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1. Needles in an ocean haystack: using environmental DNA to study marine mammals in the North Atlantic

   https://doi.org/10.7557/3.6482  

   Székely, Dóra ; Cammen, Kristina M. ; Tange Olsen, Morten ( May 2021 , NAMMCO Scientific Publications)

   Marine mammals in the North Atlantic have experienced severe depletions due to overexploitation. While some species and populations have now recovered, there are numerous other anthropogenic activities impacting their North Atlantic ecosystem. Studying marine mammals is often associated with logistical challenges, and many species have an elusive nature, resulting in substantial knowledge gaps on the distribution, abundance and diversity of marine mammals in the North Atlantic. Environmental DNA (eDNA) is an emerging tool in biodiversity monitoring and has successfully been demonstrated to complement traditional monitoring methods for a wide range of marine taxonomic groups. The promising potential of seawater eDNA is owe to advances within an array of molecular methods used to extract, detect and/or sequence the genetic material of marine organisms from a single seawater sample.  We present a literature review of eDNA studies of marine mammals and discuss the potential applications and practical challenges of eDNA in marine mammal research, management and conservation.  Environmental DNA has already been introduced to a wide range of applications within marine mammal science, from detection of endangered species to population genetic assessments. Furthermore, eDNA has the power to capture other biologically important species in the marine ecosystem and food web, which could facilitate insight into the spatiotemporal variation of different marine communities in a changing environment. With methodological and technological standardization, eDNA based approaches have a promising potential to be integrated into regular monitoring practices and management strategies. 

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2. Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples

   https://doi.org/10.1111/mec.15765  

   Andres, Kara J. ; Sethi, Suresh A. ; Lodge, David M. ; Andrés, Jose ( January 2021 , Molecular Ecology)

   Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population‐level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA‐based and individual tissue‐based estimates of allele frequencies from experimental mesocosms and in a field‐based trial. Subsequently, we used a likelihood‐based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low‐frequency alleles. With this study we document the application of eDNA and multiple amplicon‐based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population‐level genetic diversity.

    

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3. Molecular identity crisis: environmental DNA metabarcoding meets traditional taxonomy—assessing biodiversity and freshwater mussel populations (Unionidae) in Alabama

   https://doi.org/10.7717/peerj.15127  

   Hauck, Laura L. ; Atkinson, Carla L. ; Homyack, Jessica A. ; Penaluna, Brooke E. ; Mangum, Clay ; Coble, Ashley A. ; Nettles, Jami ; Thornton-Frost, Jamie E. ; Fix, Miranda J. ( January 2023 , PeerJ)

   The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay. 

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4. Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance

   https://doi.org/10.1111/2041-210X.13578  

   Doser, Jeffrey W. ; Finley, Andrew O. ; Weed, Aaron S. ; Zipkin, Elise F. ( March 2021 , Methods in Ecology and Evolution)

   Monitoring wildlife abundance across space and time is an essential task to study their population dynamics and inform effective management. Acoustic recording units are a promising technology for efficiently monitoring bird populations and communities. While current acoustic data models provide information on the presence/absence of individual species, new approaches are needed to monitor population abundance, ideally across large spatio‐temporal regions.

   We present an integrated modelling framework that combines high‐quality but temporally sparse bird point count survey data with acoustic recordings. Our models account for imperfect detection in both data types and false positive errors in the acoustic data. Using simulations, we compare the accuracy and precision of abundance estimates using differing amounts of acoustic vocalizations obtained from a clustering algorithm, point count data, and a subset of manually validated acoustic vocalizations. We also use our modelling framework in a case study to estimate abundance of the Eastern Wood‐Pewee (Contopus virens) in Vermont, USA.

   The simulation study reveals that combining acoustic and point count data via an integrated model improves accuracy and precision of abundance estimates compared with models informed by either acoustic or point count data alone. Improved estimates are obtained across a wide range of scenarios, with the largest gains occurring when detection probability for the point count data is low. Combining acoustic data with only a small number of point count surveys yields estimates of abundance without the need for validating any of the identified vocalizations from the acoustic data. Within our case study, the integrated models provided moderate support for a decline of the Eastern Wood‐Pewee in this region.

   Our integrated modelling approach combines dense acoustic data with few point count surveys to deliver reliable estimates of species abundance without the need for manual identification of acoustic vocalizations or a prohibitively expensive large number of repeated point count surveys. Our proposed approach offers an efficient monitoring alternative for large spatio‐temporal regions when point count data are difficult to obtain or when monitoring is focused on rare species with low detection probability.

    

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5. Biosystematic studies on the status of Solanum chilense

   https://doi.org/10.1002/ajb2.1621  

   Raduski, Andrew R. ; Igić, Boris ( March 2021 , American Journal of Botany)

   Common taxonomic practices, which condition species' descriptions on diagnostic morphological traits, may systematically lump outcrossing species and unduly split selfing species. Specifically, higher effective population sizes and genetic diversity of obligate outcrossers are expected to result less reliable phenotypic diagnoses. Wild tomatoes, members ofSolanumsect.Lycopersicum, are commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although the section experienced significant early work, which continues presently, the taxonomic status of many wild species has undergone a number of significant revisions and remains uncertain. Species in this section vary in their breeding systems, notably the expression of self‐incompatibility, which determines individual propensity for outcrossing

   Here, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced‐representation sequencing (RAD‐seq), a range of phylogenetic and population genetic analyses, as well as analyses of crossing and morphological data.

   Overall, each of our analyses provides a considerable weight of evidence that the Pacific coastal populations and Andean inland populations of the currently describedSolanum chilenserepresent separately evolving populations, and conceal at least one undescribed cryptic species.

   Despite its vast economic importance,Solanumsect.Lycopersiconstill exhibits considerable taxonomic instability. A pattern of under‐recognition of outcrossing species may be common, not only in tomatoes, but across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.

    

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