Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae)

Some aspects of the natural history of snakes of the colubrid genus Natrix have been well studied. With their extensive European distribution and relative abundance, their ecology, reproduction and behaviour are well known. Yet other facets of their biology remain poorly understood. These include knowledge of Natrix phylogeny, hypotheses explaining the current distribution of the three extant members of the genus, and their evolution and relationships. In this study we used molecular data, the nucleotide sequences of four protein-coding mitochondrial genes (3806 bp total), to provide a well-supported phylogeny for the genus Natrix . With these molecular data, evidence from the fossil record, and knowledge of palaeogeological events, we used two approaches in designing a time scale which we used to date the major events in Natrix speciation and intraspecific variation. Our data strongly support a phylogeny for the genus in which N. maura is basal with N. natrix and N. tessellata being sister species. The calibrated molecular clock suggests that N. maura diverged from the common ancestor of the three species 18–27 mya and that N. natrix and N. tessellata diverged 13–22 mya. Although the ranges of these estimates are large they support an early Miocene to late Oligocene origin for the three species. Intraspecific divergence is estimated to have commenced 5.3, 6.0 and 6.7 mya with evolutionary rates of 1 : 1.25 : 1.35% per million years for N. maura, N. natrix and N. tessellata , respectively.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 127–143.     

New insights into and limitations of the molecular phylogeny in the taxon-rich land snail genus Montenegrina (Mollusca: Gastropoda: Clausiliidae)

Rock-dwelling gastropods are usually patchily distributed in limestone habitats, presumably have low active and passive dispersal ability and often represent narrow-ranged endemic taxa. Their current taxonomy is predominantly shell morphology based, and it remains unknown whether the morphologically differentiated and geographically separated populations represent phylogenetic clades. In this study, we analysed the hyperdiverse, terrestrial door snail genus Montenegrina. Based on the current taxonomy defined by shell morphology, it contains 29 species and 106 subspecies distributed in the Balkan region. The constructed phylogenetic tree using three mitochondrial markers was used to test whether it agrees with the current taxonomy. In this comprehensive tree, about half of the species and subspecies are monophyletic. Some of the paraphylies could be reasonably resolved by taxonomic changes; that is, some subspecies should be reassigned or raised to species level. Other incongruencies probably arose due to introgression even between distant clades. The histone genes turned out to be unsuitable for elucidating the phylogeny of Montenegrina. In the species-delimitation tests, considerably more molecular operational taxonomic units were delimited than the number of presently described species. The present data indicate that (a) shell morphology-based taxonomy and taxon recognition can be problematic in such a large and morphologically highly variable genus; (b) the potential error due to incomplete sampling presents a problem in a genus as variable as Montenegrina; (c) multi-locus analyses should be conducted to arrive at a better basis for species delimitation; and (d) integrative approaches including genetic as well as morphological/anatomical data from a comprehensive geographic sample are necessary.     

The molecular phylogeny of the sea star Echinaster (Asteroidea: Echinasteridae) provides insights for genus taxonomy

In this study, we used sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and 16S rRNA, and one nuclear gene, 28S rRNA, to test the monophyly of the sea star genus Echinaster, and understand the phylogenetic relationships among species and subgenera within this genus. Phylogenetic analyses based on Bayesian inference and maximum likelihood methods revealed three clades with high values of genetic divergence among them (K2P distances for COI over 23%). One of the clades grouped all Echinaster (Othilia) species, and the other two clades included Echinaster (non‐Othilia) species and Henricia species, respectively. Although the relationships among Henricia, Othilia, and Echinaster could not be completely clarified, the Othilia clade was a well‐supported group with shared diagnostic morphological characters. Moreover, the approximately unbiased test applied to the phylogenetic reconstruction rejected the hypothesis of the genus Echinaster as a monophyletic group. According to these results, we suggest the revalidation of Othilia as a genus instead of a subgenus within Echinaster. Our study clarifies important points about the phylogenetic relationships among species of Echinaster. Other important systematic questions about the taxonomic classification of Echinaster and Henricia still remain open, but this molecular study provides bases for future research on the topic.     

The bee‐killing flies,genus Melaloncha Brues (Diptera: Phoridae): a combined molecular and morphological phylogeny

The phylogeny of the bee‐killing flies, genus Melaloncha Brues (Diptera: Phoridae) is analysed using six genes –cytochrome oxidase I, 16S ribosomal DNA, 12S ribosomal DNA, NADH1 dehydrogenase, 28S ribosomal DNA and CAD– plus 47 morphological characters. A total of 91 specimens, including eight out‐groups and 83 Melaloncha (representing 70 species) were included in the analyses. Parsimony analysis of the combined data set produced a single most parsimonious tree with varied Bremer and bootstrap support of interior nodes. Bayesian analysis of molecules only and of morphology + molecules produced trees largely in agreement with parsimony results, although with a few differences. Supported groups included subfamily Metopininae, genus Melaloncha, and subgenera Melaloncha s.s. and Melaloncha (Udamochiras) Enderlein. Within the subgenera, the previously recognized Melaloncha furcata, Melaloncha cingulata, Melaloncha ungulata and Melaloncha stylata groups were recovered, as well as some new groupings. The M. furcata group was placed as the sister group of other Melaloncha s.s., which is consistent with known host‐attacking behaviour.     

基于线粒体COI、COII和Cyt b基因的蚁属13种的分子系统学研究（膜翅目：蚁科：蚁亚科）

以线粒体mtDNA中的COI、COII及Cyt b基因序列为分子标记,对蚁属13种进行分析研究。结果表明,蚁属线粒体基因组成具有昆虫基因的普遍特征,如有明显的A+T偏向性,A、T密码子使用频率高等特点。基于蚁属线粒体基因进行遗传距离分析,并结合构建系统发育树,结果表明蚁属内各物种间遗传距离相差较小,遗传距离值基本在0.1以内,遗传距离较远的种发生在北京凹头蚁和掘穴蚁之间,蚁属内各种间分化与形态学研究结果基本一致。     

Development of the Osteocranium in Natrix natrix (Serpentes,Colubridae) Embryogenesis II: Development of the jaws,palatal complex and associated bones

Snakes differ from the other vertebrates with their hyperkinetic skull. To establish the developmental features of the skull bones, involved in prey capture and ingestion, the Grass snake Natrix natrix (Serpentes, Colubridae) embryos are studied at all the successive stages of embryogenesis. Thirty-five N. natrix embryos are examined. Twenty embryos are studied with histological methods; fifteen embryos are cleared and double-stained with alizarin red and alcian blue. The sequence of appearance and formation of the upper and lower jaw bones, palatal complex and associated bones is described in accordance with the table of developmental stages. New features in the ossification mode of some bones are revealed: each bone, namely, the vomer, septomaxilla and maxilla, is formed from three separate ossification centres. Three ossification centres in the maxilla, two ossification centres in the bodies of the septomaxilla and vomer, as well as the unknown additional ossification centre in the vomer had not been previously described in snake embryos. The new data can be used in further comparative research on the reptile skull development and vertebrate phylogeny.     

A molecular and morphological reassessment of the phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae)

The phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae) is investigated using molecular markers and morphological characters. We analysed the mitochondrial DNA CO1 and the nuclear 28S D2–D3 gene fragments for 74 species of Ophioninae from 25 out of the 32 recognized genera, which collectively represent 98% of described species diversity of the subfamily. Molecular markers were analysed separately and combined, with or without the adjunction of a matrix of 62 morphological characters using Bayesian inference. Our results reveal three distinct lineages, each including one of most speciose genera: Ophion, Enicospilus and Thyreodon. The comparison of the molecular data, and combined molecular plus morphological data led to the definition of the three tribes: Ophionini stat. rev. (Ophion + Alophophion + Rhopalophion + Xylophion + Afrophion); Enicospilini stat. rev. (Enicospilus + Laticoleus + Dicamptus + Hellwigiella); and Thyreodonini tribe nov. (Thyreodon + Dictyonotus + Rhynchophion). The possible association of other genera to one or another of these lineages is discussed. Ophion is a polyphyletic assemblage and requires a further revision to define the delimitation with close genera. The enigmatic Old World genus Skiapus is strongly supported as belonging to the Ophioninae, although its placement within the subfamily is ambiguous as a result of its derived genotype and phenotype. Finally, we propose a biogeographical scenario supported by this phylogeny and based on the limited available fossil data.     

A new species of the Southeast Asian genus Opisthotropis (Serpentes: Colubridae: Natricinae) from western Hunan,China

A new species of natricine snake of the Southeast Asian genus Opisthotropis Günther,1872 is described from western Hunan Province of China based on both mitochondrial DNA and morphological data.The new species is morphologically most similar and genetically most closely related to O.cheni Zhao,1999 and O.latouchii (Boulenger,1899),but possesses considerable genetic divergence (p-distance 5.1％-16.7％) and can be differentiated from all other congeners by a combination of the following morphological characters:(1) body size large (total length 514-586 mm) and strongly built;(2) dorsal scale rows 17 throughout,feebly keeled anteriorly and moderately keeled posteriorly;(3) ventral scales 147-152,subcaudal scales 54-62;(4) preocular absent,Ioreal elongated and touching orbit;(5) supralabials 8-9,fifth and sixth entering obit;(6) anterior temporals short,length 1.74-2.04 times longer than width;(7) maxillary teeth subequal,28-30;(8) dorsal surface of head with distinct irregular yellow stripes and markings edged with ochre;(9) body with clear black and yellow longitudinal streaks,partly fused to several lighter patches or thicker stripes anteriorly;and (10) venter pale yellow,with asymmetric blackish speckles along outer margin.We present an updated diagnostic key to all members of the genus Opisthotropis,and recommendations on the ecological study for the group are provided.     

Evolution of coloration, urotomy and coral snake mimicry in the snake genus Scaphiodontophis (Serpentes: Colubridae)

The Neotropical hinged-tooth, coral snake mimics of the genus Scaphiodontophis are characterized by extremely long and disproportionately thick tails that are extremely fragile. Both the coloration and tail structure are putative antipredator devices. While all examples have components of the coloration that match those of the venomous coral snakes (family Elapidae), the range of variation is extreme, leading to controversy on the status of various populations, including nine named taxa. Individual, ontogenetic and geographic variation in scutellation and head, body and tail coloration were analysed to evaluate population status and possible evolutionary trends based on a sample of 183 examples from Mexico, Central America and Colombia. Variation in subcaudal counts show population differences (higher in Mexico and upper Central America) but are not congruent with geographic variation in coloration. Generally snakes from north of Nicaragua and from central and eastern Panama have a pattern of dyads (black-light-black bands separating red bands), those from Atlantic slope Nicaragua to western Panama a pattern of monads (light-black-light bands separating the red ones) and those from Colombia have both pattern types on the same snake. The dyads and/or monads may be present the length of the body and tail, restricted to the anterior part of the body or on the entire body or on the anterior part of the body and on the tail. Two or more of these variants may occur at a single geographic locality or only a single one may be present. Head and nuchal colour patterns (Z, A, V and Du) are relatively consistent geographically. The Adantic slope Guatemala, Belize and Honduras population have the A pattern, those of Nicaragua, Costa Rica and western Panama the V pattern, and those in Colombia a Du pattern. Other populations have the Z coloration. Intermediate conditions in coloration of the body and tail and head and neck are found at localities intermediate between the main pattern types, indicating intergradation among adjacent populations. Consequently, we regard these snakes as representative of a single species, Scaphiodontophis annulatus Dumeril and Bibron and the eight other names applied to various populations and individuals as synonyms. Analysis of colour pattern leads us to the conclusion that the tricolour pattern evolved from a uniform one through a lineate-spotted condition (usually present on the non-tricolour portions of the snake) through a bicolour red and black pattern to the dyadal condition. The monadal pattern in turn was derived from the dyadal one. The data further indicates that tricolour components first appeared anteriorly and progressively expanded posteriorly. The evolutionary sequence for the head and nuchal pattern appears to be A → Z → V → Du S. annulatus has a series of jaw and tooth specializations designed for rapid processing of hard-bodied prey found during diurnal foraging in the leaf-litter. Urotomy in this species involves intervertebral tail-breakage (pseudoautotomy) without regeneration. Evidence is presented supporting the long-tail multiple break hypothesis as applicable to Scaphiodontophis and other snakes with similar tail morphology (specialized pseudoautotomy). This is in contrast to snakes with similar tail morphology (specialized pseudoautotomy). This is in contrast to Coniophanes and other snakes with a high incidence of urotomy having long but unspecialized tails (unspecialized pseudoautotomy) without multiple breaks over time. All Scaphiodontophis colour patterns have a general resemblance to that of venomous coral snakes and offer protection from generalizing predators having innate or other triggered responses to coral snake colours. The aposematic effect is enhanced by tail thrashing and head twitching behaviours. The characteristic foraging pose of S. annulatus, which tends to expose the head and anterior body, makes even the incomplete tricolour pattern effective as an antipredator defence. No evidence supports the idea that tail thrashing or the incomplete tricolour pattern directs the predator attacks to the tail to expedite pseudoautotomy. Coral snake mimicry and specialized pseudoautotomy are shown not to be co-evolved and pseudautotomy seems to have evolved long before mimetic coloration in this genus.     

A new genus and species of opisthogonimid (Digenea) of Liophis anomalus (Serpentes: Colubridae) from Uruguay

During a study on the helminth fauna of Liophis anomalus specimens deposited in the Reptile Collection of the Secci6n Zoología Vertebrados, Facultad de Ciencias, Uruguay, a new genus of Opisthogoniminae was found. Paracotyletrema n. gen. is described from the buccal cavity and esophagus of specimens from Departamento de Flores, Uruguay. This new genus differs from the other 2 Opisthogoniminae, Opisthogonimus and Westella, by having much smaller body size; maximum width at level of posterior end of oral sucker; oral sucker length more than one-fourth of body length; oral sucker and acetabulum separated by a distance of about the diameter of pharynx; cirrus pouch length more than half of body length; and testes in completely coincident zones. The type and only species, Paracotyletrema poncedeleoni n. gen., n. sp., is defined by the following diagnostic characters: mean oral sucker length one-third to one-half of body length; cirrus pouch of about body length, contorted, mainly acetabular; large, round testes in nearly adjacent fields, and an ovary nearly adjacent to right testis. Besides the type locality, Paracotyletrema poncedeleoni has been found in L. anomalus specimens from the Departamentos of Artigas and Treinta y Tres; therefore, it has a widespread distribution in Uruguay.     

基因序列在蚜虫分子系统发育研究中的应用

总结了核基因和线粒体基因在半翅目蚜虫分子系统发育研究中的应用。核基因中EF-1α应用最广泛,适用于探讨属级及属以上的问题; 核rDNA在蚜虫中应用较少,18S rDNA适用于探讨科级以上高级阶元的问题;LWO是新近在蚜虫中开发使用的一个新基因。线粒体基因中,COⅠ/COⅡ使用最多,12S rDNA/16S rDNA、ND1、Cyt b以及F-ATP6均有应用,探讨的问题从属、种级到科级不等。核基因和线粒体基因间以及不同线粒体基因间的联合分析在解决不同层次的问题中均有应用。建议不断尝试新基因以找出适合蚜虫类群的“标准基因”。并对未来蚜虫分子系统发育研究趋势进行了展望。     

Species delimitation in the Andean grasshopper genus Orotettix Ronderos & Carbonell (Orthoptera: Melanoplinae): an integrative approach combining morphological,molecular and biogeographical data

The reciprocal illumination nature of integrative taxonomy through hypothesis testing, corroboration and revision is a powerful tool for species delimitation as more than one source has to support the hypothesis of a new species. In this study, we applied an integrative taxonomy approach combining molecular and morphological data sets with distributional patterns to examine the level of differentiation between and within the grasshopper Orotettix species. Orotettix was described based on five valid species distributed in the Andes of Peru. In our study, initially a molecular‐based hypothesis was postulated and tested against morphological data and geographical patterns of distribution. Results from molecular and morphological analyses showed agreement among the species delimitation in Orotettix, and were also consistent with the geographical distribution. The analyses allowed us to delimit five new species for the genus ( O. lunatus sp. nov. , O . astreptos sp. nov. , O. colcaensis sp. nov. , O . paucartambensis sp. nov. and O . dichrous sp. nov. ) from the Eastern and Western Cordilleras of Peru. We also provide critical knowledge on the phylogenetic relationships and distribution of the genus and conduct a revision of Orotettix. © 2015 The Linnean Society of London     

A comprehensive phylogeny of the bumble bees (Bombus)

Bumble bees ( Bombus Latreille) occupy a wide diversity of habitats, from alpine meadows to lowland tropical forest, yet they appear to be similar in morphology throughout their range, suggesting that behavioural adaptations play a more important role in colonizing diverse habitats. Notwithstanding their structural homogeneity, bumble bees exhibit striking inter- and intraspecific variation in colour pattern, purportedly the outcome of mimetic evolution. A robust phylogeny of Bombus would provide the framework for elucidating the history of their wide biogeographical distribution and the evolution of behavioural and morphological adaptations, including colour pattern. However, morphological studies of bumble bees have discovered too few phylogenetically informative characters to reconstruct a robust phylogeny. Using DNA sequence data, we report the first nearly complete species phylogeny of bumble bees, including most of the 250 known species from the 38 currently recognized subgenera. Bayesian analysis of nuclear (opsin, EF-1α, arginine kinase, PEPCK) and mitochondrial (16S) sequences results in a highly resolved and strongly supported phylogeny from base to tips, with clear-cut support for monophyly of most of the conventional morphology-based subgenera. Most subgenera fall into two distinct clades ( short-faced and long-faced ) associated broadly with differences in head morphology. Within the short-faced clade is a diverse New World clade, which includes nearly one-quarter of the currently recognized subgenera, many of which are restricted to higher elevations of Central and South America. The comprehensive phylogeny provides a firm foundation for reclassification and for evaluating character evolution in the bumble bees.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 161–188.     

莽山后棱蛇Opisthotropis cheni Zhao, 1999的再描述(Serpentes:Colubridae)

作者于1999年根据湖南宦章莽山标本发表新种莽山后棱蛇Opisthotropis cheni的鉴别特征,现对该蛇加以详细描述。莽山后棱蛇足小形水栖蛇,全长500～600mm,尾长占全长的五分之一左右,身体圆柱形,头较小,与颈区分不明显。鼻间鳞前端窄,鼻孔背侧位;眼小,背侧位;前额鳞单枚,甚宽,其两外侧扩展至头侧;颊鳞长,后端人眶;无眶前鳞,眶后鳞2;颞鳞1＋2（1）;上唇鳞8（3-2-3）为主;下唇鳞10,前4或5枚接前颔片;颔片2对,前对约为后对长的2倍。背鳞通身17行,除最外行其余微棱,腹鳞159～167．肛鳞二分,尾下鳞55～59对。背面暗橄榄褐色,体侧具多数淡黄色横斑,左右横斑彼此交错或在背中线相连;腹面色白或偶有灰点斑。雄性头腹前端鳞片（如颏鳞、颔片和前4～5对下唇鳞）上有多数疣粒,雌性则无。此蛇见于山溪或小河流水中,白昼隐藏于岩洞、石下、沙砾或杂草间,晚上或黄昏外出活动觅食,共采到5号标本,其叶14号均采于晚上20～22点之间,1号采于18点左右;被捕捉的蛇离水后两三天就死掉。此蛇也曾见于农耕地灌溉渠旁的杂草中。 山     

Phylogeny of ground beetles subgenus Nialoe (s. lat.) Tanaka (Coleoptera: Carabidae; genus Pterostichus): A molecular phylogenetic approach

We constructed a phylogeny of the ground beetle subgenus Nialoe ( s. lat. ), genus Pterostichus (Coleoptera: Carabidae) based on two mitochondrial (cytochrome oxidase I and 16S ribosomal DNA) and one nuclear (28S ribosomal DNA) gene sequences. Thirty-three representative species of the group and three outgroup species were analyzed. The resultant trees (maximum parsimonious, maximum likelihood and Bayesian trees of the combined data of the three gene sequences) indicated that there are two large and three small lineages in the group, some of which were supported by a previous morphology-based phylogeny. In all the analyses, the small lineage composed of two Korean species is sister to the rest of the subgenus, but relationships of other four lineages differed among the analyses and remained unresolved. The implications of the present results are discussed in terms of taxonomy and biogeography of the group.     

Phylogeny,phylogeography, and systematics of the American pea crab genus Calyptraeotheres Campos, 1990, inferred from molecular markers

We used mitochondrial cytochrome oxidase I (COI) and the large ribosomal subunit (16S) genes to establish evolutionary relationships amongst species of Calyptraeotheres, evaluate their usefulness as DNA‐barcoding genes, and assess molecular diversity at the population level within Calyptraeotheres garthi. Bayesian, maximum likelihood, and maximum parsimony phylogenies confirmed the monophyly of Calyptraeotheres, showing that the ancestor of C. garthi, Calyptraeotheres hernandezi, and Calyptraeotheres granti radiated after the formation of the Panamanian isthmus. This finding contradicts the austral/tropical hypothesis previously proposed based on morphological data. The COI and 16S distance matrices supported separation of species as well as the genera, and corroborated that DNA barcoding is a useful tool and complements the classical taxonomy in Pinnotheridae. Phylogenetic and genetic distance analyses suggested that C. hernandezi is a junior synonym of C. garthi. Finally, C. garthi did not show a population structure across its distribution range, and showed a pattern consistent with a recent population expansion event that began 230–300 Kya. © 2013 The Linnean Society of London     

基因序列在金龟总科(Scarabaeoidea)分子系统学研究中的应用

基因序列分析是揭示金龟总科系统发育关系的重要工具。统计了应用于金龟总科中13个科的线粒体和核基因序列,综述了COⅠ、16S rRNA、28S rRNA、18S rRNA等基因序列在金龟总科分子系统学研究的新进展,探讨了不同基因序列在分类鉴定、隐存种发现、系统发育关系重建等方面的作用,对未来研究趋势进行了展望,为进一步阐明金龟总科系统发育机制奠定基础。     

A revised classification of the genus Matrona Selys, 1853 using molecular and morphological methods (Odonata: Calopterygidae)

An extensive review of the genus Matrona is presented based on mitochondrial (COI) and nuclear (ITS) sequences from 150 samples which cover all the known taxa of this genus. The separation of two main clades (oreades group: M. oreades, M. corephaea and M. taoi; basilaris group: M. basilaris, M. nigripectus, M. cyanoptera, M. japonica and M. annina) is strongly supported. The classification of all traditional recognized species is confirmed. The Hainan population separates very well from mainland M. basilaris populations, which is also confirmed by geometric morphometric analysis of wing shape. Given the implications of the molecular analysis the genus Matrona is grouped into two subgenera: subgen. Matrona (type species M. basilaris) and D ivortia subgen. nov. (type species M. oreades). A new species, M . ( M .) mazu sp. nov. , from Hainan is described. Brief taxonomic notes on the nine recognized species of the genus are given. Lectotype designations of M. basilaris and M. nigripectus are published. © 2015 The Linnean Society of London     

Chromosomal studies on five species of the genus Leptodactylus Fitzinger, 1826 (Amphibia, Anura) using differential staining

Cytogenetic studies were carried out on five species of Leptodactylus, namely L. fuscus, L. notoaktites, L. labyrinthicus, L. ocellatus, and L. podicipinus, after standard staining, Ag-NOR and C-banding as well as BrdU incorporation for three of them. The species had 2n = 22 chromosomes and two basic karyotype patterns. Chromosome 8 was a marker bearing a secondary constriction. In all species, this secondary constriction corresponded to the Ag-NOR site. The species had centromeric C-bands in all chromosomes of the complement, but some interstitial or telomeric bands seemed to differentiate some karyotypes, either at the species or the population level. In L. ocellatus, the C-banding pattern confirmed the occurrence of a heteromorphic pericentric inversion in chromosome 8 in specimens from one of the populations. The BrdU incorporation technique showed no detectable difference in the replication patterns of the major bands in the chromosomes of L. notoaktites, L. labyrinthicus, and L. ocellatus.