1
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Boëns A, Ernande B, Petitgas P, Lebigre C. Different mechanisms underpin the decline in growth of anchovies and sardines of the Bay of Biscay. Evol Appl 2023; 16:1393-1411. [PMID: 37622098 PMCID: PMC10445103 DOI: 10.1111/eva.13564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 08/26/2023] Open
Abstract
Declines in individuals' growth in exploited fish species are generally attributed to evolutionary consequences of size-selective fishing or to plastic responses due to constraints set by changing environmental conditions dampening individuals' growth. However, other processes such as growth compensation and non-directional selection can occur and their importance on the overall phenotypic response of exploited populations has largely been ignored. Using otolith growth data collected in European anchovy and sardine of the Bay of Biscay (18 cohorts from 2000 to 2018), we parameterized the breeder's equation to determine whether declines in size-at-age in these species were due to an adaptive response (i.e. related to directional or non-directional selection differentials within parental cohorts) or a plastic response (i.e. related to changes in environmental). We found that growth at age-0 in anchovy declined between parents and their offspring when biomass increased and the selective disappearance of large individuals was high in parents. Therefore, an adaptive response probably occurred in years with high fishing effort and the large increase in biomass after the collapse of this stock maintained this adaptive response subsequently. In sardine offspring, higher growth at age-0 was associated with increasing biomass between parents and offspring, suggesting a plastic response to a bottom-up process (i.e. a change in food quantity or quality). Parental cohorts in which selection favoured individuals with high growth compensation produced offspring high catch up growth rates, which may explain the smaller decline in growth in sardine relative to anchovy. Finally, on non-directional selection differentials were not significantly related to the changes in growth at age-0 and growth compensation at age-1 in both species. Although anchovy and sardine have similar ecologies, the mechanisms underlying the declines in their growth are clearly different. The consequences of the exploitation of natural populations could be long lasting if density-dependent processes follow adaptive changes.
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Affiliation(s)
- Andy Boëns
- IfremerEMH, Centre AtlantiqueNantesFrance
| | - Bruno Ernande
- Université de Montpellier – Campus Triolet – Place E. BataillonMontpellierFrance
| | | | - Christophe Lebigre
- IfremerFisheries Science and Technology Unit, Centre BretagnePlouzanéFrance
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2
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Domingo-Hernández AM, Morales-Yuste M, Buzo-Domínguez S, Adroher FJ, Benítez R. Anisakis infection in anchovies (Engraulis encrasicolus) from Iberian waters, southwestern Europe: Post-mortem larval migration. Res Vet Sci 2023; 157:26-34. [PMID: 36854200 DOI: 10.1016/j.rvsc.2023.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/25/2023]
Abstract
The Anisakis larvae presence in fish for human consumption is a health risk that needs to be monitored. The anchovy is a fish that is highly appreciated by consumers and that can harbour Anisakis. It is thus necessary to periodically evaluate the presence of anisakid larvae in them. So, anchovies from Iberian Peninsula coasts were analysed. Fish examination for macroscopic nematodes showed L3s of both Anisakis type I and Hysterothylacium aduncum. The Anisakis prevalence varies with the catching area and the fish size. The muscle prevalence was 7.45% (mean intensity 1.75; range 1-5). Molecular analysis showed 110 A. simplex s.s. (17 in muscle), 22 A. pegreffii (3) and 7 hybrid genotype individuals (1). Considering that most of the Iberian Peninsula coasts are a sympatry area between these two Anisakis species, it has been observed that A. simplex s.s./A. pegreffii ratio increases from south to north in a clockwise direction. Also, 19 larvae were detected on the fish surface from the Bay of Biscay, indicating the ability of these larvae to migrate after the fish death. The A. simplex s.s./A. pegreffii larvae proportion found on the anchovy surface is similar to the found in viscera and lower than in muscle, suggesting that most of the larvae migrating to the surface must have come from the visceral package. This confirms the importance of removing fish viscera immediately after capture, for those fish species where this is possible. As both species cause anisakiasis/anisakidosis, these data show a real risk to human health, especially in dishes highly prized in Mediterranean countries prepared with raw or semi-raw anchovies.
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Affiliation(s)
| | - Manuel Morales-Yuste
- Department of Parasitology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | - Sara Buzo-Domínguez
- Department of Parasitology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | | | - Rocío Benítez
- Department of Parasitology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
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3
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Inferring Population Structure from Early Life Stage: The Case of the European Anchovy in the Sicilian and Maltese Shelves. WATER 2022. [DOI: 10.3390/w14091427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The European anchovy is an important fishing resource in the Sicilian Channel that supports a high recruitment success variability. The presence of two spawning areas, the drifting of the larvae along the currents and the different oceanographic conditions within the region suggest the presence of different larvae subpopulations. Morphometric and biochemical approaches have been used to analyze the differences among larvae collected. The amino acid composition discriminates two larval groups closely related to the spawning regions: Adventure Bank and the shelf between the South of Sicily and Malta. In addition, there are morphometric and growth differences between recently hatched larvae in these two regions, reinforcing the hypothesis of two larval subpopulations and suggesting differences in the parental reproduction effort. Between the South of Sicily and Malta there are growth and biochemical composition differences since larvae from the Maltese coast present a higher protein content and a bigger growth rate than those from Sicily, pointing out that Malta is an area with a better nutritional condition environment. No differences in the growth rate have been observed between the Adventure Bank area and the Maltese shelf, therefore, a diverse nutritional condition cannot be suggested between these two areas despite the Maltese larvae having a higher protein content present.
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4
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Corral‐Lou A, Perea S, Perdices A, Doadrio I. Quaternary geomorphological and climatic changes associated with the diversification of Iberian freshwater fishes: The case of the genus
Cobitis
(Cypriniformes, Cobitidae). Ecol Evol 2022; 12:e8635. [PMID: 35261740 PMCID: PMC8888266 DOI: 10.1002/ece3.8635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
We studied the population genetic structure of Cobitis vettonica, an endangered freshwater fish species endemic to the Iberian Peninsula, in order to propose a biogeographic model of the responses of species to the multiple changes that occurred in the Iberian hydrological system during the Quaternary period. We also deciphered the relationship of C. vettonica with its sister species C. paludica, particularly in sympatric areas, and provide genetic information for conservation purposes. To achieve this goal, we analyzed both mitochondrial and nuclear data (the cytochrome b and the nuclear recombination activating 1 genes) and a battery of single‐nucleotide polymorphisms (SNPs) of 248 individuals of C. vettonica or C. paludica from 38 localities, including some sympatric ones, covering the entire distribution area of C. vettonica. We highlight the important role played by the hydrogeomorphological processes and climatic changes that occurred in the Iberian Peninsula during the Quaternary on both the population structure of C. vettonica and its relationship with its sister species C. paludica. Our results support the genetic introgression of populations at the eastern limit of the distribution of C. vettonica. Furthermore, we postulate genetic introgression in sympatric areas. Finally, we propose the establishment or expansion of four Operational Conservation Units (OCUs) for C. vettonica, and highlight the threat faced by its populations due to the low level of genetic diversity detected for some of its populations and genetic introgression with C. paludica, which could eventually displace C. vettonica, resulting in a loss of diversity in this species.
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Affiliation(s)
- Andrea Corral‐Lou
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
- Consultores en Biología de la Conservación S.L. Madrid Spain
| | - Silvia Perea
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
- Instituto de Biología Departamento de Zoología Universidad Nacional Autónoma de México Ciudad de México México
| | - Anabel Perdices
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
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5
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Bonhomme F, Meyer L, Arbiol C, Bănaru D, Bahri-Sfar L, Fadhlaoui-Zid K, Strelkov P, Arculeo M, Soulier L, Quignard JP, Gagnaire PA. Systematics of European coastal anchovies (genus Engraulis Cuvier). JOURNAL OF FISH BIOLOGY 2022; 100:594-600. [PMID: 34837218 DOI: 10.1111/jfb.14964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Reports of morphological differences between European anchovy (Engraulis cf. encrasicolus) from coastal and marine habitats have long existed in the ichthyologic literature and have given rise to a long-standing debate on their taxonomic status. More recently, molecular studies have confirmed the existence of genetic differentiation between the two anchovy ecotypes. Using ancestry-informative markers, we show that coastal anchovies throughout the Mediterranean share a common ancestry and that substantial genetic differentiation persists in different pairs of coastal/marine populations despite the presence of limited gene flow. On the basis of genetic and ecological arguments, we propose that coastal anchovies deserve a species status of their own (E. maeoticus) and argue that a unified taxonomical framework is critical for future research and management.
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Affiliation(s)
| | - Laura Meyer
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Daniela Bănaru
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Mediterranean Institute of Oceanography, Marseille, France
| | - Lilia Bahri-Sfar
- Biodiversité, Parasitologie et Ecologie des Écosystèmes Aquatiques, LR18ES05, 2092, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Karima Fadhlaoui-Zid
- Institut National des Sciences et Technologie de la Mer, INSTM, La Goulette, Tunisia
| | - Petr Strelkov
- Department of Ichthyology & Hydrobiology, St Petersburg State University, St Petersburg, Russia
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | - Laurent Soulier
- Centre pour l'Aquaculture, la Pêche et l'Environnement en Nouvelle-Aquitaine, Bayonne, France
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6
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Casas L, Saenz-Agudelo P, Villegas-Ríos D, Irigoien X, Saborido-Rey F. Genomic landscape of geographically structured colour polymorphism in a temperate marine fish. Mol Ecol 2021; 30:1281-1296. [PMID: 33455028 PMCID: PMC7986630 DOI: 10.1111/mec.15805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome‐wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.
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Affiliation(s)
- Laura Casas
- Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - David Villegas-Ríos
- Institute of Marine Research (IIM-CSIC), Vigo, Spain.,Instituto Mediterráneo de Estudios Avanzados (IMEDEA-CSIC-UiB), Esporles, Mallorca, Spain
| | - Xabier Irigoien
- AZTI - Marine Research, Herrera Kaia, Pasaia (Gipuzkoa), Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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7
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Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel. PLoS One 2020; 15:e0241429. [PMID: 33151981 PMCID: PMC7643961 DOI: 10.1371/journal.pone.0241429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure.
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8
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Predicting the geographic origin of Spanish Cedar (Cedrela odorata L.) based on DNA variation. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01282-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PLoS One 2019; 14:e0213992. [PMID: 30889192 PMCID: PMC6424483 DOI: 10.1371/journal.pone.0213992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/05/2019] [Indexed: 11/19/2022] Open
Abstract
Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (FST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.
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10
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Nielsen ES, Henriques R, Toonen RJ, Knapp ISS, Guo B, von der Heyden S. Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics 2018; 19:347. [PMID: 29743012 PMCID: PMC5944137 DOI: 10.1186/s12864-018-4721-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/23/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist. RESULTS Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region. CONCLUSIONS Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland,, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland,, 7602, South Africa
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Baocheng Guo
- The Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, 100101, China
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland,, 7602, South Africa.
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11
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Canales-Aguirre CB, Seeb LW, Seeb JE, Cádiz MI, Musleh SS, Arismendi I, Gajardo G, Galleguillos R, Gomez-Uchida D. Contrasting genetic metrics and patterns among naturalized rainbow trout ( Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture. Ecol Evol 2017; 8:273-285. [PMID: 29321870 PMCID: PMC5756871 DOI: 10.1002/ece3.3574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 11/29/2022] Open
Abstract
Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.
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Affiliation(s)
- Cristian B Canales-Aguirre
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
| | - Lisa W Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - James E Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - María I Cádiz
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile
| | - Selim S Musleh
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile
| | - Ivan Arismendi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad Universidad de Los Lagos Osorno Chile
| | - Ricardo Galleguillos
- Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile
| | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
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12
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Catanese G, Watteaux R, Montes I, Barra M, Rumolo P, Borme D, Buongiorno Nardelli B, Botte V, Mazzocchi MG, Genovese S, Di Capua I, Iriondo M, Estonba A, Ruggeri P, Tirelli V, Caputo-Barucchi V, Basilone G, Bonanno A, Iudicone D, Procaccini G. Insights on the drivers of genetic divergence in the European anchovy. Sci Rep 2017. [PMID: 28646131 PMCID: PMC5482869 DOI: 10.1038/s41598-017-03926-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Anchovies represent the largest world's marine fish catches and the current threats on their populations impose a sustainable exploitment based on sound scientific information. In the European anchovy (Engraulis encrasicolus), the existence of several populations has been proposed but a global view is missing. Using a multidisciplinary approach, here we assessed the divergence among different ecotypes and its possible causes. SNPs have revealed two functionally distinct ecotypes overlapping in the Central Mediterranean, with one ecotype confined near the river estuaries. The same SNPs outliers also segregated two distinct populations in the near Atlantic, despite their large spatial distance. In addition, while most studies suggested that adaptation to low salinity is key to divergence, here we show that the offshore ecotype has higher environmental tolerance and an opportunistic feeding behaviour, as assessed by the study of environmental conditions, anchovy diet and trophic levels, and passive egg dispersal. These results provide insights into the anchovy evolutionary history, stressing the importance of behaviour in shaping ecotypes.
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Affiliation(s)
- Gaetano Catanese
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Laboratorio de Investigaciones Marinas y Acuicultura (LIMIA) Govern de les Illes Balears, Av. Gabriel Roca 69, 07158, Port d'Andratx - Mallorca, Spain
| | - Romain Watteaux
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Marco Barra
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Paola Rumolo
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Diego Borme
- Department of Oceanography, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Via A. Piccard 54, 34151, Trieste, Italy
| | - Bruno Buongiorno Nardelli
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Vincenzo Botte
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Maria Grazia Mazzocchi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Simona Genovese
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Iole Di Capua
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Paolo Ruggeri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.,University of Miami, RSMAS, 4600 Rickenbacker Causeway, 33149, Miami, Florida, USA
| | - Valentina Tirelli
- Department of Oceanography, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Via A. Piccard 54, 34151, Trieste, Italy
| | - Vincenzo Caputo-Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Gualtiero Basilone
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Angelo Bonanno
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy.
| | - Daniele Iudicone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
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13
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Montes I, Laconcha U, Iriondo M, Manzano C, Arrizabalaga H, Estonba A. Reduced Single Nucleotide Polymorphism Panels for Assigning Atlantic Albacore and Bay of Biscay Anchovy Individuals to Their Geographic Origin: Toward Sustainable Fishery Management. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4351-4358. [PMID: 28489943 DOI: 10.1021/acs.jafc.7b00619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is an increasing trend upon adding a detailed description of the origin of seafood products driven by a general interest in the implementation of sustainable fishery management plans for the conservation of marine ecosystems. North Atlantic albacore ("Bonito del Norte con Eusko Label") and Bay of Biscay anchovy ("Anchoa del Cantábrico") are two commercially important fish populations with high economical value and vulnerable to commercial fraud. This fact, together with the overexploited situation of these two populations, makes it necessary to develop a tool to identify individual origin and to detect commercial fraud. In the present study, we have developed and validated a traceability tool consisting of reduced panels of gene-associated single nucleotide polymorphisms (SNPs) suitable for assigning individuals of two species to their origin with unprecedented accuracy levels. Only 48 SNPs are necessary to assign 81.1% albacore and 93.4% anchovy individuals with 100% accuracy to their geographic origin. The total accuracy of the results demonstrates how gene-associated SNPs can revolutionize food traceability. Gene-associated SNP panels are not of mere commercial interest, but they also can result in a positive impact on sustainability of marine ecosystems through conservation of fish populations through establishing a more effective and sustainable fishery management framework and contributing to the prevention of falsified labeling.
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Affiliation(s)
- Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Urtzi Laconcha
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
- Marine Research Division, AZTI , 20110 Pasaia, Spain
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Carmen Manzano
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | | | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
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14
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Abstract
Anchovy and sardine populated productive ocean regions over hundreds of thousands of years under a naturally varying climate, and are now subject to climate change of equal or greater magnitude occurring over decades to centuries. We hypothesize that anchovy and sardine populations are limited in size by the supply of nitrogen from outside their habitats originating from upwelling, mixing, and rivers. Projections of the responses of anchovy and sardine to climate change rely on a range of model types and consideration of the effects of climate on lower trophic levels, the effects of fishing on higher trophic levels, and the traits of these two types of fish. Distribution, phenology, nutrient supply, plankton composition and production, habitat compression, fishing, and acclimation and adaptation may be affected by ocean warming, acidification, deoxygenation, and altered hydrology. Observations of populations and evaluation of model skill are essential to resolve the effects of climate change on these fish.
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Affiliation(s)
- David M Checkley
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0218;
| | - Rebecca G Asch
- Program in Atmospheric and Oceanic Sciences, Princeton University, Princeton, New Jersey 08540;
| | - Ryan R Rykaczewski
- Department of Biological Sciences and Marine Science Program, University of South Carolina, Columbia, South Carolina 29208;
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15
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Lal MM, Southgate PC, Jerry DR, Bosserelle C, Zenger KR. A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera. PLoS One 2016; 11:e0161390. [PMID: 27559735 PMCID: PMC4999145 DOI: 10.1371/journal.pone.0161390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/04/2016] [Indexed: 11/18/2022] Open
Abstract
Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.
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Affiliation(s)
- Monal M. Lal
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Paul C. Southgate
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Centre for Pacific Islands Research, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Cyprien Bosserelle
- Geoscience Division, Secretariat of the Pacific Community, Nabua, Suva, Fiji Islands
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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16
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Le Moan A, Gagnaire PA, Bonhomme F. Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact. Mol Ecol 2016; 25:3187-202. [PMID: 27027737 DOI: 10.1111/mec.13627] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/28/2016] [Accepted: 03/15/2016] [Indexed: 12/19/2022]
Abstract
Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.
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Affiliation(s)
- A Le Moan
- Université Montpellier 2, Place Eugène Bataillon, Montpellier, 34095, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
| | - P-A Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, Montpellier, 34095, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
| | - F Bonhomme
- Université Montpellier 2, Place Eugène Bataillon, Montpellier, 34095, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
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17
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Biocomplexity in Populations of European Anchovy in the Adriatic Sea. PLoS One 2016; 11:e0153061. [PMID: 27074008 PMCID: PMC4830579 DOI: 10.1371/journal.pone.0153061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 01/22/2023] Open
Abstract
The sustained exploitation of marine populations requires an understanding of a species' adaptive seascape so that populations can track environmental changes from short- and long-term climate cycles and from human development. The analysis of the distributions of genetic markers among populations, together with correlates of life-history and environmental variability, can provide insights into the extent of adaptive variation. Here, we examined genetic variability among populations of mature European anchovies (n = 531) in the Adriatic (13 samples) and Tyrrhenian seas (2 samples) with neutral and putative non-neutral microsatellite loci. These genetic markers failed to confirm the occurrence of two anchovy species in the Adriatic Sea, as previously postulated. However, we found fine-scale population structure in the Adriatic, especially in northern areas, that was associated with four of the 13 environmental variables tested. Geographic gradients in sea temperature, salinity and dissolved oxygen appear to drive adaptive differences in spawning time and early larval development among populations. Resolving adaptive seascapes in Adriatic anchovies provides a means to understand mechanisms underpinning local adaptation and a basis for optimizing exploitation strategies for sustainable harvests.
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18
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Castilho R, Silva G. The European anchovy, a genetically highly diverse species displays null within-sample haplotype diversity on a single study? MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:60-61. [PMID: 33644327 PMCID: PMC7871658 DOI: 10.1080/23802359.2015.1137823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The European anchovy has been the focus of numerous population genetic studies, most of which exposing high levels of haplotype diversity. However, Keskin and Atar (2012) revealed rather singular results of null haplotype diversities. We therefore call for caution when considering these findings.
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Affiliation(s)
- Rita Castilho
- CCMAR, Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Gonçalo Silva
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Departamento de Biociências, R. Jardim do Tabaco, Lisboa, Portugal
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19
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Nayfa MG, Zenger KR. Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima). Mar Genomics 2016; 28:99-106. [PMID: 26934995 DOI: 10.1016/j.margen.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 11/19/2022]
Abstract
Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G×E effects) among populations in this region. Global Fst values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise Fst comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAFavg=0.144, Ho=0.238 and MAFavg=0.232, Ho=0.369, respectively) compared to Aru (MAFavg=0.292, Ho=0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and Fst analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville 4811, QLD, Australia.
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville 4811, QLD, Australia.
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20
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Pappalardo AM, Federico C, Sabella G, Saccone S, Ferrito V. A COI Nonsynonymous Mutation as Diagnostic Tool for Intraspecific Discrimination in the European Anchovy Engraulis encrasicolus (Linnaeus). PLoS One 2015; 10:e0143297. [PMID: 26599908 PMCID: PMC4657973 DOI: 10.1371/journal.pone.0143297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/03/2015] [Indexed: 12/01/2022] Open
Abstract
The European anchovy, Engraulis encrasicolus, is currently one of the principal target species for commercial fisheries in Europe. In this study, the mitochondrial Control Region (CR) and the Cytochrome Oxidase I (COI) mitochondrial gene were analyzed in 74 specimens of E. encrasicolus from four localities in the central Mediterranean. In both populations, the two markers revealed the presence of two main haplogroups, A and B, already detected in previous investigations of different classes of molecular markers. Both CR and COI markers consistently identified two haplogroups. The COI sequence analysis identified a non-synonymous transversion (T to G) at position 116 of the translated sequence, resulting in an amino acid change. All COI sequences of haplogroup A had an amino acid sequence with alanine in this position, while serine was present in the same position in haplogroup B. The two haplogroups A and B were also discriminated by the variable number of TACA elements at the 5’-end of the mitochondrial CR. The selection tests applied to the COI dataset revealed that codon 116 was not under positive selection, that seven amino acid changes were under purifying selection, and that two amino acids were under episodic positive selection.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Giorgio Sabella
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
- * E-mail:
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21
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Koblmüller S, Steinwender B, Weiß S, Sefc KM. Gene flow, population growth and a novel substitution rate estimate in a subtidal rock specialist, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the Adriatic Sea. J ZOOL SYST EVOL RES 2015; 53:291-299. [PMID: 26617435 PMCID: PMC4658704 DOI: 10.1111/jzs.12110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2015] [Indexed: 11/27/2022]
Abstract
Population histories depend on the interplay between exogeneous and endogeneous factors. In marine species, phylogeographic and demographic patterns are often shaped by sea level fluctuations, water currents and dispersal ability. Using mitochondrial control region sequences (n = 120), we infer phylogeographic structure and historic population size changes of a common littoral fish species, the black-faced blenny Tripterygion delaisi (Perciformes, Blennioidei, Tripterygiidae) from the north-eastern Adriatic Sea. We find that Adriatic T. delaisi are differentiated from conspecific populations in the remaining Mediterranean, but display little phylogeographic structure within the Adriatic basin. The pattern is consistent with passive dispersal of planktonic larvae along cyclonic currents within the Adriatic Sea, but limited active dispersal of adults. Demographic reconstructions are consistent with recent population expansion, probably triggered by rising sea levels after the last glacial maximum (LGM). Placing the onset of population growth between the LGM and the warming of surface waters (18 000-13 000 years BP) and employing a novel expansion dating approach, we inferred a substitution rate of 2.61-3.61% per site per MY. Our study is one of only few existing investigations of the genetic structure of animals within the Adriatic basin and is the first to provide an estimate for mitochondrial control region substitution rates in blennioid fishes.
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Affiliation(s)
| | | | - Sara Weiß
- Institute of ZoologyUniversity of GrazGrazAustria
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22
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Aykanat T, Johnston SE, Orell P, Niemelä E, Erkinaro J, Primmer CR. Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population. Mol Ecol 2015; 24:5158-74. [DOI: 10.1111/mec.13383] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Tutku Aykanat
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
| | - Susan E. Johnston
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
- Institute of Evolutionary Biology; University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Panu Orell
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Eero Niemelä
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
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23
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Silva G, Lima FP, Martel P, Castilho R. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. Proc Biol Sci 2015; 281:rspb.2014.1093. [PMID: 25143035 DOI: 10.1098/rspb.2014.1093] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.
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Affiliation(s)
- Gonçalo Silva
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Fernando P Lima
- CIBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Paulo Martel
- Centro de Biomedicina Molecular e Estrutural Instituto de Biotecnologia e Bioengenharia (CBME-Associate Laboratory), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal
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24
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Past and present drivers of population structure in a small coastal fish, the European long snouted seahorse Hippocampus guttulatus. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0728-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Lo Brutto S, Maggio T, Arculeo M. Isolation By Distance (IBD) signals in the deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) (Decapoda, Panaeidae) in the Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2013; 90:1-8. [PMID: 23769335 DOI: 10.1016/j.marenvres.2013.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/06/2013] [Accepted: 05/11/2013] [Indexed: 06/02/2023]
Abstract
The identification of boundaries of genetic demes is one of the major goals for fishery management, and few Mediterranean commercial species have not been studied from a genetic point of view yet. The deep-water rose shrimp Parapenaeus longirostris (Lucas, 1846) is one of the most important components of commercial landings in Mediterranean, its fishery aspects have received much attention, regrettably without any concern for the genetic architecture of its populations. The population structure in the central and eastern Mediterranean Sea (captures from six Italian and two Greek landings) has been analysed on the basis of surveys carried out with mitochondrial and AFLP markers. Data revealed the presence of a gradual discrepancy along a west-east axis. This species, occurring mainly at a depth of between 100 and 400 m, is not strongly confined in isolated demes, but it demonstrates an 'Isolation By Distance' model, within the Mediterranean Sea, which includes geographical areas with a some degree of isolation. The role of hydrodynamic forces, such as currents, water fronts, is discussed; and a further evidence of the 'Levantine isolation' within Mediterranean basin is shown.
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Affiliation(s)
- S Lo Brutto
- Dept. STEBICEF, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy.
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26
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SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing. PLoS One 2013; 8:e70051. [PMID: 23936375 PMCID: PMC3731364 DOI: 10.1371/journal.pone.0070051] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/13/2013] [Indexed: 11/29/2022] Open
Abstract
Increased throughput in sequencing technologies has facilitated the acquisition of detailed genomic information in non-model species. The focus of this research was to discover and validate SNPs derived from the European anchovy (Engraulis encrasicolus) transcriptome, a species with no available reference genome, using next generation sequencing technologies. A cDNA library was constructed from four tissues of ten fish individuals corresponding to three populations of E. encrasicolus, and Roche 454 GS FLX Titanium sequencing yielded 19,367 contigs. Additionally, the European anchovy genome was sequenced for the same ten individuals using an Illumina HiSeq2000. Using a computational pipeline for combining transcriptome and genome information, a total of 18,994 SNPs met the necessary minor allele frequency and depth filters. A series of further stringent filters were applied to identify those SNPs likely to succeed in genotyping assays, and for filtering of those in potential duplicated genome regions. A novel method for detecting potential intron-exon boundaries in areas of putative SNPs has also been applied in silico to improve genotyping success. In all, 2,317 filtered putative transcriptome SNPs suitable for genotyping primer design were identified. From those, a subset of 530 were selected, with the genotyping results showing the highest reported conversion and validation rates (91.3% and 83.2%, respectively) reported to date for a non-model species. This study represents a promising strategy to discover genotypable SNPs in the exome of non-model organisms. The genomic resource generated for E. encrasicolus, both in terms of sequences and novel markers, will be informative for research into this species with applications including traceability studies, population genetic analyses and aquaculture.
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Liu M, Lin L, Gao T, Yanagimoto T, Sakurai Y, Grant WS. What maintains the central North Pacific genetic discontinuity in Pacific herring? PLoS One 2012; 7:e50340. [PMID: 23300525 PMCID: PMC3532504 DOI: 10.1371/journal.pone.0050340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 10/17/2012] [Indexed: 11/18/2022] Open
Abstract
Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (Φ(ST) = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (Φ(ST) = 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (Φ(ST) = 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.
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Affiliation(s)
- Ming Liu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Longshan Lin
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Tianxiang Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, China
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Yasunori Sakurai
- Graduate School of Fisheries Science, Hokkaido University, Hakodate, Hokkaido, Japan
| | - W. Stewart Grant
- Alaska Department of Fish and Game, Anchorage, Alaska, United States of America
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