线蛱蝶亚科蝶类部分类群线粒体COI基因的分子系统发生分析

以线粒体细胞色素氧化酶I（COI）基因作分子标记,对线蛱蝶亚科蝴蝶进行序列测定．序列分析的结果表明．经比对和处理后的序列总长度是645bp,其中有199个变异位点,147个简约信息位点;所编码的氨基酸序列中有18个变异位点,7个信息位点．A＋T平均含量为69．6％,G＋C平均含量为30．4％,碱基组成出现AT偏斜．以蛱蝶亚科及秀蛱蝶亚科物种为外类群,用NJ、MP及贝叶斯法重建了该亚科的系统发生树,探讨了它们主要类群间的系统发生关系．分子系统树显示,线蛱蝶亚科由以下3大支系：环蛱蝶族＋翠蛱蝶族、线蛱蝶族、丽蛱蝶族构成;其中,环蛱蝶族为单系群（NJ树也支持线蛱蝶族的单系性）;翠蛱蝶族与环蛱蝶族亲缘关系较近：丽蛱蝶族可能是该亚科较早分化出的一支．     

Revision of Phymatolithon purpureum (Hapalidiales,Rhodophyta) based on ultrastructural and molecular data

ABSTRACT

To elucidate the taxonomy and phylogeny of Phymatolithon purpureum (P. Crouan & H. Crouan) Woelkerling & L.M. Irvine, we observed the type specimens and fresh samples using SEM (ultra-morphology) and analysed DNA sequences. Phymatolithon purpureum was originally described as Lithothamnion purpureum P. Crouan & H. Crouan from Mingant, Brittany, France. Our molecular phylogenetic analyses using psbA and COI–5P regions placed our collections from Ireland, UK and France in a clade with ‘P. borealis W.H. Adey, J.J. Hernandez-Kantun & P.W. Gabrielson (MH252286)’ from Iceland and ‘uncultured Corallinales (GQ917711 and GQ917512)’ from Roscoff, Brittany, France, near the type locality of P. purpureum. We show that P. purpureum is conspecific with P. borealis and P. polymorphum f. papillatum (Foslie) Foslie based on morphology and molecular data. Also, although P. purpureum has been often confused with P. laevigatum (Foslie) Foslie because of their similar morphology (e.g. smooth surface and sunken tetra/bisporangial conceptacles), our molecular phylogenetic analyses indicate that P. purpureum and P. laevigatum are sister taxa. Our sequences from lectotype material of P. laevigatum and syntype material of Lithothamnion emboloides Heydrich are identical.     

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.     

基于线粒体ND1和16S rRNA基因序列探讨中国蝴蝶12科的系统发育关系(鳞翅目: 双孔次亚目: 蝶类)

对中国12科共32种代表蝶类的ND1基因和16S rRNA 基因进行了序列测定（包括新测30种ND1基因和9种16S rRNA基因）和比较分析, 同时采用邻接法、最大似然法和贝叶斯法构建了12科蝶类的系统发育树, 探讨了其高级分类群的系统发育关系。序列分析的结果显示: 经比对处理后的两个基因总长度为869 bp, 其中保守位点373个, 可变位点496个, 简约信息位点375个; A+T的平均含量为80.2％, 明显高于C+G的平均含量19.8％。分子系统树表明: 蛱蝶科不是单系群; 珍蝶类、斑蝶类和喙蝶类位于蛱蝶科内; 粉蝶科和凤蝶科具有共同祖先。据此建议: 绢蝶科应归入凤蝶科; 蚬蝶科归入灰蝶科; 珍蝶类、斑蝶类和喙蝶类作为蛱蝶科中的亚科, 眼蝶类从蛱蝶科中分离出来独立成科。另外, 环蝶类的系统分类地位还有待于进一步研究。     

基于线粒体ND2基因的中国斑翅蝗科部分种类分子系统学研究（直翅目：蝗总科）

本文的目的是通过对斑翅蝗科部分种类的线粒体ND2基因进行分析,重建斑翅蝗科昆虫的系统发育关系,并探讨分子系统发育关系和传统分类结果的异同。扩增并测定了我国斑翅蝗科10属16种蝗虫的线粒体ND2全基因1 023 bp的序列,对序列的碱基组成、转换颠换、系统发育信号等进行了分析。并基于ND2全基因序列数据,分别采用邻接法（NJ）、最简约法（MP）、最大似然法（ML）和贝叶斯法重建了10属16种蝗虫的系统发育关系。结果表明：斑翅蝗科蝗虫ND2全基因A+T含量平均为74.6%;痂蝗亚科和异痂蝗亚科没能得到区分,建议合并为一个亚科;而斑翅蝗亚科和飞蝗亚科的分类地位还存在争议。     

基于线粒体ND1和COI基因序列探讨锯眼蝶亚科主要类群的系统发生关系

测定了分布于中国的锯眼蝶亚科4族10属共20个种的线粒体ND1和COI基因的部分序列,结合从GenBank中获得的4个国外种类的同源序列,以凤蝶科的迪洛尔娟凤蝶(Allancatria deyrolle)、丝带凤蝶(Sericinus montela),以及娟蝶科的西猛娟蝶(Parnassius simonius)为外类群,通过邻接法、最大简约法、最大似然法和贝叶斯法重建了分子系统树,分析了该亚科内主要类群的系统发生关系。分析结果表明:帻眼蝶族和锯眼蝶族具有较近的亲缘关系;黛眼蝶族不是单系群,该族中的黛眼蝶属、荫眼蝶属与眉眼蝶族具有较近的亲缘关系,带眼蝶属、藏眼蝶属、毛眼蝶属和帕眼蝶属聚合为一个独立的支系,其中带眼蝶属和藏眼蝶属在所有的分析方法中均以100%的置信度(BP=100%,PP=1.00)相聚合,建议将它们合并为一属。     

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

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

Evolutionary insights into the North American Necturus beyeri complex (Amphibia: Caudata) based on molecular genetic and morphological analyses

Necturus beyeri (Caudata: Proteidae), as conceived by some, contains paedomorphic salamanders distributed from the Ochlockonee drainage of Florida to the Angelina drainage of Texas. Because these salamanders differ in color pattern and karyotype across their geographic range, we performed a phylogeographic analysis that included representatives from all major drainages as well as of all congeners. The mitochondrially encoded ND2 gene was used to infer phylogenetic relationships using Bayesian inference. Morphometrics of head shape were analyzed and included as an independent data set. Our work suggests that Necturus comprises 11 lineages. A basal split within the genus separates an ancestor of two Atlantic Coastal Plain species (Necturus lewisi and Necturus punctatus) from the ancestor of nine distinct Gulf Coastal Plain lineages. One lineage is consistent with Necturus alabamensis, a species currently recognized in the Black Warrior drainage of Alabama. Two lineages comprise Necturus maculosus, as historically recognized, and six lineages comprise N. beyeri, as recognized by some, each of which occupies a unique drainage. Both of these species are demonstrated to be paraphyletic. Head morphometrics show the same patterns as the mtDNA. Overall, lineages within Necturus exhibit an east‐to‐west progression of appearance on the phylogenetic trees. This pattern corroborates biogeographic hypotheses based on previous karyological work. Within N. beyeri, this progression separates a pattern class of two eastern lineages lacking bold spotting and possessing relatively small mean body lengths from a pattern class of four western lineages possessing bold spotting and larger mean body sizes. Thus, the two eastern lineages of N. beyeri are similar in color pattern and body size to N. punctatus either through retention of the ancestral color pattern and size for the genus or through convergent selection in eastern streams of the Gulf Coastal Plain.     

Molecular phylogeny of the higher taxa of Odonata (Insecta) inferred from COI, 16S rRNA, 28S rRNA,and EF1‐α sequences

In this study, we sequenced both two mitochondrial genes (COI and 16S rRNA) and nuclear genes (28S rRNA and elongation factor‐1α) from 71 species of Odonata that represent 7 superfamilies in 3 suborders. Phylogenetic testing for each two concatenated gene sequences based on function (ribosomal vs protein‐coding genes) and origin (mitochondrial vs nuclear genes) proved limited resolution. Thus, four concatenated sequences were utilized to test the previous phylogenetic hypotheses of higher taxa of Odonata via Bayesian inference (BI) and maximum likelihood (ML) algorithms, along with the data partition by the BI method. As a result, three slightly different topologies were obtained, but the BI tree without partition was slightly better supported by the topological test. This topology supported the suborders Anisoptera and Zygoptera each being a monophyly, and the close relationship of Anisozygoptera to Anisoptera. All the families represented by multiple taxa in both Anisoptera and Zygoptera were consistently revealed to each be a monophyly with the highest nodal support. Unlike consistent and robust familial relationships in Zygoptera those of Anisoptera were partially unresolved, presenting the following relationships: ((((Libellulidae + Corduliidae) + Macromiidae) + Gomphidae + Aeshnidae) + Anisozygoptera) + (((Coenagrionidae + Platycnemdidae) + Calopterygidae) + Lestidae). The subfamily Sympetrinae, represented by three genera in the anisopteran family Libellulidae, was not monophyletic, dividing Crocothemis and Deielia in one group together with other subfamilies and Sympetrum in another independent group.     

Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Approximately 1.7 kbp of mitochondrial DNA were sequenced from 29 individuals assignable to 11 Uromastyx species or subspecies and two other agamids. U. ocellata and U. ornata had an insertion between the glutamine and isoleucine tRNA genes, which could be folded into a stable stem-and-loop structure, and the insertion for U. ornata additionally retained a sequence similar to the glutamine tRNA gene. This corroborates the role of tandem duplication in reshaping mitochondrial gene arrangements, and supports the idea that the origin of light-strand replication could be relocated within mitochondrial genomes. Molecular phylogeny from different tree-building methods consistently placed African and Arabian taxa in mutually monophyletic groups, excluding U. hardwickii inhabiting India and Pakistan. Unlike previous studies based on morphology , U. macfadyeni did not cluster with morphologically similar Arabian taxa, suggesting convergent evolution to be responsible for the morphological similarities. Divergence times estimated among the Uromastyx taxa, together with geological and palaeontological evidence, suggest that the Uromastyx agamids originated from Central Asia during the Eocene and colonized Africa after its connection with Eurasia in the early Miocene. Their radiation may have been facilitated by repeated aridification of North Africa since the middle Miocene, and geological events such as the expansion of the Red Sea and the East African Rift Valley.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 247–260.     

Phylogenetic relationships and historical biogeography of tribes and genera in the subfamily Nymphalinae (Lepidoptera: Nymphalidae)

We infer for the first time the phylogenetic relationships of genera and tribes in the ecologically and evolutionarily well‐studied subfamily Nymphalinae using DNA sequence data from three genes: 1450 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 1077 bp of elongation factor 1‐alpha (EF1‐α) and 400–403 bp of wingless (both in the nuclear genome). We explore the influence of each gene region on the support given to each node of the most parsimonious tree derived from a combined analysis of all three genes using Partitioned Bremer Support. We also explore the influence of assuming equal weights for all characters in the combined analysis by investigating the stability of clades to different transition/transversion weighting schemes. We find many strongly supported and stable clades in the Nymphalinae. We are also able to identify ‘rogue’ taxa whose positions are weakly supported (the different gene regions are in conflict with each other) and unstable. Our main conclusions are: (1) the tribe Coeini as currently constituted is untenable, and Smyrna, Colobura and Tigridia are part of Nymphalini; (2) ‘Kallimini’ is paraphyletic with regard to Melitaeini and should be split into three tribes: Kallimini s.s., Junoniini and Victorinini; (3) Junoniini, Victorinini, Melitaeini and the newly circumscribed Nymphalini are strongly supported monophyletic groups, and (4) Precis and Junonia are not synonymous or even sister groups. The species Junonia coenia, a model system in developmental biology, clearly belongs in the genus Junonia. A dispersal‐vicariance analysis suggests that dispersal has had a major effect on the distributions of extant species, and three biotic regions are identified as being centres of diversification of three major clades: the Palaearctic for the Nymphalis‐group, the Afrotropics for Junoniini and the Nearctic for Melitaeini. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86 , 227–251.     

Surprising diversity in the Pannonian populations of Marsh Fritillary (Euphydryas aurinia,Lepidoptera: Nymphalidae): Morphometric and molecular aspects

Since genetic variation is the basis of evolutionary potential of a species, its structure needs to be understood. Thus, the aim of this study was to analyze and contrast the structure of genetic and phenotypic variation in the Euphydryas aurinia populations of southeastern central Europe. Genetic variation was studied by two types of molecular genetic markers: mtDNA COI sequences and allozymes. As the great hiatus in the European distribution of E. aurinia is located in the central part of the Carpathian Basin, we expected that the populations East and West to this gap would be highly differentiated. Populations of Central Transdanubia actually represent the easternmost margin of the West European distribution of E. aurinia. In view of the peripheral position of these populations, we supposed to find some genetic sign of local adaptation, as a consequence of diversifying selection and an increased level of fluctuating asymmetry as a result of environmental stress. The analyses of the molecular genetic markers revealed a basic East–West differentiation among the populations of southeastern central Europe which was further structured in the western part of the study area. The results suggested that the genetic differentiation between the two western regions is probably the consequence of diversifying selection. The pattern of phenotypic differentiation among the western populations, however, was different. A geographic cline was revealed (decreasing wing size) toward the eastern margin of the distribution in parallel with increasing fluctuating asymmetry. The conservation inferences of the results are considered.     

Phylogenetic relationships of the callitrichinae (Platyrrhini,Primates) based on β2‐microglobulin DNA sequences

The phylogenetic relationships of callitrichine primates have been determined by DNA sequence analyses of exons 1, 2, and 3 of the β₂‐microglobulin gene. Parsimony, distance, and maximum likelihood analyses of ca. 900 base pairs of 21 taxa, representing all callitrichine genera, indicated that Saguinus was the most basal offshoot. Within Saguinus, S. fuscicollis appeared as the first divergent lineage followed by an unresolved trichotomy formed by S. mystax/S. imperator, S. midas/S. bicolor, and S. oedipus. A second callitrichine lineage was formed by Leontopithecus; each of the three species studied showed identical nucleotide sequences. Callimico appeared as the sister taxon of Callithrix/Cebuella. Genetic distances within this latter group were very small, although a stronger association between Cebuella and species of the Callithrix argentata group was observed. The inclusion of Cebuella in the genus Callithrix is suggested. These studies indicated that tamarins are more plesiomorphic than marmosets in agreement with the phyletic dwarfism hypothesis. Am. J. Primatol. 48:225–236, 1999. © 1999 Wiley‐Liss, Inc.     

Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data

Representatives of the genus Praomys occur throughout the African intertropical zone. It is unclear how many species this genus contains, nor do we know the exact distribution ranges and phylogenetic relationships of these taxa. Using molecular (16S rRNA gene sequencing) and morphological (multivariate craniometry) analyses we clarify the taxonomy and phylogenetic relationships among the Praomys occurring in Africa's lowland tropical rainforests. We studied most species known from this area, based on specimens collected in seven countries (Guinea, Ivory Coast, Cameroon, Central African Republic, Gabon, Congo Republic and Democratic Republic of Congo). In our study, Praomys appears to be monophyletic. Our results identify two species complexes: the jacksoni complex includes at least two species ( P. jacksoni and P. mutoni ) and the tullbergi complex contains at least four species ( P. tullbergi , P. rostratus , P. misonnei , P. petteri ). Although the 16S rRNA gene appears insufficient to resolve the phylogenetic relationships among all the members of the tullbergi species complex, it is suitable for the identification of most of the studied species, and its use has allowed us to redefine the geographical limits of several species.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 539–553.     

Hymenidium pilosum (Apiaceae) is a synonym of H. apiolens based on morphology and molecular data

Hymenidium apiolens and H. pilosum have been recorded to co-occur in the Himalayas, and it was found difficult to distinguish between them in the field. In this study, we reconstructed the phylogeny and estimated the genetic distance between individuals of H. apiolens, H. pilosum and related species based on nuclear ITS sequences, and rpl16 and rps16 introns, to determine the relationship between H. apiolens and H. pilosum. The analyses suggest that H. apiolens and H. pilosum are nested together, and that the ratio of genetic distance between them is smaller than that between individuals of Chamaesium spatuliferum, Hansenia forbesii or Ligusticum acuminatum. Furthermore, we found similar morphological characteristics of bracteoles, rays, petals and mericarps in H. apiolens and H. pilosum. Consequently, both molecular and morphological evidence supports that Hymenidium pilosum is a synonym of H. apiolens.     

Phylogeny of "Philoceanus complex" seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences

The Philoceanus complex is a large assemblage of lice that parasitise procellariiform seabirds (petrels, albatrosses, and their relatives). We obtained mitochondrial 12S rRNA and cytochrome oxidase I DNA sequences from 39 species from diverse hosts and localities. Resolution of deeper relationships between genera was limited, however there is evidence for two major clades, one hosted by albatrosses, the other by petrels. Based on our results, the genera hosted by albatrosses are excellent candidates for detailed analysis of cospeciation. Our results also suggest that a previous estimate of a 5-fold difference in the relative rate of sequence evolution in lice and their avian hosts is an artefact of limited taxonomic sampling.     

Conformational flexibility and loss of structural rigidity for a model hexapeptide,GRGDTP: 1H‐NMR and molecular dynamics studies

The NMR and molecular dynamics methods are used to study the conformations of a hexapeptide, GRGDTP, which has been shown to be accessible to various types of cell‐adhesion based cellular behaviors such as cell‐to‐matrix interactions, cell differentiation, immunogenicity development, gene expression, angiogenesis, metastasis, sex determination and gamete fusion. ¹H‐NMR results indicate the existence of weak 5→2 hydrogen bonded β‐turn type‐III. Molecular simulation studies using a mixed protocol of distance geometry, constrained minimization, restrained molecular dynamics followed by energy minimization resulted additional conformations that include about 64% of population of inverse γ‐turn (HB, 3→1) and about 35% population of γ‐turn (HB, 4→2). The inter‐proton distances observed in γ‐and inverse γ‐turns are also consistent with the NMR constraints. The variable internal hydrogen bonding due to γ‐turns initiated at Gly 1 and Arg 2 , and its tendency to inter‐convert between γ‐and inverse γ‐turn conformations imply that the peptide is flexible in nature. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 460–471, 2013.