Wild-caught Samples Research Articles

Fitness consequences of population bottlenecks in an invasive blowfly.

Invasive species often undergo demographic bottlenecks that cause a decrease in genetic diversity and associated reductions in population fitness. Despite this, they manage to thrive in novel environments. Investigating the effects of inbreeding and genetic bottlenecks on population fitness for invasive species is, therefore, key to understanding how they may survive in new environments. We used the blowfly Calliphora vicina (Sciences, Mathématiques et Physique, 1830, 2, 1), which is native to Europe and was introduced to Australia and New Zealand, to examine the effects of genetic diversity on population fitness. We first collected 59 samples from 15 populations across New Zealand and one in Australia, and used 20,501 biallelic SNPs to investigate population genomic diversity, structure and admixture. We then explored the impacts of repeated experimental bottlenecks on population fitness by creating inbred and outbred lines of C. vicina and measuring a variety of fitness traits. In wild-caught samples, we found low overall genetic diversity, signals of genetic admixture and limited (<3%) genetic differentiation between North and South Island populations, with genetic links between the South Island and Australia. Following experimental bottlenecks, we found significant reductions in fitness for inbred lines. However, fitness effects were not felt equally across all phenotypic traits. Moreover, they were not enough to cause population collapse in any experimental line, suggesting that C. vicina (when under relaxed selection, as in laboratory settings) may be able to compensate for population bottlenecks even when highly inbred. Our results demonstrate the value of a tractable experimental system for investigating processes that may facilitate or hamper biological invasion.

Comparison of nutritional compositions and heavy metals analysis between wild and farmed Tilapia (Oreochromis sp.) and Asian Seabass (Lates sp.) in Sabah, Malaysia

In Sabah, Malaysia, Tilapia and Asian seabass are culturally and economically important seafood choices. Understanding their nutritional content and contaminants, both wild-caught and farmed, is crucial as demand increases. This study aimed to analyze the proximate composition and heavy metals concentrations in Tilapia and Asian Seabass fish flesh, and compare the wild-caught and farmed samples. The results revealed significant nutritional variations between the two groups. Wild-caught Tilapia exhibited higher protein content (16.90 ± 0.50 %), carbohydrate levels (0.7 ± 0.10 %), moisture (80.25 ± 0.58 %), and ash content (9.22 ± 1.27 %) while farmed Tilapia displayed elevated fat content (3.55 ± 0.05 %) and energy values (94.5 kcal per 100 g). Iron concentrations in both wild and farmed Tilapia remained within safe limits for human consumption and Zinc was detected in wild Tilapia only. Meanwhile, the farmed Asian Seabass demonstrated higher protein (18.45 ± 0.25 %), fat (0.9 ± 0.10 %), carbohydrate (0.8 ± 0.20 %), ash content (21.04 ± 2.1 %), and energy values (85.5 kcal per 100 g) compared to the wild. Further study can be conducted to study the benefits of these fish species to human health upon consumption.

Microplastic Bioaccumulation in Selected Finfish Species Harvested from Northwest Coastal Waters, Sri Lanka: A Potential Risk to Human Health?

The widespread bioavailability of microplastics (MP) in the marine environment has upraised intense interest over the last few decades. However, MP trophic transfer via appetizing portions of marine organisms remains less recognized. Therefore, the present study looked at bioaccumulation potential of MPs investigating four common edible finfish species; Sardinella gibbosa, Stolephorus commersonnii, Hemiramphus archipelagicus, and Katsuwonus pelamis representing different trophic levels from Northwest Coastal waters. In the experimental protocol, the wild-caught finfish samples were analyzed considering their edible (muscle) vs non-edible (gastrointestinal (GI) tract and gills) tissues. The structural characteristics of MP materials were screened by stereomicroscope whereas elemental composition using Fourier-Transform Infrared spectroscopy. Amongst all the studied samples, around 96% exhibited MP contamination in the size range of 0.06 mm-0.11 mm. Fibers, fragments, and films were the prominent MP types detected while Polyethylene, Polypropylene, Polystyrene, and Nylon-6,6 were the polymeric substances extensively recorded. K. pelamis and S. commersonnii displayed the highest (1.1±0.54 MP/g) and lowest (0.1±0.02 MP/g) mean MP levels in edible portions, respectively. The MP quantities extracted from gills, GI tract, and flesh of each sample were significantly different (p&lt;0.05), thereby Pearson correlation test results implied the GI tract as the major possible exposure route of higher trophic finfishes while gills act as the key direction of filter feeders. Parametric One-way ANOVA test indicated that the trophic transfer interactions in the studied finfish food chains were significant (p&lt;0.05) at 95% level of confidence. Trophic Magnification Factors (TMF=2.347, 3.449) and Biomagnification Factors (1&lt;BMF) of examined food chains signified that MPs are conceivably biomagnified in edible parts of marine food webs even though the contamination in edible tissues was significantly lower than that of non-edible shares as per the Two sample T-test and Mann-Whitney tests. Therefore, the findings advocate that trophic transfer denotes an oblique, yet possible key pathway of MP ingestion for any individual who depends on seafood diets habitually. Since the MPs magnification could possibly ensure the trophic dilution. However, considering the physical and chemical toxicities and associated contaminants of MPs, there is a necessity for further studies assessing the human susceptibility to MP-related hazards via the routine consumption of seafood. Addressing this gap which implies with food safety and pollution control is a vital primacy due to the nutritional value of seafood consumption. &#x0D; Keywords: Microplastic, Trophic transfer, Biomagnification, Seafood

PCR-Based Screening of Pathogens in Bombus terrestris Populations of Turkey.

Bumblebees are an important group of insects in the pollination of various vegetables, fruits, oilseeds, legumes, and the fodder crops. Compared to honeybees, they have a wider choice of hosts and a longer flight period. These bees are used especially for the pollination of plants in greenhouses and are commercially produced for this purpose. Recently, serious decreases have been occurring in bumblebee populations due to various reasons such as pathogens, and some of species are even threatened with extinction. Due to the worldwide decline in pollinator insects, determining the distribution and prevalence of bumblebee pathogens is of great importance. Therefore, this study was conducted to determine the incidence and prevalence of pathogens in Turkish bumblebee populations and how much of each pathogen was in bumblebee samples. A total of 172 Bombus terrestris (Linnaeus,1758) samples (21 samples from commercial enterprises, 79 samples from greenhouses and 72 samples from nature) were randomly collected from 3 provinces (Antalya, Mersin and İzmir) where greenhouse cultivation is intensively carried out in Turkey. Eighty-nine of these samples were collected in the spring and eighty-three in the autumn. The presence of four pathogens (Nosema bombi, Crithidia bombi, Apicystis bombi, and Locustacarus buchneri) was investigated by PCR using universal primers. The overall prevalence of Nosema bombi, Crithidia bombi, Apicystis bombi, and Locustacarus buchneri was determined as 7.55%, 9.3%, 11.62%, and 4.65%, respectively. Co-infections (5.81%) were only detected in wild-caught (nature) samples. C. bombi and A. bombi infections were detected at higher rates in the spring samples than in the autumn samples (p < 0.05). There was no significant difference between the spring and autumn samples with respect to the presence of N. bombi and L. buchneri (p > 0.05). The results obtained could be important in determining the prevalence and spread rates of the bumblebee diseases in Turkey and to determine appropriate protection measures. The information gathered should increase our knowledge about the presence of these pathogens in Turkey and could contribute to improve apiarist's practice. More studies are needed to determine the transmission pathways of these pathogens between the populations. Also, complex pathogen interactions in bumblebee populations should be considered in the future to improve bumblebee health.

Temporal population genetic structure of Phormia regina (Diptera: Calliphoridae).

The genetic structure of forensically important blow fly (Brauer & Bergenstamm) (Diptera: Calliphoridae) populations has remained elusive despite high relatedness within wild-caught samples. This research aimed to determine if the implementation of a high-resolution spatiotemporal sampling design would reveal latent genetic structure among blow fly populations and to elucidate any environmental impacts on observed patterns of genetic structure. Adult females of the black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae), were collected from 9 urban parks in Indiana, USA over 3 yr and genotyped at 6 polymorphic microsatellite loci. The data analysis involved 3 clustering methods: principal coordinate analysis (PCoA), discriminant analysis of principal components (DAPC), and STRUCTURE. While the PCoA did not uncover any discernible clustering patterns, the DAPC and STRUCTURE analyses yielded significant results, with 9 and 4 genetic clusters, respectively. Visualization of the STRUCTURE bar plot revealed N = 11 temporal demarcations indicating barriers to gene flow. An analysis of molecular variance of these STRUCTURE-inferred populations supported strong temporally driven genetic differentiation (FST = 0.048, F'ST = 0.664) relative to geographic differentiation (FST = 0.009, F'ST = 0.241). Integrated Nested Laplace Approximation and Boosted Regression Tree analyses revealed that collection timepoint and 4 main abiotic factors (temperature, humidity, precipitation, and wind speed) were associated with the genetic subdivisions observed for P. regina. A complex interplay between environmental conditions, the unique reproductive strategies of the blow fly, and the extensive dispersal abilities of these organisms likely drives the strong genetic structure of P. regina in the Midwestern US.

INaturalist is an open science resource for ecological genomics by enabling rapid and tractable records of initial observations of sequenced biological samples.

The rapidly growing body of publicly available sequencing data for rare species and/or wild-caught samples is accelerating the need for detailed records of the samples used to generate datasets. Many already published datasets are unlikely to ever be reused, not due to problems with the data themselves, but due to their questionable or unverifiable origins. In this paper, I present iNaturalist-a pre-existing citizen science platform that allows people to post photo observations of organisms in nature-as a tool that allows genomics researchers to rapidly publish observations of samples used to generate sequencing datasets. This practice aligns with the values of the open science movement, and I also discuss how iNaturalist, along with other online resources, can be used to create an open genomics pipeline that enables future replication studies and ensures the value of genomics datasets to future research.

Genetic Diversity of the Critically Endangered Big-Headed Turtle (Platysternon megacephalum) Based on Wild and Traded Samples: Implications for Conservation

Overexploitation has driven catastrophic declines in most turtle species in Asia. Many turtles are seized annually by law enforcement officers; unfortunately, seized turtles often lack associated information on their provenance. There is also taxonomic confusion regarding the clear delineation of turtle species and subspecies in Asia. This lack of provenance data and taxonomic uncertainty is problematic as it may preclude release, make appropriate release sites hard to select, or result in genetic pollution when animals are released. In this study, we amassed and analyzed the largest number of genetic samples of the critically endangered big-headed turtle (Platysternon megacephalum) to date. Our phylogenetic and network results based on nearly 500 sequences of a mitochondrial ND4 fragment corroborate the earlier hypothesis that only two of the three currently recognized subspecies have strong molecular support and that there is greater genetic structuring within one subspecies than has been previously reported. The vast majority of P. megacephalum confiscated from the trade in Vietnam belong to Subclade 3 of P. m. peguense, and this subclade is the most broadly distributed taxon of the big-headed turtle in Vietnam based on samples with known localities. Nonetheless, for the other two subclades, all their samples originate from the trade and could not be assigned to any geographic provenance because of the lack of wild-caught samples. In addition, our results reveal two trade centers of the species, Quang Ninh Province on the border between China and Vietnam and Kon Tum Province in the Central Highlands. However, smaller animal seizures occur across the range of the species in Vietnam. While the data presented here have facilitated the selection of appropriate release sites for confiscated P. megacephalum, the significant costs of genetic screening and the shortage of samples from wild animals with good localities hinder the rewilding efforts, especially for conservation practitioners working in countries where conservation activities are not well funded and research on poorly studied species is still limited. Nevertheless, we urge that wildlife translocations include robust pre-translocation genetic screening to ensure that all individual animals are reintroduced at appropriate sites.

Better late than never: Optimising the proteomic analysis of field-collected octopus.

Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10% additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.

Stock Discrimination of Gilthead Seabream (Sparus aurata Linnaeus, 1758) through the Examination of Otolith Morphology and Genetic Structure

Reliable stock identification constitutes an integral component of effective fishery management. Current methods for the identification of putative stock units comprise the analysis of both phenotypic and genetic variability. The present study examined the spatial variation in otolith morphology (shape and asymmetry) and genetic composition of 395 wild-caught Gilthead seabream (Sparus aurata) specimens, collected from the Aegean and Ionian Seas (eastern Mediterranean) between 2014–2018. The degree of scale regeneration (SRD, % of regenerated scales) was used as an indicator to assess the potential presence of aquaculture escapees in the wild-caught samples. Otolith shape and asymmetry analyses showed a phenotypic discrimination between northwestern Aegean and Ionian Gilthead seabream populations. Genetic analyses of nine microsatellite markers revealed higher levels of genetic variation in the wild compared with samples obtained from aquaculture farms. Despite the absence of genetic structure among the wild-caught seabream populations, a low but statistically significant genetic differentiation was found between reared fish and fish collected in the field. The SRD was considered effective in detecting the presence of aquaculture escapees that may have escaped in either early or late rearing phases.

Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback.

Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. mammals, birds) but so labile in others (e.g. teleosts, amphibians). To identify general mechanisms driving transitions in sex determination systems or forces which favour their conservation, we first require empirical data on sex chromosome systems from multiple lineages. Stickleback fishes are a valuable model lineage for the study of sex chromosome evolution due to variation in sex chromosome systems between closely-related species. Here, we identify the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole-genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex-linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.

Transcriptomic profiling of Trypanosoma congolense mouthpart parasites from naturally infected flies

BackgroundAnimal African trypanosomiasis, or nagana, is a veterinary disease caused by African trypanosomes transmitted by tsetse flies. In Africa, Trypanosoma congolense is one of the most pathogenic and prevalent causes of nagana in livestock, resulting in high animal morbidity and mortality and extensive production losses. In the tsetse fly, parasites colonise the midgut and eventually reach the mouthparts, from where they can be transmitted as the fly feeds on vertebrate hosts such as cattle. Despite the extreme importance of mouthpart-form parasites for disease transmission, very few global expression profile studies have been conducted in these parasite forms.MethodsHere, we collected tsetse flies from the Shimba Hills National Reserve, a wildlife area in southeast Kenya, diagnosed T. congolense infections, and sequenced the transcriptomes of the T. congolense parasites colonising the mouthparts of the flies.ResultsWe found little correlation between mouthpart parasites from natural and experimental fly infections. Furthermore, we performed differential gene expression analysis between mouthpart and bloodstream parasite forms and identified several surface-expressed genes and 152 novel hypothetical proteins differentially expressed in mouthpart parasites. Finally, we profiled variant antigen expression and observed that a variant surface glycoprotein (VSG) transcript belonging to T. congolense phylotype 8 (i.e. TcIL3000.A.H_000381200), previously observed to be enriched in metacyclic transcriptomes, was present in all wild-caught mouthpart samples as well as bloodstream-form parasites, suggestive of constitutive expression.ConclusionOur study provides transcriptomes of trypanosome parasites from naturally infected tsetse flies and suggests that a phylotype 8 VSG gene is constitutively expressed in metacyclic- and bloodstream-form parasites at the population level.Graphical

Geographic Population Genetic Structure of the New World Screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), Using SNPs.

The New World screwworm, Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is a serious parasite of livestock, humans, and other warm-blooded animals. It has been eradicated from the northern parts of its historical range down to the Panama-Colombian border where a permanent barrier zone is maintained. This eradication was accomplished through using the sterile insect technique (SIT). In 2016 there was an outbreak of C. hominivorax in the Florida Keys. In only six months, this pest was successfully re-eradicated using SIT, but the geographic origin of the invasion has yet to be resolved. It was previously determined that the Florida flies most likely represented a single invasion, and it was recommended that a finer-scale genetic assessment should be completed. Thus, this current proof-of-concept study aimed to develop a population genetic database using single nucleotide polymorphisms (SNPs) to reference outbreaks and potentially identify the origin of the Florida outbreak. This initial database consists of wild-caught samples from 4 geographic locations as well as laboratory colony samples that originated from 7 additional locations using a genotyping by sequencing (GBS) approach. Geographic population structuring was identified for twelve populations that clustered according to geographic location. The Florida outbreak samples appeared similar to samples from the outer Caribbean cluster which included samples from Dominican Republic and Trinidad and Tobago, however, these results will be further clarified with the replacement of laboratory colony samples with future wild-caught samples.

Comprehensive assessment of chemical residues in surface and wastewater using passive sampling, chemical, biological, and fish behavioral assays

Effluents from ten full-scale municipal wastewater treatment plants (WWTPs) that discharge into the Hudson River, surface waters, and wild-caught fish samples were analyzed using liquid chromatography with tandem mass spectrometry (LC/MS/MS) to examine the influence of wastewater discharge on the concentrations of contaminants of emerging concern (CECs) and their ecological impacts on fish. Analysis was based on targeted detection of 41 pharmaceuticals, and non-targeted analysis (suspect screening) of CECs. Biological effects of treated WWTP effluents were assessed using a larval zebrafish (Danio rerio) swimming behavior assay. Concentrations of residues in surface waters were determined in grab samples and polar organic chemical integrative samplers (POCIS). In addition, vitellogenin peptides, used as biomarkers of endocrine disruption, were quantified using LC/MS/MS in the wild-caught fish plasma samples. Overall, 94 chemical residues were identified, including 63 pharmaceuticals, 10 industrial chemicals, and 21 pesticides. Eight targeted pharmaceuticals were detected in 100% of effluent samples with median detections of: bupropion (194 ng/L), carbamazepine (91 ng/L), ciprofloxacin (190 ng/L), citalopram (172 ng/L), desvenlafaxine (667 ng/L), iopamidol (3790 ng/L), primidone (86 ng/L), and venlafaxine (231 ng/L). Over 30 chemical residues were detected in wild-caught fish tissues. Notably, zebrafish larvae exposed to chemical extracts of effluents from 9 of 10 WWTPs, in at least one season, were significantly hyperactive. Vitellogenin expression in male or immature fish occurred 2.8 times more frequently in fish collected from the Hudson River as compared to a reference site receiving no direct effluent input. Due to the low concentrations of pharmaceuticals detected in effluents, it is likely that chemicals other than pharmaceuticals measured are responsible for the behavioral changes observed. The combined use of POCIS and non-target analysis demonstrated significant increase in the chemical coverage for CEC detection, providing a better insight on the impacts of WWTP effluents and agricultural practices on surface water quality.

Daily otolith ring validation, age composition, and origin of the endangered striped catfish in the Mekong

The endangered striped catfish, Pangasianodon hypophthalmus is a large-bodied, migratory catfish, and one of the most cultured catfishes in the world. This study examines the otoliths of drifting wild-caught and hatchery-raised larvae of striped catfish to validate daily ring counts, calculate fish age, and estimate spawning time and spawning location to improve our understanding of the species’ life history. We conducted daily sampling of larval/juvenile striped catfish in the Mekong mainstream in Phnom Penh in 2015 and at a fish hatchery in Cambodia. Daily water levels and river distances at and between four hydrological gauges over the Mekong River reach between Phnom Penh and Cambodia-Lao border were also collected. Standard length and otolith ring counts were examined in both hatchery-raised (150) and wild-caught (390) samples. This study revealed that (i) mass larval drift of striped catfish at the Mekong River in Phnom Penh took place from July 13th to July 23rd, 2015 corresponding with increasing flow, (ii) otolith rings are formed daily in hatchery-raised larvae, and can be used to determine the age of wild larvae/juveniles, (iii) otolith ring increments are strongly correlated with standard length in hatchery-raised larvae, but not in wild-caught larvae, (iv) mean standard length and age of striped catfish larvae collected in Phnom Penh are 14.65 mm (se = 0.07) and 27.6 days (se = 0.13), respectively, and (v) most striped catfish likely spawn in June and early July between the full and new moon, and the spawning grounds are most likely located along the Cambodian Mekong between Stung Treng and Kratie and, in 2015, travel time from spawning grounds to Phnom Penh was approximately 27 days. Upper Cambodian Mekong River is therefore likely very necessary for the persistence of all striped catfish populations and fisheries in the lower floodplains of Cambodia and Mekong delta. The existing and proposed dams in the upper Mekong River in Cambodia and beyond would drastically affect spawning sites and dry season refuge habitats and disconnect the upstream spawning from the downstream rearing habitats of the species.

Deep learning approaches for challenging species and gender identification of mosquito vectors

Microscopic observation of mosquito species, which is the basis of morphological identification, is a time-consuming and challenging process, particularly owing to the different skills and experience of public health personnel. We present deep learning models based on the well-known you-only-look-once (YOLO) algorithm. This model can be used to simultaneously classify and localize the images to identify the species of the gender of field-caught mosquitoes. The results indicated that the concatenated two YOLO v3 model exhibited the optimal performance in identifying the mosquitoes, as the mosquitoes were relatively small objects compared with the large proportional environment image. The robustness testing of the proposed model yielded a mean average precision and sensitivity of 99% and 92.4%, respectively. The model exhibited high performance in terms of the specificity and accuracy, with an extremely low rate of misclassification. The area under the receiver operating characteristic curve (AUC) was 0.958 ± 0.011, which further demonstrated the model accuracy. Thirteen classes were detected with an accuracy of 100% based on a confusion matrix. Nevertheless, the relatively low detection rates for the two species were likely a result of the limited number of wild-caught biological samples available. The proposed model can help establish the population densities of mosquito vectors in remote areas to predict disease outbreaks in advance.

Analysis of sulfonamides, fluoroquinolones, tetracyclines, triphenylmethane dyes and other veterinary drug residues in cultured and wild seafood sold in Montreal, Canada

Freshwater and marine seafood products purchased in Montreal, Canada, were screened for diverse veterinary drug residues including sulfonamides and potentiators, macrolides, lincosamides, nitrofurans, nitroimidazoles, amphenicols, quinolones and fluoroquinolones, one triphenylmethane dye and its leuco-metabolite, and tetracyclines. QuEChERS extraction ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was validated in three model matrices (fatty fish, lean fish, and shrimp edible meat). Method detection limits were in the range of 0.002–3 μg/kg, and the accuracy of matrix-matched extracted calibrants was generally within acceptance criteria. The aquaculture or wild-caught samples of pangasius (basa), cod, salmon, sole, tilapia, trout, white shrimp and giant tiger prawn originated from Canada, China, India, Southeast Asia (Indonesia, Thailand, Vietnam), and other regions worldwide. Overall, 38 % of the tested fish and shrimp samples had detectable residues of at least one veterinary drug or metabolite, and 25 % were not compliant to Canadian guidelines. Leucomalachite green was detected across various sample types (detection frequency: 13 %; maximum: 0.9 μg/kg). Other detected compounds (2–11 % of samples) included tetracycline (maximum: 36 μg/kg), 4-epi-oxytetracycline (18 μg/kg), oxytetracycline (13 μg/kg), metronidazole (13 μg/kg), sulfamethazine (4.8 μg/kg), sulfamethoxazole (4.2 μg/kg), trimethoprim (0.59 μg/kg), florfenicol (0.27 μg/kg), flumequine (0.21 μg/kg), enrofloxacin (1.6 μg/kg), and ofloxacin (0.52 μg/kg).

Wolbachia Endosymbiont of the Horn Fly (Haematobia irritans irritans): a Supergroup A Strain with Multiple Horizontally Acquired Cytoplasmic Incompatibility Genes.

The horn fly, Haematobia irritansirritans, is a hematophagous parasite of livestock distributed throughout Europe, Africa, Asia, and the Americas. Welfare losses on livestock due to horn fly infestation are estimated to cost between $1 billion and $2.5 billion (U.S. dollars) annually in North America and Brazil. The endosymbiotic bacterium Wolbachia pipientis is a maternally inherited manipulator of reproductive biology in arthropods and naturally infects laboratory colonies of horn flies from Kerrville, TX, and Alberta, Canada, but it has also been identified in wild-caught samples from Canada, the United States, Mexico, and Hungary. Reassembly of PacBio long-read and Illumina genomic DNA libraries from the Kerrville H. i. irritans genome project allowed for a complete and circularized 1.3-Mb Wolbachia genome (wIrr). Annotation of wIrr yielded 1,249 coding genes, 34 tRNAs, 3 rRNAs, and 5 prophage regions. Comparative genomics and whole-genome Bayesian evolutionary analysis of wIrr compared to published Wolbachia genomes suggested that wIrr is most closely related to and diverged from Wolbachia supergroup A strains known to infect Drosophila spp. Whole-genome synteny analyses between wIrr and closely related genomes indicated that wIrr has undergone significant genome rearrangements while maintaining high nucleotide identity. Comparative analysis of the cytoplasmic incompatibility (CI) genes of wIrr suggested two phylogenetically distinct CI loci and acquisition of another cifB homolog from phylogenetically distant supergroup A Wolbachia strains, suggesting horizontal acquisition of these loci. The wIrr genome provides a resource for future examination of the impact Wolbachia may have in both biocontrol and potential insecticide resistance of horn flies.IMPORTANCE Horn flies, Haematobia irritans irritans, are obligate hematophagous parasites of cattle having significant effects on production and animal welfare. Control of horn flies mainly relies on the use of insecticides, but issues with resistance have increased interest in development of alternative means of control. Wolbachia pipientis is an endosymbiont bacterium known to have a range of effects on host reproduction, such as induction of cytoplasmic incompatibility, feminization, male killing, and also impacts vector transmission. These characteristics of Wolbachia have been exploited in biological control approaches for a range of insect pests. Here we report the assembly and annotation of the circular genome of the Wolbachia strain of the Kerrville, TX, horn fly (wIrr). Annotation of wIrr suggests its unique features, including the horizontal acquisition of additional transcriptionally active cytoplasmic incompatibility loci. This study provides the foundation for future studies of Wolbachia-induced biological effects for control of horn flies.

Genetic convergence of industrial melanism in three geometrid moths.

The rise of dark (melanic) forms of many species of moth in heavily coal-polluted areas of nineteenth- and twentieth-century Britain, and their post-1970s fall, point to a common selective pressure (camouflage against bird predators) acting at the community level. The extent to which this convergent phenotypic response relied on similar genetic and developmental mechanisms is unknown. We examine this problem by testing the hypothesis that the locus controlling melanism in Phigalia pilosaria and Odontopera bidentata, two species of geometrid moth that showed strong associations between melanism and coal pollution, is the same as that controlling melanism in Biston betularia, previously identified as the gene cortex. Comparative linkage mapping using family material supports the hypothesis for both species, indicating a deeply conserved developmental mechanism for melanism involving cortex. However, in contrast to the strong selective sweep signature seen in British B. betularia, no significant association was detected between cortex-region markers and melanic morphs in wild-caught samples of P. pilosaria and O. bidentata, implying much older, or diverse, origins of melanic morph alleles in these latter species.

Isolation and Characterization of Antimicrobial-Producing Bacteria from the Donkey's Ear Abalone Haliotis asinina

This study was conducted to isolate, test the antimicrobial potential, and characterize bacterial isolates from the gut of Haliotis asinina collected from cage culture and wild population. Isolation was performed using dilution spread plate method and antimicrobial property was determined using streak plate method against nine test microorganisms. Results showed that of the 29 isolates from the cage-cultured samples, five isolates showed the presence of antimicrobial property against Escherichia coli, Staphylococcus aureus, Bacillus cereus, Bacillus subtilis, Bacillus megaterium, Pseudomonas aeruginosa, and Candida albicans. Among the 30 isolates from the wild-caught samples, six isolates showed the presence of antimicrobial potential when tested against E. coli, S. aureus, B. cereus, B. subtilis, B. megaterium, and C. albicans. None of the isolates inhibited Aspergillus niger or Aspergillus flavus. The bacterial strain coded C28, isolated from cage-cultured abalone, and that inhibited the most test microorganisms was subjected to cultural, morphological, and physiological characterization. It was characterized as a bacterial strain closely related to the genus Pseudomonas. The results suggest that bacteria in the gut of H. asinina have potential antimicrobial properties where bacteria related to Pseudomonas spp. are present.

Oxygen Isotope Variability within Nautilus Shell Growth Bands.

Nautilus is often used as an analogue for the ecology and behavior of extinct externally shelled cephalopods. Nautilus shell grows quickly, has internal growth banding, and is widely believed to precipitate aragonite in oxygen isotope equilibrium with seawater. Pieces of shell from a wild-caught Nautilus macromphalus from New Caledonia and from a Nautilus belauensis reared in an aquarium were cast in epoxy, polished, and then imaged. Growth bands were visible in the outer prismatic layer of both shells. The thicknesses of the bands are consistent with previously reported daily growth rates measured in aquarium reared individuals. In situ analysis of oxygen isotope ratios using secondary ion mass spectrometry (SIMS) with 10 μm beam-spot size reveals inter- and intra-band δ18O variation. In the wild-caught sample, a traverse crosscutting 45 growth bands yielded δ18O values ranging 2.5‰, from +0.9 to -1.6 ‰ (VPDB), a range that is larger than that observed in many serial sampling of entire shells by conventional methods. The maximum range within a single band (~32 μm) was 1.5‰, and 27 out of 41 bands had a range larger than instrumental precision (±2 SD = 0.6‰). The results from the wild individual suggest depth migration is recorded by the shell, but are not consistent with a simple sinusoidal, diurnal depth change pattern. To create the observed range of δ18O, however, this Nautilus must have traversed a temperature gradient of at least ~12°C, corresponding to approximately 400 m depth change. Isotopic variation was also measured in the aquarium-reared sample, but the pattern within and between bands likely reflects evaporative enrichment arising from a weekly cycle of refill and replacement of the aquarium water. Overall, this work suggests that depth migration behavior in ancient nektonic mollusks could be elucidated by SIMS analysis across individual growth bands.