Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity

Vikram Kapoor; Michael Elk; Carlos Toledo-Hernandez; Jorge W. Santo Domingo; Vikram Kapoor; Michael Elk; Carlos Toledo-Hernandez; Jorge W. Santo Domingo

doi:10.3934/environsci.2017.3.443

AIMS Environmental Science

2017, Volume 4, Issue 3: 443-455. doi: 10.3934/environsci.2017.3.443

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Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity

1.
Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
2.
U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
3.
Pegasus Technical Services, Inc., Cincinnati, OH 45268, USA
4.
Department of Biology, University of Puerto Rico, Rio Piedras, PR 00930, USA

Received: 31 January 2017 Accepted: 08 May 2017 Published: 11 May 2017

Mitochondrial signature sequences have frequently been used to study human population diversity around the world. Traditionally, this requires obtaining samples directly from individuals which is cumbersome, time consuming and limited to the number of individuals that participated in these types of surveys. Here, we used environmental DNA extracts to determine the presence and sequence variability of human mitochondrial sequences as a means to study the diversity of populations inhabiting in areas nearby a tropical watershed impacted with human fecal pollution. We used high-throughput sequencing (Illumina) and barcoding to obtain thousands of sequences from the mitochondrial hypervariable region 2 (HVR2) and determined the different haplotypes present in 10 different water samples. Sequence analyses indicated a total of 19 distinct variants with frequency greater than 5%. The HVR2 sequences were associated with haplogroups of West Eurasian (57.6%), Sub-Saharan African (23.9%), and American Indian (11%) ancestry. This was in relative accordance with population census data from the watershed sites. The results from this study demonstrates the potential value of mitochondrial sequence data retrieved from fecally impacted environmental waters to study the population diversity of local municipalities. This environmental DNA approach may also have other public health implications such as tracking background levels of human mitochondrial genes associated with diseases. It may be possible to expand this approach to other animal species inhabiting or using natural water systems.
- Human mitochondrial DNA,
- fecal pollution,
- environmental waters,
- high-throughput sequencing,
- population diversity
Citation: Vikram Kapoor, Michael Elk, Carlos Toledo-Hernandez, Jorge W. Santo Domingo. Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity[J]. AIMS Environmental Science, 2017, 4(3): 443-455. doi: 10.3934/environsci.2017.3.443

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Abstract

Mitochondrial signature sequences have frequently been used to study human population diversity around the world. Traditionally, this requires obtaining samples directly from individuals which is cumbersome, time consuming and limited to the number of individuals that participated in these types of surveys. Here, we used environmental DNA extracts to determine the presence and sequence variability of human mitochondrial sequences as a means to study the diversity of populations inhabiting in areas nearby a tropical watershed impacted with human fecal pollution. We used high-throughput sequencing (Illumina) and barcoding to obtain thousands of sequences from the mitochondrial hypervariable region 2 (HVR2) and determined the different haplotypes present in 10 different water samples. Sequence analyses indicated a total of 19 distinct variants with frequency greater than 5%. The HVR2 sequences were associated with haplogroups of West Eurasian (57.6%), Sub-Saharan African (23.9%), and American Indian (11%) ancestry. This was in relative accordance with population census data from the watershed sites. The results from this study demonstrates the potential value of mitochondrial sequence data retrieved from fecally impacted environmental waters to study the population diversity of local municipalities. This environmental DNA approach may also have other public health implications such as tracking background levels of human mitochondrial genes associated with diseases. It may be possible to expand this approach to other animal species inhabiting or using natural water systems.

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