Metabarcoding of environmental DNA (eDNA) provides more comprehensive, efficient, and non‐invasive sampling of biological communities than conventional methods. However, limitations of metabarcoding ...include taxon‐specific biases in amplification and sequencing that distort assessments of community composition. Further, hyper‐abundant species may disproportionately affect community composition assessments and impair the detection of rare species (i.e., “species masking”). In this study, we examine methodological approaches to improve eDNA metabarcoding assessments of community structure using fish community diversity in a pond in south Florida using MiFish primers modified to improve cichlid detection. Mitochondrial 12S eDNA amplicon sequencing via Illumina NovaSeq was analyzed using the DADA2 model‐based exact sequence inference. The fish species and abundances in the system were recorded during piscicide treatment and subsequent native species restocking. Our results demonstrate that (1) ultra‐high‐throughput sequencing on the newer NovaSeq patterned flow cell provided reliable detection of very rare taxa—with detections of a single individual. (2) Read numbers were significantly correlated to the total surface area of the fish population, and numerical abundance to a lesser degree; however, dominant taxa largely drove those correlations, and simulations showed that biases in the most abundant taxa will have disproportionate effects on the strength of the correlation. (3) The read number coefficient of variation for each species across spatially separated replicate samples may provide less biased abundance estimates compared with estimates based on average read counts. Finally, (4) exact sequence inference detected multiple haplotypes and population genetic diversity within a species. Our results demonstrate the real‐world metabarcoding capacity to reveal community structure and reliably detect rare species and unique haplotypes and shows that read numbers can, to a limited degree, be used to infer the size of fish populations. Careful examination of detection biases among dominant taxa and spatial variation among samples are required for rigorous eDNA‐based estimates of community structure. Our results demonstrate the capacity of NovaSeq metabarcoding to reveal freshwater fish community structure and reliably detect rare species and unique haplotypes. Metabarcoding read numbers were significantly correlated to the total surface area of the fish species' populations, allowing for conditional inferences of population sizes. However, dominant taxa largely drove those correlations, and simulations indicated that biases toward the most abundant taxa will have disproportionate effects on the strength of the correlation.
We demonstrate the capacity of NovaSeq metabarcoding to reveal community structure, reliably detect rare species and identify unique haplotypes. Our data indicated that read numbers can, with considerations, be used to infer the size of fish populations. Specifically, read numbers were significantly correlated to the total surface area of the fish population; however, dominant taxa largely drove those correlations, and simulations indicated that biases towards the most abundant taxa will have disproportionate effects on the strength of the correlation.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
To address the ongoing debate over the impact of invasive species on native terrestrial wildlife, we conducted a large-scale experiment to test the hypothesis that invasive Burmese pythons (Python ...molurus bivittatus) were a cause of the precipitous decline of mammals in Everglades National Park (ENP). Evidence linking pythons to mammal declines has been indirect and there are reasons to question whether pythons, or any predator, could have caused the precipitous declines seen across a range of mammalian functional groups. Experimentally manipulating marsh rabbits, we found that pythons accounted for 77% of rabbit mortalities within 11 months of their translocation to ENP and that python predation appeared to preclude the persistence of rabbit populations in ENP. On control sites, outside of the park, no rabbits were killed by pythons and 71% of attributable marsh rabbit mortalities were classified as mammal predations. Burmese pythons pose a serious threat to the faunal communities and ecological functioning of the Greater Everglades Ecosystem, which will probably spread as python populations expand their range.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR‐associated protein) genetic tools has given rise to applications beyond site‐directed genome editing ...for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS‐CoV‐2 and Zika virus. Despite the technology being rapid and cost‐effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field‐applicable and user‐friendly CRISPR/Cas‐based biosensor for the detection of Pseudogymnoascus destructans (Pd), the causative fungal agent of white‐nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect Pd DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing Pd‐positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of Pd‐positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease‐associated pathogen detection and monitoring applications.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Millette et al. (Ecology Letters, 2020, 23:55–67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data ...from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
This article uses two national survey data sets to analyze the effects of skin color on life outcomes for African American and Mexican American women. Using a historical framework of European ...colonialism and slavery, this article explains how skin color hierarchies were established and are maintained. The concept of social capital is used to explain how beauty, defined through light skin, works as capital and as a stratifying agent for women on the dimensions of education, income, and spousal status. The analysis shows that light skin predicts higher educational attainment for both groups of women. Light skin directly predicts higher personal earnings for African American women and indirectly affects personal earnings for Mexican American women. Light skin predicts higher spousal status for African American women but not for Mexican American women.
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BFBNIB, INZLJ, NMLJ, NUK, OILJ, PNG, SAZU, UKNU, UL, UM, UPUK, ZRSKP
Abstract
Invasive Burmese pythons (Python bivittatus) in the Everglades of Florida, United States, have drastically reduced populations of mammals, yet populations of some rodents appear unaffected ...by the invasion. To understand this pattern, we radio-tagged cotton rats (Sigmodon hispidus) in areas of high and low python occurrence densities (hereafter occurrence) and quantified the effects of python occurrence, seasonality, and sex on their survival and cause-specific mortality. Cotton rat survival was not influenced by difference in python occurrence (hazard ratio = 1.32, 95% CI = 0.77–2.26, P = 0.30). However, cotton rats were at greater risk from mortalities caused by mammals in areas of low python occurrence. In areas with elevated python occurrence, we attributed most cotton rat mortalities to birds of prey (48.6%) and reptiles (non-python = 24.3%, python = 16.2%). Where python occurrence was relatively low, we attributed cotton rat mortalities to native reptilian (28.6%), avian (35.7%), and mammalian predators (35.7%) with no python-related deaths. In total, pythons were responsible for 11.8% of all cotton rat mortalities. Finding no difference in the survival of cotton rats, despite differences in the causative agents of mortality, suggests that predation pressure from an invasive predator was compensatory for cotton rat population dynamics. This type of compensatory mortality is common for small mammals and helps explain why mammal communities in python-invaded portions of the Greater Everglades Ecosystem are increasingly dominated by cotton rats and other rodents.
This special issue of Evolutionary Applications consists of 10 publications investigating the use of next‐generation tools and techniques in population genetic analyses and biodiversity assessment. ...The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next‐generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropriate study designs, interpreting results in light of conservation concerns, and determining appropriate management actions. This special issue identifies key attributes of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genetics research.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an ...early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriate response actions to hypothetical eDNA early detections of an introduced aquatic plant in Sebago Lake (Maine, USA). The results were juxtaposed to a recent study that used a similar SDM approach to evaluate response actions to hypothetical eDNA early detections of introduced mussels in Jordanelle Reservoir (Utah, USA). We found that eDNA early detections were not actionable in Sebago Lake because the plant's invasion potential was spatially constrained and the current management activities provided acceptable levels of mitigation. In Jordanelle Reservoir, eDNA detections were actionable due to high invasion potential and analyses supported management actions to contain the invasion. The divergent outcomes of the two case studies are related to the unique attributes of the habitats and species, highlighting the utility of the SDM approach when considering an eDNA monitoring program. We use these two case studies to present a general SDM framework and a set of heuristics that can be efficiently applied to eDNA early detection rapid response scenarios and other instances associated with indeterminant eDNA detections, especially when there is an imperative to make decisions as quickly as possible.
•Decision support tools are needed to link eDNA detections to manager responses.•Structured decision making was examined as an eDNA decision support tool.•eDNA results are especially actionable when potential invader impacts are high.•Containing the invasion can be a more optimal response than control actions.•Structured decision making is useful for communicating why a decision was made.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract
Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental ...adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages—Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.
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