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Tracing the trans-pacific evolutionary history of a domesticated Seaweed (Gracilaria chilensis) with archaeological and genetic data.

Guillemin ML, Valero M, Faugeron S, Nelson W, Destombe C - PLoS ONE (2014)

Bottom Line: The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools.Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting.Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile; CNRS, Sorbonne Universités, UPMC University Paris VI, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888 Roscoff, France.

ABSTRACT
The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting. Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication. Therefore, the aquaculture of this seaweed, based essentially on clonal propagation, is occurring from genetically depressed populations and may be driving the species to an extinction vortex in Chile.

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Related in: MedlinePlus

Location of the sampling sites.ITS2 ribotype distribution and ITS2 network including 201 sequences of 481 nucleotides. Pie charts represent ribotype frequency in each population. Ribotype network was constructed using a median-joining algorithm with programme NETWORK [36]. Colours of the network correspond to those mapped with rare ribotypes in each “region” pooled under the same colour for clarity. Circle sizes are proportional to total ribotype frequency and connection lengths correspond to mutation steps (most of the ribotypes are separated by one mutational step but eight mutations separate r4 from r6).
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pone-0114039-g001: Location of the sampling sites.ITS2 ribotype distribution and ITS2 network including 201 sequences of 481 nucleotides. Pie charts represent ribotype frequency in each population. Ribotype network was constructed using a median-joining algorithm with programme NETWORK [36]. Colours of the network correspond to those mapped with rare ribotypes in each “region” pooled under the same colour for clarity. Circle sizes are proportional to total ribotype frequency and connection lengths correspond to mutation steps (most of the ribotypes are separated by one mutational step but eight mutations separate r4 from r6).

Mentions: Over the whole dataset (592 individuals), nuclear microsatellite loci displayed moderate to high numbers of alleles, ranging from three to 22 for the loci 6C7 and 7D3, respectively. For the 201 ITS2 sequences, characterised by 24 polymorphic sites and four indels, 21 ribotypes were identified. The most genetically diverse population was found in Chatham Island (Table S1). Observed heterozygosity (Ho) and Allele richness (Ae) were significantly higher in New Zealand than in Chile (Mann and Withney, P<0.05) but no significant differences were encountered for expected heterozygosity (He) and ribotype richness (Re) (Table S1). Allelic and ribotypic richness in Chile (Ae = 0.95±0.42 and Re = 0.52±0.37, Table S1) are half of those observed in New Zealand (Ae = 1.76±0.69 and Re = 0.97±0.77, Table S1), despite more sampling in Chile. The average expected heterozygosity is 25% lower in Chile than in New Zealand (He = 0.32 and 0.44 respectively, Table S1). Moreover, the allele accumulation curve describing the number of alleles observed as a function of sampling effort (Figure S1) demonstrated clearly that the saturation point was reached in Chile but not in New Zealand. It revealed that Chile is a subsample of the New Zealand genetic diversity (84% of the alleles observed in Chile were also found in New Zealand). Similarly, the ITS ribotype r1 which is ubiquitous in Chile is also the most common ribotype in the eastern coast of New Zealand (Table S1, Figure 1). The eleven individuals sequenced for rbcL from Chile (CH-MAU, N = 2; CH-ANC, N = 1), New Zealand (NZ-WIN, N = 2; NZ-SCB, N = 1; NZ-PGB, N = 1; NZ-MOU, N = 1) and Chatham Island (NZ-CHT, N = 1) displayed the same haplotype as G. chilensis sequences from Chile deposited in GenBank [27], [28]. No significant linkage disequilibrium was found among the five microsatellite loci. Most of the nineteen sampled populations were at H-W equilibrium except two populations from Chile and four populations from New Zealand (Table S1). In the population NZ-MOU, the strong heterozygote excess associated with a high number of repeated multilocus genotypes suggests the occurrence of asexual reproduction. The repeated genotypes of this population were thus removed for the analysis of the genetic structure to avoid erroneous individual assignation and flawed reconstruction of topological relationships among populations. The CH-MOL population also displayed numerous repeated genotypes but this was associated with a very low number of alleles at all loci (Table S1). These repeated genotypes were likely to have originated from distinct sexual reproduction events [14] and thus were included in all analyses.


Tracing the trans-pacific evolutionary history of a domesticated Seaweed (Gracilaria chilensis) with archaeological and genetic data.

Guillemin ML, Valero M, Faugeron S, Nelson W, Destombe C - PLoS ONE (2014)

Location of the sampling sites.ITS2 ribotype distribution and ITS2 network including 201 sequences of 481 nucleotides. Pie charts represent ribotype frequency in each population. Ribotype network was constructed using a median-joining algorithm with programme NETWORK [36]. Colours of the network correspond to those mapped with rare ribotypes in each “region” pooled under the same colour for clarity. Circle sizes are proportional to total ribotype frequency and connection lengths correspond to mutation steps (most of the ribotypes are separated by one mutational step but eight mutations separate r4 from r6).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263469&req=5

pone-0114039-g001: Location of the sampling sites.ITS2 ribotype distribution and ITS2 network including 201 sequences of 481 nucleotides. Pie charts represent ribotype frequency in each population. Ribotype network was constructed using a median-joining algorithm with programme NETWORK [36]. Colours of the network correspond to those mapped with rare ribotypes in each “region” pooled under the same colour for clarity. Circle sizes are proportional to total ribotype frequency and connection lengths correspond to mutation steps (most of the ribotypes are separated by one mutational step but eight mutations separate r4 from r6).
Mentions: Over the whole dataset (592 individuals), nuclear microsatellite loci displayed moderate to high numbers of alleles, ranging from three to 22 for the loci 6C7 and 7D3, respectively. For the 201 ITS2 sequences, characterised by 24 polymorphic sites and four indels, 21 ribotypes were identified. The most genetically diverse population was found in Chatham Island (Table S1). Observed heterozygosity (Ho) and Allele richness (Ae) were significantly higher in New Zealand than in Chile (Mann and Withney, P<0.05) but no significant differences were encountered for expected heterozygosity (He) and ribotype richness (Re) (Table S1). Allelic and ribotypic richness in Chile (Ae = 0.95±0.42 and Re = 0.52±0.37, Table S1) are half of those observed in New Zealand (Ae = 1.76±0.69 and Re = 0.97±0.77, Table S1), despite more sampling in Chile. The average expected heterozygosity is 25% lower in Chile than in New Zealand (He = 0.32 and 0.44 respectively, Table S1). Moreover, the allele accumulation curve describing the number of alleles observed as a function of sampling effort (Figure S1) demonstrated clearly that the saturation point was reached in Chile but not in New Zealand. It revealed that Chile is a subsample of the New Zealand genetic diversity (84% of the alleles observed in Chile were also found in New Zealand). Similarly, the ITS ribotype r1 which is ubiquitous in Chile is also the most common ribotype in the eastern coast of New Zealand (Table S1, Figure 1). The eleven individuals sequenced for rbcL from Chile (CH-MAU, N = 2; CH-ANC, N = 1), New Zealand (NZ-WIN, N = 2; NZ-SCB, N = 1; NZ-PGB, N = 1; NZ-MOU, N = 1) and Chatham Island (NZ-CHT, N = 1) displayed the same haplotype as G. chilensis sequences from Chile deposited in GenBank [27], [28]. No significant linkage disequilibrium was found among the five microsatellite loci. Most of the nineteen sampled populations were at H-W equilibrium except two populations from Chile and four populations from New Zealand (Table S1). In the population NZ-MOU, the strong heterozygote excess associated with a high number of repeated multilocus genotypes suggests the occurrence of asexual reproduction. The repeated genotypes of this population were thus removed for the analysis of the genetic structure to avoid erroneous individual assignation and flawed reconstruction of topological relationships among populations. The CH-MOL population also displayed numerous repeated genotypes but this was associated with a very low number of alleles at all loci (Table S1). These repeated genotypes were likely to have originated from distinct sexual reproduction events [14] and thus were included in all analyses.

Bottom Line: The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools.Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting.Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile; CNRS, Sorbonne Universités, UPMC University Paris VI, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888 Roscoff, France.

ABSTRACT
The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting. Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication. Therefore, the aquaculture of this seaweed, based essentially on clonal propagation, is occurring from genetically depressed populations and may be driving the species to an extinction vortex in Chile.

Show MeSH
Related in: MedlinePlus