Evolution of the Diploid Species of the Sub-tribe Triticineae

Abstract

Based on the phylogenetic relationships, the diploid species of the sub-tribe Triticineae are classified in five clades. The phylogenetic relationships within and between clades are discussed at length in this chapter.

11.1 Introduction

The Triticineae, the wheat lineage of the Triticeae (Clayton and Renvoize 1986; Table 2.1; Fig. 2.1), diverged from the Hordeineae, the barley lineage, during the Miocene epoch, about 8–15 million years ago (MYA) (Wolfe et al. 1989; Ramakrishna et al. 2002; Chalupska et al. 2008; Huang et al. 2002a, b; Dvorak and Akhunov 2005; Gornicki et al. 2014; Middleton et al. 2014) (Table 2.6). During this time, the global climates became warm, the Tethys Sea, that covered a large part of the East Mediterranean and Southwest Asia, disappeared and the east Mediterranean region rose (Table 2.5). This brought about diversification of temperate ecosystems and opening of new ecological niches, allowing the expansion of grasslands. These geological and climatic changes triggered the appearance first of diploid Elymus species containing the St, Ee, or Eb genomes, and somewhat later, the diploid Agropyron species, in the East Mediterranean area and Southwest and central Asia (Tables 5.1, 5.3, and 11.1). In the late Miocene, about seven MYA, the ancestral forms of Amblyopyrum, Triticum and Aegilops appeared (Marcussen et al. 2014; Huynh et al. 2019) and diverged from the lineage of Secale (Marcussen et al. 2014). Further divergence of the diploid species of Aegilops and Triticum occurred during the Pliocene (5.3–1.8 MYA). During this period the climate of the East Mediterranean and West Asia regions became seasonal. i.e., cold and humid in the winters and hot and dry in the summers, leading to a relatively short growth period in the winter and long drought in the summer. Also, today landscapes developed during the Pliocene facilitating further spread of grasslands. The climate changes and the opening of new ecological niches, applied a selection pressure that accelerated speciation processes.

Table 11.1 Time of beginning divergence in million years ago of the Triticineae lineages

In reaction to the environmentally unstable conditions of the East Mediterranean and West Asia, annualism and autogamy developed, enabling rapid colonization of new habitats by new genotypes that were ecologically isolated from their ancestral forms. Annualism enabled plants to pass the dry summer as seeds. The evolution of annual species from perennials occurred independently several times in the Triticineae, e.g., in the lineage Agropyron–Eremopyrum, in the lineage Dasypyrum–Secale, and in the divergent of the Amblyopyrum-Triticum-Aegilops linage from diploid Elymus species, presumably E. elongatus ssp. elongatus. Perennial growth habit is a dominant trait controlled by a small number of genes (Charpentier et al. 1986; Lammer et al. 2004), and mutations in these genes led to the development of annual plants. Autogamy in the Triticineae species is not an obligatory trait; occasional out-crossing may result in the production of sufficient genetic flexibility that effectively used by the rapid generation shift (Allard and Kannenberg 1968; Allard et al. 1968; Allard 1975). Changes from multi-floret spikelets to spikelets with only a few florets improved seed dispersal and reduced competition between siblings, while increased grain size ensured rapid and successful germination. More efficient seed dispersal systems were brought about by the development of awns on glume and lemma ends, that either assisted in burying the spikelet in the soil, through movements of the awns due to changes in humidity (Elbaum et al. 2007), or helped disperse the spikelets by clinging to various parts of animals. The primitive genera, Elymus, Agropyron, and Amblyopyrum, lack these specializations. Interestingly, genera or species exhibiting more advanced traits, namely, species of Eremopyrum, Taeniatherum, Crithopsis, Heteranthelium and Henrardia, occupy more xeric habitats in the peripheries of the genus distribution area.

The very wide variation in the inflorescence traits and in the seed dispersal techniques among the genera and species of the Triticineae subtribe reflects rapid adaptation to the broad radiation that occurred in the habitats of the East Mediterranean and Central Asia regions (Sakamoto 1973). In accord with the above, several molecular studies proposed that a major radiation of the Triticineae occurred during a relatively narrow period of time in the late Miocene and early Pliocene (5.3 MYA).

The initial steps of such differentiation occurred at the diploid level, i.e., the newly-formed diploid species underwent divergent evolution. This divergent evolution was accompanied by a convergent evolution, resulting from allopolyploidization of inter-generic and inter-specific hybrids, that was followed by a further divergence at the polyploid level, to new allopolyploid forms. Allopolyploidy considerably facilitates gene transfer between species and genera via hybridization and introgression (Zohary and Feldman 1962), further enhancing convergent evolution. Thus, the sub-tribe Triticineae developed in cycles of divergence at the diploid level, convergence followed by some divergence at the polyploid level and further convergence due to interspecific hybridizations. These cycles became an important factor in the evolution of the Triticineae.

Based on their geographical distributions, Sakamoto (1973, 1991) classified the Triticeae genera into two major groups: arctic-temperate group and east Mediterranean-central Asiatic group (Table 2.3), a classification that was supported by the studies of Hsiao et al. (1995a) and Fan et al. (2013). Most of the genera that developed in the east Mediterranean and central Asia regions belong to the subtribe Triticineae. This subtribe mainly contains annual species that have a solitary spikelet at each rachis node (except for Crithopsis and Taeniatherum, that have two spikelets at each rachis node). The genera Elymus and Agropyron have only perennial species, Dasypyrum and Secale have both perennial and annual species, and the remaining eight genera have only annual species (Table 2.1). Aegilops is the largest genus (24 species) and Taeniatherum, Crithopsis, Heteranthelium and Amblyopyrum are monotypic. Each genus of this group is morphologically distinct.

Speciation at the diploid level might have resulted from accumulation of mutations in coding and non-coding sequences and structural changes that led to the buildup of genetic barriers between the diverging taxa. Moreover, amplification or reduction in specific repetitive DNA sequences, mainly transposons, and their mobilization and activity, activity of genome-restructuring genes (Heneen 1963a; Feldman and Strauss 1983), as well as introgressive hybridization between the diverging taxa, may have boosted the speciation processes. Many Triticineae species have genes that either promote or suppress homoeologous pairing in interspecific and intergeneric hybrids (Table 5.2). Thus, despite the fact that the various Triticineae species are relatively young and still maintain a great deal of genetic relatedness, their chromosomes are homoeologous, rather than homologous, due to genetic and structural changes that occurred during their evolution. Consequently, the chromosomes of one species show reduced pairing with the homoeologous chromosomes of another species curtailing intergeneric and interspecific gene flow.

The most effective genetic barrier is complete sterility or semi-sterility of the interspecific F₁ hybrids, resulting, in many cases, in cryptic structural hybridity. Stebbins (1945) defined cryptic structural hybridity as chromosomal sterility due to heterozygosity for structural differences too small to materially influence chromosome pairing at meiosis. Indeed, several F₁ interspecific and intergeneric hybrids that exhibit high chromosomal pairing were completely sterile and their anthers did not dehisce (Ohta 1990). It cannot be strictly determined whether the sterility observed in the Triticineae F₁ hybrids is chromosomal or genic. This decision can be made only after chromosome doubling of the sterile hybrid. Fertile allopolyploid indicates that the sterility of the F_l hybrid is chromosomal and not genic.

A considerable number of morphological and molecular studies failed to reach a consensus concerning the phylogenetic relationships between the various diploid taxa of the Triticineae. This ambiguity is due either to a limited number of samples (Kellogg and Appels 1995; Kellogg et al. 1996; Mason-Gamer and Kellogg 1996a; Escobar et al. 2011) or to the small number of genes that were analyzed (Hsiao et al. 1995a, b; Kellogg and Appels 1995; Petersen and Seberg 1997; Helfgott and Mason-Gamer 2004; Mason-Gamer 2005). Relationships between the diploid species of the Triticineae have also been blurred by intergeneric and interspecific hybridizations and introgression events, as well as to incomplete lineage sorting of ancestral polymorphisms, indicating an intricate, reticulate pattern of evolution in this sub-tribe (Kellogg 1996; Komatsuda et al. 1999; Nishikawa et al. 2002; Mason-Gamer 2005; Kawahara 2009; Escobar et al. 2011). Such a reticulate pattern of evolution presents a considerable challenge in phylogenetic analyses, since different genes may exhibit conflicting genealogical histories (Escobar et al. 2011).

Yet, Escobar et al. (2011), using a comprehensive molecular dataset, succeeded to construct a comprehensive, multigenic phylogeny of the diploid taxa of the Triticeae tribe. The multigenic network structure (Escobar et al. 2011) highlights parts of the Triticineae history that did not evolve in a tree-like manner but rather in a reticulate pattern. Moreover, the results of Escobar et al. (2011) provided strong evidence of incongruence among single-gene trees, with different portions of the genome exhibiting different histories. They determined the role of recombination and gene location in the incongruence, and demonstrated that loci in close physical proximity are more likely to share a common history than distant ones, due to a low incidence of recombination in proximal chromosomal regions (Akhunov et al. 2003a, b; Luo et al. 2000, 2005).

Escobar et al. (2011) showed that despite strong tree conflicts, not all Triticineae clades are affected by introgression and/or incomplete lineage sorting. Notably, Agropyron, Eremopyrum and Henrardia diverge in a tree-like manner, whereas the evolution of Elymus, Dasypyrum, Secale, Heteranthelium, Taeniatherum, Amblyopyrum, Triticum and Aegilops is reticulated. There is no straightforward way to determine whether incongruence in Triticineae results from introgression or incomplete lineage sorting. Recombination could be an important evolutionary force in exacerbating the level of incongruence among gene trees.

11.2 Phylogenetic Relationships of the Diploid Elymus Species Having the St or E Genomes

Melderis (1978, 1980) transferred these species, having multiple spikelets per rachis node, from Agropyron to Elymus, leaving in Agropyron only species containing one spikelet per rachis node. Except E. spicatus that grows in western North America, all the other diploid species, that were transferred to Elymus, are native to southern Ukraine, the Mediterranean basin and Southwest Asia (Table 5.1). This group contains diploid species, some of which from autopolyploids developed and allopolyploids containing subgenomes from diploid species of this group were formed. The diploid and polyploid Elymus species of this group are perennial, and with the exception of E. elongatus, which is moderately self-fertile (Melderis 1978; Luria 1983), all the other species are cross-pollinating and self-sterile.

Genome St occurs in several diploid Elymus species, Ee in the diploid taxon E. elongatus subsp. elongatus, whereas genome Eb occurs in the diploid taxon E. farctus subsp. bessarabicus (Table 11.1). Several cytogenetic and molecular studies showed that these three genomes are closely related (de V Pienaar et al. 1988; Forster and Miller 1989; Wang 1989; Wang and Hsiao 1989; Hsiao et al. 1995a; Wei and Wang 1995; Kosina and Heslop-Harrison 1996; Petersen and Seberg 1997; Chen et al. 1998, 2003; Mason-Gamer et al. 2002; Li et al. 2007, 2008; Fan et al. 2007, 2009; Shang et al. 2007; Liu et al. 2008; Yu et al. 2008; Wang and Lu 2014). Bieniek et al. (2015) found that the nucleotide sequences at three chloroplast loci (matK, rbcL, trnH-psbA) of genomes Ee, Eb and St are almost identical, with only one substitution within the matK gene differentiating genome Eb from Ee and St. Similarly, Fan et al. (2013), using two single-copy nuclear gene (Acc1 and Pgk1) sequences, found that the St genome is closely related to the Ee genome of E. elongatus. Genome in situ hybridization (GISH) studies substantiated this conclusion by showing that genomes Ee and Eb are very similar in their repetitive DNA (Kosina and Heslop-Harrison 1996). Also, the almost complete chromosome pairing at meiosis of the F₁ hybrids between the diploid species of Elymus indicated close relatedness of these genomes (Wang 1985). The high or complete sterility of these F₁ hybrids results presumably from initial steps of divergence leading to cryptic structural hybridity.

The karyotypes of the diploid Elymus species are symmetric, the St genome consists of smaller chromosomes than genomes Ee and Eb, and Eb has larger chromosomes than Ee. These differences in chromosome size are also evident in DNA amount (Table 11.2). Since the St genome exists in the more primitive diploid species of Elymus, it is assumed that genomes Ee and Eb evolved from St. Their lager size resulted most probably from increase in repetitive DNA.

Table 11.2 Nuclear DNA amount in diploid species of Elymus

E. libanoticus grows in all parts of the Fertile Crescent and E. tauri grows in the northern part of this region only. Molecular studies have shown that these two species form one clade, while the other diploid St genome species form another clade (Mason-Gamer et al. 2010; Sun et al. 2008; Sun and Komatsuda 2010; Yan and Sun 2011). Likewise, Yu et al. (2008) found that E. libanoticus and diploid E. tauri are more closely related to one another than they are to E. stipifollius and E. reflexiaristatus. On the other hand, Yan et al. (2011) grouped the Eurasian St genome species E. libanoticus, E. reflexiaristatus and diploid E. tauri into one clade and the North American E. spicatus into a separate clade. Evidently, there are some discrepancies between various phylogenetic studies performed on this group of diploid species. The diploid subspecies of E. elongatus, subsp. elongatus, grows in the Mediterranean basin and diploid E. farctus, subsp. bessarabicus, grows in the coasts of the Black Sea, Aegean and N.E. Mediterranean Sea. These two taxa, frequently have one spikelet at each rachis node, are presumably evolved from the St-genome species. The ancestral Triticineae lineages presumably evolved from St or E genomes Elymus species in the following four, semi-independent clades: Agropyron, Eremopyrum and Henrardia clade, Dasypyrum, Secale and Heteranthelium clade, Amblyopyrum, Aegilops, and Triticum clade, and Crithopsis and Taeniatherum clade (Table 11.1). A scheme of the evolution of the Triticineae genera is presented in Fig. 2.1.

11.3 The Agropyron-Eremopyrum-Henrardia Clade

11.3.1 Clade Description

This clade contains one genus (Agropyron) with many ancestral traits and two genera (Eremopyrum and Henrardia), with many advanced traits and, therefore, may be considered younger than the former (Table 5.5). The Agropyron species are perennials, cross-fertilizing (Melderis 1978), and have tough rachises that do not disarticulate at maturity. In contrast, the species of Eremopyrum and Henrardia are, annuals, facultative autogamous, with a disarticulating rachis (wedge-type in Eremopyrum and barrel-type in Henrardia). The diploid species of these two genera have presumably evolved from diploid Agropyron.

Phylogenetic studies, based on morphology (Seberg and Frederiksen 2001), chloroplast DNA (Mason-Gamer et al. 2002; Hodge et al. 2010), chloroplast, mitochondrial, and nuclear DNA sequences (Seberg and Petersen 2007) and nuclear genes (Hsiao et al. 1995a, b; Mason-Gamer et al. 2010), separated Agropyron from Elymus, and included the genus Eremopyrum in a clade with Agropyron. The close phylogenetic relationship between Agropyron and Eremopyrum is also evident from the data of Escobar et al. (2011), who placed these two genera in the same clade. Eremopyrum species were grouped with Agropyron and Henrardia on the chloroplast DNA tree (Mason-Gamer et al. 2002). Similarly, using β-amylase gene sequences, Mason-Gamer (2005) found that Henrardia persica is close to Eremopyrum bonaepartis. Placement of both Eremopyrum and Henrardia with Agropyron has also been supported by other data sets (reviewed in Mason-Gamer 2005). reached a similar conclusion in analysis of nuclear DNA sequences. Analysis of the chloroplast gene encoding ribosomal protein rps16, led Hodge et al. (2010) also to place Eremopyrum bonaepartis and Henrardia persica in a single clade. Upon combination of Triticineae species mating system observations and data obtained from molecular analysis of 27 protein-coding loci, Escobar et al. (2010) found that Henrardia persica is very close to Eremopyrum bonaepartis and forms a clade with Eremopyrum triticeum and Agropyron mongolicum. Likewise, Escobar et al. (2011) found two well-supported sub-clades, the first formed by Henrardia and Eremopyrum bonaepartis, and the second by Agropyron mongolicum and E. triticeum. The study of Escobar et al. (2011) showed that the genera Agropyron (Astralopyrum is included), Eremopyrum and Henrardia were not affected much by introgression and/or incomplete lineage sorting. Yet, a number of hybrids between Agropyron and Elymus species have spontaneously emerged in nature. While many hybrids are sterile, a considerable number are more or less fertile, at least upon spontaneous backcrossing to one of the parents. Apparently, introgressive hybridization may have played a role in the evolution of these two genera.

11.3.2 Agropyron Gaertn.

The genus Agropyron sensu stricto contains diploid and polyploid species that are based on the P genome (Table 5.3) and are morphologically distinct from other genera in Triticineae. The diploid cytotype of Agropyron cristatum and A. mongolicum are the only diploids in the genus Agropyron s. str. Both are perennial and cross-pollinating species, but differ morphologically and in their geographical distribution (Table 5.3) The two species hybridize readily (Dewey and Hsiao 1984) and the F₁ hybrids showed reasonably good chromosome pairing at first meiotic metaphase, with an average of five to six bivalents per cell. Dewey (1969) concluded that all Agropyron species, whether diploids, autotetraploids, or autohexaploids, contain one basic genome, P, implying that autopolyploidy played an important evolutionary role in this genus.

Studies of meiotic chromosome pairing in hybrids between diploid A. cristatum and several different diploid species of Elymus showed that the P genome is closely related to the St genome and moderately related to the Ee and Eb genomes, respectively (Wang 1985, 1986, 1989, 1992). This may imply that diploid Agropyron derived from Elymus species possessing the St-genome. This assumption is supported by the analysis of 5S DNA sequences that consistently placed Elymus species with an St genome and Agropyron in one clade (Baum and Appels 1992).

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA sequence phylogeny indicated that the endemic Australian grasses Australopyrum pectinatum (genome W) are closely related to species of Agropyron (genome P) (Hsiao et al. 1995a, b). Species of the W and P genomes share certain gross morphological similarities and Australopyrum was once treated as a member of Agropyron (Löve 1984). The karyotypes of P and W genome species are also similar, but the chromosomes of the W genome are smaller (Hsiao et al. 1986). The differences in chromosome size could simply be due to a low copy number of the repetitive DNA, because the chromosomes of Australopyrum pectinatum ssp. velutinum contain much less C-banded heterochromatin than do those of Agropyron cristatum (Endo and Gill 1984).

11.3.3 Eremopyrum (Ledeb.) Jaub. and Spach

The Eremopyrum genus includes both diploid and allotetraploid taxa, namely, diploids E. bonaepartis, E. distans, and E. triticeum, and allotetraploids E. bonaepartis (=E. confusum) and E. orientale (Sakamoto 1972; Table 5.4). Following the genome analysis performed by Sakamoto (1979), the genome symbol of the Eremopyrum species are as follows: E. triticeum FF, diploid E. bonaepartis XbXb, tetraploid E. bonaepartis XbXbXdXd, E. distans XdXd, E. orientale XdXdFF (Table 5.4).

All Eremopyrum species are annual, short plants, with solitary spikelets at each rachis node, and with spikes that disarticulate at maturity (wedge-type disarticulation). Only in E. triticeum the disarticulation is at the base of each floret (floret-type disarticulation). The two tetraploid species are of recent origin, and most probably arose in the dry steppe zones of northwestern Iran, the assumed distribution center of this genus (Sakamoto 1979).

Studies of chromosome pairing at meiosis of interspecific Eremopyrum hybrids showed very little pairing between the diploid species, indicating that their genomes diverged considerably from one another, and that the tetraploid species are allotetraploids (Sakamoto 1972). Intergeneric hybridizations showed that there are strong sterility barriers between Eremopyrum species and those of other Triticeae genera (Sakamoto 1967, 1968, 1972, 1974; Frederiksen 1991b, 1993, 1994; Frederiksen and von Bothmer 1995). Sakamoto (1974) succeeded in producing the hybrid Heteranthelium piliferum x diploid Eremopyrum bonaepartis, which exhibited abnormal growth and very little chromosomal pairing at first meiotic metaphase (an average of 0.04 bivalents per cell).

Phylogenetic studies, based on morphology (Seberg and Frederiksen 2001), chloroplast DNA (Mason-Gamer et al. 2002; Hodge et al. 2010), chloroplast, mitochondrial, and nuclear DNA sequences (Seberg and Petersen 2007; Escobar et al. 2011) and nuclear genes (Hsiao et al. 1995a, b; Mason-Gamer et al. 2010), included Eremopyrum species in the same clade with species of Agropyron s. str.

11.3.4 Henrardia C.E. Hubbard

Henrardia is a small genus containing two species, H. persica and H. pubescens (Hubbard 1946). The two species differ morphologically from other genera in the Triticineae subtribe. Both species are annuals, short plants, with facultative self-pollination. The rachis harbors a solitary spikelet at each node, which are fragile, and disarticulate at maturity with the rachis segment alongside it (barrel type).

The two species are diploids (Sakamoto and Muramatsu 1965; Sakamoto 1972; Bowden 1966) and have a unique, extremely asymmetric karyotype, comprised of large chromosomes, and different from those of all other Triticineae, (Asghari-Zakaria et al. 2002), indicating an advanced genus.

Sakamoto (1972) crossed H. persica, as either female or male parent, with a number of species from different Triticeae genera, but only obtained hybrids in the cross of tetraploid Eremopyrum orientale x H. persica. The F₁ hybrid showed the wedge-type disarticulation of the Eremopyrum parent. Chromosomal pairing at first meiotic metaphase was very low (0–4 bivalents per cell), indicating lack of homology between the genomes of these two species.

Because of its very peculiar morphology, Henrardia was earlier included in genera outside the Triticineae, but Hubbard (1946) noticed that Henrardia shares several diagnostic traits with the Triticineae that have been regarded to be of diagnostic value in distinguishing the Triticeae tribe from other Poaceae tribes. Consequently, Hubbard (1946) transferred this taxon as a new genus to Triticineae.

Clayton and Renvoize (1986) considered Henrardia an offshoot of Aegilops. This is in accordance with Kellogg (1989) and Frederiksen and Seberg (1992), who, based on a cladistics analysis, concluded that Henrardia and the diploid species of Aegilops form a clade. But, in a number of molecular studies, Henrardia was grouped in a clade with the Eremopyrum species (see above).

11.4 The Dasypyrum-Secale-Heterantheliun Clade

11.4.1 Clade Description

This group contains three genera, two of which, Dasypyrum and Secale, include perennial and annual species, and one, Heteranthelium, having only one annual species. It is assumed that Dasypyrum is the most ancient genus in this clade (Blanco et al. 1996) while Secale is a younger genus and Heteranthelium is the youngest (Table 11.1). Dasypyrum diverged very early from the ancestral Triticineae, about 14 MYA (Yang et al. 2006: Table 11.1), during the early stages of separation between Triticineae and Hordeineae. Marcussen et al. (2014) concluded that Secale diverged from the ancestors of the wheat group during the Miocene, about 7 MYA, and probably at that time or somewhat earlier from Dasypyrum. Heteranthelium is the youngest in the group since it has more advanced traits than Dasypyrum and Secale (Table 5.5).

11.4.2 Dasypyrum (Coss. and Durieu) T. Durand

The genus Dasypyrum differs from the other Triticineae genera by its distinctive two-keeled glumes, with tufts of bristles along the keels. This genus comprises two allogamous species with a fragile rachis (wedge-type disarticulation), D. villosum (=Haynaldia villosa) and D. breviaristatum (=D. hordeaceum). D. villosum is an annual diploid (Frederiksen 1991a), whereas D. breviaristatum contains two cytotypes, an annual diploid and a perennial autotetraploid (Sarkar 1957; Ohta et al. 2002).

Wang et al. (1995) used the symbol Vb for the haploid genome of the diploid cytotype of D. breviaristatum and Vv for the haploid genome of D. villosum. Indeed, meiotic chromosome pairing in the interspecific F₁ hybrid D. villosum x diploid D. breviaristatum was very poor (1.44 bivalents per cell) and the hybrid was almost completely sterile, supporting the notion that the genomes of these two species are only distantly related to each other (Ohta and Morishita 2001). Yet, the shared peculiar spike morphology, indications of molecular and biochemical markers (Blanco et al. 1996), and hybridization with the species-specific repeated sequence pHv62 of D. villosum (Uslu et al. 1999), suggest a common ancestry for these two species. The genomic distance between D. villosum and D. breviaristatum, as determined by 301 RAPD loci, is smaller than their distance from Secale species (Yang et al. 2006).

Very low pairing was reported in F₁ hybrids involving Dasypyrum species and many other Triticeae species, showing little chromosome homology (Oehler 1933, 1935; Sando 1935; Kihara and Lilienfeld 1936; von Berg 1937; Kihara 1937; Kihara and Nishiyama 1937; Sears 1941b; Nakajima 1966; Chen and Liu 1982; Blanco et al. 1983a, 1983b, 1988; Lucas and Jahier 1988; von Bothmer and Claesson 1990; Yu et al. 1998, 2001; Deng et al. 2004; de Pace et al. 2011). Interestingly, low chromosome pairing was also observed in hybrid of D. villosum and Secale cereale that are included in the same phylogenetic clade. Jahier et al. (1988) crossed two amphiploids: Ae. uniaristata–D. villosum (2n = 28; genome NNVvVv) and Ae. uniaristata–S. cereale (2n = 28; genome NNRR). Despite of the low pairing in this hybrid, Jahier et al. (1988) did not reject the hypothesis that Vv and R chromosomes share homologous sequences. Rather, they attributed the Vv and R lack of pairing to factors such as asynchronous meiotic rhythm between R and Vv genomes. Similar causes can explain the lack of pairing between Vv and Vb reported above.

Morphology-based phylogenetic analyses showed that Dasypyrum and Secale form one clade (Baum 1978a, b, 1983; Kellogg 1989; Frederiksen and Seberg 1992; Seberg and Frederiksen 2001). Kellogg (1989) also placed Dasypyrum near Agropyron and Triticum monococcum, and Baum (1978a, b, 1983) considered D. villosum and Secale cereale as evolutionarily more contiguous to Triticum and Aegilops than to the rest of the Triticeae tribe. This is in accord with molecular phylogenetic studies which suggested that Secale is the closest relative of the Triticum-Aegilops genera (Kellogg et al. 1996; Huang et al. 2002a; Mason-Gamer et al. 2002). However, when Hordeum and Dasypyrum were analyzed with Secale, Triticum and Aegilops, they were positioned at the base of the tree topology, as out-groups (Yamane and Kawahara 2005; Kawahara et al. 2008), implying a much earlier divergence between D. villosum and the common ancestor of Triticum-Aegilops.

Analysis of different chloroplast and nuclear DNA sequences placed Elymus species possessing the E and St genomes and Dasypyrum species closely together (Kellogg 1992; Mason-Gamer and Kellogg 1996b, 2000; Petersen and Seberg 1997). Similarly, molecular phylogeny of the gene sequence encoding the second-largest subunit of RNA polymerase II revealed that the Vv genome of D. villosum is sister to the St genome of Elymus and that both diverged from the H-genome of barley (Sun et al. 2008). These findings fall in line with phylogenetic relationships inferred from nuclear rDNA sequences, showing a close relation of Heteranthelium and Dasypyrum to Elymus (Hsiao et al. 1995b). The Heteranthelium element of the transposon Stowaway is present in Dasypyrum but absent in other Triticeae species (Petersen and Seberg 2000). DNA/DNA hybridization of the genomes of Secale and D. villosum with labeled nuclear DNA from wheat and rye, revealed greater homology between the Vv genome of D. villosum and R genome of Secale than between Vv and the A-, B-, and D-subgenomes of wheat (Lucas and Jahier 1988). Similarly, FISH analysis involving hybridization of the genomes of different Triticeae species with species-specific molecular probes prepared from tandem repeated DNA sequences of D. villosum (pHv62) and S. cereale (pSc119.2), demonstrated greater homology between the R- and Vv-genomes than between R- or Vv-genomes and those of Triticum and Aegilops (Uslu et al. 1999).

Escobar et al. (2011) found that Dasypyrum, Heteranthelium, Secale, Taeniatherum, Triticum and Aegilops, evolved in a reticulated manner. They found that Dasypyrum and Heteranthelium form one clade, while Secale, Taeniatherum, Triticum and Aegilops formed another clade. Elymus forms a sister clade to Dasypyrum and Heteranthelium.

The formation of the Dasypyrum species was explained by a cascade of events, which began in the earlier stages of the separation of the Triticineae from the Hordeineae (13–15 MYA), and continued through the reproductive isolation of D. villosum from diploid D. breviaristatum prototype, and incipient reproductive isolation between the two cytotypes (Blanco et al. 1996). Such divergence did not occur for syntenic and gene-rich DNA segments of genomes Vv and Vb, as suggested by the strong similarity between the genomes of these two species in restriction fragment patterns of genomic DNA, the phenotypes of some isozyme systems, and the location of gliadin genes (Blanco et al. 1996). Thus, Dasypyrum was one of the earliest Triticineae genera that diverged from the basal Elymus clade. Likewise, Yang et al. (2006), studying genome relationships based on species-specific PCR markers, concluded that the formation of the Dasypyrum species began at the earlier stages of the separation of the sub-tribe Triticineae from the sub-tribe Hordeineae (13–15 MYA). Lucas and Jahier (1988) concluded that the differentiation of D. villosum (and Secale cereale) from the genera Aegilops and Triticum occurred earlier than speciation in the latter two genera. Indeed, Marcussen et al. (2014) proposed that the Secale lineage diverged from the Aegilops-Triticum lineage about 7 MYA, while Middleton et al. (2014) proposed it emerged 3–4 MYA. Lucas and Jahier (1988) assumed that the closest Aegilops-Triticum species to D. villosum is diploid wheat T. monococcum subsp. aegilopoides and not diploid species of Aegilops.

11.4.3 Secale L.

Secale is a small genus including one perennial, S. strictum and two annual species, S. sylvestre and S. cereale (Table 6.1). Most lines of the perennial S. strictum ssp. strictum and the annual S. cereale are self-incompatible, whereas the perennial S. strictum ssp. africanum, the annual S. sylvestre and some lines of S. cereale are self-compatible (Jain 1960; Kranz 1963; Kuckuck and Peters 1967; Stutz 1972). All three Secale species are diploids, (Sakamura 1918; Stolze 1925; Aase and Powers 1926; Thompson 1926; Emme 1927; Lewitsky 1929, 1931; Jain 1960; Bowden 1966; Love 1984; Petersen 1991a, b) and their genome has been designated R (Love 1984; Wang et al. 1995). B chromosomes occur in a low frequency in several lines of S. cereale and in a few populations of S. strictum subsp. strictum (Emme 1928; Darlington 1933; Hasegawa 1934; Popoff 1939; Müntzing 1944, 1950; Kranz 1963; Jones and Rees 1982; Niwa et al. 1990).

The Secale genus evolved monophyletically (Hsiao et al. 1995a; Mason-Gamer et al. 2002; Petersen et al. 2004; Bernhardt 2016). Its genome differs from that of wheat in both size and structure (Gill and Friebe 2009). Its size is the largest in the Triticineae (1C DNA of S. cereale = 8.65 pg, and that of S. strictum ssp. strictum = 9.45 pg; Table 6.3) and is 33 to 45% larger than the genome of diploid wheat (Table 3.1). This size difference is mainly due to the large amount of heterochromatin in Secale. Thus, one of the major evolutionary changes in chromosome structure in Secale has involved the addition of heterochromatin close to the telomeres (Bennett et al. 1977). The occurrence and distribution of the sub-telomeric heterochromatin in the different Secale species suggest that S. sylvestre, having a relatively small amount of heterochromatin, may be of ancient origin, while S. strictum and S. cereale may have a more recent origin (Jones and Flavell 1982).

In addition to increase in sub-telomeric heterochromatin, translocations have also played an important role in the evolution of the genus Secale (Stutz 1972; Koller and Zeller 1976; Shewry et al. 1985; Naranjo et al. 1987; Naranjo and Fernández-Rueda 1991; Liu et al. 1992; Rognli et al. 1992; Devos et al. 1993; Schlegel 2013).

Martis et al. (2013), using molecular data, suggested that also introgression from other Triticeae species may have played a role in Secale speciation and R genome evolution. However, the rarity of spontaneous formation of intergeneric hybrids involving Secale species and other Triticeae (Frederiksen and Petersen 1998), may indicates that introgression played a minor evolutionary role. Moreover, artificial intergeneric hybrids between Secale species and other Triticeae exhibited very low levels of pairing (Stebbins and Pun 1953; Heneen 1963b; Majisu and Jones 1971; Hutchinson et al. 1980; Gupta and Fedak 1985, 1987a, b; Fedak and Armstrong 1986; Wang 1987, 1988; Lu et al. 1990; Lu and von Bothmer 1991; Petersen 1991b). This low level of pairing indicates a very distant relationship between the R and the H genomes (Fedak 1979, 1986; Finch and Bennett 1980; Fedak and Armstrong 1981; Thomas and Pickering 1985; Gupta and Fedak 1985, 1987a, b; Lu et al. 1990; Petersen 1991a, 1991b), and that the R genome is slightly closer to the Eb genome than to the St genome (Wang 1987, 1988). Similarly, very little homology was observed between genomes of Aegilops and Secale species (Karpechenko and Sorokina, 1929; von Berg, 1931; Kagawa and Chizaki, 1934; Melnyk and Unrau, 1959; Majisu and Jones, 1971; Hutchinson et al. 1980; Lucas and Jahier 1988; Kawakubo and Taira 1992; Su et al. 2015), and between the genomes of diploid wheat and S. cereale (Sodkiewicz 1982), as well as between subgenomes of allopolyploid wheats and S. cereale (Longley and Sando 1930; Plotnikowa 1930; Oehler 1931; Vasiljev 1932). The absence of Ph1 has a much smaller effect on pairing between wheat and Secale chromosomes than between chromosomes of wheat subgenomes (Miller et al. 1994). Naranjo and Fernández-Rueda (1991, 1996) and Cuadrado et al. (1997) found that most of the wheat-rye pairs in the absence of Ph1 involved B subgenome chromosomes and, to a much lesser degree, D and A subgenome chromosomes.

The pairing data above show that Secale chromosomes underwent significant changes during the evolution of the genus, which affected their ability to homoeologously pair with other Triticineae species. Such alterations include, in addition to chromosomal rearrangements, also accumulation of large amounts of telomeric heterochromatin. As a result, the relative position of the telomeric regions that are involved in the commencement of meiotic pairing may shift, impairing pairing initiation of rye and other Triticineae chromosomes (Devos et al. 1995; Lukaszewski et al. 2012; Megyeri et al. 2013). Genetic and epigenetic changes, such as mutations or elimination of DNA sequences that are involved in homology recognition and pairing initiation, may also underlie this restricted pairing.

Biochemical and molecular studies have shown that S. sylvestre occupies an isolated position within the genus and differs substantially from both S. strictum and S. cereale. Its isolation may have resulted from its autogamous habit (Schiemann and Nürnberg-Krüger 1952; Khush and Stebbins 1961) or from its characteristically low sub-telomeric heterochromatin content, which results in unsynchronized mitotic cycles in embryos of hybrids with other Secale species that have larger amounts of sub-telomeric heterochromatin (Singh 1977). In contrast, hybrids between S. strictum and S. cereale are easily formed and exhibit somewhat reduced fertility, possibly because they are heterozygous for the two chromosomal translocations distinguishing S. cereale from S. strictum (Khush and Stebbins 1961; Khush 1962; Singh 1977). In areas where S. strictum grows near or even within S. cereale cultivated fields, plants resulting from hybridization and introgression between these two species were frequently observed (Stutz 1957; Khush 1962; Perrino et al. 1984; Hammer et al. 1985; Zohary et al. 2012). Biochemical and molecular studies showed that differences between S. cereale and S. strictum are not extensive (Jaaska 1975; Vences et al. 1987; Dedio et al. 1969; Sencer 1975; Reddy et al. 1990; de Bustos and Jouve 2002; Jones and Flavell 1982b; Murai et al. 1989). Yet, although S. cereale and S. strictum specimens are intermingled on the phylogenetic tree (Frederiksen and Petersen 1997), Bernhardt (2016) showed that S. strictum is somewhat different from S. cereale.

According to Kobyljanskij (1982), Protosecale, the oldest ancestor of the genus, appeared in the Oligocene Epoch (33.7–23.8 MYA) and later evolved in the Miocene (23.8–5.3 MYA) into a Protosylvestre and Protostrictum forms, from which S. sylvestre and S. strictum developed during the Pliocene epoch (5.3–1.8 MYA) (Table 2.6). The divergence of the Hordeum lineage and the Secale/Triticum/Aegilops lineage(s) occurred 8–15 MYA; Wolfe et al. (1989), Ramakrishna et al. (2002), and Marcussen et al. (2014) suggested that this event occurred 10–15 MYA, On the other hand, Huang et al. (2002a, b), Dvorak and Akhunov (2005), Chalupska et al. (2008), Gornicki et al. (2014), and Middleton et al. (2014) suggested that this divergence occurred 8–11 MYA (Table 2.6). The separation of the Secale lineage from the Triticum/Aegilops lineage occurred 7 MYA (Marcussen et al. 2014, based on nuclear genes), when the ancestral genomes of the wheat group (A. muticum, Ae. speltoides and diploid wheat) evolved.

The phylogenetic relationships between Secale and other Triticeae genera have been studied through morphological traits, genome analysis, isozymes, and cytoplasmic and nuclear DNA sequences, which have yielded contradictory results regarding the position of Secale. Taxonomical treatments by several well-known taxonomists (e.g., Nevski 1933; Melderis 1953; Tzvelev 1973, 1976) placed the genus Secale close to the genus Dasypyrum. In accord with this taxonomical treatment, Baum (1983), on the basis of a phylogenetic analysis of Triticeae by means of numerical methods, also grouped Secale and Dasypyrum close to one another. Further analysis of morphological characteristics suggested that Secale is the sister group of a clade consisting of Dasypyrum villosum, Triticum monococcum and Aegilops species (Frederiksen and Seberg 1992; Seberg and Frederiksen 2001; Seberg and Petersen 2007). In some molecular studies, Secale was classified as a sister clade to the Aegilops clade (Kellogg and Appels 1995; Mason-Gamer and Kellogg 1996a). Monte et al. (1993) place Secale in close associations with Agropyron and Elymus species bearing the E^e and E^b genomes.

Data from internal transcribed spacers (ITS) of the rDNA suggested that Secale is the sister group of Eremopyrum and Henrardia (Hsiao et al. 1995a), whereas data from the spacers between the 5S RNA genes suggested a rather basal position for Secale within Triticineae (Kellogg and Appels 1995; Kellogg et al. 1996). Mason-Gamer (2005), analyzing sequences from a portion of the tissue-ubiquitous β-amylase gene in a broad range of the mono-genomic Triticeae, found close relationships between Secale, Australopyrum (=Agropyron) and Dasypyrum. Sequencing of the ITS region of nuclear rDNA of diploid Triticeae species, brought Hsiao et al. (1995a) to conclude that Secale is close to Taeniatherum and sister clade to Elymus farctus E. elongatus and Triticum monococcum. The study of Seberg and Petersen (2007) indicated incongruence between morphological and molecular data sets. They concluded that S. strictum is close to Taeniatherum caput-medusae, followed by Dasypyrum villosum, Elymus elongatus Elymus bessarabicus, Crithopsis delileana and the genera Aegilops, Triticum and Amblyopyrum.

Thus, the phylogenetic position of Secale remains ambiguous. In conclusion, with respect to the placement of the genus Secale in the subtribe-wide phylogeny, virtually all genera of the Triticineae have been suggested–either alone or in combination with other genera–to be a sister group to Secale (Petersen et al. 2004).

11.4.4 Heteranthelium Hochst

Heteranthelium is a monotypic genus containing the species H. piliferum (Banks et Sol.) Hochst. It is an annual, facultative self-pollinating species (Luria 1983), with a very peculiar spike morphology that is different from that of other Triticeae genera. It is a diploid species (Sakamoto and Muramatsu 1965; Bowden 1966), with a symmetric karyotype (Chennaveeraiah and Sarkar 1959; Bowden 1966; Sakamoto 1974; Frederiksen 1993).

Chromosome pairing in F₁ hybrid showed that the genome of H. piliferum is distantly related to that of E. bonaepartis (Sakamoto 1974). Other artificial hybridizations involving H. piliferum and other Triticeae species were not successful. Considering the unique morphology of the spike and the dispersal unit, inter-generic crossability and the cytogenetic relationships of H. piliferum, Sakamoto (1974) concluded that the genus Heteranthelium is a distinctive entity, representing a specialized group that occupies an isolated position in the subtribe Triticineae.

In different taxonomic classifications of the Triticeae, Heteranthelium is supposed to be related to either Triticum/Aegilops complex (Nevski 1934b; Tzvelev 1976) or Hordeum (Love 1984; Clayton and Renvoize 1986; Kellogg 1989). Clayton and Renvoize (1986) regarded it as an advanced offshoot of Crithopsis. Yet, Heteranthelium has one spikelet per node like most species of the sub-tribe Triticineae, and awn-like glumes as in Hordeum (Frederiksen 1993). Thus, the phylogenetic relationships of Heteranthelium are still ambiguous. Studies of Hodge et al. (2010) of the chloroplast gene encoding ribosomal protein S16, showed that H. piliferum is in the same clade as Triticum monococcum, Secale cereale, and all the Aegilops species. Their results are consistent with the finding of Mason-Gamer et al. (2002), based on combined cpDNA sequences, of tRNA genes, spacer sequences, rpoA genes, and restriction sites. Phylogenetic relationships based on mating systems showed that H. piliferum is in a clade with Dasypyrum villosum (Escobar et al. 2010, 2011).

11.5 The Taeniatherum–Crithopsis Clade

The Taeniatherum and Crithopsis genera consist of annual, facultative autogamous, monotypic species, that have two sessile spikelets at each rachis node and contain only one hermaphrodite floret in each spikelet. Taeniatherum caput-medusae and Crithopsis delileana are considered taxonomically close to each other (Clayton and Renvoize 1986). The species of both genera are diploids (Sakamoto and Muramatsu 1965; Luria 1983) with a symmetric karyotype; the genome symbol of Taeniatherum is Ta (Wang et al. 1995) and that of Crithopsis is K (Löve 1984). The karyotype of C. delileana is similar to that of T. caput-medusae, as shown by Linde-Laursen and Frederiksen (1989). However, the C-banding patterns of the two species exhibit differences, with C. delileana having more telomeric and fewer intercalary bands than T. caput-medusae. Yet, altered distribution of C-bands is a weak diagnostic characteristic, as activity of repetitious sequences, that can affect the distribution and quantity of the C-banding, may be different in closely related species and even within a species. Taeniatherum and Crithopsis differ in their seed-dispersal system; Taeniatherum has a tough rachis and a disarticulating rachilla (like E. elongatus), so that the dispersal unit is a floret, whereas Crithopsis has a brittle rachis and wedge-type dispersal unit of spikelets.

The crossability of either T. caput-medusae or C. delileana with other Triticeae species has been difficult, and consequently, the cytogenetic relationships between these two species and other Triticeae species are poorly known. However, in the few successful intergeneric crosses, the F₁ hybrids exhibited scarce amounts of chromosomal pairing at meiosis (Sakamoto 1991; Frederiksen and von Bothmer 1989), indicating great divergence of the genomes of Taeniatherum and Crithopsis from those of the other Triticeae.

Arterburn et al. (2011) found close homology between DNA sequences of Crithopsis delileana and Taeniatherum caput-medusae. Moreover, these authors also found sizeable homology between these two species and diploid Elymus elongatus and E. farctus. The relationships between diploid E. elongatus and C. delileana were closer than those between E. elongatus and T. caput-medusae.

Based on the possession of two spikelets at each rachis node and one grain in each spikelet, taxonomists (e.g., Tzvelev 1976; Clayton and Renvoize 1986) assigned the two genera to the subtribe Hordeineae. Indeed, in most morphological trees, Taeniatherum and Crithopsis were linked to the Hordeum group (Baum 1983; Baum et al. 1987; Kellogg 1989; Frederiksen and Seberg 1992). Yet, the traditional taxonomic subdivision of the genera of the Triticeae into two sub-tribes, Hordeineae and Triticineae (Tzvelev 1976; Clayton and Renvoize 1986), is not supported by phylogenetic studies based on molecular analyses that placed Taeniatherum and Crithopsis closer to species of the Triticineae than to Hordeum (Hsiao et al. 1995a; Mason-Gamer and Kellogg 1996b; Petersen and Seberg 1997; Mason-Gamer et al. 2002; Seberg and Petersen 2007; Escobar et al. 2011). Mason-Gamer et al. (2002), analyzing new and previously published chloroplast DNA data from Elymus and from most of the mono-genomic genera of the Triticeae, concluded that their analysis agrees with previous cpDNA studies with regard to the close relationship between Secale, Taeniatherum, Triticum, and Aegilops. Escobar et al. (2011) reported that the clade containing Taeniatherum and Triticum–Aegilops is also seen on the 5S short-spacer data tree, but only if Elymus farctus and E. elongatus are included in the clade.

Sakamoto (1973, 1991) classified the Triticeae into two groups based on their geographical distribution: the Arctic-Temperate group and the Mediterranean-Central Asiatic group (Table 2.3). Hsiao et al. (1995a), analyzing ITSs of nuclear rDNA and sequences of tRNA in 30 diploid Triticeae species representing 19 genomes, found that most of the annuals of Mediterranean origin, i.e., species of Triticum, Aegilops, Crithopsis, Taeniatherum, Eremopyrum, Henrardia, Secale, and two perennials, Elymus farctus and Elymus elongatus, comprise a monophyletic group. In the parsimony tree from a more restricted species sampling, the two-perennial species Elymus farctus and E. elongatus, formed a sister group with Triticum monococcum, Aegilops speltoides, and Ae. tauschii, whereas Crithopsis, Taeniatherum, Eremopyrum, and Henrardia, were close to Secale. Based on this finding, Hsiao et al. (1995a) supported Sakamoto (1973), who suggested that the Triticeae should be classified as two major groups, a Mediterranean group and an Arctic-temperate group, where the Mediterranean lineage evolved from the Arctic-temperate species (Runemark and Heneen 1968; Sakamoto 1973). The inclusion of Crithopsis and Taeniatherum in the Mediterranean-Central Asiatic group is not merely due to their geographical distribution, but also to close phylogenetic relationships between the two genera, Crithopsis and Taeniatherum, and other Triticineae species. Their relationships with genera of the Triticineae may indicate their evolvement from the same ancestral group and suggest that evolutionary development of diagnostic morphological characteristics, e.g., number of spikelets on each rachis node and number of fertile florets in each spikelet, occurs at varying rates in different taxa. The dispersal unit of many species belonging to the Mediterranean-Central Asiatic group contains two seeds, either one in each of the two spikelets or two in a single spikelet, indicating different routes for achieving analogous adaptive traits to brace the long, dry summer of the Mediterranean and Central Asiatic regions.

The above molecular phylogenetic studies showed that Taeniatherum and Crithopsisis are closer to the species of the subtribe Triticineae than to those of the Hordeinae. Consequently, these two genera are included in this book as members of the Triticineae. Crithopsis contains more advanced traits than Taeniatherum (Table 5.5) and can be considered a younger genus, more advanced than Taeniatherum.

11.6 The Amblyopyrum-Aegilops-Triticum Clade

11.6.1 Clade Description

This clade comprises three genera, Amblyopyrum (contains one diploid species), Aegilops (contains 10 diploid, 10 allotetraploid, and 4 allohexaploid species; Table 9.3), and Triticum (contains 2 diploid, 2 allotetraploid, and 2 allohexaploid species (Table 10.5). All species are annuals, and two of the three basal species, A. muticum and Ae. speltoides are allogamous, with the former being self-incompatible (Kimber and Feldman 1987), and the latter being a predominantly cross-pollinator (Zohary and Imber 1963). Ae. longissima has been described recently as a facultative outcrossing species (Escobar et al. 2010), whereas the remainder of the species are facultative autogamous. Many of the 13-diploid species of the wheat group are differentiated from each other by their unique spike and spikelet features and specialized dispersal units, namely, wedge, barrel, and umbrella types. The diploid species also differ in their eco-geographical requirements, and distinguished well-defined habitats. These species have distinct genomes, with different genome sizes (Table 9.3) and pairing patterns in inter-specific and inter-generic hybrids (Table 9.4).

The particular eco-geographical affinities of many of the diploid species may indicate that they had undergone extensive differentiation in their early stages of development. Southeast Turkey is the geographical center of the group distribution and thus, is presumably the center of origin of the genus (Kimber and Feldman 1987). Hammer (1980) suggested that the Fertile Crescent region, which currently maintains the greatest diversity of the wheat group genera, is not necessarily the region in which the group originated and developed during its evolution. He assumed that the primary center of origin of the group was in Transcaucasia, a region where several diploid species formed and developed and later, due to climatic change, migrated in western, southern and eastern directions.

On the basis of karyomorphological studies, Senyaninova-Korchagina (1932) and Chennaveeraiah (1960) separated the diploids into two categories: those having a symmetric karyotype (the T–, A–, S–, and D– genome species) and those with an asymmetric karyotype (the C–, M–, N–, and U– genome species). Avdulov (1931) and Stebbins (1950, 1971) considered an asymmetrical karyotype more advanced than a symmetric karyotype, since the former is found in diploids with increased specialization with respect to two morphological characteristics: the type of rachis fragility and the number of awns on the glumes. Indeed, in the more primitive species, i.e., A. muticum, wild T. monococcum, Ae. speltoides ssp. ligustica, Ae. bicornis and Ae. sharonensis, the dispersal unit is wedge-type and the glumes are awnless. In Ae. tauschii, the dispersal unit is barrel-type and the glumes are awnless. In Ae. speltoides ssp. speltoides, Ae. longissima, and Ae. searsii, the spike is long, with awns only on the lemmas of the uppermost spikelet and the dispersal unit is umbrella-type, but their glumes are awnless, whereas in the more advanced species, namely, Ae. caudata, Ae. comosa, Ae. uniaristata, and Ae. umbellulata, the spike is shorter, the dispersal unit is the umbrella type and the glumes are awned. Thus, since most species of the Triticeae have median or sum-median centromeres, the ancestral taxon(s) of the genera Amblyopyrum, Aegilops and Triticum presumably had a symmetric karyotype comprised only of chromosome pairs with median or submedian centromeres and awnless glumes.

Parisod and Badaeva (2020) studied the interplay between hybridization, chromosomal evolution and biological diversification of the diploid species of the wheat group. Comparative profiling of low-copy genes, repeated sequences and transposable elements among the divergent species, characterized by different karyotypes, highlighted high genome dynamics and shed light on the processes underlying chromosomal evolution in these wild diploid species. One of the hybrid clades (e.g., species of subsection Emarginata of Aegilops section Sitopsis and Triticum) presents upsizing of metacentric chromosomes, which paralleled the proliferation of specific repeats, thus leading to a large genome size (Eilam et al. 2007), whereas other species (e.g., Ae. caudata and Ae. umbellulata) showed stable, or even reduced genome size (Eilam et al. 2007), which was associated with increasing chromosomal asymmetry.

Most morphological and molecular trees share the Aegilops–Triticum clade, while the morphological tree produced by Seberg and Petersen (2007) also included Amblyopyrum and Henrardia in this clade. Morphological trees produced by Kellogg and Appels (1995) and Mason-Gamer and Kellogg (1996a) included T. monococcum in the Secale clade, which is a sister clade to the Aegilops clade. Escobar et al. (2011), based on studies of a large number of nuclear genes, reported that T. monococcum is a branched sister of Ae. tauschii, Ae. speltoides and Ae. longissima. Hsiao et al. (1995a, b) and Kellogg et al. (1996) considered T. monococcum as a sister group of Elymus elongatus. In line with this, Hsiao et al. (1995b), based on the ITSs of the nuclear rDNA sequences, reported that the Ee and Eb genomes of Elymus clustered with the A, B, and D subgenomes of T. aestivum. Equally, Wang and Lu (2014) found that both genomes Ee and Eb are closely related to subgenomes A, B, and D of hexaploid wheat, and thus, the wheat diploid genomes may have derived from the E genome(s). In accord with these findings, also Liu et al. (2007), using genomic hybridization (both Southern and in situ hybridization), showed that the St and Eb genomes of Elymus are very closely related to the A, B and D subgenomes of T. aestivum. Interestingly, from their study of two single-copy nuclear gene (Acc1 and Pgk1) sequences, Fan et al. (2013) concluded that the relationship between Elymus farctus subsp. bessaribicus (genome Eb) and Triticum/Aegilops is closer than between Elymus elongatus (genome Ee) and Triticum/Aegilops.

A considerable number of the above morphological and molecular studies failed to reach a consensus concerning the phylogenetic relationships between the various diploid species of the wheat group (Bernhardt et al. 2020). This ambiguity is due to either a limited number of samples or to the small number of genes that were analyzed (Hsiao et al. 1995a, b; Kellogg and Appels 1995; Mason‐Gamer and Kellogg 1996; Petersen and Seberg 1997; Helfgott and Mason-Gamer 2004; Mason-Gamer 2005; Escobar et al. 2011; Bernhardt 2015; Glémin et al. 2019). Phylogenetic relationships between the diploid species of the wheat group have also been blurred by inter-generic hybridizations and introgression events, indicating an intricate, reticulate pattern of evolution in this group of species (Komatsuda et al. 1999; Nishikawa et al. 2002; Mason-Gamer 2005; Kawahara 2009; Escobar et al. 2011). In addition, an incomplete lineage sorting of ancestral polymorphisms also may lead to incongruent results. Such an intricate pattern of evolution presents a considerable challenge in phylogenetic analyses, since different genes may exhibit conflicting genealogical histories (Escobar et al. 2011).

Table 11.3 and Figs. 10.5 and 11.1 presents data on the time of beginning divergence of lineages and species of the wheat group in million years ago. The ancestral genomes of the group, T, S, and A, started diverging about 7.0–6.5 MYA from an ancestral Triticineae genome. From several morphological traits, shared by the T genome (Ambliopyrum muticum) and the Ee genome of Elymus elongatus, it can be assumed that the former derived from the latter. It is probable that also the S and the A ancestral genomes derived sequentially from diploid E. elongatus or from a closely-related species. Several hundred-thousand years later, the T and the S ancestral genomes started to diverge from one another. Homoploid hybridization involving ancestral S or T, or both, with an A ancestral genome, 6.0–5.0 MYA, formed the D-lineage that included the progenitors of Ae. tauschii, Emarginata species (Ae. bicornis, Ae. searsii, Ae. longissima, and Ae sharonensis), and the more advanced Aegilops species (Ae. caudata, Ae. comosa, Ae. uniaristata, and Ae. umbellulata). Soon after, Ae. tauschii (genome D) diverged from the D lineage. The donor of the B subgenome to allotetraploid and allohexaploid what, T. turgidum and T. aestivum, diverged from Ae. speltoides 4.5 MYA, the donor of the G subgenome to T. timopheevii diverged from Ae. speltoides about 2.85 MYA, the donor of the A subgenome to all allopolyploid wheats diverged from T. urartu 1.28 MYA, and the donor of the D subgenome to T. aestivum diverged from Ae. tauschii about 0.68 MYA. Interestingly, the four diploid progenitors that donated their genomes to allopolyploid wheat, the B, G, A, and D, are currently extinct or yet undiscovered. Similarly, the diploid donor of the Xⁿ subgenome to the allotetraploids Ae. neglecta and Ae. columnaris, and to the allohexaploid Ae recta, and the donor of the X^c subgenome to allotetraploid Ae. crassa, and to the allohexaploid Ae. crassa, Ae. vavilovii, and Ae. juvenalis, are currently extinct or yet undiscovered. Li et al. (2022) explained the extinction of all these diploid donors by assuming that competition with their more fit allopolyploid derivatives, occupying the same habitats, caused their elimination.

Table 11.3 Time of beginning divergence of lineages and species of the wheat group (Amblyopyrum, Aegilops, and Triticum)* in million years ago

Fig. 11.1

Phylogeny tree of seven diploid Triticum/Aegilops species, B-subgenome of bread wheat (cultivar Chinese Spring) and G-subgenome of T. timopheevii (an introgressed region on chromosome 2B of bread wheat cultivar “LongReach Lancer”) based on the RRGRs on chromosome 2B of Chinese Spring. [From the supplementary Fig. 5A in Li et al. (2022)]

Divergence of the diploid species of Aegilops started 3.73 MYA when the Emarginata species (Ae. bicornis, Ae. sharonensis, Ae. longissima, and Ae. searsii) diverged from the D-lineage. Divergence of the diploid species of Aegilops from one another started between 2.9 to 2.1 MYA. Within the Emarginata species, Ae. bicornis diverged from the lineage longissima-sharonensis 2.0 −1.0 MYA, Ae. searsii diverged from the other species, most probably Ae. bicornis, 1.4 MYA, and Ae. sharonensis diverged from Ae. longissima 0.4 MYA. The divergence of the more advanced diploid species of Aegilops, i.e., Ae. caudata, Ae. comosa. Ae. uniaristata, and Ae. umbellulata, from the basal Aegilops species, occurred presumably about 2.0 MYA (Marcussen et al. 2014).

Bernhardt et al. (2020) highlighted the contribution of multiple rounds of hybridization and introgression to the evolution of the diploid species of the wheat group. They analyzed DNA sequences of 244 nuclear low‐copy genes, evenly distributed across all the chromosomes, as well as genome‐wide single nucleotide polymorphisms (SNPs) for all the wild diploid species of the group. The use of a combination of different phylogenetic and network approaches together with advanced statistics revealed ancient complex reticulated processes partly involving many rounds of introgression as well as at least one homoploid hybrid speciation that occurred during the formation of the extant taxa. Based on a comprehensive taxon sampling, Bernhardt et al. (2020) were able to propose a detailed scheme of events that shaped the wild species of the wheat group and which seemed to best reflect the evolution of these species. This scheme of events is much more complex than previously suggested (Marcussen et al. 2014; Sandve et al. 2015; Li et al. 2015; El Baidouri et al. 2017; Huynh et al. 2019).

Marcussen et al. (2014) determined the divergence time of the A and B diploid ancestral genomes from a common ancestor  ~ 7 MYA and that these genomes gave rise to the D-lineage through homoploid hybrid speciation 1 to 2 million years later (Table 11.3). The A and B parental lineages contributed equally to the D lineage. This model of homoploid hybrid origin of the D lineage agrees with the fact that lineages A and B are more closely related to D individually than to each other and thus, contradicts a tree-like phylogeny. The majority of the analyses of Marcussen et al. (2014) show a slightly younger divergence of A and D lineages compared with B and D lineages, indicating that gene flow from A to D may have persisted after gene flow from B to D had ceased. Support for a homoploid hybrid origin of the D lineage is found in independent analyses using the genome sequence of bread wheat. Both at the base-pair level and in gene content [International Wheat Genome Sequencing Consortium (IWGSC) 2014], the A and B lineages are more similar to the D genome lineage than they are to each other.

However, Glémin et al. (2019) substantiated the origin of the D lineage through homoploid hybridization but suggested the involvement of the T ancestral genome instead the S ancestral genome. Bernhardt et al. (2020) were able to confirm the evolutionary scenario developed by Glémin et al. (2019), and also to uncover more complex patterns of interspecific gene flow. Their phylogenetic scheme is congruent with the proposed formation of the D lineage [refers to the progenitor of the entire S (Emarginata species) + D (Ae. tauschii) + M (Ae. comosa) clade). through homoploid hybrid speciation as suggested by Marcussen et al. (2014) and Huynh et al. (2019), but also proposes, in agreement with Glémin et al. (2019), that ancestral A. muticum, rather than ancestral Ae. speltoides, were together with the Triticum lineage, the progenitors of the group. The ancestors of A. muticum and the Triticum clade contributed approximately equal proportions (0.54 and 0.46, respectively) to the common ancestor of all other Aegilops species, except for Ae. speltoides, whose ancestral genome evolved, more or less, at the same time as the ancestral T and A genomes. Mostly progenitors of the extant diploid species of the wheat group were involved in further hybridizations and introgressions, but recent interspecific gene flow seems less significant, perhaps due to further divergence and build-up of strong genetic inter-specific isolating systems. Remarkably, despite the fact that several diploids have massive spatial eco-geographical contact (Kimber and Feldman 1987), present-day natural hybridization between diploid species of Aegilops is a rare phenomenon. Examples of current inter-specific hybridizations and introgressions were only reported between two of these species, Ae. longissima and Ae. sharonensis (Ankori and Zohary 1962).

In contrast to the current situation, Bernhardt et al. (2020) suggest that ancient inter-specific or even inter-generic hybridizations significantly contributed to the evolution of the various Aegilops species. Glémin et al. (2019) and Bernhardt et al. (2020), concluded that all the diploid Aegilops species, except Ae. speltoides, derived from an initial homoploid hybridization event involving the ancient A (Triticum) and T (A. muticum) lineages, highlighted the pivotal role of A. muticum, instead of Ae. speltoides, in the formation of the diploid Aegilops species. This hybridization event was followed by multiple introgressions affecting all taxa, except Triticum. Following the development of the diploid species of the group, Bernhardt et al. (2020) found strong signals of introgression from the caudata-umbellulata group to A. muticum. This introgression seems to have occurred in both directions. Weaker signals of introgression of Emarginata species into Ae. caudata and Ae. comosa, as well as into Ae. tauschii were also found (Bernhardt et al. 2020). These authors proposed that an ancient, now extinct, lineage was introgressed by Ae. longissima, or another species of subsection Emarginata, and possibly also by an ancestor of the caudata–umbellulata–comosa-uniaristata clade, forming Ae. tauschii. Indeed, chloroplast phylogenies (Yamane and Kawahara 2005; Bernhardt et al. 2017) trace the maternal lineage of Ae. tauschii sister to the caudata–umbellulata–comosa-uniaristata (CUMNS) clade, suggesting that one of its ancestors is an ancient, perhaps extinct lineage (El Baidouri et al. 2017). This idea is in accord with its placement in nuclear phylogenies in which Ae. tauschii shows a moderately supported sister relationship to subsection Emarginata or members of CU(MN) clade. Moreover, the data of Bernhardt et al. (2020) provide evidence of gene flow between species of section Emarginata and the B genome lineage, a hypothesis also raised by El Baidouri et al. (2017) and Glémin et al. (2019). Their study also confirms the close relationships between the members of subsection Emarginata and Ae. speltoides. Among the members of subsection Emarginata, Ae. longissima appeared as a major introgressor of B genome donor. The close relationship between Triticum species and the caudata-umbellulata-comosa-uniaristata-tauschii (genomes C, U, M, N, D) clade was confirmed, although no direction could be inferred (Bernhardt et al. 2020).

Ae. searsii, which diverged from the other Emarginata species about 2.0 -1.0 MYA (Marcussen et al. 2014) and Ae. caudata, which diverged from the advanced Aegilops species, that diverged from the basal Aegilops species about 2.5 MYA (Marcussen et al. 2014), have identical chloroplast type (Alnaddaf et al. (2012) and both were found to be close to one another (Sliari and Amer 2011). This may imply that Ae. caudata introgressed with the prototype of Ae. searsii, as suggested by Bernhardt et al. (2020). Such introgression may explain the advanced trait that exists in Ae. searsii, namely, glume length close to the length of florets, that does not exist in other Emarginata species. Also, the adaptation of Ae. searsii to Mediterranean habitats may derive from such an introgression. Hence, the evolutionary scenarios of the evolution of the diploid species of the wheat group, proposed by El Baidouri et al. (2017) and Bernhardt et al. (2020), are highly reticulated.

It is generally accepted that the divergence of the T, A and S genomes from an ancestral Triticineae genome established the basal lineages of the wheat group. Comparison of chloroplast (Yamane and Kawahara 2005; Gornicki et al. 2014; Middleton et al. 2014; Bernhardt et al. 2017) and nuclear DNA sequences (Petersen et al. 2006; Salse et al. 2008; Kawahara 2009; Marcussen et al. 2014) confirmed the basal position of Ae. speltoides on the phylogenetic Aegilops/Triticum tree. Ae. speltoides likely diverged from the progenitor of the Triticineae earlier than the ancestral A genome and much earlier than the other Aegilops species (Yamane and Kawahara 2005; Salse et al. 2008; Gornicki et al. 2014; Middleton et al. 2014; Bernhardt et al. 2017). Estimates obtained from the analyses of nuclear DNA sequences placed the possible divergence time of the three basal genomes within the period between  ~ 7 MYA (Marcussen et al. 2014). Estimates obtained from chloroplast DNA favored a more recent origin of Ae. speltoides, i.e., between 4.1–3.6 MYA (Bernhardt et al. 2017) and 2.67 ± 1.1. MYA (Middleton et al. 2014). On the other hand, the divergence of the other diploid species of the wheat group from one another occurred much later. Huang et al. (2002b) estimated that these diploid species began to diverge from one another at 4.5–2.5 MYA and Dvorak and Akhunov (2005) suggested that the divergence time of these species was about 2.7 (4.1–1.4) MYA.

It seems reasonable that the diploid species of the wheat group, other than the ancestral A. muticum, Ae. speltoides and diploid Triticum, evolved at different times–the primitive species about 4.5–2.5 MYA and the advanced ones later on, at about 2.5–1.5 MYA. This period corresponds to the geological epoch Pliocene (5.3–1.8 MYA; Table 2.5), that was characterized by development of seasonal climate (cold and humid winters and hot and dry summers) in the east Mediterranean and south west Asia, the presumed center of origin of the diploid species of this group. The adaptation to dry habitats with seasonal growth periods presumably led to the development of their annual growth habit, associated with increased self-fertilization and large grains.

Genomic divergence may result from the activity of transposable elements (TE) (McClintock 1984; Fedoroff 2012). Senerchia et al. (2013) suggested that ancestral TE families, mainly retrotransposons, followed independent evolutionary trajectories in related species, highlighting the evolution of TE populations as a key factor of genome differentiation in the diploid species of the wheat group. In accordance, Middleton et al. (2013) also found that several TE families differ strongly in their abundance across the diploid species of the wheat group, indicating that these families can thrive extremely successfully in one species, while going virtually extinct in another. Yaakov et al. (2013) also reported that several TE families have undergone either proliferation or reduction in abundance during species diversification at the diploid level. The balance between genome expansion through TE proliferation and contraction through deletion of TE sequences drives variation in genome size and organization (Bennetzen and Kellogg 1997). Hence, the large differences in genome size between the various diploid species of the wheat group (Eilam et al. 2007; Table 2.4) suggest that TE activity has played an important role in the genomic evolution of these species. Indeed, Yaakov et al. (2013) determined the relative copy numbers of TE families in diploid species of section Sitopsis of Aegilops and found high variation and genome-specificity of TEs, implying that the main genomic differences between these species are the results of differential activity of TEs. TEs, accounting for a very large fraction of the genomes of the diploid species of the wheat group [80% of well-annotated TEs, with a majority of LTR retrotransposons (Senerchia et al. 2013)], were found to be one of the main drivers of genome divergence and evolution in this group (Yaakov et al. 2013). Whole genome sequencing in the Sitopsis group confirmed that genome size variation could be largely associated with TEs proliferation (Li et al. 2022). Charles et al. (2008) estimated from the insertion dates of TEs that the majority of differential proliferation of TEs in the B and A subgenomes of bread wheat, occurred in these genomes already at the diploid level, prior to the allotetraploidization event that brought them together in Triticum turgidum, about 0.8 MYA (Marcussen et al. 2014; Gornicki et al. 2014; Middleton et al. 2014). Finally, rewiring of gene expression in hybrids might dysregulate the silencing of transposons, resulting in activation of transposons, and in reduction of the hybrid fitness or viability, thereby contributing to speciation (Levy 2013).

Another genetic system that can restructure the genome in the diploid species of the wheat group and thus lead to genomic divergence and speciation, is the activity of genome restructuring genes (McClintock 1978). These genes are normally in an inactive state and can be activated by severe stress, either physical, physiological or genetic. Upon activation, they induce a wide range of chromosomal rearrangements that lead to genome restructuring. Heneen (1963a) described an extensive chromosomal breakage occurring spontaneously in an Elymus farctus individual. Likewise, Feldman and Straus (1983) reported on a mutant line in Ae. longissima that carried a recessive gene causing a wide range of chromosomal rearrangements in meiotic and mitotic cells. None of the chromosome breaks were random, indicating that specific DNA sequences were affected. Other examples of massive chromosomal aberrations in higher plants are rare but were observed in root-tip cells of the Brazilian semi-dwarf wheat cultivar IAS-54 (Guerra et al. 1977), in the hybrid Elymus arenarius x Secale cereale (Heneen 1963b), and in the hybrid Elymus farctus x Agropyron repens (Heneen 1963c). Several other cases of spontaneous chromosome breakage in meiotic and mitotic cells of several plants and several intergeneric hybrids were reviewed by Heneen (1963a). Genome restructuring is an ongoing process in natural Ae. speltoides populations (Belyayev 2013). Indeed, numerical chromosomal aberrations, spontaneous aneuploidy and re-patterning and reduction in the species-specific tandem repeats have been detected in marginal populations of Ae. speltoides (Raskina et al. 2004; Belyayev et al. 2010).

The activation of genome restructuring genes by various stresses has important evolutionary significance. In addition to the generation of genetic variability, due to changes in small DNA sequences as well as formation of cryptic-structural hybridity that may bring about hybrid sterility even though chromosomal pairing looks complete. Genome restructuring also may lead to the formation of new linkage groups. Rapid chromosomal rearrangement can also contribute to the evolvement of isolating mechanisms between differentiating sympatric taxa. Indeed, Lewis (1966) pointed out that rapid chromosomal reorganization played a major role in the formation of many plant species. Activity of genome restructuring genes during wheat evolution may explain the wide occurrence of chromosomal rearrangements among wild as well as domesticated wheats.

11.6.2 Amblyopyrum (Jaub. and Spach) Eig

This genus contains only one species, A. muticum. Eig (1929b) regarded it as a primitive form, since he noted that this species is an intermediate in several basic morphological features between Aegilops and several species of Elymus. These traits are: a long, linear awnless spike, many cylindrical, multi-floret spikelets, absence of rudimentary spikelets, and a fragile rachilla that disarticulates into f1orets that fall separately, especially in the upper part of each spikelet.

Two of the three basal species of the wheat group, A. muticum and Ae. speltoides, are annual, allogamous and are the only species that contain B-chromosomes. The B chromosomes of A. muticum do not affect homologous pairing, but suppress homoeologous pairing in intergeneric hybrids (Mochizuki 1964; Dover and Riley 1972; Vardi and Dover 1972; Ohta and Tanaka 1982, 1983). These two species possess genes that promote pairing between homoeologous chromosomes in hybrids involving allopolyploid wheat, by counteracting the effect of the homoeologous-pairing suppressor, ph1, of allopolyploid wheat (Riley 1960: Feldman and Mello-Sampayo 1967; Dover and Riley 1972a; Dvorak 1972). Ohta (1990, 1991) crossed A. muticum with all the diploid species of the wheat group, and reported that most F₁ hybrids were completely sterile. Partial fertility was observed only in the hybrid with Ae. speltoides, leading Ohta (1990) to conclude that A. muticum is most closely related to Ae. speltoides.

Numerical analysis (Baum 1977, 1978a, b; Schultze-Motel and Meyer 1981) indicated the close relationship between Amblyopyrum and Aegilops and Triticum. Likewise, several morphological and molecular trees included Amblyopyrum in the Aegilops clade (Seberg and Petersen 2007), and Mason-Gamer et al. (1998) also included species of Elymus in this clade. Hammer (1980) and Ohta (1990, 1991) proposed that A. muticum is the ancestral species in the group, whereas Ohsako et al. (1996) studying variation in chloroplast and mitochondrial DNA by single-strand conformational polymorphism (PCR-SSCP) analysis, suggested that A. muticum is not older than Ae. speltoides.

In some phylogenetic trees, e.g., Ohsako et al. (1996) and Sasanuma et al. (2004), A. muticum was included in a different cluster than the other species of the wheat group. In-situ hybridization with several repeated DNA markers, and C-banding patterns, suggest that A. muticum occupies an isolated position, closer to the Sitopsis species than to other species of Aegilops (Badaeva et al. 1996). Sallares and Brown (2004), who analyzed the ITSs of the rRNA genes, reached a similar conclusion, namely, that A. muticum has a basal position and that it is close to Ae. speltoides. Recent studies of Glémin et al. (2019) and Bernhardt et al. (2020) presented evidence indicating the basal position of A. muticum and its contribution, together with the ancestral A genome of Triticum, and later on, through introgression with the S genome of Ae. speltoides, to the evolvement of most other species of Aegilops.

11.6.3 Aegilops L.

The Aegilops genus contains 10 diploid species (Table 9.3), all of which are annual, and facultatively autogamous, except for Ae. speltoides, which is a predominantly allogamous plant (Kimber and Feldman 1987) and Ae. longissima, which has a high percentage of cross pollination (Escobar et al. 2010). The northern region of the Fertile Crescent is the geographical center of the group distribution and thus, is presumably the center of origin of the genus (Kimber and Feldman 1987).

Eig (1929a) described principles of evolutionary succession of the Aegilops species that were based on morphological characters of the plant and particularly of the spike in comparison with other Triticeae species. His view concerning the evolutionary trends of characters in the diploid species of Aegilops was presented in the following generalization (Table 11.4): (1) tall plants represent primitive species (Ae. speltoides, Ae. sharonensis, and Ae. longissima) whereas short plants represent more advanced species (all other Aegilops species); (2) plants with awnless glumes on the apical spikelets are primitive species (species of section Sitopsis and Ae. tauschii), while single-awned glumes reflect advanced species (Ae. caudata and Ae. uniaristata), and many-awned glumes are characteristic of the most advanced species (Ae. comosa and Ae. umbellulata); (3) awns only on lemmas are seen in primitive species (Sitopsis species and Ae. tauschii), whereas main awns on glumes are seen in advanced species (Ae. caudata, Ae. comosa, Ae. uniaristata, and Ae. umbellulata); (4) wedge-type disarticulation of the spike is a feature of primitive species (Ae. speltoides var. ligustica, Ae. sharonensis, and Ae. bicornis), barrel-type of advanced type to some extent (Ae. tauschii), whereas umbrella-type is seen in the advanced species (Ae. longissima, Ae. speltoides var. speltoides, Ae. searsii, Ae. caudata, Ae. comosa, Ae. uniaristata, and umbellulata; (5) short glumes in relation to the length of the lemmas (about ½ or 2/3 of the length of the lemmas) are characteristic of primitive species (Sitopsis species, except Ae. searsii, and Ae. tauschii), whereas long glumes of a length that is almost equal to that of the lemmas is a common trait of advanced species (Ae. searsii, Ae. caudata, Ae. comosa, Ae. uniaristata and Ae. umbellulata); (6) caryopsis adhering to lemma and palea is seen in primitive species (most species of Aegilops), whereas a free caryopsis is seen in advanced species (Ae. searsii and Ae. umbellulata).

Table 11.4 Eig’s (1929a) definition of ancestral and advanced traits in the genus Aegilops

Moreover, according to Eig (1929a), the advanced species of Aegilops are mainly characterized by the following four morphological characteristics: (a) spikes with many awns, (b) ovoid spikes, (c) ovate spikelets, and (d) spikes falling entire when ripped. He found these four characteristics in Ae. umbellulata and concluded that this species is most differentiated from the other types. In contrast, these four characteristics were least distinct in section Sitopsis), which possesses many morphological characteristics common to the other genera in the Triticeae tribe. Thus, Eig concluded that the species of section Sitopsis are the most similar to the ancestral form of Aegilops.

The diploid species can be classified into three groups: those having the S genome or modified S genome (Ae. speltoides, Ae. bicornis, Ae. sharonensis, Ae. longissima, and Ae. searsii), the species having the D genome (Ae. tauschii), and those having the C, M, N, and U genomes (Ae. caudata, Ae. comosa, Ae. uniaristata, and Ae. umbellulata). Section Sitopsis was sub-divided by Eig (1929a) into two sub-sections, Truncata, containing one species (Ae. speltoides), and Emarginata, containing the other four species. Hybrids between species of the two subsections, show high pairing but are sterile, while hybrids between Emarginata species also exhibit high pairing but are fertile or partially fertile (Sears 1941a; Kihara 1949; Tanaka 1955; Kimber 1961; Riley et al. 1961; Roy 1959; Ankori and Zohary 1962; Feldman et al. 1979; Yen and Kimber 1990). The species of the two subsections also differ in karyotype structure (Riley et al. 1958), in C-banding patterns (Friebe and Gill 1996; Ruban and Badaeva 2018), in the number and distribution of certain molecular probes (Ruban and Badaeva 2018), and in the amount of nuclear DNA content (Eilam et al. 2007). On the other hand, the above cytological and molecular data imply a close relationship between the Emarginata species. Based on their studies and other reports, Ruban and Badaeva (2018) suggest the following scenario of the evolution of the five Sitopsis species: Ae. speltoides is the most distinct diploid Aegilops, that diverged from the common ancestor very early, prior to the split of the other Aegilops species (Salse et al. 2008; Gornicki et al. 2014; Marcussen et al. 2014). Divergence of Ae. speltoides from an ancestral form was not associated with major chromosomal rearrangements (Rodríguez et al. 2000; Dobrovolskaya et al. 2011). Subsequent evolution of Ae. speltoides was accompanied by several transposon insertions (Salse et al. 2008) and by the loss of the 5S rDNA locus on chromosome 1S of modern Ae. speltoides (Badaeva et al. 2016) which is present in the B subgenome of emmer and bread wheat (Mukai et al. 1990).

In this respect, Gornicki et al. (2014) and El Baidouri et al. (2017) showed that the female donor of the cytoplasm and B subgenome to T. turgidum and T. aestivum is not Ae. speltoides, but a relative of Ae. speltoides, that diverged from the latter 4.48 MYA (Li et al. 2022). The B-subgenome donor is currently either extinct or extant that yet has not been discovered. Homoploid hybridization involving the ancestral S and A genomes (Marcussen et al. 2014) or the ancestral T and A genomes (Glémin et al. 2019; Bernhardt et al. 2020) formed the D lineage, 6.0–5.0 MYA. The D lineage diverged later to the ancestral D genome (5.37 MYA (Li et al. 2022), to the Emarginata species 3.73 MYA (Li et al. 2022), and to the more advanced Aegilops species diverged from the basal Aegilops species about 2.5 MYA (Marcussen et al. 2014). The divergence of the Emarginata species was associated with an increase of high-copy DNA sequences due to the activity of transposable elements (Yaakov et al. 2013), amplification of the CTT-repeat, re-distribution of C-bands, massive amplification of Spelt-52 and gradual elimination of the D-genome-specific sequences pAs1, pTa-535 and pTa-s53 (Ruban and Badaeva 2018). The data of Ruban and Badaeva (2018) show that most drastic changes probably occurred at the stage of radiation of Ae. longissima/Ae. sharonensis, and included massive amplification of Spelt-52 and CTT-repeats, resulting in the gain of heterochromatin in these two species, and in an approximately 12% increase of nuclear DNA content in Ae. longissima/Ae. sharonensis as compared to that of Ae. searsii/Ae. bicornis (Eilam et al. 2007). The similar distribution of all analyzed DNA sequences on chromosomes of Ae. longissima and Ae. sharonensis point to a rather recent divergence of these species 0.4 MYA (Marcussen et al. 2014), which was accompanied by the species-specific 4S^l/7S^l translocation in Ae. longissima.

Morphologically, Ae. bicornis is the most primitive species in the Emarginata group (Eig 1929a). Indeed, Ae. bicornis diverged from the ancestral lineage of Ae. longissima/Ae. sharonensis 1.4 MYA (Marcussen et al. 2014). It is more difficult to produce hybrids with Ae. bicornis than with other S-genome Aegilops species (Kimber and Feldman 1987).

Morphologically, Ae. searsii resembles Ae. longissima, but molecular studies of chloroplast DNA showed that it is closer to Ae. bicornis than to Ae. longissima (Tsunewaki and Ogihara 1983). Ae. searsii differs from Ae. longissima and from the other Emarginata species by several morphological traits which are considered as evolutionarily advanced, namely, short stature, length of glumes, and free kernels (Feldman and Kislev 1977). Ae. longissima x Ae. searsii hybrids exhibit meiotic irregularities, including a reciprocal translocation, and are partial sterile (Feldman et al. 1979), and, similarly, Ae. longissima x Ae. bicornis had a reciprocal translocation, some pairing failure and the hybrid was highly sterile (Kimber 1961). By contrast, the F₁ Ae. longissima x Ae. sharonensis are fertile and show complete chromosome pairing in meiosis (five bivalents and one quadrivalent, due to a reciprocal translocation) (Tanaka 1955; Ankori and Zohary 1962). Isolation of these species is caused by different ecological requirements (Ankori and Zohary 1962; Kimber and Feldman 1987; Feldman and Levy 2015). The close relationships between the Emarginata species and the separate position of Ae. speltoides within the Sitopsis section were confirmed by molecular analyses of nuclear and cytoplasmic DNA. Based on variation of repeated nucleotide sequences (RNS), Dvorak and Zhang (1992b) showed that the Sitopsis species are phylogenetically similar, but Ae. speltoides is clearly separated from species of the Emarginata group. RAPD and AFLP analyses revealed that Ae. speltoides forms a cluster with polyploid wheats, which is separated from other Sitopsis species (Kilian et al. 2007, 2011). Likewise, the phylogenetic reconstructions of Middleton et al. (2014), showed that Ae. speltoides is not a member of Sitopsis, but together with T. turgidum, T. aestivum, and T. timopheevii lineages it forms a clade (B lineage).

Dvorak and Zhang (1992a) and Sasanuma et al. (1996, 2004) found a close relationship between Ae. caudata and Ae. umbellulata. Cytogenetic and phylogenetic studies of the four advanced species of Aegilops, i.e., caudata, comosa, umbellulata and uniaristata, showed that the N genome of Ae. uniaristata is one of the most advanced genomes in the group and is closer to the U genome of Ae. umbellulata than to the genomes of Ae. caudata and Ae. comosa (Sallares and Brown 2004; Badaeva et al. 1996). PCR fragment polymorphism analyses of chloroplast genomes placed Ae. umbellulata and Ae. comosa closer to Ae. tauschii than to the T. monococcum and Ae. speltoides (Tsunewaki et al. 1996; Gandhi et al. 2005).

Molecular analyses have shown that the diploid genomes S, D and A are much more closely related to each other than to other genomes in the wheat group (Monte et al. 1993; Dvorak and Zhang 1990; Dvorak et al. 1998). Indeed, comparisons of a large number of nuclear genes indicated that an ancestral D lineage derived from hybridization between ancient A and S lineages, about 6–7 MYA (Marcussen et al. (2014). This finding spurred a discussion regarding the hybrid origin of the extant Ae. tauschii (Sandve et al. 2015; Li et al. 2015, reevaluating the origin of Ae. tauschii by using recently published data from nuclear DNA (Marcussen et al. 2014) and chloroplast DNA sequencing (Gornicki et al. 2014), as well as additional data of chloroplast DNA of their own, confirmed the hybrid origin of the extant D genome but concluded that this genome has a more complex origin, one that may have involved multiple rounds of hybridizations. El Baidouri et al. (2017), following analysis of sequences of homoeologous genes and transposable elements derived from T. aestivum, T. turgidum ssp. durum, T. urartu, Ae. speltoides, and Ae. tauschii, deduced that, about 6 MYA, an ancestral D genome introgressed into a homoploid hybrid of the ancestral A and B genomes. The ancestral D genome became extinct sometime later. Today’s D genome, occurring in diploid Ae. tauschii and as one subgenome in T. aestivum and other allopolyploid species of Aegilops, is, therefore, a hybrid genome combining three genomes (El Baidouri et al. 2017). As the B subgenome of allopolyploid wheat is different from its closest extant relative Ae. speltoides, El Baidouri et al. (2017) assumed that the B genome itself might also have been introgressed by species of subsection Emarginata of section Sitopsis. Such introgression was also suggested by Bernhardt et al. (2020). Glémin et al. (2019), based on transcriptome data for all species of the group, proposed a complex scenario of hybridizations, and identified A. muticum (genome T), instead of Ae. speltoides (genome S), as an ancestor of the D genome lineage and of at least two more hybridization events. Bernhardt et al. (2020) also found that the ancestral T genome, and not B, was involved in the ancient hybridization with genome A.

Molecular findings relating to the chloroplast and mitochondrial genome (Tsunewaki 2009; Kawahara 2009) reinforced the studies on phylogenetic relationships of the diploid species. Tsunewaki (2009) reviewed such studies and concluded that the diploid species of the wheat group exhibit great diversification. A. muticum and Ae. speltoides, the two-outbreeding species, showed especially clear intra-specific chloroplast and mitochondrial differentiation. On the other hand, Gornicki et al. (2014) reveal low sequence variation of the chloroplast genome within Ae. speltoides as well as little haplotype variation in the Emarginata species. Yet, earlier studies (Chen et al. 1975; Hirai and Tsunewaki 1981) revealed two types of electromorphs of the Rubisco large subunit (the chloroplast subunit), H- and L-types, in these species. The H-type large subunit was found in the chloroplast of Ae. speltoides (and also in that of allopolyploid Triticum species) while the L-type large subunit exists in the chloroplast of all diploid Aegilops and Triticum species.

In many phylogenetic trees, Ae. speltoides forms a moderately supported clade with A. muticum, and, as in previous studies (Petersen et al. 2006), it was always clearly separate from the other species of Aegilops. All the analyses reported by Bernhardt et al. (2020) always classified Ae. tauschii as sister of subsection Emarginata. Marcussen et al. (2014) assumed that Ae. sharonensis is close to Ae. tauschii and is a hybrid involving the B genome lineage. The data of Bernhardt et al. (2020) showed that not only Ae. sharonensis is closely related to Ae. tauschii but that genome parts of the latter suggest the involvement of the entire subsection Emarginata, i.e., Ae. bicornis, Ae. sharonensis, Ae. longissima, and Ae. searsii. Yet, the absence of any relationship to the B genome clearly indicates a more complex evolutionary history than previously hypothesized, of the Ae. tauschii genome and perhaps also of the genome of subsection Emarginata.

11.6.4 Triticum L.

This genus contains two diploid, two tetraploid and two hexaploid species. Among the diploids, T. monococcum comprises two subspecies, wild ssp. aegilopoides and domesticated ssp. monococcum, also known as einkorn wheat, whereas T. urartu consists only of a single wild taxon. Both diploid species are annuals and facultative autogamous. The wild forms have a fragile rachis and disarticulate at maturity into wedge-type dispersal units, whereas the domesticated subspecies, that derived from ssp. aegilopoides, have a tough rachis so that at maturity the spike remains intact on the culm. The two wild taxa distribute in the northern part of the Fertile Crescent and in Transcaucasia, sympatrically in many sites. Following the spread of wheat cultivation, ssp. aegilopoides expanded its distribution as a weed, westward up to the Balkan.

Key (1966, 1968, 1981) and Hammer (1980) argued that different evolutionary tendencies exist in domesticated and wild wheat. The domesticated forms, under the selection pressure exerted by man, will further develop its greater ability to utilize fertile land and will follow a completely different trend in ear construction, namely, more specialization for tough rachis and free threshing. The wild forms will continue to occupy shrinking primary habitats or adapted as weed to various disturbed sites or cereal fields.

Hybrids between T. monococcum and the basal species of the clade, Ae. speltoides and A. muticum, had high chromosomal pairing at meiosis (Sears 1941b; Ohta 1990), which may either be due to effect of pairing promoters or indicate close phylogenetic relationships. On the other hand, hybrids between diploid wheat and the other Sitopsis species exhibit low pairing (Sears 1941b; Kushnir and Halloran 1981; Feldman 1978), indicating great divergence between the genomes of these species. Only the hybrid T. monococcum x Ae. tauschii had somewhat more pairing (4.86 bivalents and 0.21 trivalents per cell; Sears 1941b), indicating much closer cytogenetic affinities between the A and the D genomes than between the A genome and the genomes of the remaining diploid Aegilops species.

Following a morphological analysis, Baum (1983) included Amblyopyrum, Aegilops, Triticum and Henrardia in one cluster, close to species of Elymus. The findings of Escobar et al. (2011) were in agreement with previous works (Petersen and Seberg 1997), which included Triticum, Aegilops, Secale, and Taeniatherum in one clade. In some molecular studies, Triticum is a sister clade to the Aegilops clade (Kellogg and Appels, 1995; Mason-Gamer and Kellogg, 1996a), while others (Hsiao et al. 1995a, b; Kellogg et al. 1996; Liu et al. 2007) considered it to be the sister group to Elymus elongatus, assuming that Triticum may have derived from the Elymus E genome.

Yet, based on variation in repeated nucleotide sequences, Dvorak and Zhang (1992b) constructed a phylogenetic tree of the species of the Aegilops and Triticum. The tree obtained was consistent with many cyto-taxonomical data on species relationships in the two genera. Their studies clustered the two Triticum diploids, monococcum and urartu, that have been shown cytogenetically to have a common genome (Dvorak 1976; Chapman et al. 1976).

Glémin et al. (2019), Huynh et al. (2019), and Bernhardt et al. (2020) have proposed that the ancestral A. muticum and the ancestral Triticum genomes each contributed approximately equal proportions to the common ancestor of all other Aegilops species, with the exception of Ae. speltoides. Bernhardt et al. (2020), while highlighting the contribution of hybridization to the evolution of the species of Aegilops, stated that the evolution of the diploid Triticum species was not affected by inter-generic hybridization. It seems therefore, that after the ancient hybridization with the T genome, later hybridization between species of the wheat group and the A genome was restricted, presumably due to development of strong genetic barriers. As previously shown by Marcussen et al. (2014), Glémin et al. (2019), and Li et al. 2022 the Sitopsis species, the wheat subgenomes A, B, D, and G, and the T genome of A. muticum fall into three clades corresponding to the A, B and D lineages (Figs. 10.5 and 11.1).