Breeding Science 59: 471–480 (2009)

Review

Progress in phylogenetic analysis and a new infrageneric classification of the barley genus Hordeum (Poaceae: Triticeae)

Frank R. Blattner*

Leibniz Institute of Plant Genetics and Crop Research (IPK), D-06466 Gatersleben, Germany

During the last decade several phylogenetic studies of Hordeum were published using a multitude of loci from the chloroplast and nuclear genomes. In many studies taxon sampling was not representative and, thus, does not allow the inference of relationships among species. Generally, chloroplast data seem not suitable for reliable phylogenetic results, as far reaching incomplete lineage sorting result in nearly arbitrary species relationships within narrow species groups, depending on the individuals included in the analyses. Nuclear loci initially resulted at contradictory phylogenetic hypotheses. However, combining at least three nuclear loci in total evidence analyses finally provides consistent relationships among Hordeum species groups, and supports data from earlier cytological and karyological studies. Thus, recently published phylogenies agree on the monophyly of the four Hordeum genome groups (H, I, Xa, Xu), monophyly of the H/Xu and I/Xa groups, and separation between Asian and American members within the I-genome group. A new infra- generic classification of Hordeum is proposed, dividing the genus in subgenus Hordeum comprising sections Hordeum and Trichostachys, and subgenus Hordeastrum with sections Marina, Nodosa, and Stenostachys. The latter consists of two series reflecting the geographical distribution of the taxa, i.e. series Sibirica with Central Asian taxa and series Critesion comprising native taxa from the Americas. In section Nodosa all allo- polyploid taxa are grouped, which are characterized by I/Xa genome combinations.

Key Words: barley, classification, evolution, genomes, Hordeum, phylogeny, section, series, subgenus.

The genus Hordeum tribution areas. Some species like wall barley (H. murinum) and the sea barleys (H. marinum and H. gussoneanum) were Hordeum consists of about 33 species, belonging like others introduced nearly worldwide in temperate and dry regions, (wheat, rye, and several important forage grasses) to the and occur now as weeds in disturbed and agricultural habi- grass tribe Triticeae. Barley (H. vulgare) is the economically tats. Most of the species are capable of inbreeding, which most important species in the genus, used to feed livestock might contribute to successful colonization after long- and malted for beer or whisky production. Hordeum is mor- distance dispersals or human introductions. phologically well defined by three single-flowered spikelets (triplets) at each rachis node of the inflorescence, the lateral Phylogenetic analyses in Hordeum ones often sterile or only rudimentary present. The chromo- some numbers in Hordeum are all based on x = 7, and di-, Several attempts were undertaken to clarify phylogenetic tetra-, and hexaploids occur with 14, 28, and 42 chromo- relationships in the genus, since barley is a major crop on the somes, respectively. Hordeum originated in western Eurasia world scale and its wild relatives bear potential as genetic in the middle Miocene and the species are naturally distribut- resources for crop improvement. Under the influence of the ed all over the Northern Hemisphere, in South Africa and in biological species concept and to evaluate the possibility to southern South America. With 16 native species this latter use genetic diversity in wild species for crop breeding, region is also the main center of species diversity. The spe- during the 1960s crossing experiments started and pollen cies occur nearly always in open habitats, often in steppe or and seed fertility and viability of hybrids were analyzed meadow vegetation, along streams and ditches, many on (e.g., Rajhathy and Morrison 1959, 1962, Liu and Schooler salt-influenced soils, and nowadays also in disturbed habitats 1965, Subrahmanyam 1978, Bothmer and Jacobsen 1986). along streets and irrigation channels within their natural dis- These interspecific crosses resulted in the definition of dif- ferent grass genomes occurring in Triticeae (Dewey 1984, Communicated by T. Komatsuda Löve 1984), based on chromosome pairing in hybrids and Received September 3, 2009. Accepted October 1, 2009. karyological analyses of, e.g., C-banding patterns. In *Corresponding author (e-mail: [email protected]) Hordeum four genomes were described (Bothmer et al. 1986, 472 Blattner

1988a, 1988b, Linde-Laursen et al. 1992) initially named H, genome groups and geographic units of Hordeum in the I, X, and Y (Bothmer et al. 1995). Later the Y genome oc- phylogenetic tree than with particular species relationships curring in H. murinum was changed to Xu and the X genome within these groups. of H. marinum taxa to Xa (Wang et al. 1996). Shortly after- Analyses of loci of the chloroplast genome consistently wards Linde-Laursen et al. (1997) proposed to use the term showed taxa of the sea barley complex (H. marinum and H only for the genome of H. vulgare and H. bulbosum to H. gussoneanum) polyphyletic (Doebley et al. 1992, Provan make genome denomination consistent with barley chromo- et al. 1999, Nishikawa et al. 2002, Petersen and Seberg some nomenclature (i.e. 1H, 2H, … 7H). Taketa et al. 2003, Jakob and Blattner 2006), which contradicts traditional (1999b, 2005) swapped the names of the H and I genomes to taxonomy (Bothmer et al. 1995) and results derived from account for this recommendation but still used X and Y for nuclear markers (Komatsuda et al. 2001, Blattner 2004, the H. marinum and H. murinum genomes, respectively. I Petersen and Seberg 2004, Jakob et al. 2007). Moreover, the here suggest using H and I in the sense of Taketa et al. affiliation of diploid species from Central Asia were partly (2005) and Xa and Xu as proposed by Wang et al. (1996) to unclear, being either monophyletic (Doebley et al. 1992, arrive at a stable nomenclature of the basic genomes occur- Nishikawa et al. 2002) or being polyphyletic and grouping ring in Hordeum. with species from the New World and from the Mediterranean With the advent of molecular techniques, protein electro- (Petersen and Seberg 2003). Chloroplast data generally phoresis (e.g., Booth and Richards 1978, Jørgensen 1986, agree on monophyly of H. vulgare and H. bulbosum, and the Jaaska 1992) provided additional characters for analyses of H. murinum complex, respectively. An extended analysis of species relationships, which greatly increased when DNA- more than 800 individuals covering all species showed that based techniques became feasible in Hordeum (e.g., in Hordeum incomplete lineage sorting of chloroplast alleles Doebley et al. 1992, Molnar et al. 1992, Marillia and Scoles and persistence of ancient polymorphisms through specia- 1996, Komatsuda et al. 1999, El-Rabey et al. 2002, Tanno tion events can explain most of the inconsistencies (Jakob et al. 2002). Particularly DNA sequencing resulted in fast and Blattner 2006). In addition some hybridization occurs advances in molecular phylogenetics of the genus during the among closely related species that might result in chloro- last decade (Komatsuda et al. 1999, Nishikawa et al. 2002, plast capture, although hybridization does not contribute Petersen and Seberg 2003, 2004, Blattner 2004, 2006, Jakob much to overall taxonomic inconsistencies. A general fea- and Blattner 2006, Kakeda et al. 2009, Sun et al. 2009). ture of chloroplast data is that the resolution of relationships Many phylogenetic analyses suffered however from in- among the I-genome species and particularly the American complete and often arbitrary taxon sampling and/or method- taxa is quite low. This is either a result of slowly evolving ological shortcomings (e.g., Baum and Bailey 1991, Molnar marker regions like rbcL (Petersen and Seberg 2003) but et al. 1992, Svitashev et al. 1994, Marillia and Scoles 1996, also due to the occurrence of progenitor alleles together with De Bustos et al. 1998, 2002, Provan et al. 1999, El-Rabey et their descendants in single data sets (Nishikawa et al. 2002, al. 2002, Baum and Johnson 2003). Also the occurrence of Jakob and Blattner 2006), which violates basic assumptions allopolyploid Hordeum species or cytotypes, combining up of bifurcating tree algorithms (Pleines et al. 2009). There- to three parental genomes, were not always properly ac- fore, the analysis of chloroplast data of Hordeum with net- counted for when analyzed together with diploid taxa (e.g., work algorithms resulted in better-resolved allele relation- De Bustos et al. 1999). Taking into account the importance ships (Jakob and Blattner 2006). A general conclusion from of barley, surprisingly few phylogenetic studies of Hordeum the mentioned studies regarding phylogenetic analysis of with a complete or at least representative taxon sample were chloroplast markers might be that chloroplasts do not reli- conducted. Studies with higher species numbers or including ably reflect phylogenetic relationships among closely relat- at least most diploid species have been published by ed taxa in Hordeum. The only way to overcome this problem Jørgensen (1986), Doebley et al. (1992), Komatsuda et al. might be large, population-based sampling designs, which (1999), Provan et al. (1999), Nishikawa et al. (2002), allow phylogeographic analyses methods in phylogenetics Petersen and Seberg (2003, 2004), Blattner (2004, 2006), (Pleines et al. 2009). Therefore, nuclear markers seem to be Jakob and Blattner (2006), Kakeda et al. (2009), and Sun et much more useful to infer species relationships. al. (2009). The results were partly contradictory, due to (i) in- Studies of nuclear loci resulted in different phylogenetic consistencies between chloroplast and nuclear phylogenies, hypotheses, depending on the used marker techniques or (ii) differences in taxon sampling, (iii) incongruence among regions. Jørgensen (1986) studying protein variation found specific loci, and (iv) different analysis methods. I here will species of the four genome groups clearly separated, with mainly discuss studies where at least nearly all diploid spe- H. murinum (Xu genome) sister to the H-genome taxa cies were included, as unbalanced sample design alone H. vulgare and H. bulbosum, while H. marinum (Xa genome) might result in groups in phylogenetic trees that not truly was sister to the remaining taxa. The most peculiar relation- represent monophyletic taxa. Moreover, I will primarily ship resulting from this analysis was Asian H. roshevitzii look into relationships among the basic units within grouping with South American H. chilense. Komatsuda et al. Hordeum. This means that in this review I am more inclined (1999), analyzing an elongation factor locus (EF-G) linked to arrive at conclusions regarding the position of different with kernel row determination (vrs1), proposed monophyly Phylogeny and classification of the genus Hordeum 473 of the four genome groups occurring in Hordeum with the H. flexuosum, and H. euclaston/H. intercedens are mono- same overall topology as found by Jørgensen (1986). In this phyletic. These groups nicely agree with the AFLP results study resolution among I-genome taxa was quite low, thus, of Pleines and Blattner (2008). Contradictory is the position no differentiation between Asian and American taxa was of H. pubiflorum as sister to to North American H. pusillum found. Petersen and Seberg (2003) based on the analysis of in Petersen and Seberg (2009), which seems highly unlikely disrupted meiotic cDNA1 (DMC1) and combined data of to me in the light of other findings placing H. pubiflorum this locus with EF-G could not confirm monophyly of all in a group of southern Patagonian species together with genome groups. While the H and Xu genomes formed H. comosum and H. patagonicum (Blattner 2006, Jakob and monophyletic units, H. marinum grouped within Asian Blattner 2006, Pleines and Blattner 2008, Jakob et al. 2009). H. brevisubulatum and H. roshevitzii. Analysis of nuclear Generally, the data of Petersen and Seberg (2009) together rDNA ITS region (ITS) resulted in monophyly of the four with the other cited studies plus the analysis of another genomes, sister relationship of H and Xu-genome taxa, al- single-copy nuclear locus (Topo6) that resulted again in mono- though with low statistical support, sister relationship of Xa phyletic genome groups, places H and Xu and I and Xa- and I-genome taxa, and a clear separation of Asian and genome taxa in sister positions, and provides a split between American diploids within the I-genome group (Blattner Asian and American I-genome species (Jakob and Blattner 2004). In a combined analysis of EF-G, DMC1 and ITS 2009, Blattner unpublished results) indicates that nuclear (Blattner 2006) the same relationships were found, this time data finally converge towards a basic phylogeny of diploid with high support values. Sun et al. (2009) analyzed nuclear Hordeum taxa as shown in Figure 1. polymerase RPB2 and obtained H and Xu taxa grouping A maybe surprising result of the now emerging pattern of together, and H. marinum falling within the I-genome spe- Hordeum relationships from all these phylogenetic analyses cies. In this analysis H. patagonicum and H. pubiflorum, is that genomes finally seem to circumscribe real phyloge- two closely related species from southern Patagonia, are netic groups. After a long debate regarding the phylogenetic sister to this latter group, including another subspecies of utility of chromosome pairing and therefore of genomes H. patagonicum together with H. comosum. In the light of (e.g., Kellogg 1989, Seberg 1989, Seberg and Petersen other data confirming monophyly and a very close relation- 1998), it seems that genomes truly provide an overall mea- ship of the three Patagonian species (Blattner 2004, 2006, surement of phylogenetic relatedness of species, at least in Jakob and Blattner 2006, Pleines and Blattner 2008, Jakob Hordeum. Although the genome concept cannot define how et al. 2009), it seems that paralogs of RPB2 occur within different genome groups are connected in a phylogenetic this taxon group. Kakeda et al. (2009) used the single-copy sense, in Hordeum the method discerns the major units of locus of a thioredoxin-like gene closely linked to the self- the genus and is even able to indicate a separation of Asian incompatibility locus of H. brevisubulatum in a phylogenetic from American I-genome species. To arrive at the same con- analysis of H, Xa, Xu, and representative I-genome species. clusion one needs a certain number of single or low-copy They obtained monophyletic genome groups, sister relation- loci of the nuclear genome (compare Petersen and Seberg ships of H/Xu and I/Xa taxa, and American species mono- 2003 vs. 2009) to average over inconsistencies among dif- phyletic within the Asian I-genome species. Moreover, this ferent loci. Local duplications within genomes creating study provided clear evidence that the tetraploid cytotype of paralogs, transfer of genes or chromosome parts among spe- H. gussoneanum resulted from hybridization between dip- cies via hybridization, and different selective pressures on loid H. marinum and H. gussoneanum. Contradictory re- specific loci make using a single or only few nuclear single- sults were found in several studies for relationships among copy loci in phylogenetic inference a game of chance re- American species. However, in all these cases resolution garding the outcome of a phylogeny that reflects species was quite low and all hypothesized relationships not well relationships. supported. Thus, the use of amplified fragment length poly- Still lacking are studies involving a certain number of in- morphisms (AFLP), which screen genome-wide sequence dividuals per species in phylogenetic studies using nuclear diversity, was able to arrive at a clearer hypothesis of loci. Larger samples should not influence the general phylo- relationships among these species (Pleines and Blattner genetic patterns within Hordeum but within closely related 2008). In a recent publication on the evolution of transpos- groups it might provide better insights in species relation- able elements in Hordeum, Petersen and Seberg (2009) com- ships and history and speciation processes. Moreover, nearly bined data from five nuclear loci, resulting in a phylogenetic nothing is known about the extent of incomplete lineage tree that clearly separated taxon groups according to genome sorting regarding nuclear single-copy loci in grasses, al- affiliation, shows H. murinum as sister to the H-genome spe- though clear indications exist for long-term persistence of cies, and sea barley as sistergroup of the I-genome taxa. ancient polymorphisms of chloroplast markers in Hordeum Within the I-genome group the Asian species form a grade (Petersen and Seberg 2003, Jakob and Blattner 2006) and at the base of the American taxa. Diploid North American of nuclear markers in pine trees (Syring et al. 2007). As H. brachyantherum ( = H. californicum) is sister to all other effective population size of nuclear loci is twice that of species of this clade and within the closely related South chloroplasts, low-copy nuclear loci might need four times American species H. cordobense/H. muticum, H. chilense/ longer to arrive at reciprocal monophyly among species in 474 Blattner

Fig. 1. Phylogenetic tree reflecting my current understanding of relationships within Hordeum. The tree summarizes results from multiple phylo- genetic and cytological studies mentioned in this paper. Diploid taxa were drawn directly to the tree, while tetra- and hexaploids were connected by lines to their (partly putative) parental taxa. Dots behind species names depict annual taxa, dashed lines topological uncertainties. Age estima- tions are based on an assumed split between the lineages leading to barley and wheat about 13 million years ago (Gaut 2002), and were calculated with a penalized likelihood approach (Blattner 2006). comparison to plastid alleles. Higher nuclear mutation data, at least as long as not several individuals per species rates in comparison to the chloroplast can partly compensate and about five to seven nuclear marker regions are ana- for larger population size. However, with survival times of lyzed. This might, however, change in near future when next chloroplast alleles of about 4 million years in New World generation sequencing techniques become more widely Hordeum and species ages of 1–2 million years (Jakob and available. Also relationships among several polyploids are Blattner 2006) there is a high chance that also nuclear loci mainly unclear, although analyses of cloned nuclear mark- might deviate widely from reciprocal monophyly. This topic er regions or amplification with allele-specific primers can only be addressed by studies involving a certain number indicate ways to resolve this topic. Thus, for H. capense of individuals per species. and H. secalinum the involvement of H. marinum or In the light of now converging results regarding the phy- H. gussoneanum together with an I-genome species could logeny of Hordeum, it is surprising that the nuclear rDNA be shown (Petersen and Seberg 2004, Blattner 2006, ITS region with its peculiar mode of evolution (concerted Komatsuda et al. 2009), and in the H. murinum complex evolution and punctuated mode of homogenization among polyploids evolved under contribution of diploid subsp. sequences of major nucleolus organizing regions [NORs] on glaucum (Kakeda et al. 2009) and two now extinct taxa of different chromosomes; Blattner 2004) in Hordeum reflects the Xu-genome group (Jakob and Blattner 2009, Tanno et quite well the general picture resulting from several different al., in press). single and low-copy nuclear markers. Although, knowledge of NOR number within a single genome (defined by cyto- Cytological analyses within Hordeum logical methods) helps much with ITS data interpretation within closely related species groups. A large amount of cytological data was compiled in Still unclear are relationships within species with the I ge- Hordeum during the last 50 years. Karyotype definitions us- nome. It seems that in these cases fingerprint methods (e.g., ing chromosome morphology (e.g., Rajhathy and Morrison Pleines and Blattner 2008) might be more suitable to arrive 1962) were followed by more advanced methods involving at sound phylogenetic hypotheses than nuclear sequence chromosome characterization by banding technologies. For Phylogeny and classification of the genus Hordeum 475 example Giemsa C-banding (Linde-Laursen 1975) results in not very pronounced. The same might hold true for analyses specific contrasting of heterochromatic DNA within chro- of 5S rDNA variation (e.g., Baum and Johnson 2003). mosomes, while silver staining of tandemly repeated 18S– GISH data of diploid and polyploid Hordeum species 26S ribosomal RNA genes indicates the location of NORs indicate putative parental species involved in polyploid for- and satellite chromosomes. Both methods made chromo- mation. Thus, for H. capense and H. secalinum the occur- some recognition much easier. These methods resulted in rence of I together with Xa genomes were shown, indicating detailed karyograms of Hordeum species (Linde-Laursen et that either H. marinum or H. gussoneanum contributed to al. 1992) and allowed the formulation of evolutionary hy- the polyploids together with an I-genome species (Taketa potheses about species relationships (Linde-Laursen et al. et al. 1999a, 2009). Also for the hexaploid cytotype of 1995 and references therein). I here shortly review advances H. brachyantherum the occurrence of I and Xa genomes in karyology with special emphasis on in situ hybridization could be shown (Taketa et al. 1999a), indicating a cross of methods introduced during the last two decades in Hordeum tetraploid H. brachyantherum with introduced diploid research (e.g., Leitch and Heslop-Harrison 1992, De Bustos H. gussoneanum in California. These data are in accord et al. 1996, Taketa et al. 1999a, 2000b), and their special rel- with sequence data on these polyploids (Blattner 2004, evance to complement phylogenetic analyses in the genus. Petersen and Seberg 2004, Komatsuda et al. 2009). While fluorescence in situ hybridization (FISH) is mainly FISH analyses of American polyploid Hordeum species used to sensitively stain rDNA (5S, 18S–26S) loci (e.g., (Taketa et al. 2005) indicate clear differences between tetra- Leitch and Heslop-Harrison 1992) or other repetitive DNAs ploid H. depressum and the other polyploid taxa. For most of (e.g., Taketa et al. 1999b) in the genome, genomic in situ hy- these polyploids Asian H. roshevitzii is postulated to be one bridization (GISH) uses entire genomic DNA of a specific of the parental species, while it was not involved in the for- species, labeled by fluorescence dyes, to detect different mation of H. depressum. These data clearly support findings genomes occurring within a single cell. FISH helps particu- by Salomon and Bothmer (1998) and Komatsuda et al. larly to define the occurrence of rDNA tandem repeats on (2009) who also hypothesized that H. depressum was de- specific chromosomes, thus making (i) chromosome rived from hybridization of H. californicum or an extinct recognition much easier and (ii) allows also inference of the species closely related to it with H. intercedens. The other number of independent rDNA loci within a chromosome New World polyploids were all characterized as ‘jubatum’ (e.g., Leitch and Heslop-Harrison 1992, De Bustos et al. type by Taketa et al. (2005), as either H. jubatum was direct- 1996, Taketa et al. 2001). GISH data are quite helpful in the ly involved as hybridization partner in their evolution or, analysis of polyploids. In these cases the occurrence of dif- like H. jubatum, they originated via crosses between an ferent genomes in alloploid species can easily be shown Asian and an American taxon. These findings are supported (Taketa et al. 1999a), and the contribution of different pa- by earlier karyological results of Linde-Laursen et al. (1995) rental species to polyploids can be determined (Taketa et al. and by ITS sequence data (Blattner 2004). Moreover, Taketa 1999a, 2005, 2009). et al. (2005) arrive at a similar biogeographic scenario regard- As no unambiguous model of karyotype evolution exists, ing these polyploids as Blattner (2006) in a biogeographic none of the cytological methods can provide clear phylo- analysis of the entire genus Hordeum, i.e. that alloploidi- genetic relationships. However, the methods are able to zation took place in northeastern Asia or North America indicate groups of karyotypes with similar chromosome and that the polyploids then spread through the Americas. morphology, thus refining taxon groups within genomes However, mode (i.e. which diploids contributed to South (Linde-Laursen et al. 1995, Taketa et al. 2001). Particularly American polyploids and if species evolved via hybridiza- in the analysis of allopolyploids, in situ techniques provide tion or speciation on the polyploid level; Wood et al. 2009) very important information, supplementing data from DNA and sequence of origin of the American polyploids is still sequencing. For instance the knowledge of the number of mainly unresolved, although the cytological data now pro- NORs or 5S rDNA clusters within a genome (Taketa et al. vide clear and testable hypotheses for further studies. 1999b) enhances data interpretation in rDNA analysis, as In my opinion cytological data are (or will become) in- different NORs in some groups of Hordeum species harbor dispensable tools to complement phylogenetic analyses in different rDNA repeats, detectable by ITS sequencing Triticeae. Comparable to the knowledge of ploidy level that (Blattner 2004). Moreover, it provides a null hypothesis is very important in phylogenetic analysis and can be esti- about how many different rDNA sequence types can be ex- mated by careful genome size analyses (Jakob et al. 2004), pected in tetra- and hexaploid individuals derived from spe- FISH analysis can define different karyotypes and karyotype cific parental crosses. However, the proof that distinct ITS groups, which can be used to test phylogenetic hypotheses sequences, found within single individuals by cloning and with independent data sets. In contrast GISH is able to di- sequencing of PCR products, belong to NORs on different rectly visualize genomes or parts of genomes that stem from chromosomes (Blattner 2004) is still lacking. In this case different species, which might corroborate phylogenetic re- very sensitive detection methods seem necessary, and high sults or indicate that other than hypothesized species were stringency during hybridization, blocking, and washing has involved in hybridization events (Mahelka and Kopecky, in to be maintained, as differences among these sequences are press). 476 Blattner

Infrageneric classification of Hordeum Nevski (1941) came up with the first modern monograph of the genus including Asian and American species and All mentioned phylogenetic studies agree in that the infra- recognized six sections within Hordeum partly with sev- generic classification of Bothmer et al. (1995) does not re- eral series: sections Crithe (H. vulgare), Bulbohordeum flect species relationships within the genus. This was already (H. bulbosum), Hordeastrum (H. murinum, H. marinum, assumed by Jacobsen and Bothmer (1992) and Bothmer et H. pusillum, H. intercedens, H. euclaston, and H. flexuosum), al. (1995). However, N. Jacobsen and R. von Bothmer stated Anisolepis (H. chilense, H. stenostachys, H. muticum, and wisely that they are “well aware of the probably artificial na- H. cordobense), Stenostachys (H. brevisubulatum, ture of the sections Critesion, Anisolepis, and Stenostachys H. bogdanii, H. roshevitzii, and H. brachyantherum), and … but prefer to maintain an older, perhaps inconsistent, for- Critesion (H. comosum, H. jubatum, and H. procerum). His mal taxonomic grouping, than to create new ones which work was the starting point for all later revisions of the genus. might need changing within a few years” (Jacobsen and Trofimovskaya (1972) used three infrageneric levels, Bothmer 1992). Not all researchers kept to this principle, as with subgenus Hordeum (including only H. vulgare) and the plethora of different taxonomic treatments of the genus Hordeastrum, the latter with two sections: Hordeastrum (all show. I personally think that flooding the community with a annual species apart of barley) and Stenostachys (all peren- multitude of taxa results in more confusion than clarifica- nials). The sections were further divided in several series, tion, and that it therefore is more important to publish results partly in accord with Nevski (1941). describing taxon relationships and provide good phylogenetic Bothmer and Jacobsen (1985) maintained three of trees than making formal taxonomic classifications above Nevski’s sections, i.e. Anisolepis, Stenostachys, and the species level. On the other hand, I am surprisingly often Critesion, but merged taxa of sections Crithe, Bulbohordeum, confronted with studies (mostly when they are already fin- and Hordeastrum in their section Hordeum (H. vulgare, ished) where sample design was based on infrageneric H. bulbosum, and H. murinum). The other taxa of section classification, although information conflicting with such Hordeastrum were placed into sections Anisolepis classification was already available in systematics publica- (H. pusillum, H. intercedens, H. euclaston, and H. flexuosum) tions. Therefore, I think the systematics community has to be and Stenostachys (H. marinum). These sections were main- aware of a large group of scientists not trained in tree read- tained also in the last revision of the genus, although cyto- ing (Baum and Offner 2008) or even judging entire phylo- genetic data did not entirely support this classification at genetic publications, which will find it easier to follow an that time, and the authors already state that it might be accepted classification. As newer phylogenetic studies in artificial (see above). Hordeum converge on more similar results regarding species Petersen and Seberg (2003) proposed a new sectional relationships, and these are consistent with earlier results of treatment of the genus based on phylogenetic analyses of chromosome pairing studies and are backed-up by cytologi- two single copy nuclear loci and chloroplast DNA data. cal methods, I assume it timely to propose a new classifi- They delimited four sections different from Bothmer et al. cation for Hordeum, which reflects as much as possible, (1995): Hordeum, Sibirica, Stenostachys, and Critesion, the natural relationships of species in the genus and indicate still latter consisting of all American species. problematic taxon affiliations. The phylogenetic tree of likely species relationships Diverse taxonomic treatments of Hordeum exist. The within Hordeum (Fig. 1) shows that none of the up to now most extreme views are the one of A. Löve and D. Dewey proposed infrageneric classifications of Hordeum (e.g., who divided the group in Hordeum, consisting either of Nevski 1941, Trofimovskaya 1972, Bothmer and Jacobsen H. vulgare (Löve 1982, 1984) or H. vulgare and H. bulbosum 1985, Petersen and Seberg 2003) circumscribes monophy- (Dewey 1984), while all other species were subsumed in the letic units above the species level although the taxa partly re- genus Critesion Raf. This classification was based on the flect relationships. Also the split of the genus in Hordeum then emerging concept of genomes in Triticeae grasses. This and Critesion, as proposed by Dewey (1984) and Löve concept of generic delimitation was not generally agreed (1984), would result Critesion paraphyletic when H. vulgare upon and Bothmer et al. (1995) in their last revision of the and/or H. bulbosum is excluded. Thus, phylogenetic analy- genus maintained the traditional circumscription of, e.g., ses support the concept of a single genus Hordeum as pro- Nevski (1941) of Hordeum as a single genus. posed by Bothmer et al. (1995) in their last revision of the Also the infrageneric delimitation changed several times genus. In my opinion sectional classification of Hordeum during the last decades, based on morphological criteria as should conform the genome groups, as research in this topic awn length together with life cycle (e.g., Nevski 1941, during the last 50 years defined four clear units, which are Trofimovskaya 1972) and distribution (e.g., Covas 1949, still valid in the light of sequence-based molecular systemat- Bothmer and Jacobsen 1985). Different views of assumed ic approaches. However, to reflect the differences between species relationships resulted in a multitude of taxonomic H and Xu taxa on one hand and I and Xa taxa on the other, treatments of infrageneric groups within the genus. I will not a finer resolution of infrageneric categories seems necessary. review all proposed classifications here but discuss only the Therefore, I split Hordeum in subgenera Hordeum and more widely distributed or quite recent concepts. Hordeastrum (Table 1 and Table 2). These subgenera reflect Phylogeny and classification of the genus Hordeum 477

Table 1. Taxa of Hordeum L. Taxon Ploidy Haploid genome Distribution area Subgenus Hordeum Section Hordeum H. vulgare L. subsp. vulgare 2x H cultivated subsp. spontaneum (C.Koch.) Thell. 2x H SW Asia H. bulbosum L. 2x, 4x H, HH Mediterranean to C Asia Section Trichostachys Dum. H. murinum L. subsp. glaucum (Steud.) Tzvel. 2x Xu Mediterranean to C Asia subsp. murinum 4x XuXu NW Europe to Caucasus subsp. leporinum (Link) Arc. 4x, 6x XuXu, XuXuXu Mediterranean to C Asia Subgenus Hordeastrum (Doell) Rouy Section Marina (Nevski) Jaaska H. gussoneanum Parl. 2x, 4x Xa, XaXa Mediterranean to C Asia H. marinum Huds. 2x Xa Mediterranean Section Stenostachys Nevski Series Sibirica Nevski H. bogdanii Will. 2x I C Asia H. brevisubulatum (Trin.) Linka 2x, 4x, 6x I, II, III C Asia H. roshevitzii Bowden 2x I C Asia Series Critesion (Raf.) Blattner comb. & stat. nov. H. californicum Covas & Stebb. 2x I SW USA H. chilense Roem. & Schult. 2x I Chile and W Argentina H. comosum Presl 2x I S Argentina H. cordobense Bothmer et al.2xI C Argentina H. erectifolium Bothmer et al.2xI C Argentina H. euclaston Steud. 2x I C Argentina, Uruguay H. flexuosum Steud. 2x I E+C Argentina H. intercendens Nevski 2x I SW USA, NW Mexico H. muticum Presl 2x I C to N Andes H. patagonicum (Haum.) Covasa 2x I S Argentina H. pubiflorum Hook.f.a 2x I S Argentina H. pusillum Nutt. 2x I C+E USA H. stenostachys Godr. 2x I C Argentina H. depressum (Scribn. & Sm.) Rydb. 4x II W USA Interserial allopolyploids of series Critesion (all combining genomes of an American species with most probably one derived from H. roshevitzii) H. brachyantherum Nevski 4x II W North America, Kamchatka, Newfoundland H. fuegianum Bothmer et al.4xII S Argentina, S Chile H. guatemalense Bothmer et al.4xII Guatemala, S Mexico H. jubatum L. 4x II NE Asia, NW+W North America H. tetraploidum Covas 4x II C Argentina H. arizonicum Covas 6x III SW USA H. lechleri (Steud.) Schenk 6x III C+S Argentina H. parodii Covas 6x III C Argentina H. procerum Nevski 6x III S Argentina Section Nodosa (Nevski) Blattner comb. & stat. nov. H. brachyantherum Nevski 6x IIXa C California H. capense Thunb. 4x IXa S Africa H. secalinum Schreb. 4x IXa Mediterranean, C Europe a Species with subspecies not further detailed here. the major morphological differences within Hordeum, with auricles absent or inconspicuous in subgenus Hordeastrum. species with long, distinct auricles (Bothmer et al. 1995, Subgenus Hordeum in my definition corresponds to sec- Petersen and Seberg 2003) and relatively large seeds (Bothmer tion Hordeum of Bothmer and Jacobsen (1985). To account et al. 1995) in subgenus Hordeum, while seeds are small and for the different genomes, subgenus Hordeum is divided in 478 Blattner

Table 2. Hierarchical structure of infrageneric categories within Hordeum Genus Hordeum Subgenus Hordeum Hordeastrum Section Hordeum Trichostachys Marina Stenostachys Nodosa Series Sibirica Critesion Species H. bulbosum, H. murinum H. gussoneanum, Central Asian I- I-genome species naturally Allopolyploids H. vulgare H. marinum genome species occurring in the Americas combining I and Xa genomes section Hordeum consisting of the H-genome species can be debated. However, to create another series to harbor (H. bulbosum, H. vulgare) and section Trichostachys with exclusively these (segmental) allopolyploids would add an the taxa possessing the Xu genome (H. murinum). additional taxon for which I see currently no real necessity. Subgenus Hordeastrum consists of section Marina with An alternative approach would have been to merge all taxa species with the Xa genome (H. gussoneanum, H. marinum), of sections Marina, Nodosa, and Stenostachys without any the large section Stenostachys comprising all I-genome taxa, further subdivision. This would fulfill the monophyly and section Nodosa harboring allopolyploids with I/Xa ge- criterion for all I and Xa taxa including polyploids, but nome combinations (H. brachyantherum (6x), H. capense, would be much less informative in comparison to the system H. secalinum). To account for clear geographic and geno- proposed here. mic differences within section Stenostachys it is further divided in two series, i.e. series Sibirica (H. bogdanii, Taxonomic changes H. brevisubulatum, H. roshevitzii) and Critesion (all New World I-genome taxa). Hordeum L. section Nodosa (Nevski) Blattner, comb. & This infrageneric treatment more closely reflects stat. nov.—Hordeum sect. Stenostachys Nevski series phylogenetic relationships and geographic distribution of Nodosa Nevski, in Trudy Bot. Inst. Akad. Nauk S.S.S.R., the diploid species in comparison to all earlier treatments of ser. 1, 5 (1941) 152. Typus: Hordeum secalinum Schreb. the genus. The phylogenetic tree shows that annual or ( = H. nodosum L. sensu Nevski). perennial life style, a character important in earlier Hordeum L. series Critesion (Raf.) Blattner, comb. & stat. taxonomic treatments, changed several times independent- nov.—Critesion Rafinesque, in Journ. Phys. 89 (1819) ly within Hordeum. Also the distinctive long awns typical 103. Typus: Hordeum jubatum L. for barley and wall barley, evolved independently again in H. jubatum (foxtail barley) from where it was transferred to Acknowledgements H. lechleri, and within a group of southern Patagonian species (H. comosum, H. pubiflorum). Thus, apart from The author thanks Roland von Bothmer for remarks on the auricles and fruit size distinguishing subgenera Hordeum taxonomic treatment of Hordeum and discussions on the and Hordeastrum, no single qualitative morphological concept of genomes, and Takao Komatsuda and two anony- character is able to characterize the newly circumscribed mous reviewers for their helpful comments on this manu- taxonomic units. script. The new classification still bears some problems regard- ing allopolyploid species within subgenus Hordeastrum, as Literature Cited neither sections nor series are strictly monophyletic due to allopolypolyploid taxa combining genomes. Sorting I/Xa Baum, B.R. and L.G. Bailey (1991) Relationships among native and in- allopolyploids in a section of their own (Nodosa) is an ap- troduced North American species of Hordeum, based on chloro- proach similar to the taxonomic treatment of heterogenomic plast DNA restriction-site variation. Can. J. Bot. 69: 2421–2426. Triticeae genera, which are defined by their parental genome Baum, B.R. and D.A. Johnson (2003) The South African Hordeum combinations (e.g., Elymus, Leymus). Within section capense is more closely related to some American Hordeum spe- Stenostachys several allopolyploids or segmental allopoly- cies than to the European Hordeum secalinum: a perspective based ploids occur, which combine I-genome components of se- on the 5S DNA units (Triticeae: Poaceae). Can. J. Bot. 81: 1–11. ries Sibirica and Critesion (Table 1), most probably derived Baum,D.A. and S.Offner (2008) Phylogenies and tree-thinking. Am. Biol. Teach. 70: 222–229. from crosses of H. roshevitzii and H. californicum or a close Blattner, F.R. (2004) Phylogenetic analysis of Hordeum (Poaceae) as and probably extinct relative of this latter taxon. These inferred by nuclear rDNA ITS sequences. Mol. Phylogenet. Evol. species are all native to the Americas, and only two of them 33: 289–299. (H. brachyantherum, H. jubatum) occur in addition also in Blattner, F.R. (2006) Multiple intercontinental dispersals shaped the adjacent parts of northeastern Siberia. To subsume them in distribution area of Hordeum (Poaceae). New Phytol. 169: 603– series Critesion on geographical and morphological reasons 614. Phylogeny and classification of the genus Hordeum 479

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