Similar Abundance Levels Research Articles

Questioning the effectiveness of seed-reducing agents on invasive Acacia: Pod production relative to gall abundance of classical biological control agents

It has been widely accepted that the biological control agents released on invasive Australian Acacia in South Africa, have impacted on the population dynamics of their host plants. However, there are no quantitative data to support these claims and these invasive species remain at similar abundance levels prior to the release of their associated biological control agents and also show evidence of range expansion. The effect of biological control agents, two bud galling wasps (Trichilogaster acaciaelongifoliae and T. signiventris) and one gall-forming rust fungus (Uromycladium morrisii), on the pod production of their respective hosts (Acacia longifolia, A. pycnantha and A. saligna) was assessed by quantifying the reproductive and galled trees per hectare as well as the pods and galls produced per tree and per square meter over a one to two year period. It was shown that invasive Australian Acacia satiate their gall-forming biological control agents, with many pods surviving in their presence. Pod production and loss was placed into perspective using recent findings of seed rain and seed bank studies. It was concluded, based on pod production, seed rain and seed bank data that despite T. acaciaelongifoliae, T. signiventris and U. morrisii reducing pod production, they have had no impact on the population dynamics of their invasive Australian Acacia hosts in South Africa.

Two Rhabdoviruses, One Novel, Isolated from Armigeres subalbatus in China.

The family Rhabdoviridae contain important human and mammalian pathogens that are vectored by different arthropod species. The ground supernatants of mosquitoes were used to inoculate in BHK-21 and C6/36 cells for virus isolation. Then, the viral complete genome sequence was obtained and used for phylogenetic analysis. In this study, we observed a cytopathic effect (CPE) in mosquito cells (C6/36) and rod-like virion after inoculating a pool of Armigeres subalbatus samples collected in Shanxi Province, China, in 2019 (SX1916). Meta-transcriptomics sequencing revealed the presence of two distinctive rhabdoviruses with similar abundance levels, namely, Shanxi Armigeres subalbatus rhabdovirus (SXARV) and Shanxi Arboretum virus (SXABTV). Despite the fact that the SXARV genome (9590 nt) was much shorter than that of SXABTV (11,480 nt), both belonged to the Almendravirus group within Rhabdoviridae whose genomes encoded five proteins (N, P, M, G, and L) and a small hydrophobin (U1) and the difference in lengths is mainly caused by a substantially shorter N protein encoded by SXARV. On the phylogenetic tree, SXABTV was closely related (90.7% amino acid identity at L protein) with the Arboretum virus isolated from Psorophora albigenu mosquitoes in Peru in 2014, whereas SXARV was distantly related to Rio Chico virus (63.3% amino acid identity), a genetic distance large enough to be defined as a new species within Rhabdoviridae. Collectively, we report a simultaneous isolation of two related rhabdoviruses from Armigeres subalbatus that marked the circulation of almendraviruses in Shanxi, China.

Stock collapse and its effect on species interactions: Cod and herring in the Norwegian-Barents Seas system as an example.

Both the Norwegian Spring Spawning herring (Clupea harengus) and the Northeast Arctic (NEA) cod (Gadus morhua) are examples of strong stock reduction and decline of the associated fisheries due to overfishing followed by a recovery. Cod and herring are both part of the Barents Sea ecosystem, which has experienced major warming events in the early (1920–1940) and late 20th century. While the collapse or near collapse of these stocks seems to be linked to an instability created by overfishing and climate, the difference of population dynamics before and after is not fully understood. In particular, it is unclear how the changes in population dynamics before and after the collapses are associated with biotic interactions. The combination of the availability of unique long‐term time series for herring and cod makes it a well‐suited study system to investigate the effects of collapse. We examine how species interactions may differently affect the herring and cod population dynamic before and after a collapse. Particularly we explore, using a GAM modeling approach, how herring could affect cod and vice versa. We found that the effect of cod biomass on herring that was generally positive (i.e., covariation) but the effect became negative after the collapse (i.e., predation or competition). Likewise a change occurred for the cod, the juvenile herring biomass that had no effect before the collapse had a negative effect after. Our results indicate that the population collapses may alter the inter‐specific interactions and response to abiotic environmental changes. While the stocks are at similar abundance levels before and after the collapses, the system is potentially different in its functioning and may require different management action.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

BackgroundBiogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.ResultsWe intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.ConclusionsThe disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.AU1kaDmL5ojSw8dBEKS2i-Video abstract

Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data.

The emergence of next-generation sequencing (NGS) has revolutionized the way of reaching a genome sequence, with the promise of potentially providing a comprehensive characterization of DNA variations. Nevertheless, detecting somatic mutations is still a difficult problem, in particular when trying to identify low abundance mutations, such as subclonal mutations, tumour-derived alterations in body fluids or somatic mutations from histological normal tissue. The main challenge is to precisely distinguish between sequencing artefacts and true mutations, particularly when the latter are so rare they reach similar abundance levels as artefacts. Here, we present needlestack, a highly sensitive variant caller, which directly learns from the data the level of systematic sequencing errors to accurately call mutations. Needlestack is based on the idea that the sequencing error rate can be dynamically estimated from analysing multiple samples together. We show that the sequencing error rate varies across alterations, illustrating the need to precisely estimate it. We evaluate the performance of needlestack for various types of variations, and we show that needlestack is robust among positions and outperforms existing state-of-the-art method for low abundance mutations. Needlestack, along with its source code is freely available on the GitHub platform: https://github.com/IARCbioinfo/needlestack.

Relationship of biological communities to habitat structure on the largest remnant flat oyster reef (Ostrea angasi) in Australia

Oyster reef restoration is a growing field in Australia, yet formal descriptions of associated biological communities for reefs created by native flat oysters (Ostrea angasi) do not currently exist. Native flat oysters once formed extensive and complex three-dimensional habitats in bays and estuaries across southern Australia until indiscriminate fishing, sedimentation and disease led to their near disappearance. To determine the diversity and abundance on naturally occurring oyster reefs, we sampled four sites on the last known naturally occurring oyster reef ecosystem, which resides in north-eastern Tasmania, and compared them to the surrounding soft sediment regions. Assemblages were related to environmental variables to determine whether consistent patterns were present. Oyster reef sites contained three times the faunal abundance of the surrounding soft sediment regions. Abundance among echinoderms, arthropods, molluscs and fish was much elevated, whereas annelids showed similar levels of abundance but differed in terms of species composition. These results show that oyster reefs do support abundant and diverse assemblages, emphasising the probable loss of community-level biodiversity associated with their historical decline around southern Australia.

Salivary Zymogen Granule Protein 16B Drops at Onset of Chronic Graft-Versus-Host Disease: A Possible Salivary Biomarker for Oral Chronic Graft-Versus-Host Disease

Objective Chronic graft-versus-host disease (cGVHD) targets the oral mucosa and salivary glands in 30-70% of cGVHD patients after allogeneic hematopoietic stem cell transplant (HSCT). In the absence of an incisional biopsy, no diagnostic test exists to confirm clinical suspicion of cGVHD processes in oral tissues. Consequently, therapy is often withheld until severe manifestations, such as ulceration, develop. This proteomic study examined whole saliva for the presence of a diagnostic biomarker profile at first onset of oral cGVHD prior to initiation of topical steroid therapy. Methods Patients from NIH protocols (NCT00331968, NCT00520130, or NCT01851382) were sampled at oral cGVHD onset. All cases had biopsy-proven oral GVHD. Five-minute unstimulated whole saliva from 3 individual oral cGVHD patients, 3 post-transplant controls and 2 healthy volunteers was processed, iTRAQ-tagged, HPLC-fractionated, and analyzed via liquid chromatography coupled tandem mass spectrometry. High confidence protein identifications were tested using a Kruskal-Wallis test with Bonferroni correction. Selected proteins were validated by Western blot (WB) using two independent cohorts. Cohort 1: post-HSCT patients with (n=10) and without (n=10) oral cGVHD; Cohort 2: post-HSCT patients with (n=12) and without (n=12) oral cGVHD, controlled for recipient sex and prior total-body irradiation. Fluorescent immunohistochemistry (IHC) was used to further analyze zymogen granule protein 16B (ZG16B) in patient labial minor salivary glands (MSG). Results The discovery dataset contained 569 confidently-identified proteins, with 77 significantly differentially expressed at onset of cGVHD. A 6-protein panel was selected for WB validation in two independent sample cohorts; proteins were selected based on Ingenuity Pathway Analysis, biological function, and protein level. In WB analysis, MMP9, Ezrin, PIP and alpha-1-antichymotrypsin displayed similar abundance levels as in the iTRAQ screen but were not significantly different. ZG16B, a secretory lectin protein associated with the tear release in the lacrimal gland, was reduced 2-fold in saliva of post-HSCT patients with oral cGVHD (898.1 ± 371.8 AU) compared with post-HSCT patients without oral cGVHD (1905 ± 598.6 AU; p Conclusion Taken together, results indicate that ZG16B is present in lower amounts in unstimulated whole saliva and within the salivary gland acinar units at oral cGVHD onset. Reduction in this protein may indicate cGVHD activity and/or salivary gland damage and further investigation of its biological function and potential utility as a clinical biomarker of oral cGVHD onset is needed.

Small-scale agricultural landscapes and organic management support wild bee communities of cereal field boundaries

Pollinators are sensitive to agricultural intensification at both local and landscape scales. High configurational landscape heterogeneity due to small fields and a high amount of field boundaries is hypothesized to enhance farmland biodiversity. Here, we investigated the effects of organic vs. conventional farming in large- vs. small-scale agricultural landscapes on wild bee communities and their floral resources to improve conservation schemes for pollinators. We sampled bees in Central Germany at the field boundaries of 18 pairs of conventionally and organically managed winter wheat fields along the former iron curtain using pan traps and trap nests. Around traps, we surveyed species richness and flower cover of insect-pollinated forbs. Compared to conventional farming, organic farming was related to higher insect-pollinated forb species richness and flower cover in the field boundaries, presumably due to the lack of herbicide use. Interestingly, small-scale agriculture did not counteract the loss of floral resources under conventional management, as the difference to organic management was even larger in Western small-scale agriculture. Organic farming, but not small-scale agriculture, enhanced species richness of solitary bees, which is in line with their small home ranges. In contrast, bumblebees benefitted only from small-scale agriculture, which matches with their high dispersal ability. Despite similar levels of abundance and diversity of trap-nesting bees in the two landscape types, brood cell parasitism was also higher in small-scale agriculture. Both organic farming and small-scale agriculture directly and indirectly supported different groups of wild bees, suggesting long-term benefits for conservation. Agri-environment schemes should acknowledge the so far neglected benefits of small-scale agriculture for biodiversity and its potential services.

Comparative proteomic studies of a Scrippsiella acuminata bloom with its laboratory-grown culture using a 15N-metabolic labeling approach

Comparative proteomic analysis was carried out using cells isolated from a natural bloom of Scrippsiella acuminata (formerly Scrippsiella trochoidea) in the early bloom (EB) and late bloom (LB) stages as well as with laboratory-grown cultures of cells isolated from the bloom in early growth (EG) and late growth (LG) stages. For quantitative proteomics, LG cells were grown for 20 generations in the presence of 15N as a reference (i.e. common denominator) for all comparison. In comparisons with early growth laboratory grown cells (EG/LG), nearly 64% of proteins identified had similar abundance levels, with the remaining 36% mostly more abundant in EG cells. Calvin cycle, amino acid metabolism, chlorophyll biosynthesis and transcription/translation were among the up-regulated processes. Cells from the early bloom (EB/LG) had a greater abundance of transporters and enzymes related to light harvesting and oxidative phosphorylation, while the abundance of these proteins decreased in late bloom cells (LB/LG). All natural bloom samples showed either constant or lower abundance levels of enzymes involved in sugar synthesis and glycolytic pathways compared to laboratory grown cells. Our results represent the first examination of the proteomic changes in the development of a natural dinoflagellate bloom. Importantly, our results demonstrate that the proteome of cells grown in the laboratory is distinctively different from cells in a natural bloom.

Use of remote cameras to evaluate ocelot (Leopardus pardalis) population parameters in seasonal tropical dry forests of central-western Mexico

AbstractThe ocelot is one of the most studied felid species in the neotropics yet most of our current knowledge comes from tropical rain forests and protected areas. Therefore, we lack a comprehensive understanding on how the species abundance varies in terms of ecological parameters across its full distribution range. This is particularly true for the species population in the Northern Hemisphere, as data of ocelot populations occurring in tropical dry forests are scarce. In this study, we focused on: a) generating population data (density and sex ratios), based on camera-trapping, for ocelot occurring in the vast and understudied tropical dry forest of the western Pacific of Mexico. b) Comparing the variation in species abundance and density across its distribution range, including a larger set of studies from the Northern Hemisphere, contrasting parameters between rain forests and tropical seasonal ecosystems and re-examining the assumed relationship between precipitation and ocelot abundance. Overall, we identified 17 ocelots in our study sites and estimated an average density of 23.7 individuals (ind) per 100 km2with a female to male ratio >1. No significant differences in ocelot density was found between seasonal tropical forests and rain forests studies (Wilcoxon test, W=71, p=0.7675). Moreover, we found no support for the relation between ocelot density and precipitation (only when restricting our analysis to rain forest data the fit of the regression model was close to be significant, R2=0.2463, p=0.07107). Our results indicate that tropical seasonal ecosystems and dry forest in particular, may present ocelot population with similar levels of abundance than tropical rain forests. We observed that precipitation is a poor predictor of ocelot abundance. In our study, we observed that overall local ecological factors (e.g. prey abundance and interspecific interactions) influenced the spatial and temporal abundance of ocelots.

Genome-wide comparison of AP2/ERF superfamily genes between Gossypium arboreum and G. raimondii.

The APETALA2/ethylene response factor (AP2/ERF) transcription factor superfamily is known to regulate diverse processes of plant development and stress responses. We conducted a genome-wide analysis of the AP2/ERF gene in Gossypium arboreum and G. raimondii. Using RPSBLAST and HMMsearch, a total of 271 and 269 AP2/ERF genes were identified in the G. arboreum and G. raimondii genomes, respectively. A phylogenetic analysis classified diploid Gossypium spp AP2/ERF genes into 4 families and 16 subfamilies. Orthologous genes predominated the terminal branch of the phylogenetic tree. Physical mapping showed at least 30% of AP2/ERF genes clustered together. A high level of intra- and inter-species collinearity involving AP2/ERF genes was observed, indicating common (before species divergence) or parallel (after species divergence) segmental duplications, along with tandem duplications, resulting in the species-specific expansion of AP2/ERF genes in diploid Gossypium species. Motif analyses of the AP2/ERF proteins revealed that motif arrangements were highly diverse among subfamilies, but shared by orthologous gene pairs. An examination of nucleotide divergence of AP2/ERF coding regions identified small and non-significant sequence differences among orthologs. Expression profiling of AP2/ERF orthologous gene pairs showed similar abundance levels of orthologous copies between G. arboreum and G. raimondii. Thus, cotton species possess abundant and diverse AP2/ERF genes, resulting from tandem and segmental duplications. Protein and nucleotide sequence and mRNA expression analyses revealed symmetrical evolution, indicating that most AP2/ ERF genes may not have undergone significant biochemical and morphological divergence between sister species. Our study provides detailed insights into the evolutionary characteristics and functional importance of AP2/ERF genes, and could aid in the genetic improvement of agriculturally significant crops in this genus.

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing.

Reads classification is an important fundamental problem in metagenomics study. With the development of next-generation sequencing, metagenome samples can be generated using much less money and time. However, the short reads generated by next-generation sequencing make the problem of reads classification much more difficult than before. None of the existing tools can assign NGS short reads to each genome accurately, which limit their use in real application. Fortunately, in many applications, it is meaningless to separate all the species in the metagenome sample from each other. That is because we usually only focus on some specified species categories in the sample and do not care about the others. There is no existing tool that is designed technically for obtaining specified species from short metagenome reads generated by next-generation sequencing. In this paper, we propose a tool named MetaObtainer to obtain the specified species from next-generation sequencing short reads. The tool synthesizes some of newest technologies for processing of short reads, so it can have better performance than other tools. It can (1) deal with next-generation sequencing reads which are shorter than 100 bp with very high accuracy (both of precision and recall are more than 90%); (2) find unknown species using the reference genomes of species which are similar with it; (3) perform well when reads of specified species are very few in the dataset; (4) handle genomes of similar abundance levels as well as different abundance levels (1:10); and (5) obtain multiple species categories from metagenome sample.

Incomplete control of the diamondback moth, Plutella xylostella, by the parasitoid Cotesia vestalis in a cabbage field under tropical conditions

Immature Plutella xylostella (Lepidoptera: Plutellidae) and parasitoids were sampled for 39 months in an unsprayed cabbage field near Cotonou, Benin, to determine how and when host-parasitoid interactions influence the population dynamics of the moth in a tropical environment. Eighty-three samples were taken at approximately two-week intervals. There were no seasonal patterns in the abundance of immature moths, which was not correlated with weather variables, although heavy rainfall during the principal rainy season may have temporarily affected the population. The host-parasitoid system consisted almost exclusively of P. xylostella and its larval parasitoid Cotesia vestalis (Hymenoptera: Braconidae), both species occurring at similar levels of abundance (on average 7.5 ± 0.3 and 7.2 ± 0.3 individuals per plant, respectively). The tendency for host-parasitoid dynamics to cycle was apparent in the field. P. xylostella and C. vestalis showed coupled oscillations in abundance, with a time lag of about two weeks between host and parasitoid peaks. High parasitoid abundance resulted in significant decreases in moth abundance over several weeks. However, the parasitoid population in turn decreased, could not prevent the moth from rebounding, and there was no stable control of the pest. We conclude that under tropical conditions in which P. xylostella populations grow rapidly, combined with a high probability of recolonization from surrounding areas, biological control by a well-established specialist parasitoid reaches its limits and additional control measures are necessary.

Separating metagenomic short reads into genomes via clustering

BackgroundThe metagenomics approach allows the simultaneous sequencing of all genomes in an environmental sample. This results in high complexity datasets, where in addition to repeats and sequencing errors, the number of genomes and their abundance ratios are unknown. Recently developed next-generation sequencing (NGS) technologies significantly improve the sequencing efficiency and cost. On the other hand, they result in shorter reads, which makes the separation of reads from different species harder. Among the existing computational tools for metagenomic analysis, there are similarity-based methods that use reference databases to align reads and composition-based methods that use composition patterns (i.e., frequencies of short words or l-mers) to cluster reads. Similarity-based methods are unable to classify reads from unknown species without close references (which constitute the majority of reads). Since composition patterns are preserved only in significantly large fragments, composition-based tools cannot be used for very short reads, which becomes a significant limitation with the development of NGS. A recently proposed algorithm, AbundanceBin, introduced another method that bins reads based on predicted abundances of the genomes sequenced. However, it does not separate reads from genomes of similar abundance levels.ResultsIn this work, we present a two-phase heuristic algorithm for separating short paired-end reads from different genomes in a metagenomic dataset. We use the observation that most of the l-mers belong to unique genomes when l is sufficiently large. The first phase of the algorithm results in clusters of l-mers each of which belongs to one genome. During the second phase, clusters are merged based on l-mer repeat information. These final clusters are used to assign reads. The algorithm could handle very short reads and sequencing errors. It is initially designed for genomes with similar abundance levels and then extended to handle arbitrary abundance ratios. The software can be download for free at http://www.cs.ucr.edu/∼tanaseio/toss.htm.ConclusionsOur tests on a large number of simulated metagenomic datasets concerning species at various phylogenetic distances demonstrate that genomes can be separated if the number of common repeats is smaller than the number of genome-specific repeats. For such genomes, our method can separate NGS reads with a high precision and sensitivity.

Non‐random distribution of weed species abundance in arable fields

Borgy B, Gaba S, Petit S & Reboud X (2012) Non‐random distribution of weed species abundance in arable fields. Weed Research52, 383–389.SummaryMany decisions for pest control in agriculture are based on densities, rather than species presence only. Little is known about the distribution of pest abundance and even less when several species present in a field may interact. With the aim of developing an ecologically based approach to weed management, we compared observed co‐occurrence patterns with a null model, to test whether the abundances of weed species were randomly assembled. The data set covered the pattern of co‐occurrence of abundances of weeds within 200‐m2 plots located in 1143 arable fields scattered across France. Our results pinpointed a highly significant ‘similar attraction–dissimilar repulsion’ rule, as species reaching similar abundance levels co‐occurred significantly more often than expected under the hypothesis of a random distribution of abundance. A similar analysis applied to the 25% plots that had the highest weed densities indicated that the ‘similar attraction–dissimilar repulsion’ rule held true for low‐abundance classes, but not in situations where at least one species was observed at densities above 20 individuals m−2. Our analysis extends the analysis of community beyond the sole species richness index by accounting for their abundance. Overall, weed species interfered or responded similarly to an external biotic or abiotic factor, with resulting adjustment of densities at the scale of the agricultural field.

Scale-dependence of phylogenetic signal in ecological traits of ectoparasites

The non-independence of traits among closely related species is a well-documented phenomenon underpinning modern methods for comparative analyses or prediction of trait values in new species. Surprisingly such studies have mainly focused on life-history or morphological traits of free-living organisms, ignoring ecological attributes of parasite species in spite of the fact that they are critical for conservation and human health. We tested for a phylogenetic signal acting on two ecological traits, abundance and host specificity, using data for 218 flea species parasitic on small mammals in 19 regions of the Palaearctic and Nearctic, and a phylogenetic tree for these species. We tested for the presence of a phylogenetic signal at both regional and continental scales using three measures (Abouheif/Moran's I, Pagel's λ, and Blomberg et al.'s K). Our results show 1) a consistent positive phylogenetic signal for flea abundance, but only a weaker and erratic signal for host specificity, and 2) a clear dependence on scale, with the signals being stronger at the continental scale and relatively weaker or inconsistent at the regional scale. Whenever values of Blomberg et al.'s K were found significant, they were < 1 suggesting that the effects of phylogeny on the evolution of abundance and host specificity in fleas are weaker than expected from a Brownian motion model. The most striking finding is that, within a continental fauna, closely-related flea species are characterized by similar levels of abundance, though this pattern is weaker within local assemblages, possibly eroded by local biotic or abiotic conditions. We discuss the link between history (represented by phylogeny) and pattern of variation among species in morphological and ecological traits, and use comparisons between the Palaearctic and Nearctic to infer a role of historical events in the probability of detecting phylogenetic signals.

Long-term Trends in Oyster Population Dynamics in Delaware Bay: Regime Shifts and Response to Disease

We evaluate a 54-y survey time series for the Delaware Bay oyster beds in New Jersey waters to identify the characteristics of regime shifts in oyster populations and the influence of MSX and Dermo diseases on population stability. Oyster abundance was high during the 1970s through 1985. Oyster abundance was low at the inception of the time series in 1953, remained low through 1969, and has been low since 1985 and very low since 2000. Natural mortality was low in most years prior to the appearance of MSX in 1957. From 1957 through 1966, natural mortality generally remained above 10% annually and twice exceeded 20%. Natural mortality remained well below 15% during the 1970s and into the early 1980s when oyster abundance was continuously high. The largest mortality event in the time series, an MSX epizootic that resulted in the death of 47% of the stock, occurred in 1985. Mortality rose again with the incursion of Dermo in 1990 and has remained above 15% for most years since that time and frequently has exceeded 20%. The primary impact of MSX and Dermo diseases has been to raise natural mortality and ultimately to cause a dispersed stock to retreat into its habitat of refuge in the moderately low salinity reach of the bay. The time series of oyster abundance on the New Jersey oyster beds of Delaware Bay is dominated by two regime shifts, the 1970 abundance increase that was maintained for about 15 y thereafter, and the 1985 abundance decrease that continues through today. These two regime shifts ushered in long-term periods of apparent constancy in population dynamics. The 1985 regime shift was induced by the largest MSX epizootic on record that produced high mortalities throughout a population distributed broadly throughout its habitat range after 15 y of high abundance. A putative new regime commenced circa 2000 as a consequence of a series of Dermo epizootics. Mortalities routinely exceeded 20% of the population annually during this period, with the consequence of a greater degree of stock consolidation than any previous time in the 54-y record. Extreme consolidation of the stock would appear to be a characteristic of the population's response to Dermo disease. The 1970-1984 and post-1985 regimes each were ushered in by a confluence of events unique in the 54-y time series. Each was characterized by a period of relative stability in population abundance. However, the stability in total population abundance belies a more dynamic process of stock redistribution during both time intervals, demonstrating that the appearance of constancy in stock abundance is not necessarily a result of invariant stock dynamics. Rather, the Delaware Bay oyster time series suggests that regime shifts delimit periods during which differential, often offsetting, local trends impart similar abundance levels, and thus constancy at the level of the stock masks substantive changes in local population dynamics potentially fostering future catastrophic changes in population-level attributes. Understanding such regime shifts will likely determine the success of decadal management goals more so than measures designed to influence population abundance.

Limited evidence for short-term succession of microarthropods during early phases of surface litter decomposition

Succession of microarthropods during the decomposition of organic matter is an important concept in soil biology. However, few studies have tested whether the pattern of microarthropod colonisation during decomposition is independent of season. We investigated the pattern of colonisation and dominance of microarthropods on decomposing organic matter placed at two different times. Litterbags containing canola leaf or stem material were placed on the soil surface of a Western Australian agricultural field in July and September 1999. They were collected weekly to fortnightly until November. A final set of bags was collected in May 2000. Mass loss and nutrient contents (C, N, Ca, K, P and S) were measured at each sample time. Microarthropods were sorted to order and the mites to species level. Nematode abundance was determined at each sample time. Mass loss of the leaf and stem material was similar between the two placement times (≅33% and 15% ash-free dry mass lost over 33 days from leaf and stem material, respectively), although the dynamics of nutrient loss for some elements was different between the two placements. However, over the dry summer, material placed in September continued to lose nutrients whilst there was little additional loss from the material placed in July. A similar pattern of dominance of microarthropod and mite species was found on the leaf and stem material placed in July with the succession of dominant animals more rapid on the stem material. Nematode abundance appeared to increase as populations of microarthropods declined over time. Populations of microarthropods on the material placed in the September samples never achieved similar levels of abundance to that of the July samples, and the dominant fauna groups were dissimilar to those in the July samples for the same degree of decomposition. Our data indicate that the early phase of surface litter decomposition is not a successional process in terms of the microarthropod community irrespective of season and, that abiotic factors are more likely to be determining nutrient loss from organic matter within particular seasons.

An assessment of the effectiveness of Marine Protected Areas in the San Juan Islands, Washington, USA

Tuya, F. C., Soboil, M. L., and Kido, J. 2000. An assessment of the effectiveness of Marine Protected Areas in the San Juan Islands, Washington, USA. – ICES Journal of Marine Science, 57: 1218–1226. Marine protected areas (MPAs) can serve as effective sites for sheltering targeted populations. Furthermore, populations can experience increased abundance and body size in such areas. In this study we compared the abundance and body sizes of commonly collected fish and invertebrate species inside three marine preserves established eight years prior to our survey (University of Washington marine research preserves), two newly established MPAs, and three unprotected sites in the San Juan Archipelago. To determine whether population abundance and individual size were greater in protected areas within each site, these two parameters were measured for the red urchin (Strongylocentrotus franciscanus; Agasizz, 1865), sea cucumber (Parastichopus californicus; Stimpson, 1857), scallops (Chlamys rubida; Hinds, 1845; Chlamys behringiana; Midendorff, 1849; Hinnites giganteus; Gray, 1825), copper rockfish (Sebastes caurinus, Richardson, 1845), quillback rockfish (Sebastes maliger, Jordan & Jilbert, 1880), China rockfish (Sebastes nebulosus; Ayres, 1854) and lingcod (Ophiodon elongatus; Girard, 1854). The newly established MPAs and unprotected sites showed similar levels of abundance and size frequency distributions for the target species. Differences in abundance and size of small red urchins, scallops, rockfishes, and lingcod were not found among the three categories of sites, which could be attributable to a lack of effective protection within the protected sites. The UW marine preserves exhibited greater abundance of medium and large sized red urchins, which is explained because these areas lie within an urchin fishery closure zone established in the late 1970s. Ordination techniques showed that fishing pressure was the main cause of the decreased target populations assemblages. This study suggests that marine preserves have been effective in enhancing the medium and large size classes of the red urchin populations. 2000 International Council for the Exploration of the Sea

Pelagic fishes and the cod recruitment dilemma in the Northwest Atlantic

Like most other stocks of Atlantic cod (Gadus morhua) in the Northwest Atlantic, cod in the southern Gulf of St. Lawrence declined to low abundance in the early 1990s. Recovery has been slow in contrast with the rapid recovery from similar levels of abundance in the mid-1970s. This difference reflects remarkably high prerecruit survival of cod in the earlier period of low abundance rather than unusually poor survival in the 1990s. The period of high prerecruit survival of cod coincided with the collapse of herring (Clupea harengus) and mackerel (Scomber scombrus) stocks resulting from overfishing. These pelagic fishes are potential predators or competitors of the early life history stages of cod. We report a strong negative relationship between the biomass of these pelagic fishes and recruitment rate of southern Gulf cod. This is consistent with the recent suggestion that the success of large predatory fishes may depend on "cultivation" effects in which the adults crop down forage fishes that are predators or competitors of their young. Our results also point to the possibility of a triangular food web involving cod, seals, and pelagic fishes, making it difficult to predict the effect of a proposed cull of seals on the recovery of cod.