12
Triticum s.str. according to Dorofeev et al. ( 1979 ) and the revised treatment of Mac
Key by van Slageren ( 1994 ). In this work van Slagerens revision was chosen over
Mac Key ( 2005 ) since it is the most consistent and most used treatment (e.g.,
Matsuoka 2011 ; Feldman and Levy 2012 ; Zohary et al. 2012 ).
1.9 The Era of Molecular Phylogenies : What Have
We Learned?
The taxonomy within the tribe continued to evolve, particularly as improved phylo-
genetic analyses started to shed light on species relationships. Different kinds of
molecular data were generated using isozymes (McIntyre 1988 ; Jarvie and
Barkworth 1990 ), DNA/DNA hybridizations, and restriction-site analyses (Ogihara
and Tsunewaki 1988 ; Monte et al. 1993 ; Mason-Gamer and Kellogg 1996 ). In par-
ticular, DNA sequencing resulted in fast advances in molecular phylogenies within
the tribe. In the last few decades, a multitude of molecular markers have been
employed using coding and non-coding, nuclear and plastid, single-copy or low-
copy number, and repetitive loci (Hsiao et al. 1995 ; Kellogg et al. 1996 ; de Bustos
and Jouve 2002 ; Mason-Gamer et al. 2002 ; Blattner 2004 ; Petersen et al. 2006 ;
Golovnina et al. 2007 ; Mason-Gamer 2008 ; Jakob and Blattner 2010 ; Petersen et al.
2011 ; Bordbar et al. 2011 ; Yan et al. 2011 ; Brassac et al. 2012 ; Yan and Sun 2012 ;
Mason-Gamer 2013 ). Studies have mainly aimed for a better understanding within
single genera (e.g., Hordeum , Elymus ) of the tribe and/or a small subset of related
genera with the main focus being Hordeum , Pseudoroegneria, and Elymus , or the
Aegilops - Triticum complex. Petersen et al. ( 2006 ) used two single-copy nuclear
genes and one plastid marker including tetraploid and hexaploids Aegilops and
Triticum species, as well as species that represent all diploid genomes of Triticeae.
The comparison to other molecular phylogenies was severely hampered by the dif-
ferences in taxon sampling among studies. Petersen et al. ( 2006 ) suggested that
neither Aegilops and Triticum separately, nor the combination of both genera, can be
assumed monophyletic.
Generally, the comparison of studies dealing with the same genus rarely revealed
similar phylogenetic relationships. Possible reasons for incongruences between
different studies are (1) true but different evolutionary histories of distinct genes
caused by hybridization, introgressions , incomplete lineage sorting, and/or selec-
tion, (2) differently conducted analyses, and (3) limited, biased, and different taxon
sampling (Kellogg et al. 1996 ; Petersen et al. 2006 ; Blattner 2009 ). There is a con-
sensus that a good taxonomic treatment of the tribe’s members has to start with a
robust phylogeny that is based on a combination of data from different parts of the
genome (Mason-Gamer 2005 ), including all representative genera to provide con-
clusive results as well as several accessions per species to test for monophyly
within species (Petersen et al. 2006 ). So far, only a few molecular phylogenies have
been published trying to understand the tribe’s history as a whole, leaving many
N. Bernhardt