The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group

Abstract

Phylogenetic resolution is often low within groups of recently diverged taxa due to a paucity of phylogenetically informative characters. We tested the relative utility of seven noncoding cpDNA regions and a pair of homoeologous nuclear genes for resolving recent divergences, using tetraploid cottons (Gossypium) as a model system. The five tetraploid species of Gossypium are a monophyletic assemblage derived from an allopolyploidization event that probably occurred within the last 0.5-2 million years. Previous analysis of cpDNA restriction site data provided only partial resolution within this clade despite a large number of enzymes employed. We sequenced three cpDNA introns (rpl16, rpoC1, ndhA) and four cpDNA spacers (accD-psaI, trnL-trnF, trnT-trnL, atpB-rbcL) for a total of over 7 kb of sequence per taxon, yet obtained only four informative nucleotide substitutions (0.05%) resulting in incomplete phylogenetic resolution. In addition, we sequenced a 1.65-kb region of a homoeologous pair of nuclear-encoded alcohol dehydrogenase (Adh) genes. In contrast with the cpDNA sequence data, the Adh homoeologues yielded 25 informative characters (0.76%) and provided a robust and completely resolved topology that is concordant with previous cladistic and phenetic analyses. The enhanced resolution obtained using the nuclear genes reflects an approximately three- to sixfold increase in nucleotide substitution rate relative to the plastome spacers and introns.

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

“…Phylogenies of the Hawaiian mints have been reconstructed from datasets composed of commonly used DNA sequence markers, including cpDNA and nuclear ribosomal 5S non-transcribed spacer and external transcribed spacer regions (Lindqvist and Albert, 2002;Roy et al, 2013), which are rapidly evolving in many other species (Baldwin and Markos, 1998;Shaw et al, 2005;Small et al, 1998), but they fail to resolve relationships among the Hawaiian mints. A similar pattern of low genetic diversity has been noted in other recent radiations of Hawaiian plants (Appelhans et al, 2014;Baldwin and Sanderson, 1998;Cronk et al, 2005;Givnish et al, 2009;Givnish et al, 2013).…”

Allopolyploidization and evolution of species with reduced floral structures inLepidiumL. (Brassicaceae)

“…To better resolve the evolutionary pattern of floral structures in Lepidium, a phylogenetic study using a single-copy nuclear gene was required, because such markers better reflect biparental lineages of homoploid and allopolyploid hybrids and thus are powerful tools in reconstructing reticulate histories of plant groups (16)(17)(18).…”

Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

“…Resequencing of hundreds of orthologous loci that broadly sample the genomes of diploid cottons sheds light on the types and rates of evolutionary mechanisms operating in the B7 million years (Small et al, 1998;Cronn et al, 2002) since divergence of these species from common ancestors. Different DNA sequence fragments ranged widely in levels of polymorphism.…”

“…Prior studies used only small numbers of nucleotides either from chloroplast (Wendel and Albert, 1992;Small et al, 1998) or nuclear DNA (Seelanan et al, 1997;Small et al, 1999;Cronn et al, 2002;Wendel and Cronn, 2003). Early studies using cpDNA (Wendel and Albert, 1992;Small et al, 1998) suggested the C genome to have diverged first from the common ancestor shared by both A and D genome species. However, later research using genomic DNA suggested D genome species to have diverged first (Cronn et al, 2002;Wendel and Cronn, 2003).…”