Molecular phylogenetics of Triculine snails (Gastropoda: Pomatiopsidae) from southern China

Triculine (Gastropoda: Rissooidea: Pomatiopsidae) snails are involved in the transmission of schistosomiasis and paragonimiasis; their distributions are mainly across southeastern Asia and southern China. In the present investigation, partial sequences of COI, 16S, and 28S were examined to infer the phylogenetic relationships among the species rich and poorly understood gastropod. Samples were collected from 12 geographic locations in six provinces of southern China. Several methods such as maximum parsimony, maximum likelihood and distance analysis were used in phylogenetic analyses among these taxa. The resultant phylogenetic trees showed a similar topology irrespective of the phylogenetic methods used. The taxa fell into two clades, with those from Fujian, Guangxi, and Zhejiang Provinces in one clade and those from Hunan, Sichuan and Hubei in the other. Among the taxa in Hubei Province, five formed a monophyletic clade, but Tricula sp. H-SHY fell into a sister clade of Tricula hortensis of Sichuan, whilst Tricula hongshanensis formed a single clade. Sister taxa Tricula pingi and Tricula hsiangi formed well-supported clade within almost all the trees. These results, while preliminary, represent the first attempt to reconstruct a phylogeny for Triculinae across China.     

New classification of liverworts based on molecular and morphological data

Complete sequences for the 18S-rRNA gene of 22 bryophytes (12 completely new) were determined and used to construct phylogenetic trees. The evaluation of sequence data according to the maximum parsimony principle (PAUP 3.1.1) and the neighbor-joining method (MEGA) results in similar phylogenetic trees in which theBryopsida appear as a sister group to theJungermanniopsida, and both together as a sister group to theMarchantiopsida. Among theMarchantiopsida, theSphaerocarpales diverge early as a separate clade. TheMetzgeriales andJungermanniales are monophyletic. They belong to one clade and cannot be separated by either method of evaluation.     

Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction

Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.     

Phylogenetic Position of the Subgenus Lordiphosa of the Genus Drosophila (Diptera: Drosophilidae) Inferred from Alcohol Dehydrogenase (Adh) Gene Sequences

We analyzed the phylogenetic relationship between the species of Lordiphosa and other Drosophilidae using alcohol dehydrogenase (Adh) gene sequences. The phylogenetic trees consistently show that the four species Drosophila kurokawai, D. collinella, D. stackelbergi, and D. clarofinis, which include three species groups of Lordiphosa, form a monophyletic clade. This clade is placed as a sister group to the willistoni and saltans groups of Sophophora. On the other hand, three species of Lordiphosa, D. tenuicauda, D. pseudotenuicauda, and D. acutissima, all of which belong to the tenuicauda group, are not shown to be related to the major Lordiphosa lineage. In the phylogenetic trees, these species are included into the clade comprised of Drosophila and Hirtodrosophila, although it remains uncertain whether the tenuicauda group is a monophyletic group or not. These results indicate that Lordiphosa is polyphyletic and that most of the members of the subgenus have a close relationship to the neotropical groups of Sophophora. The above conclusion is compatible with the hypothesis of Okada (Mushi [1963] 37:79–100) and Lastovka and Máca (Acta Ent Bohemoslov [1978] 75:404–420) that Lordiphosa is most closely related to Sophophora; in contrast, our results contradict the hypothesis of Grimaldi (Bull Am Mus Nat Hist [1990] 197:1–139) that Lordiphosa is a sister group to the genus Scaptomyza. Received: 12 May 1999 / Accepted: 14 April 2000     

Phylogenetic structure in the grass family (Poaceae) as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among representatives of all subfamilies of the grass family (Poaceae), using Joinvillea (Joinvilleaceae) as the outgroup, placed most genera into two major clades. The first of these groups corresponds to a broadly circumscribed subfamily Pooideae that includes all sampled representatives of Ampelodesmeae, Aveneae, Brachypodieae, Bromeae, Diarrheneae, Meliceae, Poeae, Stipeae, and Triticeae. The second major clade includes all sampled representatives of four subfamilies (Panicoideae [tribes Andropogoneae and Paniceae], Arundinoideae [Arundineae], Chloridoideae [Eragrostideae], and Centothecoideae [Centotheceae]). Within this group (the “PACC” clade), the Panicoideae are resolved as monophyletic and as the sister group of the clade that comprises the other three subfamilies. Within the latter group, Danthonia (Arundinoideae) and Eragroslis (Chloridoideae) are resolved as a stable monophyletic group that excludes Phragmites (Arundinoideae); this structure is inconsistent with the Arundinoideae being monophyletic as currently circumscribed. The PACC clade is placed within a more inclusive though unstable clade that includes the woody Bambusoideae (Bambuseae) plus several disparate tribes of herbaceous grasses of uncertain affinity that are often recognized as herbaceous Bambusoideae (Brachyelytreae, Nardeae, Olyreae, Oryzeae, and Phareae). Among eight most-parsimonious trees resolved by the analysis, four include a monophyletic Bambusoideae sensu lato (comprising Bambuseae and all five of these herbaceous tribes) as the sister group of the PACC clade; in the other four trees these bambusoid elements are not resolved as monophyletic, and the PACC clade is nested among these tribes. These results are consistent with those of previous analyses that resolve a basal or near-basal branch within the family between Pooideae and all other grasses. However, resolution by the present analysis of the PACC clade, which includes Centothecoideae, Chloridoideae, and Panicoideae, but excludes Bambusoideae, is inconsistent with the results of previous analyses that place Bambusoideae and Panicoideae in a monophyletic group that excludes Centothecoideae and Chloridoideae.     

Phylogeny of Chaetonotidae and other Paucitubulatina (Gastrotricha: Chaetonotida) and the colonization of aquatic ecosystems

Kånneby, T., Todaro, M. A., Jondelius, U. (2012). Phylogeny of Chaetonotidae and other Paucitubulatina (Gastrotricha: Chaetonotida) and the colonization of aquatic ecosystems. —Zoologica Scripta, 42, 88–105. Chaetonotidae is the largest family within Gastrotricha with almost 400 nominal species represented in both freshwater and marine habitats. The group is probably non‐monophyletic and suffers from a troubled taxonomy. Current classification is to a great extent based on shape and distribution of cuticular structures, characters that are highly variable. We present the most densely sampled molecular study so far where 17 of the 31 genera belonging to Chaetonotida are represented. Bayesian and maximum likelihood approaches based on 18S rDNA, 28S rDNA and COI mtDNA are used to reconstruct relationships within Chaetonotidae. The use of cuticular structures for supra‐specific classification within the group is evaluated and the question of dispersal between marine and freshwater habitats is addressed. Moreover, the subgeneric classification of Chaetonotus is tested in a phylogenetic context. Our results show high support for a clade containing Dasydytidae nested within Chaetonotidae. Within this clade, only three genera are monophyletic following current classification. Genera containing both marine and freshwater species never form monophyletic clades and group with other species according to habitat. Marine members of Aspidiophorus appear to be the sister group of all other Chaetonotidae and Dasydytidae, indicating a marine origin of the clade. Halichaetonotus and marine Heterolepidoderma form a monophyletic group in a sister group relationship to freshwater species, pointing towards a secondary invasion of marine environments of these taxa. Our study highlights the problems of current classification based on cuticular structures, characters that show homoplasy for deeper relationships.     

Phylogeny of the East Asian botiine loaches (Cypriniformes,Botiidae) inferred from mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> gene sequences

The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, andLeptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.     

The phylogenetic position of an undescribed paedomorphic clupeiform taxon: mitogenomic evidence

Molecular characters may offer a useful alternative to confidently estimate the phylogenetic position of paedomorphic taxa otherwise difficult to place based on morphology because of the reduction or absence of characters in their larvae-like adult stage. Here, we sequenced the complete mitogenome of a remarkable undescribed marine paedomorphic clupeiform fish to gain insight into its phylogenetic position. Of a length of 17,507 bp, this mitogenome exhibits a unique gene order within the Teleostei because of the inversion of the contiguous tRNA^Gln and tRNA^Ile within the IQM region and the presence of a putative second control region inserted between these tRNAs. Mitogenomic data from 27 clupeiform species and 22 non-clupeiform species were subjected to partitioned maximum likelihood and Bayesian analyses. All resultant phylogenetic trees strongly supported the placement of this undescribed taxon within the order Clupeiformes, suborder Clupeoidei, and the family Clupeidae, as the sister group of the tribe Spratelloidini (Jenkinsia + Spratelloides) of the subfamily Dussumieriinae. Together, they form a monophyletic group with Chirocentrus and, possibly, Etrumeus. Despite its overall resemblance to Sundasalanx, this undescribed taxa (Clupeidae gen. et sp. indet.) is not closely related to that genus and represents an independent paedomorphic lineage within the Clupeoidei. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

92 Phylogenetic analysis of the caulerpales (ulvophyceae,chlorophyta) based on rbcl gene sequences

Our research seeks to clarify the phylogeny of the Caulerpales through analyses of rbcL (large subunit of ribulose 1,5 biphosphate carboxylase/oxygenase) gene sequences. In a review of caulerpalean taxonomy, Hillis‐Colinvaux (1984) recognized two suborders (Bryopsidineae and Halimedineae) on the basis of anatomical, physiological, and habitat characteristics. The Bryopsidineae (including the genera Bryopsis, Derbesia, and Codium) have cosmopolitan distributions, non‐holocarpic reproduction, and homoplasty, while the Halimedineae (including Caulerpa, Halimeda, and Udotea) have tropical to subtropical distributions, holocarpic reproduction, and heteroplasty. Previous phylogenetic analyses based on 18S rRNA sequence data supported the hypothesis of two monophyletic suborders within the Caulerpales (Zechman et al 1990). However, cladistic analyses of morphological characters (Vroom 1998) suggested that only the Halimedineae was monophyletic. Preliminary maximum likelihood and Bayesian analyses suggest the Halimedineae and Bryopsidineae form separate monophyletic groups, with robust support (bootstrap and posterior probabilities) for the former and moderate to poor support for the latter. The families of the Halimedineae (Caulerpaceae, Udoteaceae) form monophyletic sister groups with robust support. The freshwater family Dichotomosiphonaceae was inferred to be basal to the marine Halimedineae clade. The families within the Bryopsidineae (Derbesiaceae, Bryopsidaceae, Codiaceae) each form distinct monophyletic groups. The Codiaceae forms a basal monophyletic group to the sister clade of Bryopsidaceae and Derbeseaceae. This research was partially supported from a NSF grant (DEB‐0128977 to FWZ).     

Molecular phylogeny of three ambiguous ciliate genera: Kentrophoros,Trachelolophos and Trachelotractus (Alveolata,Ciliophora)

Gao, S., Strüder‐Kypke, M.C., Al‐Rasheid, K.A.S., Lin, X. & Song, W. (2010). Molecular phylogeny of three ambiguous ciliate genera: Kentrophoros, Trachelolophos and Trachelotractus (Alveolata, Ciliophora).—Zoologica Scripta, 39, 305–313. Very few molecular studies on the phylogeny of the karyorelictean ciliates have been carried out because data of this highly ambiguous group are extremely scarce. In the present study, we sequenced the small subunit ribosomal RNA genes of three morphospecies representing two karyorelictean genera, Kentrophoros, Trachelolophos, and one haptorid, Trachelotractus, isolated from the South and East China Seas. The phylogenetic trees constructed using Bayesian inference, maximum likelihood, maximum parsimony and neighbor‐joining methods yielded essentially similar topologies. The class Karyorelictea is depicted as a monophyletic clade, closely related to the class Heterotrichea. The generic concept of the family Trachelocercidae is confirmed by the clustering of Trachelolophos and Tracheloraphis with high bootstrap support; nevertheless, the order Loxodida is paraphyletic. The transfer of the morphotype Trachelocerca entzi Kahl, 1927 to the class Litostomatea and into the new haptorid genus Trachelotractus, as suggested by previous researchers based on morphological studies, is consistently supported by our molecular analyses. In addition, the poorly known species Parduczia orbis occupies a well‐supported position basal to the Geleia clade, justifying the separation of these genera from one another.     

Genetic diversity and phylogenetic position of the subclass Astomatia (Ciliophora) based on a sampling of six genera from West African oligochaetes (Glossoscolecidae, Megascolecidae), including description of the new genus Paraclausilocola n. gen

To more confidently assess phylogenetic relationships among astome ciliates, we obtained small subunit (SSU) rRNA sequences from nine species distributed in six genera and three families: Almophrya bivacuolata, Eudrilophrya complanata, Metaracoelophrya sp. 1, Metaracoelophrya sp. 2, Metaracoelophrya intermedia, Metaradiophrya sp., Njinella prolifera, Paraclausilocola constricta n. gen., n. sp., and Paraclausilocola elongata n. sp. The two new species in the proposed new clausilocolid genus Paraclausilocola n. gen. are astomes with no attachment apparatus, two files of contractile vacuoles, and an arc-like anterior suture that has differentiations of thigmotactic ciliature on the anterior ends of the left kineties of the upper surface. Phylogenetic analyses were undertaken using neighbor-joining, Bayesian inference, maximum likelihood, and maximum parsimony. The nine species of astomes formed a strongly supported clade, showing the subclass Astomatia to be monophyletic and a weakly supported sister clade to the scuticociliates. There were two strongly supported clades within the astomes. However, genera assigned to the same family were found in different clades, and genera assigned to the same order were found in both clades. Thus, astome taxa appear to be paraphyletic when morphology is used to assign species to genera.     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Phylogeny of Nematoda and Cephalorhyncha Derived from 18S rDNA

Phylogenetic relationships of nematodes, nematomorphs, kinorhynchs, priapulids, and some other major groups of invertebrates were studied by 18S rRNA gene sequencing. Kinorhynchs and priapulids form the monophyletic Cephalorhyncha clade that is the closest to the coelomate animals. When phylogenetic trees were generated by different methods, the position of nematomorphs appeared to be unstable. Inclusion of Enoplus brevis, a representative of a slowly evolving nematode lineage, in the set of analyzed species refutes the tree patterns, previously derived from molecular data, where the nematodes appear as a basal bilateral lineage. The nematodes seem to be closer to the coelomate animals than was speculated earlier. According to the results obtained, nematodes, nematomorphs, tardigrades, arthropods, and cephalorhynchs are a paraphyletic association of closely related taxa. Received: 1 December 1997 / Accepted: 9 April 1998     

Molecular phylogeny confirms Conochilidae as ingroup of Flosculariidae (Rotifera,Gnesiotrocha)

We test the hypothesis that conochilid rotifers represent an independent family‐level taxon within Superorder Gnesiotrocha, by analysing their phylogenetic position based on the 18S rDNA sequence of a large number of representatives of this taxon and its putative relatives. Both Bayesian and maximum likelihood analysis confirm a monophyletic clade of all gnesiotrochans with strong branch supports. Within Gnesiotrocha, Conochilidae form a strongly supported clade with representatives of all but some genera of Flosculariidae. These results refute Conochilidae as separate family‐level taxon within Gnesiotrocha. This finding is also supported by a phylogenetic analysis using morphology, in particular new observations on trophi morphology. Conochilid rotifers are likely specialized Flosculariidae, which evolved to a planktonic lifestyle and reduction of coloniality within the group, in contrast to other Flosculariidae. Furthermore, our analysis reveals that two genera of Flosculariidae, Beachampia and Limnias, form a single, strongly supported clade in a sister‐group relation to a clade consisting of representatives of Order Collothecacea. The present results, both regarding position of the conochild rotifers and of two genera of Flosculariidae, highlight the need for a more extensive analysis of relationships within Gnesiotrocha.     

Phylogenetic confirmation of the genus Robbea (Nematoda: Desmodoridae,Stilbonematinae) with the description of three new species

ABSTRACT

The Stilbonematinae are a monophyletic group of marine nematodes that are characterized by a coat of thiotrophic bacterial symbionts. Among the ten known genera of the Stilbonematinae, the genus Robbea Gerlach 1956 had a problematic taxonomic history of synonymizations and indications of polyphyletic origin. Here we describe three new species of the genus, R. hypermnestra sp. nov., R. ruetzleri sp. nov. and R. agricola sp. nov., using conventional light microscopy, interference contrast microscopy and SEM. We provide 18S rRNA gene sequences of all three species, together with new sequences for the genera Catanema and Leptonemella. Both our morphological analyses as well as our phylogenetic reconstructions corroborate the genus Robbea. In our phylogenetic analysis the three species of the genus Robbea form a distinct clade in the Stilbonematinae radiation and are clearly separated from the clade of the genus Catanema, which has previously been synonymized with Robbea. Surprisingly, in R. hypermnestra sp. nov. all females are intersexes exhibiting male sexual characters. Our extended dataset of Stilbonematinae 18S rRNA genes for the first time allows the identification of the different genera, e.g. in a barcoding approach.

http://zoobank.org/urn:lsid:zoobank.org:pub:D37C3F5A-CF2B-40E6-8B09-3C72EEED60B0     

The phylogenetic relationship between the Chlamydomonadales and Chlorococcales inferred from 18SrDNA sequence data

Nuclear-encoded small subunit ribosomal RNA gene (185rDNA) sequences were determined for Chlamydomonas moewusii Gerloff and five chlorococcalean algae (Chlorococcum hypnosporum Starr; Chlorococcum oleofaciens Trainor et Bold; Chlorococcum sp.; Tetracystis aeria Brown et Bold; Protosiphon botryoides (Kützingl Klebs). All these algae are characterized by a clockwise CCW) flagellar apparatus. Phylogenetic trees were constructed from sequences from these algae together with 20 green algae. All algae with a CW flagellar apparatus form a monophyletic clade (CW group). Three principal clades can be recognized in the CW group, although no morphological character supports monophyly of any of these three clades. The 185rDNA trees clearly demonstrate the non-monophyly of the Chlamydomonadales and Chlorococcales, suggesting that vegetative morphology does not reflect phylogenetic relationships in the CW group. The paraphyly or polyphyly of the genus Chlamydomonas and Chlorococcum are also revealed. Present analysis suggests that the presence or absence of a zoospore's cell wall and the multinucleate condition have limited taxonomic values at higher taxonomic ranks.     

Morphology-based phylogeny of the treehopper family Membracidae (Hemiptera: Cicadomorpha: Membracoidea)

A parsimony‐based phylogenetic analysis of eighty‐three morphological characters of adults and immatures of seventy representatives of the tribes and subfamilies of Membracidae and two outgroup taxa was conducted to evaluate the status and relationships of these taxa. Centrotinae apparently gave rise to Nessorhinini and Oxyrhachini (both formerly treated as subfamilies, now syn.n. and syn.reinst., respectively, of Centrotinae). In contrast to previous analyses, a clade comprising Nicomiinae, Centronodinae, Centrodontinae, and the unplaced genera Holdgatiella Evans, Euwalkeria Goding and Antillotolania Ramos was recovered, but relationships within this clade were not well resolved. Nodonica bispinigera, gen.n. and sp.n., is described and placed in Centrodontini based on its sister‐group relationship to a clade comprising previously described genera of this tribe. Membracinae and Heteronotinae were consistently monophyletic. Neither Darninae nor Smiliinae, as previously defined, was monophyletic on the maximally parsimonious cladograms, but constraining both as monophyletic groups required only one additional step. The monophyly of Stegaspidinae, including Deiroderes Ramos (unplaced in Membracidae), was supported on some but not all equally parsimonious cladograms. More detailed analyses of individual subfamilies, as well as morphological data on the undescribed immatures of several membracid tribes and genera, will be needed to elucidate relationships among tribes and genera. A key to the subfamilies and tribes is provided.     

A molecular and ultrastructural description of Spathidiopsis buddenbrocki and the phylogenetic position of the family Placidae (Ciliophora)

Spathidiopsis and Placus are the only two genera within the family Placidae. The family has been placed in the class Prostomatea and order Prorodontida because its members have somatic monokinetids with a radial transverse ribbon, a straight non‐overlapping postciliary ribbon, and anteriorly directed non‐overlapping kinetodesmal fibril, an apical cytostome lacking specialized oral cilia, a brosse, and toxicysts. To confirm the stability of this placement, ultrastructural morphology and small subunit rRNA gene sequences of Spathidiopsis socialis, Spathidiopsis buddenbrocki, and Placus striatus were determined. These data were combined with information from other ciliates, and phylogenetic trees were generated using maximum‐likelihood and maximum‐parsimony methods. The analyses confirmed the family Placidae to be a monophyletic group in the Prostomatea with the Placidae a sister group to a Cryptocaryon + Coleps + Prorodon clade.     

Higher and lower‐level relationships of the deep‐sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences

Fishes of the order Alepocephaliformes, slickheads and tubeshoulders, constitute a group of deep‐sea fishes poorly known in respect to most areas of their biology and systematics. Morphological studies have found alepocephaliform fishes to display a mosaic of synapomorphic and symplesiomorphic characters, resulting in great difficulties when attempting to resolve intra‐ and interrelationships. Molecular data recently added to the confusion by removing Alepocephaliformes from the Euteleostei and placed them as incertae sedis within the Otocephala. In the present study we attempt to further clarify relationships of Alepocephaliformes by adding newly determined whole mitogenome sequences from 19 alepocephaliforms in order to address 1) phylogenetic position of Alepocephaliformes within the Otocephala; and 2) intrarelationships of Alepocephaliformes. The present study includes 96 taxa of which 30 are alepocephaliforms and unambiguously aligned sequences were subjected to partitioned maximum likelihood and Bayesian analyses. Results from the present study support Alepocephaliformes as a genetically distinct otocephalan order as sister clade to Ostariophysi (mostly freshwater fishes comprising Gonorynchiformes, Cypriniformes, Characiformes, Siluriformes and Gymnotiformes). The disputed family Bathylaconidae was found to be an artificial assemblage of the two genera Bathylaco and Herwigia, with the former as the sister group of the family Alepocephalidae and the latter nested within Alepocephalidae. Platytroctidae was found to be monophyletic as sister clade to the rest of Alepocephaliformes. Previously unrecognized clades within the family Alepocephalidae are presented and a clade comprising Alepocephalus, Conocara and Leptoderma was recovered as the most derived. As long as the current classification is being followed, the genera Alepocephalus, Bathytroctes, Conocara and Narcetes were all found non‐monophyletic. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 923–936.     

Plastid phylogenomics improve phylogenetic resolution in the Lauraceae

Abstract The family Lauraceae is a major component of tropical and subtropical forests worldwide, and includes some commercially important timber trees and medicinal plants. However, phylogenetic relationships within Lauraceae have long been problematic due to low sequence divergence in commonly used markers, even between morphologically distinct taxa within the family. Here we present phylogenetic analyses of 43 newly generated Lauraceae plastomes together with 77 plastomes obtained from GenBank, representing 24 genera of Lauraceae and 17 related families of angiosperms, plus nine barcodes from 19 additional species in 18 genera of Lauraceae, in order to reconstruct highly supported relationships for the Lauraceae. Our phylogeny supports the relationships: sisterhood of the Lauraceae and a clade containing Hernandiaceae and Monimiaceae, with Atherospermataceae and Gomortegaceae being the next sister groups, followed by Calycanthaceae. Our results highlight a monophyletic Lauraceae, with nine well‐supported clades as follows: Hypodaphnis clade, Beilschmiedia–Cryptocarya clade, Cassytha clade, Neocinnamomum clade, Caryodaphnopsis clade, Chlorocardium–Mezilaurus clade, Machilus–Persea clade, Cinnamomum–Ocotea clade, and Laurus–Neolitsea clade. The topology recovered here is consistent with the patterns of plastome structural evolution and morphological synapomorphies reported previously. More specifically, flower sex, living type, inflorescence type, ovary position, anther locus number, leaf arrangement, leaf venation, lateral vein number, tree height, and inflorescence location all represent morphological synapomorphies of different lineages. Our findings have taxonomic implications and two new tribes, Caryodaphnopsideae and Neocinnamomeae, are described, and the composition of four other tribes is updated. The phylogeny recovered here provides a robust phylogenetic framework through which to address the evolutionary history of the Magnoliids, the third‐largest group of Mesangiospermae.