Molecular analysis of the recently described lizardfish Saurida lessepsianus (Synodontidae) from the Red Sea and the Mediterranean,with remarks on its phylogeny and genetic bottleneck effect

The opening of the Suez Canal in 1869 led to a massive influx of Red Sea species that invaded the Mediterranean; this was termed ‘Lessepsian migration'. Among these species was a species of lizardfish, identified by some authors as Saurida undosquamis and by others as S. macrolepis. Recently, the Red Sea and the Mediterranean populations were described according to external characteristics as a unique taxon, Saurida lessepsianus. Our molecular study confirms this finding and determines that all previous records of S. undosquamis and S. macrolepis in the Red Sea and the Mediterranean are misidentifications of S. lessepsianus. The Mediterranean population of S. lessepsianus exhibits a lower genetic variability than that of the Red Sea population, suggesting a bottleneck effect.     

Genetic diversity and population differentiation in the yellow drum Nibea albiflora along the coast of the China Sea

Nibea albiflora (yellow drum) is an important seafood fish species in East Asia. We explored the population genetic variation of N. albiflora along the coastal waters of the China Sea using microsatellite markers to facilitate a selective breeding programme that is undertaken in China. A total of 256 alleles were detected at 12 loci in four wild populations. A high level of genetic diversity was observed with the mean number of alleles and the observed and expected heterozygosity in each population ranging from 7.917 to 14.083, 0.701 to 0.764 and 0.765 to 0.841, respectively. Pairwise fixation index (F_ST) analysis indicated significant but weak genetic differentiation among populations from four localities (F_ST?=?0.030, P?<?0.01), which was also confirmed by analysis of molecular variance (AMOVA). Significant genetic differentiation was detected between Ningde and the other populations (F_ST?=?0.047–0.056, P?<?0.01). Structure analysis suggested that N. albiflora within the examined range might be composed of two stocks. The data of the present study revealed high genetic diversity and low genetic differentiation among the N. albiflora populations along the coast of the China Sea. This baseline information could be valuable for future selective breeding programmes of N. albiflora.     

Upwelling and eddies affect connectivity among local populations of the goldeye rockfish,Sebastes thompsoni (Pisces,Scorpaenoidei)

The goldeye rockfish, Sebastes thompsoni, commercial rockfish catch in the Northwest Pacific Ocean, may influence its population structure. To clarify the population genetic structure of Korean S. thompsoni and its degree of hybridization with the most close species, Sebastes joyneri, we analyzed a mitochondrial (mt) DNA control region and eleven polymorphic microsatellite (ms) loci. S. joyneri individuals were clearly distinguished from S. thompsoni by the mtDNA control region and ms loci results, with single interspecific hybridization between two species suggesting no impact on genetic structure of S. thompsoni. Analysis of mtDNA revealed no population structure within S. thompsoni, suggesting the survival of a single population in southern refugia during the glacial period. The ms loci results, in contrast, showed two genetically distinct clusters within S. thompsoni: One was predominant throughout Korean coasts (from the Yellow Sea, via the Korea Strait to the East Sea); the other was predominant at Dokdo Island in the East Sea; and both occurred in similar ratios at Wangdolcho Reef in the East Sea. A possible factor that restricts gene flow between Korean coastal and offshore populations in the East Sea may be related to the complex oceanic current patterns such as eddies and upwelling, which represent impermeable barriers to population connectivity for this species. Our findings highlight that these two populations might be representative of two separate stock within Korean waters and maintain their geographically related genetic structure.     

The Saurida undosquamis group (Aulopiformes: Synodontidae), with description of a new species from southern Japan

Four lizardfishes of Saurida (family Synodontidae), S. undosquamis, S. umeyoshii sp. nov., S. macrolepis, and S. longimanus, are described. All are recognized here as the Saurida undosquamis group, characterized by having dark dots on the upper margin of the caudal fin, pectoral fin exceeding origin to pelvic fin, anterior rays of dorsal fin neither elongate nor filamentous, predorsal length greater than distance between dorsal-fin and adipose-fin origins, 46–55 pored lateral-line scales, and vomer with 0–8 teeth. Saurida undosquamis, from northern West India and West Pacific, excluding East Asia, differs from others in having lateral-line scales ridged on the caudal peduncle, conspicuously concave posterior margin of the pectoral fin, 51–55 pored lateral-line scales, and 50–53 vertebrae. Saurida umeyoshii sp. nov., from southern Japan and the East China Sea, is defined by three rows of indistinct dark blotches on, above, and below the lateral line, distribution of scale pockets with melanophores on their posterior part extending over the entire abdominal region from the lateral line in specimens over ca. 130 mm SL, lateral-line scales not ridged on caudal peduncle, 49–52 pored lateral-line scales, and 48–50 vertebrae. Saurida macrolepis, from the Indo-West Pacific, is characterized by 46–49 pored lateral-line scales and 45–48 vertebrae. Saurida longimanus, from northern West India, northwest Australia, and southern Indonesia, differs from the others in having a long pectoral fin extending past the origin of the dorsal fin. Some geographic variations are found in S. macrolepis. Saurida grandisquamis is confirmed as a junior synonym of S. undosquamis, based on examination of the type specimens. A key to species in the S. undosquamis group is included.     

The biology of the Red Sea migrant,Saurida undosquamis in the Mediterranean and comparison with the indigenous confamilial Synodus saurus (Teleostei: Synodontidae)

A study of the biology of Red Sea — Suez Canal migrant, the lizardfish Saurida undosquamis and the indigenous Synodus saurus was carried out in the Mediterranean coast of Israel. The spawning season of S. undosquamis lasts from March to December indicating a curtailment of the year-round spawning season of the source population in the Gulf of Oman. The spawning season of S. saurus is from February to August. The diameter of ripe oocytes of S. undosquamis is 500–600 μm. Females of S. undosquamis grow slightly faster than males and reach a larger size (340 mm TL versus 280 mm TL). Niche partitioning between the two lizardfishes is primarily on the basis of depth. The invador occupying deeper water. Both species are chiefly piscivorous but as a result of their depth distribution there is little diet overlap on the specific level.     

Protein polymorphism and genetic divergence in slow loris (genusNycticebus)

In this study, protein electrophoresis was assayed to detect genetic variation in GenusNycticebus. A total of 29 samples (2N. coucang and 27N. pygmaeus) were analyzed for 42 genetic loci. In the 27 samples ofN. pygmaeus, 4 loci were observed to be polymerphic. Therefore, the estimatedP value (proportion of polymorphic loci) is 0.095, theA value (average number of alleles each locus) is 1.045, and theH value (mean individual heterozygosity) is 0.040. After comparing theH ofN. pygmaeus with those of other primates reported, we found that the protein variation inN. pygmaeus is slightly lower than the average level. Additionally, we also observed obivious allele difference betweenN. pygmaeus andN. coucang. There are no shared alleles between these two species in eight loci. TheNei's genetic distance between them was calculated as 0.2541, which falls in the spectrum of genetic difference between species in primates.     

Phylogenetic relationships inSecale (Poaceae): An isozymatic study

The genetic frequencies of 9 isozyme loci have been estimated in 23 samples of 4 species ofSecale by means of starch gel electrophoresis. The populations ofS. silvestre andS. vavilovii were monomorphic and uniform within each species, those ofS. montanum andS. cereale were polymorphic for most of the isozyme loci. On the basis of isozyme patterns as well as allelic and genotypic frequencies of isozyme loci,S. silvestre can be distinguished fromS. vavilovii, and both fromS. cereale andS. montanum; but there is no clear differentiation between the two latter species. Clusters constructed from genetic distances separateS. silvestre andS. vavilovii, whereasS. cereale andS. montanum were grouped together. The isozymatic data presented here, along with cytogenetic and life habit data, agree with the generally admitted existence of 4 species inSecale, and support the relationships suggested byKhush & Stebbins (1961).     

Genetic differentiation in populations of the polymorphic fernCeratopteris thalictroides in Japan

Analysis of isozyme variation was carried out for 27 natural populations ofCeratopteris thalictroides in Japan. Of fifteen enzyme loci examined, eight loci were genetically polymorphic. At six loci,Lap, Pgi-2, Pgm-3, Pgm-4, Idh-2, and Skd-2, a marked genetic differentiation was observed between populations to the south of Okinawa Island and those to the north of the island. Okinawa Island contained a mixture of both southern and northern variants. Thus, two genetically distinct types (the south type and the north type) ofC. thalictroides occur allopatrically in Japan. Nei's genetic identity (I) between the two was 0.64, which was within the range of the I values between congeneric pteridophyte species. Regional fixation of a null allele was detected for one duplicated PGI locus in the north type ofC. thalictroides. This finding supports the recent hypothesis of genetic diploidization of polyploids through gene silencing.     

Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae)

Sebastiscus marmoratus is a typical sedentary fish and usually lives at the bottom of the coastal zone from Japan to the East China Sea. Next-generation sequencing platform was used to obtain microsatellite loci sequences of S. marmoratus, among which forty-eight perfect microsatellite repeats were suitable for primer design. Nine polymorphic microsatellite markers were exploited and characterized for it. The allele number of all polymorphic microsatellite markers ranged from 4 to 12. Expected and observed heterozygosity varied from 0.302 to 0.909 and from 0.190 to 0.625, respectively. In further studies, the genetic variation and population structure of this species would be investigated using these microsatellite loci.     

Genetic and morphological identification of Sebastiscus tertius in the East China Sea (Scorpaeniformes: Scorpaenidae)

The allozymes and morphology of 110 specimens of three Sebastiscus species (S. marmoratus, S. tertius, and S. albofasciatus) in the East China Sea and near Japan were compared. Results of 20 allozyme loci studied showed that all three species were closely related (Nei's unbiased genetic distances, 0.057–0.133) but could be identified on the basis of informative loci with a few exceptions. Initial identification based on color patterns agreed with allozyme identification in more than 98% of Sebastiscus specimens and agreed completely in S. albofasciatus. One specimen that was initially identified as S. marmoratus because of the dark body color was actually S. tertius according to two informative allozyme loci. Number of pectoral fin rays differed between S. marmoratus (18 or fewer, 98%) and S. tertius (19 or more, 85%) in this study. The previously mentioned dark specimen had 19 pectoral fin rays, which are characteristic in S. tertius. Using seven morphological measurements, canonical discriminant analysis between S. marmoratus and S. tertius classified less than 90% of specimens into the original groups (species). Some specimens of S. tertius resembled S. marmoratus in body shape and vice versa. A combination of genetic characterization and morphological examination is necessary to identify S. marmoratus and S. tertius accurately. Distinction based on allozymes and color patterns with numbers of pectoral fin rays should provide satisfactory identification. Received: May 16, 2000 / Revised: December 19, 2000 / Accepted: January 24, 2001     

Genetic diversity of silver pomfret (Pampus argenteus) in the Southern Yellow and East China Seas

Silver pomfret (Pampus argenteus) is an important fisheries resource in China, but harvest management lacks identification of management units (genetic stocks or populations). Using amplified fragment length polymorphism (AFLP), we investigated the population genetic structure of silver pomfret from the Yellow and East China Seas. In 143 individuals examined from six locations (three locations in the Yellow Sea, three in the East China Sea), a total of 194 loci were detected by six primer combinations. In all loci, 149 loci (76.8%) were polymorphic, and the percentage of polymorphic loci varied within samples from 62.9% to 67.0%. Among the six samples, Nei’s genetic diversity was 0.23 ± 0.20–0.25 ± 0.21, and Shannon’s index was 0.34 ± 0.28–0.36 ± 0.29. Analyses revealed significant genetic differentiation among the six samples, indicating at least six separate populations of silver pomfret in the Southern Yellow and East China Seas.     

黄海和东海小黄鱼遗传多样性的RAPD分析

小黄鱼（Pseudosciaena polyactis）是我国近海重要经济鱼类之一。本文分析了采自黄海和东海5个海区共计48个个体小黄鱼的随机扩增DNA多态性（RAPD）。从40个10 bp引物中选取20个用于群体遗传多样性分析,共检测出145个位点,其中132个（91.03%） 显多态性。用Shannon多样性指数量化的平均遗传多态度为1.93（1.50～2.44）,群体内和群体间的遗传变异比例分别为69%和31%;群体间的平均遗传相似度和遗传距离分别为0.9139和0.0861。用非加权配对算数平均法（UPGMA）聚类分析的结果表明,所分析的5个群体可分为3个地理群系,从分子水平上支持了过去有关学者把黄海和东海的小黄鱼划分为北、中、南3个地理群系的观点。     

Historic speciation and recent colonization of Eurasian monkey gobies (Neogobius fluviatilis and N. pallasi) revealed by DNA sequences,microsatellites, and morphology

Aim Hidden diversity within an invasive ‘species’ can mask both invasion pathways and confound management goals. We assessed taxonomic status and population structure of the monkey goby Neogobius fluviatilis across Eurasia, comparing genetic variation across its native and invasive ranges. Location Native populations were analysed within the Black and Caspian Sea basins, including major river drainages (Dnieper, Dniester, Danube, Don and Volga rivers), along with introduced locations within the upper Danube and Vistula river systems. Methods DNA sequences and 10 nuclear microsatellite loci were analysed to test genetic diversity and divergence patterns of native and introduced populations; phylogenetic analysis of mtDNA cytochrome b and nuclear RAG‐1 sequences assessed taxonomic status of Black and Caspian Sea lineages. Multivariate analysis of morphology was used to corroborate phylogenetic patterns. Population genetic structure within each basin was evaluated with mtDNA and microsatellite data using F_ST analogues and Bayesian assignment tests. Results Phylogenetic analysis of mitochondrial and nuclear sequences discerned a pronounced genetic break between monkey gobies in the Black and Caspian Seas, indicating a long‐term species‐level separation dating to c. 3 million years. This pronounced separation further was confirmed from morphological and population genetic divergence. Bayesian inference showed congruent patterns of population structure within the Black Sea basin. Introduced populations in the Danube and Vistula River basins traced to north‐west Black Sea origins, a genetic expansion pattern matching that of other introduced Ponto‐Caspian gobiids. Main conclusions Both genetic and morphological data strongly supported two species of monkey gobies that were formerly identified as subspecies: N. fluviatilis in the Black Sea basin, Don and Volga Rivers, and the Kumo‐Manych Depression, and Neogobius pallasi in the Caspian Sea and Volga River delta. Genetic origins of introduced N. fluviatilis populations indicated a common invasion pathway shared with other introduced Ponto‐Caspian fishes and invertebrates.     

The genetic variability of the red king crab, <Emphasis Type="Italic">Paralithodes camtschatica</Emphasis> (Tilesius, 1815) (Anomura,Lithodidae) introduced into the Barents Sea compared with samples from the Bering Sea and Kamchatka region using eleven microsatellite loci

The intentional introduction of red king crab, Paralithodes camtschatica (Tilesius, 1815) in the Barents Sea represent one of a few successful cases and one that now supports a commercial fishery. Introductions of alien species into new environments are often associated with genetic bottlenecks, which cause a reduction in the genetic variation, and this could be important for the spreading potential of the species in the Atlantic Ocean. Red king crab samples collected in the Varangerfjord located on the Barents Sea (northern Norway) were compared with reference crab samples collected from the Bering Sea and Kamchatka regions in the Pacific Ocean. All samples were screened for eleven microsatellite loci, based on the development of species-specific primers. The observed number of alleles per locus was similar, and no reduction in genetic variation, including gene diversity and allelic richness, was detected between the Varangerfjord sample and the reference sample from Okhotsk Sea near Kamchatka, indicating no genetic bottlenecking at least for the microsatellite loci investigated. The same results were found in comparison with the sample from Bering Sea. The level of genetic differentiation among the samples, measured as overall F _ST across all loci, was relatively low (0.0238) with a range of 0.0035–0.1000 for the various loci investigated. The largest pairwise F _ST values were found between the Bering Sea and Varangerfjord/Barents Sea samples, with a value of 0.0194 across all loci tested. The lowest value (0.0101) was found between the Varangerfjord and Kamchatka samples. Genetic differentiation based on exact tests on allele frequencies revealed highly significant differences between all pairwise comparisons. The high level of genetic variation found in the Varangerfjord/Barents Sea sample could be of significance with respect to further spreading of the species to other regions in the North Atlantic Ocean.     

Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units

We examined the structure, intranuclear distribution and activity of ribosomal DNA (rDNA) in Nico-tiana sylvestris (2n=2x=24) and N. tomentosiformis (2n=2x=24) and compared these with patterns in N. tabacum (tobacco, 2n=4x=48). We also examined a long-established N. tabacum culture, TBY-2. Nicotiana tabacum is an allotetraploid thought to be derived from ancestors of N. sylvestris (S-genome donor) and N. tomentosiformis (T-genome donor). Nicotiana sylvestris has three rDNA loci, one locus each on chromosomes 10, 11, and 12. In root-tip meristematic interphase cells, the site on chromosome 12 remains condensed and inactive, while the sites on chromosomes 10 and 11 show activity at the proximal end of the locus only. Nicotiana tomentosiformis has one major locus on chromosome 3 showing activity and a minor, inactive locus on chromosome 11. In N. tabacum cv. 095-55, there are four rDNA loci on T3, S10, S11/t and S12 (S11/t carries a small T-genome translocation). The locus on S12 remains condensed and inactive in root-tip meristematic cells while the others show activity, including decondensation at interphase and secondary constrictions at metaphase. Nicotiana tabacum DNA digested with methylcytosine-sensitive enzymes revealed a hybridisation pattern for rDNA that resembled that of N. tomentosiformis and not N. sylvestris. The data indicate that active, undermethylated genes are of the N. tomentosiformis type. Since S-genome chromosomes of N. tabacum show rDNA expression, the result indicates rDNA gene conversion of the active rDNA units on these chromosomes. Gene conversion in N. tabacum is consistent with the results of previous work. However, using primers specific for the S-genome rDNA intergenic sequences (IGS) in the polymerase chain reaction (PCR) show that rDNA gene conversion has not gone to completion in N. tabacum. Furthermore, using methylation-insensitive restriction enzymes we demonstrate that about 8% of the rDNA units remain of the N. sylvestris type (from ca. 75% based on the sum of the rDNA copy numbers in the parents). Since the active genes are likely to be of an N. tomentosiformis type, the N. sylvestris type units are presumably contained within inactive loci (i.e. on chromosome S12). Nicotiana sylvestris has approximately three times as much rDNA as the other two species, resulting in much condensed rDNA at interphase. This species also has three classes of IGS, indicating gene conversion has not homogenised repeat length in this species. The results suggest that methylation and/or DNA condensation has reduced or prevented gene conversion from occurring at inactive genes at rDNA loci. Alternatively, active undermethylated units may be vulnerable to gene conversion, perhaps because they are decondensed and located in close proximity within the nucleolus at interphase. In TBY-2, restriction enzymes showed hybridisation patterns that were similar to, but different from, those of N. tabacum. In addition, TBY-2 has elevated rDNA copy number and variable numbers of rDNA loci, all indicating rDNA evolution in culture. Received: 17 November 1999; in revised form: 3 February 2000 / Accepted: 3 February 2000     

Phylogeny of the slow lorises (genusNycticebus): An approach using mitochondrial DNA restriction enzyme analysis

Mitochondrial DNA polymorphisms in 15 specimens of three species of slow lorises-Nycticebus coucang, N. intermedius, andN. pygmaeus-were analyzed in order to study the evolutionary relationships among the species. Eight restriction types were observed in the samples. Phylogenetic trees constructed on the basis of genetic distances showed that the slow lorises sort into two clusters: four types ofN. coucang and three types ofN. intermedius plus one type ofN. pygmaeus. Our results suggest that there are two valid species in the genusNycticebus-N. coucang, andN. pygmaeus-and thatN. intermedius should be included withinN. pygmaeus. Divergence between the two species may have begun 2.7 Ma (million years ago). Evolution of gross morphology, chromosomes, and mitochondrial DNA in the slow lorises appears to be concordant.     

Patterns of genetic differentiation in two annual bromegrasses,Bromus lanceolatus andB. hordeaceus (Poaceae)

Infraspecific genetic differentiation was analysed in two tetraploid annual bromegrasses,Bromus lanceolatus (from N Africa) andB. hordeaceus (from N Africa and France). Genetic analysis of populations was based on allozyme polymorphisms at 17 loci. Different fixed heterozygous phenotypes were scored in both species, according to their allopolyploid origin. In N Africa, more variation occurred among populations ofB. lanceolatus than ofB. hordeaceus. The variation was not randomly distributed among populations of both species. InB. lanceolatus, differentiation was correlated with climatic variables rather than with geographic distance between populations. Higher correlation of genetic differentiation with geographic distance occurred inB. hordeaceus, particularly at large geographic scale, between French and N African populations. Within each region, the populations appeared weakly genetically differentiated, even when belonging to different subspecies.     

Characterization of expressed sequence tag‐derived microsatellites from the kuruma prawn,Marsupenaeus japonicus

The kuruma prawn, Marsupenaeus japonicus, is a commercially important benthic marine crustacean in East Asia. Understanding the species’ population structures will be very important for its proper stock assessment and management strategy. Herein, 13 polymorphic microsatellite loci originating from expressed sequence tag libraries of M. japonicus were isolated and characterized. Number of alleles per locus ranged from two to 15, observed and expected heterozygosities ranged from 0.250 to 0.906 and from 0.310 to 0.932, respectively. The adequate level of variability within the population renders these microsatellite loci ideal markers for population genetic analysis of M. japonicus.     

PHYLOGENETIC RELATIONSHIPS OF BRYDE'S WHALES IN THE WESTERN NORTH PACIFIC AND ADJACENT WATERS INFERRED FROM MITOCHONDRIAL DNA SEQUENCES1

To clarify phylogenetic relationships of Bryde's whales, we examined the nucleotide sequence of the mitochondrial control region and cytochrome b gene in 33 animals: 12 from offshore waters of the western North Pacific, five from off the Solomon Islands, and 16 from the East China Sea and coastal waters of Kochi in southwestern Japan. For reference purposes, homologous sequences from four Balaenoptera species including four Bryde's whales collected in the eastern Indian Ocean were added. We found whales from the three sampling areas to be genetically distinct. The control region sequences suggested that the whales from the three areas separate at higher than the populational level from one another. The cytochrome b data indicated that genetic differences between whales off the Solomon Islands and animals in the other two areas are equivalent to values found among recognized Balaenoptera species, although such a relationship was not observed between the other two areas. We conclude that whales in the East China Sea and coastal waters of Kochi separate from Bryde's whales in offshore waters of the western North Pacific at higher than the populational level but lower than the specific level (i. e., at the subspecific level) and that whales off the Solomon Islands do not belong genetically to the Bryde's whale as previously recognized.     

The impact of Yangtze River discharge on the genetic structure of a population of the rock bream,Oplegnathus fasciatus

As a rocky reef species, Oplegnathus fasciatus displays significant geographic differences that may be congruent with patterns of molecular variation. We used 10 polymorphism microsatellite loci to characterize the genetic structure and test the impact of ocean currents and the Yangtze River on the population genetic connectivity of the rock bream, O. fasciatus, sampled from Jiaonan (JN), Zhoushan (ZS) and Taiwan (TW). The average number of alleles was 17.78, with a total of 160 alleles, and the average allele value in the East China Sea (ZS?=?13.70) was higher than that in the Yellow Sea (JN?=?6.70). The individuals at the ZS location showed the highest expected heterozygosity (He?=?0.86), Nei's genetic diversity (H?=?0.84) and Shannon genetic diversity (I?=?2.21). Genetic bottleneck tests showed that individuals had experienced a recent bottleneck effect in the JN location. AMOVA analysis showed that 12.19% of genetic variation existed among populations, indicating significant population genetic differentiation in the species. The values of the population pairwise differentiation index (F_st and Φ_pt) ranged from 0.01 to 0.29. The UPGMA tree showed two diverged genealogical branches corresponding to sampling localities (Clade A?=?JN, Clade B?=?ZS and TW) in the species. The AMOVA and STRUCTURE analyses suggested that O. fasciatus may be composed of two stocks in the examined range, and the freshwater discharge from the Yangtze River might act as a physical barrier to genetic exchange between north and south China stocks of the species.