RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories

Vendrami D, De Noia M, Telesca L, Handal W, Charrier G, Boudry P, Eberhart-Phillips L, Hoffman J (2019)
Scientific Reports 9(1): 7455.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA 2.75 MB
Autor*in
Vendrami, DavidUniBi ; De Noia, Michele; Telesca, Luca; Handal, William; Charrier, Grégory; Boudry, Pierre; Eberhart-Phillips, Luke; Hoffman, JosephUniBi
Abstract / Bemerkung
Recent developments in genomics are advancing our understanding of the processes shaping population structure in wild organisms. In particular, reduced representation sequencing has facilitated the generation of dense genetic marker datasets that provide greater power for resolving population structure, investigating the role of selection and reconstructing demographic histories. We therefore used RAD sequencing to study the great scallop Pecten maximus and its sister species P. jacobeus along a latitudinal cline in Europe. Analysis of 219 samples genotyped at 82,439 single nucleotide polymorphisms clearly resolved an Atlantic and a Norwegian group within P. maximus as well as P. jacobeus, in support of previous studies. Fine-scale structure was also detected, including pronounced differences involving Mulroy Bay in Ireland, where scallops are commercially cultured. Furthermore, we identified a suite of 279 environmentally associated loci that resolved a contrasting phylogenetic pattern to the remaining neutral loci, consistent with ecologically mediated divergence. Finally, demographic inference provided support for the two P. maximus groups having diverged during the last glacial maximum and subsequently expanded, whereas P. jacobeus diverged around 95,000 generations ago and experienced less pronounced expansion. Our results provide an integrative perspective on the factors shaping genome-wide differentiation in a commercially important marine invertebrate. Introduction
Erscheinungsjahr
2019
Zeitschriftentitel
Scientific Reports
Band
9
Ausgabe
1
Art.-Nr.
7455
ISSN
2045-2322
eISSN
2045-2322
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2935739

Zitieren

Vendrami D, De Noia M, Telesca L, et al. RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Scientific Reports. 2019;9(1): 7455.
Vendrami, D., De Noia, M., Telesca, L., Handal, W., Charrier, G., Boudry, P., Eberhart-Phillips, L., et al. (2019). RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Scientific Reports, 9(1), 7455. doi:10.1038/s41598-019-43939-4
Vendrami, David, De Noia, Michele, Telesca, Luca, Handal, William, Charrier, Grégory, Boudry, Pierre, Eberhart-Phillips, Luke, and Hoffman, Joseph. 2019. “RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories”. Scientific Reports 9 (1): 7455.
Vendrami, D., De Noia, M., Telesca, L., Handal, W., Charrier, G., Boudry, P., Eberhart-Phillips, L., and Hoffman, J. (2019). RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Scientific Reports 9:7455.
Vendrami, D., et al., 2019. RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Scientific Reports, 9(1): 7455.
D. Vendrami, et al., “RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories”, Scientific Reports, vol. 9, 2019, : 7455.
Vendrami, D., De Noia, M., Telesca, L., Handal, W., Charrier, G., Boudry, P., Eberhart-Phillips, L., Hoffman, J.: RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Scientific Reports. 9, : 7455 (2019).
Vendrami, David, De Noia, Michele, Telesca, Luca, Handal, William, Charrier, Grégory, Boudry, Pierre, Eberhart-Phillips, Luke, and Hoffman, Joseph. “RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories”. Scientific Reports 9.1 (2019): 7455.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-05-27T05:47:59Z
MD5 Prüfsumme
cb8c3b63a291d4dd1d89464fc195a423


Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

67 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Genotyping-by-sequencing in ecological and conservation genomics.
Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA., Mol. Ecol. 22(11), 2013
PMID: 23711105
Evaluating signatures of glacial refugia for North Atlantic benthic marine taxa.
Maggs CA, Castilho R, Foltz D, Henzler C, Jolly MT, Kelly J, Olsen J, Perez KE, Stam W, Vainola R, Viard F, Wares J., Ecology 89(11 Suppl), 2008
PMID: 19097488
Genomic signature of adaptation to climate in Medicago truncatula.
Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND, Tiffin P., Genetics 196(4), 2014
PMID: 24443444
An investigation of the movement of the scallop, Pecten maximus
Hartnoll RG., 1967
The pelagic life of the pectinid Pecten maximus—a review
Le M, Paugam A, Le G., 2003
Aspects of veliger larval growth and byssus drifting of the spat of Pecten maximus and Aequipecten (Chlamys) opercularis
Beaumont AR, Barnes DA., 1992
Population genetic differentiation of the great scallop Pecten maximus in western Britain investigated by randomly amplified polymorphic DNA
Heipel DA, Bishop JDD, Brand AR, Thorpe JP., 1998
Mitochondrial DNA variation in the scallop Pecten maximus (L.) assessed by a PCR-RFLP method.
Wilding CS, Beaumont AR, Latchford JW., Heredity (Edinb) 79 ( Pt 2)(), 1997
PMID: 9279012
Genetics of indigenous and transplanted populations of Pecten maximus: no evidence for the existence of separate stocks
Beaumont AR, Morvan C, Huelvan S, Lucas A, Ansell AD., 1993
Population genetics of Pecten maximus of the Northeast Atlantic coast
Ridgway GM, Dahle G, Høisœter T., 2000
Genetic structure of a commercially exploited bivalve, the great scallop Pecten maximus, along the European coasts
Morvezen R, Charrier G, Boudry P, Chauvaud L, Breton F, Strand O, Laroche J., Conserv. Genet. 17(1), 2016
PMID: IND604785997
Physical oceanography of the North Sea
Huthnance JM., 1991
Benthic macrofaunal community structure in the Norwegian Trench, deep Skagerrak
Rosenberg R, Hellman B, Lundberg A., 1996
North Sea interaction with the North Atlantic ocean
Huthnance JM., 1997
Local adaptation in marine invertebrates.
Sanford E, Kelly MW., Ann Rev Mar Sci 3(), 2011
PMID: 21329215
Effects of high temperature on survival of the giant scallop
Dickie LM., 1958
Fine-scale temperature-associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus).
Lehnert SJ, DiBacco C, Van Wyngaarden M, Jeffery NW, Ben Lowen J, Sylvester EVA, Wringe BF, Stanley RRE, Hamilton LC, Bradbury IR., Heredity (Edinb) 122(1), 2018
PMID: 29773897
Variation in size and growth of the great scallop Pecten maximus along a latitudinal gradient.
Chauvaud L, Patry Y, Jolivet A, Cam E, Le Goff C, Strand O, Charrier G, Thebault J, Lazure P, Gotthard K, Clavier J., PLoS ONE 7(5), 2012
PMID: 22649553
Proteomic-based comparison between populations of the Great Scallop, Pecten maximus.
Artigaud S, Lavaud R, Thebault J, Jean F, Strand O, Strohmeier T, Milan M, Pichereau V., J Proteomics 105(), 2014
PMID: 24704858
Differences in reproductive ecology in natural and transplanted populations of Pecten maximus: evidence for the existence of separate stocks
Mackie LA, Ansell AD., 1993
Gradient forests: calculating importance gradients on physical predictors.
Ellis N, Smith SJ, Pitcher CR., Ecology 93(1), 2012
PMID: 22486096
Population differentiation and taxonomic status of the exploited limpet Patella candei in the Macaronesian islands (Azores, Madeira, Canaries)
Côrte-Real HBSM, Hawkins SJ, Thorpe JP., 1996
Evolutionary and Zoogeographical Remarks on the Mediterranean Fauna of Brachyuran Crabs
Almaça Carlos., 1985

AUTHOR UNKNOWN, 0
Are Pecten maximus and Pecten jacobaeus different species?
Wilding CS, Beaumont AR, Latchford JW., 1999
Nucleotide diversity and Pleistocene population expansion in Atlantic and Mediterranean scallops (Pecten maximus and P. jacobaeus) as revealed by the mitochondrial 16S ribosomal RNA gene
Saavedra C, Peña JB., 2005
Allozyme variation in populations of scallops, Pecten jacobaeus (L.) and P. maximus (L.)(Bivalvia: Pectinidae), across the Almeria–Oran front
Rıos C, Sanz S, Saavedra C, Pena JB., 2002
RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity.
Vendrami DL, Telesca L, Weigand H, Weiss M, Fawcett K, Lehman K, Clark MS, Leese F, McMinn C, Moore H, Hoffman JI., R Soc Open Sci 4(2), 2017
PMID: 28386419
RADpainter and fineRADstructure: Population Inference from RADseq Data.
Malinsky M, Trucchi E, Lawson DJ, Falush D., Mol. Biol. Evol. 35(5), 2018
PMID: 29474601
Robust demographic inference from genomic and SNP data.
Excoffier L, Dupanloup I, Huerta-Sanchez E, Sousa VC, Foll M., PLoS Genet. 9(10), 2013
PMID: 24204310
LEA: an R package for landscape and ecological association studies
Frichot E, François O., 2015
APE: Analyses of Phylogenetics and Evolution in R language.
Paradis E, Claude J, Strimmer K., Bioinformatics 20(2), 2004
PMID: 14734327
Pelagic larval duration and dispersal distance revisited.
Shanks AL., Biol. Bull. 216(3), 2009
PMID: 19556601
Mitochondrial DNA variation among open-sea and enclosed populations of the scallop Pecten maximus in western Britain
Heipel DA, Bishop JDD, Brand AR., 1999

AUTHOR UNKNOWN, 0
The cockle Cerastoderma edule at Northeast Atlantic shores: genetic signatures of glacial refugia
Krakau M, Jacobsen S, Jensen KT, Reise K., 2012
Timing of the Last Glacial Maximum from observed sea-level minima
Yokoyama Y, Lambeck K, De Deckker P , Johnston P, Fifield LK., Nature 406(6797), 2000
PMID: 10963593

AUTHOR UNKNOWN, 0
Genome scan methods against more complex models: when and how much should we trust them?
de Villemereuil P, Frichot E, Bazin E, Francois O, Gaggiotti OE., Mol. Ecol. 23(8), 2014
PMID: 24611968
Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers
Wilding CS, Butlin RK, Grahame J., 2001
Biological consequences of global warming: is the signal already apparent?
Hughes I I., Trends Ecol. Evol. (Amst.) 15(2), 2000
PMID: 10652556

AUTHOR UNKNOWN, 0
Biogeographic patterns and Plio-Pleistocene extinction of Bivalvia in the Mediterranean and southern North Sea
Raffi S, Stanley SM, Marasti R., 1985
A study of an intense density front in the eastern Alboran Sea: the Almeria–Oran front
Tintore J, La PE, Blade I, Cruzado A., 1988

AUTHOR UNKNOWN, 0
Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA., PLoS ONE 3(10), 2008
PMID: 18852878
Stacks: an analysis tool set for population genomics.
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA., Mol. Ecol. 22(11), 2013
PMID: 23701397
Deriving genotypes from RAD-seq short-read data using Stacks.
Rochette NC, Catchen JM., Nat Protoc 12(12), 2017
PMID: 29189774
Lost in parameter space: a road map for stacks
Paris JR, Stevens JR, Catchen JM., 2017
The variant call format and VCFtools.
, Bioinformatics 27(15), 2011
PMID: 21653522
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC., Am. J. Hum. Genet. 81(3), 2007
PMID: 17701901
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.
Jombart T, Ahmed I., Bioinformatics 27(21), 2011
PMID: 21926124
Inference of population structure using dense haplotype data.
Lawson DJ, Hellenthal G, Myers S, Falush D., PLoS Genet. 8(1), 2012
PMID: 22291602
InbreedR: an R package for the analysis of inbreeding based on genetic markers
Stoffel MA., 2016
Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus.
Estoup A, Beaumont M, Sennedot F, Moritz C, Cornuet JM., Evolution 58(9), 2004
PMID: 15521459
A note on composite likelihood inference and model selection
Varin C, Vidoni P., 2005
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Benjamini Y, Hochberg Y., 1995
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 31092869
PubMed | Europe PMC

Suchen in

Google Scholar