Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Evolution of Protein Molecules

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Computation And Interpretation Of Biological Statistics Of Fish Populations

Ecological risk assessment for the effects of fishing

There is increasing scientific and public concern over the presence of microplastics (MPs) in the natural environment. Here, we present the results of a systematic review of the literature to assess the weight of evidence for MPs causing environmental harm. We conclude that MPs do occur in surface water and sediments. Fragments and fibers predominate with beads making up only a small proportion of the detected MP types. Concentrations detected are orders of magnitude lower than those reported to affect molecular level endpoints, feeding, reproduction, growth, tissue inflammation and mortality in organisms. The evidence for MPs acting as a vector for hydrophobic organic compounds (HOC) to accumulate in organisms is also weak. The available data therefore suggest that these materials are not causing harm to the environment. There is however a mismatch between the particle types, size ranges, and concentrations of MPs used in laboratory tests and those measured in the environment. Select environmental compartments have also received limited attention. There is an urgent need for studies that address this mismatch by performing better quality and more holistic monitoring studies alongside more environmentally realistic effects studies. Only then will we be able to fully characterize risks of MPs to the environment in order to support the introduction of regulatory controls that can make a real positive difference to environmental quality.

https://setac.onlinelibrary.wiley.com/doi/pdf/10.1002/etc.4268

Microplastics in the aquatic environment: Evidence for or against adverse impacts and major knowledge gaps.

Identification of taxonomical units underpins most biological endeavours ranging from accurate biodiversity estimates to the effective management of sustainably harvested, protected or endangered species. Successful species identification is now frequently based on a combination of approaches including morphometrics and DNA markers. Sequencing of the mitochondrial COI gene is an established methodology with an international campaign directed at barcoding all fishes. We employed COI sequencing alongside traditional taxonomic identification methods and uncovered instances of deep intraspecific genetic divergences among flathead species. Sixty-five operational taxonomic units (OTUs) were observed across the Indo-West Pacific from just 48 currently recognized species. The most comprehensively sampled taxon, Platycephalus indicus, exhibited the highest levels of genetic diversity with eight lineages separated by up to 16.37% genetic distance. Our results clearly indicate a thorough reappraisal of the current taxonomy of P. indicus (and its three junior synonyms) is warranted in conjunction with detailed taxonomic work on the other additional Platycephalidae OTUs detected by DNA barcoding.

Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding.

Genetic diversity and effective population size in mass selection lines of Pacific oyster (Crassostrea gigas)

Five polymorphic microsatellite loci were examined in 1391 yellowfin tuna (Thunnusalbacares) from eight regions of the western (Coral Sea, eastern Australia, Fiji, Indonesia, Philippines and Solomon Islands) and eastern (California and Mexico ) Pacific Ocean. Across all samples, numbers of alleles per locus ranged from 7 to 30 (mean: 17.0), and observed heterozygosities per locus ranged from 0.223 to 0.955 (mean: 0.593). Temporal collections were available for three areas: no significant temporal heterogeneity was observed for the Coral Sea (1991/1992 and 1995/1996 collections) or eastern Australia (1994/1995, 1995/1996, 1996/1997 and 1997/1998), but there was slight but significant heterogeneity at one locus (cmrTa-161) between the two Philippines collections (1994/1995 and 1996/1997). Genotypes generally showed a good fit to Hardy–Weinberg expectations within populations; only cmrTa-208 in the pooled Coral Sea population gave a significant deviation after Bonferroni correction for 40 tests, with a small but significant excess of homozygotes. Four loci showed no evidence of population differentiation following contingency Chi-squared and FST analyses. The fifth locus, cmrTa-161, showed small but significant differentiation (FST=0.002, P<0.001). This heterogeneity was largely a result of the Philippines 1994/1995 and Fiji collections; there was no correlation with geographic distance. The average FST across all five loci was very low (FST=0.002), but it was significant (P<0.001). It is unclear whether this low but significant differentiation reflects noise in the dataset, perhaps arising from experimental error, or real population differentiation. The finding of very limited population heterogeneity accords with most of the earlier allozyme and mitochondrial DNA studies of yellowfin tuna in the Pacific Ocean.

Population structure of yellowfin tuna (Thunnus albacares) in the western Pacific Ocean, inferred from microsatellite loci

Genetic differentiation was minimal and overall non-significant among five collections of bigeye tuna Thunnus obesus from the Indian Ocean, examined for variation at mitochondrial DNA (mtDNA) and at seven microsatellite loci.

Genetic stock structure of bigeye tuna in the Indian Ocean using mitochondrial DNA and microsatellites

Two mitochondrial DNA regions and seven microsatellite loci were examined in Patagonian toothfish from three locations in the Southern Ocean (Macquarie Island, five collections; Heard and McDonald Islands, four collections; Shag Rocks/South Georgia area, one collection). Striking mtDNA heterogeneity was detected between the three fishing locations (FST=0.445, P<0.001), but spatial and temporal collections within the same location were not significantly different. No significant overall microsatellite differentiation between the three locations was apparent (FST=−0.009, P=0.785). However, some individual loci showed small but significant differentiation, which in each case was attributable to between rather than within-location differentiation. Greater differentiation of mtDNA can, in principle, be explained either by female philopatry and male dispersal, or by its greater sensitivity to changes in effective population size. The latter seems more likely as tagging indicates that toothfish is generally a sedentary species. The genetic heterogeneity between the three locations indicates restricted gene flow, with the fish at each location comprising independent units. Depletion in one location is therefore unlikely to be quickly replaced by immigration from another.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0954102002000238

Sharon A. Appleyard

Papers

Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding.

Genetic diversity and effective population size in mass selection lines of Pacific oyster (Crassostrea gigas)

Population structure of yellowfin tuna (Thunnus albacares) in the western Pacific Ocean, inferred from microsatellite loci

Genetic stock structure of bigeye tuna in the Indian Ocean using mitochondrial DNA and microsatellites

Population structure of the Patagonian toothfish around Heard, McDonald and Macquarie Islands