Engyprosopon vanuatuensis, a new species of bothid flounder (Pleuronectiformes: Bothidae) from off Vanuatu, South West Pacific

A new bothid flounder, Engyprosopon vanuatuensis, is described on the basis of 15 specimens (9 males and 6 females, 41.1–55.8mm in standard length) collected from deep waters (163–165m) off Vanuatu Island in 1994 during the French exploratory cruise MUSORSTOM 8. The new species clearly differs from its congeners in having a short body, big eyes, large scales, and many gill rakers without serrations. Remarkable sexual dimorphism appears in interorbital width, anterior curve of head profile, rostral and orbital spines, length of ocular-side pectoral fin, small dots on eyes, and pigmentation of blind-side body.     

Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?

Although most genetic estimates of contemporary effective population size (Ne) are based on models that assume Ne is constant, in real populations Ne changes (often dramatically) over time, and estimates (Ne) will be influenced by Ne in specific generations. In such cases, it is important to properly match Ne to the appropriate time periods (for example, in computing Ne/N ratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity--the 'salmon' model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following. Discrete generations: (i) Temporal samples from generations 0 and t estimate the harmonic mean Ne in generations 0 through t - 1 but do not provide information about Ne in generation t; (ii) Single samples provide an estimate of Ne in the parental generation, not the generation sampled; (iii) single-sample and temporal estimates never provide information about Ne in exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations. Salmon model: (i) A pair of single-cohort (typically juvenile) samples from years 0 and t provide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (N b(0) and N b(t)), but adult samples are more difficult to interpret because they are influenced by Nb in a number of previous years; (ii) For single-cohort samples, both one-sample and temporal methods provide estimates of Nb in the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single-sample estimates of Nb as much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates of Ne in iteroparous species with overlapping generations and identify areas in need of further research.     

Systematic factor optimization for cryopreservation of shipped sperm samples of diploid Pacific Oysters, Crassostrea gigas

Despite some 26 published reports addressing oyster sperm cryopreservation, systematic factor optimization is lacking, and sperm cryopreservation has not yet found application in aquaculture on a commercial scale. In this study, the effects of cooling rate, single or combined cryoprotectants at various concentrations, equilibration time (exposure to cryoprotectant), straw size, and cooling method were evaluated for protocol optimization of shipped sperm samples from diploid oysters. Evaluation of cooling rates revealed an optimal rate of 5 degrees C/min to -30 degrees C followed by cooling at 45 degrees C/min to -80 degrees C before plunging into liquid nitrogen. Screening of single or combined cryoprotectants at various concentrations suggested that a low concentration (2%) of polyethylene glycol (FW 200) was effective in retaining post-thaw motility and fertilizing capability when combined with permeating cryoprotetcants such as dimethyl sulfoxide (DMSO), methanol (MeOH), and propylene glycol (P-glycol). However, polyethylene glycol alone was not as effective as MeOH, DMSO, and P-glycol when using the same methods. The highest post-thaw motility (70%) and percent fertilization (98%) were obtained for samples cryopreserved with 6% MeOH. However, this does not exclude other cryoprotectants such as DMSO or P-glycol identified as effective agents in other studies. There was no significant difference in post-thaw motility between straw sizes of 0.25- and 0.5-ml. Equilibration time (exposure to cryoprotectant) of 60 min could be beneficial when the cryoprotectant concentration is low and solution is added in a step-wise fashion at low temperature. Differences in post-thaw sperm quality (e.g., motility or percent fertilization) among individual males were evident in this research. As a consequence, a generalized classification describing males with different tolerances (broad, intermediate, and narrow) to cryopreservation was developed. This classification could be applied to strain or species differences in tolerances to the cryopreservation process. The present study demonstrated that oyster sperm could be collected and shipped chilled to another facility for cryopreservation, and that it could be shipped back to the hatchery for fertilization performed at a production scale yielding live larvae with >90% fertilization. Given the existence of facilities for commercial-scale cryopreservation of dairy bull sperm, the methods developed in the present study for oysters provide a template for the potential commercialization of cryopreserved sperm in aquatic species.     

Life-history divergence in Chinook salmon: historic contingency and parallel evolution

By jointly considering patterns of genetic and life-history diversity in over 100 populations of Chinook salmon from California to British Columbia, we demonstrate the importance of two different mechanisms for life-history evolution. Mapping adult run timing (the life-history trait most commonly used to characterize salmon populations) onto a tree based on the genetic data shows that the same run-time phenotypes exist in many different genetic lineages. In a hierarchical gene diversity analysis, differences among major geographic and ecological provinces explained the majority (62%) of the overall G(ST), whereas run-time differences explained only 10%. Collectively, these results indicate that run-timing diversity has developed independently by a process of parallel evolution in many different coastal areas. However, genetic differences between coastal populations with different run timing from the same basin are very modest (G(ST) < 0.02), indicating that evolutionary divergence of this trait linked to reproductive isolation has not led to parallel speciation, probably because of ongoing gene flow. A strikingly different pattern is seen in the interior Columbia River Basin, where run timing and other correlated life-history traits map cleanly onto two divergent genetic lineages (G(ST) approximately 0.15), indicating that some patterns of life-history diversity have a much older origin. Indeed, genetic data indicate that in the interior Columbia Basin, the two divergent lineages behave essentially as separate biological species, showing little evidence of genetic contact in spite of the fact that they comigrate through large areas of the river and ocean and in some locations spawn in nearly adjacent areas.     

Conservation Genetics of the East Pacific Green Turtle (Chelonia mydas) in Michoacan, Mexico

The main continental nesting rookeries of the east Pacific green turtle (EPGT), Chelonia mydas, on the Michoacan (Mexico) coast suffered drastic population declines following intense exploitation in the 1960s--1970s with annual abundance of nesting females plummeting from about 25,000 to an average of about 1400 between 1982 and 2001. Analyses of data from three nDNA microsatellite loci and 400 bp mtDNA control region sequences from a total of 123 nesting females sampled from four Michoacan rookeries found no evidence of population sub-structuring. The recent order of magnitude reduction in the population size shows no apparent impact on genetic diversity in either control region sequences (overall h = 0.48; pi = 0.0036) or microsatellite loci (overall Na = 20.8; Hexp = 0.895). Our estimates of annual effective female population size (Nef; from theta = 2Nemicron) of 1.9-2.3 x 10(3), in spite of being an order of magnitude below historical records, appear to be sufficient to allow recovery of this population without significant loss of genetic diversity. These findings highlight the importance of continued conservation to reverse the decline of this population before it becomes vulnerable to genetic erosion.     

Salmonid Opsin Sequences Undergo Positive Selection and Indicate an Alternate Evolutionary Relationship in Oncorhynchus

Positive selection can be demonstrated by statistical analysis when non-synonymous nucleotide substitutions occur more frequently than synonymous substitutions (dN>dS). This pattern of sequence evolution has been observed in the rhodopsin gene of cichlids. Mutations in opsin genes resulting in amino acid (AA) replacement appear to be associated with the evolution of specific color patterns and the evolution of courtship behaviors. Within fish, AA replacements in opsin proteins have improved vision at great depths and have occurred in deep-sea species. Salmonids experience diverse photic environments during their life history. Furthermore, sexual selection has resulted in species-specific male and female coloration during spawning. To look for evidence of positive selection in salmonid opsins, we sequenced the RH1, RH2, LWS, SWS1, and SWS2 genes from six Pacific salmon species as well as the Atlantic salmon. These salmonids include landlocked and migratory species and species that vary in their coloration during spawning. In each opsin gene comparison from all species sampled, traditional dN:dS analysis did not indicate positive selection. However, the more sensitive Creevey–McInerney statistical analysis indicates that RH1 and RH2 experienced positive selection early in the evolution and speciation of salmonids.     

Isolation and characterization of microsatellite DNA markers in the Pacific abalone,Haliotis discus hannai

We developed 17 new microsatellite markers in Haliotis discus hannai. All loci were found to be polymorphic with an average of 13.1 alleles per locus (range 3–28). The mean observed and expected heterozygosities were 0.77 (range 0.17–1.00) and 0.79 (range 0.42–0.96), respectively. Six loci deviated significantly from Hardy–Weinberg proportions, and thus should be used with caution. The high variabilities revealed in this study suggest that these microsatellite loci should provide useful markers for studies of trait mapping, kinship and population genetics.     

Untangling cultural inheritance: language diversity and long-house architecture on the Pacific northwest coast

Many recent studies of cultural inheritance have focused on small-scale craft traditions practised by single individuals, which do not require coordinated participation by larger social collectives. In this paper, we address this gap in the cultural transmission literature by investigating diversity in the vernacular architecture of the Pacific northwest coast, where communities of hunter-fisher-gatherers constructed immense wooden long-houses at their main winter villages. Quantitative analyses of long-house styles along the coastline draw on a range of models and methods from the biological sciences and are employed to test hypotheses relating to basic patterns of macro-scale cultural diversification, and the degree to which the transmission of housing traits has been constrained by the region's numerous linguistic boundaries. The results indicate relatively strong branching patterns of cultural inheritance and also close associations between regional language history and housing styles, pointing to the potentially crucial role played by language boundaries in structuring large-scale patterns of cultural diversification, especially in relation to 'collective' cultural traditions like housing that require substantial inputs of coordinated labour.     

Age‐related thermal habitat use by Pacific salmon Oncorhynchus spp.

Age‐related thermal habitat use by sockeye Oncorhynchus nerka, chum Oncorhynchus keta and pink Oncorhynchus gorbuscha salmon was examined using trawl data obtained in spring in the North Pacific Ocean. Thermal habitat use differed by species and age. Larger and older fishes inhabited cooler areas, whereas smaller and younger fishes inhabited warmer areas.