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ABSTRACT The Indo‐Pacific lionfish,Pterois volitans,is an invasive species in the western Atlantic. Since its introduction to Florida in the early 1980s, populations have surged with lionfish now found from North Carolina to Venezuela. As their range expands, these generalist predators threaten native fauna, and while they are primarily a marine species, their tolerance for low salinity conditions may allow them to expand into sensitive estuarine habitats undetected. Traditional approaches for tracking invasive species such as direct observation or trapping are impractical over large spatial scales, making environmental DNA (eDNA) an attractive alternative. Molecular assays, such as those employing quantitative polymerase chain reaction (qPCR), amplify low copy number DNA fragments in environmental samples and are increasingly employed as a complement to traditional methods for the detection of invasive species. Currently, there is one published PCR assay for the detection of lionfish eDNA. However, the specificity of this assay is unverified, and the critical performance parameters limit of detection (LOD) and limit of quantification (LOQ) have not been established. Here we evaluate the efficacy of this assay and show that it is likely to result in false negatives in the western Atlantic. As an alternative, we developed a new TaqMan probe‐based qPCR assay that is species‐specific forP. volitansand highly sensitive with a LOD of 12 copies per reaction and a LOQ of 598 copies per reaction. While our assay does not amplify the closely relatedP. miles, which was also introduced in the western Atlantic, the low prevalence of this species in the invasive population means our assay is effective for most monitoring purposes. We conclude that our assay is a robust method for the detection of lionfish and can be employed in any habitat, offering new opportunities for controlling the spread of invasive lionfish. 

Abstract Hybridization offers insight into speciation and the forces that maintain barriers to reproduction, and hybrid zones provide excellent opportunities to test how environment shapes barriers to reproduction and hybrid fitness. A hybrid zone between the killifish, Fundulus heteroclitus and Fundulus grandis, had been identified in northeastern Florida, although the spatial structure and parameters that affect the distribution of the two species remain unknown. The present study aimed to determine the fine-scale spatial genetic patterns of the hybrid zone to test the hypothesis that species ranges are influenced by changes in dominant vegetation and to determine how differences in reproductive barriers between the two species influence the observed patterns. The area of overlap between the two species spanned ~37 km and showed a mosaic pattern of hybridization, suggesting the spatial structure of the hybrid zone is largely influenced by the environment. Environmental association analysis, however, suggested that while dominant vegetation had a significant influence on the spatial structure of the hybrid zone, a combination of environmental factors was driving the observed patterns. Hybridization tended to be rare at sites where F. heteroclitus was the more abundant species, suggesting that differences in preference for conspecifics can lead to differences in rates of introgression into parental taxa and likely result in a range-shift as opposed to adaptation in the face of climate change. 

Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic diversity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world’s largest genomic data repository, we found that most archived genomic datasets (87%) lacked the spatiotemporal metadata necessary for genetic biodiversity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 39% (51% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today’s genetic biodiversity and to plug the growing metadata gap. 

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus , we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic ( h = 0.929; π  = 0.004) relative to the Indo-Pacific ( h = 0.105; π  < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species. 

Abstract Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA‐based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome‐db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards‐compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.