Mediterranean coastal lagoons are environmentally important ecosystems whose conservation has been challenged due to anthropogenic impacts that promoted the expansion of non-indigenous and, sometimes, invasive species. Therefore, it is crucial to inventory biodiversity in these areas for the development of strategies of conservation and management. Classical methods used for biodiversity surveys and detection of non-native species may be unsuccessful for the detection and identification of species in early development stages such as cryptic, microscopic, elusive, and new coming species at low population density. The development of metabarcoding techniques in the last decade offers new opportunities for reliable biodiversity surveillance and facilitates early detection of nuisance species. The objective of this study was to analyze the species occurring in the protected coastal lagoon Canet-Saint Nazaire using a simple sampling protocol based on water samples and environmental DNA (eDNA) metabarcoding with a single barcode (cytochrome c oxidase subunit I [COI] gene). Two invasive species (Polydora cornuta and Acartia tonsa), two polychaete bioindicators of pollution (Hediste diversicolor and Capitella capitata), and one alga that produces harmful algal blooms were detected from only 6 L of water, indicating environmental degradation in the lagoon despite its protected status. These results demonstrate the importance of COI as single barcode together with eDNA as an ecological early warning system and suggest the need for environmental restoration in this lagoon.

Highly polymorphic single tandem repeat loci (STR, also known as microsatellite loci) remain a familiar, cost efficient class of markers for genetic analyses in ecology, behavior, and conservation. We characterize a new universal set of ten STR loci (from 28 potential candidate loci) in seven baleen whale species, which are optimized for PCR amplification in two multiplex reactions along with a Y chromosome marker for sex determination. The optimized, universal set of STR loci provides an ideal starting point for new studies in baleen whales aimed at individual-based and population genetic studies, and facilitates data sharing among research groups. Data from the new STR loci were combined with genotypes from other published STR loci to assess the power to assign parentage (paternity) using exclusion in four species: fin whales, humpback whales, blue whales and bowhead whales. We argue that parentage studies should present a power analysis to demonstrate that the specific data are sufficiently informative to assign parentage with statistical rigor.

Current low germline mutation rate (𝜇) estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to multiple methodological errors and uncertainty. We estimated 𝜇; directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised 𝜇 values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that 𝜇 in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Peto's Paradox). We demonstrate the feasibility of estimating 𝜇 from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on 𝜇.

The movement of organisms facilitated by anthropogenic activities is a serious threat to marine diversity, especially for endemic species that may be outcompeted from non-indigenous species (NIS). In this study, we have analyzed communities inhabiting the north of the Gulf of Aqaba, Red Sea, employing environmental DNA (eDNA) metabarcoding. That gulf is especially rich in species and population endemism. We have detected NIS representing 36% of the total number of species found from eDNA. Primary producers were more abundant in the NIS than in the native fraction of species, suggesting that functional diversity could be altered if NIS thrive there. We discuss maritime traffic as a factor that may enhance the introduction of non-natives in this region and emphasize the importance of the control of these species that may threaten the rich endemic biota of the Red Sea.

Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible, enabling explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).