Dataset Information

Modernising fish and shark growth curves with Bayesian length-at-age models.

ABSTRACT: Growth modelling is a fundamental component of fisheries assessments but is often hindered by poor quality data from biased sampling. Several methods have attempted to account for sample bias in growth analyses. However, in many cases this bias is not overcome, especially when large individuals are under-sampled. In growth models, two key parameters have a direct biological interpretation: L0, which should correspond to length-at-birth and L?, which should approximate the average length of full-grown individuals. Here, we present an approach of fitting Bayesian growth models using Markov Chain Monte Carlo (MCMC), with informative priors on these parameters to improve the biological plausibility of growth estimates. A generalised framework is provided in an R package 'BayesGrowth', which removes the hurdle of programming an MCMC model for new users. Four case studies representing different sampling scenarios as well as three simulations with different selectivity functions were used to compare this Bayesian framework to standard frequentist growth models. The Bayesian models either outperformed or matched the results of frequentist growth models in all examples, demonstrating the broad benefits offered by this approach. This study highlights the impact that Bayesian models could provide in age and growth studies if applied more routinely rather than being limited to only complex or sophisticated applications.

SUBMITTER: Smart JJ

PROVIDER: S-EPMC7870076 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Modernising fish and shark growth curves with Bayesian length-at-age models.

Smart Jonathan J JJ Grammer Gretchen L GL

PloS one 20210208 2

Growth modelling is a fundamental component of fisheries assessments but is often hindered by poor quality data from biased sampling. Several methods have attempted to account for sample bias in growth analyses. However, in many cases this bias is not overcome, especially when large individuals are under-sampled. In growth models, two key parameters have a direct biological interpretation: L0, which should correspond to length-at-birth and L∞, which should approximate the average length of full- ...[more]

PMID: 33556124

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Project description:Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (?910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the 'oligo-capping' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ?6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5'-ESTs and 41,317 3'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole genome sequencing.

Dataset Information

Modernising fish and shark growth curves with Bayesian length-at-age models.

Publications

Modernising fish and shark growth curves with Bayesian length-at-age models.

Similar Datasets

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