A CHLOROPLAST-DNA PHYLOGENY OF THE WILD PERENNIAL RELATIVES OF SOYBEAN (GLYCINE SUBGENUS GLYCINE): CONGRUENCE WITH MORPHOLOGICAL AND CROSSING GROUPS

Hypotheses of evolutionary relationships among the Australian wild perennial relatives of soybean (Glycine subgenus Glycine) are based largely on patterns of meiotic pairing in intra- and interspecific experimental hybrids. This evidence has indicated a number of genome groupings within the subgenus but has not resolved most phylogenetic relationships. Restriction-endonuclease site variation of chloroplast DNA (cpDNA) within the perennial subgenus is reported here, representing a sampling of approximately 3% of the approximately 150-kilobase plastome. Seven hundred twenty-one unique restriction sites were compared within Glycine using 29 restriction endonucleases; 157 sites varied within the genus. Distance and parsimony methods using these data yielded congruent results, recognizing the existence of three major groups within subgenus Glycine: the species-rich and geographically diverse A clade consisting of G. canescens and related taxa; the B clade, which includes the stoloniferous species; and the C group, containing two species with distinctive curved pods. These results are in general agreement with hypotheses based on genome analysis; inconsistencies involve the inclusion of genetically divergent taxa such as G. falcata in well-supported plastome clades comprised of otherwise interfertile species. Such findings are not unexpected if crossing barriers are considered to be unique features of such anomalous species, paralleling their often numerous morphological and cpDNA autapomorphies. Consideration of cpDNA divergence within the three major clades of subgenus Glycine indicates that the rate of plastome evolution is uncoupled from rates of morphological or ecological diversification.     

Origins of Allium ampeloprasum horticultural groups and a molecular phylogeny of the section Allium (Allium: Alliaceae)

The subgenus Allium section Allium includes economically important species, such as garlic and leek, as well as other polyploid minor crops. Phylogenetic studies within this section, with a focus on horticultural groups within A. ampeloprasum, were performed on 31 accessions of 17 species using the nuclear ribosomal DNA internal transcribed spacer (ITS) region and the chloroplast trnL-F and trnD-T regions. The results confirmed the monophyly of section Allium. Four main clades were identified on all ITS analyses but the relationships among those and the remaining species studied within section Allium remained unresolved. Trees based on cpDNA recovered two major clades and a topology only partly congruent with that of the ITS tree. Intra-individual polymorphism of the ITS region proved useful in tracking putative parent species of polyploid taxa. The allopolyploid origin of great headed garlic (GHG), A. iranicum and A. polyanthum was confirmed. No signs of hybridization in leek or kurrat were detected but possible introgression events were identified in pearl onion and bulbous leek. Although GHG is often used as a garlic substitute, molecular analysis revealed only a distant relationship with garlic. We also clarified the previous incorrect classification of cultivated forms within A. ampeloprasum, by showing that leek, kurrat, pearl onion, and bulbous leek should be considered separately from GHG.     

A molecular phylogeny of Anopheles annulipes (Diptera: Culicidae) sensu lato: the most species-rich anopheline complex

The Australasian Annulipes Complex is the most species-rich among Anopheles mosquitoes, with at least 15 sibling species suspected. Members of this complex are the most likely vectors of malaria in the past in southern Australia and are involved in the spread of myxomatosis among rabbits. In this, the first comprehensive molecular study of the Annulipes Complex, 23 ITS2 rDNA variants were detected from collections throughout Australia and Papua New Guinea, including diagnostic variants for the previously identified An. annulipes species A-G. Specimens of each ITS2 variant were sequenced for portions of the mitochondrial COI, COII and nuclear EF-1alpha genes. Partitioned Bayesian and Maximum Parsimony analyses confirmed the monophyly of the Annulipes Complex and revealed at least 17 clades that we designate species A-Q. These species belong to two major clades, one in the north and one mainly in the south, suggesting that climate was a driver of species radiation. We found that 65% (11) of the 17 sibling species recorded here had unique COI sequences, suggesting that DNA barcoding will be useful for diagnosing species within the Annulipes Complex. A comparison of the taxa revealed morphological characters that may be diagnostic for some species. Our results substantially increase the size of the subgenus Cellia in Australasia, and will assist species-level studies of the Annulipes Complex.     

Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae)

We investigated the phylogenetic relationships and estimated the history of species diversification and biogeography in the bufonid genus Ansonia from Southeast Asia, a unique organism with tadpoles adapted to life in strong currents chiefly in montane regions and also in lowland rainforests. We estimated phylogenetic relationships among 32 named and unnamed taxa using 2461 bp sequences of the mitochondrial 12S rRNA, tRNA^val, and 16S rRNA genes with equally-weighted parsimony, maximum likelihood, and Bayesian methods of inference. Monophyletic clades of Southeast Asian members of the genus Ansonia are well-supported, allowing for the interpretation of general biogeographic conclusions. The genus is divided into two major clades. One of these contains two reciprocally monophyletic subclades, one from the Malay Peninsula and Thailand and the other from Borneo. The other major clade primarily consists of Bornean taxa but also includes a monophyletic group of two Philippine species and a single peninsular Malaysian species. We estimated absolute divergence times using Bayesian methods with external calibration points to reconstruct the relative timing of faunal exchange between the major landmasses of Southeast Asia.     

Robertsonian metacentrics of the house mouse lose telomeric sequences but retain some minor satellite DNA in the pericentromeric area

A combination of cytogenetic and molecular biology techniques were used to study the molecular composition and organisation of the pericentromeric regions of house mouse metacentric chromosomes, the products of Robertsonian (Rb) translocations between telocentrics. Regardless of whether mitotic or meiotic preparations were used, in situ hybridisation failed to reveal pericentromeric telomeric sequences on any of the Rb chromosomes, while all metacentrics retained detectable, although reduced (average 50 kb), amounts of minor satellite DNA in the vicinity of their centromeres. These results were supported by slot blot hybridisation which indicated that mice with 2n=22 Rb chromosomes have 65% of telomeric sequences (which are allocated to the distal telomeres of both Rb and telocentric chromosomes and to the proximal telomeres of telocentrics) and 15% the amount of minor satellite, compared with mice with 2n=40 all-telocentric chromosomes. Pulsed field gel electrophoresis and Southern analysis of DNA from Rb mice showed that the size of the telomeric arrays is similar to that of mice with all-telocentric chromosomes and that the minor satellite sequences were hybridising to larger fragments incorporating major satellite DNA. Since the telomeric sequences are closer to the physical end of the chromosome than the minor satellite sequences, the absence of telomeric sequences and the reduced amount of minor satellite sequences at the pericentromeric region of the Rb metacentrics suggest that the breakpoints for the Rb translocation occur very close to the minor satellite-major satellite border. Moreover, it is likely that the minor satellite is required for centromeric function, 50–67 kb being enough DNA to organise one centromere with a functionally active kinetochore.     

Polytene chromosomes of an archipelagic subgenus, <Emphasis Type="Italic">Inseliellum</Emphasis> (Diptera: Simuliidae)

The black fly subgenus Inseliellum is present on a series of archipelagos in the South Pacific. In this study, larval polytene chromosome maps of six Inseliellum species are presented. Chromosomal relationships among taxa were determined through shared fixed inversions or chromosomal landmark positioning. Three fixed inversions (IL-2, IIS-1, and IIIS-1) were shared among species, as was the position of the nucleolar organizer (NO) (IL or IIL). Comparisons to two previously studied species of Inseliellum are included to produce a cytological transformation series among eight taxa. The NO position defines two clades in the phylogeny of Inseliellum, herein named the NO-IL and NO-IIL clades. The utility of this cytological data set is discussed.     

Nuclear Ribosomal ITS Functional Paralogs Resolve the Phylogenetic Relationships of a Late-Miocene Radiation Cycad Cycas (Cycadaceae)

Cycas is the most widespread and diverse genus among the ancient cycads, but the extant species could be the product of late Miocene rapid radiations. Taxonomic treatments to date for this genus are quite controversial, which makes it difficult to elucidate its evolutionary history. We cloned 161 genomic ITS sequences from 31 species representing all sections of Cycas. The divergent ITS paralogs were examined within each species and identified as putative pseudogenes, recombinants and functional paralogs. Functional paralogs were used to reconstruct phylogenetic relationships with pseudogene sequences as molecular outgroups, since an unambiguous ITS sequence alignment with their closest relatives, the Zamiaceae, is unachievable. A fully resolved and highly supported tree topology was obtained at the section level, with two major clades including six minor clades. The results fully supported the classification scheme proposed by Hill (2004) at the section level, with the minor clades representing his six sections. The two major clades could be recognised as two subgenera. The obtained pattern of phylogenetic relationships, combined with the different seed dispersal capabilities and paleogeography, allowed us to propose a late Miocene rapid radiation of Cycas that might have been promoted by vicariant events associated with the complex topography and orogeny of South China and adjacent regions. In contrast, transoceanic dispersals might have played an important role in the rapid diversification of sect. Cycas, whose members have evolved a spongy layer in their seeds aiding water dispersals.     

A comprehensive molecular phylogeny of the starlings (Aves: Sturnidae) and mockingbirds (Aves: Mimidae): congruent mtDNA and nuclear trees for a cosmopolitan avian radiation

We generated a comprehensive phylogeny for the avian families Sturnidae (starlings, mynas, Rhabdornis, oxpeckers, and allies) and Mimidae (mockingbirds, thrashers, and allies) to explore patterns of morphological and behavioral diversification. Reconstructions were based on mitochondrial DNA sequences from five coding genes (4108 bp), and nuclear intron sequences from four loci (2974 bp), for most taxa, supplemented with NDII gene sequences (1041 bp) derived from museum skin specimens from additional taxa; together the 117 sampled taxa comprise 78% of the 151 species in these families and include representatives of all currently or recently recognized genera. Phylogenetic analyses consistently identified nine major clades. The basal lineage is comprised of the two Buphagus oxpeckers, which are presently confined to Africa where they are obligately associated with large mammals. Some species in nearly all of the other major clades also feed on or around large vertebrates, and this association may be an ancestral trait that fostered the world-wide dispersal of this group. The remaining taxa divide into sister clades representing the New-World Mimidae and Old-World Sturnidae. The Mimidae are divided into two subclades, a group of Central American and West Indian catbirds and thrashers, and a pan-American clade of mockingbirds and thrashers. The Sturnidae are subdivided into six clades. The Phillipine endemic Rhabdornis are the sister lineage to a larger and substantially more recent radiation of South Asian and Pacific island starlings and mynas. A clade of largely migratory or nomadic Eurasian starlings (within which the basal lineage is the model taxon Sturnus vulgaris) is allied to three groups of largely African species. These reconstructions confirm that Buphagus should not be included in the Sturnidae, and identify many genera that are not monophyletic. They also highlight the substantial diversity among the major Sturnidae subclades in rates of species accumulation, morphological differentiation, and behavioral variation.     

Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences

Phylogenetic relationships were examined within the southern beech family Nothofagaceae using 22 species representing the four currently recognized subgenera and related outgroups. Nuclear ribosomal DNA sequences encoding the 5.8s rRNA and two flanking internal transcribed spacers (ITS) provided 95 phylogenetically informative nucleotide sites from a single alignment of ~588 bases per species. Parsimony analysis of this variation produced two equally parsimonious trees supporting four monophyletic groups, which correspond to groups designated by pollen type. These topologies were compared to trees from reanalyses of previously reported rbcL sequences and a modified morphological data set. Results from parsimony analysis of the three data sets were highly congruent, with topological differences restricted to the placement of a few terminal taxa. Combined analysis of molecular and morphological data produced six equally parsimonious trees. The consensus of these trees suggests two basal clades within Nothofagus. Within the larger of the two clades, tropical Nothofagus (subgenus Brassospora) of New Guinea and New Caledonia are strongly supported as sister to cool-temperate species of South America (subgenus Nothofagus). Most of the morphological apomorphies of the cupule, fruit, and pollen of Nothofagus are distributed within this larger clade. An area cladogram based on the consensus of combined data supports three trans-Antarctic relationships, two within pollen groups and one between pollen groups. Fossil data support continuous ancestral distributions for all four pollen groups prior to continental drift; therefore, vicariance adequately explains two of these disjunctions. Extinction of trans-Antarctic sister taxa within formerly widespread pollen groups explains the third disjunction; this results in a biogeographic pattern indicative of phylogenetic relationship not vicariance. For the biogeographically informative vicariant clades, area relationships based on total evidence support the recently advanced hypothesis that New Zealand and Australia share a unique common ancestry. Contrary to previous thought, the distribution of extant Nothofagus is informative on the area relationships of the Southern Hemisphere, once precise phylogenetic relationships are placed in the context of fossil data.     

The telocentric tandem repeat at the p-arm is not conserved in Mus musculus subspecies

Mouse chromosomes, with the exception of the Y chromosome, are telocentric. The telomere at the p-arm is separated from the centromere by the tL1 sequence and TLC tandem repeats. A previous report showed that the TLC array was also conserved in other strains of the subgenus Mus. These results suggest that the TLC arrays promote the stable evolutionary maintenance of a telocentric karyotype in the subgenus Mus. In this study, we investigated the degree of conservation of TLC arrays among a variety of wild-derived inbred strains, all of which are descendants of wild mice captured in several areas of the world. Genomic PCR analysis indicates that the sequential order of telomere-tL1 is highly conserved in all strains, whereas tL1-TLC is not. Next, Southern blot analysis of DNAs isolated from a panel of mouse subspecies showed both Mus musculus domesticus and Mus musculus castaneus subspecies possess TLC arrays. Unexpectedly, this repeat appears to be lost in almost all Mus musculus musculus and Mus musculus molossinus subspecies, which show a clear geographic divide. These results indicate that either other unknown sequences were replaced by the TLC repeat or almost all M. m. musculus and M. m. molossinus subspecies do not have any sequence between the telomere and minor satellites. Our observation suggests that the TLC array might be evolutionarily unstable and not essential for murine chromosomal conformation. This is the first example of the subspecies-specific large genome alterations in mice.     

Molecular phylogeny and biogeography of Malagasy frogs of the genus Gephyromantis

The genus Gephyromantis is a clade within the Malagasy-Comoroan family Mantellidae composed of rainforest frogs that live and breed to varying degrees independently from water. Based on DNA sequences of five mitochondrial and five nuclear genes we inferred the phylogeny of these frogs with full taxon coverage at the species level. Our preferred consensus tree from a partitioned Bayesian analysis of 5843 base pairs of 51 nominal and candidate species supports various major clades within the genus although the basal relationships among these remain unresolved. The data provide strong evidence for the monophyly of the subgenera Gephyromantis (after exclusion of Gephyromantis klemmeri), Laurentomantis, Vatomantis, and Phylacomantis. Species assigned to the subgenus Duboimantis belong to two strongly supported clades of uncertain relationships. G. klemmeri, previously in the subgenus Gephyromantis, was placed with high support sister to the Laurentomantis clade, and the Laurentomantis + G. klemmeri clade was sister to Vatomantis. A reconstruction of ancestral distribution areas indicates a diversification of several subgenera in the northern biogeographic regions of Madagascar and the dispersal out of northern Madagascar for several clades.     

Geographical versus ecological isolation of closely related black flies (Diptera: Simuliidae) inferred from phylogeny, geography, and ecology

To investigate patterns of geographical and ecological separation among morphologically similar, closely related species of black flies, we integrated ecological, geographical, and phylogenetic information, based on multiple gene sequences, for 12 species in the subgenus Gomphostilbia in Thailand. Molecular characters supported the monophyly of the Simulium ceylonicum species group, but not of the Simulium batoense species group, suggesting that revisionary work is needed for the latter. Both ecological and geographical isolation of similar taxa were revealed. Stream velocity and altitude were among the principal ecological factors differing between closely related species. Most closely related species in the subgenus Gomphostilbia overlap geographically, suggesting the possibility of sympatric speciation driven by ecological divergence. Geographical isolation via dispersal also might have contributed to species divergence, while Pleistocene climate changes possibly influenced population genetic structure, demographic history, and speciation of some members of the subgenus.     

四照花亚属的nrDNA ITS致同进化不完全

四照花亚属(Cornus subg.Syncarpea)隶属于山茱萸科山茱萸属(Cornus),我国该亚属共有5种8亚种。为探讨四照花亚属nrDNA ITS序列的致同进化不完全现象及假基因产生的可能原因,分析了该亚属4种(每种1~2个居群)共21个个体的nrDNA ITS序列。结果表明,这些类群的nrDNA ITS存在多态性,通过分析这些nrDNA ITS克隆序列的G+C含量、5.8S保守基序和二级结构最小自由能,推测其可能存在假基因。系统发育研究结果显示所有nrDNA ITS序列分成5个分支,同一个体的不同拷贝被分别置于两个甚至多个分支中,且不同分支显示了不同种间关系。四照花亚属物种个体内部存在nrDNA ITS不完全致同进化,可能归咎于不完全的世系分选(incomplete lineage sorting)、种间杂交或多倍化等进化事件,从而导致基因组内nrITS区序列出现多态性,同时也导致难以通过外部形态来划分亚属内种间界限。     

Phylogeny of Rubus (rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences

We used nuclear ribosomal DNA internal transcribed spacer region (ITS 1 - 5.8S - ITS 2; ITS) sequences to generate the first phylogeny of Rubus based on a large, molecular data set. We sampled 57 taxa including 20 species of subgenus Rubus (blackberries), one to seven species from each of the remaining 11 subgenera, and the monotypic and closely related Dalibarda. In Rubus, ITS sequences are most informative among subgenera, and variability is low between closely related species. Parsimony analysis indicates that Rubus plus Dalibarda form a strongly supported clade, and D. repens may nest within Rubus. Of the subgenera with more than one species sampled, only subgenus Orobatus appears monophyletic. Three large clades are strongly supported: one contains all sampled species of nine of the 12 subgenera; another includes extreme Southern Hemisphere species of subgenera Comaropsis, Dalibarda, and Lampobatus; and a third clade consists of subgenus Rubus plus R. alpinus of subgenus Lampobatus. Rubus ursinus appears to be a hybrid between a close relative of R. macraei (subgenus Idaeobatus, raspberries) and an unidentified subgenus Rubus species. ITS sequences are generally consistent with biogeography and ploidy, but traditionally important morphological characters, such as stem armature and leaf type, appear to have limited phylogenetic value in Rubus.     

Giants and dwarfs: molecular phylogenies reveal multiple origins of annual spurges within Euphorbia subg. Esula

Euphorbia (Euphorbiaceae) comprises over 2150 species and is thus the second-largest genus of flowering plants. In Europe, it is represented by more than 100 species with highest diversity in the Mediterranean area; the majority of taxa belong to subgenus Esula Pers., including about 500 taxa. The few available phylogenetic studies yielded contrasting results regarding the monophyly of subg. Esula, and the phylogenetic relationships among its constituents remain poorly understood. We have sampled DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and the plastid trnT-trnF region from about 100, predominantly European taxa of subg. Esula in order to infer its phylogenetic history. The plastid data support monophyly of subg. Esula whereas the ITS phylogeny, which is generally less resolved, is indecisive in this respect. Although some major clades have partly incongruent positions in the ITS and plastid phylogenies, the taxonomic content of the major terminal clades is congruent in both trees. As traditional sectional delimitations are largely not corroborated, an improved classification is proposed. Character state reconstruction illustrates that the annual life form developed independently several times in different clades of subgenus Esula from perennial ancestors, and that several morphological traits used in previous classifications of Euphorbia developed in parallel in different lineages.     

Phylogenetic analysis of Allium subg. Melanocrommyum infers cryptic species and demands a new sectional classification

Allium subgenus Melanocrommyum (Alliaceae) from Eurasia comprises about 150 mostly diploid species adapted to arid conditions. The group is taxonomically complicated with different and contradictory taxonomic treatments, and was thought to include a considerable number of hybrid species, as the taxa show an admixture of assumed morphological key characters. We studied the phylogeny of the subgenus, covering all existing taxonomic groups and their entire geographic distribution. We analyzed sequences of the nuclear rDNA internal transcribed spacer region (ITS) for multiple individuals of more than 100 species. Phylogenetic analyses of cloned and directly sequenced PCR products confirmed the monophyly of the subgenus, while most sections were either para- or polyphyletic. The splits of the large sections are supported by differences in the anatomy of flower nectaries. ITS data (i) demand a new treatment at sectional level, (ii) do not support the hypotheses of frequent gene flow among species, (iii) indicate that multiple rapid radiations occurred within different monophyletic groups of the subgenus, and (iv) detected separately evolving lineages within three morphologically clearly defined species (cryptic species). In two cases these lineages were close relatives, while in Allium darwasicum they fall in quite different clades in the phylogenetic tree. Fingerprint markers show that this result is not due to ongoing introgression of rDNA (ITS capture) but that genome-wide differences between both lineages exist. Thus, we report one of the rare cases in plants where morphologically indistinguishable diploid species occurring in mixed populations are non-sister cryptic species.     

Molecular phylogeny of the genus Ceanothus (Rhamnaceae) using rbc L and ndh F sequences

 Intrageneric phylogeny among ten representative Ceanothus species was investigated using DNA sequences of the chloroplast encoded ndhF and rbcL genes. Parsimony analysis of the ndhF sequences identified two main clades corresponding to two subgenera Ceanothus and Cerastes. The phylogenetic results suggest that three monophyletic clades within the subgenus Ceanothus can be delimited on the basis of (1) evergreen or (2) deciduous leaves and (3) thorn presence within the evergreen clade. The estimated divergence time based on rbcL sequences suggests that the two subgenera diverged 18–39 million years ago whereas species within each subgenus diverged more recently. Taken together, the results support the division of Ceanothus into two monophyletic subgenera and are consistent with the postulated recent divergence of many species within each subgenus. Received: 25 September 1996/Accepted: 8 November 1996     

Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar

Phylogeographic analysis of the Coffea subgenus Coffea was performed using data on plastid DNA sequences and interpreted in relation to biogeographic data on African rain forest flora. Parsimony and Bayesian analyses of trnL-F, trnT-L and atpB-rbcL intergenic spacers from 24 African species revealed two main clades in the Coffea subgenus Coffea whose distribution overlaps in west equatorial Africa. Comparison of trnL-F sequences obtained from GenBank for 45 Coffea species from Cameroon, Madagascar, Grande Comore and the Mascarenes revealed low divergence between African and Madagascan species, suggesting a rapid and radial mode of speciation. A chronological history of the dispersal of the Coffea subgenus Coffea from its centre of origin in Lower Guinea is proposed. No relation was found between phylogenetic topology and the age of emergence of the volcanic islands that Coffea species have colonised in the Indian Ocean, suggesting dispersal from mainland Africa after the emergence of the youngest island, Grande Comore, 500,000 years ago. Additional sequences were obtained from GenBank for 24 species of other Rubiaceae genera, including the Rubia genus whose origin has been dated from the Upper Miocene. Estimates of substitution rates suggested that diversification in Coffea subgenus Coffea occurred about 460,000 years ago or as recently as the last 100,000 years, depending on the cpDNA region considered and calibration. The phylogenetic relationships based on plastid sequences confirmed biogeographic differentiation of coffee species, but they were not congruent with morphological and biochemical classifications, or with the capacity to grow in specific environments. Examples of convergent evolution in the main clades are given using characters of leaf size, caffeine content and reproductive mode.     

Delimitation of major lineages within Cuscuta subgenus Grammica (Convolvulaceae) using plastid and nuclear DNA sequences

Subgenus Grammica, the largest and most diverse group in the parasitic genus Cuscuta, includes 130 species distributed primarily throughout the New World, with Mexico as its center of diversity. To circumscribe the subgenus and assess the relationships among its major lineages, we conducted the first phylogenetic study of Grammica using plastid trnL-F and nrITS sequences from a wide taxonomic sampling covering its morphological, physiological, and geographical diversity. With the exception of one species belonging elsewhere, the subgenus was found to be monophyletic. The results further indicate the presence of 15 well-supported major clades within Grammica. Some of those lineages correspond partially to earlier taxonomic treatments, but the majority of groups are identified in this study for the first time. The backbone relationships among major clades, however, remain weakly supported or unresolved in some cases. The phylogenetic results indicate that the fruit dehiscence character is homoplastic, thus compromising its value as a major taxonomic and evolutionary feature. While several striking cases of long-distance dispersal are inferred, vicariance emerges as the most dominant biogeographical pattern for Cuscuta. Species placed within one of the clades with a predominantly South American distribution are hypothesized to have substantially altered plastid genomes.