Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence.

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain.

Cephalopods have evolved nervous systems that parallel the complexity of mammalian brains in terms of neuronal numbers and richness in behavioral output. How the cephalopod brain develops has only been described at the morphological level, and it remains unclear where the progenitor cells are located and what molecular factors drive neurogenesis. Using histological techniques, we located dividing cells, neural progenitors and postmitotic neurons in Octopus vulgaris embryos. Our results indicate that an important pool of progenitors, expressing the conserved bHLH transcription factors achaete-scute or neurogenin, is located outside the central brain cords in the lateral lips adjacent to the eyes, suggesting that newly formed neurons migrate into the cords. Lineage-tracing experiments then showed that progenitors, depending on their location in the lateral lips, generate neurons for the different lobes, similar to the squid Doryteuthis pealeii. The finding that octopus newborn neurons migrate over long distances is reminiscent of vertebrate neurogenesis and suggests it might be a fundamental strategy for large brain development.

Octopuses have evolved incredibly large and complex nervous systems that allow them to perform impressive behaviors, like plan ahead, navigate and solve puzzles. The nervous system of the common octopus (also known as Octopus vulgaris) contains over half a billion nerves cells called neurons, similar to the number found in small primates. Two thirds of these cells reside in the octopuses' arms, while the rest make-up a central brain that sits between their eyes. Very little is known about how this central brain forms in the embryo, including where the cells originate and which molecular factors drive their maturation in to adult cells. To help answer these questions, Deryckere et al. studied the brain of Octopus vulgaris at different stages of early development using various cell staining and imaging techniques. The experiments identified an important pool of dividing cells which sit in an area outside the central brain called the 'lateral lips'. In these cells, genes known to play a role in neural development in other animals are active, indicating that the cells had not reached their final, mature state. In contrast, the central brain did not seem to contain any of these immature cells at the point when it was growing the most. To investigate this further, Deryckere et al. used fluorescent markers to track the progeny of the dividing cells during development. This revealed that cells in the lateral lips take on a specific neuronal fate before migrating to their target region in the central brain. Newly matured neurons have also been shown to travel large distances in the embryos of vertebrates, suggesting that this mechanism may be a common strategy for building large, complex brains. Although the nervous system of the common octopus is comparable to mammals, they evolved from a very distant branch of the tree of life; indeed, their last common ancestor was a worm-like animal that lived about 600 million years ago. Studying the brain of the common octopus, as done here, could therefore provide new insights into how complex nervous systems, including our own, evolved over time.

Reconciling seascape genetics and fisheries science in three codistributed flatfishes.

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits.

Assessment of the quality of European silver eels and tentative approach to trace the origin of contaminants - A European overview.

The European eel is critically endangered. Although the quality of silver eels is essential for their reproduction, little is known about the effects of multiple contaminants on the spawning migration and the European eel management plan does not take this into account. To address this knowledge gap, we sampled 482 silver eels from 12 catchments across Europe and developed methods to assess three aspects of eel quality: muscular lipid content (N = 169 eels), infection with Anguillicola crassus (N = 482), and contamination by persistent organic pollutants (POPs, N = 169) and trace elements (TEs, N = 75). We developed a standardized eel quality risks index (EQR) using these aspects for the subsample of 75 female eels. Among 169 eels, 33% seem to have enough muscular lipids content to reach the Sargasso Sea to reproduce. Among 482 silver eels, 93% were infected by A. crassus at least once during their lifetime. All contaminants were above the limit of quantification, except the 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE), Ag and V. The contamination by POPs was heterogeneous between catchments while TEs were relatively homogeneous, suggesting a multi-scale adaptation of management plans. The EQR revealed that eels from Warwickshire were most impacted by brominated flame-retardants and agricultural contaminants, those from Scheldt were most impacted by agricultural and construction activities, PCBs, coal burning, and land use, while Frémur eels were best characterized by lower lipid contents and high parasitic and BTBPE levels. There was a positive correlation between EQR and a human footprint index highlighting the capacity of silver eels for biomonitoring human activities and the potential impact on the suitability of the aquatic environment for eel population health. EQR therefore represents a step forward in the standardization and mapping of eel quality risks, which will help identify priorities and strategies for restocking freshwater ecosystems.

Multi-species transcriptomics reveals evolutionary diversity in the mechanisms regulating shrimp tail muscle excitation-contraction coupling.

The natural flight response in shrimp is powered by rapid contractions of the abdominal muscle fibres to propel themselves backwards away from perceived danger. This muscle contraction is dependent on repetitive depolarization of muscle plasma membrane, triggering tightly spaced cytoplasmic [Ca2+] transients and rapidly rising tetanic force responses. To achieve such high amplitude and high frequency of Ca2+ transients requires a high abundance of sarcoplasmic/endoplasmic reticulum Ca2+ ATPase (SERCA) to rapidly clear cytoplasmic Ca2+ between each transient and an efficient Ca2+ release system consisting of the Ryanodine Receptor (RyR), and voltage gated Ca2+ channels (CaVs). With the aim to expand our knowledge of muscle gene function and identify orthologous genes regulating muscle excitation-contraction (EC) coupling, this study assembled nine Penaeid shrimp muscle transcriptomes. On average, the nine transcriptomes contained 27,000 contigs, with an annotation rate of 36% and a BUSCO completeness of 70%. Despite maintaining their function, the crustacean RyR and CaV proteins showed evidence of significant diversification from mammalian orthologs, while SERCA remained more conserved. Several key components of protein interaction were conserved, while others showed distinct crustacean specific evolutionary adaptations. Lastly, this study revealed approximately 1,000 orthologous genes involved in muscle specific processes present across all nine species.

Author Correction: Gene-associated markers provide tools for tackling illegal fishing and false eco-certification.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The survey and reference assisted assembly of the Octopus vulgaris genome.

The common octopus, Octopus vulgaris, is an active marine predator known for the richness and plasticity of its behavioral repertoire, and remarkable learning and memory capabilities. Octopus and other coleoid cephalopods, cuttlefish and squid, possess the largest nervous system among invertebrates, both for cell counts and body to brain size. O. vulgaris has been at the center of a long-tradition of research into diverse aspects of its biology. To leverage research in this iconic species, we generated 270 Gb of genomic sequencing data, complementing those available for the only other sequenced congeneric octopus, Octopus bimaculoides. We show that both genomes are similar in size, but display different levels of heterozygosity and repeats. Our data give a first quantitative glimpse into the rate of coding and non-coding regions and support the view that hundreds of novel genes may have arisen independently despite the close phylogenetic distance. We furthermore describe a reference-guided assembly and an open genomic resource (CephRes-gdatabase), opening new avenues in the study of genomic novelties in cephalopods and their biology.

Preeclampsia is Associated with Sex-Specific Transcriptional and Proteomic Changes in Fetal Erythroid Cells.

Preeclampsia (PE) has been associated with placental dysfunction, resulting in fetal hypoxia, accelerated erythropoiesis, and increased erythroblast count in the umbilical cord blood (UCB). Although the detailed effects remain unknown, placental dysfunction can also cause inflammation, nutritional, and oxidative stress in the fetus that can affect erythropoiesis. Here, we compared the expression of surface adhesion molecules and the erythroid differentiation capacity of UCB hematopoietic stem/progenitor cells (HSPCs), UCB erythroid profiles along with the transcriptome and proteome of these cells between male and female fetuses from PE and normotensive pregnancies. While no significant differences were observed in UCB HSPC migration/homing and in vitro erythroid colony differentiation, the UCB HSPC transcriptome and the proteomic profile of the in vitro differentiated erythroid cells differed between PE vs. normotensive samples. Accordingly, despite the absence of significant differences in the UCB erythroid populations in male or female fetuses from PE or normotensive pregnancies, transcriptional changes were observed during erythropoiesis, particularly affecting male fetuses. Pathway analysis suggested deregulation in the mammalian target of rapamycin complex 1/AMP-activated protein kinase (mTORC1/AMPK) signaling pathways controlling cell cycle, differentiation, and protein synthesis. These results associate PE with transcriptional and proteomic changes in fetal HSPCs and erythroid cells that may underlie the higher erythroblast count in the UCB in PE.

Introgressive hybridisation between two widespread sharks in the east Pacific region.

With just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypothesis of ongoing hybridisation. We sampled a large number of individuals from areas where the species co-occur (contact zones) across the Pacific Ocean and used both mitochondrial and nuclear-encoded SNPs to examine genetic admixture and introgression between the two species. Using empirical analytical approaches and simulations, we first developed a set of 1873 highly informative SNPs for these two species to evaluate the degree of admixture between them. Overall, results indicate a high discriminatory power of nuclear SNPs (FST = 0.47, p < 0.05) between the two species, unlike mitochondrial DNA (ΦST = 0.00 p > 0.05), which failed to differentiate these species. We identified four hybrid individuals (∼1%) and detected bi-directional introgression between C. galapagensis and C. obscurus in the Gulf of California along the east Pacific coast of the Americas. We emphasize the importance of including a combination of mtDNA and diagnostic nuclear markers to properly assess species identification, detect patterns of hybridisation, and better inform management and conservation of these sharks, especially given the morphological similarities within the genus Carcharhinus.

Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus galeus.

Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Dependent within Australia. Individuals are known to move between both countries, but it is disputed whether the stocks are reproductively linked. Accurate and unbiased determination of stock and population connectivity is crucial to inform effective management. In this study, we assess the genetic composition and population connectivity between Australian and New Zealand school sharks using genome-wide SNPs, while accounting for non-random kin sampling. Between 2009 and 2013, 88 neonate and juvenile individuals from Tasmanian and New Zealand nurseries were collected and genotyped. Neutral loci were analyzed to detect fine-scale signals of reproductive connectivity. Seven full-sibling groups were identified and removed for unbiased analysis. Based on 6,587 neutral SNPs, pairwise genetic differentiation from Tasmanian and New Zealand neonates was non-significant (F ST = 0.0003, CI95 = [-0.0002, 0.0009], p = 0.1163; D est = 0.0006 ± 0.0002). This pattern was supported by clustering results. In conclusion, we show a significant effect of non-random sampling of kin and identify fine-scale reproductive connectivity between Australian and New Zealand school sharks. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.pd8612j.

Integrating complementary methods to improve diet analysis in fishery-targeted species.

Developing efficient, reliable, cost-effective ways to identify diet is required to understand trophic ecology in complex ecosystems and improve food web models. A combination of techniques, each varying in their ability to provide robust, spatially and temporally explicit information can be applied to clarify diet data for ecological research. This study applied an integrative analysis of a fishery-targeted species group-Plectropomus spp. in the central Great Barrier Reef, Australia, by comparing three diet-identification approaches. Visual stomach content analysis provided poor identification with ~14% of stomachs sampled resulting in identification to family or lower. A molecular approach was successful with prey from ~80% of stomachs identified to genus or species, often with several unique prey in a stomach. Stable isotope mixing models utilizing experimentally derived assimilation data, identified similar prey as the molecular technique but at broader temporal scales, particularly when prior diet information was incorporated. Overall, Caesionidae and Pomacentridae were the most abundant prey families (>50% prey contribution) for all Plectropomus spp., highlighting the importance of planktivorous prey. Less abundant prey categories differed among species/color phases indicating possible niche segregation. This study is one of the first to demonstrate the extent of taxonomic resolution provided by molecular techniques, and, like other studies, illustrates that temporal investigations of dietary patterns are more accessible in combination with stable isotopes. The consumption of mainly planktivorous prey within this species group has important implications within coral reef food webs and provides cautionary information regarding the effects that changing resources could have in reef ecosystems.

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome.

The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus).

Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double-digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

Adverse effect of early-life high-fat/high-carbohydrate ("Western") diet on bacterial community in the distal bowel of mice.

Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced "Western-type" diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.

Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing.

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST  = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.

Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers.

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST = 0.023-0.035), mtDNA exhibited more divergence (ΦST = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.

Harnessing the Power of Genomics to Secure the Future of Seafood.

Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.

Adaptive and non-adaptive divergence in a common landscape.

Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes-three-spined and nine-spined stickleback-differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes.The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.

Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England.

A fundamental consideration for the conservation of a species is the extent of its native range, that is, regions naturally colonized. However, both natural processes and human-mediated introductions can drive species distribution shifts. Ruling out the human-mediated introduction of a species into a given region is vital for its conservation, but remains a significant challenge in most cases. The crucian carp Carassius carassius (L.) is a threatened freshwater fish thought to be native to much of Europe. However, its native status in England is based only on anecdotal evidence. Here, we devise an approach that can be used to empirically test the native status of English fauna. We use this approach, along with 13 microsatellite loci, population structure analyses, and Approximate Bayesian Computation (ABC), to test hypotheses for the origins of C. carassius in England. Contrary to the current consensus, we find strong support for the human-mediated introduction of C. carassius into England during the 15th century. This result stimulates an interesting and timely debate surrounding motivations for the conservation of species. We discuss this topic, and the potential for continued conservation of C. carassius in England, despite its non-native origins.