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Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)

Jacobsen, Magnus W ; Pujolar, Jose Martin ; Bernatchez, Louis ; Munch, Kasper ; Jian, Jianbo ; Niu, Yongchao ; Hansen, Michael M

Molecular ecology, 2014-10, Vol.23 (19), p.4785-4798 [Periódico revisado por pares]

England: Blackwell Scientific Publications

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  • Título:
    Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)
  • Autor: Jacobsen, Magnus W ; Pujolar, Jose Martin ; Bernatchez, Louis ; Munch, Kasper ; Jian, Jianbo ; Niu, Yongchao ; Hansen, Michael M
  • Assuntos: Anguilla - classification ; Anguilla - genetics ; Anguilla anguilla ; Anguilla rostrata ; Animals ; DNA ; eel ; Evolution ; Gene Flow ; gene ontology ; genes ; Genetic Drift ; Genetic Speciation ; Genomics ; Genomics - methods ; larvae ; Linkage Disequilibrium ; Marine biology ; migratory behavior ; phosphorylation ; Polymorphism, Single Nucleotide ; population size ; RAD sequencing ; selection ; Selection, Genetic ; Sequence Analysis, DNA ; spawning ; speciation-with-gene-flow ; Sympatry
  • É parte de: Molecular ecology, 2014-10, Vol.23 (19), p.4785-4798
  • Notas: http://dx.doi.org/10.1111/mec.12896
    Table S1 Information about the filtering process for the American eel and European eel samples. Table S2 Information about alignment of filtered reads for the American eel and European samples. Table S3 Summary information on reads after p-STACKS (p-stacks; M = 10) for American and European eel samples. Table S4 Filtering on the final number of loci after populations. Table S7 Individual NCBI codes of the used RAD sequenced samples. Note S1 Information about the annotation of the genome prior to analyses of nonsynonymous and synonymous substitutions in SNPeff (Cingolani et al. 2012). Fig S1 Plots of FST across the 30 longest scaffolds using a minor allele frequency (MAF) > 0.05.Table S5 Genes represented by one or several SNPs with FST > 0.8 in either the genes themselves (including both introns and exon) or ≤5000 bp upstream the gene.Table S6 Genes or upstream regions represented by lositan SNP outliers, candidates for positive selection.
    Danish Council for Independent Research, Natural Sciences - No. 09-072 120
    Elisabeth og Knud Petersen's Foundation
    ArticleID:MEC12896
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    content type line 23
  • Descrição: The importance of speciation‐with‐geneflow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated more than 3 Ma, and although low gene flow still occurs, strong postzygotic barriers are present. Restriction‐site‐associated DNA (RAD) sequencing identified 328 300 SNPs for subsequent analysis. However, despite the presence of 3757 strongly differentiated SNPs (FST > 0.8), sliding window analyses of FST showed no larger genomic regions (i.e. hundreds of thousands to millions of bases) of elevated differentiation. Overall FST was 0.041, and linkage disequilibrium was virtually absent for SNPs separated by more than 1000 bp. We suggest this to reflect a case of genomic hitchhiking, where multiple regions are under directional selection between the species. However, low but biologically significant gene flow and high effective population sizes leading to very low genetic drift preclude accumulation of strong background differentiation. Genes containing candidate SNPs for positive selection showed significant enrichment for gene ontology (GO) terms relating to developmental processes and phosphorylation, which seems consistent with assumptions that differences in larval phase duration and migratory distances underlie speciation. Most SNPs under putative selection were found outside coding regions, lending support to emerging views that noncoding regions may be more functionally important than previously assumed. In total, the results demonstrate the necessity of interpreting genomic footprints of selection in the context of demographic parameters and life‐history features of the studied species.
  • Editor: England: Blackwell Scientific Publications
  • Idioma: Inglês
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  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

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