Low mtDNA Cytb diversity and shallow population structure of Eleutheronema tetradactylum in the East China Sea and the South China Sea

Eleutheronema tetradactylum is an economically important fish species in China water. To investigate the genetic diversity and describe population structure of it, an 1151 base pair (bp) fragment of the mitochondrial DNA Cytb sequence was analyzed in 120 individuals from four populations in the East China Sea and the South China Sea. A total of 16 haplotypes were defined by 24 variable nucleotide sites. High level of haplotype diversity and low nucleotide diversity were observed in all populations. The results of AMOVA detected that 89.44% of the genetic variation occurred within populations. Significant genetic differentiations were detected among populations (0.05097, P < 0.05), but no large-scale regional differences were detected. Analysis of neutral evolution and mismatch distribution suggested no recent population expansion happened. The present results provided new information for genetic assessment, fishery management and conservation of this species.     

Evaluation of the productivity of walleye pollock generations in the northern Sea of Okhotsk

Based on data on the abundances of various age groups in the northern Sea of Okhotsk in 1984–2008, the productivity of 33 generations of walleye pollock born between 1975 and 2007 was evaluated in two ways. The first approach allowed a retrospective estimation by abundance of the first nine one-year age groups, and the second one was a perspective estimation using the abundance index of the nearest recruitment—3- and 4-year-olds—that enabled us to evaluate the productivity of a generation before it enters into spawning and commercial stocks. These productivity estimates were compared to the data of annual catches and the dynamics of spawning stock for many years. A high value of walleye pollock stock was shown to be supported by several productive and highly productive generations, a medium value—by one productive and one moderately productive or by two moderately productive generations, and a low value—by one productive, or moderately productive, and low productive generations. In addition, overall mortality rates were calculated for generations with various productivity levels. The greatest variability of mortality rates was observed in immature walleye pollock; the maximum mortality rate was typical for the recruitment of highly abundant generations, and the minimum, for the least abundant ones. The lowest mortality was recorded at the age of mass maturation. Mature individuals of generations with various productivity levels showed insignificant differences in overall mortality rates.     

Temporal genetic stability and high effective population size despite fisheries-induced life-history trait evolution in the North Sea sole

Heavy fishing and other anthropogenic influences can have profound impact on a species' resilience to harvesting. Besides the decrease in the census and effective population size, strong declines in mature adults and recruiting individuals may lead to almost irreversible genetic changes in life-history traits. Here, we investigated the evolution of genetic diversity and effective population size in the heavily exploited sole (Solea solea), through the analysis of historical DNA from a collection of 1379 sole otoliths dating back from 1957. Despite documented shifts in life-history traits, neutral genetic diversity inferred from 11 microsatellite markers showed a remarkable stability over a period of 50 years of heavy fishing. Using simulations and corrections for fisheries induced demographic variation, both single-sample estimates and temporal estimates of effective population size (N(e) ) were always higher than 1000, suggesting that despite the severe census size decrease over a 50-year period of harvesting, genetic drift is probably not strong enough to significantly decrease the neutral diversity of this species in the North Sea. However, the inferred ratio of effective population size to the census size (N(e) /N(c) ) appears very small (10(-5) ), suggesting that overall only a low proportion of adults contribute to the next generation. The high N(e) level together with the low N(e) /N(c) ratio is probably caused by a combination of an equalized reproductive output of younger cohorts, a decrease in generation time and a large variance in reproductive success typical for marine species. Because strong evolutionary changes in age and size at first maturation have been observed for sole, changes in adaptive genetic variation should be further monitored to detect the evolutionary consequences of human-induced selection.     

Distribution and abundance dynamics of jellyfish in the Sea of Okhotsk

The seasonal and interannual trends in the distribution and abundance of jellyfish (Scyphozoa and Hydrozoa) in the epipelagic and mesopelagic areas of the Sea of Okhotsk during 1992–2005 were examined on the basis of trawl survey data. The area of occurrence, biomass, and the numbers of Scyphozoa in the epipelagic layer were the smallest in spring; in summer and fall their abundance sharply increased and then decreased in winter. In contrast to the epipelagic zone, the numbers of scyphomedusae in the mesopelagic layer were significantly lower in the summer than in the winter and spring. This probably indicates that a part of scyphomedusae winter in the mesopelagic. Hydrozoa in both the epi- and mesopelagic areas were more numerous in the winter and spring. Jellyfish biomass and abundance greatly changed from year to year. Thus, in fall the biomass of scyphomedusae and hydromedusae in the epipelagic zone varied from 166 to 1271 and from 6 to 49 kg/km², respectively.     

夏季鄂霍茨克海公海区狭鳕渔场环境特征

根据鄂霍茨克公海区狭鳕资源声学评估调查资料,研究了狭鳕分布状况及渔场环境特征,并分析了狭鳕行动分布与环境的关系．结果表明,8月公海区狭鳕密集群位于55°N以北、水深小于500m的海域,其主要分布水层在150～300m之间;调查期间狭鳕只为索饵群体,主要摄食太平洋磷虾,狭鳕密集区一般也为太平洋磷虾高密度分布区;8月公海区水温跃层大致在0～50m之间,强度为0．25℃     

Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration

Effective population size (Ne) is an important genetic parameter because of its relationship to loss of genetic variation, increases in inbreeding, accumulation of mutations, and effectiveness of selection. Like most other genetic approaches that estimate contemporary Ne, the method based on linkage disequilibrium (LD) assumes a closed population and (in the most common applications) randomly recombining loci. We used analytical and numerical methods to evaluate the absolute and relative consequences of two potential violations of the closed-population assumption: (1) mixture LD caused by occurrence of more than one gene pool, which would downwardly bias Ne and (2) reductions in drift LD (and hence upward bias in Ne) caused by an increase in the number of parents responsible for local samples. The LD method is surprisingly robust to equilibrium migration. Effects of mixture LD are small for all values of migration rate (m), and effects of additional parents are also small unless m is high in genetic terms. LD estimates of Ne therefore accurately reflect local (subpopulation) Ne unless m>～5-10%. With higher m, Ne converges on the global (metapopulation) Ne. Two general exceptions were observed. First, equilibrium migration that is rare and hence episodic can occasionally lead to substantial mixture LD, especially when sample size is small. Second, nonequilibrium, pulse migration of strongly divergent individuals can also create strong mixture LD and depress estimates of local Ne. In both cases, assignment tests, Bayesian clustering, and other methods often will allow identification of recent immigrants that strongly influence results. In simulations involving equilibrium migration, the standard LD method performed better than a method designed to jointly estimate Ne and m. The above results assume loci are not physically linked; for tightly linked loci, the LD signal from past migration events can persist for many generations, with consequences for Ne estimates that remain to be evaluated.     

Implications of the variance effective population size on the genetic conservation of monoecious species

The concept of variance effective population size [Ne_(v)] and other expressions are reviewed and described for specific sampling steps in germplasm collection and regeneration of monoecious species. Special attention is given to procedures for computing the variance of the number of contributed gametes [V(k)] to the next generation. Drift, as it occurs between generations, was considered to contain a component due to the sampling of parents and a subsequent component due to the sampling of gametes. This demonstrates that drift, caused by reduction of seed viability, damages the genetic integrity of accessions stored in germplasm banks. The study shows how mating designs, such as plant-to-plant or chain crossings with additional female gametic control, can partially alleviate this problem. Optimal procedures for increasing Ne_(v) when collecting germplasm in the field are also discussed. The effect of different female and male gametic control strategies on Ne_(v) is considered under several situations. Practical examples illustrating the use of V(k) and Ne_(v) expressions are given.     

Assessment of the consumption of walleye pollock eggs by nekton and jellyfish in the northern Sea of Okhotsk in the spring

In the northern Sea of Okhotsk, nekton and jellyfish consumed as many as 831 × 10⁹ walleye pollock eggs per day in 2011. The nekton exerted the highest pressure, viz., 98.3% of the overall predation on pollock egg by aquatic animals. Of the entire quantity of consumed eggs, 55.9% were eaten by herring, 35.9% by walleye pollock, 6.5% by Sakhalin sole, and 1.7% by jellyfish. Among jellyfish, scyphomedusae Cyanea capillata and Chrysaora melonaster, as well as the hydromedusa Tima sachalinensis consumed the largest quantities of eggs. The total consumption of pollock egg by aquatic animals in 2011 was estimated at 42.4 × 10¹², or 11.4% of the entire quantity of eggs that were spawned by walleye pollock in the waters of the northern part of the sea. The total amount of pollock eggs that were eaten by herring and pollock together for 51 days in 2011 amounted to 38.9 × 10¹², which was 5.7 times as much as that in 2002. Thus, a significant growth of predation on pollock eggs by their main consumers, viz., herring and walleye pollock, was observed in 2011. This was caused by an increase in the populations of both species during the recent years and also by a higher concentration of pollock eggs.     

Glacial Holocene environment of the southeastern Okhotsk Sea: evidence from geochemical and palaeontological data

Environmental conditions and productivity changes in the southeastern Okhotsk Sea have been reconstructed for the last 20 ka using planktonic and benthic foraminiferal oxygen isotope records and calcium carbonate, organic carbon and opal content data from two sediment cores. Species variability in benthic foraminiferal and diatom assemblages provides additional palaeoceanographic evidence. AMS radiocarbon dating of the sediments and oxygen isotope stratigraphy serve as the basis for the age models of the cores for the last 20 ¹⁴C kyr and for correlation between environmental variations in the Okhotsk Sea, and regional and global climate changes. Benthic foraminiferal assemblages in the two cores (depth 1590 and 1175 m) varied with time, so that we could recognise seven zones with different species composition. Changes in the benthic foraminiferal assemblages parallel major environmental and productivity variations. During the last glaciation, fluxes of organic matter to the sea floor showed strong seasonal variations, indicated by the presence of abundant A. weddellensis and infaunal Uvigerina spp. Benthic foraminiferal assemblages changed with warming at 12.5–11 and 10–8 ¹⁴C kyr BP, when productivity blooms and high organic fluxes were coeval with global meltwater pulses 1A and 1B. Younger Dryas cooling caused a decline in productivity (11–10 kyr BP) affecting the benthic faunal community. Subsequent warming triggered intensive diatom production, opal accumulation and a strong oxygen deficiency, causing significant changes in benthic fauna assemblages from 5.26–4.4 kyr BP to present time.     

Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua)

DNA from archived otoliths was used to explore the temporal stability of the genetic composition of two cod populations, the Moray Firth (North Sea) sampled in 1965 and 2002, and the Bornholm Basin (Baltic Sea) sampled in 1928 and 1997. We found no significant changes in the allele frequencies for the Moray Firth population, while subtle but significant genetic changes over time were detected for the Bornholm Basin population. Estimates of the effective population size ( N _e ) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and N _e 's most likely range in the thousands. There was no apparent loss of genetic variability and no evidence of a genetic bottleneck for either of the populations. Calculations of the expected levels of genetic variability under different scenarios of N _e showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by N _e 's exceeding thousand. Recent fishery-induced bottlenecks can, however, not be ruled out as an explanation for the apparent discrepancy between high levels of variability and recently reported estimates of N _e  << 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species' biology and extremely low N _e / N ratios. Our data suggest that very small N _e 's are not likely to be of general concern for cod populations and, accordingly, most populations do not face any severe threat of losing evolutionary potential due to genetic drift.     

High genetic variation in leopards indicates large and long-term stable effective population size

In this paper we employ recently developed statistical and molecular tools to analyse the population history of the Tanzanian leopard (Panthera pardus), a large solitary felid. Because of their solitary lifestyle little is known of their past or present population dynamics. Eighty-one individuals were scored at 18 microsatellite loci. Overall, levels of heterozygosity were high (0.77 +/- 0.03), with a small heterozygote deficiency (0.06 +/- 0.03). Effective population size (Ne) was calculated to be 38 000-48 000. A Ne:N ratio of 0.42 (average from four cat studies) gives a present population size of about 100 000 leopards in Tanzania. Four different bottleneck tests indicated that this population has been large and stable for a minimum of several thousand years. FST values were low and no significant genetic structuring of the population could be detected. This concurs well with the large migration values (Nm) obtained (>3.3 individuals/generation). Our analysis reveals that ecological factors (e.g. disease), which are known to have had major impact on other carnivore populations, are unlikely to have impacted strongly on the population dynamics of Tanzanian leopards. The explanation may be found in their solitary life-style, their often nonconfrontational behaviour toward interspecific competitors, or that any bottlenecks have been of limited size, localized, or too short to have affected genetic variation to any measurable degree. Since the genetic structuring is weak, gene flow is not restricted to within protected areas. Local loss of genetic variation is therefore not of immediate concern.     

Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin

There is an increasing awareness that the long-term viability of endemic island populations is negatively affected by genetic factors associated with population bottlenecks and/or persistence at small population size. Here we use contemporary samples and historic museum specimens (collected 1888–1938) to estimate the effective population size (N _e) for the endangered yellow-eyed penguin (Megadyptes antipodes) in South Island, New Zealand, and evaluate the genetic concern for this iconic species. The South Island population of M. antipodes—constituting almost half of the species’ census size—is thought to be descended from a small number of founders that reached New Zealand just a few hundred years ago. Despite intensive conservation measures, this population has shown dramatic fluctuations in size over recent decades. We compare estimates of the harmonic mean N _e for this population, obtained using one moment and three likelihood based-temporal methods, including one method that simultaneously estimates migration rate. Evaluation of the N _e estimates reveals a harmonic mean N _e in the low hundreds. Additionally, the inferred low immigration rates (m = 0.003) agree well with contemporary migration rate estimates between the South Island and subantarctic populations of M. antipodes. The low N _e of South Island M. antipodes is likely affected by strong fluctuations in population size, and high variance in reproductive success. These results show that genetic concerns for this population are valid and that the long-term viability of this species may be compromised by reduced adaptive potential.     

Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.     

The effects of cyclic dynamics and mating system on the effective size of an island mouflon population

The Haute Island mouflon (Ovis aries) population is isolated on one small (6.5 km2) island of the remote Kerguelen archipelago. Given a promiscuous mating system, a cyclic demography and a strong female-biased sex ratio after population crashes, we expected a low effective population size (Ne). We estimated Ne using demographic and temporal genetic approaches based on genetic information at 25 microsatellite loci from 62 and 58 mouflons sampled in 1988 and 2003, respectively. Genetic Ne estimates were higher than expected, varying between 104 and 250 depending on the methods used. Both demographic and genetic approaches show the Haute Island Ne is buffered against population crashes. The unexpectedly high Ne likely results from the cyclic winter crashes that allow young males to reproduce, limiting the variance of male reproductive success. Based on individual-based simulations, we suggest that despite a strongly female-biased sex ratio, the effects of the mating system on the effective population size more closely resemble random mating or weak polygyny.     

Preferred habitat and effective population size drive landscape genetic patterns in an endangered species

Landscape genetics provides a framework for pinpointing environmental features that determine the important exchange of migrants among populations. These studies usually test the significance of environmental variables on gene flow, yet ignore one fundamental driver of genetic variation in small populations, effective population size, N_e. We combined both approaches in evaluating genetic connectivity of a threatened ungulate, woodland caribou. We used least-cost paths to calculate matrices of resistance distance for landscape variables (preferred habitat, anthropogenic features and predation risk) and population-pairwise harmonic means of N_e, and correlated them with genetic distances, F_ST and D_c. Results showed that spatial configuration of preferred habitat and N_e were the two best predictors of genetic relationships. Additionally, controlling for the effect of N_e increased the strength of correlations of environmental variables with genetic distance, highlighting the significant underlying effect of N_e in modulating genetic drift and perceived spatial connectivity. We therefore have provided empirical support to emphasize preventing increased habitat loss and promoting population growth to ensure metapopulation viability.     

Population genetic structure of walleye pollock <Emphasis Type="Italic">Theragra chalcogramma</Emphasis> (Gadidae,Pisces) from the Bering Sea and Sea of Okhotsk

Walleye pollock Theragra chalcogramma Pallas occupies a central place in ecosystems of the North Pacific and is an important target species of fisheries. The species is characterized by daily vertical, spawning, feeding, and wintering migrations and spawning occurring under the sea ice. Since population structure estimation by the tagging with recapture is inefficient in walleye pollock, the pollock resources are difficult to estimate by conventional methods, requiring population genetic studies with molecular markers. The population genetic structure of five spawning aggregations from the Bering Sea was for the first time studied with ten microsatellite loci: Tch5, Tch10, Tch11, Tch12, Tch14, Tch16, Tch17, Tch19, Tch20, and Tch22. A spatially distant sample from the Sea of Okhotsk was used as a reference group. Polymorphism for the markers reached 100%, and heterozygosity of individual loci ranged from 41 to 95% in different populations. It was shown the aggregations of interest are in goodness-to-fit the Hardy-Weinberg equilibrium (HWE) at hole, while the Sea of Okhotsk sample demonstrated a sex bias: the heterozygosity at Tch16 in males was significantly lower than in females. The highest discriminative power was observed for Tch10, Tch20, and Tch22. F _ST genetic distances between populations were typical for marine fishes. A mixed composition was supposed for the sample from the region of the underwater Shirshov Ridge, which serves as a natural partial geographic barrier between the Olyutor-Karagin and Koryak walleye pollock stocks. With the Shirshov sample excluded, F _ST scatter plots and the spatial autocorrelation approach supported isolation by distance for the aggregations. An influence of abiotic factors on the population structure was assumed for walleye pollock of the Bering Sea.     

The effect of optimal harvesting on the dynamics of size and genetic composition of a two-age population

The effect of optimal stationary harvesting at a constant harvest rate on the dynamics of a two-age population is considered. It has been shown analytically that harvesting a fixed rate of the population size of only one age cohort is optimal. As has been observed, the maximum of revenue function is unattainable in the case of concurrent harvesting of both age cohorts. It has been demonstrated that the direction of natural selection does not explicitly change when unselectively harvesting individuals; however, the adaptive genetic diversity of an unharvested population can be lost due to harvesting.     

Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population

We have analyzed 24 loci including autosomal and Y-chromosomal short tandem repeats (STRs), Y-indel, and sex-determining marker in a sample of 267 unrelated individuals from the Mongolian population using the GlobalFiler? PCR Amplification Kit to provide an expanded and more reliable forensic database. Khalkh among 15 Mongolian minor-groups accounts for about 80% of the entire Mongolian population. A total of 267 different DNA profiles were found in this work. The highest gene diversity was observed in the SE33 (0.9376) locus, and the lowest value was found in the TPOX (0.6142) locus. Although individual power of discrimination estimates varied at the studied loci, combined probability of match from the 21 STR loci was estimated to be 1.139?×?10^?24, which is highly informative. Based on the results of pairwise F _ST genetic distances and multi-dimensional scaling plot showed that Mongolians were clustered into Europeans and Asians, although Mongolia is geographically located in Northeastern Asia. Thus, the present survey of the Mongolian population may help establish a comprehensive reference database for forensic and population genetic analyses.     

Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population

The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms.