1
|
Maroso F, Hillen JEJ, Pardo BG, Gkagkavouzis K, Coscia I, Hermida M, Franch R, Hellemans B, Van Houdt J, Simionati B, Taggart JB, Nielsen EE, Maes G, Ciavaglia SA, Webster LMI, Volckaert FAM, Martinez P, Bargelloni L, Ogden R. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species. Mar Genomics 2018; 39:64-72. [PMID: 29496460 DOI: 10.1016/j.margen.2018.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 05/22/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/29/2023]
Abstract
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies.
Collapse
Affiliation(s)
- F Maroso
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy.
| | - J E J Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - B G Pardo
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - K Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - I Coscia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; School of Environmental and Life Science, Rm 332, Peel Building, University of Salford, Salford M5 4WT, UK
| | - M Hermida
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - R Franch
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - B Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - J Van Houdt
- Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium
| | - B Simionati
- BMR Genomics, Via Redipuglia 21a, Padova, Italy
| | - J B Taggart
- Division of Environmental and Evolutionary Biology, School of Biology and Biochemistry, The Queen's University of Belfast, Belfast BT7 INN, UK
| | - E E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - G Maes
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium; Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Marine and Environmental Sciences, Faculty of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia
| | - S A Ciavaglia
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - L M I Webster
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - F A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - P Martinez
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - L Bargelloni
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - R Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | |
Collapse
|
2
|
Coscia I, Chopelet J, Waples RS, Mann BQ, Mariani S. Sex change and effective population size: implications for population genetic studies in marine fish. Heredity (Edinb) 2016; 117:251-8. [PMID: 27507184 PMCID: PMC5026757 DOI: 10.1038/hdy.2016.50] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 11/09/2022] Open
Abstract
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.
Collapse
Affiliation(s)
- I Coscia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - J Chopelet
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - R S Waples
- NOAA Fisheries, Northwest Fisheries Science Center, Seattle, WA, USA
| | - B Q Mann
- Oceanographic Research Institute, Durban, South Africa
| | - S Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, The University of Salford, Greater Manchester, UK
| |
Collapse
|
3
|
Coscia I, Vogiatzi E, Kotoulas G, Tsigenopoulos CS, Mariani S. Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic. Heredity (Edinb) 2012; 108:537-46. [PMID: 22126850 PMCID: PMC3331784 DOI: 10.1038/hdy.2011.120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 07/20/2011] [Revised: 10/17/2011] [Accepted: 10/27/2011] [Indexed: 11/08/2022] Open
Abstract
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here, we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 expressed sequence tag-linked markers, as well as a portion of the mitochondrial DNA (mtDNA) control region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, although the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
Collapse
Affiliation(s)
- I Coscia
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| | - E Vogiatzi
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
- Department of Molecular Biology and Genetics, Democritian University of Thrace, Alexandroupolis, Greece
| | - G Kotoulas
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
| | - C S Tsigenopoulos
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology and Genetics (IMBG), Crete, Greece
| | - S Mariani
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin, Ireland
| |
Collapse
|
5
|
Abstract
Meristic identification, mitochondrial DNA and a suite of microsatellite markers were employed to estimate the incidence of hybridization in wild populations of anadromous Allis shad Alosa alosa and twaite shad Alosa fallax in southern Irish riverine and estuarine waters. It was shown that 16% of the fishes examined were misclassified using meristic count of gill rakers. Next, a significant proportion of fishes that were robustly assigned to a species using nuclear markers were shown to possess the mtDNA of the other. The genomes of A. alosa and A. fallax in Ireland are extensively introgressed, which suggests a complex history of hybridization between these species, which can only partially be explained by recent man-made habitat changes.
Collapse
Affiliation(s)
- I Coscia
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | | | | |
Collapse
|