scholarly journals HCPC: A New Parsimonious Clustering Method based on Hierarchical Characters for Morphological Phylogenetic Reconstruction

2021 ◽  
Author(s):  
Hongwei Feng ◽  
Meng Liu ◽  
Bei Wang ◽  
Jun Feng ◽  
Jian Han ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Simulated Annealing Algorithm ◽  
Phylogenetic Reconstruction ◽  
Poor Performance ◽  
Morphological Data ◽  
Clustering Method ◽  
Parsimonious Tree ◽  
Quantitative Basis ◽  
History Of ◽  
Two Stages

Abstract Background: Phylogenetic trees are reconstructed frequently to provide a better interpretation of the evolutionary history of species. However, most traditional methods ignore the hierarchical relationships among characters and neglect the inapplicable state that frequently exists in the morphological data, resulting in poor performance of the phylogenetic analysis.Results: In this study, we propose a phylogenetic clustering method based on hierarchical characters. Accordingly, we call our method Hierarchical Characters Parsimonious Clustering(HCPC). To combine prior phylogenetic knowledge and treat the inapplicable state more reasonably, two stages are proposed, i.e., Phylogenetic reconstruction and parsimonious tree search. During phylogenetic reconstruction, HCPC is able to infer the shared ancestral relationships among species. For the search of the parsimonious tree, we use a simulated annealing algorithm to heuristically search the phylogenetic tree based on the parsimony criterion. In addition, HCPC combines asymmetric binary relationships and character hierarchies to solve the problem of the ambiguity of the inapplicable state.Conclusion: The experimental results show that the proposed method provides better performance of phylogenetic analysis than existing methods and a scientific and quantitative basis for biologists to study species evolution.

scholarly journals Genome rearrangements and phylogeny reconstruction in Yersinia pestis

2017 ◽  
Author(s):  
Olga O Bochkareva ◽  
Natalia O Dranenko ◽  
Elena S Ocheredko ◽  
German M Kanevsky ◽  
Yaroslav N Lozinsky ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Phylogenetic Trees ◽  
Yersinia Pseudotuberculosis ◽  
Phylogenetic Reconstruction ◽  
Genome Rearrangements ◽  
Integrated Analysis ◽  
Nucleotide Substitutions ◽  
Large Deletions ◽  
History Of ◽  
Gain Loss

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed the evolutionary history of genome rearrangements in Y. pestis. We also reconciled phylogenetic trees for each of the three CRISPR-loci to obtain an integrated scenario of the CRISPR-cassette evolution. We detected numerous parallel inversions and gain/loss events by the analysis of contradictions between the obtained evolutionary trees. We also tested the hypotheses that large within-replichore inversions tend to be balanced by subsequent reversal events and that the core genes less frequently switch the chain by inversions. Both predictions were not confirmed. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.

scholarly journals Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

2021 ◽  
Author(s):  
Takehiro K Katoh ◽  
Ji-Min Chen ◽  
Jin-Hua Yang ◽  
Guang Zhang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Morphological Data ◽  
Sister Relationship ◽  
Mitochondrial Coi ◽  
Adaptive Diversification ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Cladistic Analyses ◽  
Species Groups

The genus Dichaetophora Duda is of 69 formally described, Old World species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. Most of these species were delimitated morphologically, with the within-genus relationship established largely via cladistic analyses of morphological characters. In the present study, we first conducted species-delimitation with aids of morphological data as well DNA barcodes (nucleotide sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I, gene), for a huge sample of Dichaetophora and allied taxa (genus Mulgravea and subgenus Dudaica of Drosophila) collected from a wide geographical range. Then, multiple-locus phylogenetic reconstruction was conducted based on elaborate taxon sampling from the known and newly recognized species in the above taxa, with the maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, 189 species (186 of Dichaetophora, 2 of Mulgravea, and 1 for Dudaica) were newly recognized. In our ML and BI trees, several well-supported species clusters equivalent to the species groups agbo (excluding of neocirricauda), tenuicauda, sinensis (inclusive of neocirricauda) and trilobita of Dichaetophora, were recovered, with the sister-relationship between the third and fourth proved. Other well-supported clusters include 1) a clade comprising of Di. acutissima group and Dudaica, with the former proved to be paraphyletic to the latter; 2) genus Mulgravea; 3) a clade comprising exclusively of newly recognized Dichaetophora species, and was placed as sister to Mulgravea. Three of the remaining five representatives of Dichaetophora species form a solid cluster, leaving the positions of the last two unresolved. The present study greatly renewed out knowledge about the species diversity in a pan-Dichaetophora clade, providing us with an unprecedented historical framework for further taxonomy revision of this clade, and valuable baseline knowledge for future reconstruction of the history of its adaptive diversification in the particular microhabitats.

scholarly journals Genome rearrangements and phylogeny reconstruction in Yersinia pestis

2017 ◽  
Author(s):  
Olga O Bochkareva ◽  
Natalia O Dranenko ◽  
Elena S Ocheredko ◽  
German M Kanevsky ◽  
Yaroslav N Lozinsky ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Phylogenetic Trees ◽  
Yersinia Pseudotuberculosis ◽  
Phylogenetic Reconstruction ◽  
Genome Rearrangements ◽  
Integrated Analysis ◽  
Nucleotide Substitutions ◽  
Large Deletions ◽  
History Of ◽  
Gain Loss

Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed the evolutionary history of genome rearrangements in Y. pestis. We also reconciled phylogenetic trees for each of the three CRISPR-loci to obtain an integrated scenario of the CRISPR-cassette evolution. We detected numerous parallel inversions and gain/loss events by the analysis of contradictions between the obtained evolutionary trees. We also tested the hypotheses that large within-replichore inversions tend to be balanced by subsequent reversal events and that the core genes less frequently switch the chain by inversions. Both predictions were not confirmed. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.

scholarly journals Tuber Fulgens Quél. A New Record for Turkish Truffles

2020 ◽  
Vol 8 (11) ◽  
pp. 2472-2475
Author(s):  
Ilgaz Akata ◽  
Mustafa Sevindik ◽  
Ergin Şahin
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Large Subunit ◽  
Morphological Data ◽  
Lsu Rdna ◽  
High Sequence Similarity ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
History Of ◽  
First Time

Tuber samples were collected from Kırklareli province on the 10th of August 2020 and they are identified by implementing both traditional methods and molecular phylogenetic analysis using the rDNA sequences including Internal Transcribed Spacer (ITS) and 28S Ribosomal Large Subunit (LSU) regions. By taking into account the high sequence similarity between the collected samples (ANK Akata 7351) and the truffle species Tuber fulgens Quél. the collected specimen was regarded as T. fulgens and the morphological data also consolidated this finding. As a result, T. fulgens was reported for the first time from Turkey. A short description of the newly reported species is given along with its macro and microphotographs, and spore images taken by a scanning electron microscope (SEM). Additionally, ITS and LSU rDNA based evolutionary history of the specimen is provided with phylogenetic trees.

Phylogenetic Reconstruction of Character Development in Physciaceae

2001 ◽  
Vol 33 (1) ◽  
pp. 3-23 ◽  
Author(s):  
A. Nordin ◽  
J.-E. Mattsson
Keyword(s):  
Phylogenetic Trees ◽  
Character Development ◽  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
The Other ◽  
New Genera ◽  
Secondary Chemistry ◽  
The Family ◽  
History Of ◽  
Basal Position

AbstractA cladistic analysis of the Physciaceae, based on morphological and chemical data, is presented. In the resulting phylogenetic reconstruction two major clades are formed, one containing the foliose genera (Anaptychia, Dirinana, Heterodermia, Hyperphyscia, Physcia, Phaeophyscia, Physconia, Pyxine) and the fruticose Tornabea and the other containing the remaining, mainly crustose genera. Rinodina appears as paraphyletic with representatives both at the base of the tree, at the same level as the two major clades and at the base of the crustose clade. Also Mobergia has a basal position. The characters used and their distribution in the phylogenetic trees are discussed as well as their significance for the identification of monophyletic groups. The history of the family is also briefly hinted at and characters of importance for the recognition of new genera are surveyed. Relevant publications and the variation in secondary chemistry are presented in tables.

scholarly journals Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

2018 ◽  
Vol 14 (6) ◽  
pp. 20180263 ◽  
Author(s):  
Robert S. Sansom ◽  
Peter G. Choate ◽  
Joseph N. Keating ◽  
Emma Randle
Keyword(s):  
Empirical Data ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Empirical Studies ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
Simulation Studies ◽  
Historic Data ◽  
Parsimony Trees ◽  
Bayesian Trees

Reconstructing evolutionary histories requires accurate phylogenetic trees. Recent simulation studies suggest that probabilistic phylogenetic analyses of morphological data are more accurate than traditional parsimony techniques. Here, we use empirical data to compare Bayesian and parsimony phylogenies in terms of their congruence with the distribution of age ranges of the component taxa. Analysis of 167 independent morphological data matrices of fossil tetrapods finds that Bayesian trees exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees. As such, taking stratigraphic data as an independent benchmark indicates that parsimony analyses are more accurate for phylogenetic reconstruction of morphological data. The discrepancy between simulated and empirical studies may result from historic data peaking practices or some complexities of empirical data as yet unaccounted for.

scholarly journals The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data

2014 ◽  
Vol 14 (1) ◽  
pp. 52 ◽  
Author(s):  
Ralph S Peters ◽  
Karen Meusemann ◽  
Malte Petersen ◽  
Christoph Mayer ◽  
Jeanne Wilbrandt ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Morphological Data ◽  
History Of

Plastic deformations in kyanites by tectonometamorphic processes: a single-crystal X-ray diffraction study

2009 ◽  
Vol 73 (3) ◽  
pp. 359-371 ◽  
Author(s):  
G. D. Gatta ◽  
N. Rotiroti ◽  
M. Zucali
Keyword(s):  
Single Crystal ◽  
X Ray Diffraction ◽  
Plastic Deformations ◽  
X Ray ◽  
Deformational History ◽  
Significant Difference ◽  
Elliptical Section ◽  
History Of ◽  
Diffraction Patterns ◽  
Two Stages

AbstractThe crystalch emistry and crystal structure of naturalky anite crystals from the Eclogitic Micaschists Complex of the Sesia-Lanzo Zone, Western Italian Alps, have been investigated by means of optical microscopy, wavelength dispersive X-ray microanalysis, and single-crystal X-ray diffraction. The association of kyanite + garnet + phengitic-mica + chloritoid suggests that the eclogite-facies stages occurred at P ≤ 2.1 GPa and T ≤ 650ºC. Kyanite grains are large (cm-sized) porphyroblasts grown dynamically during one of the deformational events related to the subduction of the Austroalpine continentalcr ust. Under the polarizing microscope, kyanite grains show almost homogeneous cores, whereas rims are sometimes symplectitic aggregates of quartz and kyanite, confirming at least two stages of growth most likely related to the multistage deformational history of these rocks. Chemical analysis shows that Fe3+ is the major substituting cation for Al3+, ranging between 0.038 and 0.067 a.p.f.u.The single-crystal X-ray diffraction investigation of the kyanites shows severely textured patterns on the (h0l)*-plane. Such evidence is not observed in the unwarped diffraction patterns on (0kl)* and (hk0)*. The most significant difference between the structuralp arameters refined in this study, with respect to those of previously published unstrained gem-quality crystals, concerns the displacement parameters. The anisotropic displacement ellipsoids of all the atomic sites are significantly larger than those previously described, and systematically oriented with the largest elliptical section almost perpendicular to [010]. The larger ellipsoids in the kyanite crystal investigated here reflect the displacement of the centre of gravity of the electron distribution, rather than an anomalous atomic thermal motion. The magnitude and orientation of the displacement parameters and the textured/strained diffraction pattern may be the result of two combined effects: (1) that the kyanite crystals are actually composed of several blocks; (2) the crystals are affected by a pervasive residual strain, as a result of tectonometamorphic plastic deformations and re-crystallization.

scholarly journals The taxonomic history of Indo-Papuan groundsnakes, genus Stegonotus Duméril et al., 1854 (Colubridae), with some taxonomic revisions and the designation of a neotype for S. parvus (Meyer, 1874)

Zootaxa ◽  
2018 ◽  
Vol 4512 (1) ◽  
pp. 1
Author(s):  
CHRISTINE M. KAISER ◽  
HINRICH KAISER ◽  
MARK O’SHEA
Keyword(s):  
New Guinea ◽  
Molecular Data ◽  
The Philippines ◽  
Morphological Data ◽  
Valid Species ◽  
Museum Specimens ◽  
Type Specimens ◽  
History Of ◽  
Original Species ◽  
Species Specific

Since its conceptualization in 1854, 29 species of the colubrid genus Stegonotus have been recognized or described, of which 15 (admiraltiensis, batjanensis, borneensis, cucullatus, derooijae, diehli, florensis, guentheri, iridis, heterurus, melanolabiatus, modestus, muelleri, parvus, poechi) are still considered valid today. Original species descriptions for the members of this genus were published in Dutch, English, French, German, and Italian and, perhaps as a consequence of these polyglot origins, there has been a considerable amount of confusion over which species names should be applied to which populations of Stegonotus throughout its range across Borneo, the Philippines, Wallacea, New Guinea, Australia, and associated archipelagos. In addition, the terminology used to notate characteristics in the descriptions of these forms was not uniform and may have added to the taxonomic confusion. In this paper, we trace in detail the history of the type specimens, the species, and the synonyms currently associated with the genus Stegonotus and provide a basic, species-specific listing of their characteristics, derived from our examination of over 1500 museum specimens. Based on our data, we are able to limit the distribution of S. modestus to the islands of Ambon, Buru, and Seram in the central Moluccas of Indonesian Wallacea. We correct the type locality of S. cucullatus to the Manokwari area on the Bird’s Head Peninsula of West Papua, Indonesian New Guinea and designate a neotype for S. parvus, a species likely to be a regional endemic in the Schouten Archipelago of Cenderawasih Bay (formerly Geelvink Bay), Indonesian New Guinea. We unequivocally identify and explain the problematic localities of the type specimens of S. muelleri and Lycodon muelleri, which currently reside in the same specimen jar. We remove L. aruensis and L. lividum from the synonymy of S. modestus and recognize them as S. aruensis n. comb. and S. lividus n. comb., respectively. We remove S. keyensis and Zamenophis australis from the synonymy of S. cucullatus and recognize them as S. keyensis n. comb. and S. australis n. comb., respectively. We further remove S. reticulatus from the synonymy of S. cucullatus, S. dorsalis from the synonymy of S. diehli, and S. sutteri from the synonymy of S. florensis. We designate lectotypes for S. guentheri, S. heterurus, S. lividus, and S. reticulatus. Lastly, we introduce S. poechi, a valid species not mentioned in the scientific literature since its description in 1924. This brings the diversity in the genus Stegonotus to 22 species. We also caution that in a complex group of organisms like Stegonotus any rush to taxonomic judgment on the basis of molecular and incomplete morphological data sets may perpetuate errors and introduce incongruities. Only through the careful work of connecting type material with museum specimens and molecular data can the taxonomy and nomenclature of complex taxa be stabilized. 

Notes on the generic position of Brassica deserti (Brassicaceae)

2019 ◽  
Vol 66 (1-2) ◽  
pp. 89-93
Author(s):  
Jotham Ziffer-Berger ◽  
Alexandra Keren-Keiserman ◽  
Adi Doron-Faigenboim ◽  
Klaus Mummenhoff ◽  
Oz Barazani
Keyword(s):  
Mediterranean Area ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Molecular Tools ◽  
East Mediterranean ◽  
Phylogenetic Groups ◽  
5.8S Rdna ◽  
The Core ◽  
Generic Position ◽  
History Of

Molecular tools provide new insights into phylogenetic relationships of plant species, and by relating phylogenetic groups to their geographical distribution, we can cast light upon the evolution history of plant clades. In the current study, we evaluated the phylogenetic position of the Sinai endemic Brassica deserti (Brassicaceae), later renamed as Erucastrum deserti, based on morphological data and 5.8S rDNA and ITS (Internal Transcribed Spacer) regions. Our results indicate that B. deserti belongs to an East-Mediterranean – Saharo Arabian clade and was not assigned to the core Brassica and Erucastrum clades, respectively, which evolved in the West Mediterranean area. We tentatively conclude that Brassica deserti evolved independently of core Brassica and Erucastrum.

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