Background: Detecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community-level analyses due to their use of species-specific (presence/absence) 'barcodes'. Metabarcoding methods provide information on entire communities based on sequencing of all taxon-specific barcodes within an eDNA sample.Aims: Evaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience. Materials and Methods:In 2016, eight limnologically diverse lakes (surface area range: 13 -1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish-specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.Results: Analysis of species accumulation curves indicated multi-locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 -62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples. | 369SARD et Al.
Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use of fish ladders or dam removal is infeasible. However, little is known about the efficacy of trap and haul conservation strategies. Here we used genetic parentage assignments to evaluate the efficacy of reintroducing adult Chinook salmon (Oncorhynchus tshawytscha) above Cougar Dam on the South Fork McKenzie River, Oregon, USA, from 2008 to 2011. We found that mean reproductive success (RS) declined as adults were released later in the spawning season in 2009 and 2010; however, release location did not affect RS. In 2010 and 2011, we tested for RS differences between hatchery and natural origin (HOR and NOR, respectively) adults. HOR males were consistently less fit than NOR males, but little evidence for fitness differences was apparent between HOR and NOR females. Interestingly, the effect of origin on RS was not significant after accounting for variation explained by body length. Our results indicate that release date and location have inconsistent or no effect on the reproductive success of reintroduced adults when active transport strategies are employed for migratory fishes.
Dams contribute to declines in fish abundance, in part, by blocking access to historical habitat. When fish ladders are infeasible, fish can be trapped below a dam and transported above to provide access to habitat. However, this conservation strategy has received little attention in the literature, and many questions regarding efficacy remain unanswered. Here, we used a genetic parentage approach to evaluate cohort replacement rate (CRR), defined as the number of future spawners produced by a spawner, for a spring Chinook salmon Oncorhynchus tshawytscha trap and transport reintroduction program. We used CRRs to determine if the population can sustain itself in the absence of immigration, which is important when assessing demographic viability. We also evaluated the effects of release locations and dates on the fitness of reintroduced fish. Counts of adult offspring per spawner were used to estimate fitness of salmon reintroduced in 2007 and 2008. We found that fitness decreased slightly as adults were released later in the spawning season in 2007, but not in 2008. Release location did not affect fitness in either year. We also found a seasonal decline in the likelihood that a Chinook salmon collected at the trap and transport facility was produced above the dam. Finally, 2007 and 2008 CRRs were both well below one, indicating that improvements are needed to achieve demographic stability. We demonstrate that genetic monitoring of a reintroduction program helped to inform demographic viability assessments, and suggest that our approach may be broadly applicable to other philopatric species.
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