Origin and Phylogeny of Metazoans as Reconstructed with rDNA Sequences
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Summary Persson, C.: Phylogenetic relationships in Polygalaceae based on plastid DNA sequences from the trnL‐F region. ‐ Taxon 50: 763–779. 2001. ‐ ISSN 0040‐0262. Seventy‐three plastid DNA sequences from the trnL‐F region were used to infer phylogenetic relationships among Polygalaceae . The analysis indicates that Xanthophyllum is the sister group to the remainder of genera in Polygalaceae . Monophyly of tribes Polygaleae and Carpolobieae is corroborated, whereas monophyly of Moutabeae could not be confirmed. Although intergeneric relationships within Polygaleae are poorly resolved, most traditional genera are corroborated as monophyletic. However, Polygala and Bredemeyera s.l. form two exceptions and are grossly polyphyletic. Acanthocladus and Badiera (incl. Hebecarpa) , taxa often assigned to Polygala , are more closely related to Bredemeyera s.str. than to other Polygala . Likewise, Bredemeyera s.l. is broadly polyphyletic since Comesperma and Bredemeyera colletioides (sect. Hualania) have their closest relatives among other genera. Furthermore, Hualania is also polyphyletic since Bredemeyera microphylla appears as the sister to the Hebecarpa‐Badiera clade. Unlike a previous morphological analysis, Monnina is strongly supported as monophyletic by trnL‐F data, but internal relationships are partly unresolved. Species of Polygala sensu Chodat have a tendency to group by geographical distribution rather than after traditional sectional affiliation. Thus, although resolution is poor, it is suspected that several sections of Polygala are not monophyletic and need to be recircumscribed.
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Monophyly, paraphyly and polyphyly are three pivotal terminologies for reconstructing natural system, but their definitions have not been generally accepted as yet. Advantages and drawbacks of every set of definitions of monophyly, paraphyly and polyphyly are discussed with the help of set theory and graph theory of discrete mathematics and transformed cladism of systematic biology. The reason that previous paraphyly couldn't be differentiated from polyphyly is first clarified based on set theory and graph theory. In addition, every species could be monophyletic based on its unique direct origin which could not be replaced by all other origins, based on comparison of the relation between individuals of the same species with the relation between this species and any other species, or based on its unique evolutionary history. As a result, their exact definitions should ensure that any species could be monophyletic, and ensure that they three are quite distinct from one another.
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A phylogeny for Agelaius blackbirds was constructed using sequence data from an 890 base-pair (bp) region of the mitochondrial cytochrome-b gene in nine species of Agelaius and a single species from all but 1 of the 28 described blackbird genera and subgenera. The genus was found to be polyphyletic with the South American members of Agelaius more closely related to other South American blackbird genera. Application of bootstrap and jackknife manipulations supports this conclusion. That this relatively well-known genus is polyphyletic represents a warning to those attempting to construct phylogenies without first demonstrating monophyly of the ingroup. The conclusion that Agelaius is polyphyletic necessitates (1) the reinterpretation of previous studies that assumed monophyly and (2) the initiation of a variety of new comparative behavioral and ecological studies suggested by this finding.
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The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric-conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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Recent studies have transferred several species previously attributed to the fern genus Oenotrichia to other genera, and even out of the Dennstaedtiaceae to other families. However, the relationship of the type species, O. maxima from New Caledonia, has not previously been investigated using DNA sequences. With phylogenetic analyses of chloroplast DNA sequences, we verify the placement of Oenotrichia within the Dennstaedtiaceae. Moreover, O. maxima actually nests along with Leptolepia in a clade of Dennstaedtia. Dennstaedtia itself is non-monophyletic, with a second clade being more closely related to Microlepia. We outline what is required to resolve the generic taxonomy of this group. We also find that samples attributed to Saccoloma are polyphyletic, with some falling inside the Dennstaedtiaceae and others outside.
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Previously proposed definitions of the terms monophyletic, paraphyletic, and polyphyletic are examined. The definitions provided by Hennig and Ashlock are internally flawed because they do not prevent a single group from being simultaneously paraphyletic and polyphyletic. The definitions provided by Nelson are internally consistent but have undesirable consequences by either precluding the existence of monotypic genera or allowing coordinate taxa to both correspond and not correspond to monophyletic groups. The definitions provided by Farris are internally consistent and lack the drawbacks of Nelson's views; it is suggested that they are successful because they identify necessary relationships between the concepts of polyphyly and parallelism and the concepts of paraphyly and character reversal.
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The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ~23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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DNA Barcoding
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