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DNA barcodes for species identification in the hyperdiverse ant genus Pheidole (Formicidae: Myrmicinae).

Ng'endo RN, Osiemo ZB, Brandl R - J. Insect Sci. (2013)

Bottom Line: However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters.Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank.The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology, Animal Ecology Faculty of Biology Philipps-Universitaet Marburg, Karl-von-Frisch-Strasse 8, D-35032 Marburg, Germany. rossangendo@yahoo.com

ABSTRACT
DNA sequencing is increasingly being used to assist in species identification in order to overcome taxonomic impediment. However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters. Mitochondrial DNA Cytochrome oxidase subunit 1 (CO1) gene was sequenced, measuring 636 base pairs, from 47 ants of the genus Pheidole (Formicidae: Myrmicinae) collected in the Brazilian Atlantic Forest to test whether the morphology-based assignment of individuals into species is supported by DNA-based species delimitation. Twenty morphospecies were identified, whereas the barcoding analysis identified 19 Molecular Operational Taxonomic Units (MOTUs). Fifteen out of the 19 DNA-based clusters allocated, using sequence divergence thresholds of 2% and 3%, matched with morphospecies. Both thresholds yielded the same number of MOTUs. Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank. The average pairwise sequence divergence for all 47 sequences was 19%, ranging between 0-25%. In some cases, however, morphology and molecular based methods differed in their assignment of individuals to morphospecies or MOTUs. The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.

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A combined phylogeny of CO1 sequences all from the genus Pheidole from the Genbank, and 47 sequences (taxa in blue) from Rio Cachoeira Nature Reserve. The 47 sequences formed distinct clusters in relation to those from the Genbank. The tree is rooted using the taxa in red. High quality figures are available online.
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f04_01: A combined phylogeny of CO1 sequences all from the genus Pheidole from the Genbank, and 47 sequences (taxa in blue) from Rio Cachoeira Nature Reserve. The 47 sequences formed distinct clusters in relation to those from the Genbank. The tree is rooted using the taxa in red. High quality figures are available online.

Mentions: Match success of the 47 sequences was further examined in relation to the CO1 sequence of species in the genus Pheidole already present in the CO1 Genbank library (NCBI, GenBank, http://www.ncbi.nlm.nih.gov/) (searches done between 2008 and 2009). In cases where the match success was above 95%, the species name for that MOTU was allocated. To establish the distribution of genetic divergence and positioning of MOTUs in relation to Pheidole species from other regions, all CO1 sequences (genus Pheidole) that contained 640 or more bp (sequences retrieved on 2 March 2011) were extracted from the Genbank. A total of 141 sequences were obtained and combined with 47 sequences from this study for further alignment. The final set of 188 sequences was trimmed to 636 bp, and a histogram and a Neighbor-Joining tree were constructed (tree in Figure 4) using Kimura two parameter distance (Kimura 1980). This was implemented using data application Package ape (Paradis et al. 2004) available in R (R Development Core Team 2009).


DNA barcodes for species identification in the hyperdiverse ant genus Pheidole (Formicidae: Myrmicinae).

Ng'endo RN, Osiemo ZB, Brandl R - J. Insect Sci. (2013)

A combined phylogeny of CO1 sequences all from the genus Pheidole from the Genbank, and 47 sequences (taxa in blue) from Rio Cachoeira Nature Reserve. The 47 sequences formed distinct clusters in relation to those from the Genbank. The tree is rooted using the taxa in red. High quality figures are available online.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3735075&req=5

f04_01: A combined phylogeny of CO1 sequences all from the genus Pheidole from the Genbank, and 47 sequences (taxa in blue) from Rio Cachoeira Nature Reserve. The 47 sequences formed distinct clusters in relation to those from the Genbank. The tree is rooted using the taxa in red. High quality figures are available online.
Mentions: Match success of the 47 sequences was further examined in relation to the CO1 sequence of species in the genus Pheidole already present in the CO1 Genbank library (NCBI, GenBank, http://www.ncbi.nlm.nih.gov/) (searches done between 2008 and 2009). In cases where the match success was above 95%, the species name for that MOTU was allocated. To establish the distribution of genetic divergence and positioning of MOTUs in relation to Pheidole species from other regions, all CO1 sequences (genus Pheidole) that contained 640 or more bp (sequences retrieved on 2 March 2011) were extracted from the Genbank. A total of 141 sequences were obtained and combined with 47 sequences from this study for further alignment. The final set of 188 sequences was trimmed to 636 bp, and a histogram and a Neighbor-Joining tree were constructed (tree in Figure 4) using Kimura two parameter distance (Kimura 1980). This was implemented using data application Package ape (Paradis et al. 2004) available in R (R Development Core Team 2009).

Bottom Line: However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters.Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank.The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology, Animal Ecology Faculty of Biology Philipps-Universitaet Marburg, Karl-von-Frisch-Strasse 8, D-35032 Marburg, Germany. rossangendo@yahoo.com

ABSTRACT
DNA sequencing is increasingly being used to assist in species identification in order to overcome taxonomic impediment. However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters. Mitochondrial DNA Cytochrome oxidase subunit 1 (CO1) gene was sequenced, measuring 636 base pairs, from 47 ants of the genus Pheidole (Formicidae: Myrmicinae) collected in the Brazilian Atlantic Forest to test whether the morphology-based assignment of individuals into species is supported by DNA-based species delimitation. Twenty morphospecies were identified, whereas the barcoding analysis identified 19 Molecular Operational Taxonomic Units (MOTUs). Fifteen out of the 19 DNA-based clusters allocated, using sequence divergence thresholds of 2% and 3%, matched with morphospecies. Both thresholds yielded the same number of MOTUs. Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank. The average pairwise sequence divergence for all 47 sequences was 19%, ranging between 0-25%. In some cases, however, morphology and molecular based methods differed in their assignment of individuals to morphospecies or MOTUs. The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.

Show MeSH