Genetic Divergence and Phylogenetic Relationships in Grey Mullets (Teleostei: Mugilidae) Using Allozyme Data

Genetic divergence and phylogenetic relationships among five species of the Mugilidae family (Liza saliens, Liza aurata, Liza ramada, Chelon labrosus, and Mugil cephalus) were investigated, in the present study, on samples taken from Messolongi lagoon in Greece, using allozyme electrophoresis. Ten enzymic systems corresponding to 22 genetic loci were assayed, among which, four were found to be polymorphic in Liza saliens, Liza aurata, and Chelon labrosus, seven in Liza ramada, while only two were polymorphic in Mugil cephalus. Several loci showed different electrophoretic patterns among the species and thus, they can be useful in species taxonomy as diagnostic markers, as well as for further evolutionary studies. It must be underlined that among them the aGPD-2* locus proved to be species-specific, while the other ones can be also used in various combinations for the same purpose. The observed heterozygosity was found to range from 0.020 to 0.051. Allele frequencies of all loci were used to estimate Nei's (1972) genetic distance, which was found to range between 0.249 and 1.171 among the five species studied. UPGMA and NJ trees, obtained by genetic distance matrix methods, as well as, a tree based on the discrete character parsimony analysis were found to exhibit the same topology. Our result show that the three species of the genus Liza are clustered together, Chelon labrosus being closer to the previous clade, while Mugil cephalus being more distinct.     

松毛虫属（Dendrolimus) 部分种类亲缘关系与遗传分化的等位酶分析

采用等位酶聚丙烯酰胺凝胶电泳技术对松毛虫属5个种和亚种的野生种群进行了亲缘关系和遗传变异的研究.8种等位酶系统(乳酸脱氢酶LDH、苹果酸脱氢酶MDH、苹果酸酶ME、乙醇脱氢酶ADH、甲酸脱氢酶FDH、谷氨酸脱氢酶GDH、过氧化物酶POD、过氧化氢酶CAT)共检测到12个基因位点,其中6个位点为多态位点,检测到15个等位基因.松毛虫属5个种和亚种的总体水平多态位点比率P＝50%,平均有效基因数A = 1.917,平均期望杂合度He =0.267,平均遗传距离为0.0730～0.5701.遗传参数表明松毛虫属昆虫种间存在较高程度的遗传变异,聚类图和遗传距离数据表明赤松毛虫与马尾松毛虫亲缘关系最近,落叶松毛虫与思茅松毛虫亲缘关系最远.     

Phylogenetic relationships of mullets (Mugilidae) in China Seas based on partial sequences of two mitochondrial genes

Phylogenetic analyses of Mugilidae species from the China coast were carried out based on 16S and 12S rRNA mitochondrial gene sequences by maximum parsimony, maximum likelihood, Bayesian inference and neighbor joining analysis in the present study. The results suggested that Mugil cephalus is the most genetically divergent species among the Mugilidae. The four Liza species clustered together and formed a monophyletic group. The genera Osteomugil showed closer affiliation with Valamugil than with Ellochelon; these three genera then grouped together to form a monophyletic clade presenting as the sister group to Liza. Analyses of phylogenetic and genetic distance indicated that Southern and Northern lineages of Liza haematocheila may be two different species; likewise, strong genetic divergence existed between Southern and Northern M. cephalus lineages. In addition, our results supported the Southern origin of Chinese Mugilids, which is contrary to the hypothesis based on morphological characters.     

Mitochondrial DNA divergence and phylogenetic relationships in mullets (Pisces: Mugilidae) of the Sea of Japan and the Sea of Azov revealed by PCR-RFLP-analysis

Three Mugilid species: Mugil cephalus (Linnaeus, 1758) and Liza haematocheila (Temminck et Schlegel, 1845; syn. Mugil soiuy, M. haematocheilus, L. soiuy, Chelon haematocheilus) from the Sea of Japan, as well as M. cephalus and Liza aurata (Risso, 1810) from the Sea of Azov were investigated on the basis of PCR-RFLP analysis of mitochondrial DNA (mtDNA) fragments, which included 12S/16S rRNA, and ND3/ND4L/ND4 genes. Among 61 individuals of three Mugilid species thirteen different haplotypes were detected. Eight and thirteen restriction endonucleases were found to be species-specific in 12S/16SrRNA and ND3/ND4L/ND4 respectively. This method may be useful for species identification. M. cephalus showed the largest genetic divergence while L. haematocheila and L. aurata were closely related and clustered together. The level of mtDNA differentiation between the two M. cephalus samples from the Sea of Japan and the Sea of Azov, i.e., nucleotide substitutions of approximately 3%, appeared to be relatively high.     

Allozyme variation and genetic relationships among species in the Carex willdenowii complex (Cyperaceae)

A taxonomic study by Naczi, Reznicek, and Ford (American Journal of Botany, 85, 434-447, 1998) has determined that three species (Carex willdenowii, C. basiantha, and C. superata) can be recognized within the C. willdenowii complex. To determine the amount of genetic divergence within and between these species, allozyme analyses were conducted on 14 populations distributed from Pennsylvania to eastern Texas. Seventeen loci were surveyed, 13 of which were polymorphic, with all populations being polymorphic at one or more loci. Interspecific genetic identities ranged from 0.560 (C. willdenowii and C. basiantha) to 0.807 (C. basiantha and C. superata). Alleles for the isozymes Aat-1, Dia-1, Idh-2, Mdh-2, Per-1, Pgm-1, and Pgm-2 served to distinguish C. willdenowii from C. basiantha and C. superata. Carex basiantha and C. superata were recognized by alleles of Mdh-2, Pgm-1, and Tpi-2. The genetic identities of populations within species were high and exceeded 0.957. A caespitose growth habit and perigynia in close proximity to the staminate flowers suggest adaptations for selfing and therefore low levels of heterozygosity. Paradoxically, the values for expected heterozygosities (Hexp) were always lower than those obtained by direct count (Hobs): F values were highly negative, indicating heterozygous excess. Disassortative mating and selection are discussed as possible mechanisms for maintaining heterozygous excess within populations.     

Genetic differentiation of white sea bream within the Lion's Gulf and the Ligurian Sea (Mediterranean Sea)

An allozymic study was conducted on 190 individuals of white sea bream, Diplodus sargus sampled on five locations throughout the Lion's Gulf and the Ligurian Sea (Mediterranean Sea), in order to identify genetic structure. Electrophoretic surveys carried out on muscle and liver tissues identified 25 loci of which 12 were polymorphic ( P 0.95). G -test analysis shows significant differences on allelic frequencies between the five stations at six loci. Examination of the spatial structure was performed using Nei's distances and F statistics, and indicated significant genetic differences between three groups. A group which clustered Blanes (Spain), Marseille (France) and Livorno (Italy) where the absence of genetic difference can be explained by migration of larvae and adults along a coastal 'continuum'. The Elba sample (Italy) shows genetic divergence from other samples and this difference may result from isolation due to limited migration of larvae and adults. Banyuls (France), differs from all other stations. Several hypotheses are proposed to explain genetic patterns including local current systems, larval dispersal, geographic isolation and historical effects, and variation in the size classes of sampled individuals between sites.     

采用SSR和RAPD标记研究黄瓜属（葫芦科）的系统发育关系

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

基于Cytb基因序列探讨蝽亚科11种昆虫的系统发育关系

对蝽亚科6属11种昆虫线粒体DNA细胞色素b基因部分序列进行PCR扩增和序列测定。比较其同源性,统计密码子使用频率并应用生物学软件构建分子系统树。在获得的432bp序列中,碱基T,C,A和G的平均含量分别是38．1,18．2,31．9和11．8％,表现出强烈的AT偏向性;就每个氨基酸密码子来看,第3位点的A＋T含量较高,达到85．5％。该序列片段中共有162个核甘酸位点发生变异（约占37．5％）,种间序列差异范围为0．9％～19．4％,平均为16．6％,变异较大。以筛豆龟蝽Megaeopta cribraria为外群,通过多种方法构建的系统发育树拓扑结构一致,这6属11种昆虫大致形成4个分支：珀蝽属、碧蝽属、菜蝽属3属的关系最接近,形成一个分支;真蝽属的3种聚为1支,与第1支形成姊妹群;曼蝽属的2种形成1支;麻皮蝽位于系统树的基部,为分化较早的1支,是蝽亚科中较为原始的类群。     

A new species of Saturnius Manter, 1969 (Digenea: Hemiuridae) from Mediterranean mullet (Teleostei: Mugilidae)

A new hemiurid digenean, Saturnius gibsoni n. sp., is described from the stomach lining of Mugil cephalus L. off Oran, Mediterranean coast of Algeria. Characteristic morphological features of the new species include small size of the body which is comprised of six pseudosegments, small ventral sucker, weakly developed mound-shaped flange at the level of the ventral sucker, and eggs being large in relation to the size of the body. Saturnius gibsoni n. sp. resembles S. minutus Blasco-Costa, Pankov, Gibson, Balbuena, Raga, Sarabeev & Kostadinova, 2006 and two unidentified Saturnius spp. in the small size of the body and most metrical features. However, in spite of the presence of five transverse septa resulting in six pseudosegments and the range overlap of some metrical features, the ventral sucker in S. minutus is much larger, the ventral sucker muscular flange is more prominent, the last pseudosegment is narrower in relation to body width and more rounded, and the eggs are smaller (mean 21 × 10 vs 25 × 12 μm). Furthermore, the partial sequences of the 28S rRNA gene region (domains D1–D3; 1,195 nt) obtained from two isolates of S. gibsoni n. sp. differed by 11 nt (0.9%) from that of S. minutus. Both unidentified forms of Saturnius are clearly distinguishable from S. gibsoni n. sp. by the presence of six stout, transverse muscular septa, forming seven pseudosegments (vs five septa forming six pseudosegments). Bayesian inference analysis of partial 28S rDNA sequences based on a total of 15 species from the families Hemiuridae and Lecithasteridae depicted the Bunocotylinae Dollfus, 1950 as a strongly supported basal clade, with Bunocotyle progenetica (Markowski, 1936) as the closest sister taxon to Saturnius spp.     

9种石斑鱼遗传多样性和系统发生关系的微卫星分析

利用实验室克隆的13个青石斑鱼微卫星分子标记, 对中国南海海域9种石斑鱼(青石斑鱼、蜂巢石斑鱼、鲑点石斑鱼、黑边石斑鱼、鞍带石斑鱼、赤点石斑鱼、七带石斑鱼、斜带石斑鱼和棕点石斑鱼)进行了遗传多样性和系统发生关系的分析。研究结果显示, 13个微卫星标记共检测到了84个等位基因, 9种石斑鱼中的平均等位基因数、平均多态信息含量(PIC)、平均观测杂合度(Ho)、平均期望杂合度(He)和平均Hardy-Weinberg遗传偏离指数(D)分别在2.69~5.38、0.1976~0.4267、0.4615~0.6239、0.3510~0.4754和0.1097~0.2836之间变动, 说明9种石斑鱼的遗传多样性都处于中等水平。用NJ法进行聚类分析的结果将9种石斑鱼分为3个支系：斜带石斑鱼、棕点石斑鱼和鞍带石斑鱼为第1支; 青石斑鱼、赤点石斑鱼和七带石斑鱼为第2支系; 蜂巢石斑鱼、黑边石斑鱼和鲑点石斑鱼为第3支系, 该支系与第2支系的关系较近。本研究支持将宽额鲈(鞍带石斑鱼)归入石斑鱼属。     

Evolutionary relationships of two balitorids (Cypriniformes,Balitoridae) revealed by comparative mitogenomics

Balitoridae, a family within the Cypriniformes, inhabit torrential mountain streams in Asia. Although they have long fascinated ichthyologists for their numerous adaptations to this tumultuous environment, the evolutionary history of this group remains poorly understood. In this study, we investigate the evolutionary relationships of the balitorids with particular attention to the phylogenetic placement of two balitorid species, Yaoshania pachychulis and Erromyzon kalotaenia. Both species have extremely limited distributions, they are limited to Mt. Dayaoshan of the Pearl River in China and require dedicated conservation plans. However, little is known about their evolutionary relationships to other balitorids. Here, we examined the evolutionary relationships of Y. pachychulis and E. kalotaenia to each other and other balitorids through sequencing the complete mitochondrial genomes of nine balitorid individuals. For the newly sequenced balitorids, the length of the whole mitogenome, gene arrangement and their base composition are similar to those of other bony fishes. Analyses based on these newly sequenced mitogenomes and an additional 50 previously published mitogenomes show that Y. pachychulis and E. kalotaenia cluster as different clade within the subfamily Gastromyzontinae. The genetic distance between these two species ranges from 0.127 ± 0.003 to 0.132 ± 0.004 which is slightly higher than that between some genera (e.g. the distance between Vanmanenia and Metahomaloptera is 0.127 ± 0.004). Therefore, it is reasonable to assign Y. pachychulis and E. kalotaenia to different genera. Phylogenetic signal assessment suggested that ND1, ND4 and ND5 genes as well as their concatenated subsets perform relatively well in reconstructing the Cobitoidea phylogeny. The divergence time estimation indicated that the balitorids distributed in Mt. Dayaoshan might have originated and evolved following the flattening and uplifting of the Yunnan–Guizhou Plateau during the late Miocene to late Pliocene.     

Phylogenetic relationships amongHomo sapiens and related species based on restriction site variations in rDNA spacers

A rapid method, using 12 restriction enzymes, was employed to analyze variations in ribosomal DNA (rDNA) spacers in a study of phylogenetic relationships betweenHomo sapiens and related species. We mapped restriction sites in the external and internal spacer regions and compared the arrangements of sites. The estimated sequence divergence betweenHomo sapiens andPan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus, Hylobates lar, H. agilis, andMacaca fuscata was 2.7, 2.3, 3.8, 7.3, 6.8, 7.8, and 14.1%, respectively. The genetic relationships inferred from these distances generally correspond to those inferred from analyses of other molecular markers in the literature. The divergence betweenH. lar andH. agilis and betweenH. lar andH. syndactylus was 0.34 and 2.4%, respectively.This study was supported in part by Grants-in-Aid for Scientific Research from the Ministry of Education, Science and Culture, Japan, and also by the Cooperative Research Program of the Primate Research Institute, Kyoto University.     

红豆杉科植物RAPD分析及其系统学意义

利用随机扩增多态性ＤＮＡ（ＲＡＰＤ）技术分析了红豆杉科（Ｔａｘａｃｅａｅ）红豆杉属（Ｔａｘｕｓ）、白豆杉属（Ｐｓｅｕｄｏｔａｘｕｓ）、穗花杉属（Ａｍｅｎｔｏｔａｘｕｓ）和榧树属（Ｔｏｒｒｅｙａ）的６种植物：红豆杉（Ｔａｘｕｓ ｃｈｉｎｅｎｓｉｓ （Ｐｉｌｇｅｒ）Ｒｅｈｄ）、南方红豆杉（Ｔａｘｕｓ ｃｈｉｎｅｎｓｉｓ ｖａｒ．ｍａｉｒｅｉ（Ｌｅｍｅｅ ｅｔＬｅｖｌ．）Ｃｈｅｎｇ ｅｔＭａｉｒｅＹｅｗ     

Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships

Pinus L. is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms. However, our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny. Thus, we analyzed the sequences of 97 Pinus plastid genomes, including four newly sequenced genomes and 93 previously published plastomes, to explore the evolution and phylogenetic relationships in the genus Pinus. The complete chloroplast genomes of Pinus species ranged in size from 109 640 bp (P. cembra L.) to 121 976 bp (P. glabra Walter), and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms. We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983 (44%), followed by tandem repeats with 2999 (33%), and then palindromic repeats with 2126 (23%). Sixteen divergence hotspot regions were identified in Pinus plastid genomes, which could be useful molecular markers for future population genetics studies. Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus (single needle section) and Pinus (double needles section). Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous. The two subgenera subsequently split 85.86 Mya, which was largely consistent with the other molecular results based on partial DNA markers. These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes.     

Phylogenetic relationships among Hystrix species and related species based on expressed sequence tag-polymerase chain reaction

Twelve species, including three Hystrix species, five Leymus species, Hordeum bogdanii, Pseudoroegneria spicata, Psathyrostachys huashanica, and Roegneria ciliaris, were used for expressed sequence tag-polymerase chain reaction (EST-PCR) assay. A total of 125 products were amplified by 72 sets of EST-PCR markers developed in barley, among which 106 (84.8%) products were found to be polymorphic. Each EST-PCR marker produced 0–6 polymorphic bands, with an average of 1.47. The relationship between H. duthiei s...     

基于ITS 序列探讨沙棘属植物的系统发育关系

对分布于青海境内的中国沙棘、肋果沙棘和西藏沙棘的ITS区进行扩增和序列分析,并以胡颓子科胡颓子属沙枣为外类群,对胡颓子科沙棘属15种植物的ITS序列进行聚类分析, 探讨沙棘属各植物的亲缘关系.结果表明： 3种沙棘属植物的ITS区长度为600～605 bp,其中,ITS-1区为201～203 bp,5.8S为166～167 bp,ITS-2区为232～236 bp.核苷酸分析显示,3种沙棘属植物的ITS区存在丰富的变异位点.聚类分析表明,棱果沙棘种的2个亚种——棱果沙棘和理塘沙棘为2个不同种,江孜沙棘与柳叶沙棘之间的亲缘关系较近,而与中国沙棘亲缘关系较远;沙棘种下9个亚种间的聚类结果与形态学分类差异较大.
     

Recurrent origin of peripheral,coastal (sub)species in Mediterranean Senecio (Asteraceae)

Background: It is argued that coastal endemic taxa may evolve in parallel at the periphery of the distributional range of a widespread species.

Aims: We tested this hypothesis for the origins of three peripheral, coastal isolates of Senecio, S. glaucus ssp. glaucus (Israel), S. g. ssp. coronopifolius p.p. (Sicily), and S. hesperidium (Morocco), from widespread S. glaucus ssp. coronopifolius. We also determined the relative roles of selection vs. genetic drift in shaping phenotypic divergence in ssp. glaucus and S. hesperidium, using Lande’s test of neutral morphological change.

Methods: We surveyed morphological and/or allozyme variation in the three peripheral isolates and mainly inland populations of S. g. ssp. coronopifolius.

Results: Genetic data supported independent origins of the coastal taxa from nearby populations of ssp. coronopifolius. These descendant and ancestral populations showed pronounced morphological but weak genetic differentiation. Phenotypic similarities between ssp. glaucus (Israel) and S. hesperidium (Morocco) in plant height and floral traits may have resulted from parallel divergent selection from ssp. coronopifolius, though drift remains an alternative cause in S. hesperidium.

Conclusions: Our results indicate parallel ecotype formation and (sub)speciation in Senecio in which primarily selective vs. neutral determinants promoted the recurrent origin of coastal types in, respectively, Israel and Morocco.     

Phylogenetic relationships among Hystrix species and related species based on expressed sequence tag‐polymerase chain reaction

Abstract Twelve species, including three Hystrix species, five Leymus species, Hordeum bogdanii, Pseudoroegneria spicata, Psathyrostachys huashanica, and Roegneria ciliaris, were used for expressed sequence tag‐polymerase chain reaction (EST‐PCR) assay. A total of 125 products were amplified by 72 sets of EST‐PCR markers developed in barley, among which 106 (84.8%) products were found to be polymorphic. Each EST‐PCR marker produced 0–6 polymorphic bands, with an average of 1.47. The relationship between H. duthiei ssp. duthiei and H. duthiei ssp. longearistata is close, but they are remote to H. patula. Hystrix duthiei ssp. duthiei and H. duthiei ssp. longearistata were clustered with Leymus species and Psathyrostachys huashanica, which suggested that they have close genetic relationships. The results of EST‐PCR analysis are basically comparable with those obtained from studies on cytology, which indicated that EST‐PCR can be used to assess the genetic relationships among the perennial species in Triticeae.     

Genetic Identification of Grey Mullet Species (Mugilidae) by Analysis of Mitochondrial DNA Sequence: Application to Identify the Origin of Processed Ovary Products (Bottarga)

Mitochondrial DNA sequencing was used to identify and distinguish four species of commercially important Mediterranean grey mullets. Partial cytochrome b and D-loop sequences were obtained from the four fish species, and these were used to perform phylogenetic analysis and to determine species-specific DNA fingerprints. Species-specific amplification primers were designed from these fingerprints, and these were used to characterize the species origin of several samples of commercial, processed mullet ovary products. In addition to differentiating between food products from different species, this method is also sensitive enough to distinguish food products from mullets of the same species from different regions.