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Travelling in time with networks: Revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis.

Moalic Y, Arnaud-Haond S, Perrin C, Pearson GA, Serrao EA - BMC Evol. Biol. (2011)

Bottom Line: Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic.Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence) and the Shared Allele (SAD; based on alleles identity) distances.Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia.

View Article: PubMed Central - HTML - PubMed

Affiliation: IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer, centre de Brest, BP70, 29280 Plouzané, France.

ABSTRACT

Background: Hybridization or divergence between sympatric sister species provides a natural laboratory to study speciation processes. The shared polymorphism in sister species may either be ancestral or derive from hybridization, and the accuracy of analytic methods used thus far to derive convincing evidence for the occurrence of present day hybridization is largely debated.

Results: Here we propose the application of network analysis to test for the occurrence of present day hybridization between the two species of brown algae Fucus spiralis and F. vesiculosus. Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic. Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence) and the Shared Allele (SAD; based on alleles identity) distances. A diagnostic level of genotype divergence and clustering of individuals from each species was obtained through RD while screening for exchanges through putative hybridization was facilitated using SAD. Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia.

Conclusion: These results suggesting rare hybridization were confirmed by simulation of hybrids and F2 with directed backcrosses. Comparison with the Bayesian method STRUCTURE confirmed the usefulness of both approaches and emphasized the reliability of network analysis to unravel and study hybridization.

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Network topology of F. spiralis and F. vesiculosus individuals with the Rozenfeld Distance (RD). Only links with value smaller than or equal to the percolation distance Dp = 7.15 are present. Nodes representing individuals are circles for F. spiralis and squares for F. vesiculosus. Colors correspond to geographical regions. One can identify 2 clusters, one for F. spiralis individuals and the other for F. vesiculosus.
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Figure 1: Network topology of F. spiralis and F. vesiculosus individuals with the Rozenfeld Distance (RD). Only links with value smaller than or equal to the percolation distance Dp = 7.15 are present. Nodes representing individuals are circles for F. spiralis and squares for F. vesiculosus. Colors correspond to geographical regions. One can identify 2 clusters, one for F. spiralis individuals and the other for F. vesiculosus.

Mentions: Networks were analyzed at the percolation threshold (see methods). This approach is based on the analysis of the network keeping only essential links illustrating the minimum genetic distance necessary to maintain connectivity across most components of the system. The network based on the Rozenfeld distance (RD; Figure 1) reveals diagnostic RD distances among both species. At the percolation threshold distance (Dp = 7.15), genotypes corresponding to sampled F_spi (left) versus F_ves (right) clearly segregate into two sub-clusters linked through a succession of 4 nodes (Figure 1). Below this percolation threshold, the network loses its integrity and the species-specific sub-clusters split into distinct clusters (see Figure A2 in additional file 2), each exclusively composed of either F_spi or of F_ves individuals. The ensuing clusters of individuals present a hierarchical structure supported by a significant average clustering coefficient: < CC > = 0.72 higher than the one expected after randomly rewiring the links (< CCo > = 0.11 with σo = 0.1, after 10,000 random simulations). Thus illustrating the modularity of the network composed of two clusters of species, with greater internal interconnection than would be expected by chance.


Travelling in time with networks: Revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis.

Moalic Y, Arnaud-Haond S, Perrin C, Pearson GA, Serrao EA - BMC Evol. Biol. (2011)

Network topology of F. spiralis and F. vesiculosus individuals with the Rozenfeld Distance (RD). Only links with value smaller than or equal to the percolation distance Dp = 7.15 are present. Nodes representing individuals are circles for F. spiralis and squares for F. vesiculosus. Colors correspond to geographical regions. One can identify 2 clusters, one for F. spiralis individuals and the other for F. vesiculosus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3040711&req=5

Figure 1: Network topology of F. spiralis and F. vesiculosus individuals with the Rozenfeld Distance (RD). Only links with value smaller than or equal to the percolation distance Dp = 7.15 are present. Nodes representing individuals are circles for F. spiralis and squares for F. vesiculosus. Colors correspond to geographical regions. One can identify 2 clusters, one for F. spiralis individuals and the other for F. vesiculosus.
Mentions: Networks were analyzed at the percolation threshold (see methods). This approach is based on the analysis of the network keeping only essential links illustrating the minimum genetic distance necessary to maintain connectivity across most components of the system. The network based on the Rozenfeld distance (RD; Figure 1) reveals diagnostic RD distances among both species. At the percolation threshold distance (Dp = 7.15), genotypes corresponding to sampled F_spi (left) versus F_ves (right) clearly segregate into two sub-clusters linked through a succession of 4 nodes (Figure 1). Below this percolation threshold, the network loses its integrity and the species-specific sub-clusters split into distinct clusters (see Figure A2 in additional file 2), each exclusively composed of either F_spi or of F_ves individuals. The ensuing clusters of individuals present a hierarchical structure supported by a significant average clustering coefficient: < CC > = 0.72 higher than the one expected after randomly rewiring the links (< CCo > = 0.11 with σo = 0.1, after 10,000 random simulations). Thus illustrating the modularity of the network composed of two clusters of species, with greater internal interconnection than would be expected by chance.

Bottom Line: Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic.Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence) and the Shared Allele (SAD; based on alleles identity) distances.Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia.

View Article: PubMed Central - HTML - PubMed

Affiliation: IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer, centre de Brest, BP70, 29280 Plouzané, France.

ABSTRACT

Background: Hybridization or divergence between sympatric sister species provides a natural laboratory to study speciation processes. The shared polymorphism in sister species may either be ancestral or derive from hybridization, and the accuracy of analytic methods used thus far to derive convincing evidence for the occurrence of present day hybridization is largely debated.

Results: Here we propose the application of network analysis to test for the occurrence of present day hybridization between the two species of brown algae Fucus spiralis and F. vesiculosus. Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic. Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence) and the Shared Allele (SAD; based on alleles identity) distances. A diagnostic level of genotype divergence and clustering of individuals from each species was obtained through RD while screening for exchanges through putative hybridization was facilitated using SAD. Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia.

Conclusion: These results suggesting rare hybridization were confirmed by simulation of hybrids and F2 with directed backcrosses. Comparison with the Bayesian method STRUCTURE confirmed the usefulness of both approaches and emphasized the reliability of network analysis to unravel and study hybridization.

Show MeSH