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Fairfield EA, Richardson DS, Daniels CL, Butler CL, Bell E, Taylor MI. Ageing European lobsters ( Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA. Evol Appl 2021; 14:2305-2318. [PMID: 34603500 PMCID: PMC8477595 DOI: 10.1111/eva.13296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022] Open
Abstract
Crustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality-filtered loci in the economically important European lobster (Homarus gammarus). Across 0- to 51-month-old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality-filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R 2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8-55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known-age individuals and tissue types before the model can be used in fisheries management.
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Affiliation(s)
| | | | | | | | - Ewen Bell
- The Centre for Environment, Fisheries and Aquaculture ScienceLowestoftUK
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2
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Bell EA, Butler CL, Oliveira C, Marburger S, Yant L, Taylor MI. Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines. Mol Ecol Resour 2021; 22:823-833. [PMID: 34407282 DOI: 10.1111/1755-0998.13489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species.
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Affiliation(s)
- Ellen A Bell
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | | | - Claudio Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, Botucatu, São Paulo, Brazil
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, UK
| | - Levi Yant
- Future Food Beacon of Excellence and the School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
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3
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Davies CS, Taylor MI, Hammers M, Burke T, Komdeur J, Dugdale HL, Richardson DS. Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population. Mol Ecol 2021; 30:2528-2542. [PMID: 33949028 DOI: 10.1111/mec.15914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/15/2022]
Abstract
Understanding where genetic variation exists, and how it influences fitness within populations is important from an evolutionary and conservation perspective. Signatures of past selection suggest that pathogen-mediated balancing selection is a key driver of immunogenetic variation, but studies tracking contemporary evolution are needed to help resolve the evolutionary forces and mechanism at play. Previous work in a bottlenecked population of Seychelles warblers (Acrocephalus sechellensis) show that functional variation has been maintained at the viral-sensing Toll-like receptor 3 (TLR3) gene, including one nonsynonymous SNP, resulting in two alleles. Here, we characterise evolution at this TLR3 locus over a 25-year period within the original remnant population of the Seychelles warbler, and in four other derived, populations. Results show a significant and consistent temporal decline in the frequency of the TLR3C allele in the original population, and that similar declines in the TLR3C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3CC genotype had lower survival, and males - but not females - that carry the TLR3C allele had significantly lower lifetime reproductive success than those with only the TLR3A allele. These results indicate that positive selection on the TLR3A allele, caused by an as yet unknown agent, is driving TLR3 evolution in the Seychelles warbler. No evidence of heterozygote advantage was detected. However, whether the positive selection observed is part of a longer-term pattern of balancing selection (through fluctuating selection or rare-allele advantage) cannot be resolved without tracking the TLR3C allele over an extended time period.
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Affiliation(s)
- Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK
| | - Martijn Hammers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.,Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK.,Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles
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4
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Butler CL, Bell EA, Taylor MI. Removal of beneficial insertion effects prevent the long-term persistence of transposable elements within simulated asexual populations. BMC Genomics 2021; 22:241. [PMID: 33827443 PMCID: PMC8025564 DOI: 10.1186/s12864-021-07569-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/30/2021] [Indexed: 01/20/2023] Open
Abstract
Background Transposable elements are significant components of most organism’s genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even in the absence of traditional molecular evolutionary explanations, transposon proliferation may occur through a process known as ‘transposon engineering’. However, their model used a fixed beneficial transposon insertion frequency of 20%, which we believe to be unrealistically high. Results Reducing this beneficial insertion frequency, while keeping all other parameters identical, prevented transposon proliferation. Conclusions We conclude that the author’s original findings are better explained through the action of positive selection rather than ‘transposon engineering’, with beneficial insertion effects remaining important during transposon proliferation events.
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Affiliation(s)
- Christopher L Butler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Ellen A Bell
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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5
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Brock RE, Crowther LP, Wright DJ, Richardson DS, Carvell C, Taylor MI, Bourke AFG. No severe genetic bottleneck in a rapidly range-expanding bumblebee pollinator. Proc Biol Sci 2021; 288:20202639. [PMID: 33563116 PMCID: PMC7893223 DOI: 10.1098/rspb.2020.2639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Genetic bottlenecks can limit the success of populations colonizing new ranges. However, successful colonizations can occur despite bottlenecks, a phenomenon known as the genetic paradox of invasion. Eusocial Hymenoptera such as bumblebees (Bombus spp.) should be particularly vulnerable to genetic bottlenecks, since homozygosity at the sex-determining locus leads to costly diploid male production (DMP). The Tree Bumblebee (Bombus hypnorum) has rapidly colonized the UK since 2001 and has been highlighted as exemplifying the genetic paradox of invasion. Using microsatellite genotyping, combined with the first genetic estimates of DMP in UK B. hypnorum, we tested two alternative genetic hypotheses ('bottleneck' and 'gene flow' hypotheses) for B. hypnorum's colonization of the UK. We found that the UK population has not undergone a recent severe genetic bottleneck and exhibits levels of genetic diversity falling between those of widespread and range-restricted Bombus species. Diploid males occurred in 15.4% of reared colonies, leading to an estimate of 21.5 alleles at the sex-determining locus. Overall, the findings show that this population is not bottlenecked, instead suggesting that it is experiencing continued gene flow from the continental European source population with only moderate loss of genetic diversity, and does not exemplify the genetic paradox of invasion.
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Affiliation(s)
- Ryan E Brock
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Liam P Crowther
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - David J Wright
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.,Earlham Institute, Norwich Research Park, Colney Lane, Norwich, Norfolk NR4 7UZ, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Claire Carvell
- UK Centre for Ecology and Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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6
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Leigh S, Rostant WG, Taylor MI, Alphey L, Chapman T. Satyrization in Drosophila fruitflies. J Evol Biol 2020; 34:319-330. [PMID: 33159350 PMCID: PMC8246970 DOI: 10.1111/jeb.13733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/02/2020] [Accepted: 10/18/2020] [Indexed: 12/26/2022]
Abstract
The satyr of Greek mythology was half‐man, half‐goat, with an animal persona signifying immoderate sexual appetites. In biology, satyrization is the disruption of reproduction in matings between closely related species. Interestingly, its effects are often reciprocally asymmetric, manifesting more strongly in one direction of heterospecific mating than the other. Heterospecific matings are well known to result in female fitness costs due to the production of sterile or inviable hybrid offspring and can also occur due to reduced female sexual receptivity, lowering the likelihood of any subsequent conspecific matings. Here we investigated the costs and mechanisms of satyrization in the Drosophila melanogaster species subgroup of fruitflies. The results showed that D. simulans females experienced higher fitness costs from a loss of remating opportunities due to significantly reduced post‐mating sexual receptivity than did D. melanogaster females, as a result of reciprocal heterospecific matings. Reciprocal tests of the effects of male reproductive accessory gland protein (Acp) injections on female receptivity in pairwise comparisons between D. melanogaster and five other species within the melanogaster species subgroup revealed significant post‐mating receptivity asymmetries. This was due to variation in the effects of heterospecific Acps within species with which D. melanogaster can mate, and significant but nonasymmetric Acp effects in species with which it cannot. We conclude that asymmetric satyrization due to post‐mating effects of Acps may be common among diverging and hybridising species. The findings are of interest in understanding the evolution of reproductive isolation and species divergence.
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Affiliation(s)
- Stewart Leigh
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Wayne G Rostant
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich, UK
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7
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Bell EA, Cable J, Oliveira C, Richardson DS, Yant L, Taylor MI. Help or hindrance? The evolutionary impact of whole-genome duplication on immunogenetic diversity and parasite load. Ecol Evol 2020; 10:13949-13956. [PMID: 33391693 PMCID: PMC7771170 DOI: 10.1002/ece3.6987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplication (WGD) events occur in all kingdoms and have been hypothesized to promote adaptability. WGDs identified in the early history of vertebrates, teleosts, and angiosperms have been linked to the large-scale diversification of these lineages. However, the mechanics and full outcomes of WGD regarding potential evolutionary impacts remain a topic of debate. The Corydoradinae are a diverse subfamily of Neotropical catfishes with over 170 species described and a history of WGDs. They are divided into nine mtDNA lineages, with species coexisting in sympatric-and often mimetic-communities containing representatives of two or more of the nine lineages. Given their similar life histories, coexisting species of Corydoras might be exposed to similar parasite loads and because of their different histories of WGD and genome size they provide a powerful system for investigating the impacts of WGD on immune diversity and function in an animal system. Here, we compared parasite counts and the diversity of the immune-related toll-like receptors (TLR) in two coexisting species of Corydoras catfish (C. maculifer and C. araguaiaensis), one diploid and one putative tetraploid. In the putative tetraploid C. araguaiaensis, we found significantly lower numbers of parasites and significantly higher diversity (measured by both synonymous and nonsynonymous SNP counts) in two TLR genes than in the diploid C. maculifer. These results provide insight into how WGD may impact evolution, in this case by providing greater immunogenetic diversity.
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Affiliation(s)
- Ellen A. Bell
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Jo Cable
- School of BiosciencesCardiff UniversityCardiffUK
| | - Claudio Oliveira
- Departmento de MorfologiaInstituto de Biosiências/UNESPSão PauloBrazil
| | | | - Levi Yant
- Department of Cell and Developmental BiologyJohn Innes CentreNorwichUK
- Present address:
Future Food Beacon of Excellence and the School of Life SciencesUniversity of NottinghamNottinghamUK
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8
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Besnier F, Solberg MF, Harvey AC, Carvalho GR, Bekkevold D, Taylor MI, Creer S, Nielsen EE, Skaala Ø, Ayllon F, Dahle G, Glover KA. Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface. BMC Genet 2020; 21:13. [PMID: 32033538 PMCID: PMC7006396 DOI: 10.1186/s12863-020-0816-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022] Open
Abstract
Background Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations. Results After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets. Discussion The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
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Affiliation(s)
- Francois Besnier
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - Monica F Solberg
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Alison C Harvey
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Einar E Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Øystein Skaala
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Fernando Ayllon
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Geir Dahle
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| | - Kevin A Glover
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
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9
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Mat Jaafar TNA, Taylor MI, Mohd Nor SA, Bruyn MD, Carvalho GR. Comparative genetic stock structure in three species of commercially exploited Indo-Malay Carangidae (Teleosteii, Perciformes). J Fish Biol 2020; 96:337-349. [PMID: 31721192 DOI: 10.1111/jfb.14202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo-Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long-distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo-Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi-pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%-99% in mtDNA and 63%-67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%-99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise FST comparisons and the nearest-neighbour statistic (Snn ) showed significant genetic differences among Kuwait and Indo-Malay yellowtail. Within the Indo-Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries.
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Affiliation(s)
- Tun N A Mat Jaafar
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
| | - Martin I Taylor
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
| | - Siti A Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor, UK
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10
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Huml JV, Harris WE, Taylor MI, Sen R, Prudhomme C, Ellis JS. Pollution control can help mitigate future climate change impact on European grayling in the UK. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- J. Vanessa Huml
- School of Science & Environment Manchester Metropolitan University Manchester UK
- School of Biological and Marine Sciences University of Plymouth Plymouth UK
| | - W. Edwin Harris
- Crop and Environment Sciences Harper Adams University Edgmond UK
| | - Martin I. Taylor
- School of Biological Sciences University of East Anglia Norwich UK
| | - Robin Sen
- School of Science & Environment Manchester Metropolitan University Manchester UK
| | | | - Jonathan S. Ellis
- School of Biological and Marine Sciences University of Plymouth Plymouth UK
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11
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Scholz GE, Popescu AA, Taylor MI, Moulton V, Huber KT. OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression. Syst Biol 2019; 68:717-729. [PMID: 30668824 DOI: 10.1093/sysbio/syz004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain "overlay" of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly data set in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder.
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Affiliation(s)
| | | | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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12
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Abstract
Venomous teeth are rare in fishes, which typically utilise spines for defence. A new study reveals the evolutionary origins of fangs and venom in the Nemophini blennies and shows that, in contrast to snakes and lizards, the fangs pre-date the venom.
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Affiliation(s)
- Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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13
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Affiliation(s)
- Georg H Engelhard
- Centre for Environment, Fisheries & Aquaculture Science (Cefas), Pakefield Road, Lowestoft, UK
- Collaborative Centre for Sustainable Use of the Seas (CCSUS), University of East Anglia (UEA), Norwich, UK
| | - John K Pinnegar
- Centre for Environment, Fisheries & Aquaculture Science (Cefas), Pakefield Road, Lowestoft, UK
- Collaborative Centre for Sustainable Use of the Seas (CCSUS), University of East Anglia (UEA), Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia (UEA), Norwich, UK
| | - Audrey J Geffen
- Department of Biological Sciences, University of Bergen (UiB), Bergen, Norway
- Faculty of Natural Sciences, Imperial College, London, UK
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14
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Evers HG, Pinnegar JK, Taylor MI. Where are they all from? - sources and sustainability in the ornamental freshwater fish trade. J Fish Biol 2019; 94:909-916. [PMID: 30746721 DOI: 10.1111/jfb.13930] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/11/2019] [Indexed: 05/22/2023]
Abstract
The global trade in ornamental fish involves c. 125 countries worldwide and is worth c. US $15-30 billion each year. This total is dominated (90%) by freshwater fishes, most of which are sourced from breeding facilities located in developing countries, typically in Asia or South America, but also in Israel, USA and Europe. Some fish are still obtained from natural (wild) sources, but the exact percentage of wild-caught fish is difficult to quantify given a lack of reliable data. Although c. 1000 species of freshwater fishes are widely available (from a total of > 5300 on sale), the most dominant freshwater fishes in the market comprise only 30 species from the orders Cyprinodontiformes, Perciformes, Characiformes and Siluriformes. In this perspectives review paper, illustrative example case studies of wild-fish collecting (Barcelos and Rio Xingu, Brazil) and breeding projects (Java, Indonesia) are described. In addition, wild-collecting expeditions to West Papua, Indonesia are discussed, focused on discovering novel species of rainbowfish (Melanotaeniidae) for breeding in captivity. Sustainability of the aquarium industry is considered in its broadest sense. The aquarium industry has been portrayed as both a major threat to natural ecosystems, but also as being part of the solution in terms of helping to maintain species when they have gone extinct in the wild or offering an income to impoverished citizens who might otherwise engage in much more destructive practices.
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Affiliation(s)
| | - John K Pinnegar
- Centre for Environment, Fisheries & Aquaculture Science, Lowestoft Laboratory, Suffolk, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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15
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Lamb PD, Hunter E, Pinnegar JK, van der Kooij J, Creer S, Taylor MI. Cryptic diets of forage fish: jellyfish consumption observed in the Celtic Sea and western English Channel. J Fish Biol 2019; 94:1026-1032. [PMID: 30746684 PMCID: PMC6850654 DOI: 10.1111/jfb.13926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
To establish if fishes' consumption of jellyfish changes through the year, we conducted a molecular gut-content assessment on opportunistically sampled species from the Celtic Sea in October and compared these with samples previously collected in February and March from the Irish Sea. Mackerel Scomber scombrus were found to feed on hydrozoan jellyfish relatively frequently in autumn, with rare consumption also detected in sardine Sardina pilchardus and sprat Sprattus sprattus. By October, moon jellyfish Aurelia aurita appeared to have escaped predation, potentially through somatic growth and the development of stinging tentacles. This is in contrast with sampling in February and March where A. aurita ephyrae were heavily preyed upon. No significant change in predation rate was observed in S. sprattus, but jellyfish predation by S. scombrus feeding in autumn was significantly higher than that seen during winter. This increase in consumption appears to be driven by the consumption of different, smaller jellyfish species than were targeted during the winter.
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Affiliation(s)
- Philip D. Lamb
- School of Biological SciencesUniversity of East AngliaNorfolkUK
| | - Ewan Hunter
- School of Environmental SciencesUniversity of East AngliaNorfolkUK
- Cefas, LowestoftSuffolkUK
| | - John K. Pinnegar
- School of Environmental SciencesUniversity of East AngliaNorfolkUK
- Cefas, LowestoftSuffolkUK
| | | | - Simon Creer
- School of Biological SciencesBangor UniversityBangorUK
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16
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Perry WB, Solberg MF, Besnier F, Dyrhovden L, Matre IH, Fjelldal PG, Ayllon F, Creer S, Llewellyn M, Taylor MI, Carvalho G, Glover KA. Evolutionary drivers of kype size in Atlantic salmon ( Salmo salar): domestication, age and genetics. R Soc Open Sci 2019; 6:190021. [PMID: 31183145 PMCID: PMC6502380 DOI: 10.1098/rsos.190021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
The diversity of reproduction and associated mating patterns in Atlantic salmon (Salmo salar) has long captivated evolutionary biologists. Salmo salar exhibit strategies involving migration, bold mating behaviours and radical morphological and physiological change. One such radical change is the elongation and curvature of the lower jaw in sexually mature males into a hook-like appendage called the kype. The kype is a secondary sexual characteristic used in mating hierarchies and a prime candidate for sexual selection. As one of the core global aquaculture fish species, however, mate choice, and thus sexual selection, has been replaced by industrial artificial fertilization seeking to develop more commercially viable strains. Removal of mate choice provides a unique opportunity to examine the kype over successive generations in the absence of sexual selection. Here we use a large-scale common-garden experiment, incorporating six experimental strains (wild, farmed and wild × farmed hybrids), experiencing one to three sea winters, to assess the impact of age and genetic background. After controlling for allometry, fork length-adjusted kype height (AKH) was significantly reduced in the domesticated strain in comparison to two wild strains. Furthermore, genetic variation at a locus on linkage group SSA1 was associated with kype height, and a locus on linkage group SSA23 was associated with fork length-adjusted kype length (AKL). The reduction in fork length-AKH in domesticated salmon suggests that the kype is of importance in mate choice and that it has decreased due to relaxation of sexual selection. Fork length-AKL showed an increase in domesticated individuals, highlighting that it may not be an important cue in mate choice. These results give us insight into the evolutionary significance of the kype, as well as implications of genetic induced phenotypic change caused by domesticated individuals escaping into the natural environment.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Monica Favnebøe Solberg
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Francois Besnier
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Lise Dyrhovden
- Matre Research Station, Institute of Marine Research, Matredal, Norway
| | - Ivar Helge Matre
- Matre Research Station, Institute of Marine Research, Matredal, Norway
| | - Per Gunnar Fjelldal
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Fernando Ayllon
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Martin Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Martin I. Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kevin Alan Glover
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
- Institute of Biology, University of Bergen, N-5020 Bergen, Norway
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17
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Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C, Taylor MI. Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes. Proc Biol Sci 2019; 285:rspb.2017.2732. [PMID: 29445022 PMCID: PMC5829208 DOI: 10.1098/rspb.2017.2732] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/25/2018] [Indexed: 01/12/2023] Open
Abstract
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
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Affiliation(s)
- Sarah Marburger
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Markos A Alexandrou
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,Wildlands Conservation Science, LLC PO Box 1846, Lompoc, CA 93438, USA
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, s/n°18618-689 Botucatu, São Paulo, Brazil
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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18
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. How quantitative is metabarcoding: A meta-analytical approach. Mol Ecol 2018; 28:420-430. [PMID: 30408260 PMCID: PMC7379500 DOI: 10.1111/mec.14920] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
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Affiliation(s)
- Philip D Lamb
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - John K Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Richard G Davies
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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19
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Vanessa Huml J, Taylor MI, Edwin Harris W, Sen R, Ellis JS. Neutral variation does not predict immunogenetic variation in the European grayling (Thymallus thymallus)-implications for management. Mol Ecol 2018; 27:4157-4173. [PMID: 30194888 DOI: 10.1111/mec.14864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/21/2018] [Accepted: 08/29/2018] [Indexed: 11/28/2022]
Abstract
Preservation of genetic diversity is critical to successful conservation, and there is increasing demand for the inclusion of ecologically meaningful genetic information in management decisions. Supportive breeding programmes are increasingly implemented to combat declines in many species, yet their effect on adaptive genetic variation is understudied. This is despite the fact that supportive breeding may interfere with natural evolutionary processes. Here, we assessed the performance of neutral and adaptive markers (major histocompatibility complex; MHC) to inform management of European grayling (Thymallus thymallus), which routinely involves supplementation of natural populations with hatchery-reared fish (stocking). This study is the first to characterize MH II DAA and DAB loci in grayling and to investigate immune genetic variation in relation to management practice in this species. High-throughput Illumina sequencing of "introduced," "stocked native" and "non-stocked native" populations revealed significantly higher levels of allelic richness and heterozygosity for MH markers than microsatellites exclusively in non-stocked native populations. Likewise, significantly lower differentiation at the MH II than for microsatellites was apparent when considering non-stocked native populations, but not stocked populations. We developed a simulation model to test the effects of relaxation of selection during the early life stage within captivity. Dependent on the census population size and stocking intensity, there may be long-term effects of stocking on MH II, but not neutral genetic diversity. This is consistent with our empirical results. This study highlights the necessity for considering adaptive genetic variation in conservation decisions and raises concerns about the efficiency of stocking as a management practice.
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Affiliation(s)
- J Vanessa Huml
- School of Science & Environment, Manchester Metropolitan University, Manchester, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - W Edwin Harris
- School of Science & Environment, Manchester Metropolitan University, Manchester, UK
| | - Robin Sen
- School of Science & Environment, Manchester Metropolitan University, Manchester, UK
| | - Jonathan S Ellis
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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20
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Affiliation(s)
| | | | - Martin I. Taylor
- School of Biological Sciences; University of East Anglia; Norwich UK
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21
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. Jellyfish on the menu: mtDNA assay reveals scyphozoan predation in the Irish Sea. R Soc Open Sci 2017; 4:171421. [PMID: 29291125 PMCID: PMC5717700 DOI: 10.1098/rsos.171421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/26/2017] [Indexed: 05/21/2023]
Abstract
Localized outbreaks of jellyfish, known as blooms, cause a variety of adverse ecological and economic effects. However, fundamental aspects of their ecology remain unknown. Notably, there is scant information on the role jellyfish occupy in food webs: in many ecosystems, few or no predators are known. To identify jellyfish consumers in the Irish Sea, we conducted a molecular gut content assessment of 50 potential predators using cnidarian-specific mtDNA primers and sequencing. We show that jellyfish predation may be more common than previously acknowledged: uncovering many previously unknown jellyfish predators. A substantial proportion of herring and whiting were found to have consumed jellyfish. Rare ingestion was also detected in a variety of other species. Given the phenology of jellyfish in the region, we suggest that the predation was probably targeting juvenile stages of the jellyfish life cycle.
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Affiliation(s)
- Philip D. Lamb
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
- Author for correspondence: Philip D. Lamb e-mail:
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
- Cefas, Lowestoft, Suffolk NR33 0HT, UK
| | - John K. Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
- Cefas, Lowestoft, Suffolk NR33 0HT, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Richard G. Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Martin I. Taylor
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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22
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Harvey AC, Solberg MF, Glover KA, Taylor MI, Creer S, Carvalho GR. Plasticity in response to feed availability: Does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? J Fish Biol 2016; 89:1754-1768. [PMID: 27460446 DOI: 10.1111/jfb.13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Growth of farmed, wild and F1 hybrid Atlantic salmon parr Salmo salar was investigated under three contrasting feeding regimes in order to understand how varying levels of food availability affects relative growth. Treatments consisted of standard hatchery feeding (ad libitum), access to feed for 4 h every day, and access to feed for 24 h on three alternate days weekly. Mortality was low in all treatments, and food availability had no effect on survival of all groups. The offspring of farmed S. salar significantly outgrew the wild S. salar, while hybrids displayed intermediate growth. Furthermore, the relative growth differences between the farmed and wild S. salar did not change across feeding treatments, indicating a similar plasticity in response to feed availability. Although undertaken in a hatchery setting, these results suggest that food availability may not be the sole driver behind the observed reduced growth differences found between farmed and wild fishes under natural conditions.
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Affiliation(s)
- A C Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
- Department of Biology, Sea Lice Research Centre, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
| | - M I Taylor
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich, U.K
| | - S Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - G R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
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23
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Harvey AC, Juleff G, Carvalho GR, Taylor MI, Solberg MF, Creer S, Dyrhovden L, Matre IH, Glover KA. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? R Soc Open Sci 2016; 3:160152. [PMID: 27493772 PMCID: PMC4968464 DOI: 10.1098/rsos.160152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios.
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Affiliation(s)
- Alison C. Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Gareth Juleff
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Martin I. Taylor
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
- Biological Sciences, University of East Anglia, Norwich, UK
| | | | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | | | | | - Kevin A. Glover
- Havforskningsinstituttet, Bergen, Norway
- Sea Lice Research Centre, Universitetet i Bergen Institutt for Biologi, Bergen, Norway
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24
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Harvey AC, Glover KA, Taylor MI, Creer S, Carvalho GR. A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evol Appl 2016; 9:435-49. [PMID: 26989435 PMCID: PMC4778114 DOI: 10.1111/eva.12346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/13/2015] [Indexed: 11/30/2022] Open
Abstract
Released individuals can have negative impacts on native populations through various mechanisms, including competition, disease transfer and introduction of maladapted gene complexes. Previous studies indicate that the level of farmed Atlantic salmon introgression in native populations is population specific. However, few studies have explored the potential role of population diversity or river characteristics, such as temperature, on the consequences of hybridization. We compared freshwater growth of multiple families derived from two farmed, five wild and two F1 hybrid salmon populations at three contrasting temperatures (7°C, 12°C and 16°C) in a common garden experiment. As expected, farmed salmon outgrew wild salmon at all temperatures, with hybrids displaying intermediate growth. However, differences in growth were population specific and some wild populations performed better than others relative to the hybrid and farmed populations at certain temperatures. Therefore, the competitive balance between farmed and wild salmon may depend both on the thermal profile of the river and on the genetic characteristics of the respective farmed and wild strains. While limited to F1 hybridization, this study shows the merits in adopting a more complex spatially resolved approach to risk management of local populations.
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Affiliation(s)
- Alison C Harvey
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
| | | | - Martin I Taylor
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK; School of Biological Sciences University of East Anglia Norwich UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
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25
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Bourlat SJ, Borja A, Gilbert J, Taylor MI, Davies N, Weisberg SB, Griffith JF, Lettieri T, Field D, Benzie J, Glöckner FO, Rodríguez-Ezpeleta N, Faith DP, Bean TP, Obst M. Genomics in marine monitoring: new opportunities for assessing marine health status. Mar Pollut Bull 2013; 74:19-31. [PMID: 23806673 DOI: 10.1016/j.marpolbul.2013.05.042] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 05/17/2013] [Indexed: 05/06/2023]
Abstract
This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.
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Affiliation(s)
- Sarah J Bourlat
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden.
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26
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Tysklind N, Taylor MI, Lyons BP, Goodsir F, McCarthy ID, Carvalho GR. Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species. Evol Appl 2013; 6:891-909. [PMID: 24062799 PMCID: PMC3779091 DOI: 10.1111/eva.12074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 04/03/2013] [Indexed: 12/19/2022] Open
Abstract
Bioindicators are species for which some quantifiable aspect of its biology, a biomarker, is assumed to be sensitive to ecosystem health. However, there is frequently a lack of information on the underlying genetic and environmental drivers shaping the spatiotemporal variance in prevalence of the biomarkers employed. Here, we explore the relative role of potential variables influencing the spatiotemporal prevalence of biomarkers in dab, Limanda limanda, a species used as a bioindicator of marine contaminants. Firstly, the spatiotemporal genetic structure of dab around UK waters (39 samples across 15 sites for four years: 2005–2008) is evaluated with 16 microsatellites. Two temporally stable groups are identified corresponding to the North and Irish Seas (average between basin = 0.007; = 0.022). Secondly, we examine the association between biomarker prevalence and several variables, including genetic structuring, age and contaminant exposure. Genetic structure had significant interactive effects, together with age and some contaminants, in the prevalence of some of the biomarkers considered, namely hyperpigmentation and liver lesions. The integration of these data sets enhanced our understanding of the relationship between biomarker prevalence, exposure to contaminants and population-specific response, thereby yielding more informative predictive models of response and prospects for environmental remediation.
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Affiliation(s)
- Niklas Tysklind
- Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, School of Biological Sciences, Bangor University Gwynedd, UK
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Briscoe AG, Goodacre S, Masta SE, Taylor MI, Arnedo MA, Penney D, Kenny J, Creer S. Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). PLoS One 2013; 8:e62404. [PMID: 23667474 PMCID: PMC3648539 DOI: 10.1371/journal.pone.0062404] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods.
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Affiliation(s)
- Andrew G. Briscoe
- Environment Centre Wales Building, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Sara Goodacre
- Institute of Genetics, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Susan E. Masta
- Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Martin I. Taylor
- Environment Centre Wales Building, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Miquel A. Arnedo
- Departament Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - David Penney
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - John Kenny
- Centre for Genomic Research, School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Simon Creer
- Environment Centre Wales Building, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
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Hemmer-Hansen J, Nielsen EE, Therkildsen NO, Taylor MI, Ogden R, Geffen AJ, Bekkevold D, Helyar S, Pampoulie C, Johansen T, Carvalho GR. A genomic island linked to ecotype divergence in Atlantic cod. Mol Ecol 2013; 22:2653-67. [DOI: 10.1111/mec.12284] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 01/20/2013] [Accepted: 01/31/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Einar E. Nielsen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Nina O. Therkildsen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | - Martin I. Taylor
- School of Biological Sciences; University of East Anglia; Norwich NR4 7TJ UK
| | - Rob Ogden
- TRACE Wildlife Forensics Network; Royal Zoological Society of Scotland; Edinburgh EH12 6TS UK
| | - Audrey J. Geffen
- Department of Biology; University of Bergen; PB 7803 Bergen N-5020 Norway
| | - Dorte Bekkevold
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Vejlsøvej 39 Silkeborg DK-8600 Denmark
| | | | | | - Torild Johansen
- Institute of Marine Research Tromsø; PO Box 6404 Tromsø N-9294 Norway
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory; School of Biological Sciences; Environment Centre Wales; Bangor University; Bangor Gwynedd LL57 2UW UK
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Helyar SJ, Limborg MT, Bekkevold D, Babbucci M, van Houdt J, Maes GE, Bargelloni L, Nielsen RO, Taylor MI, Ogden R, Cariani A, Carvalho GR, Panitz F. SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus). PLoS One 2012; 7:e42089. [PMID: 22879907 PMCID: PMC3413699 DOI: 10.1371/journal.pone.0042089] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/02/2012] [Indexed: 11/29/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.
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Affiliation(s)
- Sarah J Helyar
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom.
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Hunter E, Taylor N, Fox CJ, Maillard M, Taylor MI. Effectiveness of TaqMan probes for detection of fish eggs and larvae in the stomach contents of a teleost predator. J Fish Biol 2012; 81:320-328. [PMID: 22747822 DOI: 10.1111/j.1095-8649.2012.03298.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Experiments were conducted on the ability of TaqMan molecular probes to detect plaice Pleuronectes platessa DNA from eggs, and cod Gadus morhua DNA from eggs and larvae following ingestion by a teleost predator, whiting Merlangius merlangus. Estimated half-life detection rate (T50) for eggs was 31 h, and 26 h for larvae, with some positive detections occurring even after visual inspection indicated complete gut clearance. Because TaqMan probes are taxon specific, the results presented demonstrate that this technique can provide a means of rapid and unambiguous detection of predation by teleosts on fish eggs and larvae.
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Affiliation(s)
- E Hunter
- Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk NR33 OHT, U.K.
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Domingues CP, Creer S, Taylor MI, Queiroga H, Carvalho GR. Temporal genetic homogeneity among shore crab (Carcinus maenas) larval events supplied to an estuarine system on the Portuguese northwest coast. Heredity (Edinb) 2011; 106:832-40. [PMID: 20959862 PMCID: PMC3186222 DOI: 10.1038/hdy.2010.126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 07/30/2010] [Accepted: 09/02/2010] [Indexed: 11/09/2022] Open
Abstract
Despite the importance of larval biology in the life histories of many marine animals, relatively little information exists on the dynamics and genetic composition of larval cohorts. The supply of megalopae larvae of the shore crab, Carcinus maenas, was measured on a daily basis during 8 months spread along two larval periods (2006 and 2007) at the Ria de Aveiro estuary, on the Portuguese northwest coast. A total of 10 microsatellite DNA loci were employed to explore the genetic structure, variability and relatedness of temporally distinct megalopal events, selected from the major pulses of supply. Larval variation was also compared genetically with that of a previously studied adult crabs sample, at the same loci, collected in 2006 and 2007 along the Iberian Peninsula. Results revealed a lack of genetic differentiation and identical diversity levels among larval events over time. No evidence of reduced genetic diversity between megalopae relative to the diversity assessed from the pooled sample of adults was found. Moreover, there was no evidence of any family relatedness among larvae from temporal events. The results obtained for C. maenas contradict predictions made by the sweepstakes reproduction hypothesis, in which large variance in reproductive success is expected, which is presumably detectable as sharp genetic discontinuities among separate larval events. Data here indicate conversely a high degree of temporal genetic stability among larval supply to a given estuary under variable oceanographic conditions, consistent with the hypothesis that sampled larvae were drawn from a large number of adults that do not differ in reproductive success.
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Affiliation(s)
- C P Domingues
- CESAM & Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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Dawnay N, Dawnay L, Hughes RN, Cove R, Taylor MI. Substantial genetic structure among stocked and native populations of the European grayling (Thymallus thymallus, Salmonidae) in the United Kingdom. CONSERV GENET 2011. [DOI: 10.1007/s10592-010-0179-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Pascoal S, Creer S, Taylor MI, Queiroga H, Carvalho G, Mendo S. Development and application of microsatellites in Carcinus maenas: genetic differentiation between Northern and Central Portuguese populations. PLoS One 2009; 4:e7268. [PMID: 19789651 PMCID: PMC2748716 DOI: 10.1371/journal.pone.0007268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 08/10/2009] [Indexed: 11/18/2022] Open
Abstract
Carcinus maenas, the common shore crab of European coastal waters, has recently gained notoriety due to its globally invasive nature associated with drastic ecological and economic effects. The native ubiquity and worldwide importance of C. maenas has resulted in it becoming one of the best-studied estuarine crustacean species globally. Accordingly, there is significant interest in investigating the population genetic structure of this broadly distributed crab along European and invaded coastlines. Here, we developed polymerase chain reaction (PCR) primers for one dinucleotide and two trinucleotide microsatellite loci, resulting from an enrichment process based on Portuguese populations. Combining these three new markers with six existing markers, we examined levels of genetic diversity and population structure of C. maenas in two coastal regions from Northern and Central Portugal. Genotypes showed that locus polymorphism ranged from 10 to 42 alleles (N = 135) and observed heterozygosity per locus ranged from 0.745 to 0.987 with expected heterozygosity ranging from 0.711 to 0.960; values typical of marine decapods. The markers revealed weak, but significant structuring among populations (global F(ST) = 0.004) across a 450 km (over-water distance) spatial scale. Combinations of these and existing markers will be useful for studying population genetic parameters at a range of spatial scales of C. maenas throughout its expanding species range.
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Affiliation(s)
- Sónia Pascoal
- CESAM & Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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Blais J, Plenderleith M, Rico C, Taylor MI, Seehausen O, van Oosterhout C, Turner GF. Assortative mating among Lake Malawi cichlid fish populations is not simply predictable from male nuptial colour. BMC Evol Biol 2009; 9:53. [PMID: 19265521 PMCID: PMC2667177 DOI: 10.1186/1471-2148-9-53] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2008] [Accepted: 03/05/2009] [Indexed: 12/03/2022] Open
Abstract
Background Research on the evolution of reproductive isolation in African cichlid fishes has largely focussed on the role of male colours and female mate choice. Here, we tested predictions from the hypothesis that allopatric divergence in male colour is associated with corresponding divergence in preference. Methods We studied four populations of the Lake Malawi Pseudotropheus zebra complex. We predicted that more distantly-related populations that independently evolved similar colours would interbreed freely while more closely-related populations with different colours mate assortatively. We used microsatellite genotypes or mesh false-floors to assign paternity. Fisher's exact tests as well as Binomial and Wilcoxon tests were used to detect if mating departed from random expectations. Results Surprisingly, laboratory mate choice experiments revealed significant assortative mating not only between population pairs with differently coloured males, but between population pairs with similarly-coloured males too. This suggested that assortative mating could be based on non-visual cues, so we further examined the sensory basis of assortative mating between two populations with different male colour. Conducting trials under monochromatic (orange) light, intended to mask the distinctive male dorsal fin hues (blue v orange) of these populations, did not significantly affect the assortative mating by female P. emmiltos observed under control conditions. By contrast, assortative mating broke down when direct contact between female and male was prevented. Conclusion We suggest that non-visual cues, such as olfactory signals, may play an important role in mate choice and behavioural isolation in these and perhaps other African cichlid fish. Future speciation models aimed at explaining African cichlid radiations may therefore consider incorporating such mating cues in mate choice scenarios.
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Affiliation(s)
- Jonatan Blais
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK.
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Fox CJ, Taylor MI, Pereyra R, Villasana MI, Rico C. TaqMan DNA technology confirms likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: implications for the assessment of the cod stock and mapping of spawning areas using egg-based methods. Mol Ecol 2005; 14:879-84. [PMID: 15723679 DOI: 10.1111/j.1365-294x.2005.02439.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent substantial declines in northeastern Atlantic cod stocks necessitate improved biological knowledge and the development of techniques to complement standard stock assessment methods (which largely depend on accurate commercial catch data). In 2003, an ichthyoplankton survey was undertaken in the Irish Sea and subsamples of 'cod-like' eggs were analysed using a TaqMan multiplex, PCR (polymerase chain reaction) assay (with specific probes for cod, haddock and whiting). The TaqMan method was readily applied to the large number of samples (n = 2770) generated during the survey and when combined with a manual DNA extraction protocol had a low failure rate of 6%. Of the early stage 'cod-like' eggs (1.2-1.75 mm diameter) positively identified: 34% were cod, 8% haddock and 58% whiting. As previous stock estimates based on egg surveys for Irish Sea cod assumed that the majority of 'cod-like' eggs were from cod, the TaqMan results confirm that there was probably substantial contamination by eggs of whiting and haddock that would have inflated estimates of the stock biomass.
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Affiliation(s)
- C J Fox
- The Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk, United Kingdom, NR33 OHT.
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Maan ME, Seehausen O, Söderberg L, Johnson L, Ripmeester EAP, Mrosso HDJ, Taylor MI, van Dooren TJM, van Alphen JJM. Intraspecific sexual selection on a speciation trait, male coloration, in the Lake Victoria cichlid Pundamilia nyererei. Proc Biol Sci 2005; 271:2445-52. [PMID: 15590594 PMCID: PMC1691879 DOI: 10.1098/rspb.2004.2911] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The haplochromine cichlids of Lake Victoria constitute a classical example of explosive speciation. Extensive intra- and interspecific variation in male nuptial coloration and female mating preferences, in the absence of postzygotic isolation between species, has inspired the hypothesis that sexual selection has been a driving force in the origin of this species flock. This hypothesis rests on the premise that the phenotypic traits that underlie behavioural reproductive isolation between sister species diverged under sexual selection within a species. We test this premise in a Lake Victoria cichlid, by using laboratory experiments and field observations. We report that a male colour trait, which has previously been shown to be important for behavioural reproductive isolation between this species and a close relative, is under directional sexual selection by female mate choice within this species. This is consistent with the hypothesis that female choice has driven the divergence in male coloration between the two species. We also find that male territoriality is vital for male reproductive success and that multiple mating by females is common.
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Affiliation(s)
- Martine E Maan
- Department of Animal Ecology, Institute of Biology, University of Leiden, PO Box 9516 2300 RA Leiden, The Netherlands.
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Pereyra R, Taylor MI, Turner GF, Rico C. Variation in habitat preference and population structure among three species of the Lake Malawi cichlid genus Protomelas. Mol Ecol 2004; 13:2691-7. [PMID: 15315681 DOI: 10.1111/j.1365-294x.2004.02224.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Several studies have demonstrated strong population structuring over small distances in the rocky-shore mbuna cichlid fishes from Lake Malawi, suggesting the potential for allopatric speciation. However, many endemic Lake Malawi cichlids are neither mbuna, nor confined to rocky shores. Using microsatellites, we investigated the population structure in three species of the non-mbuna genus Protomelas. The rocky-shore P. taeniolatus showed high levels of population structure even over distances of less than 1 km, while the sandy-shore species P. similis showed no significant structure over distances up to 21 km. Protomelas fenestratus, which is generally found at the interface between rocks and sand, also showed low levels of population structure. Our results suggest that the model of allopatric speciation based on habitat fragmentation within the current lake basin may be equally applicable to rocky-shore non-mbuna as to mbuna, but that an alternative model is required to explain speciation among sandy-shore species as well as the deep-water and pelagic species.
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Affiliation(s)
- Ricardo Pereyra
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Taylor MI, Morley JI, Rico C, Balshine S. Evidence for genetic monogamy and female-biased dispersal in the biparental mouthbrooding cichlid Eretmodus cyanostictus from Lake Tanganyika. Mol Ecol 2004; 12:3173-7. [PMID: 14629396 DOI: 10.1046/j.1365-294x.2003.01964.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, we investigate whether apparent social monogamy (where a species forms a pair bond but may participate in copulations outside the pair bond) corresponds with genetic monogamy (where individuals participate only in copulations within a pair bond) in a biparental mouthbrooding cichlid fish, Eretmodus cyanostictus, from Lake Tanganyika, Africa. Our findings suggest that E. cyanostictus is both socially and genetically monogamous and that monogamy may result from limited opportunities for polygyny, rather than from reproductive benefits of monogamy. Mating systems are believed to influence the relative rate of dispersal of the sexes, and our results suggest that E. cyanostictus displays female-biased dispersal, providing some support for the 'resource competition' hypothesis driving sex-biased dispersal.
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Affiliation(s)
- Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Taylor MI, Fox C, Rico I, Rico C. Species-specific TaqMan probes for simultaneous identification of (Gadus morhua L.), haddock (Melanogrammus aeglefinus L.) and whiting (Merlangius merlangus L.). ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00269.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Taylor MI, Meardon F, Turner G, Seehausen O, Mrosso HDJ, Rico C. Characterization of tetranucleotide microsatellite loci in a Lake Victorian, haplochromine cichlid fish: a Pundamilia pundamilia x Pundamilia nyererei hybrid. ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00272.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Taylor MI, Rüber L, Verheyen E. Microsatellites reveal high levels of population substructuring in the species-poor Eretmodine cichlid lineage from Lake Tanganyika. Proc Biol Sci 2001; 268:803-8. [PMID: 11345324 PMCID: PMC1088672 DOI: 10.1098/rspb.2000.1580] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study investigated fine-scale population substructuring in an apparently monogamous, biparental mouth-brooding cichlid. Microsatellite allele frequencies were determined at four polymorphic loci for nine populations of Eretmodus cyanostictus. We provide empirical support for the hypothesis that a species employing this breeding strategy should exhibit high levels of population substructuring. Stretches of sand represent considerable barriers to dispersal and, in contrast to the rock-dwelling cichlids of Lake Malawi, distance alone, along a continuous rocky shoreline, is sufficient to reduce gene flow significantly There was a significant pattern of isolation by distance both along the whole study area and over the stretch of continuous shoreline, suggesting that this species has poor dispersal capabilities and that juveniles establish territories close to their natal site. Despite limited dispersal, E. cyanostictus populations are not significantly more inbred than a more-widely dispersing rock-dwelling cichlid from Lake Malawi. This finding may cast doubt on the hypothesis that polyandry has evolved as a mechanism for maintaining genetic diversity in Lake Malawi cichlids. High levels of substructuring may not always promote high levels of speciation, and other factors, such as the intensity of sexual selection, may be more important in determining the speciation potential of a lineage.
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Affiliation(s)
- M I Taylor
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.
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Abstract
The good genes mechanism of sexual selection predicts that secondary sexual ornaments may reliably reveal a males resistance to parasites. We studied correlates of courtship and spawning success in a species of Copadichromis, a lekking cichlid fish from Lake Malawi, Africa, which builds sand bowers. We present the first evidence of a negative relationship between the structure of an extended phenotypic character (height skew of sand bowers) and male parasite load. Males that spawned had significantly fewer dilepipid cestodes in their livers than males that did not spawn, never before demonstrated in a lekking species of fish. Furthermore, males that spawned had significantly heavier gonads than 'unsuccessful males. We also found significant correlations between relative liver weight and some measures of reproductive success. This may indicate females are choosing to mate with males in better condition. Copyright 1998 The Association for the Study of Animal Behaviour
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Affiliation(s)
- MI Taylor
- Division of Biodiversity and Ecology, University of Southampton
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Abstract
A number of iron-chelating agents are currently being considered as orally active alternatives to desferrioxamine (DFO), the therapeutic agent for the treatment of body iron overload that is available at present. These include bidentate hydroxypyridinones (HPO), tridentate desferrithiocin (DFT) analogues and hexadentate aminocarboxylate (HBED) chelators. All chelating agents have the potential to induce toxic effects when iron homoeostasis is affected within the body. This can arise when the absorption, distribution and utilization of iron is affected. Alternatively, chelating agents can induce toxicity by directly interfering with iron-dependent metalloenzymes located within the body. These effects are, however, mainly localized to non-haem enzymes such as ribonucleotide reductase and lipoxygenase. The resultant iron complexes also have the ability to induce toxicity. Depending on the coordination geometry and donor atoms associated with the metal centre, redox cycling of the iron centre with the corresponding generation of free radicals can result.
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Affiliation(s)
- S Singh
- Department of Pharmacy, King's College, University of London, U.K
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