Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations

Genetic architecture of long-distance migration and population genomics of the endangered Japanese eel

The Japanese eel (Anguilla japonica), a flagship anguillid species for conservation, is known for its long-distance-oriented migration. However, our understanding of the genetic architecture underlying long-distance migration and population genomic characteristics of A. japonica is still limited. Here, we generated a high-quality chromosome-level genome assembly and conducted whole-genome resequencing of 218 individuals to explore these aspects. Strong signals of selection were found on genes involved in long-distance aerobic exercise and navigation, which might be associated with evolutionary adaptation to long-distance migrations. Low genetic diversity was detected, which might result from genetic drift associated with demographic declines. Both mitochondrial and nuclear genomic datasets supported the existence of a single panmictic population for Japanese eel, despite signals of single-generation selection. Candidate genes for local selection involved in functions like development and circadian rhythm. The findings can provide insights to adaptative evolution to long-distance migration and inform conservation efforts for A. japonica.

Lack of genetic structure in euryhaline Chelon labrosus from the estuaries under anthropic pressure in the Southern Bay of Biscay to the coastal waters of the Mediterranean Sea

Over the last decade, xenoestrogenic effects have been reported in populations of thicklip grey mullet Chelon labrosus from contaminated estuaries in the Bay of Biscay, resulting in intersex condition. To understand the level of gene flow in individuals of different Basque estuaries microsatellite markers were used to evaluate the population structure and connectivity of C. labrosus from estuaries of the Basque coast. 46 microsatellites were tested and 10 validated for the analysis of 204 individuals collected from 5 selected Basque estuaries and 2 outgroups in the Bay of Cadiz and Thermaic Gulf. The polymorphic microsatellites revealed 74 total alleles, 2-19 alleles per locus. The mean observed heterozygosity (0.49 ± 0.02) was lower than the expected one (0.53 ± 0.01). There was no evidence of genetic differentiation (F_ST = 0.0098, P = 0.0000) among individuals or sites. Bayesian clustering analysis revealed a single population in all sampled locations. The results of this study indicate widespread genetic homogeneity and panmixia of C. labrosus across the current sampling areas spanning the Atlantic and Mediterranean basins. The hypothesis of panmixia could therefore be well supported so individuals inhabiting estuaries with high prevalence of intersex condition should be considered as members of the same single genetic group as those inhabiting adjacent estuaries without incidence of xenoestrogenicity.

Mitochondrial DNA and Microsatellite Analyses Showed Panmixia between Temporal Samples in Endangered Anguilla japonica in the Pearl River Basin (China)

The Japanese eel (Anguilla japonica) is a commercially important species in East Asia, the abundance of which has rapidly decreased in recent decades. The fishery resource in the Pearl River basin has mainly deteriorated due to overexploitation and habitat degradation. Knowledge on its genetic status is indispensable for resource management. In this study, we explored the temporal genetic structure of A. japonica on the basis of the concatenated sequences of two mitochondrial fragments (mtDNA) and eight microsatellite markers. A total of nine temporal samples (N = 127) were collected during 2019 and 2021 from Jiangmen City, China, which is located in the Pearl River estuary. mtDNA sequence analysis showed a high level of haplotype diversity, and yielded 124 haplotypes with ranging from 9 to 19 in temporal samples. All microsatellite loci were polymorphic among each of the nine temporal samples, with 150 alleles identified across all samples. Pairwise FST values were low and nonsignificant according to both mtDNA and microsatellite markers. STRUCTURE analysis showed that all temporal samples were not clearly differentiated from each other. The yielded outcomes supported a panmictic pattern in different temporal A. japonica samples. Therefore, our results call for the management of A. japonica as a single unit and joint conservation strategy of the species, since overexploitation in any region will decrease its global resource.

Spatiotemporal Variability of Trace Elements Fingerprints in Otoliths of Japanese Eel (Anguilla japonica) and Its Use in Tracing Geographic Origin

To secure traceability along supply chains of foodstuffs, the spatiotemporal variability of trace elements' fingerprints (TEF) in fish otoliths provides a powerful tool to determine and discriminate the origin. Spatiotemporal variability of TEF was examined in a commercially important seafood, Japanese eel (Anguilla japonica), by means of laser ablation-inductively coupled plasma mass spectrometry (LA-ICPMS). Six elemental ratios (Na:Ca, Mg:Ca, P:Ca, K:Ca, Sr:Ca, and Ba:Ca) were determined in the otoliths of specimens originating from four aquaculture farms to examine the spatial variability and from one wild habitat over three years to examine the temporal variation. Significant temporal variation was found in Mg:Ca and Sr:Ca ratios; however, discriminant function analysis showed a lower temporal variation (50%) for the three years. Spatial variations were significant in Sr:Ca and Ba:Ca ratios, and discriminant function analysis showed high (80%) spatial variation among the four farms. Otolith TEF in the Japanese eel showed specific spatial variation among aquaculture farms but intangible temporal variation, suggesting the otolith TEF reflect each aquaculture environment. The present study shows that otolith TEF can be a reliable tool to discriminate the geographic origin of the Japanese eel.

High genetic connectivity among large populations of Pteronotus gymnonotus in bat caves in Brazil and its implications for conservation

Bat caves in the Neotropical region harbor exceptional bat populations (> 100,000 individuals). These populations play a wider role in ecological interactions, are vulnerable due to their restriction to caves, and have a disproportionate conservation value. Current knowledge of bat caves in Brazil is still small. However, systematic monitoring of some bat caves in northeastern Brazil shows that they experience strong population fluctuations over short periods of time, suggesting large-scale movements between roosts and a much broader use of the landscape than previously considered. Spatio-temporal reproductive connectivity between distant populations would change our understanding of the use of roosts among bat species in Brazil, and important gaps in knowledge of long-distance bat movements in the country would be filled. Here, we used ddRADseq data to analyze the genetic structure of Pteronotus gymnonotus across nine bat caves over 700 km. Our results indicate the lack of a clear geographic structure with gene flow among all the caves analyzed, suggesting that P. gymnonotus uses a network of bat caves geographically segregated hundreds of kilometers apart. Facing strong anthropogenic impacts and an underrepresentation of caves in conservation action plans worldwide, the genetic connectivity demonstrated here confirms that bat caves are priority sites for bat and speleological conservation in Brazil and elsewhere. Moreover, our results demonstrate a warning call: the applied aspects of the environmental licensing process of the mining sector and its impact must be reviewed, not only in Brazil, but wherever this licensing process affects caves having exceptional bat populations.

Population genetics of a recent range expansion and subsequent loss of migration in monarch butterflies

Range expansions-whether permanent or transient-strongly influence the distribution of genetic variation in space. Monarch butterflies are best known for long-distance seasonal migration within North America but are also established as nonmigratory populations around the world, including on Pacific Islands. Previous research has highlighted stepwise expansion across the Pacific, though questions remain about expansion timing and the population genetic consequences of migration loss. Here, we present reduced-representation sequencing data for 275 monarchs from North America (n = 85), 12 Pacific Islands (n = 136) and three locations in Australia (n = 54), with the goal of understanding (i) how the monarch's Pacific expansion has shaped patterns of population genetic variation and (ii) how loss of migration has influenced spatial patterns of differentiation. We find support for previously described stepwise dispersal across the Pacific and document an additional expansion from Hawaii into the Mariana Islands. Nonmigratory monarchs within the Mariana Islands show strong patterns of differentiation, despite their proximity; by contrast, migratory North American samples form a single genetically panmictic population across the continent. Estimates of Pacific establishment timing are highly uncertain (~100-1,000,000 years ago) but overlap with historical records that indicate a recent expansion. Our data support (i) a recent expansion across the Pacific whose timing overlaps with available historical records of establishment and (ii) a strong role for seasonal migration in determining patterns of spatial genetic variation. Our results are noteworthy because they demonstrate how the evolution of partial migration can drive population differentiation over contemporary timescales.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.