Sequences of the ribosomal DNA internal transcribed spacer ITS region and the chloroplast DNA ycf 3 -trn S intergenic spacer were determined for samples representing Chilean and non-Chilean
Adn y sus bases of dating of western American Portulacaceae and their outgroups. The data refine previous inferences of generic circumscriptions and interrelations.
In particular, the data reveal that an earlier circumscription of Cistanthe Spach is polyphyletic and also reveal a North American clade comprising Claytonia L. Govaerts, and Montia L. Within the South American genera, two patterns emerge from the data: The patterns can be evaluated in terms of two phenomena: In the latter case, the gene tree patterns may distort the true timing and cladistic pattern of morphological and ecological diversification.
At present, the degree to which evidence for hybridization among the Chilean Portulacaceae will prove to be the rule or the exception is unclear. Nonetheless, spatial and temporal ecological patterns in Chile generally favor hybrid formation and persistence. The term "western American Portulacaceae" refers to a group of ca. Genera included in this group are Calandrinia Kunth, Calyptridium Nutt. Monophyly of the group remains unresolved and depends upon the relations of Phemeranthus Raf.
Species diversity of western American Portulacaceae is divided approximately equally between North America and South America, and much of it is concentrated in California and northern Chile.
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Notwithstanding several amphitropical disjunctions, most of the genera can be characterized as predominantly or completely North American or South American. However, the present data indicate that the largely South American Cistanthe sect. Amarantoides Reiche Carolin ex Hershk. The data suggest that the first two sections may be preferably classified in Calyptridium. However, this and other nomenclatural actions supported by the present analyses will be deferred pending revision of type material.
This work presents analysis of diversity of both ITS and ycf 3 -trn S spacer sequences. ITS, a typically base-pair sequence, is the most widely applied molecular marker in interspecific phylogenetic analyses in angiosperms Hershkovitz et al.
These sequences have been determined for ca. The present analyses incorporate of these samples, emphasizing the South American samples but including sufficient samples from "Adn y sus bases of dating" this region to provide appropriate phylogenetic reference.
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Superficial examination of some of the gene trees suggests evolutionary radiation too rapid to reconstruct cladistically. This would be a reasonable scenario given evidence of relatively recent, rapid, and catastrophic events that
Adn y sus bases of dating modern Chilean habitats Arroyo et al.
More detailed examination of the data in light of field observations, however, reveals evidence for an alternative scenario, in which the gene trees reflect not rapid diversification, but effective homo-genization of the marker sequences via gene flow, thus obscuring a pattern of ecological and morphological specialization that occurred over a longer historical period. This paper presents evidence for both of these models and consequent implications for diversification of the Chilean flora.
Table I provides collection data for the analyzed specimens. For field collections, above-ground parts variously, leaves, stems, flower buds, but not open flowers from one or a few identical individuals, free from insect or other apparent damage or infection, were washed thoroughly with tap water and dried in clean paper towels prior to silica preservation. Herbarium specimens were prepared at the same time. Floristic, monographic, and other taxonomic references see below and museum specimens were used to identify the materials.
For a variety of reasons, identification of many of the Chilean samples of Cistanthe was difficult and in many cases not successful: In fact, "Adn y sus bases of dating" noted in the discussion, the historical taxonomic difficulties and present inability to identify numerous specimens can be interpreted as an expectation of the diversification scenarios proposed.
Eighteen of the DNA samples are not associated with voucher specimens. Data associated with such specimens should be interpreted circumspectfully, but not dogmatically. Other DNA samples represent cultivated material that was accessioned but not vouchered. The unvouchered materials are principally those of the outgroup and North American taxa and are hence peripheral to the theme of the present work. In any case, all samples in the present work have some degree of documentation verifying their source and identity.
Furthermore, I have handled and determined nearly all of the plant materials personally and have performed all of the DNA extractions. To minimize the risk of cross contamination, especially by PCR products, extraction supplies and reagents, as well as PCR reagents, were maintained separately from those of post-PCR procedures. In several cases, DNA was extracted from the herbarium specimen corresponding to the previously-extracted silica specimen in order to confirm sequencing results Table I.
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The amplification and sequencing primers are listed in Table 2. Sequencing reactions were electrophoresed on a Gene Analyzer Applied Biosystems. Most specimens were sequenced in both directions. Exceptions were made for chromatograms that were especially clean in a single direction and which matched completely those of samples sequenced in both directions. Many sequences of Cistanthe samples were sequenced in essentially one direction, because an internal poly-T microsatellite-like repeat obliterated clarity of the downstream signal.
Phylogenetic analyses were performed using PAUP 4. Analyses were undertaken at the level of western American Portulacaceae and at the level of each of the South American clades.
ITS and ycf 3 -trn S sequences were analyzed separately and in combination. This analysis included representative sequences of the South American genera analyzed in greater detail at the infrageneric level and fewer representative sequences of the North American genera analyzed in greater detail elsewhere Hershkovitz, submitted ms.
This analysis provides an outgroup perspective relative to each of the primarily South American genera. Alignment was optimized manually. Unambiguous gaps were treated as independent characters. Up to four unordered states were permitted for superposed multistate gaps.
In general, when more than four gap states occurred, the alignment was ambiguous. Length variable regions that could not be aligned unambiguously were scored as unknown in all sequences or at least in the sequences that could not be unambiguously aligned.
Likewise, substitutions in length variable regions were scored as substitutions among the alignable sequences and as unknown in the unalignable sequences.
Unweighted parsimony and associated bootstrap replicates were applied with stepwise addition and tree bisection-reconnection. Bootstrap replicates held ten trees at each addition step with maxtrees at trees per replicate.
To visualize the total conflict in the combined data, split decomposition was performed using SplitsTree 2. Maximum likelihood and minimum evolution methods were considered unnecessary for the present analyses. At the infrageneric level, both the number of sequences and substitutions are very low, so that the variance in estimates of Markov model substitution parameters used in distance and maximum likelihood analysis would be very high e.
Likewise, the short branch lengths at the infrageneric level and separating several poorly resolved intergeneric nodes can mislead current implementations of Bayesian likelihood methods Suzuki et al. In "Adn y sus bases of dating," practical implementations of distance and likelihood analysis cannot take into account length variation characters, which provide a considerable proportion of the information, especially in the ycf 3 -trn S sequences.
Finally, statistical inconsistency that results from using inaccurate substitution models is expected
Adn y sus bases of dating when divergence is high, e. Maximum ITS divergence within the relevant taxa are on the order of: CistantheMontiopsis subg.
Montiopsis and Montiopsis subg. Ford ; and 0. Thus, net rates from a common ancestor are especially higher in the first taxon and especially low in the last. Divergences within taxa of the ycf 3 -trn S sequences are approximately in proportion to the number of variable sites relative to ITS. However, the aligned parsimony-informative sites of the ycf 3 -trn S sequences are not AT- but rather GC-rich: Relative to ITS, variation in the ycf 3 -trn S sequences is more frequently in length rather than base substitution.
At the intergeneric level, the ycf 3 -trn S spacer sequences include one region, ca.
Adn y sus bases of dating At the infrageneric level, the length differences tend to be more easily aligned than in ITS. The length differences commonly correspond to discrete direct repeats of three or more bases. The majority of the repeat variation observed involved two states or two common states and up to two additional rare states. A poly-T repeat varying in length from 11 to 17 bases occurs in the ycf 3 -trn S sequences of samples of Cistanthe sect.
Because of the high variability and difficulty determining the exact number of Ts in the longer repeats, this region was not included in the phylogenetic analysis.
Figures 1 and 2 show sample parsimony trees and parsimony bootstrap values for the ITS and ycf 3 -trn S data, respectively. F igure 3 shows the parsimony bootstrap consensus for the combined data. The ITS tree is considerably longer, indicating an overall higher rate of evolution. However, the ITS tree also has much lower consistency and retention indices than the ycf 3 -trn S data, i.
The ycf 3 -trn S data actually yield a larger number of branches with higher bootstrap proportions. The overall number of branches with higher bootstrap proportions is greater in the combined analysis than in either data set alone.
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However, individual conflicts between the two data sets can be discerned, as diagnosed by a reduction of particular bootstrap proportions in the combined analysis versus either of the separate analyses. Circumscriptions of supraspecific taxa. Monophyly of
Adn y sus bases of dating sensu Hershkovitz a is strongly refuted by the combined data.
CistantheLewisiaClaytoniaMontiopsisMontiopsis subg. MontiopsisCalandriniaand Parakeelya. The combined data show reasonably strong support for the existence of a "North American clade" comprising Lewisiopsis, LewisiaClaytoniaand Montia. Support for this clade is weak in the separate data analyses. The ycf 3 -trn S data support a sister relation between Lewisia and Lewisiopsisbut support is dramatically less in the combined analysis.
In both data sets, the branch length from the hypothetical North American clade ancestor to Lewisiopsis is much shorter than those of the other taxa. Combined data support is also high for a clade comprising Lenzia "Adn y sus bases of dating," Calyptridiumand Cistanthe sections Amarantoides and Philippiamra.
Again, support is weak in the separate data sets. The relations of Parakeelya conflict in the parsimony consensus trees of the ITS and ycf 3 -trn S sequences not shown.
In the former, the genus is sister to Calandriniaand in the latter to the North America clade. Oddly enough, neither position is supported in the majority-rule bootstrap consensus of either data set. Parsimony trees for separate and combined data analyses are presented in Figures 4 - 6. The spontaneous deamination of cytosine is a major source of transitions from C• G to T•A base pairs, which account for half of known.
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Leída el 15 de junio de These four scientists—Watson, Crick, Franklin, and Wilkins—codiscovered the double-helix structure of DNA, which formed the basis for.