Details:

Journal Title:
Molecular Ecology Resources
Personal Author:
Petrou, Eleni L. ; Drinan, Daniel P. ; Kopperl, Robert ; Lepofsky, Dana ; Yang, Dongya ; ... More +
Petrou, Eleni L. ; Drinan, Daniel P. ; Kopperl, Robert ; Lepofsky, Dana ; Yang, Dongya ; Moss, Madonna L. ; Hauser, Lorenz Less -
NOAA Program & Office:
OAR (Oceanic and Atmospheric Research)
Description:
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (a) the efficacy of bleach decontamination, (b) the effect of decontamination on RAD genotypes and (c) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and nonspawning (uncontaminated) herring. Samples were soaked for 10 min in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction site‐associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high‐quality sequences, reproducible genotypes and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high‐throughput sequencing data and can impact downstream analyses.
Keywords:
[+]
Biotechnology Ecology, Evolution, Behavior And Systematics Genetics
Source:
Molecular Ecology Resources, 19(5), 1131-1143
DOI:
https://doi.org/10.1111/1755-0998.12978
ISSN:
1755-098X;1755-0998;
Format:
PDF
Publisher:
Wiley
Document Type:
Journal Article
Funding:
Grant no. NA14OAR4170078
Rights Information:
Accepted Manuscript
Compliance:
Library
Main Document Checksum:
[+]
urn:sha256:e53aacba3e2dd5be55a98e9198c4ffc28c0126057ae39b29fe050e4530d0485c
Download URL:
https://repository.library.noaa.gov/view/noaa/57031/noaa_57031_DS1.pdf
File Type:

Supporting Files

• No Additional Files

More +