Forecasting the Genetic Impacts of Net Pen Failures on Gulf of Mexico Cobia Populations Using Individual‐based Model Simulations

Offshore net pen fish farming provides a cost‐efficient means for production of marine finfish, and there is great interest in development of net pen operations in domestic waters. However, there are concerns over the possible genetic and ecological impacts that escaped fish may have on wild populations. We used individual‐based simulations, with parameter values informed by life history and genetic data, to investigate the short‐term (50 yr) impacts of net pen failures on the genetic composition of cobia, Rachycentron canadum, stocks in the Gulf of Mexico. Higher net pen failure rates resulted in greater genetic impacts on the wild population. Additionally, the use of more genetically differentiated source populations led to larger influxes of non‐native alleles and greater temporal genetic change in the population as a result of net pen failure. Our results highlight the importance of considering the appropriate source population for broodstock collection in net pen aquaculture systems and help to provide a general set of best management practices for broodstock selection and maintenance in net pen aquaculture operations. A thorough understanding of the genetic diversity, stock structure, and population demography of target species is important to determine the impact escapees can have on wild populations.     

Understorey plant community characteristics and natural hardwood regeneration under three partial harvest treatments applied in a northern red oak (Quercus rubra L.) stand in the Great Lakes-St. Lawrence forest region of Canada

Throughout eastern North America, stands of northern red oak (Quercus rubra L.) are undergoing successional replacement by shade-tolerant competitors. In the Great Lakes-St. Lawrence (GLSL) forest region, Q. rubra approaches the northern limit of its distribution, and ecosystem-specific silvicultural directives are needed to promote regeneration. We used an inductive, ordination-based approach to explore patterns in understorey plant community composition and microenvironment under different partial harvest treatments applied in a GLSL hardwood stand, and related these to characteristics of natural seedlings of Q. rubra and its competitors Acer rubrum and Acer saccharum.Two years after harvest, we established 2 m × 2 m plots in a stratified random design under 70% (n = 20) and 50% (n = 19) crown closure uniform shelterwood, group selection (n = 15), and uncut upper slope (n = 10) and lower slope (n = 10) areas. Percent cover of understorey vascular plant species, and a suite of microclimatic and edaphic variables were measured in each plot. Density, mean diameter and mean height of seedlings in the understorey (height <1 m) were determined in each plot for Q. rubra, A. rubrum and A. saccharum.Correspondence analysis (CA) ordination extracted two major axes explaining 21.6% of the total inertia in the species cover by plot matrix. Axis one separated uncut plots from the 50% shelterwood along a gradient of canopy cover associated with partial harvest treatments. Plot scores on axis one (13.2%) reflected a shift in dominance of the understorey from shade-tolerant Acer spp. to shade-intolerant colonizers, Rubus idaeus and Carex spp. Plot scores on axis one were directly (p < 0.05) associated with total understorey plant cover, litter depth, soil temperature and pH, but not with measures of plant diversity. Axis two (8.4%) separated plots from upper slope and lower slope areas, and plot scores were inversely associated (p < 0.05) with soil pH, phosphorus and nitrogen levels. Along axis two there was a shift in dominance from competitive (e.g. A. saccharum) to stress-tolerant (e.g. A. rubrum) species as soil fertility declined. Stepwise linear regression indicated seedling diameter in Q. rubra, A. rubrum and A. saccharum was inversely related to canopy cover. This suggests all three species benefited from partial harvest, although the relationship was strongest in Q. rubra. Patterns in understorey composition, microenvironment and seedling characteristics provide the basis to identify the main competitors of Q. rubra seedlings and adjust regeneration efforts along gradients of canopy closure and soil fertility under partial harvest systems within the GLSL forest region.     

Functional CpG methylation system in a social insect

DNA methylation systems are well characterized in vertebrates, but methylation in Drosophila melanogaster and other invertebrates remains controversial. Using the recently sequenced honey bee genome, we present a bioinformatic, molecular, and biochemical characterization of a functional DNA methylation system in an insect. We report on catalytically active orthologs of the vertebrate DNA methyltransferases Dnmt1 and Dnmt3a and b, two isoforms that contain a methyl-DNA binding domain, genomic 5-methyl-deoxycytosine, and CpG-methylated genes. The honey bee provides an opportunity to study the roles of methylation in social contexts.     

Genetic diversity and relatedness estimates for captive barramundi (Lates calcarifer,Bloch) broodstock informs efforts to form a base population for selective breeding

Aquaculture of barramundi or Asian seabass (Lates calcarifer) is growing in both Australia and Southeast Asia and there is substantial interest to improve production efficiency through selective breeding. The establishment of a large and genetically diverse base population is a prerequisite for a sustainable and long‐term productive breeding program. Before selective breeding programs can begin for Australian barramundi it is important to assess the overall genetic diversity of current captive broodstock populations. To address this question, 407 captive barramundi broodstock from eight separate Australian broodstock populations were genotyped using 16 polymorphic microsatellite DNA markers. A Bayesian STRUCTURE analysis indicated that captive Australian broodstock are broadly divided into two genetic stocks. Multivariate analysis between broodstock individuals and pairwise F_ST between broodstock populations also supported the existence of two stocks. Comparisons with data obtained from natural stocks suggested that hatchery individuals were either sourced from the two stocks or represented an admixture between them. Genetic diversity was low within each broodstock population (allelic richness ranged from 2.67 to 3.42 and heterozygosity ranged from 0.453 to 0.537) and relatedness estimates within hatcheries were generally low (average r was equal to 0.141). We recommend sourcing captive individuals according to high levels of neutral genetic diversity and low levels of relatedness for the establishment of a base population. We also make recommendations about including genetically diverse wild individuals.