Relevant bibliographies by topics / Phylogeney

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  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Phylogeney'

Author: Grafiati
Published: 18 May 2024

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Journal articles on the topic "Phylogeney"

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Zeb, Umar, Xiukang Wang, Sajid Fiaz, Azizullah Azizullah, Asad Ali Shah, Sajjad Ali, Fazli Rahim, et al. "Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis." PLOS ONE 17, no. 1 (January 19, 2022): e0262040. http://dx.doi.org/10.1371/journal.pone.0262040.

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Pinus is one of the most economical and ecological important conifers, model specie for studying sequence divergence and molecular phylogeney of gymnosperms. The less availability of information for genome resources enable researchers to conduct evolutionary studies of Pinus species. To improve understanding, we firstly reported, previously released chloroplast genome of 72 Pinus species, the sequence variations, phylogenetic relationships and genome divergence among Pinus species. The results displayed 7 divergent hotspot regions (trnD-GUC, trnY-GUA, trnH-GUG, ycf1, trnL-CAA, trnK-UUU and trnV-GAC) in studied Pinus species, which holds potential to utilized as molecular genetic markers for future phylogenetic studies in Pinnus species. In addition, 3 types of repeats (tandem, palindromic and dispersed) were also studied in Pinus species under investigation. The outcome showed P. nelsonii had the highest, 76 numbers of repeats, while P. sabiniana had the lowest, 13 13 numbers of repeats. It was also observed, constructed phylogenetic tree displayed division into two significant diverged clades: single needle (soft pine) and double-needle (hard pine). Theoutcome of present investigation, based on the whole chloroplast genomes provided novel insights into the molecular based phylogeny of the genus Pinus which holds potential for its utilization in future studies focusing genetic diversity in Pinnus species.
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LÖRZ, ANNE-NINA. "Deep-sea Rhachotropis (Crustacea: Amphipoda: Eusiridae) from New Zealand and the Ross Sea with key to the Pacific, Indian Ocean and Antarctic species." Zootaxa 2482, no. 1 (May 24, 2010): 22. http://dx.doi.org/10.11646/zootaxa.2482.1.2.

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The amphipod genus Rhachotropis has a worldwide distribution. Four species new to science are described, increasing the total number of Rhachotropis species to 59. Only one species was previously known from New Zealand and none from the Ross Sea. Two species Rhachotropis chathamensis sp. nov. and R. delicata sp. nov. were collected at the same station in 420 m depth off eastern New Zealand; R. rossi sp. nov. and R. abyssalis sp. nov. were collected below 3000 m depth in the Ross Sea, Antarctica. Investigation of recently collected material as well as historic material from the NIWA Invertebrate collection revealed several specimens of Rhachotropis antarctica K.H. Barnard, 1932 sampled in the Ross Sea. Four damaged Rhachotropis specimens, recently collected from 5170 m in the Kermadec Trench, north of New Zealand, are reported. Epibionts have been discovered on the mouthparts of several specimens from New Zealand as well as the Ross Sea. Preliminary molecular investigations of the phylogeney of Rhachotropis are briefly discussed. A key to Pacific, Indian Ocean and Antarctic species of Rhachotropis is provided.
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Gawel, Nick J., Rory Mellinger, Eric Stout, and R. Sauve. "RAPD Analysis of Acer." HortScience 30, no. 4 (July 1995): 813F—813. http://dx.doi.org/10.21273/hortsci.30.4.813f.

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DNA from 27 Acer species was used for RAPD analysis. A relatively high number of phylogenically informative polymorphisms were detected, as would be expected in intraspecific comparisons. Principle coordinates analysis was used to discern groupings among the species and a RAPD-based phylogeny was constructed. As expected when making comparisons among species, very high levels of polymorphism were found. Cultivars that grouped together in the principle components analysis also grouped together in the phylogenic analysis. Parts of the phylogenic analysis do not agree with morphology-based phylogenies. This may be due to poor correlation between morphological and DNA markers, or perhaps RAPDs may be too discriminatory to be used for interspecies comparisons. The extremely high level of between-species variation coupled with the low level of within-species variation, indicates the potential of DNA-based identification and discrimination of Acer species is high.
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Golding, G. Brian. "Reconstructing the Prior Probabilities of Allelic Phylogenies." Genetics 161, no. 2 (June 1, 2002): 889–96. http://dx.doi.org/10.1093/genetics/161.2.889.

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Abstract In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually “rare” topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4Nμ (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions.
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Stadler, Tanja, and Jana Smrckova. "Estimating shifts in diversification rates based on higher-level phylogenies." Biology Letters 12, no. 10 (October 2016): 20160273. http://dx.doi.org/10.1098/rsbl.2016.0273.

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Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or family is included. We conduct a simulation study to validate our method in a maximum-likelihood framework. Further, this method has already been introduced into the Bayesian package M r B ayes , which led to new insights into the evolution of Hymenoptera.
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Palmer, Marike, Stephanus N. Venter, Alistair R. McTaggart, Martin P. A. Coetzee, Stephanie Van Wyk, Juanita R. Avontuur, Chrizelle W. Beukes, et al. "The synergistic effect of concatenation in phylogenomics: the case in Pantoea." PeerJ 7 (April 16, 2019): e6698. http://dx.doi.org/10.7717/peerj.6698.

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With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.
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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (September 12, 2011): 2462–77. http://dx.doi.org/10.1098/rstb.2011.0025.

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Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of ‘regime changes’—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be ‘downshifts’. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of ‘rules’. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.
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Xie, Pingxuan, Lilei Tang, Yanzhen Luo, Changkun Liu, and Hanjing Yan. "Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae." Biology 12, no. 2 (February 7, 2023): 263. http://dx.doi.org/10.3390/biology12020263.

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Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid protein-coding genes. PhyParts analysis was performed to assess the level of concordance and conflict among gene trees across the species tree. The results indicate that most plastomes of Plantaginaceae are largely conserved in terms of genome structure and gene content. In contrast to most previous studies, a robust phylogeny was recovered using plastome data, providing new insights for better understanding the inter-tribal relationships of Plantaginaceae. Both concatenated and coalescent phylogenies favored the sister relationship between Plantagineae and Digitalideae, as well as between Veroniceae and Hemiphragmeae. Sibthorpieae diverged into a separate branch which was sister to a clade comprising the four tribes mentioned above. Furthermore, the sister relationship between Russelieae and Cheloneae is strongly supported. The results of PhyParts showed gene tree congruence and conflict to varying degrees, but most plastid genes were uninformative for phylogenetic nodes, revealing the defects of previous studies using single or multiple plastid DNA sequences to infer the phylogeny of Plantaginaceae.
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Mehregan, I., K. Ghanbarpour, and M. M. Shamsabad. "EVOLUTION OF PERICARP SURFACE STRUCTURE IN NEPETA S. S. (LAMIACEAE) AS INFERRED FROM ANALYSIS OF ITS DATA." Acta Botanica Hungarica 64, no. 3-4 (November 18, 2022): 369–90. http://dx.doi.org/10.1556/034.64.2022.3-4.9.

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Nutlet pericarp structure is important in the taxonomy of Lamiaceae (Labiatae) at different taxonomic levels. Within the family it has also been found that variation in pericarp structure is strongly correlated with the phylogenic results obtained from molecular DNA analyses. The genus Nepeta L., with more than 200 species mainly centred in SW Asia, is one of the taxonomically most complex genera within the family. Traditional taxonomic treatments of Nepeta are mainly based on gross morphology. As in other groups of Lamiaceae, pericarp structure provides some of the diagnostic characters in this genus. In order to investigate patterns of pericarp evolution within Nepeta, we used scanning electron microscopy to examine nutlet surfaces and pericarp cross sections and explored variation of these characters against a molecular phylogeny based on ITS sequences. Based on this phylogenetic analysis, Nepeta in its present circumscription is not monophyletic. Evolutionary trends in structure of nutlet pericarps are apparent although they require confirmation with more robust phylogenies. In particular, nutlets with tuberculate/thorny-like pericarp may have evolved once within this genus, in the common ancestor of five of the six subclades identified within Nepeta, and have been lost independently several times. We also show that evolution of tubercules in Nepeta is not related to plant life span. Our results also indicate that more genetic markers (both plastid and nuclear) are necessary to reconstruct a reliable and robust organismal phylogeny.
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Etienne, Rampal S., Bart Haegeman, Tanja Stadler, Tracy Aze, Paul N. Pearson, Andy Purvis, and Albert B. Phillimore. "Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record." Proceedings of the Royal Society B: Biological Sciences 279, no. 1732 (October 12, 2011): 1300–1309. http://dx.doi.org/10.1098/rspb.2011.1439.

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The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.
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Dissertations / Theses on the topic "Phylogeney"

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Chatterjee, Chandranath. "Phylogeney of bufonidae on the basis of sperm ultrastructure and DNA analysis studies." Thesis, University of North Bengal, 2003. http://hdl.handle.net/123456789/930.

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Bernt, Matthias. "Gene order rearrangement methods for the reconstruction of phylogeny." Doctoral thesis, Universitätsbibliothek Leipzig, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-38666.

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The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes. A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that “a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole”. This kind of data is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999). The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the reconstruction of parsimonious phylogenetic trees from gene arrangement data (Bader et al., 2008; Bernt et al., 2007b; Bourque and Pevzner, 2002; Moret et al., 2002a); or the computation of the similarities of gene arrangements (Bergeron et al., 2008a; Heber et al., 2009). 1 1 Introduction The central theme of this work is to provide efficient algorithms for modified versions of fundamental genome rearrangement problems using more plausible rearrangement models. Two types of modified rearrangement models are explored. The first type is to restrict the set of allowed rearrangements as follows. It can be observed that certain groups of genes are preserved during evolution. This may be caused by functional constraints which prevented the destruction (Lathe et al., 2000; Sémon and Duret, 2006; Xie et al., 2003), certain properties of the rearrangements which shaped the gene orders (Eisen et al., 2000; Sankoff, 2002; Tillier and Collins, 2000), or just because no destructive rearrangement happened since the speciation of the gene orders. It can be assumed that gene groups, found in all studied gene orders, are not acquired independently. Accordingly, these gene groups should be preserved in plausible reconstructions of the course of evolution, in particular the gene groups should be present in the reconstructed putative ancestral gene orders. This can be achieved by restricting the set of rearrangements, which are allowed for the reconstruction, to those which preserve the gene groups of the given gene orders. Since it is difficult to determine functionally what a gene group is, it has been proposed to consider common combinatorial structures of the gene orders as gene groups (Marcotte et al., 1999; Overbeek et al., 1999). The second considered modification of the rearrangement model is extending the set of allowed rearrangement types. Different types of rearrangement operations have shuffled the gene orders during evolution. It should be attempted to use the same set of rearrangement operations for the reconstruction otherwise distorted or even wrong phylogenetic conclusions may be obtained in the worst case. Both possibilities have been considered for certain rearrangement problems before. Restricted sets of allowed rearrangements have been used successfully for the computation of parsimonious rearrangement scenarios consisting of inversions only where the gene groups are identified as common intervals (Bérard et al., 2007; Figeac and Varré, 2004). Extending the set of allowed rearrangement operations is a delicate task. On the one hand it is unknown which rearrangements have to be regarded because this is part of the phylogeny to be discovered. On the other hand, efficient exact rearrangement methods including several operations are still rare, in particular when transpositions should be included. For example, the problem to compute shortest rearrangement scenarios including transpositions is still of unknown computational complexity. Currently, only efficient approximation algorithms are known (e.g. Bader and Ohlebusch, 2007; Elias and Hartman, 2006). Two problems have been studied with respect to one or even both of these possibilities in the scope of this work. The first one is the inversion median problem. Given the gene orders of some taxa, this problem asks for potential ancestral gene orders such that the corresponding inversion scenario is parsimonious, i.e. has a minimum length. Solving this problem is an essential component 2 of algorithms for computing phylogenetic trees from gene arrangements (Bourque and Pevzner, 2002; Moret et al., 2002a, 2001). The unconstrained inversion median problem is NP-hard (Caprara, 2003). In Chapter 3 the inversion median problem is studied under the additional constraint to preserve gene groups of the input gene orders. Common intervals, i.e. sets of genes that appear consecutively in the gene orders, are used for modelling gene groups. The problem of finding such ancestral gene orders is called the preserving inversion median problem. Already the problem of finding a shortest inversion scenario for two gene orders is NP-hard (Figeac and Varré, 2004). Mitochondrial gene orders are a rich source for phylogenetic investigations because they are known for more than 1 000 species. Four rearrangement operations are reported at least in the literature to be relevant for the study of mitochondrial gene order evolution (Boore, 1999): That is inversions, transpositions, inverse transpositions, and tandem duplication random loss (TDRL). Efficient methods for a plausible reconstruction of genome rearrangements for mitochondrial gene orders using all four operations are presented in Chapter 4. An important rearrangement operation, in particular for the study of mitochondrial gene orders, is the tandem duplication random loss operation (e.g. Boore, 2000; Mauro et al., 2006). This rearrangement duplicates a part of a gene order followed by the random loss of one of the redundant copies of each gene. The gene order is rearranged depending on which copy is lost. This rearrangement should be regarded for reconstructing phylogeny from gene order data. But the properties of this rearrangement operation have rarely been studied (Bouvel and Rossin, 2009; Chaudhuri et al., 2006). The combinatorial properties of the TDRL operation are studied in Chapter 5. The enumeration and counting of sorting TDRLs, that is TDRL operations reducing the distance, is studied in particular. Closed formulas for computing the number of sorting TDRLs and methods for the enumeration are presented. Furthermore, TDRLs are one of the operations considered in Chapter 4. An interesting property of this rearrangement, distinguishing it from other rearrangements, is its asymmetry. That is the effects of a single TDRL can (in the most cases) not be reversed with a single TDRL. The use of this property for phylogeny reconstruction is studied in Section 4.3. This thesis is structured as follows. The existing approaches obeying similar types of modified rearrangement models as well as important concepts and computational methods to related problems are reviewed in Chapter 2. The combinatorial structures of gene orders that have been proposed for identifying gene groups, in particular common intervals, as well as the computational approaches for their computation are reviewed in Section 2.2. Approaches for computing parsimonious pairwise rearrangement scenarios are outlined in Section 2.3. Methods for the computation genome rearrangement scenarios obeying biologically motivated constraints, as introduced above, are detailed in Section 2.4. The approaches for the inversion median problem are covered in Section 2.5. Methods for the reconstruction of phylogenetic trees from gene arrangement data are briefly outlined in Section 2.6.3 1 Introduction Chapter 3 introduces the new algorithms CIP, ECIP, and TCIP for solving the preserving inversion median problem. The efficiency of the algorithm is empirically studied for simulated as well as mitochondrial data. The description of algorithms CIP and ECIP is based on Bernt et al. (2006b). TCIP has been described in Bernt et al. (2007a, 2008b). But the theoretical foundation of TCIP is extended significantly within this work in order to allow for more than three input permutations. Gene order rearrangement methods that have been developed for the reconstruction of the phylogeny of mitochondrial gene orders are presented in the fourth chapter. The presented algorithm CREx computes rearrangement scenarios for pairs of gene orders. CREx regards the four types of rearrangement operations which are important for mitochondrial gene orders. Based on CREx the algorithm TreeREx for assigning rearrangement events to a given tree is developed. The quality of the CREx reconstructions is analysed in a large empirical study for simulated gene orders. The results of TreeREx are analysed for several mitochondrial data sets. Algorithms CREx and TreeREx have been published in Bernt et al. (2008a, 2007c). The analysis of the mitochondrial gene orders of Echinodermata was included in Perseke et al. (2008). Additionally, a new and simple method is presented to explore the potential of the CREx method. The new method is applied to the complete mitochondrial data set. The problem of enumerating and counting sorting TDRLs is studied in Chapter 5. The theoretical results are covered to a large extent by Bernt et al. (2009b). The missing combinatorial explanation for some of the presented formulas is given here for the first time. Therefor, a new method for the enumeration and counting of sorting TDRLs has been developed (Bernt et al., 2009a).
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Jacobson, Herbert R. "Generic revision, phylogenic classification, and phylogeny of the termitophilous tribe corotocini(Coleoptera; staphylinidae)." Doctoral thesis, Universite Libre de Bruxelles, 1985. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/213647.

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Wirth, Stefan. "Phylogeny, biology and character transformations of the Histiostomatidae (Acari, Astigmata) Phylogenie, Biologie und Merkmals-Transformationen der Histiostomatidae (Acari, Astigmata) /." [S.l. : s.n.], 2004. http://www.diss.fu-berlin.de/2004/312/index.html.

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Tekle, Yonas Isaak. "Phylogeny and Taxonomy of Childia (Acoela) : New characters for unraveling acoel phylogenies from molecules, ultrastructure, immunocytochemistry and confocal microscopy." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6315.

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Kanouh, Mohamad. "Etudes taxonomiques de deux genres d'acariens prédateurs de la famille des Phytoseiidae (Acari Mesostigmata) : Phytoseiulus Evans et Neoseiulella Muma." Thesis, Montpellier, SupAgro, 2010. http://www.theses.fr/2010NSAM0029/document.

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La classification actuelle de la famille des Phytoseiidae n'est pas basée sur de réelles études phylogénétiques et par conséquent, de nombreuses questions se posent sur la validité des taxa supra-spécifiques mais également vis-à-vis des taxa spécifiques. Ce travail de thèse avait donc pour objectif de répondre à de telles questions pour deux genres : Phytoseiulus et Neoseiulella, en utilisant pour la première fois des approches phylogénétiques moléculaires et morphologiques. Ces études phylogénétiques ont été également associées à des études biogéographiques. Les résultats obtenus par ces deux approches sont congruents et semblent montrer que ces deux genres ne sont pas monophylétiques : le genre Phytoseiulus semble au mieux paraphylétique, tandis que le genre Neoseiulella serait polyphylétique. Ces résultats sont différents de ceux développés dans les diverses révisions successives de ces deux taxa. Ce travail de thèse a permis de répondre également à des questionnements sur cinq synonymies au sein du genre Neoseiulella. L'étude de pratiquement tous les types des espèces du genre Neoseiulella nous a permis de redéfinir le genre, en excluant trois espèces et en discutant certaines synonymies. Une clé d'identification des adultes femelles des espèces valides a également été proposée. Des études complémentaires, notamment des analyses moléculaires, seront nécessaires afin de conclure plus définitivement sur les relations évolutives entre les taxa étudiés
The present classification of the family Phytoseiidae is not based on solid phylogenetic studies and therefore, many taxonomic questions still arise, concerning the validity of supra-specific and specific taxa identified to-date. This thesis thus aimed to answer such questions for two genera, Phytoseiulus and Neoseiulella, using for the first time molecular and morphological phylogenetic analyses. Biogeographic analyses have been also carried out. Results obtained by both morphological and molecular approaches are congruent and seem to show that both genera are not monophyletic: Phytoseiulus seems paraphyletic whereas Neoseiulella seems polyphyletic. These results are different from those obtained with previous revisions of these two taxa. Furthermore, this study allowed to conclude on five synonymies within the genus Neoseiulella. The observation of nearly the totality of the species belonging to the genus Neoseiulella permitted to redefine this genus, excluding three species and discussing some synonymies. Lastly, an identification key of the adult females was proposed for the valid species of the genus Neoseiulella. Further experiments, including molecular investigations, are however still required in order to obtain more reliable conclusions on the evolutionary relationships of the studied taxa
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Varón, González Ceferino. "Shape and phylogeny." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/shape-and-phylogeny(f432d494-9755-41f9-b067-431023ad3248).html.

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Geometric morphometrics, the science about the study of shape, has developed much in the last twenty years. In this thesis I first study the reliability of the phylogenies built using geometric morphometrics. The effect of different evolutionary models, branch-length combinations, dimensionality and degrees of integration is explored using computer simulations. Unfortunately in the most common situations (presence of stabilizing selection, short distance between internal nodes and presence of integration) the reliability of the phylogenies is very low. Different empirical studies are analysed to estimate the degree of evolutionary integration usually found in nature. This gives an idea about how powerful the effect of integration is over the reliability of the phylogenies in empirical studies. Evolutionary integration is studied looking at the decrease of variance in the principal components of the tangent shape space using the independent contrasts of shape. The results suggest that empirical data usually show strong degrees of integration in most of the organisms and structures analysed. These are bad news, since strong degree of integration has devastating effects over the phylogenetic reliability, as suggested by our simulations. However, we also propose the existence of other theoretical situations in which strong integration may not translate into convergence between species, like perpendicular orientation of the integration patterns or big total variance relative to the distance between species in the shape space. Finally, geometric morphometrics is applied to the study of the evolution of shape in proteins. There are reasons to think that, because of their modular nature and huge dimensionality, proteins may show different patterns of evolutionary integration. Unfortunately, proteins also show strong functional demands, which influence their evolution and that cause strong integration patterns. Integration is then confirmed as a widespread property in the evolution of shape, which causes poor phylogenetic estimates.
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Poe, Stephen Joseph. "Phylogeny of anoles /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004359.

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Rehm, Peter [Verfasser]. "Cumacea (Crustacea; Peracarida) of the Antarctic shelf - diversity, biogeography, and phylogeny = Cumacea (Crustacea; Peracarida) des antarktischen Schelfs - Diversität, Biogeographie und Phylogenie / Peter Rehm." Bremerhaven : AWI, Alfred-Wegener-Institut für Polar- und Meeresforschung, 2009. http://d-nb.info/1010171909/34.

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Larsson, Karolina. "Taxonomy and Phylogeny of Catenulida (Platyhelminthes) with Emphasis on the Swedish Fauna." Doctoral thesis, Uppsala University, Department of Evolution, Genomics and Systematics, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8470.

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This thesis focuses on phylogenetic and taxonomic studies of Catenulida (Platyhelminthes). Catenulida is a group of microscopic free-living worms mainly found in freshwater habitats. The Swedish catenulid fauna was previously virtually unknown. The taxonomy of Catenulida is difficult because of the paucity of good morphological characters, which makes species identification extremely difficult.

Molecular phylogenies are inferred from DNA sequences. Based on two molecular markers, 18S rDNA and 28S rDNA, the phylogenetic position of Catenulida has now been well established as the sister group to the rest of the flatworms, Rhabditophora. Within Catenulida there is a basal split between two major clades: Retronectidae + Catenulidae and Stenostomidae. The hypothesis of the marine Retronectidae as the sister group of the limnic Catenulida is rejected.

Four molecular markers, 18S rDNA, 28S rDNA, ITS-5.8S and CO1, are used as a backbone to infer phylogeny and to generate hypotheses about species delimitation in Catenulida using parsimony jackknifing and Bayesian analysis. Anokkostenostomum comes out non-monophyletic, and Suomina nested within Catenula, so two new synonymies are proposed: Stenostomum Schmidt, 1848 (Anokkostenostomum Noreña et al. 2005) and Catenula Duges, 1832 (Suomina Marcus, 1945) are proposed.

A first report on Swedish freshwater Catenulida are given. A total of 13 species are reported from Sweden. Four of them, all belonging to the taxon Stenostomum are new to science: S. gotlandense n.sp.; S. handoelense n.sp.; S. heebuktense n.sp. and S. steveoi n.sp.

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Books on the topic "Phylogeney"

1

Phylogeny reconstruction in paleontology. New York: Van Nostrand Reinhold, 1986.

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Steel, Mike. Phylogeny. Philadelphia, PA: Society for Industrial and Applied Mathematics, 2016. http://dx.doi.org/10.1137/1.9781611974485.

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Szalay, Frederick S., Michael J. Novacek, and Malcolm C. McKenna, eds. Mammal Phylogeny. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4615-7381-4.

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Szalay, Frederick S., Michael J. Novacek, and Malcolm C. McKenna, eds. Mammal Phylogeny. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4613-9246-0.

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Szalay, Frederick S., Michael J. Novacek, and Malcolm C. McKenna, eds. Mammal Phylogeny. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4613-9249-1.

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S, Szalay Frederick, Novacek Michael J, McKenna Malcolm C, and North Atlantic Treaty Organization, eds. Mammal phylogeny. New York: Springer-Verlag, 1993.

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Gould, Stephen Jay. Ontogeny and phylogeny. Cambridge, MA: Harvard University Press, 1985.

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1967-, Purvis Andy, Gittleman John L, and Brooks Thomas, eds. Phylogeny and conservation. Cambridge: Cambridge University Press, 2005.

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J, Novacek Michael, and Wheeler Quentin 1954-, eds. Extinction and phylogeny. New York: Columbia University Press, 1992.

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Forey, Peter L., and Norman MacLeod. Morphology, shape and phylogeny. London: Taylor & Francis, 2002.

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Book chapters on the topic "Phylogeney"

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Frank, J. Howard, J. Howard Frank, Michael C. Thomas, Allan A. Yousten, F. William Howard, Robin M. Giblin-davis, John B. Heppner, et al. "Phylogeny." In Encyclopedia of Entomology, 2868. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_2936.

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Moreira, David. "Phylogeny." In Encyclopedia of Astrobiology, 1252–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_1209.

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Kovář, I. "Phylogeny." In Ecology of Coccinellidae, 19–31. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-017-1349-8_2.

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Prado, José Luis, and María Teresa Alberdi. "Phylogeny." In The Latin American Studies Book Series, 73–84. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-55877-6_4.

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Lichtwardt, Robert W. "Phylogeny." In The Trichomycetes, 274–87. New York, NY: Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4890-3_12.

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Moreira, David. "Phylogeny." In Encyclopedia of Astrobiology, 1887–90. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_1209.

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Mackenstedt, Ute. "Phylogeny." In Encyclopedia of Parasitology, 2146–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-43978-4_2423.

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Saitou, Naruya. "Phylogeny." In Introduction to Evolutionary Genomics, 69–108. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92642-1_4.

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Saitou, Naruya. "Phylogeny." In Introduction to Evolutionary Genomics, 55–87. London: Springer London, 2013. http://dx.doi.org/10.1007/978-1-4471-5304-7_3.

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Neelabh. "Phylogeny." In Encyclopedia of Animal Cognition and Behavior, 1–4. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-319-47829-6_129-1.

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Conference papers on the topic "Phylogeney"

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Oliveira, Alberto, and Anderson Rocha. "Multiple Parenting Relationships in Image Phylogeny: Tracking Down Forgeries and Their Creators Online*." In XXIX Concurso de Teses e Dissertações da SBC. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/ctd.2016.9138.

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Due to the large amount of images shared on the web, tracking the spread and evolution of their content have become an increasingly important problem. As an image might be a composition created through the combination of the semantic information existent in two or more source images, establishing a relationship between the sources and the composite is an ever-growing problem of interest. We name as Multiple Parenting Phylogeny the problem of identifying such relationships in a set containing near-duplicate subsets of source and composition images. To tackle this problem, this work presents a three-step solution: (1) separation of near-duplicate groups; (2) classification of the relations between the groups; and (3) identification of the images used to create the original composition. Furthermore, we extend upon this framework by introducing key improvements, such as better identification of when two images share content, and improved ways to compare this content. Evaluation of the proposed method is performed by means of quantitative metrics established for evaluating the accuracy in reconstructing phylogenies and finding multiple parenting relationships in the different datasets. Finally, we also analyze the results qualitatively, with images obtained from the web
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Wright, David F. "TIME, STRATIGRAPHY, AND FOSSIL PHYLOGENIES: RE-EVALUATING THE USE OF TEMPORAL DATA IN PHYLOGENY RECONSTRUCTION AND TRAIT EVOLUTION." In 66th Annual GSA Southeastern Section Meeting - 2017. Geological Society of America, 2017. http://dx.doi.org/10.1130/abs/2017se-290918.

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Gusfield, Dan. "Persistent phylogeny." In BCB '15: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2808719.2808765.

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Akimova, E. S., I. S. Koryakov, and An Kh Baymiev. "The strategy for choosing nodule bacteria by perennial leguminous plants, depending on the stage of their vegetation." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.012.

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Bonizzoni, Paola, Simone Ciccolella, Gianluca Della Vedova, and Mauricio Soto. "Beyond Perfect Phylogeny." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3107411.3107441.

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Rogers, John, and DeAngelo Wilson. "Comparing phylogeny by compression to phylogeny by NJp and Bayesian Inference." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2020. http://dx.doi.org/10.1109/bibm49941.2020.9313237.

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Araújo, Graziela S., Guilherme P. Telles, Maria Emília M. T. Walter, and Nalvo F. Almeida. "Distance-based Live Phylogeny." In 8th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS - Science and Technology Publications, 2017. http://dx.doi.org/10.5220/0006224501960201.

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Gusfield, Dan. "Haplotyping as perfect phylogeny." In the sixth annual international conference. New York, New York, USA: ACM Press, 2002. http://dx.doi.org/10.1145/565196.565218.

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Jones, Jeff A., and Katherine A. Yelick. "Parallelizing the phylogeny problem." In the 1995 ACM/IEEE conference. New York, New York, USA: ACM Press, 1995. http://dx.doi.org/10.1145/224170.224224.

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Narayan, Kartik, Harsh Agarwal, Kartik Thakral, Surbhi Mittal, Mayank Vatsa, and Richa Singh. "DeePhy: On Deepfake Phylogeny." In 2022 IEEE International Joint Conference on Biometrics (IJCB). IEEE, 2022. http://dx.doi.org/10.1109/ijcb54206.2022.10007968.

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Reports on the topic "Phylogeney"

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Tiffani L. Williams. High-Performance Phylogeny Reconstruction. Office of Scientific and Technical Information (OSTI), November 2004. http://dx.doi.org/10.2172/834325.

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Moret, Bernard M., and Tandy Warnow. Advances in Phylogeny Reconstruction from Gene Order and Content Data. Fort Belvoir, VA: Defense Technical Information Center, October 2004. http://dx.doi.org/10.21236/ada482523.

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Стригунов, Володимир Іванович, Іван Сергійович Митяй, and Олександр Володимирович Мацюра. Egg shape in the taxonomy and phylogeny of birds of prey. МДПУ імені Богдана Хмельницького, 2016. http://dx.doi.org/10.31812/0564/1510.

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Swinstrom, Kirsten, Roy Caldwell, H. Matthew Fourcade, and Jeffrey L. Boore. The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny. Office of Scientific and Technical Information (OSTI), September 2005. http://dx.doi.org/10.2172/960399.

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Foster, Michael S. Support for a Symposium on Molecular Approaches to Phylogeny, Evolution and Biogeography. Fort Belvoir, VA: Defense Technical Information Center, December 1992. http://dx.doi.org/10.21236/ada262112.

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Kalgutkar, R. M., and A. R. Sweet. Morphology, taxonomy and phylogeny of the fossil fungal genus Pesavis from northwestern Canada. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 1988. http://dx.doi.org/10.4095/126976.

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Ksepka, Daniel, and Kristin Lamm. Systematics and Biodiversity Conservation. American Museum of Natural History, 2012. http://dx.doi.org/10.5531/cbc.ncep.0024.

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This exercise uses a fictional group of turtles to demonstrate how to implement cladistic methodology. Using a step-by-step guide, students work to find the most parsimonious cladogram for these fictional turtles. Part I involves delineating characters and building a most parsimonious cladogram based on the distribution of character states, while Part II presents additional challenges by introducing homoplasy. This exercise is designed to familiarize students with the concepts of phylogeny and cladistics, expand their skills of phylogenetic analysis, and use phylogenetic information to determine conservation priority.
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Eiserhardt, Wolf. Molekularbiologische Untersuchungen zur Phylogenie der cheilanthoiden Farne (Pteridaceae-Cheilanthoideae) des südlichen Afrika. BEE-Press, December 2007. http://dx.doi.org/10.7809/thesis.examen.001.

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Pandya, Gagan A., Michael H. Holmes, Jeannine M. Petersen, Sonal Pradhan, Svetlana A. Karamycheva, Mark J. Wolcott, Claudia Molins, et al. Whole-Genome Single Nucleotide Polymorphism Based Phylogeny of Francisella tularensis and Its Application to the Development of a Strain Typing Assay. Fort Belvoir, VA: Defense Technical Information Center, October 2009. http://dx.doi.org/10.21236/ada513240.

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Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

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Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
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