Kapoor Vikram, Elk Michael, Toledo-Hernandez Carlos, Santo Domingo Jorge W
Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA.
U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
AIMS Environ Sci. 2017;4(3):443-455. doi: 10.3934/environsci.2017.3.443.
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.
线粒体特征序列经常被用于研究世界各地的人类群体多样性。传统上，这需要直接从个体获取样本，这既麻烦又耗时，而且仅限于参与这类调查的个体数量。在这里，我们使用环境DNA提取物来确定人类线粒体序列的存在和序列变异性，以此作为研究居住在受人类粪便污染影响的热带流域附近地区人群多样性的一种手段。我们使用高通量测序（Illumina）和条形码技术从线粒体高变区2（HVR2）获得了数千个序列，并确定了10个不同水样中存在的不同单倍型。序列分析表明共有19个频率大于5%的不同变体。HVR2序列与西欧亚（57.6%）、撒哈拉以南非洲（23.9%）和美洲印第安（11%）血统的单倍群相关。这与流域站点的人口普查数据相对一致。这项研究的结果证明了从受粪便污染的环境水体中获取的线粒体序列数据在研究当地市政当局人口多样性方面的潜在价值。这种环境DNA方法可能还具有其他公共卫生意义，比如追踪与疾病相关的人类线粒体基因的背景水平。有可能将这种方法扩展到栖息于或使用天然水系统的其他动物物种。
