Ancient DNA analysis of the Japanese sea lion (Zalophus californianus japonicus Peters, 1866): preliminary results using mitochondrial control-region sequences

In this study, we successfully extracted ancient DNA from skeletal remains of the Japanese sea lion-a species that is practically extinct-from archaeological sites and determined a partial sequence of its mitochondrial DNA control region. A molecular phylogenetic tree constructed by the neighbor-joining (NJ) method showed that the sequences from Japanese sea lions clustered together, with a high bootstrap value, and that this cluster was closest to the California sea lion cluster. The distinctly divergent cluster of Japanese sea lions reflected the morphological classification of these animals as a distinct species of the genus Zalophus; however, proximity to the California sea lion cluster simultaneously implied conformation with the traditional classification of these animals as a subspecies of Zalophus californianus. The average amount of nucleotide substitution between the Japanese and California sea lions was 7.02%. The Japanese and California sea lions were estimated to have diverged 2.2 million years ago, i.e., in the late Pliocene Epoch. This is the first report on a genetic analysis of the Japanese sea lion.     

珠江口崖门鲈鱼年龄和生长的研究

本文依据1983年6月至1986年1月对290尾鲈鱼年龄和生长的调查资料,阐明鲈鱼鳞片年轮特征并计算出鲈鱼体长与鳞长、体长与体重的关系式。研究表明:3龄以前属幼鱼阶段,体长和体重的相对增长率较大,生长指标较高,3龄以后进入成鱼生长阶段。其生长适合von Bertalanffy生长方程,体重生长曲线的拐点位于3.05龄。因此以3龄、体重3.5公斤左右的鲈鱼作为商品鱼加以捕捞,经济效益最高。     

Phylogeography study of Ammodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact

To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.     

Changes in Adélie penguin breeding populations in Lützow-Holm Bay, Antarctica, in relation to sea-ice conditions

The Adélie penguin, Pygoscelis adeliae, an important component of the Antarctic marine ecosystem, is closely associated with sea ice. Using data collected by Japanese Antarctic Research Expeditions since the 1960s, we examined trends in breeding populations of this species around Lützow-Holm Bay. Ten colonies ranging in size from 10 to 2,500 individuals were counted along the Soya Coast. Populations fluctuated synchronously, and overall increased at most colonies, except for two: one located deep inside the bay and another where human disturbance was substantial. Populations tended to increase during, or after, periods of sparse sea ice in summer, a condition that occurred once every decade. An increase in population size also occurred 5 years after a winter of extensive sea ice and after a winter of especially reduced sea ice.     

DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago

DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese‐breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour‐joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan‐specific cryptic species from trans‐Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans‐Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.     

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major,Temminck et Schlegel) Populations in Japan

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F_ST = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.     

Thoracic adaptation to high altitude

Growth in the thoracic region and its adaptation to higher altitude was investigated in boys between 5 to 18 years of Rajput origin at two altitudes, i. e. Rampur Bushahr (800 m above sea level) and Kinnaur (3,000 m above sea level). Both places are located in Himachal Pradesh. The sample includes 405 individuals From Bushahr and 676 individuals from Kinnaur. The results of this study reveal that as the higher altitudes are attained the vital capacity also increases relatively more, and these differences become more pronounced after adolescence, indicating longer time of apnoea. The population living at higher altitudes is also characterised by a significant greater chest length.     

Seasonal variation of chromophore composition in the eye of the Japanese dace, <Emphasis Type="Italic">Tribolodon hakonensis</Emphasis>

The relationship between seasonal variation and the effect of several different environmental factors on chromophore composition was investigated in the eye of the Japanese dace, Tribolodon hakonensis which lives either in rivers or in the sea. Eyes obtained from river and sea populations had both retinal (A1) and 3,4-didehydroretinal (A2) all through the year but the ratio of these chromophores showed seasonal variation the relative amount of A2 was higher in winter and lower in summer. Besides seasonal variation, A2 showed marked differences depending on habitat: the highest proportion of A2 was 67% in January and the lowest 13% in July, in the river population, whereas in the sea population the highest and the lowest values were only 30 and 6%, respectively, during the same months. The seasonal variation in gonadosomatic index showed no correlation to variations in A2 proportion, and the maximum difference in water temperature between summer and winter was ca. 15°C for both habitats. Because spectral conditions at the locations of capture of both river and sea populations were similar, we conclude that Japanese dace eyes are affected by exogenous factors related to differences between freshwater and seawater environments.     

Early starvation limits survival in amphidromous fishes

Newly hatched amphidromous larvae drift downstream to the sea. Since there is practically no food available for drifting larvae, an extended downstream migration may enhance the risk of starvation. We hypothesized that early survival of amphidromous fish varies among populations according to the length of the river, due to its effect on larval starvation. The hypothesis was tested with the common Japanese amphidromous goby, Rhinogobius brunneus . Based on morphological characteristics, larvae were categorized as being in an endogenous feeding state (EFS) or irrecoverable starved state (ISS). The frequency of ISS larvae in the population from a long river was nearly twice the frequency in the population from a short stream. More than half of larvae were judged to be dying during downstream migration in the comparatively long river, although this was possibly an underestimation. It is suggested that early starvation limits reproductive success far from the sea.     

臭氧处理海水对扇贝卵的孵化及幼虫生长的影响

主要研究了用臭氧处理海水在经过连续充气曝气12、24h、不经充气曝气的处理水及没经臭氧处理的正常海水,进行海湾扇贝、虾夷扇贝受精卵的孵化和幼虫培育实验。结果表明,海湾扇贝受精卵在经过24h曝气的处理水中孵化率最高为92％,其次为没经过处理的正常海水为76％,曝气12h为16％,没经过曝气的为0;虾夷扇贝受精卵在经过24h曝气的处理水中孵化率最高为88%,其次为没经过处理的正常海水为85％,曝气12h为15％,没经过曝气为0。海湾扇贝幼虫培养在没经过处理的正常海水和经24h曝气的处理水中生长较快,曝气12h较慢;虾夷扇贝幼虫则是没经过处理的正常海水生长最快,其次是经24h曝气的处理水,而曝气12h较慢,成活率方面也表现出一定的差异,从而为臭氧处理海水在贝类育苗上的应用提供一定的指导。     

花鲈群体的遗传变异

采用水平淀粉凝胶电泳技术对花鲈群体的遗传结构进行了研究 ,共检测了中国沿海花鲈 14 6尾和 40尾日本东京湾花鲈。其群体的多态位点比例为 0 2 667— 0 53 3 3 ,观测杂合度和预期杂合度分别为 0 0 2 11— 0 0 515和0 0 3 98— 0 0 797。中日花鲈在LDH ,GPI 1 ,GPI 2 基因位点上的等位基因接近完全置换。中国花鲈各群体之间的根井遗传距离为 0 0 0 0 4— 0 0 0 11,平均值约为 0 0 0 80 ;而中日花鲈间的根井遗传距离为 0 1870— 0 1954,平均值为 0 192 6。以上结果表明中国花鲈群体间遗传变异很小 ,中日花鲈间遗传变异远大于中国花鲈群体间的遗传距离。     

Aplysiallene,a New Bromoallene as an Na,K-ATPase Inhibitor from the Sea Hare,Aplysia kurodai

A new bromoallene metabolite, named aplysiallene, was isolated from the Japanese sea hare, Aplysia kurodai, as an Na,K-ATPase inhibitor. Its structure was elucidated by spectroscopic methods. The known metabolites, laurinterol and debromolaurinterol, isolated from this animal were also evaluated for their Na,K-ATPase inhibitory activity.     

The effects of climate change on harp seals (Pagophilus groenlandicus)

Harp seals (Pagophilus groenlandicus) have evolved life history strategies to exploit seasonal sea ice as a breeding platform. As such, individuals are prepared to deal with fluctuations in the quantity and quality of ice in their breeding areas. It remains unclear, however, how shifts in climate may affect seal populations. The present study assesses the effects of climate change on harp seals through three linked analyses. First, we tested the effects of short-term climate variability on young-of-the year harp seal mortality using a linear regression of sea ice cover in the Gulf of St. Lawrence against stranding rates of dead harp seals in the region during 1992 to 2010. A similar regression of stranding rates and North Atlantic Oscillation (NAO) index values was also conducted. These analyses revealed negative correlations between both ice cover and NAO conditions and seal mortality, indicating that lighter ice cover and lower NAO values result in higher mortality. A retrospective cross-correlation analysis of NAO conditions and sea ice cover from 1978 to 2011 revealed that NAO-related changes in sea ice may have contributed to the depletion of seals on the east coast of Canada during 1950 to 1972, and to their recovery during 1973 to 2000. This historical retrospective also reveals opposite links between neonatal mortality in harp seals in the Northeast Atlantic and NAO phase. Finally, an assessment of the long-term trends in sea ice cover in the breeding regions of harp seals across the entire North Atlantic during 1979 through 2011 using multiple linear regression models and mixed effects linear regression models revealed that sea ice cover in all harp seal breeding regions has been declining by as much as 6 percent per decade over the time series of available satellite data.     

The contrasted evolutionary fates of deep‐sea chemosynthetic mussels (Bivalvia,Bathymodiolinae)

Bathymodiolinae are giant mussels that were discovered at hydrothermal vents and harboring chemosynthetic symbionts. Due to their close phylogenetic relationship with seep species and tiny mussels from organic substrates, it was hypothesized that they gradually evolved from shallow to deeper environments, and specialized in decaying organic remains, then in seeps, and finally colonized deep‐sea vents. Here, we present a multigene phylogeny that reveals that most of the genera are polyphyletic and/or paraphyletic. The robustness of the phylogeny allows us to revise the genus‐level classification. Organic remains are robustly supported as the ancestral habitat for Bathymodiolinae. However, rather than a single step toward colonization of vents and seeps, recurrent habitat shifts from organic substrates to vents and seeps occurred during evolution, and never the reverse. This new phylogenetic framework challenges the gradualist scenarios “from shallow to deep.” Mussels from organic remains tolerate a large range of ecological conditions and display a spectacular species diversity contrary to vent mussels, although such habitats are yet underexplored compared to vents and seeps. Overall, our data suggest that for deep‐sea mussels, the high specialization to vent habitats provides ecological success in this harsh habitat but also brings the lineage to a kind of evolutionary dead end.     

Fertilization potential and polyspermy prevention in the egg of the nemertean, Cerebratulus lacteus

We investigated the electrical properties of the egg of the nemertean worm Cerebratulus, and found evidence that an electrically-mediated polyspermy block operates for a period of about 1 hr after fertilization. At fertilization, in natural or artificial sea water, the membrane potential shifts from its resting level of about -66 mV to a peak of about +43 mV, and in most cases remains greater than 0 mV for more than 1 hr. The average potential during the first 30 min is +22 +/- 8 mV (SD, n = 12). When the external Na+ concentration is reduced from 486 to 51 mM (choline substituted) the fertilization potential amplitude is reduced; the average potential during the first 30 min is -27 +/- 21 mV (SD, n = 5). Eggs inseminated in 51 mM Na+ sea water become polyspermic, indicating that polyspermy prevention depends on an electrically-mediated mechanism. The electrical block is required for about 60 min, since transfer to 51 mM Na+ sea water during this period results in polyspermy. During the first hour following fertilization, the egg is also developing a permanent, nonelectrical block; the degree of polyspermy which results upon transfer to low Na+ sea water decreases progressively with time. The permanent block appears to be at the level of the egg plasma membrane or glycocalyx, since the egg envelope is not a barrier to sperm penetration, nor does its removal induce polyspermy. Electron micrographs show no obvious changes in the morphology of the extracellular layers, plasma membrane or cortex of the egg after fertilization.     

Aplysiallene, a new bromoallene as an Na, K-ATPase inhibitor from the sea hare, Aplysia kurodai

A new bromoallene metabolite, named aplysiallene, was isolated from the Japanese sea hare, Aplysia kurodai, as an Na, K-ATPase inhibitor. Its structure was elucidated by spectroscopic methods. The known metabolites, laurinterol and debromolaurinterol, isolated from this animal were also evaluated for their Na, K-ATPase inhibitory activity.     

Genetic structure of Japanese sea cucumbers (<Emphasis Type="Italic">Apostichopus japonicus</Emphasis>) along the Sanriku coast supports the effect of earthquakes and related tsunamis

The Japanese common sea cucumber (Apostichopus japonicus) is a major marine product from Sanriku, Japan, but its populations were severely affected by the 2011 Tohoku earthquake, possibly decreasing its genetic diversity and increasing its extinction risk. In this study, we estimated the genetic structure and diversity of sea cucumbers from Touni and Yamada Bays of Sanriku over 4 years after the earthquake. The between-population genetic structure was estimated using two mitochondrial DNA regions (cytochrome c oxidase subunit I and 16S rDNA). Genetic differentiation (as measured by pairwise F_ST) was not significant between locations. Thus, even after the tsunami, gene flow and genetic diversity among the two sea cucumber populations were maintained. Our data also suggested that sea cucumbers in Sanriku experienced population expansion of about 0.20–0.24 million years ago, during the stable Mindel-Riss interglacial period. We conclude that A. japonicus populations in Sanriku could maintain their genetic structure throughout multiple disastrous tsunamis over the past several 1000 years. The high dispersal ability of planktonic larvae may enable the entrance of new recruits, thereby reducing risks associated with genetic structure and diversity changes stemming from mass die-offs in a given body of water from the past to the present.     

The Chehr Abad "Salt men" and the isotopic ecology of humans in ancient Iran

We have carried out isotopic analysis (δ(13)C and δ(15)N) on five salt-preserved bodies from the salt mine at Chehr Abad, Iran, dating from the 4th C. BC through to the 4th C. AD. In an attempt to identify the geographical origins of these people, we have analyzed over a hundred archeological bone samples from various archeological sites in Iran. From the faunal remains, we observe that the entire ecosystem appears to be enriched in (15)N, which we suggest is due to the semi-arid nature of the region. We have also observed a number of cattle remains from one site (Nargas Tepe) which have a significant C(4) component to their diet from the 4th millennium BC. By combining our data with those published by [Bocherens et al.: Environ Archaeol 5 (2000) 1-19; Bocherens et al.: J Arch Sci 33 (2006) 253-264], we suggest that two of the "mummies" may have come from the Tehran/Qazvin Plain region (i.e., relatively local to the salt mine), and a further two appear on isotopic grounds to have come from the northeast of Iran or the Turkmenistan steppes. The fifth (no. 4), the best preserved, appears to have come from further afield. Collectively, these mummies and their contexts augment our knowledge of social mobility and technical innovation in Iran during the Achaemenid period.     

And the Last Shall Be First: Heterochrony and Compensatory Marine Growth in Sea Trout (Salmo trutta)

Early juvenile growth is a good indicator of growth later in life in many species because larger than average juveniles tend to have a competitive advantage. However, for migratory species the relationship between juvenile and adult growth remains obscure. We used scale analysis to reconstruct growth trajectories of migratory sea trout (Salmo trutta) from six neighbouring populations, and compared the size individuals attained in freshwater (before migration) with their subsequent growth at sea (after migration). We also calculated the coefficient of variation (CV) to examine how much body size varied across populations and life stages. Specifically, we tested the hypothesis that the CV on body size would differ between freshwater and marine environment, perhaps reflecting different trade-offs during ontogeny. Neighbouring sea trout populations differed significantly in time spent at sea and in age-adjusted size of returning adults, but not on size of seaward migration, which was surprisingly uniform and may be indicative of strong selection pressures. The CV on body size decreased significantly over time and was highest during the first 8 months of life (when juvenile mortality is highest) and lowest during the marine phase. Size attained in freshwater was negatively related to growth during the first marine growing season, suggesting the existence of compensatory growth, whereby individuals that grow poorly in freshwater are able to catch up later at sea. Analysis of 61 datasets indicates that negative or no associations between pre- and post-migratory growth are common amongst migratory salmonids. We suggest that despite a widespread selective advantage of large body size in freshwater, freshwater growth is a poor predictor of final body size amongst migratory fish because selection may favour growth heterochrony during transitions to a novel environment, and marine compensatory growth may negate any initial size advantage acquired in freshwater.