Abstract
The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon - UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis.
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Claims 5
Claim · model-written summary
Five of the tested chloroplast regions (UPA, rpoB, rpoC1, accD, rbcL) were predominantly invariant across Myristicaceae species.
- Taxon
- MyristicaceaeMyristicaceaet0
- Outcome
- predominantly invariant across speciese0
Verbatim
t0“Myristicaceae”
e0“Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL)”
Claim · model-written summary
Two chloroplast regions, matK and trnH-psbA, had significant variation and show promise for barcoding in nutmegs.
- Taxon
- MyristicaceaeMyristicaceaet0
- Gene
- matK and trnH-psbAe0
- Outcome
- significant variatione0
Verbatim
t0“Myristicaceae”
e0“Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs”
Claim · model-written summary
A two-gene approach using matK and trnH-psbA provided resolution among all sampled Compsoneura species, including the recently evolved C. sprucei and C. mexicana.
Verbatim
e0“a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana”
Claim · model-written summary
Using two regions decreased the range of intraspecific variation relative to interspecific divergence.
- Taxon
- MyristicaceaeMyristicaceaet0
- Outcome
- range of intraspecific variatione0
Verbatim
t0“Myristicaceae”
e0“the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence”
Claim · model-written summary
In a sequence identification analysis with the two-region approach, 95% of the samples were correctly identified.
Verbatim
e0“95% of the samples correctly identified in a sequence identification analysis”