Bay-scale population structure in coastal Atlantic cod in Labrador and Newfoundland, Canada

Polymorphisms at five microsatellite DNA loci provide evidence that Atlantic cod Gadus morhua inhabiting Gilbert Bay, Labrador are genetically distinguishable from offshore cod on the north-east Newfoundland shelf and from inshore cod in Trinity Bay, Newfoundland. Antifreeze activity in the blood suggests that Gilbert Bay cod overwinter within the Bay. Gilbert Bay cod are also smaller (weight and length) for their age and consequently less fecund for their age, than cod elsewhere within the northern cod complex. The productivity and recruitment potential of coastal cod off Labrador may thus be much lower than that of offshore northern cod or of inshore cod farther south, implying that a more conservative management strategy may be required for cod from coastal Labrador than traditionally practised for northern cod inhabiting less harsh environments. Relatively high F _ST and R _ST measures of population structure suggest that important barriers to gene flow exist among five components that include two inshore (Gilbert and Trinity Bay) and three offshore cod aggregations on the north-east Newfoundland Shelf and the Grand Bank. D _A and D _SW estimates of genetic distance that involve Gilbert Bay cod are approximately three- and 10–fold larger, respectively, than estimates not involving Gilbert Bay cod. The differences between inshore cod from Gilbert Bay and Trinity Bay raise the possibility that other genetically distinguishable coastal populations may exist, or may have existed prior to the northern cod fishery collapse. Harvesting strategies for northern cod should recognize the existence of genetic diversity between inshore and offshore components as well as among coastal components.     

Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic

Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome‐wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analysed genome‐wide polymorphisms to measure genetic differentiation between an offshore migratory and a nonmigratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11k single nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and nonmigratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and nonmigratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and nonmigratory ecotypes on both sides of the Atlantic Ocean.     

Mitochondrial DNA sequence variation and genetic stock structure of Atlantic cod (Gadus morhua) from bay and offshore locations on the Newfoundland continental shelf

Bay cod, Atlantic cod (Gadus morhua) that over-winter in the deep-water bays of northeastern Newfoundland, have historically been regarded as distinct in migration and spawning behaviour from offshore (Grand Bank) cod stocks. To investigate their genetic relationships, we determined the DNA sequence of a 307-base-pair portion of the mitochondrial cytochrome b gene for 236 adult cod taken from the waters off northeastern Newfoundland, including fish found over-wintering and spawning in Trinity Bay. Although 17 genotypes were found, a single common genotype occurs at a frequency of greater than 80% in all samples, and no alternative genotype occurs at a frequency of greater than 3%. Genotype proportions did not differ significantly among samples. Measures of genetic subdivision among sampling locations are nil. Cod over-wintering in Trinity Bay are not genetically distinct from offshore cod. In combination with tagging and physiological studies, these data suggest that there is sufficient movement of cod between bay and offshore locations to prevent the development or maintenance of independent inshore stocks. Adult cod that over-winter in Trinity Bay appear to represent an assemblage of temporarily nonmigratory fish that have become physiologically acclimated to cold-water inshore environments. The pattern of genetic variation in northern cod suggests a recent population structure characterized by extensive movement of contemporary individuals superimposed on an older structure characterized by a bottleneck in the population size of cod in the north-western Atlantic.     

Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research

The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.     

Does a No-Take Marine Protected Area Benefit Seahorses?

Seahorses are iconic charismatic species that are often used to ‘champion’ marine conservation causes around the world. As they are threatened in many countries by over-exploitation and habitat loss, marine protected areas (MPAs) could help with their protection and recovery. MPAs may conserve seahorses through protecting essential habitats and removing fishing pressures. Populations of White''s seahorse, Hippocampus whitei, a species endemic to New South Wales, Australia, were monitored monthly from 2006 to 2009 using diver surveys at two sites within a no-take marine protected areas established in 1983, and at two control sites outside the no-take MPA sites. Predators of H. whitei were also identified and monitored. Hippocampus whitei were more abundant at the control sites. Seahorse predators (3 species of fish and 2 species of octopus) were more abundant within the no-take MPA sites. Seahorse and predator abundances were negatively correlated. Substantial variability in the seahorse population at one of the control sites reinforced the importance of long-term monitoring and use of multiple control sites to assess the outcomes of MPAs for seahorses. MPAs should be used cautiously to conserve seahorse populations as there is the risk of a negative impact through increased predator abundance.     

Genetic evidence of <Emphasis Type="Italic">Ranavirus</Emphasis> in toe clips: an alternative to lethal sampling methods

Amphibian populations have been undergoing declines on a global scale. Among the many threats to these populations are emergent infectious diseases (EIDs). The Ranavirus in particular has been found within many declining amphibian populations. Although non-lethal sampling methods exist for some amphibian groups, such as salamanders, the anurans are traditionally tested using a lethal method. By comparing traditional liver samples and a new non-lethal method of toe clipping we prove that the Ranavirus can also be determined in frogs using a non-lethal method, a much needed tool in threatened populations. This method will allow for ranaviral detection without further impacting declining populations, and can further be used for other research questions.     

Reliability of non-lethal surveillance methods for detecting ranavirus infection

Ranaviruses have been identified as the etiologic agent in many amphibian die-offs across the globe. Polymerase chain reaction (PCR) is commonly used to detect ranavirus infection in amphibian hosts, but the test results may vary between tissue samples obtained by lethal and non-lethal procedures. Testing liver samples for infection is a common lethal sampling technique to estimate ranavirus prevalence because the pathogen often targets this organ and the liver is easy to identify and collect. However, tail clips or swabs may be more practicable for ranavirus surveillance programs compared with collecting and euthanizing animals, especially for uncommon species. Using PCR results from liver samples for comparison, we defined false-positive test results as occurrences when a non-lethal technique indicated positive but the liver sample was negative. Similarly, we defined false-negative test results as occurrences when a non-lethal technique was negative but the liver sample was positive. Using these decision rules, we estimated false-negative and false-positive rates for tail clips and swabs. Our study was conducted in a controlled facility using American bullfrog Lithobates catesbeianus tadpoles; false-positive and false-negative rates were estimated after different periods of time following exposure to ranavirus. False-negative and false-positive rates were 20 and 6%, respectively, for tail samples, and 22 and 12%, respectively, for swabs. False-negative rates were constant over time, but false-positive rates decreased with post-exposure duration. Our results suggest that non-lethal sampling techniques can be useful for ranavirus surveillance, although the prevalence of infection may be underestimated when compared to results obtained with liver samples.     

Analyses of genetic change-over in Drosophila populations

Genetic change-overs in Drosophila populations similar to those frequently observed in microbial ones maintained in chemostats are described. In two cases, the change-overs were revealed by an abrupt and sustained increase in the probability that two independently sampled lethal chromosomes proved to be allelic. These favored lethals (or closely linked non-lethal elements) were estimated to have fitnesses 1.30–1.35 in combination with “ordinary” lethals or 1.05–1.10 in combination with non-lethal chromosomes (fitness 1.00 is assigned to carriers of non-lethal chromosomes only). A decrease in the frequency of lethal chromosomes in a third population was adequately explained by postulating the origin of a non-lethal “favored” element whose relative fitness was 1.25, a value similar to those estimated above. Genetic change-over in populations is discussed in relation to biochemical and morphological conservatism.     

Population Connectivity Shifts at High Frequency within an Open-Coast Marine Protected Area Network

A complete understanding of population connectivity via larval dispersal is of great value to the effective design and management of marine protected areas (MPA). However empirical estimates of larval dispersal distance, self-recruitment, and within season variability of population connectivity patterns and their influence on metapopulation structure remain rare. We used high-resolution otolith microchemistry data from the temperate reef fish Hypsypops rubicundus to explore biweekly, seasonal, and annual connectivity patterns in an open-coast MPA network. The three MPAs, spanning 46 km along the southern California coastline were connected by larval dispersal, but the magnitude and direction of connections reversed between 2008 and 2009. Self-recruitment, i.e. spawning, dispersal, and settlement to the same location, was observed at two locations, one of which is a MPA. Self-recruitment to this MPA ranged from 50–84%; within the entire 60 km study region, self-recruitment accounted for 45% of all individuals settling to study reefs. On biweekly time scales we observed directional variability in alongshore current data and larval dispersal trajectories; if viewed in isolation these data suggest the system behaves as a source-sink metapopulation. However aggregate biweekly data over two years reveal a reef network in which H. rubicundus behaves more like a well-mixed metapopulation. As one of the few empirical studies of population connectivity within a temperate open coast reef network, this work can inform the MPA design process, implementation of ecosystem based management plans, and facilitate conservation decisions.     

A non-lethal technique for detecting the chytrid fungus Batrachochytrium dendrobatidis on tadpoles

Batrachochytrium dendrobatidis (Bd) infection on post-metamorphic frogs and salamanders is commonly diagnosed using polymerase chain reaction (PCR) of skin scrapings taken with mildly abrasive swabs. The technique is sensitive, non-lethal, and repeatable for live animals. Tadpoles are generally not sampled by swabbing but are usually killed and their mouthparts excised to test for the pathogen. We evaluated a technique for non-lethal Bd diagnosis using quantitative PCR (qPCR) on swabs scraped over the mouthparts of live tadpoles. The sensitivity of non-lethal (swabbing) and lethal (removal of mouthparts) sampling was assessed using 150 Bd-infected Rana subaquavocalis tadpoles. Swabbing was consistently less sensitive than lethal sampling, but still detected Bd. Experimental Bd prevalence was 41.1% when estimated by destructively sampling mouthparts and 4.7 to 36.6% (mean = 21.4%) when estimated with swabs. Detection rates from swabbing varied with investigator and time since infection. The likelihood of detecting Bd-infected tadpoles was similar regardless of size and developmental stage. Swabbing mouthparts of live tadpoles is a feasible and effective survey technique for Bd, but, because it is less sensitive, more tadpoles must be sampled to estimate prevalence at a confidence level comparable to destructive sampling.     

湛江湾角毛藻群落的时空分布及其影响因素

2009年2-11月以水采、网采和显微鉴定的方法分别对湛江湾的浮游植物进行了周年的季节调查,分析了湛江湾角毛藻(Chaetoceros)群落的时空分布和影响因素.结果表明:湛江湾角毛藻共有32种,其中有17种为赤潮种,优势种有旋链角毛藻(C.curvisetus)、假弯角毛藻(C.pseudocurvisetus)和牟氏角毛藻(C.muelleri)3种;种类丰富度和细胞丰度在季节分布上表现为春夏季高于秋冬季,而在空间分布上总体表现为湾口高,向内湾逐渐降低.相关分析表明:角毛藻细胞丰度与水温、盐度、pH、叶绿素a浓度及浮游植物细胞丰度呈极显著的正相关,与DIN、SiO32-呈极显著的负相关,与PO43-相关性不显著:角毛藻细胞丰度的季节变化主要取决于水温,由季节更替而产生的种间竞争和浮游动物的摄食压力也是重要的影响因素,而空间变化则受到光照、盐度、pH和高丰度养殖贝类滤食压力的影响.     

野猪与人冲突防控对策研究的系统评价

在中国,野猪(Sus scrofa)与人冲突问题亟需采取有效、科学的对策进行防控。通过了解野猪与人冲突防控对策的文献数量、研究范围、防控对策的种类及有效性等方面,对国内外野猪与人冲突防控对策进行系统分析与评价,以期为我国防控野猪与人冲突提供理论依据。检索中英文数据库建库至2021年5月31日的文献,提取文献的研究起始年份、研究所在地理单元、使用的防控措施种类、措施是否有效、措施的具体内容评价等。共搜集文献446篇,最终纳入77篇,分别来自欧洲、亚洲、北美洲、大洋洲、南美洲五大洲,研究时间主要在1981年后。防控对策类型主要分为致死性防控(药物、猎捕)及非致死性防控(干扰技术、设置障碍物、补充喂养、生育控制、生物防控)两大类;致死性防控对策的有效性(81.5%)高于非致死性防控对策的有效性(68.4%)。相比于非致死性防控对策,致死性防控对策是目前有效性较高的防控策略,而猎捕是现阶段调控野猪种群可行性较高的主要致死性防控对策。国外在猎捕方面的经验可为我国开展野猪防控工作提供参考。     

Reproductive potential of the eastern baltic cod <Emphasis Type="Italic">Gadus morhua callarias</Emphasis> L. population

Trends in interannual variation in maturation and spawning terms of various age cohorts in the Eastern Baltic cod population in 1997–2009 were studied. Specific features in the age structure of the mature population part that were established by the end of the first decade of the 21st century were clarified. The role of cod age cohorts in the current population reproduction was considered taking into account the data on cod recruitment and fecundity.     

Stock-specific changes in growth rates, food conversion efficiencies, and energy allocation in response to temperature change in juvenile Atlantic cod

Under common environments, populations of laboratory reared (Grand Banks, GB and Gulf of Maine, GOM) and wild caught (Fortune Bay, FB and Bonavista Bay, BB; Newfoundland) juvenile cod Gadus morhua responded similarly to temperature change in specific growth rates, food conversion efficiencies, condition factors, liver water content, and muscle water content. However, GOM cod had higher condition factors, and showed differences from GB cod in phenotypic plasticity of hepatosomatic index to temperature. These differences were not present in a different population comparison between FB and BB cod. All populations had higher growth rates and food conversion efficiencies at warmer temperatures, and exhibited compensatory growth when temperature was increased. The results suggest relatively larger genetic differences between GB and GOM cod than between FB and BB cod, and indicate that the faster growth of southern populations in the wild is not due to a higher genetic capacity for growth rate.     

Population dynamics of a threatened giant millipede: implications for restoration

The population dynamics of threatened invertebrates have important implications for their conservation and restoration. The Seychelles giant millipede (SGM), Sechelleptus seychellarum, is a threatened and functionally important macro‐detritivore endemic to the Seychelles granitic islands. Here, we studied the population dynamics of the SGM from 1998 to 2009 on Cousine Island, Seychelles, to make practical restoration recommendations. Large fluctuations in millipede densities were found between 1998 and 2009. In 2002, 2003, 2005, and 2007 millipede densities were low, while densities were high in 1998 and 2009. Although the SGM is active all year round, millipede surface activity was positively correlated with rainfall, with millipede density high during the wet NW monsoon period (i.e., October to April) and low during the SE trade wind period (i.e., May to September). Female:male:juvenile ratios were ～3:1:1. The implications of these results for restoration are that translocations should preferably be done in years of high millipede densities and during the wet season. Furthermore, chemical control of the invasive ant Pheidole megacephala, which is currently being carried out on Cousine Island and in future could be conducted on other Seychelles islands, should preferably be done during the low rainfall months, as the SGM readily consumes the hydramethylnon‐based bait.     

Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity

Adaptive differences across species’ ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene–environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired‐end restriction site‐associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene–association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature‐ and precipitation‐related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.     

Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network

The use of marine protected area (MPA) networks to sustain fisheries and conserve biodiversity is predicated on two critical yet rarely tested assumptions. Individual MPAs must produce sufficient larvae that settle within that reserve's boundaries to maintain local populations while simultaneously supplying larvae to other MPA nodes in the network that might otherwise suffer local extinction. Here, we use genetic parentage analysis to demonstrate that patterns of self-recruitment of two reef fishes (Amphiprion percula and Chaetodon vagabundus) in an MPA in Kimbe Bay, Papua New Guinea, were remarkably consistent over several years. However, dispersal from this reserve to two other nodes in an MPA network varied between species and through time. The stability of our estimates of self-recruitment suggests that even small MPAs may be self-sustaining. However, our results caution against applying optimization strategies to MPA network design without accounting for variable connectivity among species and over time.     

Threat of predation negates density effects in larval gray treefrogs

While density-dependence is central to most theory regarding population regulation and community structure, specific mechanisms that modify its effects in the absence of changes in consumer-resources ratios (e.g., thinning) are not well understood. To determine if the threat of predation alters effects of density, we investigated the interaction between density of larval treefrogs (Hyla chrysoscelis) and the non-lethal presence of a predatory fish (Enneacanthus obesus). A significant density by fish interaction was consistent for all response variables (e.g., larval survivorship, mass, and time to metamorphosis) driven by a complete lack of density effects in the presence of predators, while predator-free tanks showed classic density-dependent responses. Given that female H. chrysoscelis strongly avoid ovipositing in ponds containing fish, certain larval adaptations are apparently not constrained by maternal behavior and suggest redundancy in response to predators. Our data suggest that non-lethal effects of predators can determine larval performance irrespective of larval density, and that the non-lethal effects of predators can be strong whether lethal effects are strong or weak.     

Natural regulatory (CD4+CD25+FOXP+) T cells control the production of pro-inflammatory cytokines during Plasmodium chabaudi adami infection and do not contribute to immune evasion

Different functions have been attributed to natural regulatory CD4+CD25+FOXP+ (Treg) cells during malaria infection. Herein, we assessed the role for Treg cells during infections with lethal (DS) and non-lethal (DK) Plasmodium chabaudi adami parasites, comparing the levels of parasitemia, inflammation and anaemia. Independent of parasite virulence, the population of splenic Treg cells expanded during infection, and the absolute numbers of activated CD69+ Treg cells were higher in DS-infected mice. In vivo depletion of CD25+ T cells, which eliminated 80% of CD4+FOXP3+CD25+ T cells and 60-70% of CD4+FOXP3+ T cells, significantly decreased the number of CD69+ Treg cells in mice with lethal malaria. As a result, higher parasite burden and morbidity were measured in the latter, whereas the kinetics of infection with non-lethal parasites remained unaffected. In the absence of Treg cells, parasite-specific IFN-gamma responses by CD4+ T cells increased significantly, both in mice with lethal and non-lethal infections, whereas IL-2 production was only stimulated in mice with non-lethal malaria. Following the depletion of CD25+ T cells, the production of IL-10 by CD90(-) cells was also enhanced in infected mice. Interestingly, a potent induction of TNF-alpha and IFN-gamma production by CD4+ and CD90(-) lymphocytes was measured in DS-infected mice, which also suffered severe anaemia earlier than non-depleted infected controls. Taken together, our data suggest that the expansion and activation of natural Treg cells represent a counter-regulatory response to the overwhelming inflammation associated with lethal P.c. adami. This response to infection involves TH1 lymphocytes as well as cells from the innate immune system.     

Effects of predator-induced thinning and activity changes on life history in a damselfly

We investigated how the lethal and non-lethal presence and absence of a fish predator, perch (Perca fluviatils), influenced behaviour, numbers emerging, size at emergence, and development rate of the damselfly Lestes sponsa. The experiment was carried out in outdoor artificial ponds and spanned from the egg stage to emergence of the damselflies. During the experiment food resources for the damselflies were continuously monitored. Damselflies exposed to a lethal predator showed a significantly lower activity level than those in the absence of predators or subjected to a non-lethal predator. Half-way through the larval stage the reduction in activity level was correlated with the presence of lethal predators, and at the end of the larval stage with higher zooplankton densities. Though larvae decreased activity level, size at emergence was larger and development time faster for individuals in the lethal predator treatment. Since fewer larvae emerged from that treatment we interpret the larger size at emergence to be an effect of a combination of thinning and higher zooplankton densities.