Using environmental DNA (eDNA) from water to study the genetics of different species is becoming increasingly popular. Most studies have focused on the mitochondrial genome to understand genetic differences in various animals. Mitochondrial DNA (mtDNA) is helpful because it is easy to extract from water samples and shows clear differences between populations due to its fast mutation rate.
However, mtDNA mainly tells us about female ancestry and does not recombine, limiting its usefulness. Additionally, nuclear insertions of mitochondrial DNA and changes in the mitochondrial genome can cause confusion. Scientists are now exploring nuclear eDNA for genetic studies to overcome these issues. Although this research is still new, some studies are promising. For example, research on the round goby fish showed that genetic data from eDNA matched well with data from tissue samples. This method also successfully showed genetic differences between populations in different locations. However, first, let us introduce an important term: Single nucleotide polymorphism (SNPs; pronounced as ‘snips’), which are variations at a single position in a DNA sequence among individuals. They are commonly used to identify genetic differences and study population genetics.
Recently, research on Cichlid fish (Astatotilapia calliptera) aimed to see if single nucleotide polymorphism (SNP) variants from the nuclear genome can be used to study genetic structures within a single lake. Specifically, the main objective was to determine if eDNA can reliably reflect the genetic divergence among cichlid fish populations along a depth gradient in Lake Masoko.
Sample Collection and Methods at Lake Masoko, Tanzania
Lake Masoko is a 35-meter-deep crater lake with no surface connection to rivers. It hosts two genetically distinct types of fish—one adapted to shallow waters and the other to deeper waters. Researchers collected eDNA samples from different depths (3, 7, 12, 18, and 22 meters) by SCUBA diving. They extracted and sequenced DNA, focusing on 120 specific genetic markers (SNPs). The sequences were then compared to a reference genome of Cichlid fish. Statistical tests were performed to see how the genetic variations found in the eDNA samples matched those in actual fish samples. This helped determine if the eDNA accurately reflects the genetic makeup of the fish populations.
Study Reveals Genetic Differences in Fish Populations Using eDNA
The study found that genetic variations in eDNA closely matched those in fish samples from the same depths, confirming eDNA’s ability to reflect fine-scale genetic structures. Significant genetic differences were observed between fish living in shallow waters (less than 5 meters deep) and those in deep waters (deeper than 20 meters). These differences were linked to environmental factors like temperature and oxygen levels.
When examining the population structure, the researchers used 71 specific genetic markers (SNPs) to identify distinct genetic clusters at the 12-meter and 18-meter depths. These depths correspond to the lake’s thermo-oxycline, a barrier where temperature and oxygen levels change drastically.
There were environmental and methodological considerations. The study acknowledged potential biases due to PCR amplification methods and limitations in genomic databases, which can affect the accuracy of identifying species-specific sequences. Also, there were significant shifts in the microbial communities, indicating distinct biological zones within the lake.
Practical Implications and Future Directions From this Study
Conservation and Ecological Studies: Using eDNA to detect fine-scale genetic structures offers new possibilities for managing and conserving aquatic populations. This method is particularly valuable for species that are hard to sample directly due to their rarity, behaviour, or ethical concerns.
Enhancing eDNA Techniques: The study emphasised the need to improve eDNA methodologies. These improvements include designing better primers to reduce biases and using more effective hybridisation-capture techniques to target specific genomic regions.
Potential for Broader Applications: Beyond describing genetic structures, eDNA could also help monitor ecological responses to environmental changes, such as shifts in species distributions due to climate change.
Overall, this study demonstrates the effectiveness of eDNA in detecting fine-scale genetic structures within aquatic species, showing that eDNA data can accurately reflect population genetics. It supports further developing eDNA-based methods as a non-invasive, effective tool for ecological and conservation research. By amplifying nuclear loci from eDNA and generating genetic variation data, researchers can infer population structures, offering a promising approach to studying and managing aquatic biodiversity.
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