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First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers.

Nagy ZT, Sonet G, Glaw F, Vences M - PLoS ONE (2012)

Bottom Line: Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages.Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.

View Article: PubMed Central - PubMed

Affiliation: Joint Experimental Molecular Unit, Royal Belgian Institute of Natural Sciences, Brussels, Belgium. lustimaci@yahoo.com

ABSTRACT

Background: DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar.

Methodology/principal findings: Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7-100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41-48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.

Conclusions/significance: The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.

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Related in: MedlinePlus

Plot of bootstrap values supporting genera and families with different DNA sequence length.Values for genera (top) and families (bottom) were obtained by neighbor-joining analyses based on DNA sequence fragments of 664 bp (original data set), 450, 300, 200 and 100 bp, respectively.
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pone-0034506-g004: Plot of bootstrap values supporting genera and families with different DNA sequence length.Values for genera (top) and families (bottom) were obtained by neighbor-joining analyses based on DNA sequence fragments of 664 bp (original data set), 450, 300, 200 and 100 bp, respectively.

Mentions: Neighbor-joining analyses based on shorter sequences (450, 300, 200, and 100 bp, respectively) showed that the number of well supported groups (with bootstrap values over 90%) decreased with shorter marker length (Figure 4), both on family- and genus-level. A few genera were found—mostly including a single or a couple of species only—which were highly supported in all subsets testing the effect of marker length. Also, none of the six species-rich monophyletic genera was supported significantly in the data set of mini-barcodes (100 bp). On the family level, even mini-barcodes of 100 bp length were sufficient to obtain highest support values in Chamaeleonidae, Pelomedusidae, and Psammophiidae, but low or no support was recovered for the other eight families. Results of distance-based comparisons showed that short marker sequences of 100 bp remained unique on species level, and, therefore, could be used for unambiguous identification of the samples.


First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers.

Nagy ZT, Sonet G, Glaw F, Vences M - PLoS ONE (2012)

Plot of bootstrap values supporting genera and families with different DNA sequence length.Values for genera (top) and families (bottom) were obtained by neighbor-joining analyses based on DNA sequence fragments of 664 bp (original data set), 450, 300, 200 and 100 bp, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3316696&req=5

pone-0034506-g004: Plot of bootstrap values supporting genera and families with different DNA sequence length.Values for genera (top) and families (bottom) were obtained by neighbor-joining analyses based on DNA sequence fragments of 664 bp (original data set), 450, 300, 200 and 100 bp, respectively.
Mentions: Neighbor-joining analyses based on shorter sequences (450, 300, 200, and 100 bp, respectively) showed that the number of well supported groups (with bootstrap values over 90%) decreased with shorter marker length (Figure 4), both on family- and genus-level. A few genera were found—mostly including a single or a couple of species only—which were highly supported in all subsets testing the effect of marker length. Also, none of the six species-rich monophyletic genera was supported significantly in the data set of mini-barcodes (100 bp). On the family level, even mini-barcodes of 100 bp length were sufficient to obtain highest support values in Chamaeleonidae, Pelomedusidae, and Psammophiidae, but low or no support was recovered for the other eight families. Results of distance-based comparisons showed that short marker sequences of 100 bp remained unique on species level, and, therefore, could be used for unambiguous identification of the samples.

Bottom Line: Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages.Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.

View Article: PubMed Central - PubMed

Affiliation: Joint Experimental Molecular Unit, Royal Belgian Institute of Natural Sciences, Brussels, Belgium. lustimaci@yahoo.com

ABSTRACT

Background: DNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar.

Methodology/principal findings: Representatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7-100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41-48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.

Conclusions/significance: The new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.

Show MeSH
Related in: MedlinePlus