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DNA-Based Taxonomy in Ecologically Versatile Microalgae: A Re-Evaluation of the Species Concept within the Coccoid Green Algal Genus Coccomyxa (Trebouxiophyceae, Chlorophyta).

Malavasi V, Škaloud P, Rindi F, Tempesta S, Paoletti M, Pasqualetti M - PLoS ONE (2016)

Bottom Line: Our results are compared with those of a recent integrative study of Darienko and colleagues that reassessed the taxonomy of Coccomyxa, recognizing 7 species in the genus.We conclude that the 27-species scenario is presently the most realistic for Coccomyxa and we suggest that well-supported lineages distinguishable by ecological preferences should be recognized as different species in this genus.We also recommend that for microbial lineages in which the overall diversity is unknown and taxon sampling is sparse, as is often the case for green microalgae, the results of analyses for algorithmic DNA-based species delimitation should be interpreted with extreme caution.

View Article: PubMed Central - PubMed

Affiliation: Interdepartmental Center of Environmental Science and Engineering (CINSA), University of Cagliari, Cagliari, Italy.

ABSTRACT
Coccomyxa is a genus of unicellular green algae of the class Trebouxiophyceae, well known for its cosmopolitan distribution and great ecological amplitude. The taxonomy of this genus has long been problematic, due to reliance on badly-defined and environmentally variable morphological characters. In this study, based on the discovery of a new species from an extreme habitat, we reassess species circumscription in Coccomyxa, a unicellular genus of the class Trebouxiophyceae, using a combination of ecological and DNA sequence data (analyzed with three different methods of algorithmic species delineation). Our results are compared with those of a recent integrative study of Darienko and colleagues that reassessed the taxonomy of Coccomyxa, recognizing 7 species in the genus. Expanding the dataset from 43 to 61 sequences (SSU + ITS rDNA) resulted in a different delimitation, supporting the recognition of a higher number of species (24 to 27 depending on the analysis used, with the 27-species scenario receiving the strongest support). Among these, C. melkonianii sp. nov. is described from material isolated from a river highly polluted by heavy metals (Rio Irvi, Sardinia, Italy). Analyses performed on ecological characters detected a significant phylogenetic signal in six different characters. We conclude that the 27-species scenario is presently the most realistic for Coccomyxa and we suggest that well-supported lineages distinguishable by ecological preferences should be recognized as different species in this genus. We also recommend that for microbial lineages in which the overall diversity is unknown and taxon sampling is sparse, as is often the case for green microalgae, the results of analyses for algorithmic DNA-based species delimitation should be interpreted with extreme caution.

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Comparison of different species scenarios resulting from GMYC and bPTP analyses, along with the species clusters proposed by Darienko et al.[4].The topologies shown were obtained by BEAST analyses based on concatenated SSU + ITS rDNA (A) and ITS rDNA (B) datasets, using alignments reduced to include only well-aligned ITS positions. The red coloration delimits species clusters recognized by GMYC analyses; a hatched (red) pattern indicates the GMYC clusters containing genetically identical sequences. The pink coloration delimits the eight species clusters proposed by Darienko et al.[4]. Different species scenarios proposed by GMYC and bPTP analyses are indicated by vertical bars next to the phylogenetic trees. For each topology, two different datasets were analysed (including original and reduced ITS rDNA alignment to include only well-aligned ITS positions). The species clusters are either assigned to previously described Coccomyxa species or labelled alphabetically. Clade colouring follows the Fig 4. Scale bars represent the expected number of substitutions per site.
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pone.0151137.g005: Comparison of different species scenarios resulting from GMYC and bPTP analyses, along with the species clusters proposed by Darienko et al.[4].The topologies shown were obtained by BEAST analyses based on concatenated SSU + ITS rDNA (A) and ITS rDNA (B) datasets, using alignments reduced to include only well-aligned ITS positions. The red coloration delimits species clusters recognized by GMYC analyses; a hatched (red) pattern indicates the GMYC clusters containing genetically identical sequences. The pink coloration delimits the eight species clusters proposed by Darienko et al.[4]. Different species scenarios proposed by GMYC and bPTP analyses are indicated by vertical bars next to the phylogenetic trees. For each topology, two different datasets were analysed (including original and reduced ITS rDNA alignment to include only well-aligned ITS positions). The species clusters are either assigned to previously described Coccomyxa species or labelled alphabetically. Clade colouring follows the Fig 4. Scale bars represent the expected number of substitutions per site.

Mentions: Values at the nodes indicate statistical support estimated by three methods—MrBayes posterior-node probability (left), maximum-likelihood bootstrap (middle), and weighted maximum parsimony bootstrap (right). Full statistical support (1.00/100/100) is marked with an asterisk. Thick branches represent nodes receiving the highest PP support (1.00). The newly sequenced strain of Coccomyxa SCCA 048 is marked in bold. Sequences obtained from authentic strains are marked by arrowheads. Clades belonging to four species circumscribed by Darienko et al.[4], i.e., C. simplex, C. subellipsoidea, C. polymorpha and C. viridis, are marked in blue, green, yellow, and red, respectively. The clades recognized are either assigned to previously described Coccomyxa species or labelled alphabetically based on GMYC analyses (see Fig 5). Scale bar represents the expected number of substitutions per site.


DNA-Based Taxonomy in Ecologically Versatile Microalgae: A Re-Evaluation of the Species Concept within the Coccoid Green Algal Genus Coccomyxa (Trebouxiophyceae, Chlorophyta).

Malavasi V, Škaloud P, Rindi F, Tempesta S, Paoletti M, Pasqualetti M - PLoS ONE (2016)

Comparison of different species scenarios resulting from GMYC and bPTP analyses, along with the species clusters proposed by Darienko et al.[4].The topologies shown were obtained by BEAST analyses based on concatenated SSU + ITS rDNA (A) and ITS rDNA (B) datasets, using alignments reduced to include only well-aligned ITS positions. The red coloration delimits species clusters recognized by GMYC analyses; a hatched (red) pattern indicates the GMYC clusters containing genetically identical sequences. The pink coloration delimits the eight species clusters proposed by Darienko et al.[4]. Different species scenarios proposed by GMYC and bPTP analyses are indicated by vertical bars next to the phylogenetic trees. For each topology, two different datasets were analysed (including original and reduced ITS rDNA alignment to include only well-aligned ITS positions). The species clusters are either assigned to previously described Coccomyxa species or labelled alphabetically. Clade colouring follows the Fig 4. Scale bars represent the expected number of substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814044&req=5

pone.0151137.g005: Comparison of different species scenarios resulting from GMYC and bPTP analyses, along with the species clusters proposed by Darienko et al.[4].The topologies shown were obtained by BEAST analyses based on concatenated SSU + ITS rDNA (A) and ITS rDNA (B) datasets, using alignments reduced to include only well-aligned ITS positions. The red coloration delimits species clusters recognized by GMYC analyses; a hatched (red) pattern indicates the GMYC clusters containing genetically identical sequences. The pink coloration delimits the eight species clusters proposed by Darienko et al.[4]. Different species scenarios proposed by GMYC and bPTP analyses are indicated by vertical bars next to the phylogenetic trees. For each topology, two different datasets were analysed (including original and reduced ITS rDNA alignment to include only well-aligned ITS positions). The species clusters are either assigned to previously described Coccomyxa species or labelled alphabetically. Clade colouring follows the Fig 4. Scale bars represent the expected number of substitutions per site.
Mentions: Values at the nodes indicate statistical support estimated by three methods—MrBayes posterior-node probability (left), maximum-likelihood bootstrap (middle), and weighted maximum parsimony bootstrap (right). Full statistical support (1.00/100/100) is marked with an asterisk. Thick branches represent nodes receiving the highest PP support (1.00). The newly sequenced strain of Coccomyxa SCCA 048 is marked in bold. Sequences obtained from authentic strains are marked by arrowheads. Clades belonging to four species circumscribed by Darienko et al.[4], i.e., C. simplex, C. subellipsoidea, C. polymorpha and C. viridis, are marked in blue, green, yellow, and red, respectively. The clades recognized are either assigned to previously described Coccomyxa species or labelled alphabetically based on GMYC analyses (see Fig 5). Scale bar represents the expected number of substitutions per site.

Bottom Line: Our results are compared with those of a recent integrative study of Darienko and colleagues that reassessed the taxonomy of Coccomyxa, recognizing 7 species in the genus.We conclude that the 27-species scenario is presently the most realistic for Coccomyxa and we suggest that well-supported lineages distinguishable by ecological preferences should be recognized as different species in this genus.We also recommend that for microbial lineages in which the overall diversity is unknown and taxon sampling is sparse, as is often the case for green microalgae, the results of analyses for algorithmic DNA-based species delimitation should be interpreted with extreme caution.

View Article: PubMed Central - PubMed

Affiliation: Interdepartmental Center of Environmental Science and Engineering (CINSA), University of Cagliari, Cagliari, Italy.

ABSTRACT
Coccomyxa is a genus of unicellular green algae of the class Trebouxiophyceae, well known for its cosmopolitan distribution and great ecological amplitude. The taxonomy of this genus has long been problematic, due to reliance on badly-defined and environmentally variable morphological characters. In this study, based on the discovery of a new species from an extreme habitat, we reassess species circumscription in Coccomyxa, a unicellular genus of the class Trebouxiophyceae, using a combination of ecological and DNA sequence data (analyzed with three different methods of algorithmic species delineation). Our results are compared with those of a recent integrative study of Darienko and colleagues that reassessed the taxonomy of Coccomyxa, recognizing 7 species in the genus. Expanding the dataset from 43 to 61 sequences (SSU + ITS rDNA) resulted in a different delimitation, supporting the recognition of a higher number of species (24 to 27 depending on the analysis used, with the 27-species scenario receiving the strongest support). Among these, C. melkonianii sp. nov. is described from material isolated from a river highly polluted by heavy metals (Rio Irvi, Sardinia, Italy). Analyses performed on ecological characters detected a significant phylogenetic signal in six different characters. We conclude that the 27-species scenario is presently the most realistic for Coccomyxa and we suggest that well-supported lineages distinguishable by ecological preferences should be recognized as different species in this genus. We also recommend that for microbial lineages in which the overall diversity is unknown and taxon sampling is sparse, as is often the case for green microalgae, the results of analyses for algorithmic DNA-based species delimitation should be interpreted with extreme caution.

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