Journal
BMC EVOLUTIONARY BIOLOGY
Volume 13, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2148-13-35
Keywords
Adaptive radiation; Island biogeography; Lobeliads; Next-generation sequencing; Progression rule; Single-copy nuclear genes
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Funding
- Gordon and Betty Moore Foundation
- Washington State University
- Direct For Education and Human Resources
- Division Of Human Resource Development [0833211] Funding Source: National Science Foundation
- Office Of The Director
- EPSCoR [0903833] Funding Source: National Science Foundation
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Background: DNA barcoding of land plants has relied traditionally on a small number of markers from the plastid genome. In contrast, low-copy nuclear genes have received little attention as DNA barcodes because of the absence of universal primers for PCR amplification. Results: From pooled-species 454 transcriptome data we identified two variable intron-less nuclear loci for each of two species-rich genera of the Hawaiian flora: Clermontia (Campanulaceae) and Cyrtandra (Gesneriaceae) and compared their utility as DNA barcodes with that of plastid genes. We found that nuclear genes showed an overall greater variability, but also displayed a high level of heterozygosity, intraspecific variation, and retention of ancient alleles. Thus, nuclear genes displayed fewer species-diagnostic haplotypes compared to plastid genes and no interspecies gaps. Conclusions: The apparently greater coalescence times of nuclear genes are likely to limit their utility as barcodes, as only a small proportion of their alleles were fixed and unique to individual species. In both groups, species-diagnostic markers from either genome were scarce on the youngest island; a minimum age of ca. two million years may be needed for a species flock to be barcoded. For young plant groups, nuclear genes may not be a superior alternative to slowly evolving plastid genes.
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