Sample size requirements for genetic studies on yellowfin tuna

In population genetics, the amount of information for an analytical task is governed by the number of individuals sampled and the amount of genetic information measured on each of those individuals. In this work, we assessed the numbers of individual yellowfin tuna (Thunnus albacares) and genetic markers required for ocean-basin scale inferences. We assessed this for three distinct data analysis tasks that are often employed: testing for differences between genetic profiles; stock delineation, and; assignment of individuals to stocks. For all analytical tasks, we used real (not simulated) data from four sampling locations that span the tropical Pacific Ocean. Whilst spatially separated, the genetic differences between the sampling sites were not substantial, a maximum of approximately Fst = 0.02, which is quite typical of large pelagic fish. We repeatedly sub-sampled the data, mimicking a new survey, and performed the analyses. False positive rates were also assessed by re-sampling and randomly assigning fish to groups. Varying the sample sizes indicated that some analytical tasks, namely profile testing, required relatively few individuals per sampling location (n ≳ 10) and single nucleotide polymorphisms (SNPs, m ≳ 256). Stock delineation required more individuals per sampling location (n ≳ 25). Assignment of fish to sampling locations required substantially more individuals, more in fact than we had available (n > 50), although this sample size could be reduced to n ≳ 30 when individual fish were assumed to belong to one of the groups sampled. With these results, designers of molecular ecological surveys for yellowfin tuna, and users of information from them, can assess whether the information content is adequate for the required inferential task.

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An Effective Sample Size for Predicting Plant Disease Incidence in a Spatial Hierarchy

Phytopathology ◽

10.1094/phyto.1999.89.9.770 ◽

1999 ◽

Vol 89 (9) ◽

pp. 770-781 ◽

Cited By ~ 42

Author(s):

L. V. Madden ◽

G. Hughes

Keyword(s):

Sample Size ◽

Binomial Distribution ◽

Disease Incidence ◽

Simulated Data ◽

Heterogeneous Data ◽

Sampling Unit ◽

Effective Sample Size ◽

Incidence Data ◽

Eutypa Dieback ◽

Number Of Individuals

For aggregated or heterogeneous disease incidence, one can predict the proportion of sampling units diseased at a higher scale (e.g., plants) based on the proportion of diseased individuals and heterogeneity of diseased individuals at a lower scale (e.g., leaves) using a function derived from the beta-binomial distribution. Here, a simple approximation for the beta-binomial-based function is derived. This approximation has a functional form based on the binomial distribution, but with the number of individuals per sampling unit (n) replaced by a parameter (v) that has similar interpretation as, but is not the same as, the effective sample size (ndeff ) often used in survey sampling. The value of v is inversely related to the degree of heterogeneity of disease and generally is intermediate between ndeff and n in magnitude. The choice of v was determined iteratively by finding a parameter value that allowed the zero term (probability that a sampling unit is disease free) of the binomial distribution to equal the zero term of the beta-binomial. The approximation function was successfully tested on observations of Eutypa dieback of grapes collected over several years and with simulated data. Unlike the beta-binomial-based function, the approximation can be rearranged to predict incidence at the lower scale from observed incidence data at the higher scale, making group sampling for heterogeneous data a more practical proposition.

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A Study Design For The Assessment Of Fish Tumour Prevalence In The Lower St. Clair River

10.32920/ryerson.14653107.v1 ◽

2021 ◽

Author(s):

Liliya Baranova

Keyword(s):

Sample Size ◽

Statistical Methods ◽

Study Design ◽

Histopathological Examination ◽

Sentinel Species ◽

Sampling Location ◽

Special Focus ◽

Anecdotal Evidence ◽

Sampling Locations ◽

Area Of Concern

A conclusive fish tumour prevalence assessment has never been conducted in the lower part of the St. Clair River Area of Concern, despite possible re-contamination of the river and anecdotal evidence of fish abnormalities. This paper provides a study design for a comprehensive fish tumour prevalence assessment of the Lower St. Clair River with special focus on Walpole Island First Nation and surrounding waters. Study details such as area of focus, sentinel species, suggested sampling locations, sample size, field protocols and statistical methods are identified. A brief guide for histopathological examination and interpretation is provided. An alternate method of sampling location siting is suggested. This study design is intended to provide a guide and background reference for the implementation of a future full scale fish tumour assessment in the Lower St. Clair River.

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A Study Design For The Assessment Of Fish Tumour Prevalence In The Lower St. Clair River

10.32920/ryerson.14653107 ◽

2021 ◽

Author(s):

Liliya Baranova

Keyword(s):

Sample Size ◽

Statistical Methods ◽

Study Design ◽

Histopathological Examination ◽

Sentinel Species ◽

Sampling Location ◽

Special Focus ◽

Anecdotal Evidence ◽

Sampling Locations ◽

Area Of Concern

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Spatial covariation in survival rates of Northeast Pacific pink salmon (Oncorhynchus gorbuscha)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f01-096 ◽

2001 ◽

Vol 58 (8) ◽

pp. 1501-1515 ◽

Cited By ~ 54

Author(s):

Brian J Pyper ◽

Franz J Mueter ◽

Randall M Peterman ◽

David J Blackbourn ◽

Chris C Wood

Keyword(s):

Spatial Scales ◽

Pink Salmon ◽

Survival Rates ◽

Ocean Basin ◽

Oncorhynchus Gorbuscha ◽

Pink Salmon Oncorhynchus Gorbuscha ◽

Geographical Regions ◽

Basin Scale ◽

Stock Recruitment ◽

Best Fit

We examined spatial patterns of covariation in indices of survival rate (residuals from the best-fit stock- recruitment curve) across four decades among 43 wild pink salmon (Oncorhynchus gorbuscha) stocks from 14 geographical regions in Washington, British Columbia, and Alaska. We found strong evidence of positive covariation among stocks within each region and between certain adjacent regions (e.g., correlations from 0.3 to 0.7) but no evidence of covariation between stocks of distant regions (e.g., separated by 1000 km or more). This suggests that important environmental processes affecting temporal variation in survival rates of pink salmon from spawners to recruits operate at regional spatial scales rather than at the larger ocean basin scale. Based on limited fry abundance data, we found that this covariation in spawner-to-recruit survival rates may be strongly influenced by marine processes.

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Can We Compare Effect Size of Spatial Genetic Structure Between Studies and Species Using Moran Eigenvector Maps?

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.612718 ◽

2021 ◽

Vol 9 ◽

Author(s):

Celia Hein ◽

Hossam E. Abdel Moniem ◽

Helene H. Wagner

Keyword(s):

Genetic Structure ◽

Effect Size ◽

Stationary Process ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Meta Analysis ◽

Empirical Studies ◽

Sampling Locations ◽

Number Of Individuals ◽

Moran Eigenvector Maps

As the field of landscape genetics is progressing toward comparative empirical studies and meta-analysis, it is important to know how best to compare the strength of spatial genetic structure between studies and species. Moran’s Eigenvector Maps are a promising method that does not make an assumption of isolation-by-distance in a homogeneous environment but can discern cryptic structure that may result from multiple processes operating in heterogeneous landscapes. MEMgene uses spatial filters from Moran’s Eigenvector Maps as predictor variables to explain variation in a genetic distance matrix, and it returns adjusted R2 as a measure of the amount of genetic variation that is spatially structured. However, it is unclear whether, and under which conditions, this value can be used to compare the degree of spatial genetic structure (effect size) between studies. This study addresses the fundamental question of comparability at two levels: between independent studies (meta-analysis mode) and between species sampled at the same locations (comparative mode). We used published datasets containing 9,900 haploid, biallelic, neutral loci simulated on a quasi-continuous, square landscape under four demographic scenarios (island model, isolation-by-distance, expansion from one or two refugia). We varied the genetic resolution (number of individuals and loci) and the number of random sampling locations. We considered two measures of effect size, the MEMgene adjusted R2 and multivariate Moran’s I, which is related to Moran’s Eigenvector Maps. Both metrics were highly sensitive to the number of locations, even when using standardized effect sizes, SES, and the number of individuals sampled per location, but not to the number of loci. In comparative mode, using the same Moran Eigenvector Maps for all species, even those with missing values at some sampling locations, reduced bias due to the number of locations under isolation-by-distance (stationary process) but increased it under expansion from one or two refugia (non-stationary process). More robust measures of effect size need to be developed before the strength of spatial genetic structure can be accurately compared, either in a meta-analysis of independent empirical studies or within a comparative, multispecies landscape genetic study.

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STRUKTUR POPULASI DAN KANDUNGAN LOGAM BERAT PADA GASTROPODA (Telescopium telescopium) DI KAWASAN MANGROVE TAMAN NASIONAL RAWA AOPA WATUMOHAI

BioWallacea : Jurnal Penelitian Biologi (Journal of Biological Research) ◽

10.33772/biowallacea.v5i2.5879 ◽

2019 ◽

Vol 5 (2) ◽

Author(s):

Gusni Sri Ningsih ◽

Analuddin Kangkuso ◽

Nasaruddin Nasaruddin

Keyword(s):

Heavy Metals ◽

Population Structure ◽

Atomic Absorption ◽

Size Distribution ◽

Absorption Spectroscopy ◽

Atomic Absorption Spectroscopy ◽

Sea Water ◽

Quality Standard ◽

Sampling Location ◽

Number Of Individuals

ABSTRAKPenelitian ini bertujuan untuk mengetahui struktur populasi dan kandungan logam berat gastropoda (Telescopium telescopium) di Taman Nasional Rawa Aopa Watumohai. Penelitian ini dilaksanakan pada bulan Januari sampai Maret 2018. Lokasi pengambilan sampel penelitian terletak pada mangrove yang tumbuh di Sungai Lanowulu dan Roraya di TNRAW. Penelitian ini menggunakan metode purposive sampel. Penelitian ini menggunakan plot kuadrat ukuran 1 m2 diletakkan di setiap stasiun. Jumlah individu dari T. telescopium dihitung berat dan panjangnya. Selain itu, kandungan logam berat Timbal (Pb) dan Cadmium (Cd) di dalam daging T. telescopium dihitung menggunakan Atomic Absorption Spectroscopy (AAS) di Laboratorium Fakultas Perikanan dan Ilmu Kelautan Universitas Halu Oleo. Struktur populasi T. telescopium ditentukan dengan analisis histogram, distribusi ukurannya ditentukan dengan analisis koefisien variasi (CV). Hasil penelitian menunjukkan struktur populasi gastropoda membentuk kurva normal dengan ukuran kecil. Kandungan logam Pb dan Cd di dalam sedimen dan air laut dari Sungai Roraya lebih tinggi secara signifikan dibandingkan dengan Sungai Lanowulu, disisi lain, kandungan logam berat Pb dan Cd dalam daging T. telescopium tidak berbeda signifikan. Dengan demikian, kandungan logam berat Pb dan Cd pada air laut, sedimen dan daging T. telescopium di sungai Lanowulu dan sungai Roraya berada di atas baku mutu sesuai dengan Kepmen LH. No. 51. 2004. Kata kunci: Gastropoda, Mangrove, Logam Berat, TNRAW. ABSTRACTThis study aims todetermine the population structure and heavy metals contents of gastropods (Telescopiumtelescopium) living in RawaAopaWatumohai National RAWN Park. This research was conducted from January until March 2018. The sampling location of research was in mangroves grown along the Lanowulu and Roraya rives at RAWN Park. This research uses purposive sampling method. This study used the plot quadrate of 1 m2 widethat placed in each station. The number of individuals of.T. telecopium was counted, while their fresh weight and length of T.telescopiumwere measured. In addition, the content of heavy metals of Lead (Pb) and Cadmium (Cd) into meat of T. telescopium were measured by using Atomic Absorption spectroscopy (AAS) in Laboratory at Faculty of Fisheries andMarine Science at Halu Oleo University. The population structure of T. telescopium was determined by histrogram analysis, its size distribution was determined by coefficient of variation (CV) analysis. The results showed that population structure of gastropods was normal curve with small ranges of size distribution. The content of Pb and Cd into sediment and sea water of Rorayariver were significantly higher as compared than that in Lanowulu river. On the other hand, the content of heavy metals Pb and Cd into meat of T. telescopium was not significantly different. However, the heavy metals contents of Pb and Cd into sea water, sediment and meat of T. telescopiumboth in Lanowuluand Roraya riverswere above the quality standard according to Ministry of Environment No. 51/LH/2004. Keywords : Gastropods, mangroves, Lanowulu and Roraya rivers, heavy metals, Rawa Aopa Watumohai National Park

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Presence of CAT genetic markers as an indicator of accelerated rate of liver fibrosis progression in patients with chronic hepatitis

Experimental and Clinical Gastroenterology ◽

10.31146/1682-8658-ecg-189-5-39-43 ◽

2021 ◽

Vol 1 (5) ◽

pp. 39-43

Author(s):

I. A. Bulatova ◽

T. P. Shevlyukova ◽

A. P. Shchekotova ◽

A. V. Krivtsov

Keyword(s):

Chronic Hepatitis ◽

Liver Fibrosis ◽

Genetic Markers ◽

Rapid Progression ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Risk Alleles ◽

Slow Progression ◽

Polymerase Chain ◽

Number Of Individuals

Goal. To evaluate the genetic profi le of patients with chronic hepatitis C (CHC) by the CAT gene polymorphism in the region-262G/A (rs1001179), GPX4 in the region-718C/T (rs713041), IL28B in the region C/T (rs12979860) and VEGFA in the region- 634G/C (rs2010963) to analyze the association of the rate of progression of liver fi brosis with polymorphic genetic markers.Materials and methods. We examined 36 patients with CHC with a rapidly progressive rate of fi brosis (up to 10 years) and 56 patients with a slowly progressive course of the disease (more than 10 years). The study of single- nucleotide polymorphisms of genes was carried out by the method of polymerase chain reaction.Results. In the group with rapid progression of liver fi brosis, individuals with multiple risk alleles for the studied polymorphisms were more common, which confi rms the association of the risk of liver fi brosis progression with the genetic markers CAT in the region-262G/A (rs1001179) and GPX4 in the region-718C/T (rs713041) with their combined carrier. Among patients with rapid progression of fi brosis, a greater number of individuals had simultaneously 4–6 risk alleles in 27.5%, while patients with slow progression of the process only in 11% of cases.Conclusion. This set of genetic markers can be used as genetic testing of patients with liver fibrosis to determine the prognosis of the disease.

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