorpha. These taxa have been analysed using cladistic methodology which, in combination with an excellent fossil record, provides a well established morphological phylogeny. Sequence analysis of cox2 revealed a high degree of sequence divergence among the species, reflecting in part the antiquity of the family, but also a significant acceleration of sequence evolution in the ceratopogonids compared to other nematoceran Diptera. Phylogenetic reconstruction by neighbor-joining and maximum parsimony gave strong support for an early separation of an ancient lineage that includes the two genera, Austroconops and Leptoconops, from the remainder of the family. The results support the existence of a clade that includes two subfamilies, Dasyheleinae and Forcipomyiinae, and this clade appears as sister to the remaining subfamily, Ceratopogoninae. The molecular phylogeny also supports monophyly of the Ceratopogonidae, and either a sister or paraphyletic relationship of this family with the Chironomidae.     

Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology

Higher‐level phylogenetics of Pycnogonida has been discussed for many decades but scarcely studied from a cladistic perspective. Traditional taxonomic classifications are yet to be tested and affinities among families and genera are not well understood. Pycnogonida includes more than 1300 species described, but no systematic revisions at any level are available. Previous attempts to propose a phylogeny of the sea spiders were limited in characters and taxon sampling, therefore not allowing a robust test of relationships among lineages. Herein, we present the first comprehensive phylogenetic analysis of the Pycnogonida based on a total evidence approach and Direct Optimization. Sixty‐three pycnogonid species representing all families including fossil taxa were included. For most of the extant taxa more than 6 kb of nuclear and mitochondrial DNA and 78 morphological characters were scored. The most parsimonious hypotheses obtained in equally weighted total evidence analyses show the two most diverse families Ammotheidae and Callipallenidae to be non‐monophyletic. Austrodecidae + Colossendeidae + Pycnogonidae are in the basal most clade, these are morphologically diverse groups of species mostly found in cold waters. The raising of the family Pallenopsidae is supported, while Eurycyde and Ascorhynchus are definitely separated from Ammotheidae. The four fossil taxa are grouped within living Pycnogonida, instead of being an early derived clade. This phylogeny represents a solid framework to work towards the understanding of pycnogonid systematics, providing a data set and a testable hypothesis that indicate those clades that need severe testing, especially some of the deep nodes of the pycnogonid tree and the relationships of ammotheid and callipallenid forms. The inclusion of more rare taxa and additional sources of evidence are necessary for a phylogenetic classification of the Pycnogonida. © The Willi Hennig Society 2006.     

Reconstructing the phylogeny of the Sipuncula

Sipunculans are marine spiralian worms with possible close affinities to the Mollusca or Annelida. Currently 147 species, 17 genera, 6 families, 4 orders and 2 classes are recognized. In this paper we review sipunculan morphology, anatomy, paleontological data and historical affiliations. We have conducted cladistic analyses for two data sets to elucidate the phylogenetic relationships among sipunculan species. We first analyzed the relationships among the 45 species of Phascolosomatidea with representatives of the Sipunculidea as outgroups, using 35 morphological characters. The resulting consensus tree has low resolution and branch support is low for most branches. The second analysis was based on DNA sequence data from two nuclear ribosomal genes (18S rRNA and 28S rRNA) and one nuclear protein-coding gene, histone H3. Outgroups were chosen among representative spiralians. In a third analysis, the molecular data were combined with the morphological data. Data were analyzed using parsimony as the optimality criterion and branch support evaluated with jackknifing and Bremer support values. Branch support for outgroup relationships is low but the monophyly of the Sipuncula is well supported. Within Sipuncula, the monophyly of the two major groups, Phascolosomatidea and Sipunculidea is not confirmed. Of the currently recognized families, only Themistidae appears monophyletic. The Aspidosiphonidae, Phascolosomatidae and Golfingiidae would be monophyletic with some adjustments in their definition. The Sipunculidae is clearly polyphyletic, with Sipunculus nudus as the sister group to the remaining Sipuncula, Siphonosoma cumanense the sister group to a clade containing Siphonosoma vastumand the Phascolosomatidea, and Phascolopsis gouldi grouping within the Golfingiiformes, as suggested previously by some authors. Of the genera with multiple representatives, only Phascolosoma and Themiste are monophyletic as currently defined. We are aiming to expand our current dataset with more species in our molecular database and more detailed morphological studies.     

Cladistic analysis of the family Baetidae (Insecta: Ephemeroptera) in South America

The family Baetidae, which belongs to the order Ephemeroptera, was first described by Leach in 1815 . Since then, almost 100 genera and 900 species have been described. Although diverse, this family is relatively homogeneous. The adults are extremely similar to one another, the wings vary little and the penes are membranous, features that significantly reduce differentiation among taxa. In contrast, the larvae have more conspicuous differences. Most are collector–gatherers, but a few are carnivorous or filter feeders. In South America, although knowledge concerning the 27 genera and 132 species of Baetidae described for this region has improved in the last three decades, phylogenetic relationships remain unknown. The present study, the first cladistic analysis of Baetidae in South America, included 70 species (55 are Neotropical) and 126 morphological characters. The matrix was analysed using tnt , under implied weights. Although the monophyly of the family Baetidae was obtained with good support, the subfamilies proposed originally (Baetinae, Cloeoninae and Callibaetinae) were recovered as paraphyletic. The Baetodes complex, as well as the relationships between genera, is discussed. The validity of some structures or characters as support of different groupings is also discussed.     

Phylogeny of the Polycentropodidae (Insecta: Trichoptera) based on protein-coding genes reveal non-monophyletic genera

We tested the previous hypotheses of the phylogenetic position and monophyly of the caddisfly family Polycentropodidae. We also tested previous hypotheses about the internal generic relationship within the family by including 15 ingroup genera, many of them also represented by the genotype. All families that were previously taxonomically associated with the polycentropodids were included in the analysis. The total data set of 2225bp representing sequences of combined nuclear and mitochondrial genes and 171 taxa, was analyzed using Bayesian inference. We found strong support for a monophyletic Polycentropodidae with Ecnomidae as the closest sister group. The recently erected families Kambaitipsychidae and Pseudoneureclipsidae were monophyletic and distantly related to the Polycentropodidae. Within Polycentropodidae, monophyly and validity of the genera Neucentropus, Neureclipsis, Cyrnus, Holocentropus, Tasmanoplegas, Pahamunaya, Cernotina and Cyrnellus was strongly supported, while the genera Polycentropus, Polyplectropus, Plectrocnemia, Placocentropus and Nyctiophylax were all polyphyletic. The New Caledonian species were polyphyletic and represented three distinct clades. The sister group to the New Caledonian clades are from Australia, New Zealand and Chile, respectively. The Vanuatu species evolved after dispersal from the Fiji Islands. New internal primers for cytochrome oxidase I sequences of Trichoptera are introduced.     

Molecular phylogeny of the moonseed family (Menispermaceae): implications for morphological diversification

We used the chloroplast gene ndhF to reconstruct the phylogeny of the moonseed family (Menispermaceae), a morphologically diverse and poorly known cosmopolitan family of dioecious, primarily climbing plants. This study includes a worldwide sample of DNA sequences for 88 species representing 49 of the 70 genera of all eight traditionally recognized tribes. Phylogenetic relationships were estimated, and the Shimodaira-Hasegawa test was used to compare the likelihood of alternative phylogenetic hypotheses and to evaluate the monophyly of tribes currently in use. The monospecific Indo-Malesian Tinomiscium is sister to the remaining members of the family, within which are two major clades. Within these two clades, well-supported clades correspond to four of the eight traditionally recognized tribes, while others, such as Menispermeae, are polyphyletic. Mapping of major morphological characters on the phylogeny indicates that the crescent-shaped seed is derived from a straight seed, the tree habit has arisen multiple times, endosperm has been lost many times, but unicarpellate flowers evolved only once. Morphological synapomorphies for Menispermaceae include the presence of a condyle, a large embryo, and druplets. The phylogeny provides for the first time a detailed molecular-based assessment of relationships in Menispermaceae and clarifies our understanding of morphological diversification within the family.     

Links between host-plant type and site of feeding as revealed by the evolution of Palaearctic Eriococcidae (Sternorrhyncha: Coccoidea)

This work is an assessment of the biogeographical, taxonomic, biological and phylogenetic knowledge of the poorly defined family Eriococcidae. The study of its geographical diversity shows the richness of the Palearctic fauna on which the present analysis focuses. The numerous systems dealing with the taxonomy of Eriococcidae are detailed, and the specific taxonomical status of the genus Eriococcus, which contains 155 out of the 175 known Palearctic species is reevaluated. The phylogeny of the palaearctic members of the scale insect family Eriococcidae is reconstructed, using 9 genera and 52 species. Three more scale insect species belonging to 3 families were used as outgroups. The cladistic analysis of 130 morphological characters of the adults resulted in 10 most parsimonious trees, placing Eriococcus buxi as the sister-group of all other sampled Eriococcidae. The genera Acanthococcus, Rhizococcus, Greenisca and Anophococcus appear as para- or polyphyletic, but the weakness of most of the clades does not allow to denounce strictly the monophyly of these genera. However, some clades are supported with high confidence, like (Kaweckia + Neokaweckia), (Anophococcus parvispinus(Anophococcus inermis+Greenisca placida) and (Gossyparia spuria+Acanthococcus aceris). Concerning host-plant relationships, the phylogeny supports an evolutionary scenario whereby the ancestor of the family Eriococcidae fed originally on woody plants, and more typically on leaves. The switch observed from Poaceae to other herbaceous plants is correlated to the switch from leaves as preferred site of nutrition to branches and stems. The supported scenario shows another switch, back from other herbs to Poaceae, associated to the choice of leaves as nutrition site.     

A phylogenetic study of krill (Crustacea: Euphausiacea) reveals new taxa and co-evolution of morphological characters

The first comprehensive phylogenetic study of Euphausiacea (all 86 valid species) is presented. It is based on four molecular markers and 168 morphological characters (including 58 characters of the petasma). Phylogenetic analyses support the monophyly and robustness of the families Bentheuphausidae and Euphausiidae and reveal three major clades for which we erect three new subfamilies: Thysanopodinae, Euphausiinae and Nematoscelinae. All genus-level clades are statistically supported (except Thysanopoda in molecular analyses), deeply nested within the subfamily-level clades, and encompass 14 new species groups. Copulatory structures have a major impact on tree topology in the morphological analysis, the removal of which resulted in only half the number of supported clades and genera. We revealed three groups of morphological characters, which are probably coupled with the same biological role and thus interlinked evolutionarily: (i) antennular peduncle and petasma (copulation); (ii) eyes and anterior thoracopods (feeding); and (iii) shape of carapace and pleon (defence). We analysed the evolutionary pathways of the clades into main oceanic biotopes and compared them with morphological adaptations most likely to be coupled with this process.     

Sociality in theridiid spiders: repeated origins of an evolutionary dead end

Evolutionary "dead ends" result from traits that are selectively advantageous in the short term but ultimately result in lowered diversification rates of lineages. In spiders, 23 species scattered across eight families share a social system in which individuals live in colonies and cooperate in nest maintenance, prey capture, and brood care. Most of these species are inbred and have highly female-biased sex ratios. Here we show that in Theridiidae this social system originated eight to nine times independently among 11 to 12 species for a remarkable 18 to 19 origins across spiders. In Theridiidae, the origins cluster significantly in one clade marked by a possible preadaptation: extended maternal care. In most derivations, sociality is limited to isolated species: social species are sister to social species only thrice. To examine whether sociality in spiders represents an evolutionary dead end, we develop a test that compares the observed phylogenetic isolation of social species to the simulated evolution of social and non-social clades under equal diversification rates, and find that sociality in Theridiidae is significantly isolated. Because social clades are not in general smaller than their nonsocial sister clades, the "spindly" phylogenetic pattern-many tiny replicate social clades-may be explained by extinction rapid enough that a nonsocial sister group does not have time to diversify while the social lineage remains extant. In this case, this repeated origin and extinction of sociality suggests a conflict between the short-term benefits and long-term costs of inbred sociality. Although benefits of group living may initially outweigh costs of inbreeding (hence the replicate origins), in the long run the subdivision of the populations in relatively small and highly inbred colony lineages may result in higher extinction, thus an evolutionary dead end.     

Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str.

We present phylogenetic analyses of Malpighiales, which are poorly understood with respect to relationships within the order, using sequences from rbcL, atpB, matK and 18SrDNA from 103 genera in 23 families. From several independent and variously combined analyses, a four-gene analysis using all sequence data provided the best resolution, resulting in the single most parsimonious tree. In the Malpighiales [bootstrap support (BS) 100%], more than eight major clades comprising a family or group of families successively diverged, but no clade containing more than six families received over 50% BS. Instead, ten terminal clades that supported close relationships between and among families (>50% BS) were obtained, between, for example, Balanopaceae and Chrysobalanaceae; Lacistemataceae and Salicaceae; and Phyllanthaceae and Picrodendraceae. The monophyly of Euphorbiaceae sens. str. were strongly supported (BS 100%), but its sister group was unclear. Euphorbiaceae sens. str. comprised two basally diverging clades (BS 100%): one leading to the Clutia group (Chaetocarpus, Clutia, Pera and Trigonopleura), and the other leading to the rest of the family. The latter shared a palisadal, instead of a tracheoidal exotegmen as a morphological synapomorphy. While both Acalyphoideae (excluding Dicoelia and the Clutia group) and Euphorbioideae are monophyletic, Crotonoideae were paraphyletic, requiring more comprehensive analyses.