Distinguishing between two sympatric Acanthopagrus species from Dapeng Bay, Taiwan, using morphometric and genetic characters

Morphometric and genetic data were used to compare two sympatric and morphologically similar species, Acanthopagrus berda and Acanthopagrus taiwanensis , in Dapeng Bay, South-western Taiwan. A principle component analysis of morphological data indicated a distinction between the two species, with pectoral fin length and eye diameter accounting for 32·27% of the variation. Interspecific sequence divergence, based on mtDNA cytochrome b (0·118 ± 0·01), was larger than intraspecific divergences between haplotypes (0·007 for A. taiwanensis and 0·003 for A. berda ). Individuals of the two species clustered into different groups in three phylogenetic trees with 100% bootstrap support. The mean observed heterozygosity for eight microsatellite loci was 0·471 ± 0·202 for A. taiwanensis and 0·637 ± 0·145 for A. berda . Nei's unbiased measure of interspecific genetic distance ( D _S) was 1·334. F _ST (0·134) and R _ST (0·404) values indicated significant differentiation between species. An unrooted neighbour-joining tree was constructed by allele-sharing distances and the factorial correspondence analysis split all specimens into two distinct clusters. The results of morphometric, mtDNA and microsatellite analyses indicated the presence of two species, A. taiwanensis and A. berda .     

Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Mitochondrial DNA sequence divergence between two cryptic species of Lethenteron, with reference to an improved identification technique

Genetic divergences and population structures were examined in the cryptic Lethenteron sp. N and sp. S, based on mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (CO I) region sequences. An improved method of discrimination between L . sp. N and sp. S was found using PCR, with diagnostic primers for each species-specific sequence in the mtDNA CO I region. Identification of 50 individuals of each species by this analysis was consistent with that by allozyme analysis of nuclear DNA. L . sp. N and sp. S, identified on the basis of diagnostic alleles at five allozymic loci, were independently grouped in a neighbour-joining (NJ) tree, with a large sequence difference (mean ±  s . d . = 9·10 ± 0·36%) between them. Within each species, the values of sequence divergence among localities were significantly higher in L . sp. S (1·61 ± 0·44%) than in L . sp. N (1·10 ± 0·48%). On the tree and nested clade analyses, several phylogenetic groups comprising geographically close localities were detected in the former, although scarcely detected in the latter, probably resulting from dispersal pattern differences between them.     

Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific Ocean

To clarify the taxonomic status of Gymnura crebripunctata and Gymnura marmorata , the extent of morphological and nucleotide variation between these nominal species was examined using multivariate morphological and mitochondrial DNA comparisons of the same characters with congeneric species. Discriminant analysis of 21 morphometric variables from four species ( G. crebripunctata , G. marmorata , Gymnura micrura and Gymnura poecilura ) successfully distinguished species groupings. Classification success of eastern Pacific species improved further when specimens were grouped by species and sex. Discriminant analysis of size-corrected data generated species assignments that were consistently accurate in separating the two species (100% jackknifed assignment success). Nasal curtain length was identified as the character which contributed the most to discrimination of the two species. Sexual dimorphism was evident in several characters that have previously been relied upon to distinguish G. crebripunctata from G. marmorata . A previously unreported feature, the absence of a tail spine in G. crebripunctata , provides an improved method of field identification between these species. Phylogenetic and genetic distance analyses based on 698 base pairs of the mitochondrial cytochrome b gene indicate that G. crebripunctata and G. marmorata form highly divergent lineages, supporting their validity as distinct species. The closely related batoid Aetoplatea zonura clustered within the Gymnura clade, indicating that it may not represent a valid genus. Strong population structuring (overall Φ _ST = 0·81 ,P < 0·01) was evident between G. marmorata from the Pacific coast of the Baja California peninsula and the Gulf of California, supporting the designation of distinct management units in these regions.     

The Systematics and Reproductive Biology of the Galeus arae Subspecific Complex (Chondrichthyes: Scyliorhinidae)

Galeus arae is currently classified as a complex of three subspecies (Galeus arae arae, Galeus arae antillensis, and Galeus arae cadenati). Morphometric and meristic analyses, size at maturity, and variation in color patterns, support the recognition of these taxa as distinct species. All species have well-developed nidamental glands and are oviparous. Galeus arae comprises two geographically disjunct populations that are not distinguishable by the characters we examined. A northern population occurs along the east and Gulf coasts of North America from South Carolina to the Mississippi delta, and the northern coast of Cuba to the north-eastern tip of the Yucatan. A southern population occurs along the Caribbean coasts of Honduras, Nicaragua, and Costa Rica, and some neighboring islands. Galeus antillensis occurs on the northern coasts of Hispaniola and Puerto Rico, and off many of the Leeward Islands. Galeus cadenati occurs off the Caribbean coasts of Panama and Colombia. Distributional data suggest that the three species are distributed allopatrically.     

Temporal resource partitioning varies with individual competitive ability: a test with Arctic charr Salvelinus alpinus visiting a feeding site from a refuge

The relationship among relative size, growth rate and diel visits into a feeding compartment were studied in Arctic charr Salvelinus alpinus , a species known for its flexible activity patterns. Individual swimming activity from a refuge compartment into an uncovered feeding compartment was studied using an automated passive integrated transponder system. Approximately half of the individuals in four groups of S. alpinus spent 70–80% of their time in the feeding compartment, regardless of the time of day. The remaining individuals spent nearly as much time (70–80%) in the feeding compartment during the night, but only spent c. 20% of their time in the feeding compartment during the day. These individuals had a lower mean ± s . d . masses (13·17 ± 4·34 g) and growth rate (daily growth coefficient, G = 0·80 ± 1·19) than those individuals that spent most of their time in the feeding compartment during the day (mass = 16·65 ± 5·73 g and G = 2·04 ± 0·81). This indicated that some smaller fish were absent from the feeding compartment during daytime, possibly to avoid aggression from larger conspecifics. In the open compartment, the aggressive interactions were more frequent in daylight than during night and always low in the covered compartment.     

A low rate of replacement substitutions in two major Ovis aries mitochondrial genomes

Two mitochondrial DNA molecules which represent major Ovis aries mtDNA haplogroups were cloned and comparatively sequenced to assess the degree of intraspecific variation. A total of 9623 bp that correspond to 58% of both mitochondrial genomes were determined. The control region, the Cyt b , ND2, ND3, ND4L, COIII and 12 tRNA genes, including the origin of L-strand replication, were completely characterized. Partial sequence information was obtained from the 12S and 16S rRNA and an additional six protein coding and six tRNA genes. The control regions of the two mtDNAs showed a nucleotide divergence of 4·34% while coding regions differed by 0·44%. The number of sheep coding region substitutions was similar to values observed in intraspecific comparisons of mitochondrial DNAs that represent remote points in genealogical trees of mice and humans. However, replacement substitutions were only observed at ∼30% of the rate in mice and ∼20% of the rate in humans. Nucleotide substitutions with a potential for phenotypic effects were found in the 12S and 16S rRNA and in the ND1 and COIII genes.     

The genetic architecture of correlations among growth‐related traits and male age at maturation in rainbow trout

Heritabilities and genetic correlations among growth‐related traits of two cultured strains (Rainbow Springs and Spring Valley) of rainbow trout Oncorhynchus mykiss were estimated using restricted maximum likelihood methods with a three‐generation pedigree. Heritability was high (>0·50 ± 0·03) for body mass and condition factor but moderate (0·35 ± 0·04) for age at sexual maturity in males. Body mass and age at sexual maturation were phenotypically correlated in the families of one experimental strain, Rainbow Springs, and had a positive genetic correlation (0·26 ± 0·03) across families from both test strains (Rainbow Springs and Spring Valley). This indicates that faster growing individuals were more likely to mature at 2 years of age than slower growing individuals in the two hatchery strains investigated. Microsatellite markers of body mass quantitative tract loci (QTL) were reconfirmed as being located on linkage groups B, G, N, 5 and new markers on Oi were detected. Some QTL effects were restricted to specific sampling dates suggesting temporal expression of QTL. QTL for condition factor were limited to linkage group G in both strains. Three suggestive QTL for precocious maturation mapped to similar regions as those for body mass in the Rainbow Springs families while no associations were evident in the Spring Valley families. The results suggest that these regions may play a role in the basis for genetic and phenotypic correlations between body mass and precocious maturation in this species.     

Genetic population structure of red snappers (Lutjanus malabaricus Bloch & Schneider, 1801 and Lutjanus erythropterus Bloch, 1790) in central and eastern Indonesia and northern Australia

The genetic population structure of red snapper Lutjanus malabaricus and Lutjanus erythropterus in eastern Indonesia and northern Australia was investigated by allozyme electrophoresis and sequence variation in the control region of mtDNA. Samples were collected from eight sites in Indonesia and four sites in northern Australia for both species. A total of 13 allozyme loci were scored. More variable loci were observed in L. malabaricus than in L. erythropterus . Sequence variation in the control region (left domain) of the mitochondrial genome was assessed by RFLP and direct sequencing. MtDNA haplotype diversity was high ( L. erythropterus , 0·95 and L. malabaricus , 0·97), as was intraspecific sequence divergence, ( L. erythropterus , 0·0–12·5% and L. malabaricus , 0·0–9·5%). The pattern of mtDNA haplotype frequencies grouped both species into two broad fisheries stocks with a genetic boundary either between Kupang and Sape ( L. malabaricus ) or between Kupang and Australian Timor Sea ( L. erythropertus ). The allozyme analyses revealed similar boundaries for L. erythropterus . Seven allozymes stocks compared to two mtDNA stocks of L. malabaricus including Ambon, which was not sampled with mtDNA, however, were reported. Possible reasons for differences in discrimination between the methods include: i) increased power of multiple allozyme loci over the single mtDNA locus, ii) insufficient gene sampling in the mtDNA control region and iii) relative evolutionary dynamics of nuclear (allozyme loci) and mitochondrial DNA in these taxa. Allozyme and haplotype data did not distinguish separate stocks among the four Australian locations nor the central Indonesian (Bali and Sape locations) for both L. malabaricus and L. erythropterus.     

Studies on the nature of the Z-discs in skeletal muscle fibres of sharks, Etmopterus spinax L. and Galeus melastomus Rafinesque-Schmaltz

The ultrastructural details of Z-discs from red, intermediate, and white axial muscle fibres from the sharks Etmopterus spinax and Galeus melastomus are described. Red fibre Z-discs contain the most amorphous matrix material, and are thicker (100–115 nm) than intermediate (85–88 nm) and white Z-discs (75–80 nm). Four sets of oblique bars extend tangentially from each thin filament. In each set two bars are present, those of white fibres are close together (approximately 5 nm), while those of red fibres are separated by a distance of 15 nm. A model of shark Z-disc structure is proposed. The denaturation (heat transition) temperatures of the muscle proteins were studied by differential scanning calorimetry (DSC). The heat transitions of collagen, actin, and myosin were identified; the actin heat transition temperature increased in the sequence red, intermediate, and white. The total protein pattern of red and white muscle were studied by SDS electrophoresis. A protein with a molecular weight of about 55000 may represent a Z-disc protein.     

Diet and feeding strategy of blackmouth catshark Galeus melastomus

Diet and feeding strategy of the blackmouth catshark Galeus melastomus in the deep waters of the eastern Ionian Sea were investigated. Sampling was carried out using experimental bottom longline fishing at depths ranging from 300 to 855 m in summer and autumn 2010. Diet variability with fish size, season, area, sex and depth zone was tested and only season was found to significantly affect the diet of the species. Of the 870 stomachs examined, only 1·4% were empty. Cumulative prey curves showed that the sample sizes were adequate to describe the main prey items of the diet for both seasons. Prey identified belonged primarily to three major groups: fishes, cephalopods and dendrobranchiatan and caridean shrimps. In autumn, the above three major groups were found as principal prey, whereas in summer cephalopods followed by fishes were the principal prey and shrimps were found as secondary prey. SIMPER analysis indicated high dissimilarity between seasons and highlighted that Sepiolidae, Myctophidae, fishes, cephalopods, shrimps and other crustaceans contributed to seasonal differences in the diet of G. melastomus. The prey diversity index was higher in autumn than in summer. A high dietary overlap was observed between the two seasons. Galeus melastomus behaved as an opportunistic predator with a variety of unimportant prey in its diet. Feeding strategy indicated that G. melastomus holds a generalist niche with a considerable specialization at the individual level. This strategy seems to be an adaptation to a food‐scarce environment, as typified in deep‐water habitats.     

Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation

Aphyocypris kikuchii is a cyprinid species endemic to northern and eastern Taiwan and is the only primary freshwater fish native east of the Coastal Mountain Range. In total, 92 individuals of A. kikuchii from seven populations in three regions of the island were surveyed for mitochondrial DNA (mtDNA) variation. High haplotype diversity ( h = 0·989) and low nucleotide diversity ( π = 0·009) of mtDNA were detected. Negative values of Tajima's D and unimodal mismatch distributions probably reflect a history of recent demographic expansions from small populations. Three major haplotype clusters displayed geographically non-overlapping distributions, indicating a long-term isolation between regions. Hierarchical analysis of molecular variance showed significant genetic structuring among populations ( Φ _ST= 0·66). Significant haplotype heterogeneity was also detected among populations within regions ( Φ _SC= 0·41, P < 0·001) and among regions ( Φ _CT= 0·43, P < 0·05). Molecular clock estimates of coalescence in the three major mtDNA lineages indicated coalescence in the most recent common ancestor c. 0·11–0·39 million years ago. Haplotypes of cluster B nested as interior nodes in the haplotype network, indicating that migrations from Shueilian (SL) populations to the northern region (cluster A) and to the eastern region (cluster C) may have occurred independently. Lineages A and B + C should be managed as two distinct evolutionarily significant units, while the northern, SL and southern groups should be managed as separate management units.     

On Argyripnus atlanticus, Maul 1952 (Pisces, Stomiatoidei), with a description of post-larval forms

Twelve specimens standard length 16·8–53·0 mm, including 2 post-larvae (hitherto unknown to the genus), of Argyripnus atlanticus Maul 1952 are reported. The external characteristics of adults are summarized and the internal features of 2 specimens described. A swimbladder is present. The post-larvae are described and their distinction from other maurolicid genera given. Development of the species is considered in terms of morphometric growth changes and increase with age of photophore number. A relatively longer tail and shorter preventral length is characteristic of juveniles and post-larvae, but other body proportions remain approximately constant at all growth stages. A full complement of photophores is attained at approximately 43 mm standard length. Morphological examination of the ovaries of 7 females indicate that first full maturation has not been reached. Development, geographic variation and habits of the species are discussed.     

Galeus longirostris,a new species of the sawtail catshark from Japan

Galeus longirostris sp. nov. is described based on 46 specimens taken off the southern part of Japan. It is distinguished from all known species ofGaleus in having a considerably longer snout. This species is morphologically close toG. nipponensis, which commonly occurs off the southern part of Japan, but differs in having longer preoral length than the mouth width, a bluntly rounded snout, larger pectoral fins, a shorter interspace between anal and lower caudal fins, and a greater number of monospondylous vertebrae.     

Population dynamics of fisheries stock enhancement

A comparative analysis was performed on sixteen morphometric characters, in three different juvenile sterlet Acipenser ruthenus L. populations. Specimens were collected from a wild population in the Serbian part of the Danube River ( n  = 46), from aquaculture stocks in the Czech Republic originating from Russia ( n  = 40), and aquaculture stocks in the Slovak Republic originating from Slovakian part of the Danube River ( n  = 28). Average values for total length were 29·9 ± 3·9 cm, 29·1 ± 3·7 cm and 27·3 ± 7·7 cm for Serbia, Czech Republic and Slovak Republic, respectively. Populations were compared using t ‐test and sequential Bonferroni correction for multiple comparisons was applied in order to determine significant differences between them. Results of analysis showed that all three populations differed in prebarbel length, interocular distance and maximum head width. Although all these characters are head‐related, head length itself was very uniform among all populations. The natural population from the Serbian part of the Danube River differed from the populations reared in aquaculture in seven morphometric characters. The two populations reared in aquaculture consistently showed lower morphological variability than the wild population, even though they had different genetic backgrounds (Russia and Slovakia). Future genetic studies will show if this tendency is caused by a reduction in genetic variability.     

小口白甲鱼都柳江种群mtDNA D环的序列变异及遗传多样性

采用PCR结合DNA测序技术,测定分析了易危鱼类小口白甲鱼(Onychostoma lini)都柳江种群36个个体mtDNA D环约470bp序列的变异及遗传多样性。结果表明,在36个个体中,该序列的长度为469～475bp,其碱基组成为A+T的平均含量(68.4%)高于G+C(31.6%)。共检测到25个多态位点,其中转换19个、颠换6个。核苷酸多样性(π)为0.00575,平均核苷酸差异数(K)为2.695。36个个体分属5个单倍型,单倍型多样度(Hd)为0.260,单倍型间的平均遗传距离(P)为0.026。5个单倍型构建的UPGMA系统树聚为2个分支。目前小口白甲鱼都柳江种群mtDNA D环序列存在着较丰富的变异和遗传多样性。     

Differentiation of Salvelinus malma charr and Taranetz Charr Salvelinus taranetzi from PCR-RFLP analysis of mitochondrial DNA

Genetic differentiation of two sympatric charr species, the Dolly Varden charr (Salvelinus malma Walbaum) and the Taranetz charr (S. taranetzi Kaganovski), has been studied. Restriction fragment length polymorphism (RFLP) analysis has been used to compare three mitochondrial DNA (mtDNA) fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified via polymerase chain reaction (PCR). The divergence between S. malma and S. taranetzi inferred from mtDNA nucleotide sequences is 2.8%; between S. leucomaenis and S. taranetzi, 7.1%; and between S. malma and S. leucomaenis, 7.5%. The absence of common haplotypes and the degree of divergence indicate that the Dolly Varden charr and the Taranetz charr are genetically isolated and confirm that S. taranetzi may be regarded as a separate species.     

Morphological and molecular tools in identifying the Mediterranean limpets Patella caerulea, Patella aspera and Patella rustica

Allozyme electrophoresis, a partial nucleotide sequence of a mitochondrial gene for cytochrome oxidase I (COI) and discriminant analysis of shell morphometric characters were used to study the relationships among the Sicilian marine gastropods of the Patella genus. Allozyme and mtDNA markers unequivocally distinguished the species and were very useful markers in correctly classifying the different species when morphological characters overlapped each other. Several allozyme loci and many nucleotide positions were diagnostic of species. In contrast, the discriminant analysis of simple morphometric shell characters failed to adequately discriminate the species, suggesting that environmental factors influence colouration and morphological patterns in the Patella species. Our results underline the importance of a genetic approach, as compared to a morphological approach, in discriminating the Mediterranean Patella species.     

Population genetic structure of northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis> in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D-loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplo-type and nucleotide diversity were 0.5261 ± 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise G4ST values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Genetic isolation between Atlantic and Mediterranean albacore populations inferred from mitochondrial and nuclear DNA markers

Genetic population structure of Atlantic and Mediterranean albacore Thunnus alalunga was investigated using nucleotide sequence variations of the glucose‐6‐phosphate dehydrogenase gene intron ( G6PD ) and the mitochondrial DNA (mtDNA) D‐loop region ( Dloop ). Restriction analysis using Ase I digestion detected two major restriction types ( A and B ) at the Dloop locus with strong frequency differences between Atlantic and Mediterranean samples. Thirty‐six individuals of 100 Mediterranean albacore were of the B type whereas no B type individuals were found in the Atlantic samples ( n  = 102). Phylogenetic analysis using nucleotide sequence data of the Dloop locus indicated that the B type lineage recently arose from the ancestral A lineage in the Mediterranean Sea and has not dispersed into the Atlantic Ocean. The frequencies of two alleles ( L and S ) at the G6PD locus were significantly different between the samples from the Atlantic ( L  = 0·495) and the Mediterranean ( L  = 0·725), but no significant heterogeneity was observed between mtDNA‐ A and ‐ B types of the Mediterranean sample. These molecular data indicate that gene flow between the Atlantic and Mediterranean albacore populations have been considerably restricted and strongly suggest these populations should continue to be treated as two distinct management units.