Deep phylogeographic break among white croaker Pennahia argentata (Sciaenidae, Perciformes) populations in North-western Pacific

Abstract:   The Quaternary cold periods in the North-western Pacific are thought to have greatly influenced the genetic structures of marine species. One hundred and thirty-two individuals of white croaker Pennahia argentata were sampled from 12 localities throughout its distribution range to estimate the demographic history and genetic structure based on mitochondrial DNA cytochrome b gene and control region sequences. Two distinct clades with net genetic divergence of 3% in the control region were detected, one in Chinese coastal waters and the other in Japanese coastal waters. These clades may have been isolated and diverged during Pleistocene low sea levels. Nucleotide diversity was much higher in the Chinese clade than in the Japanese clade. The demographic history of the two clades was examined using neutrality tests and mismatch analyses, and the results indicated Pleistocene population expansion in both clades. Molecular variance and pairwise F _ST analyses revealed significant differentiation between two Japanese populations and lack of genetic structure in the Chinese populations. The significant geographic structure in white croaker suggests a low level of dispersal in this species. The lack of phylogeographic structure in Chinese coastal waters may reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.     

Genetic population structure of <Emphasis Type="Italic">Nibea albiflora</Emphasis> in Yellow Sea and East China Sea

ABSTRACT:   The population genetic structure and level of gene flow of Nibea albiflora from the Yellow Sea and the East China Sea were examined with a 479-bp segment of a mtDNA control region. In total, 65 samples were collected from three locations and 37 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the three populations ranged from 0.9130 ± 0.0308 (Zhoushan) to 0.9926 ± 0.0230 (Xiamen), and from 0.0073 ± 0.0043 (Qingdao) to 0.0099 ± 0.0057 (Xiamen). Analysis of molecular variance and pairwise F _ST revealed little genetic structure between the Yellow Sea and the East China Sea in N. albiflora . But based on the exact test of differentiation, the null hypothesis that N. albiflora within the Yellow Sea and the East China Sea constitutes a panmictic mtDNA gene pool was rejected. This might be caused by the broad spawning areas but not by the Yangtze River outflow. Mismatch distribution revealed that N. albiflora has undergone population expansion, possibly before the last 85 000–170 000 years. The existence of high gene flow between stocks in the studied area was supported by our results. Annual migrations, larval drift in the ocean currents, and recent range expansion could be the reasons for little genetic structure in the studied area.     

Historical DNA as a tool to genetically characterize the Mediterranean sand tiger shark (Carcharias taurus,Lamniformes: Odontaspididae): A species probably disappeared from this basin

1. The sand tiger shark (Carcharias taurus) is a coastal species distributed in temperate and sub‐tropical waters, classified as ‘Vulnerable’ at global level and ‘Critically endangered’ in eastern Australia, south‐western Atlantic Ocean, and Mediterranean Sea. Six populations (north‐western Atlantic, Brazil, South Africa, Japan, eastern Australia, and western Australia) with low genetic diversity and limited gene flow were identified worldwide, but genetic information for many other geographic areas are still missing. Specifically, this species is listed in several reports as part of the Mediterranean fauna, even if there has been a lack of catches and sightings in recent years in this basin. To clarify the origin of C. taurus individuals caught in the past in the Mediterranean Sea, historical samples were genetically analysed.
2. Nine samples with certain Mediterranean origin were collected from different European museums. DNA was extracted and ~600 bp of the mitochondrial DNA control region were amplified using eight overlapping species‐specific primer pairs. Sequences obtained were aligned with all the haplotypes globally known so far.
3. Genetic analysis revealed the misidentification of one museum specimen. Among the remaining Mediterranean historical samples, three different haplotypes were recovered. Two of them previously observed only in South Africa and one described in both South African and Brazilian populations.
4. Results suggest a genetic relationship between Mediterranean sand tiger sharks and those from the western Indian Ocean. According to previous studies, we hypothesized that, during the Pleistocene, the cold Benguela upwelling barrier was temporarily reduced allowing the passage of C. taurus individuals from the Indian to Atlantic Ocean. After the restoration of this phylogeographic barrier some individuals were trapped in the Atlantic Ocean and probably migrated northward colonizing the western African coasts and the Mediterranean Sea.

     

Microsatellite polymorphism in Italian populations of northern pike (Esox lucius L.)

Northern pike (Esox lucius) is not considered an endangered species in Italy, but since recent studies indicate the decline of this population, conservation and management strategies based on the genetic differentiation of natural northern pike populations are needed. In this paper, genetic diversity was analysed in 10 Italian and 2 East European northern pike populations by means of seven microsatellite loci. Data indicated an appreciable genetic differentiation, in spite of a low genetic variation, and agreed with the low level of genetic polymorphism already observed for this species in North America and North Europe. Results of statistical tests revealed genetic peculiarities of the Italian populations, even though signals of recent contact between populations were found and discussed in relation to anthropic impacts, particularly to the stocking practice. This investigation represents the first approach to the knowledge of the genetic variability of Italian pike populations using microsatellite markers, and reported results could be of interest for future management and conservation programmes of this species in Italy.     

Reintroduction of a dioecious aquatic macrophyte (Stratiotes aloides L.) regionally extinct in the wild. Interesting answers from genetics

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Evidence for genetic differentiation in the european conger eel Conger conger based on mitochondrial DNA analysis

ABSTRACT:   The European conger eel Conger conger is an important marine benthic fish in the North-East Atlantic and represents a valuable fishery resource. However, little is known about its reproductive biology. In an attempt to gain a better understanding of the conger eel population structure, mitochondrial DNA (mtDNA) sequences were examined. A region with 432 bp of the control region of the mtDNA was sequenced from 40 individuals from six different locations around the central and eastern North Atlantic Ocean. Thirty variable positions defined 28 distinct haplotypes. The average sequence difference within samples (1.3–4.2%) was comparable to those between samples (1.4–3.6%). MtDNA sequence-based statistical tests showed significant geographic differentiation between some local population samples, suggesting that the conger eel does not comprise a single panmictic population. However, given our sample sizes, these preliminary results should be interpreted with caution and more individuals from more sites, including the Mediterranean Sea, should be analyzed in detail. The genetic variability detected in this study is an initial step to elucidate the genetic background of the conger eel population structure.     

Conservation genetics and management implications for European grayling, Thymallus thymallus: synthesis of phylogeography and population genetics

Abstract  European grayling, Thymallus thymallus (L.), populations have steadily declined since the mid-1980s, mostly because of habitat degradation and increased predation pressure. To provide guidelines for conservation strategies and future management programmes, delineation of conservation and management units is warranted. Over the last decade, several studies have investigated the phylogeography and population genetic structure of T. thymallus using mitochondrial and nuclear microsatellite DNA markers. However, no study has covered the distribution range of T. thymallus across Europe; thus, a comprehensive survey of the evolutionary history of the species is lacking. This paper synthesises the major findings of the molecular studies and provides guidelines for the conservation and management of genetic resources of T. thymallus . At least five major mtDNA lineages have evolved in geographical isolation during the Pleistocene and these lineages should be recognised as the basic evolutionary significant units for T. thymallus in northern, central and southern Europe. There is also evidence for a high level of admixture among major lineages and sublineages, especially in the contact zones of drainages (e.g. in mainland Sweden and Norway and in central Germany), most probably resulting from a complex process of post-glacial and inter-glacial colonisation and re-colonisation events from different refugia during the Pleistocene ice ages. Based on the microsatellite data, T. thymallus shows a substantial level of inter-population genetic differentiation and, compared with other freshwater fish species, a relatively low level of within-population genetic diversity. The species develops discrete population structure, both within hydrologically connected rivers or lakes on comparatively small scales as well as in large river systems.     

中国沿海平疣桑椹石磺CO I 基因的遗传多样性与遗传分化

基于CO I序列,对中国沿海5个平疣桑椹石磺(Platevindex mortoni)群体的遗传多样性及遗传分化进行了分析,84个样本中共检测出单倍型41个,多态性位点117个。总体来说,平疣桑椹石磺具有高的单倍型多样性(0.835±0.039)和核苷酸多样性(0.0572±0.0060)。分子方差分析(AMOVA)表明,65.98%的变异存在于种群间,34.02%的变异发生在种群内。群体间遗传分化固定指数(Fst)、基因流(Nem)及遗传距离分析表明,平疣桑椹石磺已产生了明显的群体间分化。厦门(XM)、湛江(ZJ)和广西(GX)群体间无明显分化,基因流较大(Nem5),而海南(HN)、苍南(CN)群体分别与其他群体存在显著的分化。单倍型网络图及谱系树同样证实了群体遗传差异的存在。遗传距离模式(IBD)检测显示出,平疣桑椹石磺群体的遗传距离与地理距离之间不存在明显的线性关系。中性检验及历史动态检验推断,ZJ和GX群体可能经历过历史上的瓶颈效应,XM群体经历过历史上的种群扩张,扩张时间推测大约为0.12 Ma BP,可能伴随更新世冰期的气候变暖,海平面上升发生。本研究通过对平疣桑椹石磺mt DNA的CO I基因进行分析,探讨其遗传多样性及遗传分化过程,旨在为该物种种质保护,资源合理开发及生物进化方面研究提供基础资料和理论依据。     

Stocking of native Mediterranean brown trout (Salmo trutta) into French tributaries of Lake Geneva does not contribute to lake-migratory spawners

Abstract –  We studied the contribution of stocking with Mediterranean autochthonous brown trout ( Salmo trutta ) to the lake-migratory spawners in French tributaries of Lake Geneva. This singular lake system is inhabited by both the resident and the migratory life-history form, and by trout of Atlantic and Mediterranean origins. Using two discriminatory microsatellite loci between the Atlantic and Mediterranean alleles, we compared the genetic composition of the migratory Atlantic populations of the four main tributaries before (1999; N  = 113) and after (2004, 2005 and 2006; N  = 137) recent introductions of native Mediterranean trout. No significant modification of the genetic composition was detected in all four populations over time and only two individuals were statistically assigned to the Mediterranean strain by the Bayesian method implemented in the structure program. These results suggest a negligible contribution of the stockings with autochthonous Mediterranean trout to the lake-migratory spawners migrating into the four tributaries.     

基于CO I和Cyt b序列的丹江口水库鲢群体遗传结构特征分析

有效的人工增殖放流应监控放流群体和野生群体的遗传结构特征,以避免放流群体对天然群体遗传多样性的负面影响。本研究利用线粒体CO I和Cyt b基因分析了丹江口鲢库区、鲢亲本和鲢子代3 个群体的遗传结构特征。分析结果显示,104 条646 bp线粒体CO I序列中共检测到多态位点15 个,简约信息位点5 个,单一变异位点10 个,定义了7 个单倍型,单倍型多样性为0.544~0.676,核苷酸多样性为0.00221~0.00254;103 条1058 bp线粒体Cyt b序列中共检测到多态位点19 个,简约信息位点13 个,单一变异位点6 个,定义了14 个单倍型,单倍型多样性为0.609~0.714,核苷酸多样性为0.00262~0.00424,总体上处于较高单倍型多样性和较低核苷酸多样性。CO I和Cyt b序列遗传距离、遗传分化指数以及基因流分析结果显示,群体间遗传距离为0.002（CO I）、0.003~0.004（Cyt b）,总的遗传分化指数为-0.00468（P>0.05）（CO I）、0.03180（P>0.05）（Cyt b）,差异均不显著,群体间基因流为14.69～41.47（CO I）、5.49～40.47（Cyt b）,分子方差分析（AMOVA）结果表明群体的遗传变异主要来自群体内。单倍型聚类关系树表明,3 个鲢群体间均存在共享单倍型,不同地理群体间单倍型散乱分布于各支,未形成地理群体的聚集。以上分析结果显示,3 个鲢群体间不存在明显的遗传分化,表明增殖放流鲢群体与丹江口库区野生群体的遗传多样性和遗传结构相近,可开展增殖放流。本研究结果可为丹江口鱼类增殖站鲢群体的增殖放流提供科学依据。     

Reproductive ecology of two cyprinid fishes in an oligotrophic lake near the southern limits of their distribution range

Abstract –  The reproductive activities of two dominant fish species, roach Rutilus rutilus and rudd Scardinius erythrophthalmus were investigated from August 2000 to July 2002 in an oligotrophic lake, Lake Sapanca, in the northwest of Turkey. A total of 907 roach and 593 rudd individuals were examined. Macroscopic appearance of ovary, gonadosomatic index and oocyte diameter frequency distribution suggested that the spawning season of roach and rudd were from early April (13 °C) to late May (18 °C) and from early May (17.5 °C) to late June (23.5 °C), respectively. The spawning cycles of both species showed the same tendency in two successive years. The estimated mean total lengths at first maturity ( L _T50) were 12.26 and 14.98 cm for male and female roach, respectively, and 7.12 and 8.10 cm for male and female rudd, respectively. The sizes at 50% maturity corresponded to 3 years for roach and 1 year for rudd, for both sexes. The ratio of males to females was 1.3:1 and 1.2:1 for roach and rudd, respectively. The average condition factor K was 1.21 for rudd and 1.14 for roach, and it was not affected by sex or reproductive effort. Absolute fecundity varied from 7829 to 95,387 eggs between ages 3 and 9 for roach and from 1807 to 35,629 eggs between ages 1 and 7 for rudd. Comparisons of these results with earlier studies from more northern regions revealed that spawning of both species in this area started earlier, but spawning temperature and the duration of spawning was approximately the same.     

Population structure of purple sea urchin <Emphasis Type="Italic">Strongylocentrotus purpuratus</Emphasis> along the Baja California peninsula

Abstract:   Purple sea urchin Strongylocentrotus purpuratus is fished from British Columbia, Canada to Punta Baja, Mexico. The North American population has been divided into northern and southern fishery stocks at the break of Point Conception, but little is known about its southernmost distribution along the Mexican Pacific coast of the Baja California peninsula. In this study purple sea urchin populations in six sites along the Baja California peninsula were analyzed using mitochondrial deoxyribonucleic acid restriction fragment length polymorphism (mtDNA RFLP). A homogeneous distribution of three common haplotypes among all sites was observed. A significant F _ST value, however, indicated genetic structure mainly due to the haplotype array in San Miguel, Isla Todos Santos and Punta Baja sites, which were characterized by having high haplotype diversity and several unique haplotypes. Homogeneous distribution of haplotypes along the peninsula could have been influenced by the unidirectional California Current system, flowing north to south. Unique haplotypes in Punta Baja and the structure found could be the result of local oceanographic features specific to this major upwelling zone. It may be necessary to consider the Punta Baja populations individually when managing the purple sea urchin fishery in Baja California, as they show signs of being a unique stock.     

基于mtDNACytb基因序列的我国不同水系野生鲇种群遗传多样性与种群历史分析

为进一步了解鲇这一广布种的遗传多样性与种群遗传结构,阐明该经济鱼类的种群历史动态,本研究对我国长江(上游、中游)、珠江、福建、海南、辽河地区的野生鲇样本进行mtDNA Cytb基因序列测定与种群遗传多样性和遗传结构分析。结果显示,在所分析的216个序列样本中,共检测出78个单倍型,其中Hap_45在鲇不同群体中分布最为广泛;鲇总群体具有较高的单倍型多样性(Hd=0.948±0.009)和核酸多样性(Pi=0.017 99±0.000 55),暗示了其自然种群数量的相对稳定;单倍型系统发育与网络关系图分析显示,78种单倍型被分为4个分支,且不同单倍型分布相对集中,划分为4个谱系。中性检验与错配分析表明,不同水系野生鲇种群(4个谱系)在约晚更新世时期(0.04~0.05百万年)经历过近期种群扩张事件。     

Stock structure of Japanese flounder inferred from morphological and genetic analyses

ABSTRACT:   Stock structure of Japanese flounder Paralichthys olivaceus has been inferred mainly from either morphological or genetic analyses. However, because the results of both analyses did not always agree with each other, an inclusive conclusion has never been obtained. In this study, the stock structure has been inferred from both morphological and genetic analyses using 722 wild Japanese flounder collected from nine locations along the Japanese coast. The dorsal and anal fin ray counts were larger in the southern than in the northern populations. In total, 1041 bp of mitochondrial NADH dehydrogenase subunit-2 ( ND2 ) and 1830 bp of ND5 sequences were aligned. There are 578 variable sites in the concatenated sequence from the two genes, which defined a total of 490 haplotypes. Both results of morphological and genetic analyses indicated that the western Kyushu group, which included the Nagasaki and Kagoshima populations, was divided from the other seven populations. This is the first report to reveal the heterogeneity of the western Kyushu group based on statistical analysis.     

Genetic structure and phylogeographic relationships of the Bellamya complex: A nascent aquacultural snail in the Pearl River basin,China

The current genetic structure of a species is determined by both historical demographics and contemporary gene flow among populations. As an economically important snail in China, Bellamya has attracted much attention for its breeding and aquaculture and has provided a good study system for this theoretical structure. Our results showed that high genetic diversity occurred in most populations distributed in the Pearl River basin, except for the population in Nanning, Guangxi Zhuang Autonomous Region. A lack of distinct genealogical branches or geographic clades was found for the Bellamya complex across the Pearl River basin. Nevertheless, low but significant genetic structure and high differentiation were detected between Anshun (in Guizhou Province) and other geographic populations segregated by the Yunnan–Guizhou Plateau, suggesting that geographic barriers exist around this region, while this scenario was not applicable to the populations in Yuxi, Yunnan Province. The demographic history described a relatively stable pattern before the last glacial period, but the effective population sizes have drastically decreased since the late Pleistocene. The lack of genetic structure across the Pearl River basin is mainly attributed to a high level of gene flow by passive migration due to flooding and anthropogenic and animal translocation. The vicariance caused by the uplift of the Yunnan–Guizhou Plateau during the early Pleistocene likely contributed to the divergence of the plateau and plain sublineages in the Pearl River basin. A genetic diversity and phylogeography analysis are valuable to developing further guidance on breeding and conservation strategies for Bellamya germplasm resources.     

基于线粒体Cyt b基因序列的绿鳍马面鲀6个野生群体的遗传结构分析

利用线粒体细胞色素b(cytochrome b,Cyt b)基因分析了我国沿海绿鳍马面鲀(Thamnaconus septentrionalis)6个野生群体(大连、秦皇岛、蓬莱、日照、舟山和汕头)的遗传多样性和群体遗传结构。结果显示,在176个个体915 bp的Cyt b部分序列中共检测到32个变异位点和30个单倍型;6个群体的单倍型多样性为0.883~0.953,核苷酸多样性0.0032~0.0039;群体间固定指数较小,呈中低度分化;AMOVA分析表明,遗传变异主要来源于群体内,群体间遗传分化未达到显著水平。群体历史动态分析表明,绿鳍马面鲀在16.9万~42.2万年前经历种群扩张。总体上,各群体间的遗传分化较小,并未形成相应的地理支系,推测黑潮的输送作用以及绿鳍马面鲀的洄游习性维持了各群体间高强度的基因交流;中更新世中晚期的气候波动对绿鳍马面鲀的种群扩张以及地理分布格局可能具有重要影响。本研究结果加深了人们对于绿鳍马面鲀资源情况的认识,为绿鳍马面鲀资源的保护和合理利用提供了理论依据。     

基于控制区序列分析河鲈遗传多样性

河鲈为我区优质经济鱼类之一,在我国仅分布于新疆阿勒泰地区。为更好的保护和合理开发利用这一有限资源,我们基于mtDNA控制区序列对额尔齐斯河-乌伦古河水系的5个野生群体进行了遗传多样性和遗传结构进行了研究。PCR-SSCP标记结果显示,18个单倍型分布于5个群体的100个个体中。对这18个单倍型个体的mtDNA控制区序列克隆和测序,最终确定13个单倍型,检测到14个变异位点,占分析序列的1.60%。河鲈总种群表现高的单倍型多样度（0.942±0.034）和偏低的核苷酸多样度（0.00242±0.00450）。Tajima’s D和Fuand Li’s D指数的估算结果显示,河鲈5个群体遗传分化不显著（P〉0.1）,具有较稳定的种群结构。YBW,BEJH和LSW群体间存在着一定的基因流（Nm〉1）,WLGH群体与其他群体间的基因流水平低（Nm〉0.6）,存在着由于遗传漂变而产生分化的危险。5个群体间的单倍型序列差异为0.003,说明单倍型间未出现分化。     

Mitochondrial DNA variation in the East China Sea and Yellow Sea populations of Japanese Spanish mackerel <Emphasis Type="Italic">Scomberomorus niphonius</Emphasis>

Japanese Spanish mackerel Scomberomorus niphonius is a commercially important species in the East China Sea and Yellow Sea, but there is limited knowledge of its genetic population structure. In order to detect its genetic structure, sequence variation of the first hypervariable segment of the control region was analyzed among eight populations of S. niphonius from the East China Sea and Yellow Sea. A total of 119 polymorphic sites were detected in the 505-bp segment of the control region among 134 individuals of S. niphonius, defining 112 haplotypes. Mean haplotype diversity and nucleotide diversity for the eight populations were 0.9963 ± 0.0017 and 0.0236 ± 0.0119, respectively. As expected, analysis of molecular variance detected no significant differences at all hierarchical levels, and most of the conventional population Φ_ST statistics were negative, indicating that no significant population genetic structure exists in the East China Sea and Yellow Sea. Moreover, the exact test of differentiation supported the null hypothesis that S. niphonius within the East China Sea and Yellow Sea constitutes a panmictic mtDNA gene pool. Neutrality tests and mismatch distribution revealed that S. niphonius underwent population expansion in the late Pleistocene. Strong dispersal capacity of larvae and adults, long-distance migrations, and ocean currents in the studied area could be the reasons for genetic homogeneity in this species in the East China Sea and Yellow Sea. Insufficient time to accumulate genetic variation might be another explanation for the lack of genetic structure in the East China Sea and Yellow Sea.     

基于线粒体16SrRNA基因序列的长江下游重要水体脆弱象鼻溞群体遗传结构分析

为了解长江下游地区10个水体脆弱象鼻溞群体的遗传结构,研究测定了脆弱象鼻溞(Bosmina fatalis)线粒体16SrRNA基因序列,结果显示,100个样本中共有8个变异位点,定义了9个单倍型,单倍型多样性(Hd=0.284)和核苷酸多样性(Nd=0.000 76)均较低。AMOVA分子变异分析结果表明,脆弱象鼻溞遗传分化主要来自群体内,占93.33%,群体间的变异低,占6.67%。Fst值统计检验表明,各水体之间遗传分化不显著。系统发育树和中介网络图说明脆弱象鼻溞单倍型间关系较近,未形成明显谱系地理格局。中性检验和错配分布结果说明脆弱象鼻溞出现过群体扩张现象。     

Low genetic variability in an endangered population of fiddler crab <Emphasis Type="Italic">Uca arcuata</Emphasis> on Okinawajima Island: analysis of mitochondrial DNA

ABSTRACT:   Restriction fragment length polymorphism analysis was performed on polymerase chain reaction-amplified DNA fragments containing the D-loop , ND2 , and CO I genes of fiddler crab Uca arcuata mitochondrial DNA. In total, 316 individuals from six populations in Japan and two populations in Taiwan were analyzed using five restriction endonucleases ( Afa I, Bcn I, Cfr 13I, Hae III and Hin fI), yielding 85 haplotypes. Samples were taken from Nakagusuku Bay, Okinawajima Island, which is the only known distribution of U. arcuata in the Ryukyu Archipelago. The Okinawajima Island population is isolated geographically from others and showed a marked low genetic variability ( h  = 0.2539, π  = 0.0005) and significant differentiation from other population samples in haplotype composition. We suggest that a substantial decrease in the genetic variability of the Okinawajima Island population was caused by genetic drift under the conditions of small population size and low gene flow from other populations. It is important to conserve the intertidal zone in Nakagusuku Bay for the maintenance of this endangered population.