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Spurious genotypes in female nematodes resulting from contamination with male DNA
J D Anderson1, S Williams-Blangero, T J C Anderson
1Southwest Foundation for Biomedical Research, P.O. Box 760549, San Antonio, Texas 78245-0549, USA. janderson@darwin.sfbr.org
Abstract:
Females of many invertebrates contain stored sperm or fertilized eggs or both, causing potential genotyping errors. We investigated errors caused by male DNA contamination by amplifying 5 microsatellites in DNA isolated from various tissue types in the nematode Ascaris lumbricoides. We observed additional alleles in 30/135 uterus-derived samples when compared with muscle controls, resulting in 20/135 (15%) incorrect genotypes and an underestimation of inbreeding. In contrast, we observed additional alleles in only 5/143 ovary-derived samples, resulting in 4/143 (3%) incorrect genotypes and no significant influence on inbreeding estimates. Because uterus constitutes approximately 17% of a female's organ weight, a substantial proportion of samples isolated from female tissue may contain male-derived DNA. Male contamination is easily avoided when using large nematodes such as A. lumbricoides. However, we urge caution for studies using DNA isolated from small invertebrates that store sperm or fertilized eggs or both.
Insights
Male DNA contamination in female invertebrates can cause genotyping errors. Uterus samples from Ascaris lumbricoides showed higher contamination rates (15%) than ovary samples (3%), impacting genetic analyses.
Area of Science:
- Genetics
- Invertebrate Biology
- Molecular Ecology
Background:
- Female invertebrates often store sperm or fertilized eggs, posing risks for genetic studies.
- Male DNA contamination can lead to inaccurate genotyping and skewed population genetics analyses.
- Understanding contamination sources is crucial for reliable molecular data in invertebrates.
Purpose of the Study:
- To investigate the prevalence and impact of male DNA contamination in different tissue types of female Ascaris lumbricoides.
- To assess the potential for genotyping errors and altered inbreeding estimates due to male DNA contamination.
- To provide recommendations for minimizing DNA contamination in invertebrate genetic research.
Main Methods:
- DNA was isolated from various tissue types (uterus, ovary, muscle) of female Ascaris lumbricoides.
- Five microsatellite markers were amplified to detect the presence of additional alleles indicative of male DNA.
- Genotyping accuracy and inbreeding coefficients were compared between tissue types.
Main Results:
- Additional alleles, suggesting male DNA contamination, were observed in 15% of uterus-derived samples (30/135).
- This contamination led to 15% incorrect genotypes and an underestimation of inbreeding in uterus samples.
- Ovary-derived samples showed significantly lower contamination rates (3%, 4/143), with minimal impact on inbreeding estimates.
Conclusions:
- Uterus tissue in Ascaris lumbricoides is a significant source of male DNA contamination, potentially compromising genetic data.
- While contamination is manageable in large nematodes, researchers using smaller invertebrates should exercise caution.
- Careful sample selection and tissue type consideration are essential to avoid male DNA contamination in invertebrate genetic studies.
