Relevant bibliographies by topics / Phylogenetic

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Phylogenetic'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 May 2024

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Journal articles on the topic "Phylogenetic"

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Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (September 21, 2022): 782. http://dx.doi.org/10.3390/d14100782.

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Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.
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Ziegler, Willi, and Charles A. Sandberg. "Conodont Phylogenetic-Zone Concept." Newsletters on Stratigraphy 30, no. 2 (July 14, 1994): 105–23. http://dx.doi.org/10.1127/nos/30/1994/105.

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LI, JIA-XIN, MAO-QIANG HE, and RUI-LIN ZHAO. "Three new species of Micropsalliota (Agaricaceae, Agaricales) from China." Phytotaxa 491, no. 2 (March 19, 2021): 167–76. http://dx.doi.org/10.11646/phytotaxa.491.2.6.

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Species diversity of Micropsalliota in China remains poorly known, especially in southwestern China, a hotspot of biodiversity. Based on morphological characteristics and molecular phylogenetic analyses using ITS and nrLSU sequences, three new species named Micropsalliota delicatula, M. dentatomarginata and M. digitatocystis are introduced from China. Phylogenetc analyses results indicated the unique phylogenetic positions of three new species in Micropsalliota. Full descriptions, photo plates, illustrations and a phylogenetic tree to show the placement of three new species are presented.
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Blomquist, Gregory E. "Adaptation, phylogeny, and covariance in milk macronutrient composition." PeerJ 7 (November 13, 2019): e8085. http://dx.doi.org/10.7717/peerj.8085.

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Background Milk is a complicated chemical mixture often studied through macronutrient concentrations of fat, protein, and sugar. There is a long-standing natural history tradition describing interspecific diversity in these concentrations. However, recent work has shown little influence of ecological or life history variables on them, aside from maternal diet effects, along with a strong phylogenetic signal. Methods I used multivariate phylogenetic comparative methods to revisit the ecological and life history correlates of milk macronutrient composition and elaborate on the nature of the phylogenetic signal using the phylogenetic mixed model. I also identified clades with distinctive milks through nonparametric tests (KSI) and PhylogeneticEM evolutionary modeling. Results In addition to the previously reported diet effects, I found increasingly aquatic mammals have milk that this is lower in sugar and higher in fat. Phylogenteic heritabilities for each concentration were high and phylogenetic correlations were moderate to strong indicating coevolution among the concentrations. Primates and pinnipeds had the most outstanding milks according to KSI and PhylogeneticEM, with perissodactyls and marsupials as other noteworthy clades with distinct selection regimes. Discussion Mammalian milks are diverse but often characteristic of certain higher taxa. This complicates identifying the ecological and life history correlates of milk composition using common phylogenetic comparative methods because those traits are also conservative and clade-specific. Novel methods, careful assessment of data quality and hypotheses, and a “phylogenetic natural history” perspective provide alternatives to these traditional tools.
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Zhang, Xiaorong. "Teaching molecular phylogenetics through investigating a real-world phylogenetic problem." Journal of Biological Education 46, no. 2 (June 2012): 103–9. http://dx.doi.org/10.1080/00219266.2011.634018.

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Duarte, Leandro D. S., Vanderlei J. Debastiani, André V. L. Freitas, and Valério D. Pillar. "Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics." Methods in Ecology and Evolution 7, no. 8 (March 10, 2016): 937–46. http://dx.doi.org/10.1111/2041-210x.12547.

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Agorreta, Ainhoa, Diego San Mauro, Ulrich Schliewen, James L. Van Tassell, Marcelo Kovačić, Rafael Zardoya, and Lukas Rüber. "Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies." Molecular Phylogenetics and Evolution 69, no. 3 (December 2013): 619–33. http://dx.doi.org/10.1016/j.ympev.2013.07.017.

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FAITH, DANIEL P., FRANK KÖHLER, LOUISE PUSLEDNIK, and J. W. O. BALLARD. "Phylogenies with Corroboration Assessment." Zootaxa 2946, no. 1 (July 8, 2011): 52. http://dx.doi.org/10.11646/zootaxa.2946.1.11.

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Mooi & Gill (2010) argued that careful character study and well-understood synapomorphies do not have the strong role that they deserve as the basis for evidence in phylogenetics. We agree, but suggest that the problem is even greater. Not only character synapomorphies, but also other forms of phylogenetic evidence, typically do not receive the critical assessment that would support phylogenetic inference. In this paper, our goal is to not simply to highlight problems but to suggest solutions. We will suggest that a stronger role for corroboration assessment in systematics could overcome these problems in phylogenetic inference.
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Petersen, G., and O. Seberg. "Phylogenetic Analysis of allopolyploid species." Czech Journal of Genetics and Plant Breeding 41, Special Issue (July 31, 2012): 28–37. http://dx.doi.org/10.17221/6129-cjgpb.

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Hegewald, Eberhard, and Nobutaka Hangata. "Phylogenetic studies on Scenedesmaceae (Chlorophyta)." Algological Studies/Archiv für Hydrobiologie, Supplement Volumes 100 (December 20, 2000): 29–49. http://dx.doi.org/10.1127/algol_stud/100/2000/29.

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Dissertations / Theses on the topic "Phylogenetic"

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Jirásková, Kristýna. "Metody rekonstrukce fylogenetických superstromů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219518.

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The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.
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Kosíř, Kamil. "Metody rekonstrukce fylogenetických superstromů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-220860.

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The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.
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Mecham, Jesse L. "Jumpstarting phylogenetic searches /." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1403.pdf.

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McHugh, Sean W. "Phylogenetic Niche Modeling." Thesis, Virginia Tech, 2021. http://hdl.handle.net/10919/104893.

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Projecting environmental niche models through time is a common goal when studying species response to climatic change. Species distribution models (SDMs) are commonly used to estimate a species' niche from observed patterns of occurrence and environmental predictors. However, a species niche is also shaped by non-environmental factors--including biotic interactions and dispersal barrier—truncating SDM estimates. Though truncated SDMs may accurately predict present-day species niche, projections through time are often biased by environmental condition change. Modeling niche in a phylogenetic framework leverages a clade's shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche implemented in R. Under our model, species SDM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving under multivariate Brownian motion random walk. Through simulation analyses, we demonstrated model accuracy and precision that improved as phylogeny size increased. We also demonstrated our model on a clade of eastern United States Plethodontid salamanders by accurately estimating species niche, even when no occurrence data is present. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and niche in data deficient species.
Master of Science
As many species face increasing pressure in a changing climate, it is crucial to understand the set of environmental conditions that shape species' ranges--known as the environmental niche--to guide conservation and land management practices. Species distribution models (SDMs) are common tools that are used to model species' environmental niche. These models treat a species' probability of occurrence as a function of environmental conditions. SDM niche estimates can predict a species' range given climate data, paleoclimate, or projections of future climate change to estimate species range shifts from the past to the future. However, SDM estimates are often biased by non-environmental factors shaping a species' range including competitive divergence or dispersal barriers. Biased SDM estimates can result in range predictions that get worse as we extrapolate beyond the observed climatic conditions. One way to overcome these biases is by leveraging the shared evolutionary history amongst related species to "fill in the gaps". Species that are more closely phylogenetically related often have more similar or "conserved" environmental niches. By estimating environmental niche over all species in a clade jointly, we can leverage niche conservatism to produce more biologically realistic estimates of niche. However, currently a methodological gap exists between SDMs estimates and macroevolutionary models, prohibiting them from being estimated jointly. We propose a novel model of evolutionary niche called PhyNE (Phylogenetic Niche Evolution), where biologically realistic environmental niches are fit across a set of species with occurrence data, while simultaneously fitting and leveraging a model of evolution across a portion of the tree of life. We evaluated model accuracy, bias, and precision through simulation analyses. Accuracy and precision increased with larger phylogeny size and effectively estimated model parameters. We then applied PhyNE to Plethodontid salamanders from Eastern North America. This ecologically-important and diverse group of lungless salamanders require cold and wet conditions and have distributions that are strongly affected by climatic conditions. Species within the family vary greatly in distribution, with some species being wide ranging generalists, while others are hyper-endemics that inhabit specific mountains in the Southern Appalachians with restricted thermal and hydric conditions. We fit PhyNE to occurrence data for these species and their associated average annual precipitation and temperature data. We identified no correlations between species environmental preference and specialization. Pattern of preference and specialization varied among Plethodontid species groups, with more aquatic species possessing a broader environmental niche, likely due to the aquatic microclimate facilitating occurrence in a wider range of conditions. We demonstrated the effectiveness of PhyNE's evolutionarily-informed estimates of environmental niche, even when species' occurrence data is limited or even absent. PhyNE establishes a proof-of-concept framework for a new class of approaches for studying niche evolution, including improved methods for estimating niche for data-deficient species, historical reconstructions, future predictions under climate change, and evaluation of niche evolutionary processes across the tree of life. Our approach establishes a framework for leveraging the rapidly growing availability of biodiversity data and molecular phylogenies to make robust eco-evolutionary predictions and assessments of species' niche and distributions in a rapidly changing world.
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Mecham, Jesse Lewis. "Jumpstarting Phylogenetic Searches." BYU ScholarsArchive, 2006. https://scholarsarchive.byu.edu/etd/483.

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Phylogenetic analysis is a central tool in studies of comparative genomics. When a new region of DNA is isolated and sequenced, researchers are often forced to throw away months of computation on an existing phylogeny of homologous sequences in order to incorporate this new sequence. The previously constructed trees are often discarded, and the researcher begins the search again from scratch. The jumpstarting algorithm uses trees from the prior search as a starting point for a new phylogenetic search. This technique drastically decreases search time for large data sets. This kind of analysis is necessary as researchers analyze tree of life size data sets.
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Faller, Beáta. "Combinatorial and probabilistic methods in biodiversity theory." Thesis, University of Canterbury. Mathematics and Statistics, 2010. http://hdl.handle.net/10092/3985.

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Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how much of an evolutionary tree is spanned by a subset of species. In this thesis, we study optimization problems that aim to find species sets with maximum PD in different scenarios, and examine random extinction models under various assumptions to predict the PD of species that will still be present in the future. Optimizing PD with Dependencies is a combinatorial optimization problem in which species form an ecological network. Here, we are interested in selecting species sets of a given size that are ecologically viable and that maximize PD. The NP-hardness of this problem is proved and it is established which special cases of the problem are computationally easy and which are computationally hard. It is also shown that it is NP-complete to decide whether the feasible solution obtained by the greedy algorithm is optimal. We formulate the optimization problem as an integer linear program and find exact solutions to the largest food web currently in the empirical literature. In addition, we give a generalization of PD that can be used for example when we do not know the true evolutionary history. Based on this measure, an optimization problem is formulated. We discuss the complexity and the approximability properties of this problem. In the generalized field of bullets model (g-FOB), species are assumed to become extinct with possibly different probabilities, and extinction events are independent. We show that under this model the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows. When extinction probabilities are influenced by some binary character on the tree, the state-based field of bullets model (s-FOB) represents a more realistic picture. We compare the expected loss of PD under this model to that under the associated g-FOB model and find that the former is always greater than or equal to the latter. It is natural to further generalize the s-FOB model to allow more than one binary character to affect the extinction probabilities. The expected future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is compared to that for the associated g-FOB model and our previous result is generalized.
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Krig, Kåre. "Methods for phylogenetic analysis." Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.

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In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix d.

In this thesis I present a few methods for constructing a phylogenetic tree from d. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When d does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.

Finally I have tested the methods both on real measured data and constructed test cases.

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Pardi, Fabio. "Algorithms on phylogenetic trees." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611685.

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Wang, Min-Hui. "Classification using phylogenetic trees /." The Ohio State University, 1999. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488190595939375.

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Sundberg, Kenneth A. "Partition Based Phylogenetic Search." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2583.

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Evolutionary relationships are key to modern understanding of biological systems. Phylogenetic search is the means by which these relationships are inferred. Phylogenetic search is NP-Hard. As such it is necessary to employ heuristic methods. This work proposes new methods based on viewing the relationships between species as sets of partitions. These methods produce more parsimonious phylogenies than current methods.
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Books on the topic "Phylogenetic"

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Bininda-Emonds, Olaf R. P., ed. Phylogenetic Supertrees. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-1-4020-2330-9.

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Scherson, Rosa A., and Daniel P. Faith, eds. Phylogenetic Diversity. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-93145-6.

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Lemey, Philippe, Marco Salemi, and Anne-Mieke Vandamme, eds. The Phylogenetic Handbook. Cambridge: Cambridge University Press, 2009. http://dx.doi.org/10.1017/cbo9780511819049.

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Basic phylogenetic combinatorics. New York: Cambridge University Press, 2011.

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Bakker, Peter, Finn Borchsenius, Carsten Levisen, and Eeva Sippola, eds. Creole Studies – Phylogenetic Approaches. Amsterdam: John Benjamins Publishing Company, 2017. http://dx.doi.org/10.1075/z.211.

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Wägele, Johann Wolfgang. Foundations of phylogenetic systematics. München: Pfeil, 2005.

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1968-, Salemi Marco, Vandamme Anne-Mieke 1960-, and Lemey Philippe, eds. The phylogenetic handbook: A practical approach to phylogenetic analysis and hypothesis testing. 2nd ed. Cambridge, UK: Cambridge University Press, 2009.

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1968-, Salemi Marco, Vandamme Anne-Mieke 1960-, and Lemey Philippe, eds. The phylogenetic handbook: A practical approach to phylogenetic analysis and hypothesis testing. 2nd ed. Cambridge, UK: Cambridge University Press, 2009.

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C, Holmes Edward, ed. Molecular evolution: A phylogenetic approach. Oxford: Blackwell Science, 1998.

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Bickel, David R. Phylogenetic Trees and Molecular Evolution. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-11958-3.

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Book chapters on the topic "Phylogenetic"

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Gooch, Jan W. "Phylogenetic." In Encyclopedic Dictionary of Polymers, 915. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14499.

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Rieppel, Olivier. "The Evolutionary Turn in Comparative Anatomy." In Phylogenetic Systematics, 1–33. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-1.

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Rieppel, Olivier. "Epilogue." In Phylogenetic Systematics, 323–25. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-10.

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Rieppel, Olivier. "Of Parts and Wholes." In Phylogenetic Systematics, 35–66. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-2.

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Rieppel, Olivier. "The Turn against Haeckel." In Phylogenetic Systematics, 67–106. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-3.

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Rieppel, Olivier. "The Rise of Holism in German Biology." In Phylogenetic Systematics, 107–47. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-4.

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Rieppel, Olivier. "The Rise of German (“Aryan”) Biology." In Phylogenetic Systematics, 149–85. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-5.

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Rieppel, Olivier. "Ganzheitsbiologie." In Phylogenetic Systematics, 187–242. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-6.

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Rieppel, Olivier. "The Ideological Instrumentalization of Biology." In Phylogenetic Systematics, 243–80. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-7.

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Rieppel, Olivier. "A New Beginning." In Phylogenetic Systematics, 281–302. Boca Raton : Taylor & Francis, 2016. | Series: Species and systematics: CRC Press, 2016. http://dx.doi.org/10.1201/b21805-8.

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Conference papers on the topic "Phylogenetic"

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STANLEY, SCOTT, and BENJAMIN A. SALISBURY. "PHYLOGENETIC GENOMICS AND GENOMIC PHYLOGENETICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0047.

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Daskalakis, Constantinos, Elchanan Mossel, and Sébastien Roch. "Optimal phylogenetic reconstruction." In the thirty-eighth annual ACM symposium. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1132516.1132540.

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Snell, Q., M. Whiting, M. Clement, and D. McLaughlin. "Parallel Phylogenetic Inference." In ACM/IEEE SC 2000 Conference. IEEE, 2000. http://dx.doi.org/10.1109/sc.2000.10062.

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Bansal, Mukul S. "Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation." In 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2016. http://dx.doi.org/10.1109/iccabs.2016.7802785.

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Berry, Vincent, and David Bryant. "Faster reliable phylogenetic analysis." In the third annual international conference. New York, New York, USA: ACM Press, 1999. http://dx.doi.org/10.1145/299432.299457.

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Katariya, Priyank Raj, and Sathish S. Vadhiyar. "Phylogenetic Predictions on Grids." In 2009 5th IEEE International Conference on e-Science (e-Science). IEEE, 2009. http://dx.doi.org/10.1109/e-science.2009.17.

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Hwa, Kuo-Yuan, Hsing-Hsang Hung, and Chen-Hsing Chen. "Phylogenetic Analysisof Trichomonade Xylosyltransferases." In 2007 Frontiers in the Convergence of Bioscience and Information Technologies. IEEE, 2007. http://dx.doi.org/10.1109/fbit.2007.109.

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Hayden, James E. "Phylogenetic prediction: Analytical considerations." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.110120.

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Blackburn, Michael B. "Phylogenetic analysis of insecticidalChromobacterium." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.112826.

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Hunt, Warren A., and Serita M. Nelesen. "Phylogenetic trees in ACL2." In the sixth international workshop. New York, New York, USA: ACM Press, 2006. http://dx.doi.org/10.1145/1217975.1217996.

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Reports on the topic "Phylogenetic"

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Nierzwicki-Bauer, S. A. Phylogenetic relationships among subsurface microorganisms. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/6106595.

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Nierzwicki-Bauer, S. A. Phylogenetic relationships among subsurface microorganisms. Progress report. Office of Scientific and Technical Information (OSTI), December 1991. http://dx.doi.org/10.2172/10106325.

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Bruice, Thomas C. DNG and RNG Phylogenetic Single Cell Probes. Fort Belvoir, VA: Defense Technical Information Center, February 1999. http://dx.doi.org/10.21236/ada360479.

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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using rRNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, June 1989. http://dx.doi.org/10.21236/ada209595.

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Lapedes, A. S., B. G. Giraud, L. C. Liu, and G. D. Stormo. Correlated mutations in protein sequences: Phylogenetic and structural effects. Office of Scientific and Technical Information (OSTI), December 1998. http://dx.doi.org/10.2172/296863.

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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using Tau RNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, February 1991. http://dx.doi.org/10.21236/ada254451.

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Nierzwicki-Bauer, S. A. Phylogenetic relationships among subsurface microorganisms. Project technical progress report. Office of Scientific and Technical Information (OSTI), August 1993. http://dx.doi.org/10.2172/10171574.

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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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9

Balkwill, D. L., and R. H. Reeves. Physiological and phylogenetic study of microbes from geochemically and hydrogeologically diverse subsurface environments. Office of Scientific and Technical Information (OSTI), January 1991. http://dx.doi.org/10.2172/5026959.

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10

Gardner, S., and C. Jaing. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees. Office of Scientific and Technical Information (OSTI), March 2012. http://dx.doi.org/10.2172/1047247.

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