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Genetic structure of Daphnia galeata populations in Eastern China.

Wei W, Gießler S, Wolinska J, Ma X, Yang Z, Hu W, Yin M - PLoS ONE (2015)

Bottom Line: Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity.Overall, populations did not cluster by geographical origin.Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.

View Article: PubMed Central - PubMed

Affiliation: Yangzhou University, College of Animal Science and Technology, Yangzhou, China.

ABSTRACT
This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.

No MeSH data available.


Taxon identity of individuals from the D. longispina complex sampled from eight lakes in Eastern China.(a) Similarity of Chinese samples to 49 reference clones representing three species and two hybrid taxa (indicated by crosses; for a list of all reference clones see Yin et al. 2010). Factorial correspondence analysis scores from the first two axes are shown. FCA based on allelic variation at up to 15 microsatellite loci was used to extract factorial axes. (b) Individuals were reclassified by discriminant functions to taxa using FCA scores from four axes to discriminate among groups. Shown are values from the first two discriminant functions per individual and five group centroids representing the five taxa.
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pone.0120168.g001: Taxon identity of individuals from the D. longispina complex sampled from eight lakes in Eastern China.(a) Similarity of Chinese samples to 49 reference clones representing three species and two hybrid taxa (indicated by crosses; for a list of all reference clones see Yin et al. 2010). Factorial correspondence analysis scores from the first two axes are shown. FCA based on allelic variation at up to 15 microsatellite loci was used to extract factorial axes. (b) Individuals were reclassified by discriminant functions to taxa using FCA scores from four axes to discriminate among groups. Shown are values from the first two discriminant functions per individual and five group centroids representing the five taxa.

Mentions: Among 313 individuals from eight lakes in and around Yangzhou city (allowing missing data at up to four loci), 250 had a unique MLG genotype. Those unique MLGs were used in species assignment tests by DFCA. Altogether, ten factorial axes were extracted by FCA (cut-off: eigenvalue > 0.1) in a joint analysis with 49 well-defined reference genotypes [10]. Although the eigenvalues of the first two factorial axes were relatively low (0.73 and 0.58) and only 13.75% of the variance was explained, the plot of respective factorial axis scores resolved at least three species clusters (Fig. 1a). The Chinese samples clustered nearby the D. galeata reference MLGs but away from two hybrid clusters. When individuals were classified to five groups corresponding to the five reference taxa (D. cucullata, D. galeata, D. longispina, F1 D. cucullata × D. galeata and F1 D. galeata × D. longispina) discriminant analysis on all ten FCA scores confirmed the D. galeata species identity of the Chinese samples (Fig. 1b). Wilks´ lambdas from the first three discriminant functions were significant (P < 0.001). Only the first two functions had eigenvalues > 1 (74.72 and 49.87) and explained 99.8% of the variance in the data. Group centroids of taxonomic units were clearly separated and all Chinese samples unambiguously clustered with eight reference D. galeata genotypes from Europe and one from North America. Also, when using GENECLASS to assign individuals to one of two species (D. galeata and D. longispina) all Chinese Daphnia were clearly assigned to D. galeata (p > 99.7).


Genetic structure of Daphnia galeata populations in Eastern China.

Wei W, Gießler S, Wolinska J, Ma X, Yang Z, Hu W, Yin M - PLoS ONE (2015)

Taxon identity of individuals from the D. longispina complex sampled from eight lakes in Eastern China.(a) Similarity of Chinese samples to 49 reference clones representing three species and two hybrid taxa (indicated by crosses; for a list of all reference clones see Yin et al. 2010). Factorial correspondence analysis scores from the first two axes are shown. FCA based on allelic variation at up to 15 microsatellite loci was used to extract factorial axes. (b) Individuals were reclassified by discriminant functions to taxa using FCA scores from four axes to discriminate among groups. Shown are values from the first two discriminant functions per individual and five group centroids representing the five taxa.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358959&req=5

pone.0120168.g001: Taxon identity of individuals from the D. longispina complex sampled from eight lakes in Eastern China.(a) Similarity of Chinese samples to 49 reference clones representing three species and two hybrid taxa (indicated by crosses; for a list of all reference clones see Yin et al. 2010). Factorial correspondence analysis scores from the first two axes are shown. FCA based on allelic variation at up to 15 microsatellite loci was used to extract factorial axes. (b) Individuals were reclassified by discriminant functions to taxa using FCA scores from four axes to discriminate among groups. Shown are values from the first two discriminant functions per individual and five group centroids representing the five taxa.
Mentions: Among 313 individuals from eight lakes in and around Yangzhou city (allowing missing data at up to four loci), 250 had a unique MLG genotype. Those unique MLGs were used in species assignment tests by DFCA. Altogether, ten factorial axes were extracted by FCA (cut-off: eigenvalue > 0.1) in a joint analysis with 49 well-defined reference genotypes [10]. Although the eigenvalues of the first two factorial axes were relatively low (0.73 and 0.58) and only 13.75% of the variance was explained, the plot of respective factorial axis scores resolved at least three species clusters (Fig. 1a). The Chinese samples clustered nearby the D. galeata reference MLGs but away from two hybrid clusters. When individuals were classified to five groups corresponding to the five reference taxa (D. cucullata, D. galeata, D. longispina, F1 D. cucullata × D. galeata and F1 D. galeata × D. longispina) discriminant analysis on all ten FCA scores confirmed the D. galeata species identity of the Chinese samples (Fig. 1b). Wilks´ lambdas from the first three discriminant functions were significant (P < 0.001). Only the first two functions had eigenvalues > 1 (74.72 and 49.87) and explained 99.8% of the variance in the data. Group centroids of taxonomic units were clearly separated and all Chinese samples unambiguously clustered with eight reference D. galeata genotypes from Europe and one from North America. Also, when using GENECLASS to assign individuals to one of two species (D. galeata and D. longispina) all Chinese Daphnia were clearly assigned to D. galeata (p > 99.7).

Bottom Line: Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity.Overall, populations did not cluster by geographical origin.Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.

View Article: PubMed Central - PubMed

Affiliation: Yangzhou University, College of Animal Science and Technology, Yangzhou, China.

ABSTRACT
This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.

No MeSH data available.