Phylogeny of Vestimentifera (Siboglinidae, Annelida) inferred from morphology

Vestimentifera, formerly considered a phylum, are here included in the annelid clade Siboglinidae which also encompasses Frenulata and Sclerolinum . All Siboglinidae inhabit reducing habitats, mostly in the deep sea. Vestimentifera are known from hydrothermal vents and cold seeps. Cladistic analyses of vestimentiferan relationships are performed on three levels: (1) among the vestimentiferan species, (2) among the reconstructed ancestral vestimentiferan and other siboglinids and (3) on the level of the families included in the annelidan clade Sabellida. The monophyly of vestimentiferans is confirmed in all analyses. A group of exclusively vent-inhabiting species forms a derived monophyletic clade. The sister group to the vent clade is the Escarpia complex. Lamellibrachia appears to be paraphyletic. Except for the paraphyly of Lamellibrachia , the reconstructed pattern agrees with the molecular phylogeny based on cytochrome c oxidase subunit I. Ancient ridge systems can be invoked to explain modern day geographical distributions. The Pacific Kula Ridge that spanned the Pacific in an east–west direction during the Early Tertiary, may have been a pathway for the ancestor of the vent clade to reach the eastern Pacific. The biogeography is consistent with the recent divergence of Vestimentifera as inferred from molecular data. The reconstructed phylogeny of the Siboglinidae supports the monophyly of the Frenulata and within those, the Thecanephria and Athecanephria. In contrast to molecular and other morphological analyses, Sclerolinum appears as the sister group to the Frenulata. The family level analysis supports the sister group relationship of the Siboglinidae to a clade formed by Sabellariidae, Sabellidae and Serpulidae. Hypothesized homologies of the vestimentiferan obturaculum and vestimentum to structures in related taxa need further investigation.     

Phylogeny of Holothuroidea (Echinodermata) inferred from morphology

Holothuroids, or sea cucumbers, are an abundant and diverse group of echinoderms with over 1400 species occurring from the intertidal to the deepest oceanic trenches. In this study, we report the first phylogeny of this class, based on a cladistic analysis of 47 morphological characters. We introduce several previously unconsidered synapomorphic characters, examine the relationships between representatives from all extant families and assess the assumptions of monophyly for each order and subclass. Maximum-parsimony analyses using three rooting methods recovered well-supported and identical topologies when two small and apparently derived families, Eupyrgidae and Ge-phyrothuriidae, were removed. The results suggest that the higher-level arrangement of Holothuroidea warrants a considerable revision. Apodida was sister to the other holothuroids. The monophyly of Dendrochirotida was not supported and the group may be paraphyletic. A randomization test using Wills' gap excess ratio found significant congruence between the phylogeny and the stratigraphic record of fossil members, suggesting that the fossil record of holothuroids is not as incomplete as is often stated. The fossil-calibrated tree indicated that several groups of holothuroids survived the end-Permian mass extinction and that the clade composed of Dendrochirotida, Dactylochirotida, Aspidochirotida and Molpadiida rapidly radiated during the Triassic.     

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

Background  

Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole.     

Phylogeny and systematics of Protodrilidae (Annelida) inferred with total evidence analyses

Protodrilidae is a group of small, superficially simple‐looking annelids, lacking chaetae and appendages, except for two prostomial palps. Originally considered to be one of the primitive “archiannelid” families, its affinity within Annelida is still highly debated. Protodrilids are found worldwide in the interstices of intertidal and subtidal marine sediments. Despite their simple appearance they constitute one of the most species‐rich interstitial families, with 36 described species in two genera, Protodrilus and the gutless Astomus. Here we present the first phylogenetic study of Protodrilidae employing five gene fragments, 55 morphological characters and 73 terminals (including seven outgroups) analysed under direct optimization and parsimony as well as model‐based methods. The large data set includes all 36 described species of Protodrilidae (17 of which are represented only by the morphological partition) as well as 30 undescribed or uncertain species (represented by both morphology and molecules). This comprehensive, inclusive and combined analysis revealed a new perspective on the phylogeny of Protodrilidae: the family is shown to contain six cosmopolitan subclades, each supported by several morphological apomorphies, and with the genus Astomus consistently nested among the other five clades rather than next to these. Consequently, the diagnosis of Protodrilus is emended, Astomus remains unchanged and the four remaining lineages are diagnosed and named Megadrilus n. gen, Meiodrilus gen. nov., Claudrilus n. gen and Lindrilus gen. nov. Character transformations showed that large size and presence of pigmentation, oviducts and eyes are plesiomorphies of the family, retained in Protodrilus, Megadrilus gen. nov. and Lindrilus gen. nov. These features are secondarily lost in the gutless Astomus with epidermal uptake of nutrients, as well as in Meiodrilus gen. nov. and some species of Claudrilus n. gen, with smaller size correlated to life in interstices of finer sediments.     

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.     

Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology

Subfamily Barnadesioideae (Asteraceae) consists of nine genera and 91 species endemic to South America. They include annual and perennial herbs, arching shrubs and trees up to 30 m tall. Presumed sister to all other Asteraceae, its intergeneric relationships are key to understanding the early evolution of the family. Results of the only molecular study on the subfamily conflict with relationships inferred from morphology. We investigate inter- and intrageneric relationships in Barnadesioideae with novel DNA sequence data and morphological characters using parsimony, likelihood and Bayesian inference. All results verify Barnadesioideae as monophyletic and sister to the rest of the family. A basal split within the subfamily is recognized, with Chuquiraga, Doniophyton and Duseniella in one clade, and Arnaldoa, Barnadesia, Dasyphyllum, Fulcaldea, Huarpea and possibly Schlechtendalia in another. The largest genus, Dasyphyllum, is revealed as biphyletic with the two clades separating along subgeneric and geographic lines. Schlechtendalia, suggested as the earliest diverging lineage of the subfamily by morphological studies and parsimony analyses, is found in a more derived position under model-based inference methods. Competing phylogenetic hypotheses, both previous and present, are evaluated using likelihood-based tests. Evolutionary trends within Barnadesioideae are inferred: hummingbird pollination has developed convergently at least three times. An early vicariance in the subfamily’s distribution is revealed. X = 9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole.     

Molecular phylogeny of lugworms (Annelida, Arenicolidae) inferred from three genes

Arenicolids comprise a group of four genera in which about 30 nominal species are described. Whereas the biology of many arenicolids is well known, the phylogenetic relationships of these worms are inadequately studied. A close relationship of Arenicolidae and Maldanidae is generally accepted. The phylogenetic relationships of arenicolid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA gene, the nuclear 18S rRNA gene, and a small fraction of the nuclear 28S rRNA gene. Members of all described arenicolid genera are included in the data set. Phylogenetic analyses were conducted using Maximum Likelihood, Bayesian inference, and Maximum Parsimony. The monophyly of the Maldanidae, as well as of the Arenicolidae is supported by all conducted analyses. Two well supported major clades are highest ranked sister taxa in the Arenicolidae: one containing all Abarenicola species and one containing Arenicola, Arenicolides, and Branchiomaldane. Evidence is given for a closer relationship between the two investigated Branchiomaldane species and Arenicolides ecaudata in the combined analysis. In the light of the molecular data the best explanation for structural and morphological observations is that Branchiomaldane evolved by progenesis.     

Phylogenetic relationships within Serpulidae (Sabellida, Annelida) inferred from molecular and morphological data

We assessed phylogenetic relationships within Serpulidae (including Spirorbinae) using parsimony and Bayesian analyses of 18S rDNA, the D1 and D9−D10 regions of 28S rDNA, and 38 morphological characters. In total, 857 parsimony informative characters were used for 31 terminals, 29 serpulids and sabellid and sabellariid outgroups. Following ILD assessment the two sequence partitions and morphology were analysed separately and in combination. The morphological parsimony analysis was congruent with the results of the 2003 preliminary analysis by Kupriyanova in suggesting that a monophyletic Serpulinae and Spirorbinae form a clade, while the remaining serpulids form a basal grade comprising what are normally regarded as Filograninae. Bremer support values were, however, quite low throughout. In contrast, the combined analyses of molecular and morphological data sets provided highly resolved and well-supported trees, though with some conflict when compared to the morphology-only analysis. Spirorbinae was recovered as a sister group to a monophyletic group comprising both 'filogranin' taxa ( Salmacina , Filograna , Protis , and Protula ) and 'serpulin' taxa such as Chitinopoma , Metavermilia , and Vermiliopsis . Thus the traditionally formulated subfamilies Serpulinae and Filograninae are not monophyletic. This indicates that a major revision of serpulid taxonomy is needed at the more inclusive taxonomic levels. We refrain from doing so based on the present analyses since we feel that further taxon sampling and molecular sequencing are required. The evolution of features such as the operculum and larval development are discussed.     

Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological data

A phylogeny of the meiofaunal polychaete family Nerillidae based on morphological, molecular and combined data is presented here. The data sets comprise nearly complete sequences of 18S rDNA and 40 morphological characters of 17 taxa. Sequences were analyzed simultaneously with the morphological data by direct optimization in the program POY, with a variety of parameter sets (costs of gaps: transversions: transitions). Three outgroups were selected from the major polychaete group Aciculata and one from Scolecida. The 13 nerillid species from 11 genera were monophyletic in all analyses with very high support, and three new apomorphies for Nerillidae are identified. The topology of the ingroup varied according to the various parameter settings. Reducing the number of outgroups to one decreased the variance among the phylogenetic hypotheses. The congruence among these was tested and a parameter set, with equal weights (222) and extension gap weighted 1, yielded minimum incongruence (ILD). Several terminal clades of the combined analysis were highly supported, as well as the position of Leptonerilla prospera as sister terminal to the other nerillids. The evolution of morphological characters such as segment numbers, chaetae, appendages and ciliation are traced and discussed. A regressive pathway within Nerillidae is indicated for several characters, however, generally implying several convergent losses. Numerous genera are shown to require revision. © The Willi Hennig Society 2005.     

Phylogeny of Labidodemas and the Holothuriidae (Holothuroidea: Aspidochirotida) as inferred from morphology

The Holothuriidae is one of the three established families within the large holothuroid order Aspidochirotida. The approximately 185 recognized species of this family are commonly classified in five nominal genera: Actinopyga , Bohadschia , Holothuria , Pearsonothuria and Labidodemas. Maximum parsimony analyses on morphological characters, as inferred from type and nontype material of the five genera, revealed that Labidodemas comprises highly derived species that arose from within the genus Holothuria . The paraphyletic status of the latter, large (148 assumed valid species) and morphologically diverse genus has recently been recognized and is here confirmed and discussed. Nevertheless, we adopt a Darwinian or eclectic classification for Labidodemas , which we retain at generic level within the Holothuriidae. We compare our phylogeny of the Holothuriidae with previous classifications of its genera and subgenera, and make suggestions concerning possible systematic changes.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 103−120.     

Further revisions of the Sabellidae subfamilies and cladistic relationships among the Fabriciinae (Annelida: Polychaeta)

Cladistic relationships of the sabellid subfamilies Fabriciinae and Sabellinae are examined in light of recent revisions of fabriciin taxa. The potential placement of Caobangia in the Sabellinae is suggested from an initial analysis of selected fabriciin species and genera. Subsequent cladistic analyses at the family level produced over 1800 cladograms, among which Caobangia is the most plesiomorphic taxon of either the Fabriciinae or Sabellinae. Successive approximations weighting reduced this ambiguity, consistently placing Caobangia in the Sabellinae. Subfamilies are emended on the basis of these results. Cladistic relationships of fabriciin taxa, exclusive of Caobangia , display topological instability among some genera and species. Genera are, however, monophyletic in all topologies. Incorporating ontogenetic data for branching ventral filamentous appendages in Augeneriella reduces ambiguity among genera and suggests alternative transformation series for ventral filamentous appendages.     

Phylogenetic relationships within the leaf-mining flies (Diptera: Agromyzidae) inferred from sequence data from multiple genes

The leaf-mining flies (Diptera: Agromyzidae) are a diverse group whose larvae feed internally in leaves, stems, flowers, seeds, and roots of a wide variety of plant hosts. The systematics of agromyzids has remained poorly known due to their small size and morphological homogeneity. We investigated the phylogenetic relationships among genera within the Agromyzidae using parsimony and Bayesian analyses of 2965 bp of DNA sequence data from the mitochondrial COI gene, the nuclear ribosomal 28S gene, and the single copy nuclear CAD gene. We included 86 species in 21 genera, including all but a few small genera, and spanning the diversity within the family. The results from parsimony and Bayesian analyses were largely similar, with major groupings of genera in common. Specifically, both analyses recovered a monophyletic Phytomyzinae and a monophyletic Agromyzinae. Within the subfamilies, genera found to be monophyletic given our sampling include Agromyza, Amauromyza, Calycomyza, Cerodontha, Liriomyza, Melanagromyza, Metopomyza, Nemorimyza, Phytobia, and Pseudonapomyza. Several genera were found to be polyphyletic or paraphyletic including Aulagromyza, Chromatomyia, Phytoliriomyza, Phytomyza, and Ophiomyia. We evaluate our findings and discuss host-use evolution in light of current agromyzid taxonomy and two recent hypotheses of relationships based on morphological data.     

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.     

Phylogeny of penaeoid shrimps (Decapoda: Penaeoidea) inferred from nuclear protein-coding genes

Penaeoidea is a diverse group of economically important marine shrimps. Attention to the evolutionary history of the penaeoids has been raised since studies using mitochondrial DNA markers and sperm ultrastructure contradict classification of the penaeoid families based on morphology and hence challenge the long standing taxonomy of this superfamily. In this study, DNA sequences of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α-subunit, were determined from 37 penaeoid genera to reconstruct the evolutionary relationships and to estimate divergence ages of the penaeoid shrimps. Phylogenetic analyses using maximum likelihood and Bayesian approaches strongly support the monophyly of Solenoceridae, Aristeidae and Benthesicymidae, but find Sicyoniidae nested within Penaeidae, making this family paraphyletic. Penaeoidea comprises two lineages: the former three families in one while the latter two in another. The diversification of these lineages may be related to bathymetry. The penaeid-like lineage diversified in the Triassic, earlier than the aristeid-like lineage with an origin in the Jurassic. Taxonomic revisions within Penaeoidea are also proposed for further investigation. Due to the paraphyly of Penaeidae and the high genetic divergence among the three penaeid tribes of Burkenroad [Burkenroad, M.D., 1983. Natural classification of Dendrobranchiata, with a key to recent genera. In: Schram, F.R. (Ed.), Crustacean Issues I. Crustacean Phylogeny. A.A. Balkema, Rotterdam, pp. 279–290], these tribes should be treated as having the same taxonomic rank as Sicyoniidae, while the family ranking of Benthesicymidae has to be re-considered owing to the low genetic divergence between the benthesicymids and the aristeids.     

Phylogeny of colletid bees (Hymenoptera: Colletidae) inferred from four nuclear genes

Colletidae comprise approximately 2500 species of bees primarily distributed in the southern continents (only two colletid genera are widely distributed: Colletes and Hylaeus). Previously published studies have failed to resolve phylogenetic relationships on a worldwide basis and this has been a major barrier to the progress of research regarding systematics and evolution of colletid bees. For this study, data from four nuclear gene loci: elongation factor-1alpha (F2 copy), opsin, wingless, and 28S rRNA were analyzed for 122 species of colletid bees, representing all subfamilies and tribes currently recognized; 22 species belonging to three other bee families were used as outgroups. Bayesian, maximum likelihood, and parsimony methods were employed to investigate the phylogenetic relationships within Colletidae and resulted in highly congruent and well-resolved trees. The phylogenetic results show that Colletidae are monophyletic and that all traditionally recognized subfamilies (except Paracolletinae) are also strongly supported as monophyletic. Our phylogenetic hypothesis provides a framework within which broad questions related to the taxonomy, biogeography, morphology, evolution, and ecology of colletid bees can be addressed.     

Phylogeny and classification of the leafhopper subfamily Eurymelinae (Hemiptera: Cicadellidae) inferred from molecules and morphology

Phylogenetic analysis of the globally distributed arboreal leafhopper subfamily Eurymelinae was conducted based on DNA sequence data from three nuclear and two mitochondrial genes in addition to 86 discrete morphological characters. The analysis included 89 species representing 61 genera from all major biogeographic regions including six species from outgroups, Megophthalminae and Ulopinae. Trees resulting from partitioned Bayesian and maximum likelihood analyses of the combined data were well resolved and largely congruent, differing mainly in the relationships among the earliest diverging lineages. The results are consistent with an expanded concept of Eurymelinae, including tribes Austroagalloidini and Macropsini. Six monophyletic groups are recognized as new tribes, Balocerini, Chiasmodolini, Chileanoscopini, Idioceroidini, Kopamerrini and Nesocerini, tribe n. , and the previously recognized tribes Eurymelini, Idiocerini and Megipocerini are redefined. A new synonym, Busonini Zhang & Li, 2015 syn.n. is proposed here for Megipocerini Isaev, 1988. Molecular divergence time estimates were calibrated using two fossil taxa and suggested that the earliest divergences occurred in the Lower Cretaceous and that most major lineages of this group arose during the Cretaceous. Reconstruction of ancestral areas revealed considerable continental-scale biogeographical structure. The place of origin of Eurymelinae is equivocal but major lineages arose in the Neotropical, Australian and Afrotropical regions. A key to tribes and a checklist of genera showing current tribal placements are provided.     

Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions

For Nicotiana, with 75 naturally occurring species (40 diploids and 35 allopolyploids), we produced 4656bp of plastid DNA sequence for 87 accessions and various outgroups. The loci sequenced were trnL intron and trnL-F spacer, trnS-G spacer and two genes, ndhF and matK. Parsimony and Bayesian analyses yielded identical relationships for the diploids, and these are consistent with other data, producing the best-supported phylogenetic assessment currently available for the genus. For the allopolyploids, the line of maternal inheritance is traced via the plastid tree. Nicotiana and the Australian endemic tribe Anthocercideae form a sister pair. Symonanthus is sister to the rest of Anthocercideae. Nicotiana sect. Tomentosae is sister to the rest of the genus. The maternal parent of the allopolyploid species of N. sect. Polydicliae were ancestors of the same species, but the allopolyploids were produced at different times, thus making such sections paraphyletic to their extant diploid relatives. Nicotiana is likely to have evolved in southern South America east of the Andes and later dispersed to Africa, Australia, and southwestern North America.     

Phylogeny of the order Tintinnida (Ciliophora, Spirotrichea) inferred from small- and large-subunit rRNA genes

Concatenated sequences of small- and large-subunit rRNA genes were used to infer the phylogeny of 29 species in six genera of Tintinnida. We confirmed previous results on the positions of major clusters and the grouping of various genera, including Stenosemella, the paraphyletic Tintinnopsis, the newly investigated Helicostomella, and some species of the polyphyletic Favella. Tintinnidium and Eutintinnus were found to be monophyletic. This study contributes to tintinnid phylogenetic reconstruction by increasing both the number of species and the range of genetic markers analyzed.     

Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology

Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loesener's subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.