Signature of an early genetic bottleneck in a population of Moroccan sardines (Sardina pilchardus)

Hierarchical Neutral and Non-Neutral Spatial Genetic Structuring in the European Sardine (Sardina pilchardus) Revealed by Genomic Analysis: Implications for Management

The European sardine (Sardina pilchardus) sustains some of the most important East Atlantic fisheries and is exhibiting pronounced phenotypic and distributional changes linked to environmental changes. The application of high-resolution genomic methods is recommended to provide insights into population demographics and patterns of ecological and evolutionary diversification. This study performed genome wide SNP analysis of samples collected across understudied NE Atlantic waters as well as geographical outgroup samples from Morocco and the Western Mediterranean. The data revealed pronounced differentiation of three regional groups (NE Atlantic, Morocco, and Western Mediterranean) that can be linked to glacial vicariance and contemporary dispersal limitations. Structuring was also apparent at outlier loci adding to evidence that genome architecture and non-neutral processes are influencing sardine populations at various spatial scales. The highly resolved Morocco group may be a previously undescribed and localized lineage and confirms complex stock structure along the North African coast. Among the NE Atlantic samples, genome wide patterns confirm restricted gene flow between Biscay and North Sea sardine with signatures of isolation by distance. F ST, individual assignment, and introgression tail analyses of outlier loci revealed further structuring and identify a North Sea-Eastern Channel group distinct from a Bay of Biscay-Celtic Sea-Western Channel group. This pattern contradicts current management boundaries and indicates that increasing sardine numbers in the North Sea reflect an expansion of an eastern English Channel-North Sea fringe population. While this confirms the ability of the species' northern peripheral populations to expand in response to changing conditions, the genetically differentiated southern populations may differ in this regard. Overall, this study adds to a developing genetic framework for understanding sardine biocomplexity and provides resources for management.

Tracing metals in Mediterranean and Atlantic Sardina pilchardus: Unveiling impacts on food safety

This study evaluates the concentration of metals and trace elements (Al, Cd, Cu, Fe, Li, Pb, Zn) in the muscle tissue of Sardina pilchardus from three northeast Atlantic localities (Lisbon, Canary Islands, Rabat) and two western Mediterranean sites (Málaga, Cartagena) to assess food safety and environmental impact. A total of 100 sardines were sampled between January and June 2019, with specimens collected, homogenized by size and weight, and analyzed for metal content using Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES). Results show significant geographical variation in metal concentrations, with Cartagena exhibiting the highest levels due to industrial and urban activities, while the Canary Islands had the lowest, likely influenced by geographical isolation and stringent environmental regulations. Intermediate levels were observed in Lisbon, Rabat, and Málaga, with Rabat ranking second highest. Importantly, none of the samples exceeded EU safety limits for lead (0.3 mg/kg) or cadmium (0.25 mg/kg), confirming their suitability for human consumption regarding metal content. These findings emphasize the role of local environmental and industrial factors in influencing metal bioaccumulation in marine ecosystems. Genetic and ecological dynamics, such as the Almería-Oran Front and the Canary Islands' isolation, likely contribute to these patterns. The study underscores the importance of continuous monitoring to safeguard food safety and marine ecosystem health. Despite Cartagena's elevated contamination levels, which pose a higher potential risk if sardine consumption is frequent, sardines from all locations remain within safety limits. Moving forward, research should prioritize long-term monitoring and explore genetic and ecological factors influencing bioaccumulation trends, contributing to sustainable management and effective pollution control measures. This highlights the interconnectedness of environmental health and human dietary safety, emphasizing the need for a proactive approach to monitoring marine contamination.

Genomic analysis of NE Atlantic sardine (Sardina pilchardus) reveals reduced variation in a recently established North Sea population and directs reconsideration of management units

The European sardine (Sardina pilchardus) is under intense fishing pressure and exhibits distributional/abundance shifts linked to environmental change. The current understanding of population demographics needed for sustainable management is uncertain due to concerns that previous genetic studies lacked resolution and limited sampling of sardine north of the Bay of Biscay. To address these issues, we performed mtDNA sequencing and genome wide SNP analysis of samples collected across the Bay of Biscay, Celtic Sea, English Channel and North Sea. The complete SNP data reported a lack of structure throughout the sampled area compatible with high gene flow. A consensus suite of positive outlier SNPs was identified which reported a significant correlation with geographical distance with the largest differentiation between the southern Bay of Biscay and North Sea samples which also reported a significant mtDNA ΦST. While the roles of dispersal limitation and environmental heterogeneity underpinning this require further study, this adds to growing evidence that selection is influencing sardine population structure against a background of high gene flow. The results indicate that while there may be a level of demographic independence between North Sea and South Biscay sardine, the current delimitation of central (Biscay) and northern (Channel and Celtic Sea) operational stocks may misrepresent connectivity between the Biscay and Channel. The North Sea sample exhibited markedly lower mtDNA and nuclear variation than other samples. As sardine have only recently invaded the North Sea such reduced genetic variation is compatible with predictions for peripheral leading-edge populations but contrasts with patterns for other small pelagic species and emphasises the need to consider species-specific genetic structure in ecosystem-based management. Nascent management of the North Sea sardine fishery must ensure that current low levels of genetic diversity are not eroded further as this may decrease the species adaptive potential and inhibit its expansion.

Santamaría MT, Faria R, Machado AM, Fonseca MM, Froufe E, C. Castro LF. Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia

The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.

Comparing otolith shape descriptors for population structure inferences in a small pelagic fish, the European sardine Sardina pilchardus (Walbaum, 1792)

Otolith shape analysis has been one of the most used approaches to study population structure in the past decades. Currently, two sets of shape descriptors are used to perform otolith shape analysis, namely, Elliptic Fourier descriptor (EFd), which focuses on the overall otolith shape differences, and Discrete Wavelet descriptor (DWd), which is sensible to local differences along the otolith contour. Here, the authors conducted a comparative analysis of the performance of both the descriptors in reconstructing the population structure and connectivity patterns in a small pelagic fish species with a wide geographical distribution and fast growth rate, the European sardine Sardina pilchardus (Walbaum, 1792), for the first time. A combination of each otolith shape descriptor and shape indices was explored using multivariate statistical methods. The two otolith shape descriptors showed similar, although limited, overall classification success associated with the population dynamic characteristics of the species. Both descriptors point to migration among adjacent areas, such as northern Atlantic locations, eastern Mediterranean and even across well-defined physical obstacles, such as the Strait of Gibraltar, among Atlantic and western Mediterranean locations. Both descriptors supported the division of the populations of Mediterranean waters into three main groups but slightly differed in the group limits of the Atlantic waters. A comparison of the present results with those from previous otolith shape analysis studies using EFd on a decadal time scale revealed differences in the population structure and connectivity patterns compared to the earlier period. These differences not only may be attributed to changes in environmental variables leading to changes in population dynamics but can also be the result of the sardine biomass sharp decrease that occurred in the past decade.

Population Genetic Study on the European Flounder (Platichthys flesus) from the Southern Baltic Sea Using SNPs and Microsatellite Markers

The European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen's observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive alterations in its gene pool due to increased fishing pressure. For this purpose, 190 fish were collected from four locations along the central coastline of Poland, i.e., Mechelinki, Władysławowo, the Vistula Lagoon in 2018, and the Słupsk Bank in 2020. The fish were morphologically analyzed and then genetically screened by the application of nineteen microsatellite DNA and two diagnostic SNP markers. The examined European flounder specimens displayed a high level of genetic diversity (PIC = 0.832-0.903, I = 2.579-2.768). A lack of significant genetic differentiation (Fst = 0.004, p > 0.05) was observed in all the examined fish, indicating that the European flounder in the sampled area constitutes a single genetic cluster. A significant deficiency in heterozygotes (Fis = 0.093, p < 0.05) and overall deviations from Hardy-Weinberg expectations (H-WE) were only detected in fish sampled from the Słupsk Bank. The estimated effective population size (Ne) among the sampled fish groups varied from 712 (Słupsk Bank) to 10,115 (Władysławowo and Mechelinki). However, the recorded values of the Garza-Williamson indicator (M = 0.574-0.600) and the lack of significant (p > 0.05) differences in Heq > He under the SMM model did not support the species' population size changes in the past. The applied SNP markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. The analysis of an association between biological traits and patterns of genetic diversity did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish that might be caused by increased fishing pressure.

Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter includes how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to global change. Here, under a seascape genomic approach, ddRAD data of 4609 single nucleotide polymorphisms (SNPs) from 398 sardines (Sardina pilchardus) collected in 11 Mediterranean and one Atlantic site were generated. These were used along with oceanographic and ecological information to detect signals of adaptive divergence with gene flow across environmental gradients. The studied sardines constitute two clusters (F_ST  = 0.07), a pattern attributed to outlier loci, highlighting putative local adaptation. The trend in the number of days with sea surface temperature above 19°C, a critical threshold for successful sardine spawning, was crucial at all levels of population structuring with implications on the species' key biological processes. Outliers link candidate SNPs to the region's environmental heterogeneity. Our findings provide evidence for a dynamic equilibrium in which population structure is maintained by physical and ecological factors under the opposing influences of migration and selection. This dynamic in a natural system warrants continuous monitoring under a seascape genomic approach that might benefit from a temporal and more detailed spatial dimension. Our results may contribute to complementary studies aimed at providing deeper insights into the mechanistic processes underlying population structuring. Those are key to understanding and predicting future changes and responses of this highly exploited species in the face of climate change.

Molecular phylogenetic and morphometric analysis of population structure and demography of endangered threadfin fish Eleutheronema from Indo-Pacific waters

The threadfin Eleutheronema are the important fishery resources in Indo-Pacific regions and classified as the endangered species with considerable conservation values. Their genetic diversity and population structure remain essentially unknown but are critical for the proper management and sustainable harvests of such important fisheries. Here, the mitochondrial DNA sequences of CO1 and 16s rRNA were determined from 75 individuals of Eleutheronema tetradactylum and 89 individuals of Eleutheronema rhadinum collected from different locations of South China Sea and Thailand coastal waters. Genetic diversity analysis revealed that both E. tetradactylum (Haplotype diversity, H = 0.105–0.211; Nucleotide diversity, π = 0.00017–0.00043) and E. rhadinum (H = 0.074–0.663, π = 0.00013–0.01088) had low diversity. Population structure analysis demonstrated the shallow genetic differentiation among the South China Sea populations. The limited communication between China and Thailand populations caused the high genetic differentiation in all groups due to the low dispersal ability. Reconstruction of CO1 phylogenetic relationships and demographic studies across Indo-West-Pacific regions provided strong evidence for a shared common origin or ancestor of E. tetradactylum and E. rhadinum. Eleutheronema rhadinum were further subdivided into two distinct genetic lineages, with Clade A dominantly distributing in Thailand and Malaysia and Clade B distributing in China coastal waters. Phenotypic divergence, characterized mainly by the depth of caudal peduncle and length of caudal peduncle, was also observed for all populations, which was possibly associated with specific local adaptations to environmental changes. Our study suggested a strong need for the development of proper fishery management strategies and conservation actions for the imperiled Eleutheronema species.

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

Background

The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.

Findings

The genome of a single female individual was sequenced using Illumina HiSeq X Ten 10x Genomics linked reads, generating 113.8 gigabase pairs of data. Three draft genomes were assembled: 2 haploid genomes with a total size of 935 megabase pairs (N50 103 kilobase pairs) each, and a consensus genome of total size 950 megabase pairs (N50 97 kilobase pairs). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of 11 tissues were sequenced to aid the functional annotation of the genome, resulting in 40,777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of >2.3 million phased single-nucleotide polymorphisms with heterozygous loci.

Conclusions

A draft genome was obtained, despite a high level of sequence repeats and heterozygosity, which are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data will be a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.

Genetic diversity and population structure of the blue jack mackerel Trachurus picturatus across its western distribution

Blue jack mackerel Trachurus picturatus collected at six sampling locations of the north-east Atlantic Ocean (Azores, Madeira, Canaries, and Matosinhos, Peniche and Portimão, mainland Portugal) and one location in the Mediterranean (Sicily), were used to examine the genetic structure of this species. Three mitochondrial gene regions (cytochrome c oxidase subunit I, cytochrome b and control region) were used to study the genetic structure of the species in Macaronesia, as well as to compare the genetic diversity of this region with published results from its eastern distribution. All markers indicated the absence of genetic structure among populations, with high indices of genetic diversity. These results suggest that the species went through a bottleneck event, followed by a recent population expansion. Moreover, the comparison with previously published results from the T. picturatus Mediterranean distribution suggests the existence of a single panmictic population throughout the species' full range. This was, however, an unexpected result since other methodologies have shown the presence of, at least, three different population-units in the NE Atlantic Ocean.

Testing spatial heterogeneity with stock assessment models

This paper describes a methodology that combines meta-population theory and stock assessment models to gain insights about spatial heterogeneity of the meta-population in an operational time frame. The methodology was tested with stochastic simulations for different degrees of connectivity between sub-populations and applied to two case studies, North Sea cod (Gadus morua) and Northeast Atlantic sardine (Sardina pilchardus). Considering that the biological components of a population can be partitioned into discrete spatial units, we extended this idea into a property of additivity of sub-population abundances. If the additivity results hold true for putative sub-populations, then assessment results based on sub-populations will provide information to develop and monitor the implementation of finer scale/local management. The simulation study confirmed that when sub-populations are independent and not too heterogeneous with regards to productivity, the sum of stock assessment model estimates of sub-populations’ SSB is similar to the SSB estimates of the meta-population. It also showed that a strong diffusion process can be detected and that the stronger the connection between SSB and recruitment, the better the diffusion process will be detected. On the other hand it showed that weak to moderate diffusion processes are not easy to identify and large differences between sub-populations productivities may be confounded with weak diffusion processes. The application to North Sea cod and Atlantic sardine exemplified how much insight can be gained. In both cases the results obtained were sufficiently robust to support the regional analysis.

High genetic diversity and low-population differentiation in the Patagonian sprat (Sprattus fuegensis) based on mitochondrial DNA

The Patagonian sprat, Sprattus fuegensis, is a small pelagic marine fish that inhabits the continental shelf along the coasts of Chilean Patagonian and Argentina, a distribution that was highly impacted during the Last Glacial Maximum (LGM). In order to identify how the LGM played a role on the current observed genetic diversity and population structure of S. fuegensis, we analyzed 1438 nucleotide positions from the control region of 335 individuals collected at 12 sites across its distribution. Genetic diversity and differentiation indices were calculated to identify population structure, and a Bayesian skyride plot (BSRP) reconstruction was carried out to infer the historic population dynamics. Extremely high genetic diversity was found at all locations analyzed, non-population structure was found across its distribution, and the BSRP showed two increases in effective population size over time. Our outcomes suggest that the current genetic diversity, population structure and population expansion may have occurred during the medium and late Pleistocene.

Sharing fishers´ ethnoecological knowledge of the European pilchard (Sardina pilchardus) in the westernmost fishing community in Europe

BACKGROUND

With the present difficulties in the conservation of sardines in the North Atlantic, it is important to investigate the local ecological knowledge (LEK) of fishermen about the biology and ecology of these fish. The ethnoecological data of European pilchard provided by local fishermen can be of importance for the management and conservation of this fishery resource. Thus, the present study recorded the ethnoecological knowledge of S. pilchardus in the traditional fishing community of Peniche, Portugal.

METHODS

This study was based on 87 semi-structured interviews conducted randomly from June to September 2016 in Peniche. The interview script contained two main points: Profile of fishermen and LEK on European pilchard. The ethnoecological data of sardines were compared with the scientific literature following an emic-etic approach. Data collected also were also analysed following the union model of the different individual competences and carefully explored to guarantee the objectivity of the study.

RESULTS

The profile of the fishermen was investigated and measured. Respondents provided detailed informal data on the taxonomy, habitat, behaviour, migration, development, spawning and fat accumulation season of sardines that showed agreements with the biological data already published on the species. The main uses of sardines by fishermen, as well as beliefs and food taboos have also been mentioned by the local community.

CONCLUSIONS

The generated ethnoecological data can be used to improve the management of this fishery resource through an adaptive framework among the actors involved, in addition to providing data that can be tested in further ecological studies. Therefore, this local knowledge may have the capacity to contribute to more effective conservation actions for sardines in Portugal.

Spatio-temporal patterns of genetic variations in populations of yellowtail kingfish Seriola lalandi from the south-eastern Pacific Ocean and potential implications for its fishery management

The genetic population structure and genetic diversity of yellowtail kingfish Seriola lalandi from the coastal south-eastern Pacific Ocean (SEP) were evaluated at spatiotemporal scale in order to understand the ecology of this species. Between 2012 and 2015, temporal and spatial population genetic structure and a low genetic diversity were detected in S. lalandi from SEP. These results suggest that S. lalandi specimens arriving annually from offshore to the SEP coast could come from at least two genetically distinct populations, revealing a particular life strategy (i.e. reproductive or habitat segregation) for this fish species. Therefore, the SEP coast might constitute a point of population mixing for this species. Additionally, the low genetic diversity of S. lalandi in the SEP could be a result of a founder effect or overfishing. Regardless of the process explaining the genetic diversity and structure of S. lalandi in this geographical area, this new information should be considered in order to implement successful fishery management of this resource in the South Pacific.

Population genetic structure of Indian oil sardine, Sardinella longiceps along Indian coast

Genetic stock structure and historical demography of Indian oil sardine, a commercially and ecologically important small pelagic fish, was studied using mitochondrial control region and Cytochrome C Oxidase I (COI) sequences. A 758 bp portion of the control region in 287 individuals and a 576 bp portion of the COI gene in 291 individuals from 10 locations along the distribution range were amplified resulting in 236 and 84 haplotypes, respectively. The high haplotype and low nucleotide diversity values (0.99 and 0.19 for control region and 0.85 and 0.004 for COI, respectively) are characteristic of populations having undergone a demographic expansion. Genetic differentiation, ΦST, was low and insignificant between populations using both control region and COI gene markers. Mismatch analysis showed a recent demographic and spatial expansion coinciding with the late Pleistocene epoch. Mantel tests revealed the lack of isolation by distance which is attributable either to high levels of migration overriding the effect of genetic drift or to insufficient time for accomplishing a balance between migration and drift after a recent range expansion.

Hidden diversity in sardines: genetic and morphological evidence for cryptic species in the goldstripe sardinella, Sardinella gibbosa (Bleeker, 1849)

Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine.

Pelagic life and depth: coastal physical features in West Africa shape the genetic structure of the Bonga Shad, Ethmalosa fimbriata

The bonga shad, Ethmalosa fimbriata, is a West African pelagic species still abundant in most habitats of its distribution range and thought to be only recently affected by anthropogenic pressure (habitat destruction or fishing pressure). Its presence in a wide range of coastal habitats characterised by different hydrodynamic processes, represents a case study useful for evaluating the importance of physical structure of the west African shoreline on the genetic structure of a small pelagic species. To investigate this question, the genetic diversity of E. fimbriata was assessed at both regional and species range scales, using mitochondrial (mt) and nuclear DNA markers. Whereas only three panmictic units were identified with mtDNA at the large spatial scale, nuclear genetic markers (EPIC: exon-primed intron-crossing) indicated a more complex genetic pattern at the regional scale. In the northern-most section of shad’s distribution range, up to 4 distinct units were identified. Bayesian inference as well as spatial autocorrelation methods provided evidence that gene flow is impeded by the presence of deep-water areas near the coastline (restricting the width of the coastal shelf), such as the Cap Timiris and the Kayar canyons in Mauritania and Senegal, respectively. The added discriminatory power provided by the use of EPIC markers proved to be essential to detect the influence of more subtle, contemporary processes (e.g. gene flow, barriers, etc.) acting within the glacial refuges identified previously by mtDNA.

Population genetic structure of the striped silverside, Atherinomorus endrachtensis (Atherinidae, Atheriniformes, Teleostei), inhabiting marine lakes and adjacent lagoons in Palau: marine lakes are "Islands" for marine species

Although evidence for the evolution of terrestrial species on islands continues to rapidly accumulate, little is known about the evolution of marine species in geographically isolated environments such as islands as ocean currents often facilitate gene flow among populations. In this study, we focused on marine lakes of the Palau Islands, which are considered to be true analogues of terrestrial islands for marine species. To examine evolutionary processes in marine lakes, we conducted population genetic analyses on marine lake and lagoon populations of the striped silverside, Atherinomorus endrachtensis, using two mitochondrial DNA markers differing in evolutionary rate, the cytochrome b gene and the control region. The analyses revealed that the amount of genetic diversity of marine lake populations is much lower than that of lagoon populations and high levels of genetic differentiation occur among marine lake and lagoon populations. The present study has shown that marine lake populations have been completely isolated and have differentiated from lagoon populations, and each marine lake population is experiencing different evolutionary processes. These findings clearly demonstrate that marine lakes are excellent environments for the evolutionary study of marine species.

Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus)

Background

Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (Sardina pilchardus) is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies (S. p. pilchardus and S. p. sardina).

Results

We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods (hierarchical AMOVA test and R_ST pairwise comparisons) supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test.

Conclusion

We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.

Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break?

The geological history of the Mediterranean Sea, its hydrography and connection with the Atlantic Ocean have been well documented. Despite a wealth of historical and oceanographic data, the Atlantic-Mediterranean transition remains controversial at the biological level as there are discordant results regarding the biogeographical separation between the Atlantic and Mediterranean biota. The opening of the Strait of Gibraltar at the end of the Messinian Salinity Crisis (some 5.33 million years ago), removed the land barrier that impeded the marine biota allowing it to disperse freely into the Mediterranean Sea. However, present day genetic patterns suggest a limitation to gene flow for some marine species, preventing population admixture. In the last few years, a large number of studies have challenged the hypothesis of the Strait of Gibraltar representing a phylogeographical break. A review of more than 70 papers reveals no obvious relationship between either dispersal ability or life history, and observed patterns of partial or complete genetic isolation between Atlantic and Mediterranean populations. We re-analysed a selection of this large body of data (20 studies in total) in order to provide a homogeneous and coherent view on the generality of the phylogeographical patterns and the presence of a phylogeographical barrier. This offered the opportunity to summarize the state of the art on this matter and reach some general conclusions on the evolutionary history across the Atlantic-Mediterranean range. Geographically, some species in the transition zone showed step changes of allele frequencies associated with the Almeria-Oran Front rather than with the Strait of Gibraltar itself. A major part of the data describe evolutionary events well within the time frame of the Quaternary age as very few taxa pre-date closure of the Tethys Sea. Results point to a combined signature of vicariance, palaeoclimate fluctuation and life-history traits on the Atlantic-Mediterranean phylogeographical patterns. Principal component analysis failed to show any particular association between biological traits and genetic variables. It would argue that organismal determinism may play a far less significant role than marine biogeographers have generally believed.

Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis)

Climatic oscillations during the Pleistocene ice ages produced great changes in species' geographical distribution and abundance, which could be expected to have genetic consequences. Living in the temperate upwelling zones of the northwestern Pacific, Japanese anchovy (Engraulis japonicus) might have been affected by these severe climatic oscillations. To investigate the effects of Pleistocene climatic changes on the evolution in Japanese anchovy, fragments of 522 bp at the 5' end of mitochondrial DNA control region were sequenced for 241 individuals from 13 localities and 37 individuals of Australian anchovy. Japanese anchovy and Australian anchovy are reciprocally monophyletic and a late Pleistocene transequatorial divergence between the two species was indicated. High levels of haplotype diversity (>0.99) were found for all samples, indicating a high level of genetic diversity. Analyses of molecular variance and the conventional population statistic F(ST) revealed no significant genetic structure throughout the range of Japanese anchovy. Both mismatch distribution analyses and neutrality tests suggested a late Pleistocene population expansion for both Japanese anchovy (79,000-317,000 years ago) and Australian anchovy (45,000-178,000 years ago).