Usefulness of cpDNA markers for phylogenetic and phylogeographic analyses of closely related cactus species

Abstract

ABSTRACT. Although plastid DNA has been widely explored as a marker of choice for phylogeny and phylogeography studies, little is known about its utility for examining relationships between closely related species. The slow evolutionary rates inherent to chloroplast (cp) DNA make it difficult to perform lower level taxonomic analyses, particularly at the population level. We characterized the nucleotide variation and investigated the utility of eight noncoding cpDNA regions in four closely related species of the Pilosocereus aurisetus group (Cactaceae), an endemic taxon of eastern South America. The plastid intergenic spacers 5'-trnS-trnG, 3'-trnS-trnG and trnT-trnL were the most variable regions and were the most useful for lower level taxonomic comparisons, especially when used together. We conclude that an adequate combination of regions alongside indels as an additional character improves the usefulness of cpDNA for phylogenetic studies.

Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies

“…The samples (157 in total; Table ) were sequenced to cover the noncoding intergenic spacers trnT‐trnL and trnS‐trnG of the chloroplast DNA (cpDNA) following the PCR protocols described by Bonatelli et al . (). We also amplified and sequenced Exon‐1 of the low‐copy nuclear photoreceptor gene ( PhyC ) in 34 individuals (one individual per population, except for the population ART, from which two individuals were sequenced; Table ) using the primers and PCR conditions reported by Helsen et al .…”

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

“…These segments were selected based on previous variability screening for Cereus (Romeiro‐Brito, Moraes, Taylor, Zappi, & Franco, ; Silva et al., ). Amplification reactions for trnS‐trnG and PHYC were performed following Bonatelli, Zappi, Taylor, and Moraes () and Helsen, Browne, Anderson, Verdyck, and Dongen (), respectively. The direct sequencing was prepared using the Big Dye terminator 3.1 kit (Applied Biosystems) and conducted in Gene Amp PCR System 9700 (Applied Biosystems).…”

Lineage‐specific evolutionary rate in plants: Contributions of a screening for Cereus (Cactaceae)

“…Although most of the segments that revealed variability in the three levels of analysis were previously used in cactus studies to establish evolutionary relationships for phylogeographic analyses ( trnQ (UUG) -5′rps16 , psbJ-petA , and rpL16 [Korotkova et al, 2011]; trnS-trnG [Bonatelli et al, 2013]), some of the plastid regions previously used at the intraspecific level did not present enough variation in this work ( trnT-trnL and psbA-trnH [Korotkova et al, 2011; Bonatelli et al, 2013]).…”

“…We selected 16 plastid molecular markers: 14 intergenic spacers ( trnT-trnL , 3′trnK-matK partial, trnL-trnF , 3′rps16-5′trnK (UUU) , trnS-trnG , trnH-psbA , trnQ (UUG) -5′rps16 , rpl32-trnL (UAG) , psbJ-petA , atpI-atpH , petL-psbE , psbD-trnT (GGU) , 3′trnV (UAC) -ndhC , and ndhF-rpl32 ) and two introns ( rpL16 and rpS16 ), which are considered the most variable regions on average for angiosperms as a whole in both Shaw et al publications (Shaw et al, 2007, 2014: 3′rps16-5′trnK (UUU) , trnQ (UUG) -5′rps16 , rpl32-trnL (UAG) , psbJ-petA , atpI-atpH , petL-psbE , psbD-trnT (GGU) , 3′trnV (UAC) -ndhC , ndhF-rpl32 ), and also other variable markers previously used in Cactaceae ( trnT-trnL , 3′trnK-matK partial, trnL-trnF , trnS-trnG , trnH-psbA , and rpL16 ; Nyffeler, 2002; Bonatelli et al, 2013). The rpS16 intron was included because it is among the most used in species-level studies due to the early development of universal primers for this region (Shneyer, 2009).…”