Where do you think you’re going? Accounting for ontogenetic and climate‐induced movement in spatially stratified integrated population assessment models

Understanding spatial population structure and biocomplexity is critical for determining a species’ resilience to environmental and anthropogenic perturbations. However, integrated population models (IPMs) used to develop management advice for harvested populations have been slow to incorporate spatial dynamics. Therefore, limited research has been devoted to understanding the reliability of movement parameter estimation in spatial population models, especially for spatially dynamic marine fish populations. We implemented a spatial simulation–estimation framework that emulated a generic marine fish metapopulation to explore the impact of ontogenetic movement and climate‐induced distributional shifts between two populations. The robustness of spatially stratified IPMs was explored across a range of movement parametrizations, including ignoring connectivity or estimating movement with various levels of complexity. Ignoring connectivity was detrimental to accurate estimation of population‐specific biomass, while implementing spatial IPMs with intermediate levels of complexity (e.g. estimating movement in two‐year and two‐age blocks) performed best when no a priori information about underlying movement was available. One‐way distributional shifts mimicking climate‐induced poleward migrations presented the greatest estimation difficulties, but the incorporation of auxiliary information on connectivity (e.g. tag‐recapture data) reduced bias. The continued development of spatially stratified modelling approaches should allow harvested resources to be better utilized without increased risk. Additionally, expanded collection and incorporation of unique spatially explicit data will enhance the robustness of IPMs in the future.     

A Comparison of the Effects of Two Prey Enrichment Media on Growth and Survival of Pacific Bluefin Tuna,Thunnus orientalis,Larvae

Three experiments were conducted to investigate the growth, survival, and standardized cohort biomass of Pacific bluefin tuna, Thunnus orientalis, larvae fed nutritionally enhanced prey during the first week of feeding using two commonly used, commercially available enrichment media, AlgaMac Enrich and Marine Glos. T. orientalis larvae exhibited exponential growth in standard length and dry weight. The daily specific growth rates in length and weight are the first reported for T. orientalis larvae and the averages ranged from 3.8 to 4.1% and 27.5%, respectively, for larvae in the AlgaMac treatment and from 4.1 to 6.1% and 31.5%, respectively, in the Marine Glos treatment. Average daily growth rates in length ranged from 0.16 to 0.23 mm/d for larvae in the AlgaMac treatment and from 0.17 to 0.27 mm/d for those in the Marine Glos treatment. Daily growth rates in length were similar to those reported for other tuna larvae reared in the laboratory but slower than most published estimates for larval tunas in situ at similar water temperatures. Mean prey number per gut was positively associated with mean prey level in the tank. Both enrichment media appear to be good sources of nutritional improvement of planktonic prey for T. orientalis larvae.     

Potential for reintroduction of lake sturgeon in five northern Lake Michigan tributaries: a habitat suitability perspective

• 1. Conservation and rehabilitation efforts for lake sturgeon Acipenser fulvescens throughout the Great Lakes include the re‐establishment of self‐sustaining stocks in systems where they have been extirpated.
• 2. Information on the suitability of potential lake sturgeon habitat in tributaries is important for determining their capacity to support lake sturgeon stocking and to develop system‐specific rehabilitation strategies.
• 3. Geo‐referenced habitat information characterizing substrate composition, water depth, and stream gradient were applied to a life‐stage specific lake sturgeon habitat suitability index in a geographic information system to produce spatially explicit models of life‐stage specific habitat characteristics in five northern Lake Michigan tributaries from which lake sturgeon have been extirpated.
• 4. Habitat models indicated that high quality lake sturgeon spawning and staging habitat comprised 0 to 23% and 0 to 9% of the available habitat, respectively, whereas high quality juvenile lake sturgeon habitat was relatively ubiquitous throughout each river and comprised 39 to 99%.
• 5. Comparison of these data to lake sturgeon habitat availability in Lake Michigan tributaries currently supporting populations indicated that spawning and staging habitats may limit the ability of these systems to support spawning. Efforts to re‐establish lake sturgeon populations in these systems should consider the creation of spawning and staging habitat to increase reproductive and recruitment potential prior to the initiation of stocking efforts.

Copyright © 2007 John Wiley & Sons, Ltd.     

Most fish destined for fishmeal production are food‐grade fish

Marine fisheries target and catch fish both for direct human consumption (DHC) as well as for fishmeal and fish oil, and other products. We derived the fractions used for each for 1950–2010 by fishing country, and thus provide a factual foundation for discussions of the optimal use of fisheries resources. From 1950 to 2010, 27% (~20 million tonnes annually) of globally reconstructed marine fisheries landings were destined for uses other than DHC. Importantly, 90% of fish destined for uses other than DHC are food‐grade or prime food‐grade fish, while fish without a ready market for DHC make up a much smaller proportion. These findings have implications for how we are using fish to feed ourselves or, more appropriately, how we are not using fish to feed ourselves.     

Visualisation of standardized life-history patterns

The life‐history patterns of fish and invertebrate species are complex. But much of this complexity can be captured in simple diagrams of coastal transects, where juveniles usually occur in larger numbers in shallow waters, while adults generally inhabit deeper, offshore waters. Iconographic representations of generalized life‐history patterns and depth profiles, with specific key life‐history parameters can capture much of these standardized patterns, including spawning areas, nursery/juvenile distributions, adult distributions and spawning migrations. Several examples presented here from a wide range of habitats and ecosystems (temperate and tropical waters, demersal, deep water, pelagic and coral reefs), including an example of different stocks of the same species, illustrate some general patterns with regard to water depth and distance from shore. The present approach should be viewed as a first step towards obtaining standardized patterns about key life‐history parameters, and will hopefully lead to incorporation into management of life‐history interconnectivity between different fishery sectors or gears. This may contribute to sustainable, ecosystem‐based approaches to management by informing policy options when faced with decisions to rationalize overcapitalized fisheries.     

Movement rules for juvenile steelhead: dynamic linking of movement behaviour to habitat and density

We incorporated explanatory factors including stream habitat type and fish density into individual‐based models with dynamic connections among adjacent habitat units to infer dispersal behaviour of juvenile steelhead Oncorhynchus mykiss in a Great Lakes watershed. We used mark–recapture data and an inverse modelling approach to estimate daily probability of steelhead moving out of a habitat unit, P(move), according to four competing models. The models used included (i) a null model where all fish had equal movement probability; (ii) a habitat‐dependent model where P(move) depended on the habitat type; (iii) a density‐dependent model of P(move); and (iv) a model where P(move) depended on both density and habitat type. The habitat‐dependent model provided the most parsimonious fit to the observed data according to Akaike's information criteria (AICc). In the null model, P(move) averaged 0.70, whereas P(move) averaged 0.75 in pools, 0.68 in riffles and 0.73 in runs in the habitat‐dependent model.     

Targeted identification of genomic regions using TAGdb

Background

The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes.

Results

We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.

Conclusions

The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly.     

An unholy disease in the Holy Land: The history of anthrax between the Jordan River and the Mediterranean Sea (1909–2012)

The history of recorded cases of anthrax in human beings and animals from 1909 to 2012 in the area between the Jordan River and the Mediterranean Sea is reviewed. The disease was endemic until the middle of the 20th century, but the incidence decreased thereafter, with only sporadic cases from the 1980s onwards. Human cases have not been diagnosed in the region since 1984 and the number of episodes of animal disease has reduced to less than one per year. This decline is mostly due to the disruption of the infective cycle by improved veterinary control, including vaccination, treatment and outbreak management. A policy of reactive vaccination for 10 years of affected herds and herds grazing in their proximity has been applied. No new outbreaks have been observed in such herds after the cessation of vaccination, despite continued grazing on the same sites, so it is assumed that spore survival in such areas is shorter than 10 years. This is independent of the soil composition, which is calcareous throughout most of the relevant area. However, reemergence of anthrax, even after decades, has occurred following disturbance and heavy rainfall.     

Bayesian structural equation models for inferring relationships between phenotypes: a review of methodology, identifiability, and applications

Structural equation models provide a general statistical modelling technique for estimating and testing relationships among variables. Such relationships are often not revealed by standard linear models, but are of importance for understanding mechanisms underlying e.g., production-related diseases, such as mastitis. This paper gives a review of Bayesian structural equation models concerning methodology and identifiability, focused on animal breeding and genetics modelling. Applications of this type of methods in animal breeding are also reviewed critically, with discussion on advantages and disadvantages of these approaches.