'On the Application of Hierarchical Coevolutionary Genetic Algorithms: Recombination and Evaluation Partners'

This paper examines the use of a hierarchical coevolutionary genetic algorithm under different partnering strategies. Cascading clusters of sub-populations are built from the bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations potentially search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the sub-populations on solution quality are examined for two constrained optimisation problems. We examine a number of recombination partnering strategies in the construction of higher-level individuals and a number of related schemes for evaluating sub-solutions. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

A Pyramidal Evolutionary Algorithm with Different Inter-Agent Partnering Strategies for Scheduling Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

Exploiting problem structure in a genetic algorithm approach to a nurse rostering problem

There is considerable interest in the use of genetic algorithms to solve problems arising in the areas of scheduling and timetabling. However, the classical genetic algorithm paradigm is not well equipped to handle the conflict between objectives and constraints that typically occurs in such problems. In order to overcome this, successful implementations frequently make use of problem specific knowledge. This paper is concerned with the development of a GA for a nurse rostering problem at a major UK hospital. The structure of the constraints is used as the basis for a co-evolutionary strategy using co-operating sub-populations. Problem specific knowledge is also used to define a system of incentives and disincentives, and a complementary mutation operator. Empirical results based on 52 weeks of live data show how these features are able to improve an unsuccessful canonical GA to the point where it is able to provide a practical solution to the problem.

Partnering Strategies for Fitness Evaluation in a Pyramidal Evolutionary Algorithm

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes for (sub-)fitness evaluation purposes are examined for two multiple-choice optimisation problems. It is shown that random partnering strategies perform best by providing better sampling and more diversity.

A Pyramidal Evolutionary Algorithm with Different Inter-Agent Partnering Strategies for Scheduling Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

A Pyramidal Genetic Algorithm for Multiple-Choice Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence, higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

'Exploiting problem structure in a genetic algorithm approach to a nurse rostering problem'

There is considerable interest in the use of genetic algorithms to solve problems arising in the areas of scheduling and timetabling. However, the classical genetic algorithm paradigm is not well equipped to handle the conflict between objectives and constraints that typically occurs in such problems. In order to overcome this, successful implementations frequently make use of problem specific knowledge. This paper is concerned with the development of a GA for a nurse rostering problem at a major UK hospital. The structure of the constraints is used as the basis for a co-evolutionary strategy using co-operating sub-populations. Problem specific knowledge is also used to define a system of incentives and disincentives, and a complementary mutation operator. Empirical results based on 52 weeks of live data show how these features are able to improve an unsuccessful canonical GA to the point where it is able to provide a practical solution to the problem.

Etude électrophorétique des protéines solubles du cristallin de la sardine (Clupea pilchardus Walb.) du Golfe du Lion

The eye lens proteins electrophoresis of pilchard of the Gulf of Lion (Clupea pilchardus Walb.) shows the existence of 2 sub-populations. The hypothesis of an hereditary control by two co-dominant allels is in agreement with the expected Hardy-Weinberg distribution.

Morphometric characteristics of Prochilodus lineatus (Valenciennes 1847), of the migratory and resident stocks of the river Mogí-Guaçu, São Paulo State, Brazil

A espécie Prochilodus lineatus é de grande importância comercial na região dos rios Grande, Pardo e Mogi-Guaçu e tem como característica a formação de grandes cardumes, apta a desenvolver amplos deslocamentos migratórios. O presente trabalho objetivou avaliar, por meio das características morfométricas e etária, se os curimbatás (P. lineatus) dos diferentes estoques migradores e residentes constituem uma única população, havendo interação entre as sub-populações no período de piracema (migração reprodutiva). Utilizou-se um delineamento inteiramente casualizado em esquema fatorial 4 x 2, com quatro tipos de estoques (um residente e três migradores) e dois sexos (macho e fêmea) com trinta repetições, considerando cada peixe como unidade experimental. Foi observada variação de 80,19% para o primeiro componente principal e 8,09% do segundo componente principal fornecida pelas dez variáveis morfométricas dos estoques residentes e migradores. O estoque residente correspondeu aos maiores valores para todas as variáveis morfométricas. Houve sobreposição dos escores individuais das mesmas características entre os estoques migradores. Observou-se predominância de machos entre os estoques residentes e migrador I e II. As semelhanças morfométricas verificadas entre os estoques migradores indicam tratar-se de uma única população, com pequenas variações interpopulacional.

High interannual variability in connectivity and genetic pool of a temperate clingfish matches oceanographic transport predictions

Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats. Genetic analyses based on microsatellites countered our prediction and a biophysical dispersal model showed that oceanographic transport was a good explanation for the patterns observed. Adult sub-populations separated by up to 300 km of coastline displayed no genetic differentiation, revealing a single connected population with larvae potentially dispersing long distances over hundreds of km. Despite this, parentage analysis performed on recruits from one focal site within the Marine Park of Arrábida (Portugal), revealed self-recruitment levels of 2.5% and 7.7% in 2011 and 2012, respectively, suggesting that both long- and short-distance dispersal play an important role in the replenishment of these populations. Population differentiation and patterns of dispersal, which were highly variable between years, could be linked to the variability inherent in local oceanographic processes. Overall, our measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations.

Synonymous co-variation across the E1/E2 gene junction of hepatitis C virus defines virion fitness

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3′-end of E1 highly conserved and the 5′-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.

Provenance of Holocene beach sand in the Western Iberian

Detrital zircons from Holocene beach sand and igneous zircons from the Cretaceous syenite forming Cape Sines (Western Iberian margin) were dated using laser ablation – inductively coupled plasma – mass spectrometry. The U–Pb ages obtained were used for comparison with previous radiometric data from Carboniferous greywacke, Pliocene–Pleistocene sand and Cretaceous syenite forming the sea cliff at Cape Sines and the contiguous coast. New U–Pb dating of igneous morphologically simple and complex zircons from the syenite of the Sines pluton suggests that the history of zircon crystallization was more extensive (ca 87 to 74 Ma), in contrast to the findings of previous geochronology studies (ca 76 to 74 Ma). The U–Pb ages obtained in Holocene sand revealed a wide interval, ranging from the Cretaceous to the Archean, with predominance of Cretaceous (37%), Palaeozoic (35%) and Neoproterozoic (19%) detrital-zircon ages. The paucity of round to subrounded grains seems to indicate a short transportation history for most of the Cretaceous zircons (ca 95 to 73 Ma) which are more abundant in the beach sand that was sampled south of Cape Sines. Comparative analysis using the Kolmogorov–Smirnov statistical method, analysing sub-populations separately, suggests that the zircon populations of the Carboniferous and Cretaceous rocks forming the sea cliff were reproduced faithfully in Quaternary sand, indicating sediment recycling. The similarity of the pre- Cretaceous ages (>ca 280 Ma) of detrital zircons found in Holocene sand, as compared with Carboniferous greywacke and Pliocene–Pleistocene sand, provides support for the hypothesis that detritus was reworked into the beach from older sedimentary rocks exposed along the sea cliff. The largest percentage of Cretaceous zircons (

First Report of a Toxic Nodularia spumigena (Nostocales/Cyanobacteria) Bloom in Sub-Tropical Australia. II. Bioaccumulation of Nodularin in Isolated Populations of Mullet (Mugilidae)

Fish collected after a mass mortality at an artificial lake in south-east Queensland, Australia, were examined for the presence of nodularin as the lake had earlier been affected by a Nodularia bloom. Methanol extracts of muscle, liver, peritoneal and stomach contents were analysed by HPLC and tandem mass spectrometry; histological examination was conducted on livers from captured mullet. Livers of sea mullet (Mugil cephalus) involved in the fish kill contained high concentrations of nodularin (median 43.6 mg/kg, range 40.8-47.8 mg/kg dry weight; n = 3) and the toxin was also present in muscle tissue (median 44.0 mu g/kg, range 32.3-56.8 mu g/kg dry weight). Livers of fish occupying higher trophic levels accumulated much lower concentrations. Mullet captured from the lake 10 months later were also found to have high hepatic nodularin levels. DNA sequencing of mullet specimens revealed two species inhabiting the study lake: M. cephalus and an unidentified mugilid. The two mullet species appear to differ in their exposure and/or uptake of nodularin, with M. cephalus demonstrating higher tissue concentrations. The feeding ecology of mullet would appear to explain the unusual capacity of these fish to concentrate nodularin in their livers; these findings may have public health implications for mullet fisheries and aquaculture production where toxic cyanobacteria blooms affect source waters. This report incorporates a systematic review of the literature on nodularin measured in edible fish, shellfish and crustaceans.

Sub-Arctic populations of European lobster (Homarus gammarus) in Northern Norway.

The European lobster is distributed throughout the south and western regions of the Norwegian coast. A previous lobster allozyme investigation (1993) in the Tysfjord region, north of the Arctic Circle demonstrated that the lobster population from this region was genetically different from lobster samples collected in other parts of Norway. More detailed investigation including supplementary extensive sampling and additional allozyme, microsatellite and mtDNA analyses are reported here. This investigation supports the genetic distinctness of the Tysfjord population and shows that this is mainly due to a reduction (60�70%) in gene diversity (observed heterozygosities and number of alleles) compared with lobsters from more southern regions. In addition to the Tysfjord region, the comprehensive sampling also included lobsters found in the adjacent Nordfolda fjord system. Genetic analyses provided evidence for significant differences between the lobster populations of Tysfjord and Nordfolda, even though they are separated by a coastal distance of only 142 km. The two populations were also different with regards to several biological characteristics such as body size. The genetic difference between these two geographically close populations is likely to be due to the local hydrological conditions, preventing larval dispersal between the fjord systems. Assessment of lobster abundance in the north-west region suggests that the sub-arctic lobster populations are geographically isolated.

The biogeographical status of Alnus crispa (Ait.) Pursch in sub-Arctic southern Greenland : do pollen records indicate local populations during the past 1500 years?

Peer reviewed