Chloroplast DNA Restriction Site Variation Research Articles

Chloroplast DNA restriction site variation in theVernonieae (Asteraceae), an initial appraisal of the relationship of New and Old World taxa and the monophyly ofVernonia

Chloroplast DNA restriction site variation was examined for 35 taxa in theVernonieae and four outgroup tribes, using 17 restriction enzymes mapped for ca. 900 restriction sites per species; 139 mutations were found to be phylogenetically informative. Phylogenetic trees were constructed using Wagner and weighted parsimony, and evaluated by bootstrap and decay analyses. Relationships of Old and New World taxa indicate complex geographical relationships; there was no clear geographic separation by hemisphere. The relationships between Old and New World Vernonias found here support prior morphological analyses. The sister group to all New and most Old World taxa was composed of a small group of Old World species including yellow-flowered, trinervate-leaved species previously postulated to be basal in the tribe. The majority of both New and Old World taxa are derived from a lineage beginning with the monotypic genusStokesia, an endemic of the southeastern United States. The genusVernonia was also found to be paraphyletic within both the New and Old World. Available data do not support either the separation ofVernonia or the tribeVernonieae into geographically distinct lineages. The pattern of relationships within theVernonieae for taxa from North America, Asia, Africa, Central and South America is most similar to that of several other groups of both plants and animals with a boreotropical origin, rather than an origin in Gondwanaland. Such a pattern of distribution suggests more ancient vicariant events than are routinely postulated for theAsteraceae.

Phylogenetic relationships among Puccinellia and allied genera of Poaceae as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among accessions of Catabrosa P. Beauv., Phippsia (Trin.) R. Br., Sclerochloa P. Beauv., and Puccinellia Pari, resolved a monophyletic Puccinellia, with Sclerochloa as its sister group, Phippsia the sister of the Puccinellia + Sclerochloa clade, and Catabrosa situated more distantly. These results suggest that the taxonomic fusion of Phippsia and Puccinellia, which has been proposed in light of the existence of natural hybrids between them (currently recognized as the nothogenus × Pucciphippsia Tsvelev), would yield a grouping that would not be monophyletic unless Sclerochloa also was included. The set of restriction site characters that resolve these relationships provides minimal support for species groupings within Puccinellia, and the groupings that are resolved are inconsistent in some cases with species boundaries as determined by morphology and isozymes.

Phylogenetic Relationships Among Puccinellia and Allied Genera of Poaceae as Inferred from Chloroplast DNA Restriction Site Variation

Phylogenetic Relationships Among Puccinellia and Allied Genera of Poaceae as Inferred from Chloroplast DNA Restriction Site Variation

Phylogenetic structure in the grass family (Poaceae) as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among representatives of all subfamilies of the grass family (Poaceae), using Joinvillea (Joinvilleaceae) as the outgroup, placed most genera into two major clades. The first of these groups corresponds to a broadly circumscribed subfamily Pooideae that includes all sampled representatives of Ampelodesmeae, Aveneae, Brachypodieae, Bromeae, Diarrheneae, Meliceae, Poeae, Stipeae, and Triticeae. The second major clade includes all sampled representatives of four subfamilies (Panicoideae [tribes Andropogoneae and Paniceae], Arundinoideae [Arundineae], Chloridoideae [Eragrostideae], and Centothecoideae [Centotheceae]). Within this group (the “PACC” clade), the Panicoideae are resolved as monophyletic and as the sister group of the clade that comprises the other three subfamilies. Within the latter group, Danthonia (Arundinoideae) and Eragroslis (Chloridoideae) are resolved as a stable monophyletic group that excludes Phragmites (Arundinoideae); this structure is inconsistent with the Arundinoideae being monophyletic as currently circumscribed. The PACC clade is placed within a more inclusive though unstable clade that includes the woody Bambusoideae (Bambuseae) plus several disparate tribes of herbaceous grasses of uncertain affinity that are often recognized as herbaceous Bambusoideae (Brachyelytreae, Nardeae, Olyreae, Oryzeae, and Phareae). Among eight most‐parsimonious trees resolved by the analysis, four include a monophyletic Bambusoideae sensu lato (comprising Bambuseae and all five of these herbaceous tribes) as the sister group of the PACC clade; in the other four trees these bambusoid elements are not resolved as monophyletic, and the PACC clade is nested among these tribes. These results are consistent with those of previous analyses that resolve a basal or near‐basal branch within the family between Pooideae and all other grasses. However, resolution by the present analysis of the PACC clade, which includes Centothecoideae, Chloridoideae, and Panicoideae, but excludes Bambusoideae, is inconsistent with the results of previous analyses that place Bambusoideae and Panicoideae in a monophyletic group that excludes Centothecoideae and Chloridoideae.

Phylogenetic Structure in the Grass Family (Poaceae) as Inferred from Chloroplast DNA Restriction Site Variation

Phylogenetic Structure in the Grass Family (Poaceae) as Inferred from Chloroplast DNA Restriction Site Variation

Phylogenetic Significance of Chloroplast DNA Restriction Site Varition in the Ipomopsis aggregata Complex and Related Species (Polemoniaceae)

The Ipomopsis aggregata complex comprises diploid, perennial, montane herbs, dis- tributed across western North America. We used chloroplast DNA (cpDNA) restriction site variation to examine phylogenetic relationships among the three species in the complex, I. aggregata, I. arizonica and I. tenuituba, and several related species. Twenty-one restriction site mutations and four length mutations were used to reconstruct a phylogenetic tree by cladistic methods. With -a few exceptions, patterns of cpDNA variation within I. aggregata were consistent with current taxonomy and reflected the geographic distributions of subspecies and populations. However, cpDNA-based relationships among species were not congruent with a pre-1992 taxonomy of the group. Ipomopsis tenuituba did not form a distinct clade; two populations of this species had the same primitive cpDNA as I. arizonica and I. rubra, whereas two other populations emerged on branches within I. aggregata, and one population (of I. tenuituba subsp. macrosiphon) shared mutations with I. thurberi. It is not clear whether this pattern is the result of cpDNA transfer during periods of hybridization or the ten- uituba morphology has arisen independently more than once. Ipomopsis tenuituba subsp. macrosiphon has subsequently been segregated as a species. The level of sequence divergence among species was similar in magnitude to that among populations within each species, consistent with patterns of recent divergence and subsequent hybridization among the three species in the complex. In addition, relationships based on cpDNA variation reflected taxonomy and geographic distribution more congruently than did allozymes. The results from this study suggest that evolution of the I. aggregata complex has involved cases of chloroplast DNA transfer between taxa, convergent evo- lution for certain floral characters, or both.

Phylogenetic Relationships in North American Astragalus (Fabaceae) Based on Chloroplast DNA Restriction Site Variation

Chloroplast DNA restriction site variation was surveyed in 58 accessions of aneuploid (n = 11-15) North American Astragalus plus outgroup taxa consisting of Oxytropis lambertii, and two species from euploid (n = 8, 16 . . .), predominantly Old World, sections of Astragalus. A set of 52 site mutations was analyzed using Wagner parsimony. The resulting strict consensus tree revealed that the North American aneuploid series forms a monophyletic ingroup relative to the Old World euploid outgroups. In addition, a diverse assemblage of taxa comprising some 20% of the North American species is monophyletic. A method for characterizing large sets of equally parsimonious trees in terms of the diversity of distinct component clades is described and applied to these data.

Molecular relationships in subtribe Brassicinae (Cruciferae, tribe Brassiceae)

Restriction-site variation for 17 endonucleases was compared in the large single-copy region of the chloroplast genome in 74 taxa of the genera Brassica, Coincya, Diplotaxis, Eruca, Erucastrwn, Hirschfeldia, Raphanus, Sinapidendron, Sinapis, and Trachystoma (subtribe Brassicinae, tribe Brassiceae, Cruciferae). A total of 422 restriction-site mutations was observed, with 228 (54%) showing variation among taxa. Phylogenetic analyses indicated a clear division of the subtribe into two main lineages designated here as Rapa–Oleracea and Nigra. Polyphyly was evident in five genera (Brassica, Diplotaxis, Erucastrum, Sinapis, and Trachystoma) as indicated by their placement in both lineages and (or) further separation into groups within a lineage. The genera Coincya, Hirschfeldia, and Sinapidendron were monophyletic within the Nigra lineage, as were Eruca and Raphanus in the Rapa–Oleracea lineage. Four major groups were recognized within each lineage. The lowest levels of chloroplast DNA divergence were observed among taxa belonging to the same cytodeme or crossing group and were highest for Brassica rapa and Brassica oleracea versus Brassica nigra at 2.10–3.91% and 2.00–3.78%, respectively. The chloroplast DNA data were incongruent with traditional taxonomic circumscription of 5 of the 10 genera but concordant with other data sets that support the close genetic relatedness of all 10 genera. Key words: Brassica, Coincya, Erucastrum, Sinapidendron, Trachystoma, chloroplast DNA restriction-site variation.

Cladistic Analysis of Chloroplast DNA Restriction Site Characters in Erythrina (Leguminosae: Phaseoleae)

Chloroplast DNA restriction site variation was examined in 60 species of Erythrina (Leguminosae: Phaseoleae). This sample represents four of the five subgenera and most sections of this pantropical, woody, and ornithophilous genus of 112 species. Cladistic analysis of restriction site characters resulted in numerous most parsimonious trees, but the strict consensus tree was highly resolved. Low levels of resolution because of absence of characters were confined to a single clade representing plastomes sampled from a large group of closely related species. The groupings obtained from the chloroplast DNA characters were generally consistent with the traditional in- frageneric classification scheme for the genus. Plastome lineages of only one of the four subgenera surveyed was monophyletic, but those of most sections or of groups of closely related sections were monophyletic. The gene tree suggests that members of the African subg. Chirocalyx and of the Paleotropical subg. Erythraster are closely related and sister to African and Asian members of subg. Erythrina. Chloroplast DNA relationships indicate that hummingbird pollination, considered derived relative to passerine pollination, evolved convergently in at least three distinct lineages and that reversals to passerine pollination also may have occurred. Erythrina L. (Leguminosae: Phaseoleae) is an

Cladistic Characters and Cladogram Stability

Phylogenetic stability is the tendency for monophyletic groups that are resolved by an analysis to continue to be resolved when either the data or the analytical method is altered. Bootstrapping and similar procedures assess the stability of monophyletic groups, but provide little information to indicate which characters are crucial in the support of particular groups. We present a method that does so. Sequential Character Removal consists of a series of cladistic analyses, each conducted with a different subset of a complete data set; the subsets are obtained by the sequential and exhaustive removal of characters, individually and in all combinations of two or more. A character or combination of characters is critical to the resolution of a monophyletic group when the removal of that character or set of characters results in the loss of resolution of the group. Thus, for any monophyletic group, Sequential Character Removal generates a list of characters and char- acter combinations that are critical to the resolution of the group, in the context of an otherwise complete data set. An analysis of a real data set, representing chloroplast DNA restriction site variation among 27 species of Poaceae, demonstrates that characters critical to the recognition of a monophyletic group need not be synapomorphies of that group, and that a clade that is resolved by a complete data set, and fails to be resolved when a particular set of characters is removed, may reappear when additional characters are removed.

Chloroplast DNA Phylogenetic Studies in New World Phaseolinae (Leguminosae: Papilionoideae: Phaseoleae)

Chloroplast DNA restriction site variation was examined in several species of Pha- seolus, Vigna, and Ramirezella, and in four potential outgroups (Dipogon, Macroptilium, Oxyrhynchus and Strophostyles) of the Phaseolus-Vigna complex. Cladistic analyses of restriction site characters yielded 22 equally parsimonious trees with a consistency index of 0.60. Results of the chloroplast DNA analysis are consistent with current hypotheses from morphological studies in suggesting that Phaseolus is monophyletic, but that Vigna is polyphyletic. The Vigna plastomes are divided into two clades. One consists of all the Old World subgenera surveyed and the New World subg. Lasiospron, supporting morphological evidence that this distinct New World subgenus may be more closely related to the Old World groups than to other New World subgenera. The second clade is strictly New World and comprises Vigna subg. Srgmotdotropts, V. populnea, Ramirezella and Oxyrhynchus. The close relationship of Ramirezella chloroplast DNA's with New World Vigna and Oxyrhynchus plastomes follows recent cladistic analyses of morphological characters. Relationships of plastomes of the New World clade to the mostly Old World Vigna clade depends on rooting of the tree. Within Phaseolus, species from three small and distinct Mexican endemic sections have monophyletic chlo- roplast DNA's. Plastomes of the larger sect. Phaseolus are not monophyletic, but subgroups within the section follow relationships proposed by non-molecular studies. If rooted with Dipogon, the chloroplast DNA gene tree places Phaseolus, along with Macroptilium and Strophostyles, as sister group to the New World Vigna clade. Otherwise, if rooted with the Macroptilium and Strophostyles plastomes, Phaseolus chloroplast DNA's are sister group to plastomes of both Vigna clades and of Dipogon.

Genetic Diversity and Origin of the Hawaiian Islands Cotton, Gossypium tomentosum

Gossypium tomentosum is the only member of the cotton genus endemic to the Hawaiian archipelago. It is morphologically distinct from other allopolyploid Gossypium species, and its phylogenetic relationships with them are uncertain. Chloroplast and ribosomal DNA restriction site variation were used to estimate the phylogeny of the allopolyploids. Gossypium mustelinum is resolved as sister to the remaining allopolyploid species, which include two species-pairs, G. barbadense-G. darwinii and G. hirsutum (including G. lanceolatum)-G. tomentosum. This indication that G. tomentosum is sister to G. hirsutum is supported by allozyme data. Gossypium tomentosum is proposed, based on biogeographic evidence and molecular data, to have originated by transoceanic dispersal from a Mesoamerican progenitor. Few restriction site variants were observed among the allopolyploids, suggesting that present lineages diverged relatively rapidly following polyploidization. Allozyme analysis of 30 G. tomentosum accessions collected from seven islands revealed relatively low levels of genetic diversity: 11 of 50 loci were polymorphic, mean number of alleles per locus was 1.24, and mean panmictic heterozygosity was 0.033. Little geographic patterning of allelic distributions was observed. Despite historical cultivation of G. barbadense and G. hirsutum in Hawaii and the existence of their naturalized derivatives, no allozyme evidence of interspecific introgression into G. tomentosum was detected.

GENETIC DIVERSITY AND ORIGIN OF THE HAWAIIAN ISLANDS COTTON, GOSSYPIUM TOMENTOSUM

Gossypium tomentosum is the only member of the cotton genus endemic to the Hawaiian archipelago. It is morphologically distinct from other allopolyploid Gossypium species, and its phylogenetic relationships with them are uncertain. Chloroplast and ribosomal DNA restriction site variation were used to estimate the phylogeny of the allopolyploids. Gossypium mustelinum is resolved as sister to the remaining allopolyploid species, which include two species‐pairs, G. barbadense‐G. darwinii and G. hirsutum (including G. lanceolatum)‐G. tomentosum. This indication that G. tomentosum is sister to G. hirsutum is supported by allozyme data. Gossypium tomentosum is proposed, based on biogeographic evidence and molecular data, to have originated by transoceanic dispersal from a Mesoamerican progenitor. Few restriction site variants were observed among the allopolyploids, suggesting that present lineages diverged relatively rapidly following polyploidization. Allozyme analysis of 30 G. tomentosum accessions collected from seven islands revealed relatively low levels of genetic diversity: 11 of 50 loci were polymorphic, mean number of alleles per locus was 1.24, and mean panmictic heterozygosity was 0.033. Little geographic patterning of allelic distributions was observed. Despite historical cultivation of G. barbadense and G. hirsutum in Hawaii and the existence of their naturalized derivatives, no allozyme evidence of interspecific introgression into G. tomentosum was detected.

Phylogenetic systematics of New WorldIpomoea (Convolvulaceae) based on chloroplast DNA restriction site variation

Chloroplast DNA restriction site variation was studied in 31 New World species ofIpomoea, representing a majority of the New World sections and series within the genus. Using 14 endonucleases, a total of 124 phylogenetically informative restriction sites was detected. Dollo parsimony, Wagner parsimony, and bootstrap methods were employed to construct phylogenetic trees and evaluate confidence intervals of monophyletic groups. With a few exceptions, groups circumscribed on the basis of morphological variation are in agreement with groupings based on restriction site variation. Relationships between subgeneric groupings, however, disagree substantially with those proposed in the past. Although conflicting hypotheses for some intersectional relationships are not presently resolvable, cpDNA restriction site analyses propose the following refinements of existing classification schemes.Ipomoea ser.Setosae is divided into distantly related groups, as is sect.Pharbitis. SeriesTyrianthinae, a proposed segregate of sect.Pharbitis, is associated with sect.Calonyction and the Tricolor complex (subg.Quamoclit).Ipomoea sect.Batatas is segregated from other herbaceous groups of the heterogeneous subg.Quamoclit sensu lato and aligned as a derivative ofI. setosa, subg.Eriospermum. To test for homology of key characters weighted in traditional schemes, morphological features were studied with respect to their distribution on lineages defined by restriction site data. Characters such as setose sepals, foliose-pubescent sepals, and erect growth habit, among others, are interpreted as having multiple origins, while 3-locular ovaries, 4-locular ovaries, and long-haired seeds have evolved only once.

Reexamination of Series Relationships of Mexican and Central American Wild Potatoes (Solanum sect. Petota): Evidence from Chloroplast DNA Restriction Site Variation

Chloroplast DNA restriction analysis has been used to test the series classifications of the Mexican and Central American representatives of Solanum sect. Petota of Rydberg, Bukasov, Hawkes, and Correll. Three clades are supported: 1. all species in series Morelliformia, Pinnatisecta, and Polyadenia exclusive of S. bulbocastanum and S. cardiophyllum. Subclades within clade 1 include S. trifidum and S. tarnii; S. x michoacanum and S. pinnatisectum; S. brachistotrichum and S. stenophyllidium; S. clarum and S. morelliforme; and series Polyadenia; 2. S. bulbocastanum and S. cardiophyllum; 3. S. verrucosum (a Mexican diploid), the Mexican polyploid species, and the South American species. Within clade 3, series Conicibaccata forms a well-defined subclade, whereas S. verrucosum, series Longipedicellata, series Demissa, and the South American species form another. In reference to the latest classification of Hawkes, series Conicibaccata and Polyadenia are supported as monophyletic; the Mexican diploids are paraphyletic; and series Demissa, Longipedicellata, and S. verrucosum (series Tuberosa) form one monophyletic assemblage. Species within series Longipedicellata and Demissa are polyploid, possibly of hybrid origin, and may need less conservative markers or biparentally- inherited probes to distinguish them. These molecular results are compared to the diverse data sets that have led to this classification. Solanum sect. Petota Dumort., the potato and its wild relatives, traditionally has been consid- ered to be taxonomically difficult, and conflict- ing taxonomic interpretations of species bound- aries and series relationships are common. The group contains much morphological and phys- iological variability. An earlier taxonomic in- terpretation of the group (Correll 1962) recog- nized 157 species, while the latest (Hawkes 1990) recognizes 232 species. Bitter (1912) was the first to describe series in Solanum sect. Petota (series Conicibaccata and Maglia), although he failed to designate series affiliations for many species. Rydberg (1924) di- vided the Mexican and Central American po-

Phylogenetic and Evolutionary Implications of Interspecific Chloroplast DNA Variation in Krigia (Asteraceae-Lactuceae)

Chloroplast DNA restriction site and length variation was examined among 12 taxa of Krigia, using 34 restriction endonucleases, filter hybridization experiments, and comparative mapping procedures. A total of 252 restriction site mutations was detected, 159 of which were phylogenetically informative. The resulting phylogenetic trees correlated well with cytological and morphological data. The two sects. Krigia and Cymbia differed by at least 73 restriction site mutations. Most species within each section were characterized by many restriction site changes. Interspecific sequence divergence in Krigia was much higher than in any other previously studied genus of the Asteraceae and was comparable to the high levels of divergence found in genera of other angiosperm families. Relative rates of chloroplast DNA evolution in Krigia were significantly different among the various chromosome number groups, resulting in the rejection of a molecular clock. However, a molecular clock could not be rejected within each chromosome number group. Different regions of the chloroplast genome also showed extremely different frequencies of mutations and four hotspot areas were identified. The areas occurred in long spacer regions between gene coding sequences. Furthermore, most of the homoplasy and length variation also occurred within these hotspots. Chloroplast DNA trees were consistent with the hypothesis that an ancient allopolyploid event between species with low chromosome base numbers, followed by subsequent aneuploid reduction, resulted in K. wrightii with n = 9. The results also suggest that x = 5 is the probable ancestral base number for the genus and that aneuploid reduction is the major mode of chromosome number change in Krigia and related genera.

Molecular systematics of Brassica and allied genera (Subtribe Brassicinae, Brassiceae) — chloroplast DNA variation in the genus Diplotaxis

Chloroplast DNA restriction site variation for 17 endonucleases was surveyed for the large single-copy region of the genome in 26 taxa of the genus Diplotaxis and compared with previously mapped site mutations in other members of the Subtribe Brassicinae (Tribe Brassiceae, Cruciferae). A total of 259 restriction site and length mutations were observed, 206 (80%) of which showed variation at the interspecific level. Phylogenetic analysis indicated a clear division of the genus Diplotaxis into the same two lineages for the Subtribe Brassicinae, described previously by Warwick and Black as Rapa/ Oleracea and Nigra. Levels of genetic divergence and taxon groupings suggested by the restriction site variation were highly consistent with previously recognized cytodemes or crossing groups and the geographical distribution of Diplotaxis taxa. However, the data were inconsistent with the morphologically based taxonomic delimitation of the genus, certain subgeneric circumscriptions, and even species delimitation in the case of D. virgata. Diplotaxis species were separated into three major groups in each of the two lineages. In the Rapa/ Oleracea lineage, Group A included D. erucoides ssp. erucoides and D. cossoniana. Group B included two subgroups: B (i) D. tenuifolia, D. cretacea, and D. simplex and B (ii) D. harra. Group C included D. viminea and D. muralis. Within the Nigra lineage, group D included D. siettiana, D. ibicensis, D. brevisiliqua, and D. gomezcampoi. Group E included D. brachycarpa. Group F included three subgroups: F (i) D. assurgens, D. tenuisiliqua, an accession of D. virgata from southern Morocco (DVA), and D. siifolia; F (ii) D. berthautii and D. virgata f. sahariensis; and F (iii) D. catholica, D. catholica var. rivulorum, D. virgata ssp. virgata. These groups often showed greater genetic closeness to other species from other genera in the Subtribe than to other species of Diplotaxis.

CHLOROPLAST DNA VARIATION IN GLIRICIDIA SEPIUM (LEGUMINOSAE): INTRASPECIFIC PHYLOGENY AND TOKOGENY

An analysis of chloroplast DNA restriction site variation in Gliricidia sepium reveals two geographically distinct chloroplast lineages, one in the Yucatan Peninsula and the other along the Pacific Coast in Mexico and Central America. Geographical, morphological, biochemical, and habitat distinctions suggest that these two chloroplast lineages reflect organismal lineages. Within the Pacific coastal chloroplast lineage, there exist sublineages that most likely reflect tokogenetic systems of relationship rather than organismal phytogeny, a hypothesis supported by the co‐occurrence of more than one of these chloroplast sublineages in a single population. The genetic distance between any two of these chloroplast lineages ranges from 0.0001 to 0.0024 nucleotide substitutions per site and reveals relatively high levels of intraspecific divergence. We suggest that assessing intraspecific chloroplast DNA variation is important generally in higher level phylogenetic analysis because it enables one to obtain truer estimates of homoplasy, detect potentially cryptic species, and distinguish among molecular markers that reflect phylogenetic vs. tokogenetic relationships. This is in addition to determining the extent of potential complicating factors such as introgression and lineage sorting from polymorphic ancestry.

Chloroplast DNA Variation in Gliricidia sepium (Leguminosae): Intraspecific Phylogeny and Tokogeny

An analysis of chloroplast DNA restriction site variation in Gliricidia sepium reveals two geographically distinct chloroplast lineages, one in the Yucatan Peninsula and the other along the Pacific Coast in Mexico and Central America. Geographical, morphological, biochemical, and habitat distinctions suggest that these two chloroplast lineages reflect organismal lineages. Within the Pacific coastal chloroplast lineage, there exist sublineages that most likely reflect tokogenetic systems of relationship rather than organismal phytogeny, a hypothesis supported by the co-occurrence of more than one of these chloroplast sublineages in a single population. The genetic distance between any two of these chloroplast lineages ranges from 0.0001 to 0.0024 nucleotide substitutions per site and reveals relatively high levels of intraspecific divergence. We suggest that assessing intraspecific chloroplast DNA variation is important generally in higher level phylogenetic analysis because it enables one to obtain truer estimates of homoplasy, detect potentially cryptic species, and distinguish among molecular markers that reflect phylogenetic vs. tokogenetic relationships. This is in addition to determining the extent of potential complicating factors such as introgression and lineage sorting from polymorphic ancestry.

Relationships among native and introduced North American species of Hordeum, based on chloroplast DNA restriction-site variation

Restriction-site analysis of chloroplast DNA was carried out on a total of 13 North American species of Hordeum, 7 native and 6 introduced. Sites associated with polymorphic banding patterns were omitted so that only invariant sites within species were used in the analyses. A number of taxa whose species status is in dispute can indeed be supported at species rank, i.e., H. brachyantherum, H. californicum, H. pusillum, H. intercedens, H. marinum, and H. geniculatum. The maternal progenitor of H. arizonicum is H. pusillum, and this is further discussed in light of other possibilities. Both phenetic and cladistic analyses indicate a tripartite relationship whereby H. vulgare is distant from the group of H. leporinum, H. glaucum, and H. murinum and from a second group comprising the native species H. brachyantherum, H. californicum, H. arizonicum, H. jubatum, H. pusillum, H. intercedens, and H. depressum. Hordeum marinum and H. geniculatum occupy a central position in this relationship. Speculation that the putative ancient form of Hordeum resembled a H. murinum – H. geniculatum-like species is discussed. Key words: chloroplast DNA, Hordeum, phylogenetic relationships.