Monitoring newt communities in urban area using eDNA metabarcoding

PeerJ

article

Léo Charvoz¹  Laure Apothéloz-Perret-Gentil¹  Emanuela Reo¹  Jacques Thiébaud³  Jan Pawlowski¹ 

[1]Department of Genetics and Evolution, University of Geneva

[2]ID-Gene ecodiagnostics, Campus Biotech Innovation Park

[3]KARCH-GE ,(Swiss Coordination Center for the Protection of Amphibians and Reptiles)—Geneva Regional Branch

[4]Polish Academy of Sciences, Institute of Oceanology

关键词: eDNA;    Metabarcoding;    Newt;    Illumina;    Invasive;    Water;    16S;    Monitoring;   

DOI  :  10.7717/peerj.12357

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Newts are amphibians commonly present in small ponds or garden pools in urban areas. They are protected in many countries and their presence is monitored through visual observation and/or trapping. However, newts are not easy to spot as they are small, elusive and often hidden at the bottom of water bodies. In recent years, environmental DNA (eDNA) has become a popular tool for detecting newts, with a focus on individual species using qPCR assays. Here, we assess the effectiveness of eDNA metabarcoding compared to conventional visual surveys of newt diversity in 45 ponds within urban areas of Geneva canton, Switzerland. We designed newt-specific mitochondrial 16S rRNA primers, which assign the majority of amplicons to newts, and were able to detect four species known to be present in the region, including the invasive subspecies Lissotriton vulgaris meridionalis, native to the Italian peninsula, that has been introduced in the Geneva area recently. The obtained eDNA results were congruent overall with conventional surveys, confirming the morphological observations in the majority of cases (67%). In 25% of cases, a species was only detected genetically, while in 8% of cases, the observations were not supported by eDNA metabarcoding. Our study confirms the usefulness of eDNA metabarcoding as a tool for the effective and non-invasive monitoring of newt community and suggests its broader use for the survey of newt diversity in urban area at larger scales.

【 授权许可】

CC BY