Biology subjects

Stoeckle, M. Y.

Publications and source records attributed to Stoeckle, M. Y..

4 recordsLinked to original sources

bioRxiv2025

Biomonitoring in the Anthropocene: Urban estuary environmental DNA tracks marine fish, terrestrial wildlife, and human diet

Managing human impacts in urban estuaries asks for up-to-date monitoring of marine life. Here we analyze vertebrate eDNA in New York Citys East River, a rocky estuary channel difficult to survey with mechanical gear and subject to wastewater discharge. We collected water samples weekly for one year and applied spike-in metabarcoding to quantify vertebrate eDNA. Replication experiments demonstrated good reproducibility above about 10 eDNA copies/PCR. We propose a fish censusing scale based on absolute eDNA abundance. Local marine fish eDNA followed a classic hollow curve species abundance distribution over four orders of magnitude, with abundant and common taxa comprising about 25% of species and 95% of fish eDNA. There was a 10-fold increase in local marine fish eDNA in summer and seasonal differences among taxa consistent with known phenology. Two fish species were newly abundant in comparison to an eDNA survey at the same site in 2016. Levels of other vertebrate eDNA--domesticated animal, non-fish wildlife, and dietary fish--were correlated with human eDNA levels, consistent with a shared wastewater source. Wastewater eDNA identified the commonest urban mammals, land birds, and household pets. Proportions of dietary animal eDNA in wastewater closely approximated proportions in national consumption statistics, opening a window into human diet assessment. Effort and cost for the weekly shoreline survey were modest. Vertebrate eDNA metabarcoding with spike-in quantification enabled weekly monitoring of urban estuary fish populations, identified overlooked newly abundant species, and reported on terrestrial wildlife and human diet.

ecology↗

bioRxiv2022

12S Gene Metabarcoding with DNA Standard Quantifies Marine Bony FishEnvironmental DNA, Identifies Threshold for Reproducible Amplification, and Overcomes Distortion Due to Non-Fish Vertebrate DNA

Single-species PCR assays accurately measure eDNA concentration. Here we test whether multi-species PCR, i.e., metabarcoding, with an internal standard can quantify eDNA of marine bony fish. Replicate amplifications with Riaz 12S gene primers were spiked with known amounts of a non-fish vertebrate DNA standard, indexed separately, and sequenced on an Illumina MiSeq. Fish eDNA copies were calculated by comparing fish and standard reads. Relative reads were directly proportional to relative DNA copies, with average and maximum variance between replicates of about 1.3- and 2.0-fold, respectively. There was an apparent threshold for consistent amplification of about 10 eDNA copies per PCR reaction. The internal DNA standard corrected for distortion of read counts due to non-fish vertebrate DNA. To assess potential amplification bias among species, we compared reads obtained with Riaz 12S primers to those with modified MiFish primers. Our results provide evidence that Riaz 12S gene metabarcoding with an internal DNA standard quantifies marine bony fish eDNA over a range of about 10 to 5,000 copies per reaction, without indication of significant PCR bias among teleost species. In mid-Atlantic coastal samples, eDNA rarity was the main limitation to reproducible detection and quantification, and this was partly overcome by increasing the amount of a DNA sample amplified. Our findings support incorporating a DNA standard in 12S metabarcoding to help quantify eDNA abundance for marine bony fish species.

ecology↗

bioRxiv2018

GoFish: A Streamlined Environmental DNA Presence/Absence Assay for Marine Vertebrates

Here we describe GoFish, a streamlined environmental DNA (eDNA) presence/absence assay. The assay amplifies a 12S segment with broad-range vertebrate primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis. We first obtained 12S sequences from 77 fish specimens representing 36 northwestern Atlantic taxa not well documented in GenBank. Using the newly obtained and published 12S records, we designed GoFish assays for 11 bony fish species common in the lower Hudson River estuary and tested seasonal abundance and habitat preference at two sites. Additional assays detected nine cartilaginous fish species and a marine mammal, bottlenose dolphin, in southern New York Bight. GoFish sensitivity was equivalent to Illumina MiSeq metabarcoding. Unlike quantitative PCR (qPCR), GoFish does not require tissues of target and related species for assay development and a basic thermal cycler is sufficient. Unlike Illumina metabarcoding, indexing and batching samples are unnecessary and advanced bioinformatics expertise is not needed. The assay can be carried out from water collection to result in three days. The main limitations so far are species with shared target sequences and inconsistent amplification of rarer eDNAs. We think this approach will be a useful addition to current eDNA methods when analyzing presence/absence of known species, when turnaround time is important, and in educational settings.

ecology↗

bioRxiv2018

Why Should Mitochondria Define Species?

More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes--drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

evolutionary biology↗