cpDNA Phylogeny Research Articles

Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand

Lepidium sensu stricto (s.s.) (Brassicaceae) (ca. 150 species) is distributed worldwide with endemic species on every continent. It is represented in Australia and New Zealand by 19 and seven native species, respectively. In the present study we used a nuclear ribosomal internal transcribed spacer (ITS) phylogeny in comparison with a cpDNA phylogeny to unravel the origin of Australian/New Zealand species. Although phylogenetic relationships within Lepidium s.s. were not fully resolved, the cpDNA data were in agreement with a Californian origin of Lepidium species from Australia/New Zealand. Strongly conflicting signals between the cp- and nuclear DNA phylogenetic analysis clearly indicated hybridogenous genomic constitution of Australian Lepidium s.s. species: All 18 studied Australian/New Zealand Lepidium s.s. species examined shared a Californian cpDNA type. While eleven Australian/New Zealand species appeared to harbor a Californian ITS type, a group of seven species shared a South African ITS type. This pattern is most likely explained by two trans-oceanic dispersals of Lepidium from California and Africa to Australia/New Zealand and subsequent hybridization followed by homogenization of the ribosomal DNA either to the Californian or South African ITS type in the two different lineages. Calibration of our molecular trees indicates a Pliocene/Pleistocene origin of Lepidium in Australia/New Zealand. Low levels of cpDNA and ITS sequence divergence and unresolved topologies within Australian/New Zealand species suggest a rapid and recent radiation of Lepidium after the hybridization event. This coincides with dramatic climatic changes in that geological epoch shaping the composition of the vegetation.

Phylogenetic positions of Actites megalocarpa and Sonchus hydrophilus (Sonchinae: Asteraceae) based on ITS and chloroplast non-coding DNA sequences

Phylogenetic positions of the Australian endemic taxa Actites megalocarpa and Sonchus hydrophilus within the subtribe Sonchinae were determined on the basis of ITS sequences of nuclear rDNA and the psbA–trnH(GUG) intergenic spacer of chloroplast DNA. Both ITS and cpDNA phylogenies suggest that the monotypic genus Actites is not closely related to the members of Sonchus section Asperi, as previously suggested. Rather, this study indicates that it is more closely related to the members of Sonchus sections Maritimi (S.�maritimus) and Arvenses (S. arvensis). It also suggests that S. maritimus from section Maritimi is one of the closest relatives of Actites in Australia, although an alternative origin from section Arvenses is possible. Actites and Embergeria, once treated as congeneric taxa, appear to have originated independently in Australia and New Zealand, respectively. Sonchus hydrophilus is closely related to the S. asper complex, S. oleraceus and S. kirkii. This study suggests that S. kirkii may be involved in the origin of S. hydrophilus in Australia.

Phylogenetic split of Larix : evidence from paternally inherited cpDNA trn T- trn F region

A molecular phylogeny of Larix comprising 12 species was constructed from the sequence analysis of the paternally inherited cpDNA trnT-trnF region of 46 individuals. The most parsimonious tree split Larix into three sister clades: one clade was composed of two North American species, the other two were short-bracted and long-bracted species of Eurasia respectively except that L. sibirica was clustered in the long-bracted clade. The difference between the present cpDNA phylogeny and previous nrDNA ITS phylogeny in the position of L. sibirica seems to suggest that ancient cytoplasmic gene flow might exist between sections Larix and Multiserialis. The short-bracted L. laricina and long-bracted L. occidentalis have an identical sequence of the trnT-trnF region, which implies that the bract length divergence among North American larches might have occurred recently or chloroplast capture happened during the early differentiation of the two species. The cpDNA results also shed some light on the biogeography of Larix.

Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the urophyllum group of the genus Fagopyrum (Polygonaceae).

We performed phylogenetic analyses of Fagopyrum species in the urophyllum group based on nucleotide sequences of two nuclear genes, FLORICAULA/LEAFY (FLO/LFY) and AGAMOUS (AG), and three segments of chloroplast DNA (cpDNA), rbcL-accD, trnK intron, and trnC-rpoB spacer. The FLO/LFY and AG sequences turned out to be phylogenetically more informative at the intrageneric level than the cpDNA sequences. Congruence among these gene trees, inferred by a maximum-likelihood (ML) method, demonstrated that topologies were partially incongruent between the nuclear and chloroplast DNA phylogenies. The nuclear DNA sequence data supported a monophyletic relation of F. statice, F. gilesii, and F. jinshaense, whereas the former two species formed another monophyletic relation with the F. capillatum-F. gracilipes-F. gracilipedoides-F. rubifolium clade excluding F. jinshaense in the synthetic cpDNA phylogeny. In addition, two divergent sequences of FLO/LFY were found in F. rubifolium (tetraploid). One of these was sister to F. gracilipedoides and another was sister to F. statice, and a monophyletic relation of these two genes was rejected by a bootstrap analysis. These results suggest that hybridization may have occurred during diversification of Fagopyrum species in the urophyllum group, and that F. rubifolium is possibly allotetraploid species.

Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets.

Although the monogenomic genera of the Triticeae have been analyzed in numerous biosystematic studies, the allopolyploid genera have not been as extensively studied within a phylogenetic framework. We focus on North American species of Elymus, which, under the current genomic system of classification, are almost all allotetraploid, combining the St genome of Pseudoroegneria with the H genome of Hordeum. We analyze new and previously published chloroplast DNA data from Elymus and from most of the monogenomic genera of the Triticeae in an attempt to identify the maternal genome donor of Elymus. We also present a cpDNA phylogeny for the monogenomic genera that includes more data than, and thus builds on, those previously published. The chloroplast DNA data indicate that Pseudoroegneria is the maternal genome donor to all but one of the Elymus individuals. There is little divergence among the Elymus and Pseudoroegneria chloroplast genomes, and as a group, they show little divergence from the rest of the Triticeae. Within the monogenomic Triticeae, the problematic group Thinopyrum is resolved as monophyletic on the chloroplast DNA tree. At the intergeneric level, the data reveal several deeper-level relationships that were not resolved by previous cpDNA trees.

Historical biogeography and the origin of stomatal distributions inBanksiaandDryandra(Proteaceae) based on their cpDNA phylogeny

Banksia and Dryandra have undergone extensive speciation and adaptive radiation, especially in Australia's isolated Southwest Botanical Province. We derive a phylogeny for these groups based on cpDNA sequences and use it to reconstruct their historical biogeography and evolution of leaf traits thought to be adapted to drought and/or nutrient poverty. Slowly evolving regions (trnL intron, trnL/trnF spacer) are used to resolve large-scale relationships; faster evolving regions (rp116 intron, psbA/trnH and trnT/trnL spacers) are used to resolve relationships among closely related species. Banksia is paraphyletic with respect to Dryandra. The lineage underwent a basal split into two clades (here named /Cryptostomata and /Phanerostomata), and four infrageneric taxa supported by morphological cladistic analyses (series Spicigerae, Abietinae, Tetragonae, and Banksia) are not monophyletic. Dispersal-vicariance analysis resolves a southwestern Australian origin for the lineage, with two later expansions to the east followed by vicariance events. Stomatal crypts arose with the /Cryptostomata, which is characterized by tough, long-lived leaves and common in southwestern Australia. Sequestering of stomata also arose multiple times in /Phanerostomata, which is characterized by softer, short-lived leaves and common in moister coastal areas, via inrolling of the margins of narrow leaves and restricting stomata to shallow pits. The hypothesis that sclerophylly preadapted the plants to xeromorphy is supported in the case of shallow stomatal pits and deep stomatal crypts, but not narrow, needle-like leaves.

A chloroplast DNA phylogeny of easternPhlox(Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny

The comparison of independent phylogenies is a valuable approach to the study of evolutionary pattern and process. Available data on eastern North American Phlox, including our recent ITS phylogeny, suggest that relationships are complicated in the group and that hybridization may have been a contributing factor. We used restriction site data from the chloroplast genome to develop a second phylogeny for eastern Phlox. Sampling was the same as that for the ITS study and consisted of 79 samples (including all 22 eastern Phlox species and most eastern subspecies, as well as multiple populations of many taxa). The resulting cpDNA phylogeny agrees with the ITS phylogeny in many respects, strengthening earlier conclusions. Nevertheless, incongruence between the trees is noteworthy: many samples, particularly of members of the P. pilosa and P. glaberrima complexes, are placed in different clades. A variety of tests were carried out to assess congruence in terms of topological patterns, character congruence, and homogeneity of data sets. Significant conflict between the phylogenies is discussed in light of the hypothesis that hybridization has affected relationships in this genus.

Chloroplast DNA evidence for the roles of island colonization and extinction in Tolpis (Asteraceae: Lactuceae)

Tolpis consists of ∼13 species native to Africa, Europe, and Macaronesia, with at least one species endemic to each of the four major archipelagos of the Azores, Madeira Islands, Canary Islands, and Cape Verde Islands. All but two of these species develop woody stems by maturity. Chloroplast DNA restriction site variation was analyzed for all species of Tolpis and four outgroups in order to understand the patterns of island colonization and evolution of woodiness in this genus. Parsimony analyses revealed a strongly supported monophyletic Tolpis. Within the genus, the following three well-supported groups were detected: all species from the Canary Islands and Cape Verde Islands, both Azorean species, and both continental species. The Canary Island/Cape Verde clade was sister to the two continental species, and the Azorean clade was sister to this group. The two Madeiran species of Tolpis occupied the basalmost positions within the genus. When biogeography was mapped onto this phylogeny, nine equally parsimonious reconstructions (five steps each) of dispersal history were detected, which fell into two groups: eight reconstructions implied that Tolpis colonized Madeira from the continent, followed by continental extinction and subsequent continental recolonization, while one reconstruction implied that Tolpis colonized Macaronesia four times. Two of the reconstructions involving continental extinction required the least amount of overall dispersal distance. The cpDNA phylogeny also suggests that woodiness arose in the common ancestor of all extant Tolpis, followed by two independent reversals to an herbaceous habit. Assuming that one of the eight reconstructions favoring continental extinction and recolonization is true, our results suggest that Tolpis may represent the first documented example of a woody plant group in Macaronesia that has recolonized the mainland in herbaceous form.

Historical biogeography of Androcymbium Willd. (Colchicaceae) in Africa: evidence from cpDNA RFLPs

The cpDNA restriction variation in 39 populations representing a geographical sampling of 18 species ofAndrocymbium in southwestern and northern Africa was examined to assess the historical biogeography of the genus. The cpDNA phylogeny indicates that the disjunction between South and North Africa is best explained by the dispersal of southern African ancestors into North Africa. Divergence time estimates suggest that the geographic range of the genus may have extended considerably north (perhaps to Tanzania and Kenya) prior to the global desiccation of Africa in the Miocene. Further expansion of the genus northward was probably stalled until climatic changes in the late Miocene brought about the gradual replacement of a subtropical woodland savanna with the arid landscape that gave rise to the Sahara. Aridification of the northern quarter of the continent provided the ecological conditions for fostering the expansion of Androcymbium along the Mediterranean fringe (probably east to west) and its introduction into the Canary Islands. Unlike their South African congeners, the northern species have experienced expansions, fragmentations, and local extinctions in response to the severe climatic shifts in this area during the Pliocene-Pleistocene. According to our divergence time estimates, the arid track may have already existed as a continuous area connecting southern and northern Africa in the late Miocene.

Historical biogeography of Androcymbium Willd. (Colchicaceae) in Africa: evidence from cpDNA RFLPs

The cpDNA restriction variation in 39 populations representing a geographical sampling of 18 species ofAndrocymbium in southwestern and northern Africa was examined to assess the historical biogeography of the genus. The cpDNA phylogeny indicates that the disjunction between South and North Africa is best explained by the dispersal of southern African ancestors into North Africa. Divergence time estimates suggest that the geographic range of the genus may have extended considerably north (perhaps to Tanzania and Kenya) prior to the global desiccation of Africa in the Miocene. Further expansion of the genus northward was probably stalled until climatic changes in the late Miocene brought about the gradual replacement of a subtropical woodland savanna with the arid landscape that gave rise to the Sahara. Aridification of the northern quarter of the continent provided the ecological conditions for fostering the expansion of Androcymbium along the Mediterranean fringe (probably east to west) and its introduction into the Canary Islands. Unlike their South African congeners, the northern species have experienced expansions, fragmentations, and local extinctions in response to the severe climatic shifts in this area during the Pliocene-Pleistocene. According to our divergence time estimates, the arid track may have already existed as a continuous area connecting southern and northern Africa in the late Miocene.

Evolution of Endemic Sideritis (Lamiaceae) in Macaronesia: Insights from a Chloroplast DNA Restriction Site Analysis

Abstract Sideritis L. subgenus Marrubiastrum (Lamiaceae) comprises 24 species of Macaronesian endemic perennials. The constituent taxa encompass a wide array of life forms that have exploited all ecological zones present in the Macaronesian archipelagos of Madeira and the Canary Islands. Though recently revised, an explicit phylogeny of the subgenus is still lacking. This group is especially intriguing because it exhibits the largest aneuploid series ever reported in oceanic island plants. The present study uses a chloroplast DNA restriction site analysis to elucidate the pattern of evolution within and among the islands. The insular taxa form a strongly supported monophyletic group, indicating a single colonization of Macaronesia. Monophyly of the sections is not supported. Integrating geographical and ecological distribution with the cpDNA phylogeny reveals a pattern of diversification within the islands consistent with adaptive radiation. Most other Macaronesian plant groups studied thus far have diver...

Incongruence between chloroplast and species phylogenies in Eucalyptus subgenus Monocalyptus (Myrtaceae)

Seventy-eight polymorphic cpDNA (chloroplast DNA) characters were found in 13 closely related taxa from Eucalyptus series Amygdalinae (subgenus Monocalyptus) and seven potential outgroup taxa. The strict consensus of six cladograms generated from cpDNA data confirmed monophyly of Monocalyptus. However, cpDNA phylogeny within Monocalyptus was incongruent with taxonomic classification, being more related to geography, even when accessions were from divergent series. Monocalyptus cpDNA formed two major clades. On the island of Tasmania cpDNA was restricted to a single clade, exhibited very little variation, and was phylogenetically related to cpDNA found in central and western Victoria. In contrast, cpDNA of mainland monocalypt taxa was more variable, even within the Amygdalinae. Four out of six Tasmanian Amygdalinae species were polymorphic. The difference between cpDNA of replicates was often greater than differences between species from different series. The low level of cpDNA variation and extensive morphological intergradation between the Tasmanian endemics suggest recent speciation. However, the transfer of cpDNA through hybridization between lineages is the most likely explanation for the observed sharing of cpDNA across series. This study highlights that the geographical pattern to cpDNA variation in Eucalyptus may be an important source of information on past plant distributions in Australia.

Reconstructing Hybrid Speciation Using Sequences of Low Copy Nuclear Genes: Hybrid Origins of Five Paeonia Species Based on Adh Gene Phylogenies

Alcohol dehydrogenase (Adh) genes were amplified with PCR, cloned, and sequenced for five putative hybrid species of the genus Paeonia (Paeoniaceae): P sinjiangensis, P arietina, P humilis, P officinalis, and P parnassica. Two to three diverged types of sequences were found at each of the AdhiA and Adh2 loci for each species. Parsimony analyses of these sequences together with previously obtained Adh sequences of non-hybrid species of Paeonia indicated that two major types of Adh sequences of each of the five species were phylogenetically separated on the AdhiA and Adh2 trees. Along with nrDNA and cpDNA phylogenies, it is most parsimonious to hypothesize that these diverged sequences represent alleles derived from different parents through hybrid speciation. The approach of separating parental alleles of a nuclear gene in a hybrid genome and reconstructing phylogenies of these alleles offers a solution to the long standing methodological difficulty of reconstructing reticulate evolution. Phylogenies of plant nuclear genes, however, may be con- founded by dynamic evolutionary processes of the gene families, such as gene duplication/ deletion, gene conversion, and recombination. Thus, a strong hypothesis of hybrid speciation should rely on the congruence of multiple gene phylogenies as well as the congruence between gene phylogenies and other lines of evidence.

Molecular Phylogeny of Artemisia Section Tridentatae (Asteraceae) Based on Chloroplast DNA Restriction Site Variation

Chloroplast DNA restriction site variation was used to examine phylogenetic relationships in Artemisia sect. Tridentatae, a complex of eleven species of woody shrubs, which are dominant components of sagebrush communities of western North America. Twenty-seven endonucleases were utilized to identify 82 variable site mutations, 27 of which were phylogenetically informative. The resulting cpDNA phylogeny indicates that sect. Tridentatae is monophyletic, with the exception of A. palmeri and A. bigelovii, two historically anomolous species. A sister-group relationship between A. palmeri and species of subg. Artemisia supports the exclusion of A. palmeri from sect. Tridentatae (subg. Seriphidium), and its inclusion within subg. Artemisia. Artemisia bigelovii, a species with heterogamous capitula, is nested within the Tridentata clade, supporting its inclusion within the section. Introgression and subsequent chloroplast capture of the Tridentatae genome by two unrelated species, A. californica and A. fihlifolia, may explain the unexpected placement of these two species in the Tridentata clade. Low cpDNA sequence divergence provides only limited resolution of phylogenetic relationships within sect. Tridentatae, indicative of a recently differentiated and/or hybridizing polymorphic species complex. In addition, the cpDNA data provide only equivocal evidence for either of two competing hypotheses regarding the origin and phylogenetic relationship of sect. Tridentatae within Artemisia s.l.

Intraspecific Phylogeny Analysis Using ITS Sequences: Insights from Studies of the Streptanthus glandulosus Complex (Cruciferae)

Within many lineages diversity of the internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes has proven comparable to that of restriction sites of chloroplast DNA (cpDNA). Al- though cpDNA polymorphism has proven useful in many phylogenetic studies at the intraspecific level, the utility of ITS sequences in this application has been subjected only to limited testing. The Streptanthus glan- dulosus complex is an ideal candidate for this evaluation, given the substantial variation in cpDNA restriction site and enzyme electrophoretic markers present among populations. ITS sequences were obtained for 31 populations within the complex; phylogenetic patterns derived from these data were compared to a cpDNA phylogeny based on restriction site data from a previous study. No population exhibited the same ITS se- quence, and average divergence among populations was 2.57%. The ITS strict consensus tree bears clades that are geographically distinct, but lacking in internal resolution; we suspect that some combination of gene flow, lineage sorting, and recombination has led to low resolution within these major clades. The ITS tree shares many features with the cpDNA tree, but the two also display substantial incongruities, including one that may have arisen via cytoplasmic introgression. Greater consistency is exhibited by the cpDNA tree, most likely due to the haploid and non-recombining nature of the chloroplast genome. Combining the ITS and cpDNA data results in a more highly resolved tree than those from either of the separate analyses. Despite the pitfalls of using a diploid, recombining data source like ITS at the intraspecific level, potential benefits include tracking of maternal and paternal lineages as well as insight into patterns and levels of gene flow among populations. Furthermore, the joint use of ITS and cpDNA markers facilitates independent assessment of intraspecific phylogenetic hypotheses and can expose cases in which introgression or phylogenetic sorting has caused incongruencies among haplotype trees.

Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)

The coding region of the mat K gene and two intergenic spacers, psb A-trn H and trn L(UAA)-trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psb A-trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped-strand mispairing, provided relatively reliable phylogenetic information. The mat K coding region, evolving more rapidly than the trnL-trn F spacer and more slowly than the psb A-trn H spacer, produced the best resolved phylogenetic tree. The mat K phylogeny was compared with the phylogeny obtained from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent. The Eurasian and western North American disjunct distribution of the genus may have resulted from interrruption of the continuous distribution of ancestral populations of extant peony species across the Bering land bridge during the Miocene. Pleistocene glaciation may have played an important role in triggering extensive reticulate evolution within section Paeonia and shifting distributional ranges of both parental and hybrid species.

Evolution of the Eastern Asian and Eastern North American Disjunct Genus Symplocarpus (Araceae): Insights from Chloroplast DNA Restriction Site Data

Chloroplast DNA (cpDNA) variation was surveyed with 20 restriction endonucleases for the eastern Asian and eastern North American disjunct genus Symplocarpus (Araceae). The cpDNA phylogeny reveals a sister group relationship between S. foetidus from eastern North America and S. renifolius from eastern Asia. The cpDNA divergence between the two intercontinental sister species is 0.61%, which suggests an estimated divergence time of 6.1 million years ago during the late Miocene. The Bering land bridge hypothesis is compatible with the estimated time of divergence for the migration of Symplocarpus between eastern Asia and North America. Furthermore, a single origin of the exothermic spadices in Symplocarpus is suggested by the phylogeny. The cpDNA data also provide independent support for the recognition of three species within the genus.

Evolution of the Eastern Asian and Eastern North American disjunct genus Symplocarpus (Araceae): insights from chloroplast DNA restriction site data

Chloroplast DNA (cpDNA) variation was surveyed with 20 restriction endonucleases for the eastern Asian and eastern North American disjunct genus Symplocarpus (Araceae). The cpDNA phylogeny reveals a sister group relationship between S. foetidus from eastern North America and S. renifolius from eastern Asia. The cpDNA divergence between the two intercontinental sister species is 0.61%, which suggests an estimated divergence time of 6.1 million years ago during the late Miocene. The Bering land bridge hypothesis is compatible with the estimated time of divergence for the migration of Symplocarpus between eastern Asia and North America. Furthermore, a single origin of the exothermic spadices in Symplocarpus is suggested by the phylogeny. The cpDNA data also provide independent support for the recognition of three species within the genus.

Chloroplast DNA study of the genera Ambrosia s.l. and Hymenoclea (Asteraceae): Systematic implications

The relationship ofAmbrosia (ragweed) andFranseria has long been debated. Their treatment as separate genera has been repeatedly challenged. In this study, chloroplast DNA restriction site variation was examined for species from bothAmbrosia andFranseria as well as taxa from the closely related genusHymenoclea. The chloroplast genomes of members of these three genera were examined using 21 restriction endonucleases and the restriction mutations were used to construct phylogenetic trees. Wagner and Dollo parsimony as well as weighted parsimony were employed to compare the different phylogenies. The results support a close relationship betweenAmbrosia andFranseria, but indicate that the two groups are well separated. Compared toFranseria, Ambrosia is a much more strongly supported group, and the results indicate thatHymenoclea is closer toFranseria than toAmbrosia. The cpDNA phylogeny was used as a framework to examine evolutionary trends in morphology and secondary chemistry.

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.