Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence. Recovery was rapid and now there are over 200,000 individuals. We sequenced 260 modern and 8 historical northern elephant seal nuclear genomes to assess the impact of the population bottleneck on individual northern elephant seals and to better understand their recovery. Here we show that inbreeding, an increase in the frequency of alleles compromised by lost function, and allele frequency distortion, reduced the fitness of breeding males and females, as well as the performance of adult females on foraging migrations. We provide a detailed investigation of the impact of a severe bottleneck on fitness at the genomic level and report on the role of specific gene systems.

Monitoring of Delphinidae species population patterns in the Mediterranean Sea was carried out in a sequence of surveys employing different approaches. Data from seven-year surveys with small catamaran sailing boats were analyzed under model-based approaches. Density Surface Models were used to produce spatial distribution prediction of three Delphinidae species (Stenella coeruleoalba, Tursiops truncatus, and Delphinus delphis) in an extended study area covering much of the Mediterranean Sea. A classical distance sampling protocol was applied in order to calculate the detection probability of clusters. Static (depth, slope, distance from the coast, and distance from isobaths of 200 m) and nonstatic (sea surface temperature and chlorophyll) variables were used to predict the species distribution/abundance in a generalized additive model context. Stenella coeruleoalba was found to be the dominant species, with an extended distribution in the study area; its abundance was significantly affected by both depth and distance. Tursiops truncatus and Delphinus delphis illustrated a significant abundance correlation with depth and chlorophyll, respectively, while both species showed a robust longitude correlation. Our model pinpoints the significance of nondesigned transect line surveys, suggesting the importance of specific habitat areas for future monitoring and conservation aspects of marine mammals.

Population dynamics in the marine realm can shape species’ spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species’ population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, using a panel of four microsatellite markers. Recorded low F_ST values within the study area indicate little evidence of genetic differentiation among populations. Results suggest high gene flow which may imply near-panmixia between populations, indicating the possibility of a probable movement of adult migrants, or strong passive drift at sea in early life stages of the species. To this extent, bibliographically speaking, different species within the Sparidae family favor altered population dynamics patterns with respect to local populations and genetic divergence, in the context of the molecular marker used.

The authentication of food products and the verification of their identity are of major importance for consumers. Food fraud through mislabeling is an illegal practice consisting of the substitution of an expensive food product by a relatively cheaper one, misleading false labelling of their origin and adulteration in processed or frozen products. This issue is particularly of high importance concerning fish and seafood, which are easily adulterated primarily due to difficult morphological identification. Fish species of the Mullidae family are considered among the most high-valued seafood products traded in Greece and Eastern Mediterranean in general, in terms of the price and demand. Specifically, the red mullet (Mullus barbatus) and the striped red mullet (Mullus surmuletus) are both indigenous in the Aegean (FAO Division 37.3.1) and the Ionian (FAO Division 37.2.2) Seas, with high levels of consumers’ preferences. However, they could be easily adulterated or misidentified by the invasive Aegean Sea Lessepsian migrator goldband goatfish (Upeneus moluccensis) as well as by the imported West African goatfish (Pseudupeneus prayensis). Keeping this in mind, we designed two novel, time-saving and easy-to-apply multiplex PCR assays and one multiple Melt–Curve analysis real-time PCR for the identification of these four species. These methodologies are based on species-specific primers targeting single nucleotide polymorphisms (SNPs) detected via sequencing analysis of the mitochondrial cytochrome C oxidase subunit I (CO1) and of the cytochrome b (CYTB) genes in newly collected individuals, with additional comparison with congeneric and conspecific haplotypes obtained from the GenBank database. Both methodologies, targeting CO1 or CYTB, utilize one common and four diagnostic primers, producing amplicons of different length that are easily and reliably separated on agarose gel electrophoresis, yielding a single clear band of diagnostic size for each species or a certain Melt–Curve profile. The applicability of this cost-effective and fast methodology was tested in 328 collected specimens, including 10 cooked samples obtained from restaurants. In the vast majority (327 out of the 328) of the specimens tested, one single band was produced, in agreement with the expected products with a single exception a M. barbatus sample that was identified as M. surmuletus, the identity of which was confirmed using sequencing, indicating erroneous morphological identification. The developed methodologies are expected to contribute to the detection of commercial fraud in fish authentication.

Admixture and hybridization may play a key role in population dynamics and speciation with respect to habitat, demographic history, and adaptive selection. The present study examines the genetic diversity of two congeneric—but in different subgenera—holothurians that live in sympatry in mixed populations. Strong evidence of admixture was provided by analyzing RAD sequencing data from 90 and 67 individuals of Holothuria (Holothuria) tubulosa and Holothuria (Roweothuria) poli, respectively, from various areas of the Hellenic Seas (eastern Mediterranean). Coalescent demographic analysis revealed a recent directional gene flow from H. poli to H. tubulosa. The two species populations diverged around 13.5 thousand years ago, just after the Last Glacial Maximum. According to the pairwise sequential Markovian coalescent approach, the historical population effective sizes for both species declined during the last Pleistocene glaciations, probably due to population decline, followed by a relative rapid recovery as it is calculated using LD methods. The presented results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.

Background: Comprehensively detailed information on population dynamics for benthic species is crucial since potential admixture of individuals could shift the genetic subdivision and age structure during a full breeding period. The apparent genetic impact of the potential recruitment strategy of Norway lobsterNephrops norvegicusis still under research. For this reason the present study was focused on genetic variation of the species over a given continuous year period in a semi-enclosed gulf of the Aegean Sea.Results: Analyses revealed that the relative smaller size class in females and the apparent faster growth of males may represent a key-role differential strategy for the two sexes, whereas females tend to mature slower. Heterozygosity fitness correlations (HFCs) showed substantially significant associations suggesting that inbreeding depression for females and outbreeding depression for males are the proximate fitness mechanisms, respectively.Conclusions: Nephrops norvegicusuniformal genetic composition (background of high gene flow), could be attributed to potential population recolonization, due to a hypothesized passive larval movement from deeper waters, which may suggest that some offspring of local residents and potential male non-breeders from other regions admixture randomly.