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Mantel test correlating pairwise linearized genetic distances (FST/(1−FST)) vs. geographical distances (shortest waterway distance in kilometre) between all glass eel sampling locations considering (a) all RAD sequences and (b) mitochondrial RAD sequences only.
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Next generation sequencing and the collection of genome-wide data allow identifying adaptive variation and footprints of directional selection. Using a large SNP data set from 259 RAD-sequenced European eel individuals (glass eels) from 8 locations between 34 to 64oN, we examined patterns of genome-wide genetic diversity across locations. We tested...
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... testing. An MDS plotting the first and second coordi- nates obtained from pairwise genetic distances showed all samples clustering together fitting no apparent geo- graphical pattern (Fig. S1a, Supporting information). A Mantel test showed no correlation between genetic and waterway distances (r = À0.232; P = 0.250), which suggests no IBD pattern (Fig. ...
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... locations after Bonfer- roni correction. However, pairwise F ST values were significant at five of 28 comparisons, all involving Iceland. Concordantly, Iceland was the most distant sample in the MDS analysis (Fig. S1b, Supporting infor- mation) and also contributed to the observed positive but nonsignificant pattern of IBD (r = 0.311; P = 0.107; Fig. ...
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Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla) and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphologica...
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... These approaches have shown to be a combination to reduce type I and II error rates [16,61,62]. Some authors suggest that the SNP-environment association approach may be more sensitive to variations in allele frequencies and that it might be difficult to capture the adequate environmental factors [63,64]. When comparing both approaches, the two loci were identified in common: dDo-cent_Contig_17536, dDocent_Contig_31244; in this case, we used all o-SNP with both approaches. ...
Populations of highly mobile species that undertake long distance migrations are typically considered to be panmictic. Nonetheless, mechanisms related to behavior or local environmental conditions promote genetic isolation in the absence of physical barriers. Highly migratory shark species exhibit varying levels of fidelity to specific regions, shaping the genetic architecture of different populations and resulting in geographically based genetic variation with potential adaptive value. An understanding of the genetic variation of highly migratory species is needed to develop effective conservation strategies. This study aimed to assess the neutral and adaptive variation of the smooth hammerhead shark (Sphyrna zygaena) in the northern Mexican Pacific (NMP) via single nucleotide polymorphisms (SNPs). We analyzed 1480 SNPs in 92 individuals from four geographic regions in the NMP, of which 1469 SNPs were neutral loci (n-SNP), and 11 were putatively under selection (o-SNP) using four genoma scan methods. Genetic diversity was geographically similar among regions (Ho = 0.275). The neutral variation showed panmixia (n-SNPs; FST = 0.0012, p = 0.44), which may be associated with the high dispersal capacity of S. zygaena. A pattern of adaptive variation between individuals from the Gulf of California and Pacific coast was revealed using o-SNPs FST-based methods (24 oSNPs; FST = 0.061, p < 0.001), which may be promoted by individual preferences based on physiological limitations. The estimated effective population size (Ne) of S. zygaena was 1390 individuals, which is theoretically optimal for the population to persist over time.
... The absence of intermediate forms suggests that strong disruptive selection plays a role in the observed pattern of variation (Cucherousset et al., 2011). However, random mating and larval dispersal ensure no apparent genetic structuring or reproductive isolation between these forms (Als et al., 2011;Pujolar et al., 2014). In this species (and probably many others), phenotypic structuring may be purely plastic through the mechanism of differential gene expression (De Meyer et al., 2016). ...
Patterns in phenotypic and genotypic diversity within many species are becoming increasingly apparent, although there remain many species for which such patterns have yet to be described adequately.
Fishes from recently glaciated ecosystems are likely to be particularly rich in intraspecific diversity, yet current conservation management strategies are, in many parts of the world, particularly in Europe, conventionally and overwhelmingly focused on species, regardless of competing species concepts, and appropriate policies for managing diversity at a sub‐specific level still have to be developed.
Occasional attempts to protect certain vulnerable ecotypes and proposed alternative units of conservation (e.g. ‘Pragmatic Species’ or ‘Evolutionarily Significant Units’) reinforce the conventional primacy of contemporary expressed patterns of variation.
Intraspecific phenotypic and genotypic patterns are ultimately the result of complex processes of divergence; conservation approaches that focus on the products of evolution largely ignore the processes that generate and maintain those patterns. Policies that acknowledge the continuation of evolution, the derivation of novel diversity over often very short time spans and the role of environment in initiating and perpetuating these processes are poorly integrated into management strategy.
To address possible deficits, where intraspecific diversity is not addressed in management practice, we believe it to be important first to characterize hidden genetic and phenotypic diversity, which may intimate eco‐evolutionary processes, initially among species of high conservation status. A second step should be to use an approach to intraspecific diversity that illuminates the ultimate processes and mechanisms that bring about that diversity, which also concedes the central role of the environment and affords adequate protection to the ecosystems that drive these processes, such as the United Nations Convention on Biological Diversity (CBD) Ecosystems approach.
... To address the bad state of this species, the European Union adopted a management plan for the recovery of eel stock through an EU regulation (i.e., Regulation EU 2017/1004), which provides for the release of 40 % silver eel caught. Because the species is a unique stock with a European distribution [10], [11], and its conservation depends on recruitment and emigration from each basin, it is very important to collect the data on the presence of migrating eels and their stage of maturity. ...
The eel (Anguilla anguilla) population in Europe has declined dramatically since the 1980s and shows no signs of recovery. There are several threats to this species: migratory barriers, loss of habitats, hydroelectric dams, overfishing, and illegal trade. As a result, the eel has become part of the ICUN endangered species and is protected by various institutions. Information data on the maturation stage is needed to monitor silver eel escapement and assess population trends. In the sampling activities spanning from 2012 to 2022 silver index was calculated on 1852 eels in the northern Adriatic Sea. With the help of machine learning technology, we trained an algorithm in pupil recognition and the calculation of horizontal eye diameter in eels. This study allowed us: a) to identify a single parameter to discriminate the sexual maturity of the eel and thus to know the female with a migratory instinct; b) to use this parameter as a proxy to develop an easy and user-friendly app for all management operators.
... For example, Washburn et al. (2020) described low levels of genetic structure in the Tuxedo Darter (E. lemniscatum; F st = 0.01); see also Heggenes and Røed (2006); Als et al. (2011);Feijoo et al. (2011);and Pujolar et al. (2014) for panmictic vertebrate populations with F st < 0.01. Fluker et al. (2010Fluker et al. ( , 2014a showed moderate-high levels of population structure with F st > 0.20 for three groundwater-dependent darters (see also Online Resource 1; Table S4). ...
The southeastern United States is a hotspot of biodiversity, but aquatic habitats are fragmented by anthropogenic activities such as hydrologic alteration. Small-stream-inhabiting fish can suffer population declines, loss of genetic diversity, and migration impediment from riverine impoundment. The Trispot Darter (Etheostoma trisella) is a small, freshwater fish endemic to the southeastern United States. E. trisella was previously believed to be extinct and has now been listed as threatened under the U.S. Endangered Species Act, due to destruction of its limited habitat and a restricted range. We used mitochondrial DNA (NADH dehydrogenase subunit 2 gene), seven microsatellite loci, and 9732 single nucleotide polymorphisms (SNPs) to evaluate population structure and diversity in E. trisella. Mitochondrial data provided evidence of historical connectivity between populations, with haplotype sharing across populations and weak support for population structure. Microsatellite and SNP data, however, indicate that populations have more recently become isolated. Furthermore, we detect three distinct management units (i.e., genetic groups) which reflect isolated geographic localities (i.e., Little Canoe Creek, Ballplay Creek, and a system including the Conasauga and Coosawattee rivers). We also detected a recent bottleneck event in the Ballplay Creek population as well as a low effective population size. Tests of isolation by distance further suggest that populations are structured by riverine isolation rather than geographic distance. A better understanding about the distribution, abundance, and habitat occupancy of all E. trisella populations will be important for informing future decisions for conservation of the species.
... The pertinence of using otoliths to study development and environmental adaptations in this species may be related to the conservation status of the eel, which is actually in decline and listed as critically endangered, and may support a better understanding of the roles of different habitats to sustain and conserve the species [39,40]. Due to its catadromous life cycle, its wide geographical distribution range, its genomic panmixia, and its ability to live in different aquatic environments, the eel is particularly well suited for understanding how growth is influenced by environmental conditions [28,29,41]. Nevertheless, the body growth of eels can vary significantly within the same subpopulation because of interindividual variation and geographically different habitats [24,29,38,42,43]. ...
An otolith shape and morphometric analysis was performed on European eel (Anguilla anguilla) subpopulations from five rivers and three coastal lagoons of Sardinia (central-western Mediterranean) to assess the role of different habitats on otolith development. Sagittal otolith shape was described by 11 harmonics from elliptic Fourier descriptors. Comparisons among the harmonics were run through canonical discriminant analyses (CDAs). The CDA reclassification rate (75.7%) demonstrated a spatial environmental discrimination among local eel subpopulations of Sardinia. The Euclidean distance values demonstrated a dissimilarity between the river and lagoon groups. The form factor and roundness shape indices were significantly higher in the river group than in the lagoon group. The distances of the first three rings to the otolith core revealed site-specific otolith development. Moreover, the annual otolith growth rate was faster in the lagoon group than in the river group. The differences among the studied sites in terms of sagittal otolith shape could relate to changes in different local stocks potentially related to environmental peculiarities. Establishing a direct correlation between otolith morphology and environmental factors is challenging, and further studies are needed to investigate the relationship between habitat type/environmental variation and growth/body characteristics of eels. Nevertheless, the achieved results suggest that this method can be considered to be a valuable tool for studying the ontogeny of the European eel. Key Contribution: An otolith shape analysis was performed on European eel subpopulations from five rivers and three lagoons of Sardinia. The obtained differences could lead to changes in different local stocks related to environmental peculiarities.
... Genomic studies of other marine species revealed the occurrence of outliers in metapopulations that were also exhibiting structure at neutral markers (Nielsen et al., 2009;Bradbury et al., 2010;Limborg et al., 2012;Laconcha et al., 2015). However, outlier loci were also discovered in metapopulations where no significant spatial structure was observed at neutral loci (Lamichhaney et al., 2012;Pujolar et al., 2014;Grewe et al., 2015). It is possible that blackfin tunas utilize their high capacity for movement to select habitats with favourable characteristics across their range leading to little or no local selection, although the wide range utilized by the species suggests that regional populations would differ by some environmental characteristics such as the differences in reproductive season timing discussed above for the South American group. ...
Blackfin tuna (Thunnus atlanticus) is a small tuna distributed in the western Atlantic Ocean where it is exploited by growing recreational and commercial regional fisheries. In this work, genome-wide genetic variation was analysed to investigate the occurrence of stock subdivision. A de novo assembly of the blackfin tuna genome was generated using Illumina paired-end sequencing data and applied as a reference for population genomic analysis of specimens from nine localities (average sample size per locality n = 72) spanning most of the blackfin tuna distribution range. A total of 2139 single-nucleotide polymorphisms were discovered and genotyped using the double-digest restriction associated DNA sequencing. Pairwise exact homogeneity tests were significant in 24 out of 36 population pairs and significant spatial autocorrelation of genotypes was observed for specimens collected within 2250 km of each other. However, divergence among locality samples was very low (pairwise FST range 0.0002–0.0025) and significant temporal variations were detected in localities sampled multiple times. Approaches to detect cryptic groups de novo were unsuccessful. Additional sampling is warranted to determine if multiple stocks need to be defined for management and assess temporal and spatial patterns of gene flow connecting them.
... We also assume evolutionarily stable ESD (Charnov and Bull 1989), meaning that the proportions of males and females initially established are determined by selection acting through environmental conditions )-and that no mutant strategy based on different proportions can achieve higher fitness. Although eel panmixia (Pujolar et al. 2014) would prevent any occurrence of heritable local adaptation (Schmidt 1925;Tesch 2003), genetic differentiation could be generated by spatial and temporal segregation in the reproductive events (Wirth and Bernatchez 2001;Jacobsen et al. 2018) and in the alternative migration timing and pathways of larvae across the ocean, as observed in the phenology of arrivals of glass eels (Pujolar et al. 2014;Bornarel et al. 2018). Moreover, the colonization of contrasted habitats within the downstream-upstream gradient of river basins could generate epigenetic (e.g. ...
... We also assume evolutionarily stable ESD (Charnov and Bull 1989), meaning that the proportions of males and females initially established are determined by selection acting through environmental conditions )-and that no mutant strategy based on different proportions can achieve higher fitness. Although eel panmixia (Pujolar et al. 2014) would prevent any occurrence of heritable local adaptation (Schmidt 1925;Tesch 2003), genetic differentiation could be generated by spatial and temporal segregation in the reproductive events (Wirth and Bernatchez 2001;Jacobsen et al. 2018) and in the alternative migration timing and pathways of larvae across the ocean, as observed in the phenology of arrivals of glass eels (Pujolar et al. 2014;Bornarel et al. 2018). Moreover, the colonization of contrasted habitats within the downstream-upstream gradient of river basins could generate epigenetic (e.g. ...
We implement a newly developed framework, expressed as a mathematical model that we solve numerically, for understanding environmental sex determination in populations with consistent trends in abundance. Though broadly applicable, the analysis here focuses on the steadily declining North Atlantic eel populations. This enables us to show how the eco-evolutionary dynamics of eels reflect sex-specific and habitat-specific relationships among demographic features. When increasing stress levels resulting from Human-Induced Rapid Environmental Change are imposed on these populations, they become increasingly vulnerable to highly biased sex ratios. Our analysis is both prescriptive (identifying the key components and the priorities for deepening our understanding of them) and predictive (indicating expected qualitative patterns to be tested in future work). Priorities include establishing sex ratios and age/sex structure by habitat, measuring the magnitude and effects of social and individual stress levels, estimating effects of fishing pressure, and investigating reproduction in the Sargasso Sea. Key predictions address expected biases and trends in sex ratios, habitats more likely to be population sources (e.g. river basins) or sinks (e.g. estuary), expected trends in bimaturism (sex-specific maturation times), implications of the relative speed of adaptation and of environmental deterioration, and fitness responses to stress levels, early-stage mortality, and female demographic parameters.
... This drastic reduction of eel population led the European eel to be listed in 2007 on the IUCN red list as a critically endangered species (Jacoby and Gollock, 2014;Pike et al., 2020) and the European Union to mandate each of its member country to write an eel management plan to restore eel population (European Council, 2007). The second consequence of eel life cycle, is that eel population is a single panmictic population (Als et al., 2011;Pujolar et al., 2014;Enbody et al., 2021). The panmixia in eel population plead for a global management of this population all over its transnational repartition (Als et al., 2011). ...
The European eel, Anguilla anguilla, is an emblematic facultative catadromous species that spawns in the Sargasso Sea and grow in continental waters of Europe and North Africa. In most of its growing habitats its population has dropped since 1980. Although Mediterranean lagoons represent particularly important habitats for eel, knowledge of eel ecology in lagoons is not as developed as it is in rivers. Particularly, data on the phenology, drivers and biometrics characteristics of glass eel entering lagoons are scarce. To address this lack of data, the abundance, pigmentation stage, size, and weight of glass eel entering the Bages-Sigean lagoon (western French Mediterranean) were monitored during 647 d from December 2018 to April 2021 using passive floating traps. Simultaneously, different environmental drivers were measured (flow velocity, temperature, rainfalls…). The highest abundances of glass eels were observed between mid-November and mid-March especially when the discharge of the main tributary of the lagoon was higher than its base flow. The glass eels captured during the peak of entrance were less pigmented, longer, and bigger than during other months. This work enabled us to identify periods when anthropogenic activities should be limited to decrease human-based impact on glass eel in similar habitats.
... An ability to withstand environmental variability is often key to a species' range expansions, whether they be natural or human-mediated. Environmental tolerance can be related to or controlled by such mechanisms of adaptation as differences in gene family expression, gene splicing, methylation, past gene duplications and other genomic mechanisms also related to pangenome functions (Pujolar et al. 2014;Malachowicz et al. 2015;Kijewska et al. 2016Kijewska et al. , 2018Bitter et al. 2019;Malachowicz & Wenne 2019;Clark et al. 2021;Corrochano-Fraile et al. 2022;Liu et al. 2022). For example, there is now a growing body of evidence to indicate that M. galloprovincialis is the best adapted smooth-shelled mussel to tolerate thermal variation, an adaptation that may be both facilitating its spread into non-native areas and its ability to outcompete congenerics (e.g., Braby & Somero 2006;Jones et al. 2010;Tomanek & Zuzow 2010). ...
Blue mussels of the genus Mytilus are important ecosystem engineers in intertidal and subtidal communities. The distribution of Mytilus mussels is influenced by a number of benthic and pelagic environmental variables (e.g., substratum type and availability, water movement, phytoplankton production, physical disturbance) as well as interactions between these variables. Because of its broad tolerance of environmental variation the Mediterranean species, Mytilus galloprovincialis, has the greatest ability of all blue mussels to colonise new geographic regions. Understanding how population genetic
variation is related to, or caused by, environmental variation is important but has long been a challenge. The present study examined the genetic differentiation of native populations of M. galloprovincialis throughout its entire geographic range in the Mediterranean Sea, the Black Sea and the Sea of Azov using 53 single nucleotide polymorphisms (SNP loci). Mussels, in total 1004 individuals collected from 36 locations, were genotyped and combined with existing SNP data for mussels from 11 reference sites. Pairwise comparisons of FST values, correspondence analysis (CA) and STRUCTURE analysis all revealed four groups of populations: the Atlantic Ocean; the western Mediterranean; the Aegean Sea; and the Azov, Black and Marmara Seas. One population – from Algeria (Oran West) – was intermediate between the two main groups of the Mediterranean Sea and Atlantic Ocean. Seascape genetic analyses using GLM and DistLM analyses were employed to test site-specific genetic variation as a function of 13 environmental variables. The GLM identified five environmental variables that explained variation in site-specific FST values, whilst in the DistLM best-fit model only four were significant. These analyses suggest that a complex mix of environmental variables contribute to explaining genetic variation of M. galloprovincialis populations within the Mediterranean Sea, which most likely reflects the complex geological history of formation,
isolation and reconnection among the regional sub-basins of the Sea.
... In this case, additional information from the RADseq dataset is provided by separating organellar reads from the nuclear ones without further sequencing effort. The utility of this approach, what we may term as 'organellar mining', was only addressed in a handful of studies (Clugston et al., 2019;Du et al., 2020;Feng et al., 2017;Forsman et al., 2017;McVay et al., 2017;Meger et al., 2019;Pujolar et al., 2014;Terraneo et al., 2018). All these studies either use existing software-such as Stacks (Rochette et al., 2019) as applied by Stobie et al. (2019) or ipyRAD (Eaton & Overcast, 2020) utilised by Du et al. (2020) or GATK (McKenna et al., 2010) as demonstrated by Meger et al. (2019)-to sort reads from the different genomes, which are sometimes proprietary solutions (e.g. ...
Different versions of Restriction‐site‐Associated DNA sequencing (RADseq) have become powerful and popular tools in molecular ecology. Although RADseq datasets are generally regarded as representative of the nuclear genome, reduced representation genomic libraries may also sample the organellar (i.e. the mitochondrial and, in the case of plants, the plastid) DNA. This cytoplasmic genetic variance provides a better understanding of evolutionary history by uncovering past hybridisation and identifying maternal or, rarely, paternal lineage due to rapid lineage sorting.
We developed a pipeline that is based on existing bioinformatic tools to automatically mine and genotype organellar loci from RADseq libraries. The efficacy of our pipeline is tested on eight publicly available datasets spanning different phylogenetic levels (i.e. from family‐level phylogenies to phylogeography) and RADseq methods (sdRAD, ddRAD, ezRAD, GBS) for genotyping mitochondrial and plastid loci, which were subject to phylogenetic tree reconstruction.
In all cases, organellar phylogenies adequately supplemented the original studies by corroborating the large‐scale picture based on RADseq or by bringing additional evidence on past or contemporary hybridisation. RADseq methods designed to achieve larger horizontal coverage (i.e. ddRAD, ezRAD) yielded longer organellar alignments, but sdRAD and GBS still provided valuable polymorphic organellar loci at no additional sequencing effort.
Our newly developed pipeline can be run under a Unix‐like operating system and is freely accessible at https://doi.org/10.5281/zenodo.6619190
