Movement patterns of endangered Roanoke logperch (Percina rex)

Abstract –  Using mark–recapture methods, we studied movements of endangered Roanoke logperch ( Percina rex Jordan & Evermann), a benthic darter, at 12 riffle–run sites over a 9-year-long period in the Roanoke River, Virginia, USA. Our primary objective was to characterise movements among transects within sites, but we opportunistically recorded two between-site movements as well. Our recapture rate was low (22 of 485 marked fish), but most recaptured fish exhibited movements between tagging and recapture, relocating either to another transect within a site (12 fish) or to another site altogether (two fish). Within sites, Roanoke logperch exhibited fidelity over time to the areas in which they were initially marked. These restricted areas were lengthier than transects (>15 m) but shorter than entire riffle–runs (<150 m). The two between-site movements were extensive (3.2 and 2.5 km), observed over a long mark–recapture interval (2 and 5 years, respectively), and may have represented migratory or dispersal movements. Their detection required an unusually extensive study design. Both small- and large-scale movements fulfil important ecological functions for Roanoke logperch, and greater study of such movements in this and other darter species is needed to inform conservation choices.     

Low genetic variation and isolation of northern peripheral populations of a red seaweed (Grateloupia lanceola)

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An assessment of hatchery effects on Florida bass (Micropterus salmoides floridanus) microsatellite genetic diversity and sib‐ship reconstruction

Black bass populations have been augmented with aggressive aquaculture as a fisheries management tool over the past several decades. The purpose of our study was to estimate changes in genetic diversity and effective number of breeders (N_b) contributing to and represented in fingerling samples from two stages in the Florida bass (Micropterus salmoides floridanus) production process: post‐fry grow‐out and post‐feed training. We screened 120 wild‐sourced brood fish and 900 fingerlings representing two periods at nine microsatellite loci and determined relatedness (R_xy), effective number of breeders (N_b) and general diversity trends over the hatchery production process. The construction of putative full‐sib partitions revealed that cohorts within stage 1 and 2 fingerling samples consisted of large numbers of small sib groups (80 and 55 groups respectively). Effective number of breeders calculated using the linkage disequilibrium method was estimated at 60–100 depending on the N_b parameters, representing a N_b/N of >0.5. Our assessment suggests that the current raceway breeding practice appear to be adequate at maintaining substantial portions of the genetic diversity of the breeding stock.     

Microsatellite DNA analysis and hydrodynamic modelling reveal the extent of larval transport and gene flow between management zones in an exploited marine fish (Glaucosoma hebraicum)

Determining the extent of dispersal in exploited marine fishes is essential for understanding their population dynamics and optimising management. The West Australian dhufish, Glaucosoma hebraicum, is a highly sought‐after, large and long‐lived reef‐dwelling species, endemic to south‐western Australia. Stock assessments indicate that this indicator species is overexploited. The fishery is managed using a zone‐based system, which implicitly assumes a high degree of demographic independence among zones. While tagging studies indicate limited movement of adult G. hebraicum, there is no understanding of the spatial scale of dispersal of its larvae and thus the true extent of interdependence of management zones. We analysed 13 microsatellite DNA loci to characterise the extent of gene flow, and conducted particle tracking simulations to model larval transport in this species. Genetic data demonstrated that some local recruitment was likely, but that on a broad scale gene flow between the management zones was extensive, and the entire fishery represents a single genetic stock. Hydrodynamic modelling predicted that the majority of dhufish larvae recruit from within the management zone where they are spawned, and that inter‐annual variation in current velocities has limited effect on the extent of larval transport. Because management zones are likely to be largely independent in terms of both larval and adult recruitment, heavy localised fishing pressure has the potential to reduce the abundance and reproductive capacity of this species in highly fished areas, but it should have limited impact on neutral genetic diversity.     

Direct evidence of limited dispersal of the reef fish Parapercis colias (Pinguipedidae) within a marine reserve and adjacent fished areas

1. Spillover of organisms from marine reserves may augment adjacent areas, and is often cited as an important reason for the establishment of marine protected areas. Spillover is dependent on residence or limited dispersal of organisms resulting in an increase in their abundance and size within a marine reserve. 2. To investigate movement (i.e. spillover versus residence) we tagged and released 90 blue cod Parapercis colias (Pinguipedidae) at each of four sites, two in and two adjacent to Long Island–Kokomohua Marine Reserve, Marlborough Sounds, New Zealand. The study was done 4–5 years after establishment of the no‐take reserve. 3. Abundances of blue cod were similar in and out of the marine reserve, but mean estimated size was 4 cm larger in the reserve than at fished sites. 4. Fewer tag resights were made in the reserve than at fished sites, and tagged blue cod were resighted at greater depths in the reserve than at fished sites. 5. Most resights (75% for fished sites, 73% for reserve sites) were made within 100 m of the tagging sites, and the number of resights declined through time, though tagged individuals were resighted up to 31 months after tagging. 6. The lower number of tag resights at reserve sites, despite the lack of extraction, is consistent with some blue cod at reserve sites moving longer distances than those at fished sites. 7. The greater size of individuals in the reserve and limited dispersal of a proportion of the population show that survivorship of blue cod is increased within marine reserves. 8. Computer simulations based on measured dispersals indicate that even marine reserves of a few hundred metres long‐shore extent have the potential to supplement fished populations nearby. 9. These data provide direct evidence of limited dispersal of the most common edible reef fish in the Marlborough Sounds. Blue cod will grow to larger sizes in marine reserves and via spillover will become available to fishers in adjacent areas of contiguous coast. Copyright © 2000 John Wiley & Sons, Ltd.     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

The landscape genetics of syntopic topminnows (Fundulus notatus and F. olivaceus) in a riverine contact zone

The metapopulation dynamics of a species are influenced by the spatial arrangement of preferred habitats across a landscape. Increasing habitat patchiness can result in greater population subdivision, leading to more pronounced population genetic structure. Therefore, even subtle differences in habitat preferences among species could lead to substantial differences in genetic structure. Members of the Fundulus notatus species complex of topminnows include a headwater specialist and a large river specialist with broadly overlapping geographical distributions. Both species are often found in the same drainage systems, but partially isolated by divergent habitat preferences. The purpose of this research was to determine whether distribution along a stream continuum in a contact zone influences population genetic patterns in two species of topminnow (Fundulus olivaceus and Fundulus notatus). Fish were collected in the summers of 2010–2012, and habitat data were collected in summer 2012, within all major tributaries of the Saline River in southern Illinois. In total, 523 fish were genotyped using seven microsatellite loci to assess genetic variation. Species distributions in F. notatus and F. olivaceus were associated with habitat factors that covaried with cumulative drainage area. Populations of F. olivaceus showed a greater level of genetic structure reflected in a significant pattern of isolation by distance, while populations of F. notatus showed no such pattern. Spatial autocorrelation analysis revealed that at an individual level, both species became increasingly divergent with waterway distance. Overall, clear interspecific differences in habitat preferences were translated into measurable but relatively subtle differences in population genetic structure.     

大西洋鳕微卫星引物对太平洋鳕的适用性

利用Genbank中大西洋鳕的7对微卫星引物,对太平洋鳕基因组DNA进行PCR扩增。这7对引物均可较稳定地扩增出条带,它们分别是Gmo2、Gmo3、Gmo8、Gmo19、Gmo35、Gmo36、Gmo37,并且扩增出的7个位点均表现出多态性,共获得69个等位基因,每个位点的等位基因数目为4～17,大小为111～227bp。在7个位点上2种鱼的等位基因的大小存在着不同程度的差异。其中Gmo37在大西洋鳕和太平洋鳕中扩增出的条带的长度差异最大,基本无重合部分,分别为220～290bp和144～226bp,本研究结果以期对2种鳕科鱼类遗传结构的进一步研究提供帮助。     

Influences of in-stream habitat and upstream land-use on site occupancy of the Kanawha darter (Etheostoma kanawhae): A narrowly distributed species from the New River (Upper Kanawha Basin)

1. Freshwater communities are threatened by the conversion of natural landscapes for urban and agricultural purposes. Changes to land use may disrupt stream nutrient and geomorphological processes and reduce water quality, increase sedimentation, and decrease habitat heterogeneity eventually leading to species loss and decreases in ecosystem productivity. Endemic species are frequently at greater risk of habitat-mediated fragmentation and extirpation due to their constrained distributions.
2. The Kanawha darter (Etheostoma kanawhae) is an understudied fish endemic to the New River Drainage in North Carolina and Virginia, USA. To investigate the potential effect(s) of land-use change on Kanawha darters, naïve occupancy was modelled using instream habitat characteristics and upstream forest cover.
3. Generalized linear models revealed that instream habitat and forest cover are reliable predictors of Kanawha darter site occupancy. Specifically, models demonstrated that occupancy increased in reaches with reduced stream width, velocity, and bedrock substrate but higher concentrations of coarse woody material. Kanawha darter occupancy was also positively associated with the extent of forest cover in upstream catchments.
4. Although Kanawha darters are not currently considered imperilled, most populations occurred in isolated reaches separated by large sections of unoccupied habitat. Continuing ex-urban development in riparian zones is likely to be the primary threat to Kanawha darters and other endemic species in this catchment. Resource managers and stakeholders should preserve forest cover in headwaters and occupied tributaries and protect or restore riparian zones along the main-stem South and North Forks of the New River to preserve high-quality habitat and enhance connectivity among isolated Kanawha darter populations.
5. As human populations in montane regions continue to grow, there is a need to understand how land-use change affects endemic freshwater species. This study further supports the importance of retaining forest cover as an effective strategy for protecting and restoring populations of endemic fishes in high-gradient streams.

     

Efficacy of calcein as a chemical marker of green‐lipped mussel (Perna canaliculus) larvae and its potential use for tracking larval dispersal

An optimal chemical shell marking protocol was developed for the New Zealand green‐lipped mussel, Perna canaliculus with a view to its future use in larval tracking experiments. Larval P. canaliculus aged either 10, 15 or 19 days post fertilization were immersed in treatments of 50, 100 and 200 mg L^?1 of calcein for a period of 24 h before measurements of shell mark brightness were taken. There was 100% marking success in all calcein treatments for all age classes, with 19‐day larvae immersed in 200 mg L^?1 calcein producing the brightest mark. Growth was not affected by calcein immersion; however, 10‐day larvae exhibited significantly higher levels of mortality compared with 15‐ and 19‐day larvae suggesting a reduced resilience to the marking protocols in younger larvae. In a mass staining experiment, a solution of 100 mg L^?1 calcein was used to successfully stain15.6 million hatchery reared P. canaliculus larvae. Calcein, therefore, offers a low impact method with which to stain the sensitive early life stages of this species thus providing a rapid method for identifying individuals of interest, i.e. individuals released in the wild or specific family lines within a hatchery environment.     

鲢微卫星标记研制及其在鲢和鳙遗传多样性研究中的应用

鲢(Hypophthalmichthys molitrix)和鳙(Aristichys nobilis)是中国特有的四大家鱼中2个重要成员,主要分布于黑龙江、长江和珠江水系.传统人工养殖依靠天然鱼苗.但是,人口增长和人类经济活动加剧使其天然产卵和孵化场消失或遭到破坏.人工育苗技术虽然解决了鱼苗供应问题,但由于遗传资源管理和使用方法的不完善,使两种鱼的生长表现、抗病抗逆性和遗传多样性等都有明显的降低.另外,因洪水导致的养殖个体逃逸也使天然群体的遗传多样性受到干扰.近年来,比较大规模的人工鱼苗放流实践也加剧了对天然群体遗传多样性的扰动.对这些问题的深入研究迫切需要一套适用的分子标记.为评价鲢和鳙的遗传多样性、确定它们的遗传分化和地理分化、科学合理地管理和开发利用遗传资源,本研究构建了富集GT微卫星序列的基因组短片段文库.随机选择并测序的97个克隆中有87个含有微卫星序列.根据其中的21条序列,设计了22对微卫星标记引物并用来分析了在长江荆州段捕获的32尾野生鲢和7尾野生鳙的遗传多样性.所有标记引物在两种鱼中通用.在全部样品中共发现129个等位基因.每位点等位基因数在3～10个,平均5.9个.不同标记揭示的遗传多样性指数在0.33～2.00,平均1.22.由于使用的鱼个体数少,如鳙,只有7个个体,样品也只来源于长江荆州江段.本研究无法基于两种鱼的天然分布,对两种鱼的遗传分化、地理种群多样性比较、养殖群体和天然群体差异等问题进行深入分析.但是,这组标记的研制将有助于这2个中国特有经济鱼种的遗传多样性分析、遗传资源的管理及开发利用等相关研究.本研究中,微卫星DNA标记的研制使用了固定有微卫星核心序列的磁珠.这样的磁珠与两端接有已知序列的DNA片段杂交能富集出含有微卫星核心序列的片段.通过扩增和连接转化,可方便地获得大量含微卫星核心序列的片段.与已有的方法不同的是,本研究用AFLP方法的某些步骤使片段两端加上已知引物序列,方便易行.迄今,这两种鱼还没有微卫星标记连锁图谱.构建这样的图谱是本项目研究的长远目标.     

Effects of Protein Concentration,Plasticiser, and pH on the Properties of Protein Films from Whitemouth Croaker (Micropogonias furnieri) Residues

ABSTRACT

Proteins have been used extensively because of their relative abundance, nutritional qualities, and film-forming ability with a good structural integrity and mechanical properties. This study investigated the effects of protein isolate and glycerol concentration and pH on the properties of protein films obtained from Whitemouth croaker (Micropogonias furnieri) residues. The films were evaluated for mechanical properties, thickness, water solubility, water vapor permeability (WVP), and morphological properties. The lowest water solubility of the films occurred at low pHs and low glycerol concentrations. The films had high elongation and higher tensile strength when prepared with higher concentrations of protein isolate, lower concentrations of glycerol, and at lower pHs. The WVP and thickness of the films had a low correlation coefficient. The films were rough and had irregular surfaces. These results indicated that protein isolates from fish of low commercial value can be used as a component of new polymeric films for packaging. However, more studies are needed to assess their barrier action against oxygen, thermal behaviors, and their performance in different types of packaging.     

Incidence and timing of wild and escaped farmed Atlantic salmon (Salmo salar) in Norwegian rivers inferred from video surveillance monitoring

Run timing of escaped farmed Atlantic salmon Salmo salar vs. wild fish was compared by the use of video camera surveillance in 15 rivers over several years, covering 1600 km of the Norwegian coastline (from 58°N to 69°N). Annual runs of wild salmon varied among rivers from <200 fish to more than 10 000. During the surveillance period that for most rivers extended from late May to early October, larger‐sized salmon (fish ≥ 65 cm) generally entered the rivers earlier than small fish. The percentage of salmon identified as escaped farmed fish ranged from 0.1% to 17% across rivers with an average of 4.3%. Estimates of escapees are, however, assumed to represent minimum values because an unknown number of farmed fish passing the video cameras may have been misclassified as wild fish. By the use of a linear mixed model and generalised additive mixed models, it was found that the relationship between run timing and fish length differed significantly between farmed and wild salmon. While small‐sized farmed and wild fish (<65 cm) entered the river at about the same time, wild large salmon returned on average 1–2 weeks earlier than similarly sized escapees. The proportion of large‐sized farmed escapees also increased until late August and decreased thereafter. In contrast, there was a relatively constant and lower proportion of small‐sized escapees throughout the season. Within the surveillance period, there was no evidence of any exceptionally late runs of fish classified as escaped farmed salmon.     

Comparative assessment of the genetic variation in selectively bred generations from two geographic populations of ivory shell (Babylonia areolata)

Ivory shell, Babylonia areolata, is one of the commercially important mariculture species in southern China and South‐East Asia. The selection programme for growth trait has been conducted since 2010 in two selected lines for three generations, namely the Hainan (H) and Thailand (T) selected lines. Ten polymorphic microsatellite loci were used to monitor changes in their genetic diversity and structure during the selection process. A relatively high level of overall genetic diversity was observed, while the number of microsatellite allele declined slightly in the mass selection lines. Comparative diversity estimates indicated greater genetic diversity in H line than T line. Moreover, a relatively weak but significant genetic differentiation was found in both of the selected generations. In addition, the higher genetic variation observed in H line is most likely caused by artificial selection while selection bias on a growth advantage for the T population. These findings suggest no significant decline of genetic diversity was observed in the presently selected lines and that a potential exists for genetic improvement and development for B. areolata.     

Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA

Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean, Western Pacific Ocean and Eastern Atlantic Ocean were investigated using mitochondrial (mt) DNA sequence data. A total of 380 specimens were sampled from four regions in the Indian Ocean (Cocos Islands, Southeastern Indian Ocean, Southwestern Indian Ocean and Seychelles), and one region each from the Atlantic (Guinea) and the Western Pacific Oceans, respectively. The reconstructed neighbor-joining phylogeny based on the first hypervariable region (HVR-1) of the mitochondrial control region sequence data showed that haplotypes from the Indian and the Western Pacific Oceans could be grouped into two clades (Clades I and III), whereas in the Atlantic Ocean, two divergent clades (Clades I and II) coexisted. A single stock of bigeye tuna in the Indian Ocean was supported by hierarchical AMOVA tests and pairwise Φ_ST analyses. Clade I was the dominant population in the Indian and the Western Pacific Oceans which consisted of more than 96% of the specimens and Clade II was a specific group exclusively restricted to the Atlantic Ocean which made up 77% of its specimens. A new minor Clade, Clade III was discovered in the Indian and the Western Pacific Ocean. Overall, these analyses indicated that bigeye tuna of the Indian Ocean constituted a single panmictic population.     

Isolation and characterization of koi herpesvirus (KHV) from Indonesia: identification of a new genetic lineage

Koi herpesvirus (KHV) is the aetiological agent of an emerging disease (KHVD) associated with mass mortalities in koi and common carp and reported from at least 30 countries. We report the first isolation of KHV from koi and common carp in Indonesia and initial characterization of the isolates. Clinical signs, histopathology and virion morphology are similar to those of isolates from other countries. Phylogenetic analyses using the thymidine kinase gene amplified from each isolate and from carp tissue samples collected from KHVD outbreaks throughout Indonesia indicated that the Indonesian isolates are more closely related to the Asian than the European KHV lineage. Sequence analysis of two other variable regions between ORF29 and ORF31 (marker I) and near the start of ORF 133 (marker II) indicated that all Indonesian isolates displayed a marker I allele (I(++)) previously identified only in isolates of the Asian lineage. However, in the marker II region, all Indonesian isolates displayed the II(-) allele, which has been reported previously only amongst isolates of the European lineage, and nine of these displayed a mixed genotype (II(+)II(-)). The I(++)II(-) genotype has not been reported previously and appears to represent a new intermediate lineage that may have emerged in Indonesia.     

Interannual and spatial variation in the population genetic composition of young‐of‐the‐year Pacific ocean perch (Sebastes alutus) in the Gulf of Alaska

Little is known about the population structure of Alaskan rockfishes, including Pacific ocean perch (POP, Sebastes alutus), and how persistent and variable oceanographic features may influence their structures. Moreover, early life history information is sparse for many species. We used data from 14 microsatellite loci to characterize the genetic structure of young‐of‐the‐year Pacific ocean perch collected during 1998–2003 from the Gulf of Alaska and Bering Sea. Broad‐scale geographic variation in genetic structure of the young‐of‐the‐year (F_ST = 0.005, P < 10^?4) had similarities to that observed in a previous adult study. The overall correlation between genetic and geographic distance (isolation by distance) was nearly identical to that observed in the adults. Fine‐scale geographic divergence was also observed and may be the result of oceanographic circulation features within the Gulf of Alaska. Interannual variation (between cohorts) at locations sampled in more than one year is consistent with variable oceanography and fine‐scale population structure rather than the influence of a sweepstakes effect. The similarities of the young‐of‐the‐year with the adults and the pattern of genetic divergence confirm that dispersal of Pacific ocean perch is limited in all life stages.     

A simple non-enzymatic method for the preparation of white spot syndrome virus (WSSV) DNA from the haemolymph of Marsupenaeus japonicus using FTA matrix cards

White spot syndrome virus (WSSV) is an important shrimp pathogen responsible for large economic losses for the shrimp culture industry worldwide. The nucleic acids of the virus must be adequately preserved and transported from the field to the laboratory before molecular diagnostic analysis is performed. Here, we developed a new method to isolate WSSV-DNA using Flinders Technology Associates filter paper (FTA matrix card; Whatman) without centrifugation or hazardous steps involved. FTA technology is a new method allowing the simple collection, shipment and archiving of nucleic acids from haemolymph samples providing DNA protection against nucleases, oxidation, UV damage, microbial and fungal attack. DNA samples prepared from 10-fold dilutions of moribund shrimp haemolymph using FTA matrix cards were analysed using semi-quantitative and quantitative polymerase chain reaction (PCR) and were compared with two commercially available DNA isolation methods, the blood GenomicPrep Mini Spin Kit (GE Healthcare) and the DNAzol (Invitrogen). Sequence analysis was performed for the DNA samples prepared using the various isolation procedures and no differences in the sequence among these methods were identified. Results based on the initial copy number of DNA prepared from the GenomicPrep Mini Spin Kit are a little more sensitive than the DNA prepared from FTA matrix cards, whereas the DNAzol method is not suitable for blood samples. Our data shows the efficiency of retention capacity of WSSV-DNA samples from impregnated FTA matrix cards. Matrix cards were easy to store and ship for long periods of time. They provide ease of handling and are a reliable alternative for sample collection and for molecular detection and characterization of WSSV isolates.     

Environmental and spatial effects on the distribution of blue marlin (Makaira nigricans) as inferred from data for longline fisheries in the Pacific Ocean

Blue marlin is distributed throughout tropical and temperate waters in the Pacific Ocean. However, the preference of this species for particular habitats may impact its vulnerability to being caught. The relationship between spatio‐temporal patterns of blue marlin abundance and environmental factors is examined using generalized additive models fitted to catch and effort data from longline fisheries. The presence of blue marlin, and the catch rate given presence, are modeled separately. Latitude, longitude, and sea‐surface temperature explain the greatest proportion of the deviance. Spatial distributions of relative density of blue marlin, based on combining the probability of presence and relative density given presence, indicate that there is seasonal variation in the distribution of blue marlin, and that the highest densities occur in the tropics. Seasonal patterns in the relative density of blue marlin appear to be related to shifts in SST. The distribution and relative abundance of blue marlin are sufficiently heterogeneous in space and time that the results of analyses of catch and effort data to identify ‘hotspots’ could be used as the basis for time‐area management to reduce the amount of blue marlin bycaught in longline fisheries.