Multilocus ribosomal RNA phylogeny of the leaf beetles (Chrysomelidae)

Basal relationships in the Chrysomelidae (leaf beetles) were investigated using two nuclear (small and partial large subunits) and mitochondrial (partial large subunit) rRNA (≈ 3000 bp total) for 167 taxa covering most major lineages and relevant outgroups. Separate and combined data analyses were performed under parsimony and model‐based tree building algorithms from dynamic (direct optimization) and static (Clustal and BLAST) sequence alignments. The performance of methods differed widely and recovery of well established nodes was erratic, in particular when using single gene partitions, but showed a slight advantage for Bayesian inferences and one of the fast likelihood algorithms (PHYML) over others. Direct optimization greatly gained from simultaneous analysis and provided a valuable hypothesis of chrysomelid relationships. The BLAST‐based alignment, which removes poorly aligned sequence segments, in combination with likelihood and Bayesian analyses, resulted in highly defensible trees obtained in much shorter time than direct optimization, and hence is a viable alternative when data sets grow. The main taxonomic findings include the recognition of three major lineages of Chrysomelidae, including a basal “sagrine” clade (Criocerinae, Donaciinae, Bruchinae), which was sister to the “eumolpine” (Spilopyrinae, Eumolpinae, Cryptocephalinae, Cassidinae) plus “chrysomeline” (Chrysomelinae, Galerucinae) clades. The analyses support a broad definition of subfamilies (i.e., merging previously separated subfamilies) in the case of Cassidinae (cassidines + hispines) and Cryptocephalinae (chlamisines + cryptocephalines + clytrines), whereas two subfamilies, Chrysomelinae and Eumolpinae, were paraphyletic. The surprising separation of monocot feeding Cassidinae (associated with the eumolpine clade) from the other major monocot feeding groups in the sagrine clade was well supported. The study highlights the need for thorough taxon sampling, and reveals that morphological data affected by convergence had a great impact when combined with molecular data in previous phylogenetic analyses of Chrysomelidae. © The Willi Hennig Society 2007.     

Higher‐level phylogeny of longhorn beetles (Coleoptera: Chrysomeloidea) inferred from mitochondrial genomes

Cerambycidae (longhorn beetles) and related families in the superfamily Chrysomeloidea are important components of forest ecosystems and play a key role in nutrient cycling and pollination. Using full mitochondrial genomes and dense taxon sampling, the phylogeny of Chrysomeloidea with a focus on Cerambycidae and allied families was explored. We used 151 mitochondrial genomes (75 newly sequenced) covering all families and 29 subfamilies of Chrysomeloidea. Our results reveal that (i) Chrysomelidae (leaf beetles) are sister to all other chrysomeloid families; (ii) Cerambycidae sensu stricto (s. s.) is polyphyletic due to the inclusion of other families that split Cerambycidae into a ‘lamiine’ clade comprising Lepturinae sensu lato (s. l.) + (Lamiinae + Spondylidinae) and a ‘cerambycine’ clade comprising Dorcasominae + (Cerambycinae + Prioninae s. l.); (iii) the subfamilies within the two clades of Cerambycidae s. s. were monophyletic, except for the placement of Necydalinae nested in Lepturinae, and the placement of Parandrinae within Prioninae (now considered as tribes Necydalini and Parandrini, respectively); (iv) smaller families were grouped into two major clades: one composed of Disteniidae+Vesperidae and the other composed of Orsodacnidae + (Megalopodidae + Oxypeltidae); (v) relationships among the four major clades were poorly supported but were resolved as ((cerambycines + (Disteniidae + Vesperidae) + Orsodacnidae + (Megalopodidae + Oxypeltidae)) + lamiines. Divergence time analyses estimated that Chrysomeloidea originated ca. 154.1 Mya during the late Jurassic, and most subfamilies of Cerambycidae originated much earlier than subfamilies of Chrysomelidae. The diversification of families within Chrysomeloidea was largely coincident with the radiation of angiosperms during the Early Cretaceous.     

The complete mitochondrial genome of Paracymoriza prodigalis (Leech, 1889) (Lepidoptera), with a preliminary phylogenetic analysis of Pyraloidea

The complete mitochondrial genome sequence is determined for Paracymoriza prodigalis (Leech, 1889). The 15,326 bp circular molecule possesses a gene organization and order identical to other sequenced Pyraloidea mitochondrial genomes. All tRNAs have the typical clover-leaf structure except for tRNA^Ser(AGN), which lacks the dihydrouridine (DHU) arm. The A+T-rich region of 343 bp includes the features common to the Lepidoptera, including the ‘ATAGA’ followed by an 19-bp poly-T stretch, but the tandem repeat sequences often appearing in available insects are not found. Phylogenetic relationships of eight subfamilies of 14 Pyraloidea species were constructed based on 13 PCGs of mitochondrial genomes using Bayesian inference (BI) and maximum likelihood (ML) methods. These phylogenies of the subfamilies within Pyraloidea accord well with morphological phylogenetic analysis except for the position of Schoenobiinae.     

Molecular systematics of Eumolpinae and the relationships with Spilopyrinae (Coleoptera, Chrysomelidae)

The 3400 species of Eumolpinae constitute one of the largest subfamilies of leaf beetles (Chrysomelidae). Their systematics is still largely based on late 19th century monographs and remains highly unsatisfactory. Only recently, some plesiomorphic lineages have been split out as separate subfamilies, including the southern hemisphere Spilopyrinae and the ambiguously placed Synetinae. Here we provide insight into the internal systematics of the Eumolpinae based on molecular phylogenetic analyses of three ribosomal genes, including partial mitochondrial 16S and nuclear 28S and complete nuclear 18S rRNA gene sequences. Sixteen morphological characters considered important in the higher-level systematics of Eumolpinae were also included in a combined analysis with the molecular characters. All phylogenetic analyses were performed using parsimony by optimizing length variation directly on the tree, as implemented in the POY software. The data support the monophyly of the Spilopyrinae outside the clade including all sampled Eumolpinae, corroborating their treatment as a separate subfamily within the Chrysomelidae. The systematic placement of the Synetinae remains ambiguous but consistent with considering it a different subfamily as well, since the phylogenetic analyses using all the available evidence show the representative sequence of the subfamily also unrelated to the Eumolpinae. The Megascelini, traditionally considered a separate subfamily, falls within the Eumolpinae. Several recognized taxonomic groupings within Eumolpinae, including the tribes Adoxini or Typophorini, are not confirmed by molecular data; others like Eumolpini seem well supported. Among the morphological characters analyzed, the presence of a characteristic groove on the pygidium (a synapomorphy of the Eumolpini) and the shape of tarsal claws (simple, appendiculate or bifid) stand out as potentially useful characters for taxonomic classification in the Eumolpinae.     

Molecular systematics reveals the origins of subsociality in tortoise beetles (Coleoptera,Chrysomelidae, Cassidinae)

Subsocial behaviour is known to occur in at least 19 insect orders and 17 families of Coleoptera. Within the leaf beetle family, Chrysomelidae, extended maternal care is reported in only 2 of 15 subfamilies: Cassidinae and Chrysomelinae. Although the emergence of subsociality in insects has received much attention, extensive analyses on the evolution of this behaviour based on phylogenetic approaches are missing. Subsociality is recorded in 33 species of tortoise beetles belonging to the tribes Mesomphaliini and Eugenysini. A molecular phylogenetic reconstruction of these tribes and the remaining five Neotropical tribes of cassidine tortoise beetles was used to investigate the evolution of maternal care and to elucidate the phylogenetic relationships among Neotropical cassidine tribes. A phylogeny was constructed using 90 species and three loci from both mitochondrial and nuclear genes (COI, CAD and 28S). Bayesian inference and maximum likelihood analyses based on a concatenated dataset recovered two independent origins, with no evidence of reversal to solitary behaviour. One origin comprises three Mesomphaliini genera tightly associated with Convolvulaceae, and the other consists of the genus Eugenysa Chevrolat (Eugenysini), a small clade embedded within a group feeding exclusively on Asteraceae. A previous hypothesis suggesting dual origins on different host plants was confirmed, whereas other hypotheses based on a phylogenetic reconstruction of Cassidinae could not be sustained. Our analysis also revealed that the tribe Mesomphaliini is a monophyletic taxon if Eugenysini is included, and for this reason, we re-establish synonymy of both tribes. We also provide nine new records of subsociality for tortoise beetles species.     

Phylogenetic relationships among Bombycidae s.l. (Lepidoptera) based on analyses of complete mitochondrial genomes

The family Bombycidae (sensu Minet, 1994) is a diverse group of species belonging to the superfamily Bombycoidea. It is an economically important group of moth species, containing well‐known silk‐producing insects, as well as many pests of agriculture and forestry. The morphology‐based hypothesis of Minet (1994) on the composition of Bombycidae is in conflict with subsequent phylogenetic hypotheses for the superfamily based on nuclear genes. In this paper, the complete mitochondrial genomes of nine species of Bombycidae are presented for the first time. Based on these genomes, four dataset partitions and three gblocks parameter settings, phylogenetic relationships among Bombycidae were reconstructed using maximum likelihood and Bayesian inference methods. Bombycidae was confirmed as a polyphyletic group, with the traditional subfamilies Prismostictinae and Oberthueriinae forming a single well‐supported clade that is distant to Bombycinae. The phylogenetic relationships within Bombycoidea were supported as ((((Bombycinae, Sphingidae), Saturniidae), (Prismostictinae, Oberthueriinae)), Eupterotidae).     

Complete mitochondrial genome sequence and phylogenetic position of the Amu Darya sturgeon,Pseudoscaphirhynchus kaufmanni (Acipenseriformes: Acipenseridae)

In this study, we successfully assembled the complete mitochondrial genome of the Amu Darya sturgeon Pseudoscaphirhynchus kaufmanni. Based on this mitochondrial genome and previously published mitochondrial genomes of members of the Acipenseridae family, we assessed the phylogenetic position of P. kaufmanni using maximum likelihood and Bayesian inference for phylogeny reconstruction. The resultant phylogenetic trees were well-resolved, with congruence between different phylogenetic methods. This robust phylogenetic analysis elucidated the relationship among the four acipenserid genera and strongly supported the division of the family into three main clades. Evaluation of molecular phylogeny using maximum likelihood and Bayesian analysis led to the following conclusions: (a) the most basal position within the Acipenseridae remains in the clade containing Acipenser oxyrinchus and Acipenser sturio; (b) the genus Scaphirhynchus belongs to the Atlantic clade and is a sister group of the remaining species of the clade; and (c) the close relationship between P. kaufmanni and Acipenser stellatus is well supported.     

The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Characterization of four mitochondrial genomes of Crambidae (Lepidoptera,Pyraloidea) and phylogenetic implications

Loxostege turbidalis, Loxostege aeruginalis, Pyrausta despicata, and Crambus perlellus belong to Crambidae, Pyraloidea. Their mitochondrial genomes (mitogenomes) were successfully sequenced. The mitogenomes of L. turbidalis, L. aeruginalis, P. despicata, and C. perlellus are 15 240 bp, 15 339 bp, 15 389 bp, and 15 440 bp. The four mitogenomes all have a typical insect mitochondrial gene order, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one A + T rich region (control region). The PCGs are initiated by the typical ATN codons, except CGA for the cox1 gene. Most PCGs terminate with common codon TAA or TAG, the incomplete codon T is found as the stop codon for cox2, nad4, and nad5. Most tRNA genes exhibit typical cloverleaf structure, except trnS1 (AGN) lacking the dihydrouridine (DHU) arm. The secondary structure of rRNA of four mitogenomes were predicted. Poly-T structure and micro-satellite regions are conserved in control regions. The phylogenetic analyses based on 13 PCGs showed the relationships of subfamilies in Pyraloidea. Pyralidae, and Crambidae are monophyletic, respectively. Pyralidae comprises four subfamilies, which form the following topology with high support values: (Galleriinae + ((Pyralinae + Epipaschiinae)+ Phycitinae)). Crambidae includes seven subfamilies and is divided into two lineages. Pyraustinae and Spilomelinae are sister groups of each other, and form the “PS clade.” Other five subfamilies (Crambinae, Acentropinae, Scopariinae, Schoenobiinae, and Glaphyriinae) form the “non-PS clade” in the Bayesian inference tree. However, Schoenobiinae is not grouped with the other four subfamilies and located at the base of Crambidae in two maximum likelihood trees.     

Craniid brachiopods: aspects of clade structure and distribution reflect continental drift (Brachiopoda: Craniiformea)

We present maximum likelihood and Bayesian inference relative time‐tree analyses of aligned gene sequences from a worldwide collection of craniiform brachiopods belonging to two genera, Novocrania and Neoancistrocrania. Sequences were obtained from one mitochondrial and three nuclear‐encoded ribosomal RNA genes from varying numbers of specimens. Data‐exploration by network (splits) analyses indicates that each gene identifies the same divergent clades and (with one minor exception) the same inter‐clade relationships. Neoancistrocrania specimens were found only in the Pacific Ocean, near Japan, on the Norfolk and Chesterfield Ridges, and near the Solomon Islands. The Novocrania clades, in approximate order of increasing distance from the root comprise 1. a ‘Northern’ clade of animals collected in the NE. Atlantic, W. Mediterranean and Adriatic; 2. a ‘Tethyan’ clade comprising animals from the E. Mediterranean, Cape Verde islands and the Caribbean (Belize and Jamaica); 3. a ‘NE. Pacific’ clade containing animals from Vancouver Island and from localities near Japan and south of Taiwan; 4. a ‘Southern’ clade that contains two widely separated subclades, one from New Zealand and the other with an extraordinarily wide distribution, ranging from near Japan in the north to the Chesterfield Ridge and Solomon Islands in the West, and in the East to the Galapagos Islands, the coast of South America (Chile) and Richardson seamount (off South Africa) in the South Atlantic. To the South, members of this clade were found in the Weddell, Scotia and Bellinghausen Antarctic Seas. The root of the extant craniid radiation was previously found (by relaxed‐clock analysis) to lie on the branch connecting the two genera so that, in effect, the one clade of Neoancistrocrania serves to polarise evolutionary relationships within the several clades of Novocrania. As previously suggested, all results confirm that Neoancistrocrania is sister to the ‘Northern’ Novocrania clade, and this leads to a proposal that Neoancistrocrania represents one extreme of a wide range of variation in ancestral ventral valve mineralisation, speciation (～90 Ma) resulting from competitive exclusion in rapidly‐growing reef environments. To the extent possible, the identified molecular clades are correlated with named species of Novocrania. The reproductive and population biology of craniid brachiopods is not well known, but from available evidence they are considered to have low‐dispersal potential and, except in enclosed localities such as cold‐water fjords, to have small effective population sizes, features which are consistent with the observed divergent populations in well‐separated localities. Exceptionally slow craniid molecular (rDNA) evolution is suggested by the short branch of Novocrania where it has been used as an outgroup for large‐scale analyses of metazoans. Slow molecular evolution is also indicated by the existence of a distinct Tethyan clade, reflecting restricted dispersal at former times, and by the uniform, short, genetic distances and exceptionally wide geographical distribution of the Southern clade. Thus, the geographical distribution and phylogenetic divergence of craniid brachiopods is an example of phylotectonics, in which relationships revealed by phylogenetic analyses reflect opportunities for dispersal and settlement that were created by tectonic plate movements associated, in this case, with opening and closure of Tethys and the breakup of Gondwana. Molecular dating of craniid divergences and radiochemical dating of tectonic events thus illuminate one another. © 2014 The Linnean Society of London     

Phylogeny and systematics of mitriform gastropods (Mollusca: Gastropoda: Neogastropoda)

With about 800 Recent species, ‘miters’ are a widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo‐West Pacific. They include the two families Mitridae and Costellariidae, similar in shell morphology and traditionally treated as close relatives. Some genera of deep‐water Ptychatractidae and Volutomitridae are close to miters in shell morphology, and the term ‘mitriform gastropods’ has been introduced to refer to Mitridae, Costellariidae, and this assortment of convergent forms. The present study aimed at the reconstruction of phylogenetic relationships of mitriform gastropods based on representative taxon sampling. Four genetic markers [cytochrome c oxidase subunit I (COI), 16S and 12S rRNA mitochondrial genes, and H3 (Histone 3) nuclear gene] were sequenced for over 90 species in 20 genera, and the molecular data set was supplemented by studies of radula morphology. Our analysis recovered Mitridae as a monophyletic group, whereas the genus Mitra was found to be polyphyletic. Of 42 mitrid species included in the analysis, 37 formed a well‐supported ‘core Mitridae’ consisting of four major clades, three of them consistent with the subfamilies Cylindromitrinae, Imbricariinae, and Mitrinae, and Strigatella paupercula standing out by itself. Basal to the ‘core Mitridae’ are four minor lineages, with the genus Charitodoron recognized as sister group to all other Mitridae. The deep‐water family Pyramimitridae shows a sister relationship to the Mitridae, with high support for a Pyramimitridae + Mitridae clade. Our results recover the monophyly of the Costellariidae, which form a well‐supported clade that also includes Ptychatractidae, Columbariinae, and Volutomitridae, but not Mitridae. Most derived and diverse amongst Costellariidae are species of Vexillum, characterized by a bow‐shaped, multicuspidate rachidian tooth. Several previously unrecognized deep‐water costellariid lineages are revealed. Their members retain some plesiomorphies – in particular a tricuspidate rachidian tooth – that makes them morphologically intermediate between ptychatractids and Vexillum. The taxa of Ptychatractidae included in the analysis are not monophyletic, but form three well‐supported, unrelated groupings, corresponding respectively to Ceratoxancus + Latiromitra, Exilia, and Exiliodea. None of them shows an affinity to Pseudolividae. © 2015 The Linnean Society of London     

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades

Despite their ecological significance as decomposers and their evolutionary significance as the most speciose eusocial insect group outside the Hymenoptera, termite (Blattodea: Termitoidae or Isoptera) evolutionary relationships have yet to be well resolved. Previous morphological and molecular analyses strongly conflict at the family level and are marked by poor support for backbone nodes. A mitochondrial (mt) genome phylogeny of termites was produced to test relationships between the recognised termite families, improve nodal support and test the phylogenetic utility of rare genomic changes found in the termite mt genome. Complete mt genomes were sequenced for 7 of the 9 extant termite families with additional representatives of each of the two most speciose families Rhinotermitidae (3 of 7 subfamilies) and Termitidae (3 of 8 subfamilies). The mt genome of the well supported sister-group of termites, the subsocial cockroach Cryptocercus, was also sequenced. A highly supported tree of termite relationships was produced by all analytical methods and data treatment approaches, however the relationship of the termites+Cryptocercus clade to other cockroach lineages was highly affected by the strong nucleotide compositional bias found in termites relative to other dictyopterans. The phylogeny supports previously proposed suprafamilial termite lineages, the Euisoptera and Neoisoptera, a later derived Kalotermitidae as sister group of the Neoisoptera and a monophyletic clade of dampwood (Stolotermitidae, Archotermopsidae) and harvester termites (Hodotermitidae). In contrast to previous termite phylogenetic studies, nodal supports were very high for family-level relationships within termites. Two rare genomic changes in the mt genome control region were found to be molecular synapomorphies for major clades. An elongated stem-loop structure defined the clade Polyphagidae + (Cryptocercus+termites), and a further series of compensatory base changes in this stem-loop is synapomorphic for the Neoisoptera. The complicated repeat structures first identified in Reticulitermes, composed of short (A-type) and long (B-type repeats) defines the clade Heterotermitinae+Termitidae, while the secondary loss of A-type repeats is synapomorphic for the non-macrotermitine Termitidae.     

Morphology, molecules, and character congruence in the phylogeny of South American geophagine cichlids (Perciformes, Labroidei)

Phylogenetic relationships among the Neotropical cichlid subfamily Geophaginae were examined using 136 morphological characters and a molecular dataset consisting of six mitochondrial and nuclear genes. Topologies produced by morphological and combined data under parsimony were contrasted, congruence among different partitions was analysed, and potential effects of character incongruence and patterns of geophagine evolution on phylogenetic resolution are discussed. Interaction of morphological and molecular characters in combined analysis produced better resolved and supported topologies than when either was analysed separately. Combined analyses recovered a strongly supported Geophaginae that was closely related to Cichlasomatinae. Within Geophaginae, two sister clades included all geophagine genera. Acarichthyini (Acarichthys+Guianacara) was sister to the ‘B clade’, which contained the ‘Geophagus clade’ (‘Geophagus’steindachneri+Geophagus sensu stricto, and both sister to Gymnogeophagus) as sister to the ‘Mikrogeophagus clade’ (Mikrogeophagus+‘Geophagus’brasiliensis), and in turn, the Geophagus and Mikrogeophagus clades were sister to the crenicarine clade (Crenicara+Dicrossus) and Biotodoma. The second geophagine clade included the ‘Satanoperca clade’ (Satanoperca+Apistogramma and Taeniacara) as sister to the ‘Crenicichla clade’ (Crenicichla+Biotoecus). Several lineages were supported by unique morphological synapomorphies: the Geophaginae + Cichlasomatinae (5 synapomorphies), Geophaginae (1), Crenicichla clade (3), crenicarine clade (1), the sister relationship of Apistogramma and Taeniacara (4) and of Geophagus sensu stricto and‘Geophagus’steindachneri (1), and the cichlasomine tribe Heroini (1). Incorporation of Crenicichla in Geophaginae reconciles formerly contradictory hypotheses based on morphological and molecular data, and makes the subfamily the most diverse and ecologically versatile clade of cichlids outside the African great lakes. Results of this study support the hypothesis that morphological differentiation of geophagine lineages occurred rapidly as part of an adaptive radiation.     

Complete mitochondrial genome of Tubulipora flabellaris (Bryozoa: Stenolaemata): the first representative from the class Stenolaemata with unique gene order

Mitochondrial genomes play a significant role in the reconstruction of phylogenetic relationships within metazoans. There are still many controversies concerning the phylogenetic position of the phylum Bryozoa. In this research, we have finished the complete mitochondrial genome of one bryozoan (Tubulipora flabellaris), which is the first representative from the class Stenolaemata. The complete mitochondrial genome of T. flabellaris is 13,763 bp in length and contains 36 genes, which lacks the atp8 gene in contrast to the typical metazoan mitochondrial genomes. Gene arrangement comparisons indicate that the mitochondrial genome of T. flabellaris has unique gene order when compared with other metazoans. The four known bryozoans complete mitochondrial genomes also have very different gene arrangements, indicates that bryozoan mitochondrial genomes have experienced drastic rearrangements. To investigate the phylogenetic relationship of Bryozoa, phylogenetic analyses based on amino acid sequences of 11 protein coding genes (excluding atp6 and atp8) from 26 metazoan complete mitochondrial genomes were made utilizing Maximum Likelihood (ML) and Bayesian methods, respectively. The results indicate the monopoly of Lophotrochozoa and a close relationship between Chaetognatha and Bryozoa. However, more evidences are needed to clarify the relationship between two groups. Lophophorate appeared to be polyphyletic according to our analyses. Meanwhile, neither analysis supports close relationship between Branchiopod and Phoronida. Four bryozoans form a clade and the relationship among them is T. flabellaris + (F. hispida + (B. neritina + W. subtorquata)), which is in coincidence with traditional classification system.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes

With efficient sequencing techniques, full mitochondrial genomes are rapidly replacing other widely used markers, such as the nuclear rRNA genes, for phylogenetic analysis but their power to resolve deep levels of the tree remains controversial. We studied phylogenetic relationships of leaf beetles (Chrysomelidae) in the tribes Galerucini and Alticini (root worms and flea beetles) based on full mitochondrial genomes (103 newly sequenced), and compared their performance to the widely sequenced nuclear rRNA genes (full 18S, partial 28S). Our results show that: (i) the mitogenome is phylogenetically informative from subtribe to family level, and the per‐nucleotide contribution to nodal support is higher than that of rRNA genes, (ii) the Galerucini and Alticini are reciprocally monophyletic sister groups, if the classification is adjusted to accommodate several ‘problematic genera’ that do not fit the dichotomy of lineages based on the presence (Alticini) or absence (Galerucini) of the jumping apparatus, and (iii) the phylogenetic results suggest a new classification system of Galerucini with eight subtribes: Oidina, Galerucina, Hylaspina, Metacyclina, Luperina, Aulacophorina, Diabroticina and Monoleptina.     

Phylogenetic relationships within parrots (Psittacidae) inferred from mitochondrial cytochrome-b gene sequences

Blood and tissue samples of 40 individuals including 27 parrot species (15 genera; 3 subfamilies) were collected in Indonesia. Their phylogenetic relationships were inferred from 907 bp of the mitochondrial cytochrome-b gene, using the maximum-parsimony method, the maximum-likelihood method and the neighbor-joining method with Kimura two-parameter distance. The phylogenetic analysis revealed that (1) cockatoos (subfamily Cacatuinae) form a monophyletic sister group to other parrot groups; (2) within the genus Cacatua, C. goffini and C. sanguinea form a sister group to a clade containing other congeners; (3) subfamily Psittacinae emerged as paraphyletic, consisting of three clades, with a clade of Psittaculirostris grouping with subfamily Loriinae rather than with other Psittacinae; (4) lories and lorikeets (subfamily Loriinae) emerged as monophyletic, with Charmosyna placentis a basal sister group to other Loriinae, which comprised the subclades Lorius; Trichoglossus+Eos; and Chalcopsitta+ Pseudeos.     

Mitogenomic phylogeny of the Naticidae (Gastropoda: Littorinimorpha) reveals monophyly of the Polinicinae

The Naticidae is a species-rich family of predatory marine gastropods with substantial interspecific morphological diversity. The classification of the Naticidae has been traditionally based on morphology data, but the phylogenetic relationships within the family are debated due to conflicting molecular results, especially regarding the monophyly of subfamilies Polinicinae and Naticinae. To further resolve the phylogenetic controversies within the Naticidae, we undertake a phylogenetic approach using 14 newly sequenced complete or nearly complete (only lacking a control region) mitochondrial genomes. Both the maximum likelihood and Bayesian inference analyses supported monophyly of the Polinicinae, but paraphyly of the Naticinae due to the placement of the enigmatic genus Notocochlis. The ancestral character reconstruction suggests that the operculum, a character that currently defines the two subfamilies, evolved from an ancestor with a calcareous operculum in the evolutionary history of naticids. In addition, the chronogram estimates that naticids was originated in late Triassic (about 227 million years ago), consistent with previous hypotheses. Our study highlights the importance of using complete mitochondrial genomes while reconstructing phylogenetic relationships within the Naticidae. The evolution scenario of the naticid operculum contributes new insights into the classification of Naticidae.     

Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data

Extensive phylogenetic analyses of the updated sequence data of mammalian mitochondrial genomes were carried out using the maximum likelihood method in order to resolve deep branchings in eutherian evolution. The divergence times in the mammalian tree were estimated by a relaxed molecular clock of the mitochondrial proteins calibrated with multiple references. A Chiroptera/Eulipotyphla (i.e. bat/mole) clade and a close relationship of this clade to Fereuungulata (Carnivora+Perissodactyla+Cetartiodactyla) were reconfirmed with high statistical significance. However, a support for a monophyly of Fereuungulata relative to the Chiroptera/Eulipotyphla clade was fragile, and we suggest that the three branchings among Carnivora, Perissodactyla, Cetartiodactyla and Chiroptera/Eulipotyphla occurred successively in a short time period, estimated to be approximately 77Myr BP. The Chiroptera/Eulipotyphla divergence was estimated to roughly coincide with the Cretaceous-Tertiary boundary (65Myr BP). The monophyly of Rodentia, the Lagomorpha/Rodentia clade (traditionally called Glires), and the Afrotheria/Xenarthra clade were preferred over alternative relationships, but the supports of these clades were not strong enough to exclude other possibilities. Although several super-order taxa of eutherians were strongly supported by the analyses of the mitochondrial genome data, the branching order in the deepest part of the eutherian tree remained ambiguous from the data presently available.