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Current monitoring methods to assess benthic impacts of marine finfish aquaculture are based on complex biological indices and/or geochemistry data. The former requires benthic macrofauna morpho‐taxonomic characterization that is time‐ and cost‐intensive, while the latter provides rapid assessment of the organic enrichment status of sediments but does not directly measure biotic impacts. In this study, sediment samples were collected from seven stations at six salmon farms in British Columbia, Canada, and analyzed for geochemical parameters and by eDNA metabarcoding to investigate linkages between geochemistry and foraminifera. Sediment texture across farm sites ranged from sand to silty loam, while the maximum sediment pore‐water sulphide concentration at each site ranged from 1,000 to 13,000 μM. Foraminifera alpha diversity generally increased with distance from cage edge. Adonis analyses revealed that farm site explained the most variation in foraminifera community, followed by sediment type, enrichment status, and distance from cage edge. Farm‐specific responses were observed in diversity analyses, taxonomic difference analyses, and correlation analyses. Results demonstrated that species diversity and composition of foraminifera characterized by eDNA metabarcoding generated signals consistent with benthic biodiversity being impacted by finfish farming activities. This substantiates the validity of eDNA metabarcoding for augmenting current approaches to benthic impact assessments by providing more cost‐effective and practicable biotic measures than traditional morpho‐taxonomy. To capitalize on this potential, further work is needed to design a new nomogram that combines eDNA metabarcoding data and geochemistry data to enable accurate monitoring of benthic impacts of fish farming in a time‐ and cost‐efficient way. [ABSTRACT FROM AUTHOR]

DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with 'success/failure' of barcoding), and we recommend their further consideration for barcoding studies. [ABSTRACT FROM AUTHOR]

1. We used historical sources, morphology-based taxonomy and mtDNA sequence data to address questions about the signal crayfish Pacifastacus leniusculus. These included evaluating unrecognised cryptic diversity and investigating the extent to which P. leniusculus may have been introduced within its presumed native range in the Pacific Northwest region of North America. Our study builds and expands on Pacific Northwest phylogeographic knowledge, particularly related to patterns of glacial refugia for freshwater species. 2. Extensive collections (824 specimens) from British Columbia (Canada), Idaho, Nevada, Oregon and Washington (United States) were used to characterise P. leniusculus at the mitochondrial 16S rRNA gene. Genetic groups within the species were elucidated by phylogenetics and amova; evolutionary relationships within the most common and diverse group were investigated using a statistical parsimony haplotype network, a nested amova, and tests of isolation by distance. Morphological measurements were used to relate findings of molecular analyses to three historically recognised P. leniusculus subspecies and characterise cryptic diversity by morphology. 3. We found substantial cryptic diversity, with three groups highly distinct from P. leniusculus in discrete geographic regions: the Chehalis River glacial refugium, Central Oregon and the Okanagan Plateau. Disjunct distributions of P. leniusculus relative to these cryptic groups and known patterns of Pleistocene glaciation and landscape evolution cast doubt on whether P. leniusculus is native to some areas such as coastal drainages of northern Washington and southern British Columbia. Morphological traits previously used to characterise P. leniusculus subspecies still persist but may be incapable of distinguishing P. leniusculus from newly discovered cryptic groups. 4. Cryptic diversity found within P. leniusculus highlights the pressing need for a thorough investigation of the genus Pacifastacus using data based on more extensive gene and taxon sampling. It also warrants conservation attention, as introductions of P. leniusculus within the Pacific Northwest may carry risks of hybridisation and introgression for cryptic groups. Owing to high genetic diversity and limited dispersal capacity relative to more vagile organisms like freshwater fish, crayfish of the genus Pacifastacus offer powerful potential insights into the geological history and phylogeography of the Pacific Northwest region. Finally, by shedding light on the long-neglected native range of P. leniusculus, our results should also better inform our understanding of potential source populations for, and the ecology of, this important invasive species in regions including Europe, Japan and elsewhere in North America. [ABSTRACT FROM AUTHOR]

Molecular ecologists, in search of suitable molecular markers, frequently PCR-amplify regions of mitochondrial DNA from total DNA extracts. This approach, although common, is prone to the co-amplification of nuclear copies of transposed DNA sequences (numts), which can then generate apparent mitochondrial sequence heteroplasmy. In this study we describe the discovery of apparent mitochondrial sequence heteroplasmy in Thalassarche albatrosses but eliminate the possibility of true sequence heteroplasmy and numts and instead reveal the source of the apparent heteroplasmy to be a duplicated control region. The two control regions align easily but are not identical in sequence or in length. Comparisons of functionally significant conserved sequence blocks do not provide evidence of degeneration in either duplicate. Phylogenetic analyses of domain I of both control region copies in five Thalassarche species indicate that they are largely evolving in concert; however, a short section within them is clearly evolving independently. To our knowledge this is the first time contrasting evolutionary patterns have been reported for duplicate control regions. Available evidence suggests that this duplication may be taxonomically widespread, so the results presented here should be considered in future evolutionary studies targeting the control region of all Procellariiformes and potentially other closely related avian groups. [ABSTRACT FROM AUTHOR]

Six variable microsatellite loci were used to examine genetic structuring in the closely related shy albatross ( Thalassarche cauta) and white-capped albatross ( T. steadi). First, levels of genetic differentiation between the species, and among three populations within each species, were analysed using amova, FST and RST. We found high levels of genetic structuring and detected many unshared alleles between the species, which provide strong evidence against any contemporary gene flow between them. Within each species, shy albatross populations were found to be genetically distinct whereas white-capped albatross populations were undifferentiated, which implies that dispersal events are much rarer in the former than in the latter. These results formed the basis for the recommendation that the three white-capped albatross populations (as a whole) and each shy albatross population be treated as separate units for conservation. Second, levels of genetic diversity and allelic patterns in shy and white-capped albatrosses were assessed for whether they support earlier mtDNA results suggesting that shy albatrosses arose through range expansion of white-capped albatrosses. All measures indicated lower genetic diversity within shy albatrosses than within white-capped albatrosses and upheld the hypothesis that shy albatrosses were founded by white-capped albatrosses. [ABSTRACT FROM AUTHOR]

Abstract The evolutionary relationship between shy (Thalassarche cauta ) and white-capped (T. steadi ) albatrosses was examined using mitochondrial control region sequences. Results were interpreted in the context of a recent and contentious taxonomic revision that recommended full species status for shy and white-capped albatrosses. Low sequence divergence between shy and white-capped albatrosses (1.8%) and between their close relatives, Salvin's and Chatham albatrosses (2.9%), was observed. Much higher sequence divergence was found between the shy/white-capped pair and the Salvin’s/Chatham pair (7.0%). Phylogenetic analyses confirmed the separation of the shy/white-capped pair from the Salvin’s/Chatham pair but did not provide species-level resolution. Phylogeographic analyses, including a nested clade analysis, F [sub ST] estimates and an analysis of molecular variance, indicated unambiguous genetic structuring between shy and white-capped albatrosses, thus confirming the demographic isolation of the species, but showed little to no structuring within each species. The geographical distribution of mtDNA haplotypes and other evidence suggest that shy albatrosses arose through range expansion by white-capped albatrosses. [ABSTRACT FROM AUTHOR]

Presents a study that examined the apportionment of genetic diversity in the noisy miner Manorina melanocephala in Brisbane, Queensland. Analysis of the DNA microsatellite loci of the birds; Estimation of the heterozygosity and number alleles of the microsatellite; Examination of the pairwise patterns of genetic differentiation in noisy miners.

Incidental detection of species of concern (e.g., invasive species, pathogens, threatened and endangered species) during biodiversity assessments based on high‐throughput DNA sequencing holds significant risks in the absence of rigorous, fit‐for‐purpose data quality and reporting standards. Molecular biodiversity data are predominantly collected for ecological studies and thus are generated to common quality assurance standards. However, the detection of certain species of concern in these data would likely elicit interest from end users working in biosecurity or other surveillance contexts (e.g., pathogen detection in health‐related fields), for which more stringent quality control standards are essential to ensure that data are suitable for informing decision‐making and can withstand legal or political challenges. We suggest here that data quality and reporting criteria are urgently needed to enable clear identification of those studies that may be appropriately applied to surveillance contexts. In the interim, more pointed disclaimers on uncertainties associated with the detection and identification of species of concern may be warranted in published studies. This is not only to ensure the utility of molecular biodiversity data for consumers, but also to protect data generators from uncritical and potentially ill‐advised application of their science in decision‐making. [ABSTRACT FROM AUTHOR]

Non‐indigenous species (NIS) reach every corner of the world, at times wreaking havoc on ecosystems and costing the global economy billions of dollars. A rapid and accurate biosurveillance tool tailored to a particular biogeographic region is needed to detect NIS when they are first introduced into an area as traditional detection methods are expensive and require specialized expertise. Metabarcoding of environmental and community DNA meets those biosurveillance requirements; a novel tool tailored to the Northwest Pacific Ocean is presented here using an approach that could revolutionize early detection of NIS. Eight newly designed genetic markers for multiple gene regions were implemented to meet the stringent taxonomic requirements for the detection of NIS across four major marine phyla. The tool was considered highly successful because it identified 12 known NIS in the study area and a further seven species representing potential new records. Overall community composition detected here was statistically different between substrate types; zooplankton sampling accounted for significantly higher species richness than filtered sea water in most cases, but this was dominated by mollusk and arthropod species. Both substrate types sampled were required to identify the wide taxonomic breadth of known NIS in the study area. Intensive sampling is known to be paramount for the detection of rare species, including new incursions of NIS, thus it is recommended to include diverse DNA sampling protocols based on species' life‐history characteristics for broad detection capacity. Application of a metabarcoding‐based molecular biosurveillance tool optimized for biogeographic regions enables rapid and accurate early detection across a wide taxonomic range to allow quick implementation of eradication or control efforts and potentially mitigate some of the devastating effects of NIS worldwide. [ABSTRACT FROM AUTHOR]

Metabarcoding combines DNA barcoding with high‐throughput sequencing, often using one genetic marker to understand complex and taxonomically diverse samples. However, species‐level identification depends heavily on the choice of marker and the selected primer pair, often with a trade‐off between successful species amplification and taxonomic resolution. We present a versatile metabarcoding protocol for biomonitoring that involves the use of two barcode markers (COI and 18S) and four primer pairs in a single high‐throughput sequencing run, via sample multiplexing. We validate the protocol using a series of 24 mock zooplanktonic communities incorporating various levels of genetic variation. With the use of a single marker and single primer pair, the highest species recovery was 77%. With all three COI fragments, we detected 62%–83% of species across the mock communities, while the use of the 18S fragment alone resulted in the detection of 73%–75% of species. The species detection level was significantly improved to 89%–93% when both markers were used. Furthermore, multiplexing did not have a negative impact on the proportion of reads assigned to each species and the total number of species detected was similar to when markers were sequenced alone. Overall, our metabarcoding approach utilizing two barcode markers and multiple primer pairs per barcode improved species detection rates over a single marker/primer pair by 14% to 35%, making it an attractive and relatively cost‐effective method for biomonitoring natural zooplankton communities. We strongly recommend combining evolutionary independent markers and, when necessary, multiple primer pairs per marker to increase species detection (i.e., reduce false negatives) in metabarcoding studies. [ABSTRACT FROM AUTHOR]

Background: Intracellular symbionts often undergo genome reduction, losing both coding and non-coding DNA in a process that ultimately produces small, gene-dense genomes with few genes. Among eukaryotes, an extreme example is found in microsporidians, which are anaerobic, obligate intracellular parasites related to fungi that have the smallest nuclear genomes known (except for the relic nucleomorphs of some secondary plastids). Mikrocytids are superficially similar to microsporidians: they are also small, reduced, obligate parasites; however, as they belong to a very different branch of the tree of eukaryotes, the rhizarians, such similarities must have evolved in parallel. Since little genomic data are available from mikrocytids, we assembled a draft genome of the type species, Mikrocytos mackini, and compared the genomic architecture and content of microsporidians and mikrocytids to identify common characteristics of reduction and possible convergent evolution. Results: At the coarsest level, the genome of M. mackini does not exhibit signs of extreme genome reduction; at 49.7 Mbp with 14,372 genes, the assembly is much larger and gene-rich than those of microsporidians. However, much of the genomic sequence and most (8075) of the protein-coding genes code for transposons, and may not contribute much of functional relevance to the parasite. Indeed, the energy and carbon metabolism of M. mackini share several similarities with those of microsporidians. Overall, the predicted proteome involved in cellular functions is quite reduced and gene sequences are extremely divergent. Microsporidians and mikrocytids also share highly reduced spliceosomes that have retained a strikingly similar subset of proteins despite having reduced independently. In contrast, the spliceosomal introns in mikrocytids are very different from those of microsporidians in that they are numerous, conserved in sequence, and constrained to an exceptionally narrow size range (all 16 or 17 nucleotides long) at the shortest extreme of known intron lengths. Conclusions: Nuclear genome reduction has taken place many times and has proceeded along different routes in different lineages. Mikrocytids show a mix of similarities and differences with other extreme cases, including uncoupling the actual size of a genome with its functional reduction. [ABSTRACT FROM AUTHOR]

Summary: DNA-based methods continue to unveil the diversity and evolutionary origins of life on Earth. ‘Next generation’ methods have just solved a long-standing puzzle by uncovering previously unseen yet globally distributed diversity within a lineage of amitochondriate parasites affecting commercially exploited aquatic hosts. This discovery will impact both pure and applied research fields. [ABSTRACT FROM AUTHOR]

The common blue mussel ( Mytilus edulis ) was introduced to British Columbia, Canada, in the 1980s as an aquaculture alternative to native mussel species. Since then, the mussel industry in Pacific Canada has expanded and includes operations utilizing traditional methods of broodstock selection based on visual qualitative and quantitative traits. The impacts of hatchery propagation on genetic diversity and implications for animal fitness have been previously studied for other aquatic species, and this study further examines the effect of hatchery production on three M. edulis aquaculture populations in relation to a wild originator population. Prior to microsatellite genetic analysis, animals were identified to species using nuclear markers and were found to contain varying proportions of pure M. edulis as well as other pure species and hybrids from the ‘ Mytilus edulis complex’. Subsequently seven microsatellite markers were used to genotype 166 pure adult M. edulis individuals, all of which exhibited high levels of polymorphism. Allele frequencies at multiple loci did not conform to Hardy–Weinberg expectations and substantially less genetic diversity and very low effective population size estimates ( N e , calculated from linkage disequilibrium) were observed in farmed populations compared to the wild reference population. All populations were found to be genetically distinct based on F ST estimates. Mean allelic richness was approximately three times higher in the wild reference population than the three farmed populations (21 compared to 7.51, 7.91 in the two populations selecting for size and 8.24 in the population selecting for a colour morph). Observed heterozygosity was not significantly decreased in the cultured colour morph population, but was significantly different in the two other culture populations in comparison to the wild group. Reduced genetic diversity of the aquaculture populations is likely at least partially due to small effective breeding groups during hatchery propagation, creating genetic drift over successive generations. Speculations about the influence of broodstock selection practices are tentative and should be addressed in further temporal studies. These results indicate the need for the effective management of hatchery operations, the importance of rigorous site inventory, genetic broodstock characterization, and that ideally pedigree programs should be developed to help maintain healthy and productive shellfish culture populations with adaptive fitness capacity. Statement of relevance Hatchery methods impact species purity and genetic diversity. [ABSTRACT FROM AUTHOR]

Marine Protected Areas (MPAs) have been adopted globally as a tool to combat biodiversity loss and restore marine ecosystems. Successful application of MPAs will be predicated on the ability to monitor biodiversity in a synoptic and noninvasive manner. Environmental DNA (eDNA) methods have important advantages over traditional biodiversity survey methods for monitoring conservation areas. To evaluate the efficacy of eDNA metabarcoding for fish biodiversity monitoring, we sampled 19 coastal eelgrass (Zostera marina) beds in Canada, as eelgrass beds are known for high biodiversity and significant conservation value. At each site, beach seines were used to survey fish and water samples were collected contemporaneously for eDNA metabarcoding. In total, beach seining caught 32 672 individuals across 59 fish taxa, and eDNA detected 129 fish taxa. eDNA captured site-level variation and detected higher species richness at both site and regional levels compared to seining. eDNA abundance had a positive association with capture abundance. Collectively these results highlight how eDNA metabarcoding offers an efficient approach for monitoring fish biodiversity in coastal eelgrass beds, thus providing a valuable and noninvasive tool for MPA planning and coastal monitoring. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities, thus it has high potential utility for routine assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected at six salmon farms in British Columbia, Canada. Benthic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analysing 11,466 individuals using a combination of morphology‐based taxonomy and DNA barcoding. Study objectives were to: (i) compare biotic signals associated with benthic impacts of salmon farming in the two data sources, and (ii) identify potential eDNA indicators to facilitate monitoring in Canada. Alpha diversity parameters were consistently reduced near fish cage edge and negatively correlated with pore‐water sulphide concentration, with coefficients ranging from −0.62 to −0.48. Although Polychaeta are a common indicator group, the negative correlation with pore‐water sulphide concentration was much stronger for Nematoda OTU richness (correlation coefficient: −0.86) than for Polychaeta (correlation coefficient: −0.38). Presence/absence of Capitella generally agreed well between the two methods despite that they differed in the volume of sediments sampled and the molecular marker used. Multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop local biotic indices. [ABSTRACT FROM AUTHOR]

Successful invasion by nonindigenous species is often attributed to high propagule pressure, yet some foreign species become widespread despite showing reduced genetic variation due to founder effects. The signal crayfish ( Pacifastacus leniusculus) is one such example, where rapid spread across Japan in recent decades is believed to be the result of only three founding populations. To infer the history and explore the success of this remarkable crayfish invasion, we combined detailed phylogeographical and morphological analyses conducted in both the introduced and native ranges. We sequenced 16S mitochondrial DNA of signal crayfish from across the introduced range in Japan (537 samples, 20 sites) and the native range in western North America (700 samples, 50 sites). Because chela size is often related to aggressive behavior in crayfish, and hence, their invasion success, we also measured chela size of a subset of specimens in both introduced and native ranges. Genetic diversity of introduced signal crayfish populations was as high as that of the dominant phylogeographic group in the native range, suggesting high propagule pressure during invasion. More recently established crayfish populations in Japan that originated through secondary spread from one of the founding populations exhibit reduced genetic diversity relative to older populations, probably as a result of founder effects. However, these newer populations also show larger chela size, consistent with expectations of rapid adaptations or phenotypic responses during the invasion process. Introduced signal crayfish populations in Japan originate from multiple source populations from a wide geographic range in the native range of western North America. A combination of high genetic diversity, especially for older populations in the invasive range, and rapid adaptation to colonization, manifested as larger chela in recent invasions, likely contribute to invasion success of signal crayfish in Japan. [ABSTRACT FROM AUTHOR]

Digeneans and cestodes are species-rich taxa and can seriously impact human health, fisheries, aqua- and agriculture, and wildlife conservation and management. DNA barcoding using the COI Folmer region could be applied for species detection and identification, but both 'universal' and taxon-specific COI primers fail to amplify in many flatworm taxa. We found that high levels of nucleotide variation at priming sites made it unrealistic to design primers targeting all flatworms. We developed new degenerate primers that enabled acquisition of the COI barcode region from 100% of specimens tested (n = 46), representing 23 families of digeneans and 6 orders of cestodes. This high success rate represents an improvement over existing methods. Primers and methods provided here are critical pieces towards redressing the current paucity of COI barcodes for these taxa in public databases. [ABSTRACT FROM AUTHOR]

Mikrocytos mackini is an internationally regulated pathogen and causative agent of Denman Island disease in Pacific oysters Crassostrea gigas . Recent phylogenetic breakthroughs have placed this parasite within a highly divergent and globally distributed eukaryotic lineage that has been designated a new taxonomic order, Mikrocytida. The discovery of this new radiation of parasites is accompanied by a heightened awareness of the many knowledge gaps that exist with respect to the general biology, epizootiology, and potential impact of mikrocytid parasites on hosts, ecosystems, and commercial fisheries. It has also highlighted current shortcomings regarding our ability to detect these organisms. In this study, we developed a species-specific, sensitive, and quantitative method for detecting M. mackini DNA from host tissues using probe-based real-time qPCR technology. A limit of sensitivity between 2 and 5 genome copy equivalents was achieved in a reaction matrix containing ≥40 ng/μL host gDNA without inhibition. This detection proved superior to existing methods based on conventional PCR, histology or gross pathology and is the first species-specific diagnostic test for M. mackini . Quantitative assessment of parasite DNA using this assay remained accurate to between 10 and 50 copies identifying that during infection, M. mackini DNA was significantly more prevalent in hemolymph, labial palp, and mid-body cross-sections compared to mantle or adductor muscle. DNA extracted from a mid-body cross-section also provided the highest likelihood for detection during diagnostic screening of infected oysters. Taken together, these findings provide strong analytical evidence for the adoption of qPCR as the new reference standard for detecting M. mackini and give preliminary insight into the distribution of the parasite within host tissues. Standardised operating methodologies for sample collection and qPCR testing are provided to aid in the international regulatory diagnosis of M. mackini and serve as a useful platform for the future development of multiplexed or alternate mikrocytid species detection. [ABSTRACT FROM AUTHOR]

Summary: Mikrocytos mackini is an intracellular protistan parasite of oysters whose position in the phylogenetic tree of eukaryotes has been a mystery for many years [1,2]. M. mackini is difficult to isolate, has not been cultured, and has no defining morphological feature. Furthermore, its only phylogenetic marker that has been successfully sequenced to date (the small subunit ribosomal RNA) is highly divergent and has failed to resolve its evolutionary position [2]. M. mackini is also one of the few eukaryotes that lacks mitochondria [1], making both its phylogenetic position and comparative analysis of mitochondrial function particularly important. Here, we have obtained transcriptomic data for M. mackini from enriched isolates and constructed a 119-gene phylogenomic data set. M. mackini proved to be among the fastest-evolving eukaryote lineages known to date, but, nevertheless, our analysis robustly placed it within Rhizaria. Searching the transcriptome for genetic evidence of a mitochondrion-related organelle (MRO) revealed only four mitochondrion-derived genes: IscS, IscU, mtHsp70, and FdxR. Interestingly, all four genes are involved in iron-sulfur cluster formation, a biochemical pathway common to other highly reduced “mitosomes” in unrelated MRO-containing lineages [7]. This is the first evidence of MRO in Rhizaria, and it suggests the parallel evolution of mitochondria to mitosomes in this supergroup. [Copyright &y& Elsevier]

Abstract: Within Canadian waters there are two distinct stocks of Pacific hake (Merluccius productus); an inshore resident stock and an offshore, migratory stock. From 2006 to 2008, a change in the migratory behavior of the offshore stock resulted in a shift of the entire fishery from the typical grounds off the west coast of Vancouver Island to the more northerly region of Queen Charlotte Sound. Management concerns regarding the unknown exploitation of any resident stocks prompted a re-examination of Pacific hake stock structure in Canadian waters. Population genetic techniques determined a connectivity of Pacific hake found in Queen Charlotte Sound in the summer to (1) the offshore migratory population; (2) the inshore resident population and (3) the populations in adjacent deepwater inlets. We provide evidence that supports the delineation of the resident and migratory stocks; and evidence of two other genetically differentiated resident groups. These results were supported by differences in biological parameters and parasite infection levels. Of note is the first record of the occurrence of the parasite Kudoa paniformis in the resident population. [Copyright &y& Elsevier]

Abstract: Hundreds of thousands of seabirds are killed each year as a result of interacting with longline and trawl fishing operations, and the severity of the impact varies regionally. Shy and white-capped albatrosses, Thalassarche cauta and Thalassarche steadi respectively, are phenotypically similar species known to be incidentally killed by fishing operations. The magnitude of this mortality has not previously been assessed across their range. Here we examine recent effort and bycatch rates in fisheries known to incidentally kill these species and qualitatively evaluate the level of impact of each fishery. Results indicate that over 8500 of these albatrosses may be killed annually, although the reliability of this estimate is low due to the paucity of comprehensive observer data in most fisheries. Of the estimated deaths of all seabird species in the fisheries assessed, trawl and longline fisheries killed birds in approximately equal proportions, but when the mortality levels of shy-type albatrosses were examined, trawl fisheries were responsible for 75% of all deaths. Data suggest most of these birds were killed in South African, Namibian and New Zealand demersal trawl fisheries and the South Africa pelagic longline fishery. Because most adult shy albatrosses are comparatively sedentary and rarely found outside Australian waters, it is primarily juvenile shy albatrosses that regularly encounter fishing fleets known to kill large numbers of albatrosses. In contrast, throughout most of their range juvenile and adult white-capped albatrosses are exposed to fisheries that collectively kill many thousands of these albatrosses each year. These data emphasise the urgent need for robust assessments of the impact of bycatch at a species and population level, and the urgent implementation of effective mitigation measures. [Copyright &y& Elsevier]