Testing the variability of chloroplast sequences for plant phylogeography

Abstract

Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…A recent analysis of chloroplast genomes focusing on non-coding regions from 25, mostly congeneric species pairs suggests that a few regions are generally highly variable across most angiosperms, including ndhF-rpl32, rpl32-trnL, ndhC-trnV, and 5'rps16-trnQ . These regions have also been found to be highly variable in other studies using different sets of taxa and approaches (Byrne and Haninson, 2012;Dong et al, 2012;Shaw et al, 2007). All of these regions were moderately to highly variable among Stachys species.…”

Centros de origen, domesticación y diversidad genética de la ciruela mexicana, Spondias purpurea (Anacardiaceae)

“…Los marcadores moleculares de DNA de cloroplasto son los que se han privilegiado en los estudios filogeográficos de las plantas, porque tienen mayor probabilidad de retener la información biogeográfica (Burger et al, 2008;Byrne y Hankinson, 2012;Nybom et al, 2014). En términos generales se asume que la diversidad genética de las especies cultivadas es menor que la de sus ancestros silvestres como consecuencia de la selección direccional y los cuellos de botella a que se someten las especies domesticadas.…”

Phylogeographic evidence for two mesic refugia in a biodiversity hotspot

“…The level of variation for 13 non-coding regions of the chloroplast genome has been tested in six plant species from south-west Western Australia, including C. quadrifidus (Byrne and Hankinson, 2012). Three of the most polymorphic regions (D4 loop introns rpl16 and petB; intergenic spacer trnQ-rps16) were selected for amplification using the PCR on DNA from five plants from each population of C. quadrifidus.…”