Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples.

Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235× (90× - 352× per base position) coverage of the whale shark mitogenome. Using a minor allele frequency of 5%, we find 29 variable sites throughout the mitogenome, indicative of at least five contributing individuals. We also retrieved numerous mitochondrial reads from an abundant nontarget species, mackerel tuna (Euthynnus affinis), showing a clear relationship between sequence similarity to the capture probes and the number of captured reads. The nuclear target capture probes retrieved only a few reads and polymorphic variants from the whale shark, but we successfully obtained millions of reads and thousands of polymorphic variants with different allele frequencies from E. affinis. We demonstrate that target capture of complete mitochondrial genomes and thousands of nuclear loci is possible from aquatic eDNA samples. Our results highlight that careful probe design, taking into account the range of divergence between target and nontarget sequences as well as presence of nontarget species at the sampling site, is crucial to consider. eDNA sampling coupled with target capture approaches provide an efficient means with which to retrieve population genomic data from aggregating and spawning aquatic species.

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats.

Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates, spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish genera previously recorded in the Gulf. Sites of similar habitat type were also similar in eDNA composition. The species accumulation analyses showed that the number of sample replicates was insufficient for some sampling sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate diversity in the study area. Our results confirm that seawater samples contain habitat-characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.

ADN Ambiental de Vertebrados Tomado del Agua Marina para Realizar Biomonitoreos de los Hábitats Marinos Resumen La conservación y el manejo de la biodiversidad marina depende del biomonitoreo de los hábitats marinos, pero las estrategias actuales requieren de muchos recursos y de diferentes estrategias para diferentes organismos. El ADN ambiental (ADNa) extraído de muestras de agua es una estrategia eficiente y versátil para detectar animales acuáticos. En el océano, la composición del ADNa refleja la fauna local a escalas espaciales finas, pero se sabe poco sobre la efectividad del monitoreo basado en el ADNa de las comunidades marinas a grandes escalas. Investigamos el potencial del ADNa para caracterizar y distinguir las comunidades marinas a escalas espaciales grandes mediante una comparación de la composición de especies de vertebrados entre los hábitats marinos de Qatar, en el Golfo Arábigo (también conocido como el Golfo Persa), con base en el meta-código de barras del ADNa extraído de muestras de agua de mar. Realizamos análisis de acumulación de especies para estimar cuánta de la diversidad de vertebrados logramos detectar. Obtuvimos secuencias de ADNa de diversos ensamblajes de vertebrados marinos, los cuales abarcaron 191 taxones de 73 familias. Estos taxones incluyeron a especies raras y en peligro de extinción y cubrieron el 36% de los géneros de peces óseos previamente registrados en el golfo. Los sitios con tipos similares de hábitat también fueron similares en cuanto a la composición del ADNa. Los análisis de acumulación de especies mostraron que el número de réplicas de muestras fue insuficiente para algunos sitios de muestreo, pero sugieren que unos cientos de muestras de ADNa podrían capturar potencialmente >90% de la diversidad de vertebrados marinos en el área de estudio. Nuestros resultados confirman que las muestras de agua marina contienen firmas moleculares características del hábitat y que el monitoreo de ADNa puede cubrir eficientemente la diversidad de vertebrados a escalas relevantes para la conservación y el manejo nacional y regional.

Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA.

Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.