Fine-scale environmental effects on Cape hake survey catch rates in the northern Benguela, using data from a trawl-mounted instrument package

2017 ◽  
Vol 584 ◽  
pp. 185-198
Author(s):  
P Kainge ◽  
K Wieland
Keyword(s):  
Environmental Effects ◽  
Fine Scale ◽  
Catch Rates ◽  
Using Data ◽  
Instrument Package

Spatial distribution patterns, abundance and population structure of deep-sea crab Chaceon macphersoni, based on complementary analyses of trap and trawl data

2013 ◽  
Vol 64 (6) ◽  
pp. 507 ◽  
Author(s):  
Johan C. Groeneveld ◽  
Bernadine I. Everett ◽  
Sean T. Fennessy ◽  
Stephen P. Kirkman ◽  
Jorge Santos ◽  
...  
Keyword(s):  
Population Structure ◽  
Deep Sea ◽  
Distribution Patterns ◽  
Marine Species ◽  
Austral Spring ◽  
Mean Size ◽  
Spatio Temporal ◽  
Catch Rates ◽  
Using Data ◽  
Hard Substrata

Marine species such as deep-sea geryonid crabs often exhibit high spatio-temporal variability in abundance and size over depth, substratum type and season, therefore data collected from a single gear type may not represent the whole population. Complementary data from trawl (soft substratum) and trap (hard substratum) fisheries were analysed within a general linear modelling (GLM) framework to assess distribution, abundance and population structure of Chaceon macphersoni off eastern South Africa. Catch rates, mean size, maturation size and sex ratio were modelled relative to year, month, depth, latitude and gear effects. Trap and trawl analyses indicated higher abundance as depth increased up to 500 m, and during the austral spring and summer. The mean size of crabs remained constant at all depths sampled, and sex ratios were skewed towards females. Females were smaller than males, and achieved maturity at a smaller size. A standardised index based on trawl data (1988–2010) showed a long-term decline in abundance, with some recovery after 2002, whereas the trap index showed recent local depletions on hard substrata. Using data from two gear types confirmed broad gradients in abundance, but also emphasised subtle trends, such as local depletions on hard substrata, that would not have been apparent from trawl data only.

Trawl operations in the South East Fishery, Australia: spatial distribution and intensity

2001 ◽  
Vol 52 (4) ◽  
pp. 419 ◽  
Author(s):  
James W. P. Larcombe ◽  
Kevin J. McLoughlin ◽  
Richard D. J. Tilzey
Keyword(s):  
Interannual Variation ◽  
Fine Scale ◽  
Scale Analysis ◽  
Coarse Scale ◽  
Depth Stratum ◽  
North East ◽  
Management Area ◽  
Catch Rates ◽  
High Effort ◽  
Total Effort

Trawl areas and intensities were mapped at coarse (22 km 1986–99)and fine (1 km 1995–99)scales, and statistics reported by area and depth stratum. Total effort in hours was relatively stable to 1992, then increased substantially to 1999. The total distance trawled from fine-scale analysis showed a similar trend for the 1995–99 period. Coarse-scale analysis from 1986–99 indicated effort increases in north-east Bass Strait in particular, and also off western Tasmania and west of Bass Strait. There was little change in the total area of the fishery from 1995 to 1999, but grid cells on the periphery showed considerable interannual variation in the presence or absence of fishing. Increased or redistributed effort tended to further concentrate in the relatively small high-effort areas, rather than increasing equally across the grounds, or spreading to new grounds. In the total management area, a small proportion of the 1 km grids was fished. However, in 200–1000 m depth strata, ≥50%of the grids were fished with some intensity. The consequences and compromises of spatial scale are discussed in terms of data quality, the use of trawl effort as a surrogate for marine disturbance, and the interpretation of catch rates.

Role of large- and fine-scale variables in predicting catch rates of larval Pacific lamprey in the Willamette Basin, Oregon

2014 ◽  
Vol 25 (2) ◽  
pp. 261-271 ◽  
Author(s):  
Luke D. Schultz ◽  
Mariah P. Mayfield ◽  
Gabe T. Sheoships ◽  
Lance A. Wyss ◽  
Benjamin J. Clemens ◽  
...  
Keyword(s):  
Fine Scale ◽  
Pacific Lamprey ◽  
Willamette Basin ◽  
Catch Rates

Incidental Catch of Cetaceans with Salmon Gillnet

1975 ◽  
Vol 32 (7) ◽  
pp. 1229-1235 ◽  
Author(s):  
Seiji Ohsumi
Keyword(s):  
United States ◽  
The United States ◽  
Negligible Effect ◽  
Catch Rate ◽  
Incidental Catch ◽  
Phocoenoides Dalli ◽  
Catch Rates ◽  
Using Data

Using data on number of cetaceans caught per 1000 "tans" (= approximately 50 m) of salmon drift gillnet, incidental catch rates by salmon research vessels of the Japanese Fisheries Agency averaged 0.476. The maximum was 1.42. The average ranged between 0.37 and 0.65 from 1962 to 1971, indicating negligible effect on porpoise populations. These figures are much lower than the average incidental catch rate (6.66) in the United States salmon drift net research. The main catch is Phocoenoides dalli.

scholarly journals Revealing multi-scale population structure in large cohorts

2018 ◽  
Author(s):  
Alex Diaz-Papkovich ◽  
Luke Anderson-Trocmé ◽  
Simon Gravel
Keyword(s):  
Population Structure ◽  
Large Scale ◽  
Large Population ◽  
Computational Cost ◽  
General Purpose ◽  
Exploratory Analysis ◽  
Fine Scale ◽  
Using Data ◽  
The Uk ◽  
Unbalanced Sampling

AbstractGenetic structure in large cohorts results from technical, sampling and demographic variation. Visualisation is therefore a first step in most genomic analyses. However, existing data exploration methods struggle with unbalanced sampling and the many scales of population structure. We investigate an approach to dimension reduction of genomic data that combines principal components analysis (PCA) with uniform manifold approximation and projection (UMAP) to succinctly illustrate population structure in large cohorts and capture their relationships on local and global scales. Using data from large-scale genomic datasets, we demonstrate that PCA-UMAP effectively clusters closely related individuals while placing them in a global continuum of genetic variation. This approach reveals previously overlooked subpopulations within the American Hispanic population and fine-scale relationships between geography, genotypes, and phenotypes in the UK population. This opens new lines of investigation for demographic research and statistical genetics. Given its small computational cost, PCA-UMAP also provides a general-purpose approach to exploratory analysis in population-scale datasets.Author summaryBecause of geographic isolation, individuals tend to be more genetically related to people living nearby than to people living far. This is an example of population structure, a situation where a large population contains subgroups that share more than the average amount of DNA. This structure can tell us about human history, and it can also have a large effect on medical studies. We use a newly developed method (UMAP) to visualize population structure from three genomic datasets. Using genotype data alone, we reveal numerous subgroups related to ancestry and correlated with traits such as white blood cell count, height, and FEV1, a measure used to detect airway obstruction. We demonstrate that UMAP reveals previously unobserved patterns and fine-scale structure. We show that visualizations work especially well in large datasets containing populations with diverse backgrounds, which are rapidly becoming more common, and that unlike other visualization methods, we can preserve intuitive connections between populations that reflect their shared ancestries. The combination of these results and the effectiveness of the strategy on large and diverse datasets make this an important approach for exploratory analysis for geneticists studying ancestral events and phenotype distributions.

scholarly journals Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species

2018 ◽  
Vol 27 (3) ◽  
pp. 647-658 ◽  
Author(s):  
Elena Mosca ◽  
Erica A. Di Pierro ◽  
Katharina B. Budde ◽  
David B. Neale ◽  
Santiago C. González-Martínez
Keyword(s):  
Genetic Structure ◽  
Environmental Effects ◽  
Tree Species ◽  
Spatial Genetic Structure ◽  
Forest Tree ◽  
Fine Scale ◽  
Forest Tree Species

Estimation of genetic parameters for lambing ease, birthweight and gestation length in Australian sheep

2016 ◽  
Vol 56 (5) ◽  
pp. 934 ◽  
Author(s):  
L. Li ◽  
D. J. Brown
Keyword(s):  
Animal Models ◽  
Environmental Effects ◽  
Genetic Parameters ◽  
Genetic Correlations ◽  
Gestation Length ◽  
Phenotypic Variance ◽  
Full Dataset ◽  
Australian Sheep ◽  
Using Data ◽  
Estimation Of Genetic Parameters

This study presents estimates of genetic parameters for lambing ease (LE), birthweight (BW) and gestation length (GL) in Australian terminal sire sheep breeds using data from the Sheep Genetics LAMBPLAN database. LE was scored on lambs on a 1–5 scale, with 1 being no assistance and 5 being other such as special veterinary assistance. The full dataset consisted of 43 448 records on LE and its two subsets (the single and twin subsets) based on the birth type of the litter were analysed. Four models with different combinations of random effects consisting of direct genetic, maternal genetic and maternal permanent environmental effects were compared. All traits were analysed using linear animal models and linear sire models with LE further analysed by threshold sire models for all datasets to evaluate the influence of datasets and models on the estimation of genetic parameters. The results showed that multiple-born lambs had shorter GL, less BW and less lambing difficulty than single-born lambs. Lambing difficulty decreased with the increase of dam age from 1.5 to 4.5 years, and then increased afterwards. Genetic parameters using linear animal models were similar to those using linear sire models for all traits. Phenotypic variance and direct heritability were higher for single-born lambs compared with twin-born lambs. No significant maternal permanent environmental effect was detected for LE. Based on results using linear animal models with the full dataset, the direct heritabilities were 0.06 ± 0.01, 0.15 ± 0.01 and 0.52 ± 0.02, the maternal heritabilities were 0.03 ± 0.01, 0.15 ± 0.01 and 0.13 ± 0.02 for LE, BW and GL, respectively. The proportions of maternal permanent environmental effects to the total variances were 0.13 ± 0.01 for BW. Low to moderate direct genetic correlations of 0.31 ± 0.09 (LE and BW), 0.24 ± 0.11 (LE and GL) and 0.08 ± 0.08 (BW and GL) were estimated using tri-variate analysis from the full dataset, indicating the trend that lambs with greater BW and longer GL would result in more lambing difficulty.

A Bayesian hierarchical formulation of the De Lury stock assessment model for abundance estimation of Falkland Islands' squid (Loligo gahi)

2004 ◽  
Vol 61 (6) ◽  
pp. 1048-1059 ◽  
Author(s):  
Murdoch K McAllister ◽  
Simeon L Hill ◽  
David J Agnew ◽  
Geoffrey P Kirkwood ◽  
John R Beddington
Keyword(s):  
Sampling Error ◽  
Stock Assessment ◽  
Assessment Model ◽  
Abundance Estimation ◽  
Falkland Islands ◽  
Parameter Estimates ◽  
Bayesian Hierarchical ◽  
Stock Assessments ◽  
Catch Rates ◽  
Using Data

In stock assessments of short-lived species, De Lury depletion models are commonly applied in which commercial catches and changing catch rates are used to estimate resource abundance. These methods are applied within fishing seasons to decide when to close the fishery and can be reliable if the data show a distinct decline in response to the catch removals. However, this is not always the case, particularly when sampling error variation masks trends in abundance. This paper presents a Bayesian hierarchical formulation of the De Lury model in which data from previous years are combined hierarchically in the same stock assessment model to improve parameter estimation for future stock assessments. The improved precision in parameter estimates is demonstrated using data for the Falkland Islands' Loligo gahi squid fishery.

Sign in / Sign up

Export Citation Format

Share Document