Continuum in MDGC Technology: From Classical Multidimensional to Comprehensive Two-Dimensional Gas Chromatography.

Recent advances in multidimensional gas chromatography (MDGC) comprise methods such as multiple heart-cut (H/C) analysis and comprehensive two-dimensional gas chromatography (GC × GC); however, clear approaches to evaluate the MDGC results, choice of the most appropriate method, and optimized separation remain of concern. In order to track the capability of these analytical techniques and select an effective experimental approach, a fundamental approach was developed utilizing a time summation model incorporating temperature-dependent linear solvation energy relationship (LSER). The approach allows prediction of optimized analyte distribution in the 2D space for various MDGC approaches employing different experimental variables such as column lengths, temperature programs, and stationary phase combinations in order to evaluate separation performance (apparent (1)D, (2)D, total number of separated peaks, and orthogonality) for simulated MDGC results. The methodology applied LSER to generate results for nonpolar-polar and polar-nonpolar 2D column configurations for separation of 678 compounds in an oxidized kerosene-based jet fuel sample. Three-dimensional plots were generated in order to illustrate the dependency of separation performance on (2)D column length and number of injections for different stationary phase combinations. With a given limit of analysis time, a MDGC approach to obtain an optimized total separated peak number for a particular column set was proposed depending on (1)D and (2)D analyte peak distribution. This study introduces fundamental concepts and establishes approaches to design effective GC × GC or multiple H/C systems for different column combinations, to provide the best overall separation outcomes with the highest separated peak number and/or orthogonality.

Consequences of domestication in eastern oyster: Insights from whole genomic analyses.

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.

Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.

The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.

Confirmation of the shell-boring oyster parasite Polydora websteri (Polychaeta: Spionidae) in Washington State, USA.

Invasions by shell-boring polychaetes such as Polydora websteri Hartman have resulted in the collapse of oyster aquaculture industries in Australia, New Zealand, and Hawaii. These worms burrow into bivalve shells, creating unsightly mud blisters that are unappealing to consumers and, when nicked during shucking, release mud and detritus that can foul oyster meats. Recent findings of mud blisters on the shells of Pacific oysters (Crassostrea gigas Thunberg) in Washington State suggest a new spionid polychaete outbreak. To determine the identity of the polychaete causing these blisters, we obtained Pacific oysters from two locations in Puget Sound and examined them for blisters and burrows caused by polychaete worms. Specimens were also obtained from eastern oysters (Crassostrea virginica Gmelin) collected in New York for morphological and molecular comparison. We compared polychaete morphology to original descriptions, extracted DNA and sequenced mitochondrial (cytochrome c oxidase I [mtCOI]) and nuclear (small subunit 18S rRNA [18S rRNA]) genes to determine a species-level molecular identification for these worms. Our data show that Polydora websteri are present in the mud blisters from oysters grown in Puget Sound, constituting the first confirmed record of this species in Washington State. The presence of this notorious invader could threaten the sustainability of oyster aquaculture in Washington, which currently produces more farmed bivalves than any other US state.

Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci.

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.

Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus.

Previous work on the harpacticoid copepod Tigriopus californicus has focused on the extensive population differentiation in three mtDNA protein coding genes (COXI, COXII, Cytb). In order to get a more complete understanding of mtDNA evolution in this species, we sequenced three complete mitochondrial genomes (one from each of three California populations) and compared them to two published mtDNA genomes from an Asian congener, Tigriopus japonicus. Several features of the mtDNA genome appear to be conserved within the genus: 1) the unique order of the protein coding genes, rRNA genes and most of the tRNA genes, 2) the genome is compact, varying between 14.3 and 14.6 kb, and 3) all genes are encoded on the same strand of the mtDNA. Within T. californicus, extremely high levels of nucleotide divergence (>20%) are observed across much of the mitochondrial genome. Inferred amino acid sequences of the proteins encoded in the mtDNAs also show high levels of divergence; at the extreme, the three ND3 variants in T. californicus showed >25% amino acid substitutions, compared with <3% amino acid divergence at the previously studied COXI locus. Unusual secondary structures make functional assignments of some tRNAs difficult. The only apparent tRNA(trp) in these genomes completely overlaps the 5' end of the 16S rRNA in all three T. californicus mtDNAs. Although not previously noted, this feature is also conserved in T. japonicus mtDNAs; whether this sequence is processed into a functional tRNA has not been determined. The putative control region contains a duplicated segment of different length (from 88 to 155 bp) in each of the T. californicus sequences. In each case, the duplicated segments are not tandem repeats; despite their different lengths, the distance between the start of the first and the start of the second repeat is conserved (520 bp). The functional significance, if any, of this repeat structure remains unknown.

NMR Profiling of Metabolites in Larval and Juvenile Blue Mussels (Mytilus edulis) under Ambient and Low Salinity Conditions.

Blue mussels (Mytilus edulis) are ecologically and economically important marine invertebrates whose populations are at risk from climate change-associated variation in their environment, such as decreased coastal salinity. Blue mussels are osmoconfomers and use components of the metabolome (free amino acids) to help maintain osmotic balance and cellular function during low salinity exposure. However, little is known about the capacity of blue mussels during the planktonic larval stages to regulate metabolites during osmotic stress. Metabolite studies in species such as blue mussels can help improve our understanding of the species' physiology, as well as their capacity to respond to environmental stress. We used 1D ¹H nuclear magnetic resonance (NMR) and 2D total correlation spectroscopy (TOCSY) experiments to describe baseline metabolite pools in larval (veliger and pediveliger stages) and juvenile blue mussels (gill, mantle, and adductor tissues) under ambient conditions and to quantify changes in the abundance of common osmolytes in these stages during low salinity exposure. We found evidence for stage- and tissue-specific differences in the baseline metabolic profiles of blue mussels, which reflect variation in the function and morphology of each larval stage or tissue type of juveniles. These differences impacted the utilization of osmolytes during low salinity exposure, likely stemming from innate physiological variation. This study highlights the importance of foundational metabolomic studies that include multiple tissue types and developmental stages to adequately evaluate organismal responses to stress and better place these findings in a broader physiological context.

Multidimensional gas chromatography of oxidative degradation products in algae-derived fuel oil samples using narrow heartcuts and rapid cycle times.

To characterize a fuel's thermal and storage stability an understanding of the process of oxidation and oxidation pathways is essential. Oxidation pathways commence with hydroperoxides which quickly decompose to form a range of alcohols, acids and other oxygen-containing species. In the presence of significant levels of hydrocarbon-based matrix, analysis of these heteroatomic species is difficult. Applying multidimensional gas chromatography with very narrow heart-cut windows (0.20 min) minimizes the number of compounds transferred to the second dimension (2D) column during each heart-cut. Successive heart-cuts every 2.00 min are taken throughout the analytical run, since each heart-cut has a maximum retention on 2D of <2.00 min on the fast elution 2D column. Subsequent analyses involve incrementing or offsetting the heart-cut windows by 0.20 min, so after 10 analyses, a complete coverage of the sample components can be obtained. On the polar 1D and non-polar 2D phase column arrangement, non-polar matrix compounds elute last on the 2D column, and this determines the largest (2t)R; i.e., (2t)R < P(M) to ensure retained components on 2D will not overlap with subsequent heart-cuts. Heartcutting is supported by cryotrapping at the start of the 2D column in order to provide significantly better resolution. Good quality MS library match data generally demonstrate the high resolution separation of oxygenates achieved. Whilst 1D GC-MS was unsuccessful in identifying any of the oxygen-containing compounds reported here, good correlation of MS data (with average MS library similarity data) for acids (903), alcohols (909), ketones (941) and aldehydes (938) in the sample is obtained. The method requires ten sequential runs, and this can be accomplished automatically once the events table is set up. However if fewer target compounds are to be transferred, a reduced number of sequential runs can be implemented.

Highly divergent duplicate mannose-6-phosphate isomerase (Mpi) genes in the blue mussel, Mytilus edulis.

Gene duplication has been hypothesized to play a major role in the evolution of genes and genomes and in generating phenotypic diversity among the proteins those genes encode. We have identified duplicate genes for the glycolytic enzyme mannose-6-phosphate isomerase (MPI: EC 5.3.1.8) in marine mussels in the genus Mytilus. Overall, there was only 52% sequence identity (72% similarity) between the proteins encoded by these two genes, designated as Mpi-A and Mpi-B. Based on a comparison of the rate of non-synonymous substitution between orthologous and paralogous Mpi coding sequences obtained from Mytilus edulis and the congener M. trossulus we estimate that the duplication of Mpi in mussels occurred ~170 MYA. We detected paralog-specific differences in the ratio of non-synonymous to synonymous substitutions (k(a)/k(s)) and in the predicted net charge for MPI-A and MPI-B. Using a real-time quantitative RT-PCR assay we observed substantial changes in Mpi-A and Mpi-B transcript levels between tissue types; the strongest expression of Mpi-A was observed in mantle tissue while Mpi-B expression exceeded that of Mpi-A in gill and hepatopancreas tissues. Taken together, these observations suggest that different functional roles have evolved for these two Mytilus Mpi genes subsequent to gene duplication.

Immunolocalization of a Galphaq protein to the chemosensory organs of Dipolydora quadrilobata (polychaeta: spionidae).

Chemoreception in marine invertebrates mediates a variety of ecologically important behaviors including defense, reproduction, larval settlement and recruitment, and feeding. The sensory pathways that regulate deposit-feeding activity by polychaetes living in sedimentary habitats are of particular interest because such feeding has profound effects on the physical and chemical properties of the habitat. Nevertheless, little is known concerning the molecular mechanisms of chemical signal transduction associated with deposit feeding and other behaviors in polychaetes. Chemosensory-based feeding behaviors are typically regulated by G-protein-coupled signal transduction pathways. However, the presence and role of such pathways have not been demonstrated in marine polychaetes. Methodologies involving degenerate primer-based reverse transcription with the polymerase chain reaction and rapid amplification of cDNA ends were used to identify and characterize a Galphaq subunit expressed in the feeding palps of the spionid polychaete Dipolydora quadrilobata. The D. quadrilobata Galphaq protein had high sequence similarity with previously reported Galphaq subunits from both invertebrate and vertebrate taxa. Immunhistochemistry and immunocytochemistry were used with confocal laser scanning microscopy and transmission electron microscopy to visualize the distribution of a Galphaq antibody in whole worms and in cilia of the feeding palps. Galphaq immunoreactivity was concentrated in the nuchal organs, food-groove cilia, and lateral/abfrontal cilia of the feeding palps. Because these structures are known to be involved in chemoreception, we propose that Galphaq isolated from D. quadrilobata is a key component of chemosensory signal transduction pathways in this species.

FTIR analysis and monitoring of synthetic aviation engine oils.

Synthetic turbine oils from military aircraft engines were analysed for antioxidant content and total acid number using infrared (IR) spectroscopy. Two-dimensional IR correlation analysis was employed to investigate and interpret observed trends in the spectra, as acid was formed and antioxidant species were depleted in the oils, as a function of aging and engine wear. Principal components and partial least squares algorithms were used and compared for the development of calibration and prediction models. Transmission IR spectrometry is demonstrated to be effective for the analysis and monitoring of synthetic aviation turbine engine oils and shown to provide rapid and accurate information as compared with traditional analytical techniques and methods.

Comment on "Divergent induced responses to an invasive predator in marine mussel populations".

Freeman and Byers (Reports, 11 August 2006, p. 831) presented evidence for the rapid evolution of antipredator defenses in the mussel Mytilus edulis. However, their analysis is confounded by three issues. Samples from some sites are likely to have included a second species, M. trossulus; their manipulation of chemical cues does not preclude other interpretations; and they failed to establish an adaptive significance to shell thickening.

Molecular evolution at the cytochrome oxidase subunit 2 gene among divergent populations of the intertidal copepod, Tigriopus californicus.

The cytochrome c oxidase subunit 2 gene (COII) encodes a highly conserved protein that is directly responsible for the initial transfer of electrons from cytochrome c to cytochrome c oxidase (COX) crucial to the production of ATP during cellular respiration. Despite its integral role in electron transport, we have observed extensive intraspecific nucleotide and amino acid variation among 26 full-length COII sequences sampled from seven populations of the marine copepod, Tigriopus californicus. Although intrapopulation divergence was virtually nonexistent, interpopulation divergence at the COII locus was nearly 20% at the nucleotide level, including 38 nonsynonymous substitutions. Given the high degree of interaction between the cytochrome c oxidase subunit 2 protein (COX2) and the nuclear-encoded subunits of COX and cytochrome c (CYC), we hypothesized that some codons in the COII gene are likely to be under positive selection in order to compensate for amino acid substitutions in other subunits. Estimates of the ratio of nonsynonymous to synonymous substitution (omega), obtained using a series of maximum likelihood models of codon substitution, indicated that the majority of codons in T. californicus COII are under strong purifying selection (omega << 1), while approximately 4% of the sites in this gene appear to evolve under relaxed selective constraint (omega = 1). A branch-site maximum likelihood model identified three sites that may have experienced positive selection within the central California sequence clade in our COII phylogeny; these results are consistent with previous studies showing functional and fitness consequences among interpopulation hybrids between central and northern California populations.

Nonhomologous recombination between the large unassigned region of the male and female mitochondrial genomes in the mussel, Mytilus trossulus.

Doubly uniparental inheritance of mtDNA (DUI) is commonly observed in several genera of bivalves. Under DUI, female offspring inherit mtDNA from their mothers, while male offspring inherit mtDNA from both parents but preferentially transmit the paternally inherited mtDNA to their sons. Several studies have shown that the female- and male-specific mtDNA lineages in blue mussels, Mytilus spp., vary by upward of 20% at the nucleotide level. In addition to high levels of nucleotide substitution, the present study observed substantial gender-based length polymorphism in the presumptive mitochondrial control region (=large unassigned region; LUR) of North American M. trossulus. In this species, female lineage LUR haplotypes are over 2 kb larger than male lineage LUR haplotypes. Analysis of sequence data for these length variants indicates that the F LUR haplotypes of North American M. trossulus contain sequences similar to the F lineage control region in the congeners M. edulis and M. galloprovincialis. Relative to the F LUR in the latter two species, however, the F lineage LUR haplotypes in M. trossulus contain two large sequence insertions, each nearly 1 kb in size. One of these insertions has high sequence similarity to the male lineage LUR of M. trossulus. The tandem arrangement of F and M control region sequences in the F lineage LUR of M. trossulus is most likely the result of nonhomologous recombination between the male and the female mitochondrial genomes in M. trossulus, a finding that has important implications regarding the transmission and evolution of blue mussel mitochondrial genomes.

GENOTYPE-ENVIRONMENT INTERACTION FOR JUVENILE GROWTH IN THE HARD CLAM MERCENARIA MERCENARIA (L.).

Offspring from half-sib and full-sib families of the hard clam, Mercenaria mercenaria were reared in five locations along the Atlantic Coast to test for the presence of genotype-environment interaction for juvenile growth rate. Location effects upon growth rate variation were prevalent; of the genetic effects, the additive genetic by location variance was predominant with the nonadditive genetic by location component contributing to a lesser degree to the interaction variance. The additive and nonadditive variation over all environments was negligible. Genotype-environment interaction was found to be at least partially due to a change in the amount of genetic variation expressed at each location; with significant additive variation detected at Charleston and Georgetown, SC sites and significant nonadditive variation at Millsboro, DE. Genetic covariance/correlation analysis indicated that reversals in relative family performance across locations were prevalent, implying the possibility of habitat specialization among genotypes. In addition, graphical analysis produced no evidence of a ubiquitously superior genotype. These analyses suggest that genotype-environment interaction should act to constrain the evolution of juvenile growth rate in Mercenaria, preserve any heritable variation associated with this trait and may lead to the development of phenotypic plasticity for growth.

Functional coadaptation between cytochrome c and cytochrome c oxidase within allopatric populations of a marine copepod.

Geographically isolated populations may accumulate alleles that function well on their own genetic backgrounds but poorly on the genetic backgrounds of other populations. Consequently, interpopulation hybridization may produce offspring of low fitness as a result of incompatibilities arising in allopatry. Genes participating in these epistatic incompatibility systems remain largely unknown. In fact, despite the widely recognized importance of epistatic interactions among gene products, few data directly address the functional consequences of such interactions among natural genetic variants. In the marine copepod, Tigriopus californicus, we found that the cytochrome c variants isolated from two different populations each had significantly higher activity with the cytochrome c oxidase derived from their respective source population. Three amino acid substitutions in the cytochrome c protein appear to be sufficient to confer population specificity. These results suggest that electron transport system (ETS) proteins form coadapted sets of alleles within populations and that disruption of the coadapted ETS gene complex leads to functional incompatibilities that may lower hybrid fitness.

ASYMMETRIC INTROGRESSION OF MITOCHONDRIAL DNA AMONG EUROPEAN POPULATIONS OF BLUE MUSSELS (MYTILUS SPP.).

-Mytilus edulis and M. galloprovincialis are two blue mussel species that coexist in western Europe. Previously, we reported that M. galloprovincialis populations contain female and male haplotypes that are fixed in M. edulis populations as well as unique haplotypes. This study assesses whether paraphyly for these species is due to introgression or incomplete lineage extinction. The lineage extinction hypothesis predicts that the shared mtDNA haplotypes in M. galloprovincialis will be significantly diverged from those in M. edulis and form distinct sequence clades. In contrast, the introgression hypothesis proposes that M. edulis haplotypes have only recently been introduced into M. galloprovincialis through hybridization with relatively little divergence accumulating between the shared RFLP haplotypes. We examined 80 mtl6S gene sequences for both the maternal and paternal mtDNA lineages from mussels sampled from various European populations and found strong support for the introgression hypothesis. In addition, we found that M. edulis mtDNA haplotypes appear to be introgressing into mussel populations in the Baltic Sea, which have predominantly M. trossulus nuclear genotypes, indicating that introgressive hybridization is prevalent among European mussel populations.