Comparison and optimization for DNA extraction of archived fish specimens

Silva, Priscilla Caroline; Malabarba, Maria Claudia; Vari, Richard P.; Malabarba, Luiz Roberto

doi:10.1016/j.mex.2019.06.001

Cited by 8 publications

(6 citation statements)

References 17 publications

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“…Almost since the inception of isolating hDNA from museum specimens, researchers have experimented with alternative approaches and specimen types for acquiring DNA [16,[83][84][85][86]. This practice has continued through contemporary research that includes evaluating different types and parts of the specimen, testing commercial kits, and modifying 'home-brew' approaches [87][88][89]. One of the general findings is that DNA concentration varies among parts of the specimen and preservation techniques [59,87,89,90], tissue types [54], and sources of genomic DNA [47].…”

Section: Unresolved Challengesmentioning

confidence: 99%

Mining museums for historical DNA: advances and challenges in museomics

Raxworthy

Smith

2021

Trends in Ecology & Evolution

150

102

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Section: Unresolved Challengesmentioning

confidence: 99%

Mining museums for historical DNA: advances and challenges in museomics

Raxworthy

Smith

2021

Trends in Ecology & Evolution

150

102

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“…The future improvement in reference databases requires collaborating with aquariums and museums to sequence some fish species like deep‐sea fishes or rare species which are difficult to capture in the wild. Extraction of ancient DNA from museum samples is challenging but the advances in this field are promising (Silva et al, 2019 ) and initiatives such the one of Margaryan et al ( 2020 ) for vertebrates in Denmark open new perspectives for the development of genetic databases. Currently, few studies (Gaither et al, 2018 ; Tenggardjaja et al, 2014 ) have focused on the vertical connectivity of fish species and their potential ecotypes across depth which is a key information in conservation.…”

Section: Discussionmentioning

confidence: 99%

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

Duhamet

Albouy

Marques

et al. 2023

Ecology and Evolution

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“…rate of fragmentation, concentration and rate of contaminants, respectively) showing that it is highly dependent on the tissue processed, the storage conditions and the species [e.g. (Silva et al, 2019;Martincováand Aghova, 2020;Lutz et al, 2023)]. Martincovaá nd Aghová (2020), tested 12 different DNA extraction methods from eight manufacturers, including some the most widely used commercial silica membrane-based kits.…”

Section: Isolation Of High Quality Dnamentioning

confidence: 99%

A review of genomics methods and bioinformatics tools for the analysis of close-kin mark-recapture

Casas

Saborido‐Rey

2023

Front. Mar. Sci.

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Stock assessments serve to monitor the condition of fish stocks and exploit them sustainably but require accurate data such as growth and mortality rates as input parameters. Most species fished worldwide lack the data needed to assess their status and even those closely assessed are often based on parameters that are known to contain uncertainty. This has resulted in an increased share of overfished stocks over the last half century, demanding urgently innovative methodologies that can provide novel means to reduce uncertainty of fish stocks assessments and expand the range of assessed species. CKMR has emerged recently attracting a great interest due to its potential to provide accurate demographic parameters of interest in stock assessments. The method is at the crossroads between fisheries science and genomics, requiring specialized knowledge that is usually outside of the experience of fisheries scientist and modellers, complicating the application of the method and its uptake in regular fisheries assessments. In this review, we provide useful information to perform the genomics and bioinformatics steps required to complete successfully a CKMR study. We discuss the most suitable genomics assays, considering the amount of information they provide, their easiness of use and cost of genotyping accurately the large number of individuals needed to assess most fish stocks. We provide an overview of methods of analysis and statistical methodologies that can be used to infer kinship with the accuracy required in a large population setting with sparse sampling, where most individuals are unrelated, determining a low probability of finding closely related individuals. We analyse potential sources of biases and errors and provide recommendations to facilitate the application of CKMR to a wider range of fish stocks.

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Comparison and optimization for DNA extraction of archived fish specimens

Abstract: Graphical abstract

Cited by 8 publications

References 17 publications

Mining museums for historical DNA: advances and challenges in museomics

Mining museums for historical DNA: advances and challenges in museomics

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

A review of genomics methods and bioinformatics tools for the analysis of close-kin mark-recapture

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