cpDNA Restriction Site Variation Research Articles

The Phylogenetic Position of Eastern Asian Sedoideae (Crassulaceae) Inferred from Chloroplast and Nuclear DNA Sequences

Abstract The phylogenetic position of 74 taxa of Asian Sedoideae (Crassulaceae) was estimated based on analyses of the trnL-trnF intergenic spacer sequence of cpDNA and the ITS region, including the 5.8S rDNA sequence, of nDNA. Our analyses suggest that the subfamily Sedoideae is not monophyletic and the genus Sedum especially is highly paraphyletic. Recent studies based on cpDNA restriction-site variation and the matK region recognized seven clades of “major importance.” In our analyses, four major clades were recovered: Kalanchoe, Sempervivum, Aeonium, and Acre. All Asian Sedum (s.s.) tested are included in the Acre clade, and all other eastern Asian genera are in groups corresponding to the Telephium clade. The Telephium clade is split into four strongly supported subclades, Rhodiola, Hylotelephium, Phedimus, and Umbilicus, and is determined to be polyphyletic. All eastern Asian genera that were segregated from Sedum are separated in a lineage distinct from Sedum (s.s.). Hylotelephium, Orostachys, Mete...

Implications for the Phylogeny, Classification, and Biogeography of Solanum from cpDNA Restriction Site Variation

A phylogenetic analysis of Solanum based on chloroplast DNA restriction site variation confirms previous findings that Lycopersicon and Cyphomandra are derived from within Solanum. Three out of four Solanum subgenera with more than one representative in this analysis (Minon, Potatoe, Solanum) are found to be polyphyletic, suggesting that the subgeneric classification of the genus needs revision. Subgenus Leptostemonum is monophyletic within the context of our sampling. Three primary clades can be distinguished within Solanum. Clade I includes representatives of sections Archaesolanum, Dulcamara, Holophylla, Jasminosola- num, and Solanum. Clade II includes members of subgenus Potatoe (sections Basarthrum, Lycopersicon, and Petota). Clade III includes all representatives sampled from subg. Leptostemonum, sects. Allophyllum, Brevan- therum, Gemninata, Pseduocapsicum, and Cyphomandropsis, and species formerly assigned to Cyphomandra. Solanum as a whole and each of the three primary clades apppear to be New World in origin. Within Leptostemonum, African and Australian members are derived from New World ancestors.

DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE HEUCHERA GROUP (SAXIFRAGACEAE).

Various factors, including taxon density, sampling error, convergence, and heterogeneity of evolutionary rates, can potentially lead to incongruence between phylogenetic trees based on different genomes. Particularly at the generic level and below, chloroplast capture resulting from hybridization may distort organismal relationships in phylogenetic analyses based on the chloroplast genome, or genes included therein. However, the extent of such discord between chloroplast DNA (cpDNA) trees and those trees based on nuclear genes has rarely been assessed. We therefore used sequences of the internal transcribed spacer regions (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA) to reconstruct phylogenetic relationships among members of the Heuchera group of genera (Saxifragaceae). The Heuchera group presents an important model for the analysis of chloroplast capture and its impact on phylogenetic reconstruction because hybridization is well documented within genera (e.g., Heuchera), and intergeneric hybrids involving six of the nine genera have been reported. An earlier study provided a well-resolved phylogenetic hypothesis for the Heuchera group based on cpDNA restriction-site variation. However, trees based on ITS sequences are discordant with the cpDNA-based tree. Evidence from both morphology and nuclear-encoded allozymes is consistent with the ITS trees, rather than the cpDNA tree, and several points of phylogenetic discord can clearly be attributed to chloroplast capture. Comparison of the organellar and ITS trees also raises the strong likelihood that ancient events of chloroplast capture occurred between lineages during the early diversification of the Heuchera group. Thus, despite the many advantages and widespread use of cpDNA data in phylogeny reconstruction, comparison of relationships based on cpDNA and ITS sequences for the Heuchera group underscores the need for caution in the use of organellar variation for retrieving phylogeny at lower taxonomic levels, particularly in groups noted for hybridization.

Parsimony analysis of cpDNA restriction site variation in subfamily Nepetoideae (Labiatae)

Parsimony analysis of cpDNA restriction site variation supports monophyly of subfamily Nepetoideae. However, a close relationship among Nepetoideae and other gynobasic‐styled Labiatae is not supported, indicating that a gynobasic style has evolved independently in at least two clades of Labiatae. The inferred relationships are congruent with the classification of Cantino, Harley, and Wagstaff (1992, Advances in labiate sciences, 27–37, Royal Botanic Gardens, Kew) but conflict to varying degrees with traditional classifications. Monophyly of four tribes of Nepetoideae also is supported.

Parsimony Analysis of cpDNA Restriction Site Variation in Subfamily Nepetoideae (Labiatae)

Parsimony analysis of cpDNA restriction site variation supports monophyly of subfamily Nepetoideae. However, a close relationship among Nepetoideae and other gynobasic-styled Labiatae is not supported, indicating that a gynobasic style has evolved independently in at least two clades of Labiatae. The inferred relationships are congruent with the classification of Cantino, Harley, and Wagstaff (1992, Advances in labiate sciences, 27–37, Royal Botanic Gardens, Kew) but conflict to varying degrees with traditional classifications. Monophyly of four tribes of Nepetoideae also is supported.

Molecular phylogeny ofIva (Asteraceae, Heliantheae) based on chloroplast DNA restriction site variation

Iva s.str. (comprising ten species) was examined by cpDNA restriction site variation to determine phyletic relationships within the group. The results were compared with relationships proposed from other data. A total of 86 restriction site mutations was detected, 47 of which proved phylogenetically informative. A single most parsimonious tree was obtained using both Wagner and Dollo parsimony. The tree revealed three main lineages that are congruent with the three chromosome lineages (base numbers of x = 16, 17, 18). The monophyly of the x = 16 and 18 groups was supported strongly by molecular data, while the monophyly of x = 17 lineage was only supported moderately. Relationships among the three lineages indicate that the sect.Iva is paraphyletic because sect.Linearbractea is nested within it. Both morphological data and the secondary chemical data are in agreement with the proposed cpDNA phylogeny. Because of this agreement, sect.Iva is revised such that,I. axillaris was excluded and positioned within the newly proposed sect.Rhizoma. Patterns and rates of cpDNA evolution were also examined. The results indicated an uneven evolution in the chloroplast genome with different rates of cpDNA evolution in at least a few species ofIva. However, the evolutionary clock hypothesis can not be rejected within most of the lineages inIva.

Evolution in the Andean Epiphytic Genus Columnea (Gesneriaceae). II. Chloroplast DNA Restriction Site Variation

A cladistic analysis of chloroplast DNA (cpDNA) restriction site variation was per- formed on Columnea (Gesneriaceae) sections Pentadenia and StVgnan,he. Two species of Alloplectus were included in the analyses and one of Drymonia was used as the outgroup. Restriction site variation was analyzed using Wagner parsimony and character state weighting that favors conver- gent losses over convergent gains. The large numbers of equally most parsimonious trees prevented examination of each tree independently. Thus, examination of phvlogenetic relationships was based on a strict consensus of all most parsimonious trees. The resulting phylogeny is largely congruent with recent classification schemes, although the positions of several species are not in accordance with traditional relationships. As a result of the cladistic analysis of the cpDNA restriction site variation, section Pentadenia is at least paraphyletic, and possibly polyphyletic with section Styg- nanthe. The lack of resolution among the several clades within section Stygnanthe does not provide evidence for or against monophyly of this section. Several clades are strongly supported with cpDNA data and provide insight into biogeography and origin of morphological adaptations.

Chloroplast DNA phylogeny of Lens (Leguminosae): origin and diversity of the cultivated lentil

A restriction-site analysis of chloroplast DNA (cpDNA) variation in Lens was conducted to: (1) assess the levels of variation in Lens culinaris ssp. culinaris (the domesticated lentil), (2) identify the wild progenitor of the domesticated lentil, and (3) construct a cpDNA phylogeny of the genus. We analyzed 399 restriction sites in 114 cultivated accessions and 11 wild accessions. All but three accessions of the cultivar had identical cpDNAs. Two accessions exhibited a single shared restriction-site loss, and a small insertion was observed in the cpDNA of a third accession. We detected 19 restriction-site mutations and two length mutations among accessions of the wild taxa. Three of the four accessions of L. culinaris ssp. orientalis were identical to the cultivars at every restriction site, clearly identifying ssp. orientalis as the progenitor of the cultivated lentil. Because of its limited cpDNA diversity, we conclude that either the cultivated lentil has passed through a genetic bottleneck during domestication and lost most of its cytoplasmic variability or else was domesticated from an ancestor that was naturally depauperate in cpDNA restriction-site variation. However, because we had access to only a small number of populations of the wild taxa, the levels of variation present in ssp. orientalis can only be estimated, and the extent of such a domestication bottleneck, if applicable, cannot be evaluated. The cpDNA-based phylogeny portrays Lens as quite distinct from its putative closest relative, Vicia montbretii. L. culinaris ssp. odemensis is the sister of L. nigricans; L. culinaris is therefore paraphyletic given the current taxonomic placement of ssp. odemensis. Lens nigricans ssp. nigricans is by far the most divergent taxon of the genus, exhibiting ten autapomorphic restriction-site mutations.

Geographic structuring of chloroplast DNA genotypes inTiarella trifoliata (Saxifragaceae)

Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of “intraspecific phylogeography” to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.

Phylogenetic and evolutionary implications of nuclear ribosomal DNA variation in dwarf dandelions (Krigia, Lactuceae, Asteraceae)

Restriction site and length variations of nrDNA were examined for 51 populations of seven species ofKrigia. The nrDNA repeat ranged in size from 8.7 to 9.6 kilobase (kb). The transcribed region, including the two ITSs, was 5.35 kb long in all examinedKrigia populations. In contrast, the size of the nontranscribed IGS varied from 3.35 to 4.25 kb. Eight different types of length-variations were identified among the 51 populations, including distinct nrDNA lengths in the tetraploid and diploid populations of bothK. biflora andK. virginica. However, a few variations were detected among populations of the same species or within a cytotype. All populations ofKrigia sect.Cymbia share a 600 bp insertion in IGS near the 18 S gene, and this feature suggests monophyly of the section. AllKrigia spp. had a conjugated type of subrepeat composed of approximately 75 basepairs (bp) and 125 bp. Base modifications in the gene coding regions were highly conserved among species. Forty-five restriction sites from 15 enzymes were mapped, 24 of which were variable among populations. Only four of the variable sites occurred in the rRNA coding region while 20 variable sites were detected in the noncoding regions. Collectively, 25 enzymes generated about 66 restriction sites in each nrDNA; this amounts to about 4.3% of the nrDNA repeat. A total of 50 restriction sites was variable, 28 of which were phylogenetically informative. Phylogenetic analyses of site mutations indicated that two sections ofKrigia, sect.Cymbia and sect.Krigia, are monophyletic. In addition, relationships among several species were congruent with other sources of data, such as cpDNA restriction site variation and morphology. Both length and restriction site variation supported an allopolyploid origin of the hexaploidK. montana. The average sequence divergence value inKrigia nrDNA was 40 times greater than that of the chloroplast DNA. The rapid evolution of nrDNA sequences was primarily due to changes of the IGS sequences.

Chloroplast DNA evolves slowly in the palm family (Arecaceae).

A survey of cpDNA restriction-site variation for 22 species representing five of the six subfamilies of the palm family was conducted. Phylogenetic reconstructions based on the restriction-site data are in general agreement with conventional analyses based on morphological characters. Base-substitution estimates, derived from the restriction-site data, indicate a potential 5-13-fold decrease in substitution rates within the palms relative to rate estimates for annual plant taxa. Approximately 1,000 bp of the rbcL gene (ribulose-1,5-bisphosphate carboxylase, large subunit) were sequenced from species representing two subfamilies of the palms. The complete DNA sequence data are in accord with the restriction-site data and indicate a total rate of nucleotide substitution that is about eightfold lower than that observed for annual plants.

Phylogenetics in Clarkia (Onagraceae): Restriction Site Mapping of Chloroplast DNA

Restriction site maps of chloroplast DNA (cpDNA), maternally inherited in Clarkia, were obtained in representative species of all seven diploid sections, the allotetraploid sect. Clarkia, and the outgroup Epilobium brachycarpum. CpDNA restriction site variation was analyzed by Wagner and Dollo parsimony, bootstrapping, and genetic distance methods. Four shortest Wagner trees, one of which was also the shortest Dollo and Bootstrap majority-rule tree, were examined along with 21 one-step longer trees. Section Myxocarpa was placed as basal in Clarkia followed by a trichotomy of the Rhodanthos lineage, the Eucharidium I Clarkia lineage, and the lineage including sects. Sympherica, Phaeostoma, Fibula, and Godetia. However, when trees only one step longer are considered, many of these sectional alignments are lost. Early and rapid divergence of most sectional lineages, coupled with higher rates of cpDNA restriction site homoplasy, is proposed to account for the lack of many synapomorphic restriction site characters at the sectional level in Clarkia. A comparison of the cpDNA results to morphology, cytology, and biogeography with respect to intersectional relationships is presented. Diploid sect. Fibula, previously believed to have originated through intersectional cross- ing between sects. Phaeostoma and Sympherica, has a chloroplast genome similar to one species of sect. Phaeostoma. Monophyletic lineages as previously described on the basis of the distribution of duplicated PGI genes are supported, but not fully so. The origin of the allotetraploid C. pulchella involved sect. Eucharidium as the maternal diploid parent and sect. Myxocarpa as the paternal diploid parent. The origin of C. pulchella was ancient, predating the divergence of the two extant species of sect. Eucharidium.