Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region

Abstract

Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase.

Explosive radiation in high Andean Hypericum—rates of diversification among New World lineages

“…Likewise, the amount and influence of hybridization and/or incomplete lineage sorting needs to be investigated by incorporation of both further nuclear and chloroplast markers (Rieseberg and Soltis, 1991; Jakob and Blattner, 2006; Carine et al, 2007). Comparison of nuclear low copy genes and cpDNA marker will offer to investigate the amount of reticulation, and incomplete lineage sorting/introgression (Peters et al, 2007; Nosil et al, 2009; Brassac et al, 2012) involved in diversification of Hypericum in the Andes.…”

A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA

“…However, there are several investigations on grasses at the tribe or genus level (Brassac et al, 2012;Fan et al, 2007Fan et al, , 2009Hand et al, 2010;Huang et al, 2002;Jakob and Blattner, 2010;Mason-Gamer, 2005, 2013Sha et al, 2010;Triplett et al, 2012).…”

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

“…This is because of their evolutionary dynamics. LCNGs experience gene duplication and recombination (Wendel and Doyle, 1998;Small et al, 2004;Feliner and Rossello, 2007) and can be transferred among taxa through hybridization or other horizontal gene transfer events (e.g., Ghatnekar et al, 2006;Vallenback et al, 2008Vallenback et al, , 2010Mahelka and Kopecký , 2010;Brassac et al, 2012). More practical issues include the lack of universal PCR primers and often-limited understanding of copy numbers and evolutionary rates.…”