Phylogenetic relationships among the Iranian Triticum diploid gene pool as inferred from the loci Acc1 and Pgk1

Abstract

In this study, 129 individuals belonging to the Iranian wild diploid Triticum gene pool were screened using PCR-SSCP based on Acc1 and Pgk1 loci. Sequencing of the representatives of different SSCP patterns allowed for detection of three haplotypes for each of the loci. The phylogenetic relationships among the Iranian wild diploid Triticum haplotypes and related genera were analyzed using DNA sequences from these two single copy loci. Despite previous reports that recommended the usefulness of nuclear single copy genes for phylogenetic inference, the Bayesian and parsimony analyses carried out in this study showed that these two loci were not applicable tools in the phylogeny reconstruction of diploid Triticum gene pool. Thus, our findings confirm that phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees.

Peer Review #3 of "A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions (v0.1)"

“…Triticum lineage, recovery of major subclades in the lineage is congruent with other studies (Petersen et al, 2006;Gornicki et al, 2014;Bernhardt et al, 2017). The Aegilops speltoides + Triticum timopheevii sublineage has been found in other studies (Golovnina et al, 2007;Gornicki et al, 2014;Gogniashvili et al, 2015) plastome (Gornicki et al, 2014) and nuclear (Petersen et al, 2006;Nasernakhaei et al, 2015) trees, but none of those studies sampled the Georgian endemic Triticum macha. Golovnina et al Aegilops clade is congruent with other plastid trees with similar sampling (Petersen et al, 2006; PeerJ reviewing PDF | (2017:08:19682:2:0:NEW 4 Jan 2018)…”

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

“…& Menabde) MacKey), T. turgidum and T. aestivum “Chinese Spring,” whose relationships conflict strongly among the plastome trees. Close relationships among multiple subspecies of T. turgidum (sometimes recognized at species level) and T. aestivum “Chinese Spring” were found in earlier plastome ( Gornicki et al, 2014 ) and nuclear ( Petersen et al, 2006 ; Nasernakhaei et al, 2015 ) trees, but none of those studies sampled the Georgian endemic T. macha . Golovnina et al (2007) sampled one individual of T. macha in their matK tree, which was identical to multiple other taxa, including Triticum durum Desf.…”