Description and relationships of Chaetopterus pugaporcinus, an unusual pelagic polychaete (Annelida, Chaetopteridae)

An extraordinary new species, Chaetopterus pugaporcinus, is described from eight specimens collected from deep mesopelagic waters off Monterey Bay, California, by remotely operated vehicles. All specimens exhibit a consistent combination of both adult and larval characteristics, leaving in question the maturity of the specimens. All specimens lack ciliated larval bands and the stout, modified chaetae (cutting spines) typically found in segment A4 of chaetopterids. If the specimens described here are larvae, they are remarkable for their size, which ranged from 10 to 21 mm total length, nearly twice the length of the largest polychaete larvae previously reported and 5 to 10 times larger than known chaetopterid larvae. Then too, their lack of segment addition prior to settlement would be atypical. If adult, they are particularly unusual in their habitat choice and body form. Morphology of the uncini and comparison to larval morphology indicated a close relationship to either Chaetopterus or Mesochaetopterus. However, the lack of cutting spines and typical adult morphology made it impossible to determine to what genus this species should be allied. Thus, we carried out the first molecular phylogenetic analysis of the Chaetopteridae in order to appropriately place and name the new species. Three partial genes were sequenced for 21 annelid species. The sequencing also provides the first molecular evidence that Chaetopterus variopedatus sensu Hartman (1959) is not a single cosmopolitan species. The question of C. pugaporcinus being a delayed larva or a genuine holopelagic chaetopterid is discussed.     

Phylogenetic status of the family Naididae (Oligochaeta, Annelida) as inferred from DNA analyses

Phylogenetic analyses based upon the D3 domain of the nuclear 23S rRNA gene and part of the mitochondrial COI gene indicate that the family Naididae is a subordinate group within the family Tubificidae and most closely related to the subfamily Rhyacodrilinae. Based upon relative genetic distances we hypothesize that the origin of Naididae occurred relatively early in the evolution of Tubificidae, but this was a fairly late event compared to the basic radiation among Annelida.     

Loss of complexity from larval towards adult nervous systems in Chaetopteridae (Chaetopteriformia,Annelida) unveils evolutionary patterns in Annelida

Organisms Diversity & Evolution - Chaetopteridae — the parchment worms — comprise a group of early branching annelids with a scarcely investigated neuroanatomy and neurogenesis. Due...     

Phylogenetic relationships within Nephtyidae (Polychaeta,Annelida)

Ravara, A., Wiklund, H., Cunha, M. R. & Pleijel, F. (2010). Phylogenetic relationships within Nephtyidae (Polychaeta, Annelida). —Zoologica Scripta, 39, 394–405. We present the first phylogeny of nephtyids, a common, soft‐bottom living polychaete family comprising five genera and over 100 species. Characters used to distinguish nephtyid genera are a matter of controversy and considerable confusion remains as to the generic delineations. The phylogeny is estimated with molecular data from the mitochondrial genes cytochrome oxidase I and 16S rDNA, the nuclear genes 18S rDNA and 28S rDNA and morphological data. The results reveal two well‐supported major clades, corresponding in part to the two main genera of the family, Aglaophamus and Nephtys. The species Nephtys pulchra and Nephtys australiensis are transferred to Aglaophamus, and new diagnoses for the genera are provided. Dentinephtys is synonymized with Nephtys, and Nephtys cornuta is sister to the remaining nephtyids and is referred to the new genus Bipalponephtys, together with Nephtys danida and Micronephthys neotena. Micronephthys is sister to Nephtys and Inermonephtys is of uncertain position.     

Phylogenetic affinities of the Flabelligeridae (Annelida, Polychaeta)

Cirratuliformia includes Acrocirridae, Cirratulidae, Ctenodrilidae, Flabelligeridae, Flotidae and Sternaspidae. The phylogenetic affinities have not been settled due to a limited availability of type or non-type material and the relationship between acrocirrids and flabelligerids have been problematical. In our study, the type material of all type species for all flabelligerid, and most acrocirrid genera have been studied and the morphological features have been used in a phylogenetic analysis. The results indicate that Acrocirridae, Ctenodrilidae, Fauveliopsidae, Flabelligeridae and Flotidae are monophyletic and that Sternaspidae falls within Cirratulidae; however, the latter conclusion might be reversed through increased taxon-sampling. The flabelligerid genera Brada, Flabelligera, Pherusa and Stylarioides each consists of several monophyletic groups and may be split. Conversely, Bradiella includes Diversibranchius, and the pelagic Buskiella includes Flota. The generic affinities of Poeobius remain uncertain, collecting better materials may resolve this issue.     

Phylogenetic analyses of Andromedeae (Ericaceae subfam. Vaccinioideae)

Phylogenetic relationships within the Andromedeae and closely related taxa were investigated by means of cladistic analyses based on phenotypic (morphology, anatomy, chromosome number, and secondary chemistry) and molecular (rbcL and matK nucleotide sequences) characters. An analysis based on combined molecular and phenotypic characters indicates that the tribe is composed of two major clades—the Gaultheria group (incl. Andromeda, Chamaedaphne, Diplycosia, Gaultheria, Leucothoe¨, Pernettya, Tepuia, and Zenobia) and the Lyonia group (incl. Agarista, Craibiodendron, Lyonia, and Pieris). Andromedeae are shown to be paraphyletic in all analyses because the Vaccinieae link with some or all of the genera of the Gaultheria group. Oxydendrum is sister to the clade containing the Vaccinieae, Gaultheria group, and Lyonia group. The monophyly of Agarista, Lyonia, Pieris, and Gaultheria (incl. Pernettya) is supported, while that of Leucothoe¨ is problematic. The close relationship of Andromeda and Zenobia is novel and was strongly supported in the molecular (but not morphological) analyses. Diplycosia, Tepuia, Gaultheria, and Pernettya form a well-supported clade, which can be diagnosed by the presence of fleshy calyx lobes and methyl salicylate. Recognition of Andromedeae is not reflective of our understanding of geneological relationships and should be abandoned; the Lyonia group is formally recognized at the tribal level.     

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.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.     

Phylogenetic analysis of Tubificidae (Annelida, Clitellata) based on 18S rDNA sequences

Tubificids are aquatic clitellate worms, but recent analyses of morphological characters suggested that this family, as currently recognized, is paraphyletic. Sequences of the 18S rDNA gene of 40 protostome worm species (including 13 representatives of the Tubificidae) and 2 mollusc species were cladistically analyzed to test the monophyly of the Tubificidae and that of some of its constituent subfamilies. Under all alignments tested, the same general phylogenetic pattern emerged. The data support the idea that the Naididae, another clitellate taxon, is associated with some "rhyacodriline" groups within the Tubificidae. The data also corroborate the idea that the Tubificinae and the Limnodriloidinae are monophyletic but indicate that the Rhyacodrilinae and the Phallodrilinae are not. Bathydrilus does not appear to be closely related to other "phallodriline" genera.     

Phylogenetic analyses of the family Tetraonchidae (Platyhelminthes: Monogenea)

A phylogenetic reconstruction of the monogenean family Tetraonchidae was carried out by methods of parsimony-based cladistics. The analysis included 20 species of tetraonchids and two out-groups (Sundanonchus tomanorum and Dactylogyrus amphibothrium) and was based on 34 morphofunctional characters. Software PAUP 4.0 and Winclada were used for the phylogenetic reconstructions. Obtained results allow proposing a preliminary phylogenetic hypothesis of the family Tetraonchidae along with the discussion of host-parasite association. According to the current taxonomic view, the family Tetraonchidae included two genera. Cladistic analysis showed a monophyly of the family and the genus Tetraonchus Diesing, 1858. Two representative of the former genus, Tetraoncus monenteron and T. borealis, parasitize the pikes (Esocoformes: Esocidae) and the grayling (Salmonidae: Thymallinae) respectively. The genus Salmonchus Spassky et Roytman, 1958 has a complicated structure and its intrageneric relationships were not completely resolved; in general, the analysis allows to recognise several species groups: Salmonchus oncorhynchi--the parasite of the Oncorhynchus masou smolt living during the first year of life in fresh water; four species (S. variabilis, S. gussevi, S. grumosus, S. alaskensis) inhabiting specifically the whitefishes (Salmonidae: Coregoninae); all reminder of Salmonchus species occurring on the salmons (Salmonidae: Salmoninae). The bootstrap test gives a support only for the following clades: family Tetraonchidae (75%), genus Tetraonchus (88%); a group of Salmonchus species associated with the whitefishes (93%) and grouping of four species (S. huhonis, S. pseudolenoki, S. skrjabini and S. lenoki) from the lenoks (Brachymystax) and taimens (Hucho) (61%).     

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.     

Phylogenetic systematics of Erythronium (Liliaceae): morphological and molecular analyses

For a nearly complete set of species of Erythronium (Liliaceae), we examined two plastid loci (the rps16 intron and the 5′ trnK intron, excluding the matK exon), one nuclear locus (nrITS) and morphology to evaluate species relationships and that of Erythronium to Amana, the putatively most closely allied genus. A matrix of morphological characters was developed through observation of around 900 living and herbarium specimens; evolution of these was examined using character optimization on the combined (total‐evidence) tree. Parsimony methods were used to examine the morphological and molecular data sets produced, both separately and in combination, with Bayesian methods also used on the molecular data sets. These established that the genus is probably sister to Amana (although most analyses placed Amana inside Erythronium) and that Tulipa is sister to the pair of Erythronium and Amana. Within Erythronium, there are three strongly supported geographically distinct clades: (1) Eurasian and (2) eastern and (3) western North American. Separation of species in these three clades is less clear, particularly among the western North American taxa. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Phylogenetic information from three mitochondrial genomes of Terebelliformia (Annelida) worms and duplication of the methionine tRNA

Mitochondrial genomes have been useful for inferring animal phylogeny across a wide range of clades, however they are still poorly sampled in some animal taxa, limiting our knowledge of mtDNA evolution. For example, despite being one of the most diverse animal phyla, only 5 complete annelid mitochrondial genomes have been published. To address this paucity of information, we obtained complete mitochondrial genomic sequences from Pista cristata (Terebellidae) and Terebellides stroemi (Trichobranchidae) as well as one nearly complete mitochondrial genome from Eclysippe vanelli (Ampharetidae). These taxa are within Terebelliformia (Annelida), which include spaghetti worms, icecream cone worms and their relatives. In contrast to the 37 genes found in most bilaterian metazoans, we recover 38 genes in the mitochondrial genomes of T. stroemi and P. cristata due to the presence of a second methionine tRNA (trnM). Interestingly, the two trnMs are located next to each other and are possibly a synapomorphy of these two taxa. The E. vanelli partial mitochondrial genome lacks this additional trnM at the same position, but it may be present in the region not sampled. Compared to other annelids, gene orders of these three mitochondrial genomes are generally conserved except for the atp6-mSSU region. Phylogenetic analyses reveal that mtDNA data strongly supports a Trichobranchidae/Terebellidae clade.     

Phylogenetic analyses of Cloeodes Traver and related genera (Ephemeroptera: Baetidae)

Cloeodes Traver is atypical among Baetidae (Ephemeroptera) because it seems to possess a unique Pantropical distribution. Thirty‐nine species have been described to date, 26 from the Neotropics, four from the Southern Nearctic, seven from the Afrotropics and two from the Oriental region. Several genera have been considered related to Cloeodes during the last decades, of which the following remain valid: Crassabwa Lugo‐Ortiz & McCafferty, Dabulamanzia Lugo‐Ortiz & McCafferty (both Afrotropical), Bungona Harker (Australasian) and Chopralla Waltz & McCafferty (Oriental). Despite their supposed relationship, a phylogenetic analysis between all of these genera has never been performed. In the present paper, based on an extensive analysis of all genera that have been considered related to Cloeodes, a phylogenetic analysis using morphological characters (continuous and discrete) was performed in order to address the monophyly of the genus Cloeodes within the Cloeodes complex of genera. According to our results, Cloeodes and the complex are paraphyletic. Based on this, Cloeodes is restricted to the New World, Potamocloeon is revalidated to include most representatives of Afrotropical Cloeodes and is divided into two subgenera: Potamocloeon (Africa) and the new Aquaediva (Madagascar). In addition, the concept of Bungona is expanded to include Australasian and Oriental taxa – namely the subgenera Chopralla and the revalidated Centroptella – and finally the new genus Crassolus is established to include C. inzingae comb.n. from Africa. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:C416090E-C43D-481A-9A3D-F3B1EEE41176 .     

Phylogenetic relationships within Maldanidae (Capitellida,Annelida), based on morphological characters

The Maldanidae annelid worms are reviewed and the phylogenetic relationships of their subgroups provided, based on Hennigian principles and maximum parsimony. Characters were coded as binary and multistate (transformation series). We used 33 terminal taxa (species), and 50 characters. Characters were treated as unordered and of equal weight, and analysis was run in TNT. Three equally most-parsimonious trees were obtained with heuristic searches, with lengths of 64 steps; CI = 0.95, and RI = 0.98. The monophyly of Maldanidae was supported with 100% of bootstrap and jackknife values. As a result of our analysis, Arenicolidae remains the sister-group of Maldanidae, and both should be referred to Maldanomorpha. Maldanidae was supported by the following synapomorphies: dorsal prostomium; prostomium keel-shaped and fused to peristomium; torus globose behind median chaetigers; median chaetigers greatly elongated; number of pre-anal segments reduced. The subfamily Bogueinae was not monophyletic; Boguea and Boguella were included within Rhodininae. Clymenura, previously included in the Clymenurinae, was included within Euclymeninae. The taxa Notoproctinae, Maldaninae, Nicomachinae and Euclymeninae were grouped in the Maldanoplaca, a new taxon. Eight further new clades have been found, but were not named.     

Molecular and morphometric analyses identify new lineages within a large Eumida (Annelida) species complex

We report on two new lineages of the Eumida sanguinea complex from Great Britain and describe one of them as a new species using a multilocus approach, including the mitochondrial DNA COI-5P and the nuclear markers ITS (ITS1, 5.8S rRNA and ITS2) and 28S rRNA. The molecular analysis placed Eumida mackiei sp. nov. in a monophyletic clade with 19.1% (COI), 10.1% (ITS) and 1.7% (28S) mean distance to its nearest neighbour. Molecular diagnoses were also applied to nine lineages within the E. sanguinea complex. This was complemented with morphometric data employing multivariate statistical analysis and the incorporation of statistical dissimilarities against three other described species from the complex. Eumida mackiei sp. nov. can be distinguished from E. notata and E. maia by the larger distance between the eyes and differences in morphometric proportions mainly in the dorsal and ventral cirri as well as in the prostomial appendages. E. sanguinea sensu stricto failed to produce a cluster of its own in the morphometric analysis, probably due to juvenile bias. Integrative taxonomy provided strong evidence to formally describe a new cryptic species that can now be used in biomonitoring or other relevant ecological research.     

采用SSR和RAPD标记研究黄瓜属（葫芦科）的系统发育关系

野黄瓜Cucumis hystrix（2n=24）是在亚洲发现的第一个染色体基数为12的黄瓜属物种。这一发现对现行的以染色体基数和地理分布为基础的黄瓜属分类系统提出了质疑。采用SSR和RAPD两种分子标记对黄瓜属22份不同类型材料的亲缘关系进行了研究。结果表明,野黄瓜C.hystrix与黄瓜C.sativus var.sativus（2n=14）间的遗传距离（SSR:0.59,RAPD:0.57）小于其与甜瓜C.melo var.melo（2n=24）间的距离（SSR:0.87,RAPD:0.70）。SS     

Radiocarbon dating and metal analyses of `fossil' and living tubes of Protula (Annelida: Polychaeta)

Since the initiation of benthic and trawling studies in southern California over 50 years ago, empty calcareous tubes, measuring up to 36 cm in length and 2.1 cm in diameter, have been collected and presumed to belong to the serpulid genus Protula. ¹⁴C dating of these `fossil' tubes, ranged from 631 ±34 to 3987 ±42 yrs. In connection with monitoring programs, living specimens of Protula superba Moore, 1909 were collected from the benthos off southern California. A comparison of the elemental profile of the ancient and extant tubes was conducted to ascertain the effects of time and the recent increase in various anthropogenically mobilized metals on the incorporation of Al, As, Ba, Cd, Ce, Co, Cr, Fe, Mo, Ni, Pb, U, V and Zn in the calcareous tube. Surprisingly, inductively coupled plasma mass spectroscopy (ICP-MS) analysis of the digested tubes showed the concentrations of the elements were generally higher in `fossil' tubes than those obtained from living animals. However, the concentration of elements was higher in `fossil' tubes collected from the vicinity of municipal outfall discharges compared to `fossil' tubes collected from near an offshore island. Laser ablation ICP-MS analyses across transverse sections of `fossil' and living tubes showed spatial heterogeneity of elements in the structure. Elevated signals for Pb, Gd, Ce, La, Pr, Sm, Eu and Nd were observed on both internal and external surfaces on all tubes. Elevated responses for Fe, Zn, Sr, Mn, Tb, Dy, Ho, Er and Bi were primarily noted on the outer surfaces. It is hypothesized that the higher concentrations of metals in the `fossil' tubes may be the result of surface contamination facilitating elemental adsorption or substitution over the years. It is concluded that the use of biomineralized structures as biomonitors of water quality should involve rigorous chelating procedures to remove contaminating metals from lattice bound elements locked in the mineral matrix.