On the pile-up effect and priors for Linf and M/K: Response to a Comment by Hordyk et al. on “A new approach for estimating stock status from length frequency data”

There is a recognized need for new methods with modest data requirements to provide preliminary estimates of stock status for data-limited stocks (e.g. Rudd and Thorson, 2018). Froese et al. (2018) provide such a method, which derives estimates of relative stock size from length frequency (LF) data of exploited stocks. They show that their length-based Bayesian biomass estimation method (LBB) can reproduce the “true” parameters used in simulated data and can approximate the relative stock size as estimated independently by more data-demanding methods in 34 real stocks. However, in a comment on LBB, Hordyk et al. (2019) claim (i) that the master equation of LBB is incomplete because it does not correct for the pile-up effect caused by aggregating length measurements into length classes or “bins”, (ii) that LBB is highly sensitive to equilibrium assumptions and wrongly uses maximum observed length (Lmax) for guidance in setting a prior for the estimation of asymptotic length (Linf), and (iii) that the default prior used by LBB for the ratio between natural mortality and somatic growth rate (M/K) of 1.5 (SD = 0.15) is inadequate for many exploited species. These comments are addressed belo

A new approach for estimating stock status from length frequency data

This study presents a new method (LBB) for the analysis of length frequency data from commercial catches. LBB works for species that grow throughout their lives, such as most commercially-important fish and invertebrates, and requires no input in addition to length frequency data. It estimates asymptotic length, length at first capture, relative natural mortality, and relative fishing mortality. Standard fisheries equations can then be used to approximate current exploited biomass relative to unexploited biomass. In addition, these parameters allow the estimation of length at first capture that would maximize catch and biomass for a given fishing effort, and estimation of a proxy for the relative biomass capable of producing maximum sustainable yields. Relative biomass estimates of LBB were not significantly different from the “true” values in simulated data and were similar to independent estimates from full stock assessments. LBB also presents a new indicator for assessing whether an observed size structure is indicative of a healthy stock. LBB results will obviously be misleading if the length frequency data do not represent the size composition of the exploited size range of the stock or if length frequencies resulting from the interplay of growth and mortality are masked by strong recruitment pulses

Decreased PM10 exposure attenuates age-related lung function decline: genetic variants in p53, p21, and CCND1 modify this effect.

BACKGROUND: Decreasing exposure to airborne particulates was previously associated with reduced age-related decline in lung function. However, whether the benefit from improved air quality depends on genetic background is not known. Recent evidence points to the involvement of the genes p53 and p21 and of the cell cycle control gene cyclin D1 (CCND1) in the response of bronchial cells to air pollution. OBJECTIVE: We determined in 4,326 participants of the Swiss Cohort Study on Air Pollution and Lung and Heart Diseases in Adults (SAPALDIA) whether four single-nucleotide polymorphisms in three genes [CCND1 (rs9344 [P242P], rs667515), p53 (rs1042522 [R72P]), and p21 (rs1801270 [S31R])] modified the previously observed attenuation of the decline in the forced expiratory flow between 25% and 75% of the forced vital capacity (FEF(25-75)) associated with improved air quality. METHODS: Subjects of the prospective population-based SAPALDIA cohort were assessed in 1991 and 2002 by spirometry, questionnaires, and biological sample collection for genotyping. We assigned spatially resolved concentrations of particulate matter with aerodynamic diameter < or = 10 microm (PM(10)) to each participant's residential history 12 months before the baseline and follow-up assessments. RESULTS: The effect of diminishing PM(10) exposure on FEF(25-75) decline appeared to be modified by p53 R72P, CCND1 P242P, and CCND1 rs667515. For example, a 10-microg/m(3) decline in average PM(10) exposure over an 11-year period attenuated the average annual decline in FEF(25-75) by 21.33 mL/year (95% confidence interval, 10.57-32.08) among participants homozygous for the CCND1 (P242P) GG genotype, by 13.72 mL/year (5.38-22.06) among GA genotypes, and by 6.00 mL/year (-4.54 to 16.54) among AA genotypes. CONCLUSIONS: Our results suggest that cell cycle control genes may modify the degree to which improved air quality may benefit respiratory function in adults

Conserving European biodiversity across realms

Terrestrial, freshwater, and marine ecosystems are connected via multiple biophysical and ecological processes. Identifying and quantifying links among ecosystems is necessary for the uptake of integrated conservation actions across realms. Such actions are particularly important for species using habitats in more than one realm during their daily or life cycle. We reviewed information on the habitats of 2,408 species of European conservation concern and found that 30% of the species use habitats in multiple realms. Transportation and service corridors, which fragment species habitats, were identified as the most important threat impacting ∼70% of the species. We examined information on 1,567 European Union (EU) conservation projects funded over the past 25 years, to assess the adequacy of efforts toward the conservation of “multi‐realm” species at a continental scale. We discovered that less than a third of multi‐realm species benefited from projects that included conservation actions across multiple realms. To achieve the EU's conservation target of halting biodiversity loss by 2020 and effectively protect multi‐realm species, integrated conservation efforts across realms should be reinforced by: (1) recognizing the need for integrated management at a policy level, (2) revising conservation funding priorities across realms, and (3) implementing integrated land‐freshwater‐sea conservation planning and management

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

1000 Genomes-based metaanalysis identifies 10 novel loci for kidney function

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-Analysis of kidney function based on the estimated glomerular filtration rate (EGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10-8 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, wh

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways

Groundfish survey data from the German Bight from 1902-08, 1919-23, and 1930-1932 and ICES International Bottom Trawl Survey (IBTS) quarter 3 data from 1991 to 2009

Groundfish survey data from the German Bight from 1902-08, 1919-23, and 1930-1932 and ICES International Bottom Trawl Survey (IBTS) quarter 3 data from 1991 to 2009 were analysed with respect to species frequencies, maximum length, trends in catch-per-unit-effort, species richness parameters (SNR) and presence of large fish (Phi40), the latter defined as average presence of species per haul with specimens larger than 40 cm given. Four different periods are distinguished: (a) before 1914 with medium commercial CPUE and low landings, Phi40 approx. 2, high abundance in elasmobranchs and SNR conditions indicating highly diverse assemblages, (b) conditions immediately after 1918 with higher commercial CPUE, recovering landings, Phi40 at > 4 in 1919, and SNR conditions indicating highly diverse assemblages, (c) conditions from 1920 to the early 1930's with decreasing commercial CPUE, increased landings, decreasing Phi40, SNR conditions similar to later years indicating less diverse assemblages, and a decrease in elasmobranchs. In the IBTS series (d), Phi40 remains low indicating an increased rarity of large specimens, and SNR characteristics are similar to the third period. Dab, whiting and grey gurnard have increased considerably in the IBTS series as compared to the historic data. Phi40 is suggested an alternative indicator reflecting community functional diversity when weight based indicators cannot be applied

The association of a variant in the cell cycle control gene CCND1 and obesity on the development of asthma in the Swiss SAPALDIA study

OBJECTIVE: The molecular mechanisms underlying the association between obesity (BMI ≥ 30 kg/m(2)) and asthma are poorly understood. Since shifts in the fate of bronchial cells due to low-grade systemic inflammation may provide a possible explanation, we investigated whether two of the best documented functional variants in cell cycle control genes modify the obesity-asthma association. METHODS: We genotyped 5930 SAPALDIA cohort participants for the single-nucleotide polymorphisms (SNPs) rs9344 in the cyclin D1 gene (CCND1) and rs1042522 in the gene encoding tumor protein 53 (TP53). We assessed the independent association of these SNPs and obesity with asthma prevalence and incidence. RESULTS: The CCND1 SNP modified the association between obesity and asthma prevalence (p(interaction )= 0.03). The odds ratios (ORs) and 95% confidence intervals (CIs) for reporting a physician diagnosis of asthma at baseline, comparing obese with non-obese participants, were 1.09 (0.51-2.33), 1.64 (0.94-2.88), and 3.51 (1.63-7.53) for GG, GA, and AA genotypes, respectively. We found comparable genotype differences for incident asthma within the 11 years of follow-up. As for the TP53 SNP, the interactions with obesity status with respect to asthma were not statistically significant. CONCLUSIONS: Our results suggest that obesity may contribute to asthma and associated tissue remodeling by modifying the processes related to the CCND1 gene activity