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Eulachon (Thaleichthys pacificus), a culturally and ecologically important anadromous smelt (Family Osmeridae), ranges from Northern California to the southeast Bering Sea. In recent decades, some populations have experienced declines. Here we use a contig-level genome assembly combined with previously published restriction site-associated DNA sequencing (RADseq)-derived markers to construct an amplicon panel for eulachon. Using this panel, we develop a filtered genetic baseline of 521 variant loci genotyped in 1989 individuals from 14 populations ranging from Northern California through central Alaska. Consistent with prior genetic studies, the strongest separation occurs among three main regions: from Northern California up to and including the Fraser River; north of the Fraser River to southeast Alaska; and within the Gulf of Alaska. Separating the Fraser River from southern US populations and refining additional substructure within the central coast may be possible in mixed-stock analysis; this will be addressed in future work. The amplicon panel outperformed the previous microsatellite panel and thus will be used in future mixed-stock analyses of eulachon to provide new insights for management and conservation of eulachon.

This study presents the first microsatellite DNA study of population structure of Pacific hake, Merluccius productus (also known as Pacific whiting) within the Salish Sea, which has been identified as a distinct population segment under the US Endangered Species Act and is currently listed as a federal Species of Concern. In contrast, a separate coastal stock component of Pacific hake represents the most abundant commercial groundfish species on the US West Coast. We surveyed variation at 10 microsatellite DNA loci in a total of 655 individuals from three Salish Sea locations (Port Susan (PTS) and Dabob Bay in Washington and south-central Strait of Georgia (SOG) in British Columbia), three coastal locations (two off southern California and one in the Gulf of Alaska), and the Northern Gulf of California (GOC), México. No significant differences were detected among temporal samples from both PTS and SOG locations. Multilocus measures of population subdivision between coastal and Salish Sea populations (all pairwise FST ≥ 0.03) and between PTS and SOG populations (FST ≥ 0.01) suggest a moderate degree of demographic isolation among these spawning populations. No significant genetic differences were found among the three coastal Pacific hake samples; however, Pacific hake from the GOC were significantly differentiated from both coastal (FST > 0.05) and Salish Sea (FST ≥ 0.03) Pacific hake. Correlations between genetic and geographic distance showed that Pacific hake display a very strong isolation by distance signal, both over the whole study area (∼4500 km; r2 = 0.94) and within the Salish Sea (∼280 km; r2 = 0.72). This study suggests that PTS and SOG populations are to some extent demographically isolated from each other.

Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analysed for genetic variability at 12 microsatellite loci and compared to 17 present-day O. nerka populations-exhibiting either anadromous (sockeye salmon) or nonanadromous (kokanee) life histories-from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee Rivers (pairwise F(ST) = 0.004 and 0.002, respectively), and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise F(ST) = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration timing, suggesting that this group represents a historical ESU originating in headwater lakes in British Columbia that was probably extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.

Eulachon (Thaleichthys pacificus), an anadromous smelt in the Northeast Pacific Ocean was examined for listing under the USA’s Endangered Species Act (ESA). A southern Distinct Population Segment (DPS) of eulachon – that occurs in the California Current and is composed of numerous subpopulations that spawn in rivers from northern California to northern British Columbia – was identified on the basis of ecological and environmental characteristics, and to a lesser extent, genetic and life history variation. Although the northern terrestrial boundary of this DPS remains uncertain, our consensus opinion was that this northern boundary occurs south of the Nass River and that the DPS was discrete from more northern eulachon, as well as significant to the biological species as a whole and thus is a ‘species’ under the ESA. Eulachon have been nearly absent in northern California for over two decades, have declined in the Fraser River by over 97% in the past 10 years, and are at historically low levels in other British Columbia rivers in the DPS, and nearly so in the Columbia River. Major threats to southern eulachon include climate change impacts on ocean and freshwater habitat, by-catch in offshore shrimp trawl fisheries, changes in downstream flow timing and intensity owing to dams and water diversions, and predation. These threats, together with large declines in abundance, indicate that the southern DPS of eulachon is at moderate risk of extinction throughout all of its range. The southern DPS was listed as threatened under the ESA in May 2010 – the first marine forage fish to be afforded these statutory protections, which apply only to waters under U.S. jurisdiction.

This 20th Wakefield Symposium, ‘The genetics of subpolar fish and invertebrates’, is the successor of the 11th Wakefield Symposium, ‘Genetics of sub- arctic fish and shellfish’, which was held in Juneau, Alaska in 1993. In the introduction to that sympo- sium (Gharrett & Smoker 1994), it was noted that: ‘beginning in the 1960s, modern tools of genetic analysis began to be broadly applied in fisheries science’, and that ‘within the past decade (referring to the 1980s), fisheries genetics had entered the main- stream of fisheries resource utilization’. That obser- vation may be an understatement in today’s world of fisheries science. Once-vigorous fisheries in many parts of the world have failed, growing demand for fisheries products has led to full utilization of many remaining capture resources and is driving an increase in aquaculture productivity, and the role of aquacul- ture has increased dramatically ([FAO 2002]). Looming over concerns of lost stocks and persistent erosion of genetic variability are predictions of global warming, which may further tax genetic resources. One of the consequences of these developments is an increased interest in and reliance on genetic applications to many aspects of fisheries management, aquaculture, and conservation.

Information developed during recently completed evaluations of the status of seven species of anadromous Pacific salmonids (Oncorhynchus spp.) in the Pacific Northwest was used to characterize patterns of intraspecific diversity along three major axes: ecology, life history and biochemical genetics. Within the study area, the species' ranges, and therefore the number of distinct ecological regions inhabited differ considerably, with pink and chum salmon limited to the northern areas and chinook salmon and steelhead distributed over the widest geographic range. The species showed comparable differences in the patterns of life history and genetic diversity, with chinook and sockeye salmon and steelhead having the most major diversity groups and pink, chum and coho salmon having the least. Both life history and genetic diversity showed a strong, positive correlation with the extent of ecological diversity experienced by a species, and the correlation between the number of major genetic and life history groups within a species was even stronger (r=0.96; P

Phylogenetic relationships among vesicomyid clams (Bivalvia: Vesicomyidae) and their placement within the order Heterodonta were examined using mitochondrial encoded cytochrome oxidase subunit I (COI) DNA sequences. The presently analyzed vesicomyids represent a recent monophyletic radiation that probably occurred within the Cenozoic. Nucleotide phylogenetic analyses resolved discrete clades that were consistent with currently recognized species: Calyptogena magnifica, C. ponderosa, Ectenagena extenta, C. phaseoliformis, Vesicomya cordata, Calyptogena n. sp. (Gulf of Mexico), C. kaikoi, C. nautilei, C. solidissima and C. soyoae (Type-A). However, specimens variously identified as: V. gigas, C. kilmeri, C. pacifica, and V. lepta comprised two “species complexes”, each composed of multiple evolutionary lineages. Most taxa are limited to hydrothermal-vent or cold-seep habitats, but the “vent” versus “seep” clams do not constitute separate monophyletic groups. Current applications of the generic names Calyptogena, Ectenagena, and Vesicomya are not consistent with phylogenetic inferences.

A protein electrophoretic survey of mytilids inhabiting deep-sea hydrothermal vents and cold-water methane/sulfide seeps revealed electromorph patterns diagnostic of 10 distinct species. From hydrothermal vents located at sites on the Galapagos Rift, the Mid-Atlantic Ridge, and the Mariana Back Arc Basin, we detected four species of mytilids. Six additional species were detected from three cold-water seep sides in the Gulf of Mexico. The patchy distribution and temporal stability of seeps may provide a greater opportunity for mytilid diversification and persistence than vent sites Nei's genetic distances (D) between species were relatively large (range: 0.528 to ∞) both within and among habitat types. This pronounced degree of genetic differentiation suggests a relatively ancient common ancestor for the group. Phylogenetic trees were generated using distance Wagner and parsimony analyses of allozyme and morphological characters. The tree topologies obtained from both methods support: (1) the hypothesis that a seep ancestor gave rise to the deep-sea hydrothermal vent mytilids, (2) a historical progression from shallow-water to deep-water habitats, and (3) a co-evolutionary progression from external to internal localization of bacterial symbionts. Whether the seep mytilid taxa constitute paraphyletic or polyphyletic groups remains unresolved. Our phylogenetic hypotheses also provide a benchmark for the phylogeny of mytilid bacterial symbionts.

Widespread population extirpations and the consequent loss of ecological, genetic, and life-history diversity can lead to extinction of evolutionarily significant units (ESUs) and species. We attempted to systematically enumerate extinct Pacific salmon populations and characterize lost ecological, life history, and genetic diversity types among six species of Pacific salmon (Chinook [Oncorhynchus tshawytscha], sockeye [O. nerka], coho [O. kisutch], chum [O. keta], and pink salmon [O. gorbuscha] and steelhead trout [O. mykiss]) from the western contiguous United States. We estimated that, collectively, 29% of nearly 1400 historical populations of these six species have been lost from the Pacific Northwest and California since Euro-American contact. Across all species there was a highly significant difference in the proportion of population extinctions between coastal (0.14 extinct) and interior (0.55 extinct) regions. Sockeye salmon (which typically rely on lacustrine habitats for rearing) and stream-maturing Chinook salmon (which stay in freshwater for many months prior to spawning) had significantly higher proportional population losses than other species and maturation types. Aggregate losses of major ecological, life-history, and genetic biodiversity components across all species were estimated at 33%, 15%, and 27%, respectively. Collectively, we believe these population extirpations represent a loss of between 16% and 30% of all historical ESUs in the study area. On the other hand, over two-thirds of historical Pacific salmon populations in this area persist, and considerable diversity remains at all scales. Because over one-third of the remaining populations belong to threatened or endangered species listed under the U.S. Endangered Species Act, it is apparent that a critical juncture has been reached in efforts to preserve what remains of Pacific salmon diversity. It is also evident that persistence of existing, and evolution of future, diversity will depend on the ability of Pacific salmon to adapt to anthropogenically altered habitats.

Solemya reidi Bernard 1980 is a gutless protobranch bivalve known to possess intracellular chemoautotrophic bacterial symbionts in its gill. A light and electron microscope study on the embryology and larval development of S. reidi provides data for the bivalve Subclass Cryptodonta. S. reidi spontaneously spawned large eggs (271 μm in diameter), which developed within individual gelatious egg capsules. The first several cleavages were equal and a distinct molluscan cross was formed at the animal pole of the embryo, features previously unreported in bivalve development. Lecithotrophic pericalymma larvae (similar to the larvae of paleotaxodont protobranch bivalves and aplacophoran molluscs) hatched at 18 to 24 h and remained in the water column for a further 5 d at 10°C. At hatching, larvae measured from 360 to 440 μm in length and from 225 to 265 μm in cross-sectional diameter. Definitive adult structures developed within an epithelial locomotory test entirely covered with compound cilia. The test histolysed at metamorphosis and was ingested throught the mouth into the perivisceral cavity. Length and height of the shell following metamorphosis was 433 μm (±42 μm, n=16) and 282 μm (± 29 μm, n=13), respectively. Primary data and data from the literature show that the type of larval development in both paleotaxodont and cryptodont bivalves cannot be reliably estimated from egg or prodissoconch sizes.

Rod-shaped bacteria were consistently observed by transmission electron microscopy in the locomotory test of larvae and in the perivisceral cavity of post-larvae of Solemya reidi, a gutless protobranch bivalve known to possess intracellular chemoautotrophic bacterial symbionts in the adult gill. Bacteria develop within granular vesicles in the larval test, where they either remain to be ingested at metamorphosis, or are released into the space separating the test and embryo, to be subsequently ingested through the larval mouth. In either case, bacteria lie within the perivisceral cavity following metamorphosis. Bacteria were not seen either in or on gametes or in gills of juveniles. It is hypothesized that these bacteria represent a transmission stage of the gill symbionts present in adult S. reidi and are not evident in gametes or gills of juveniles due to cryptic packaging within granular vesicles. Perpetuation of this symbiosis would therefore be assured through vertical transmission, as is typical of other marine invertebrate-bacteria endosymbioses.

Structural changes occurring in the alimentary tract, perivisceral cavity, foot, hypobranchial gland, and gills of larval and post-larval Solemya reidi, a gutless protobranch bivalve, were examined using both light and electron microscopy at 1, 3, 5, 18, 34 and 42 d after fertilization. A fully developed mouth, esophagus, and anus, together with the rudiments of a stomach and rectum are present before metamorphosis. At metamorphosis, the cells making up the dorsal and lateral walls of the stomach dissociate, and by 18 d the mouth and anus are the only remaining portions of the alimentary tract. The larval test is ingested into the perivisceral cavity at metamorphosis and its autolysis continues through at least the 42nd day after fertilization. The foot, gills, and hypobranchial gland, poorly developed at metamorphosis, develop slowly and are still undergoing extensive morphogenesis at 42 d.