Livestock trade history, geography, and parasite strains: the mitochondrial genetic structure of Echinococcus granulosus in Argentina

A sample of 114 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from different host species and sites in Argentina has been sequenced for 391 bp from the mitochondrial cytochrome c oxidase subunit I gene to analyze genetic variability and population structure. Nine different haplotypes were identified, 5 of which correspond to already characterized strains. Analysis of molecular variance and nested clade analysis of the distribution of haplotypes among localities within 3 main geographic regions indicate that geographic differentiation accounts for the overall pattern of genetic variability in E. granulosus populations. Significant geographic differentiation is also present when the sheep strain alone is considered. Our results suggest that geographic patterns are not due to actual restricted gene flow between regions but are rather a consequence of past history, probably related to the time and origin of livestock introduction in Argentina.     

基于线粒体COI基因序列探讨泥蚶的遗传分化

采用PCR技术对我国沿海地区7个泥蚶群体的线粒体COI基因部分序列进行了测定和遗传分析。在来自7个群体的38个泥蚶样本均得到660 bp的COI基因片段序列,共103个多态位点,组成17种单倍型;数据分析表明：7个群体形成了二大类群：福建以北(包括福建)的5个群体（江苏盐城、浙江奉化、浙江乐清养殖和自然群体、福建福鼎）形成一个类群,类群内的遗传距离为0.0016;福建以南的类群（广东湛江、海南海口）形成一个类群,遗传距离为0.0006;二个类群之间的遗传距离为0.1529,表现为高度的分化。因此我国沿海泥蚶已分化形成福建以南和以北二大类群,二大类群之间的遗传分化已达到亚种水平。     

Mitochondrial <Emphasis Type="Italic">cox</Emphasis>1 and plastid <Emphasis Type="Italic">rbc</Emphasis>L genes of <Emphasis Type="Italic">Gracilaria vermiculophylla</Emphasis> (Gracilariaceae,Rhodophyta)

The mitochondrial cytochrome c oxidase subunit I gene sequence was recently developed for DNA barcoding of red algal species. We determined the 1245 base pairs of the gene from 27 taxa of an agar-producing species, Gracilaria vermiculophylla, and putative relatives and compared the results with rbcL data from the same species. A total of 392 positions (31.5%) were variable, 282 positions (22.6%) were parsimoniously informative, and average sequence divergence was 13% in an ingroup. Within G. vermiculophylla, pairwise divergence of the gene was variable up to 11 bp (0.9%). Seven recognized haplotypes of cox1 tended to be geographically related. In the aligned 1386 bp of rbcL, three haplotypes were recognized. These results suggest that cox1 is a valuable molecular marker within species and will be very useful in haplotype analyses.     

Genetic Variation and Population Structure of Hair Crab (<Emphasis Type="Italic">Erimacrus isenbeckii</Emphasis> ) in Japan Inferred from Mitochondrial DNA Sequence Analysis

Genetic variation and population structure of hair crab (Erimacrus isenbeckii) were examined using nucleotide sequence analysis of 580 base pairs (bp) in the 3′ portion of the mitochondrial cytochrome c oxidase subunit I gene (COI) of 20 samples collected from 16 locales in Japan (the Hokkaido and Honshu Islands) and one in Korea. A total of 27 haplotypes was defined by 23 variable nucleotide sites in the examined COI region. Pairwise population F _ST estimates and neighbor-joining tree inferred distinct genetic differentiation between the representative samples from the Pacific Ocean off the Eastern Hokkaido Island and the Sea of Japan, while others were intermediate between these two groups. AMOVA also showed a weak but significant differentiation among these three groups. The present results suggest a moderate population structure of hair crab, probably influenced by high gene flow between regional populations due to sea current dependent larval dispersal of this species.     

Assessing the use of mitochondrial cox1 gene and cox2-3 spacer for genetic diversity study of Malaysian Gracilaria changii (Gracilariaceae, Rhodophyta) from Peninsular Malaysia

Advances in DNA-based genetic markers provide the essential tools in measurement of genetic diversity relating to the evolution, biogeography, and systematics of red algae by exploiting genetic variation in the entire genome of organisms. The understanding of genetic diversity in Gracilaria changii (Gracilariaceae, Rhodophyta) will provide valuable information for conservation, plant breeding management, and strain selection for cultivation. However, information of intraspecific genetic variation is still rudimentary. In this study, two mitochondrial encoded markers, cytochrome oxidase subunit 1 (cox1) and intergenic spacer between the cytochrome oxidase subunits 2 and 3 (cox2-3 spacer) were used to investigate genetic diversity in 40 individuals of G. changii collected from 11 different geographically distinct populations from Peninsular Malaysia. Seven distinct mitochondrial haplotypes were identified with the cox1 gene and three mitochondrial haplotypes with the cox2-3 spacer. Intraspecific nucleotide differences ranged from 0 to 6 bp for the cox1 and 0–4 bp for the cox2-3 spacer, respectively. This is the first report comparing the suitability of mitochondrial markers of the cox1 gene and the cox2-3 spacer for genetic diversity studies on G. changii. The present study showed that the cox1 gene is a potential molecular marker to infer intraspecific genetic variation in red macroalgae. The cox1 marker is more variable compared to the cox2-3 spacer and revealed genetic variation and phylogeographic structure for this ecologically and economically important species.     

Population genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI gene sequences

Chinese sea bass (Lateolabrax maculatus), an important commercial and recreational fishery species in China, whose natural resources have decreased dramatically for decades due to overfishing and environmental changes. To provide guidelines for the source conservation and management, genetic diversity and population structure of L. maculatus were analyzed based on the mitochondrial cytochrome oxidase subunit I (COI) gene. Totally 192 individuals were sampled from five locations: Qingdao (QD), Chongming (CM), Dongtou (DT), Lieyu (LY) and Fangcheng (FC). After sequencing of a 586 bp fragment of COI gene, 20 haplotypes were defined. H4 (haplotype 4) and H8 were the dominant haplotypes and existed in all populations. Haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.572 to 0.721 and from 0.00129 to 0.00271, respectively. The highest Hd and π were found in DT and LY populations, while the lowest value of Hd and π were in the QD population. Genetic distance ranged from 0.0031 to 0.0027 within populations and from 0.0018 to 0.0035 between populations. Analysis of molecular variance (AMOVA) revealed that significant genetic divergence was found in QD and FC populations. In addition, neutrality tests and mismatch distribution analysis indicated that this species experienced potential population expansion events.     

Population structure of Macrobrachium australiense (Decapoda: Palaemonidae) in Western Queensland, Australia: the role of contemporary and historical processes

Rivers of Western Queensland, Australia, represent a discontinuous and variable aquatic habitat for the freshwater fauna of the region. Rivers periodically fluctuate between being highly fragmented, with numerous disconnected waterholes and ephemeral channels, and being highly connected by a dominant system of anastomosing channels. We used mitochondrial sequences to investigate the genetic structure and inferred patterns of dispersal associated with this flow regime for the freshwater prawn, Macrobrachium australiense (Decapoda: Palaemonidae), sampling 28 localities throughout eight catchments. Based on a 505 base pair fragment of mitochondrial cytochrome c oxidase subunit I, we identified 98 haplotypes in a sample of 402 individuals. The haplotypes clustered into two main clades corresponding geographically to the major drainages: the Lake Eyre and Murray-Darling basins. Populations of M. australiense inhabiting the two basins appear to have diverged around 800,000 years ago (estimated sequence divergence of 1.6%). Analysis of population differentiation indicated contemporary high levels of genetic subdivision and restricted gene flow among populations within and among catchments. Phylogenetic analysis detected a series of historical range expansions in the region and we suggest that climate fluctuations during the Pleistocene have resulted in extensive floods that have promoted historical movements of aquatic organisms across catchment boundaries.     

Cryptic divergence and strong population structure in the colonial invertebrate Pycnoclavella communis (Ascidiacea) inferred from molecular data

We studied sequence variation in the mitochondrial gene cytochrome c oxidase subunit I (COI) for 135 individuals from eight Mediterranean populations of the colonial ascidian Pycnoclavella communis across most of its presently known range of distribution in the Mediterranean. Three haplotypes from Atlantic locations were also included in the study. Phylogenetic, phylogeographic and population genetic analyses were used to unravel the genetic variability within and between populations. The study revealed 32 haplotypes for COI, 29 of them grouped within two Mediterranean lineages of P. communis (mean nucleotide divergence between lineages was 8.55%). Phylogenetic and network analyses suggest the possible existence of cryptic species corresponding to these two lineages. Population genetic analyses were restricted to the five populations belonging to the main genetic lineage, and for these localities we compared the information gleaned from COI sequence data and from eight microsatellite loci. A high genetic divergence between populations was substantiated using both kinds of markers (COI, global Fst=0.343; microsatellite loci, global Fst=0.362). There were high numbers of private haplotypes (COI) and alleles (microsatellites) in the populations studied. Restricted gene flow and inbreeding occur in the present range of distribution of the species. Microsatellite loci showed a strong incidence of failed amplifications, which we attribute to the marked intraspecies variability that hampered the application of these highly specific markers. Our results show important genetic variability at all levels studied, from within populations to between basins, possibly coupled to speciation processes. This variability is attributable to restricted gene flow among populations due to short-distance dispersal of the larvae.     

厚壳贻贝养殖群体与野生群体线粒体DNA的遗传分析(英文）

采用线粒体DNA COI基因序列对厚壳贻贝2个养殖群体与2个野生群体的遗传多样性进行了研究。4个群体共获得30个单倍型。结果显示：在养殖群体中单倍型的数量和遗传多样性要比野生群体的低,可能是由于只有少量的有效父母本对养殖群体的遗传变异有贡献所致。养殖群体与当地野生群体之间也未发生显著的遗传分化,可能是因为它们之间存在基因流。在今后厚壳贻贝养殖过程中,本研究可以用在对养殖群体进行遗传监测,从而保证养殖群体的遗传多样性水平。     

Comparison of three organelle markers for phylogeographic inference in Batrachospermum helminthosum (Batrachospermales, Rhodophyta) from North America

Phylogeographic signal provided by the newly developed 23S plastid rRNA marker (universal plastid amplicon, UPA) and the cytochrome oxidase subunit I gene marker (COI) in the freshwater red alga Batrachospermum helminthosum, throughout its range in North America, was investigated. These markers were compared in individuals from a previous study using the cytochrome oxidase 2–3 spacer region ( cox 2–3), which has yielded the most useful data to date with 13 haplotypes among geographic locations. Five haplotypes were resolved for the UPA, differing by only one to two base pairs (bp), and we conclude that this marker may be more appropriate for studying interspecific variation. In contrast, the COI gene revealed 16 haplotypes, differing from one to 44 base pairs or up to 6.6% sequence variation. The intraspecific variation of COI in this taxon is much greater than that reported thus far for marine red algae (generally <5 bp). The intraspecific variation within B. helminthosum is in accord with levels shown in Batrachospermum macrosporum (48 bp within distant locations in Brazil). The COI gene is comparable to the cox 2–3 spacer for phylogeographic studies as the haplotype networks were similar and showed the same geographic patterns. To our knowledge, this is the first comparison of these three regions for phylogeographic research in the red algae.     

Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations

Due to their maternal mode of inheritance, mitochondrial markers can be regarded as almost 'ideal' tools in evolutionary studies of conifer populations. In the present study, polymorphism was analysed at one mitochondrial intron (nad 1, exon B/C) in 23 native European Pinus sylvestris populations. In a preliminary screening for variation using a polymerase chain reaction-restriction fragment length polymorphism approach, two length variants were identified. By fully sequencing the 2.5 kb region, the observed length polymorphism was found to result from the insertion of a 31 bp sequence, with no other mutations observed within the intron. A set of primers was designed flanking the observed mutation, which identified a novel sequence-tagged-site mitochondrial marker for P. sylvestris. Analysis of 747 trees from the 23 populations using these primers revealed the occurrence of two distinct haplotypes in Europe. Within the Iberian Peninsula, the two haplotypes exhibited extensive population differentiation (PhiST = 0.59; P < or = 0.001) and a marked geographical structuring. In the populations of central and northern Europe, one haplotype largely predominated, with the second being found in only one individual of one population.     

Occurrence of a novel strain of Scirtothrips dorsalis (Thysanoptera: Thripidae) in Japan and development of its molecular diagnostics

Scirtothrips dorsalis Hood is a cosmopolitan and polyphagous thrips species. Recently, a novel strain of S. dorsalis attacking capsicum crops was found in Japan. A molecular phylogenetic analysis using mitochondrial cytochrome c oxidase subunit I sequences revealed that the capsicum-associated populations were genetically different from Japanese native strains and were closely related to Southeast Asian populations. We named the capsicum-associated populations “strain C” and the Japanese native ones “strain YT”. A total of 10 haplotypes were found in strain C and 26 in strain YT. To differentiate the two strains, we developed a multiplex-PCR method using the ribosomal ITS2 region.     

厚壳贻贝养殖群体与野生群体线粒体DNA的遗传分析(英文)

采川线粒体DNA COI基因序列对厚壳贻贝2个养殖群体与2个野生群体的遗传多样性进行了研究.4个群体共获得30个单倍型.结果显示:在养殖群体中单倍型的数量和遗传多样性要比野生群体的低,可能是由于只有少量的有效父母本对养殖群体的遗传变异有贡献所致.养贿群体与当地野生群体之间也未发生显著的遗传分化,可能足因为它们之间存在基因流.在今后厚壳贻贝养殖过程中,本研究可以用在对养殖群体进行遗传监测,从而保证养殖群体的遗传多样性水平.     

Phylogeographic Analysis of the Firefly, Luciola lateralis, in Japan and Korea Based on Mitochondrial Cytochrome Oxidase II Gene Sequences (Coleoptera: Lampyridae)

Luciola lateralis is widely distributed throughout the Korean Peninsula, northeast China, Sakhalin, and Japan. Two ecological types are recognized in Japan based on flash and hatching time characteristics. The mitochondrial cytochrome oxidase II gene was surveyed by restriction fragment length polymorphism analysis for Japan (46 populations) and Korea (two populations). Eleven haplotypes were detected. Gene trees revealed that haplotypes between Japan and Korea are much more differentiated in nucleotide sequences (8.1%) than those within Japan (0.3-1.4%) and Korea (0.7%). Haplotypes between Honshu and Hokkaido are not separated as clades, and the two ecological types cannot be segregated from each other phylogenetically. We suggest that the Japanese populations of this species may have dispersed within one million years ago and that ecological differences may be the result of physiological adaptation to cold climates.     

Survey of mitochondrial DNA haplotypes of Potamopyrgus antipodarum (Caenogastropoda: Hydrobiidae) introduced into Japan

Potamopyrgus antipodarum from 13 locations in central and western Japan were investigated for mitochondrial DNA haplotypes. Two haplotypes (JA and JB) were found based on an analysis of a 343-bp sequence of the cytochrome c oxidase subunit I gene. The JB type comprised two subhaplotypes (JB-I and JB-II), which were distinguishable by an additional sequence of 289 bp. Eleven populations were likely monomorphic in the mtDNA haplotype, while two populations, which were supposed to have been established recently, were polymorphic, encompassing JA and JB haplotypes. This result suggests that different haplotypes invaded Japan via different routes and that polymorphic populations were formed by colonization from more than one source population.     

入侵我国红火蚁的三种单倍型

红火蚁Solenopsis invicta Buren是重要的经济害虫,特别是在农业和生态系统危害方面。2004年底在广东和香港的部分地区发现红火蚁入侵。本文用线粒体细胞色素氧化酶Ⅰ（CO Ⅰ）基因对境内的13个种群进行了入侵蚁巢是否独立传入进行了分析。通过对共计28个蚁巢56个体的包含904个碱基的CO Ⅰ基因分析,发现入侵中国的红火蚁中存在3种单倍型。基于未修正的配对序列变异分析表明,单倍型Ⅱ与单倍型Ⅲ之间的变异最小。而香港种群同时具有这三种单倍型,是入侵中国的红火蚁种群中多样性最丰富的地区。这三种单倍型都分别在阿根廷红火蚁种群中有记录。同源性分析显示,中国的红火蚁可能起源于阿根廷或南美洲,而香港可能是所研究种群的第一入侵地点。     

Phylogenetic analysis of cryptic speciation in the polychaete Pygospio elegans

Development in marine invertebrate species can take place through a variety of modes and larval forms, but within a species, developmental mode is typically uniform. Poecilogony refers to the presence of more than one mode of development within a single species. True poecilogony is rare, however, and in some cases, apparent poecilogony is actually the result of variation in development mode among recently diverged cryptic species. We used a phylogenetic approach to examine whether poecilogony in the marine polychaete worm, Pygospio elegans, is the result of cryptic speciation. Populations of worms identified as P. elegansooded, and intermediate larvae; these modes are found both within and among populations. We examined sequence variation among partial mitochondrial cytochrome c oxidase subunit I sequences obtained for 279 individual worms sampled across broad geographic and environmental scales. Despite a large number of unique haplotypes (121 haplotypes from 279 individuals), sequence divergence among European samples was low (1.7%) with most of the sequence variation observed within populations, relative to the variation among regions. More importantly, we observed common haplotypes that were widespread among the populations we sampled, and the two most common haplotypes were shared between populations differing in developmental mode. Thus, our results support an earlier conclusion of poecilogony in P elegans. In addition, predominantly planktonic populations had a larger number of population-specific low-frequency haplotypes. This finding is largely consistent with interspecies comparisons showing high diversity for species with planktonic developmental modes in contrast to low diversity in species with brooded developmental modes.     

粤东海域口虾蛄遗传多样性

采用线粒体COI基因序列对粤东汕尾和深圳2个海域口虾蛄(Oratosquilla oratoria)的遗传多样性进行了分析.研究表明,所分析的口虾蛄mtDNA CO I基因(592 by)共检测到21个变异位点,占总位点的3.55%.转换和颠换位点数分别为18和3个,碱基替换的饱和性分析表明,口虾蛄CO I基因碱基替换...     

利用COI基因序列分析长江与澜沧江水系日本沼虾群体的遗传结构

测定了我国长江水系和澜沧江水系的日本沼虾9个群体,共79个个体的线粒体COI基因序列片段(约450bp),结果发现有89个变异位点,共计有46个单倍型。其中云南昆明(KM)群体具有较丰富的遗传多样性(h=1.000,π=0.028),而重庆(CQ)群体的遗传多样性最小(h=0.700,π=0.008)。AMOVA分析表明,群体间的遗传变异占总遗传变异的9.66%,而90.34%的遗传变异源于群体内。采用邻接法(NJ)构建的分子系统树显示,46个单倍型明显地聚为长江中下游和长江上游与澜沧江两个族群。其结果可以为合理开发和利用日本沼虾自然野生资源,以及建立和保护日本沼虾种质资源库及基因库提供必要的参考。     

基于线粒体COⅡ基因序列的双斑长跗萤叶甲中国北方地理种群的遗传多样性研究

双斑长跗萤叶甲Monolepta hieroglyphica (Motschulsky)是自2001年以来在我国北方为害玉米呈加重趋势的一种害虫。为初步探讨中国北方不同地理种群间和种群内该害虫的遗传分化程度、 遗传多样性以及基因流水平, 对来自中国北方的26个不同地理种群的线粒体COⅡ (细胞色素C氧化酶亚基Ⅱ) 基因片段序列的核苷酸多态性进行了研究。结果表明： 在515头个体的长度为484 bp COⅡ片段中共发现了28个变异位点和15种单倍型。单倍型间的系统进化分析发现, 15种单倍型主要分为两大分支。总种群单倍型多样性指数Hd为0.257, 种群内单倍型多样度在0.100～0.515范围内。总种群的Fst为0.585, Gst为0.417, 基因流Nm为0.35。AMOVA分子变异分析结果发现, 双斑长跗萤叶甲的遗传分化主要来自种群之间, 占方差比率的58.58%。实验总种群及大部分种群的中性检验符合中性突变, 说明我国北方双斑长跗萤叶甲在近期没有出现种群扩张现象。研究结果揭示中国北方双斑长跗萤叶甲不同地理种群间基因流水平低, 种群间已发生明显的遗传分化, 分化主要来自种群之间。