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Topic: Phylogenetics

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	CLC bio: Phylogenetics
		Phylogenetics is therefore an integral part of the science of systematics that aims to establish the phylogeny of organisms based on their characteristics.
		Furthermore, phylogenetics is central to evolutionary biology as a whole as it is the condensation of the overall paradigm of how life arose and developed on earth.
		The phylogenetic tree in figure 2.1 is rooted at the most recent common ancestor of all Hominidae species, and therefore represents a hypothesis of the direction of evolution e.g.
	www.clcbio.com /index.php?id=46 (1390 words)

	Britain.tv Wikipedia - Phylogenetics
		In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations).
		Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of, phylogenetic systematics, constitutes a means of classifying groups of organisms according to degree of evolutionary relatedness.
		All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.
	www.britain.tv /wikipedia.php?title=Phylogenetics (617 words)

	Phylogenetics Factsheet
		Phylogenetic systematics is that field of biology that does deal with identifying and understanding the evolutionary relationships among the many different kinds of life on earth, both living (extant) and dead (extinct).
		A phylogenetic tree is composed of nodes, each representing a taxonomic unit (species, populations, individuals), and branches, which define the relationship between the taxonomic units in terms of descent and ancestry.
		Branches on phylogenetic trees may be scaled (top panel) representing the amount of evolutionary change, time, or both, when there is a molecular clock, or they may be unscaled (middle panel) and have no direct correspondence with either time or amount of evolutionary change.
	www.ncbi.nlm.nih.gov /About/primer/phylo.html (5910 words)

	Teaching Animal Molecular Phylogenetics (Site not responding. Last check: 2007-10-12)
		Annelida and Arthropoda are not sister taxa: A phylogenetic analysis of spiralian metazoan morphology.
		Phylogenetic relationships among extant classes of echinoderms, as inferred from sequences of 18S rDNA, coincide with relationships deduced from the fossil record.
		Phylogenetic position of the mitochondrion-lacking protozoan Trichomonas tenax, based on amino acid sequences of elongation factors 1∝ and 2.
	www.mhhe.com /biosci/pae/zoology/animalphylogenetics/references.mhtml (1118 words)

	29+ Evidences for Macroevolution: Phylogenetics
		Phylogenetics is the scientific discipline concerned with describing and reconstructing the patterns of genetic relationships among species and among higher taxa.
		Phylogenetic trees are normally portrayed with two dimensions: a time dimension and a morphological dimension.
		In order to establish their validity in reliably determining phylogenies, phylogenetic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed.
	www.talkorigins.org /faqs/comdesc/phylo.html (5163 words)

	[No title]
		The goal of phylogenetics, whether based on molecules or morphology, is to reconstruct the evolutionary history of groups of organisms.
		Molecular phylogenetics has gained wide acceptance in spite of these and other problems because it provides a large amount of evidence that is independent of morphology, as well as other advantages.
		Molecular Phylogenetic Trees as Alternative Hypotheses As noted before, if a character is not consistent with one phylogenetic tree, then a molecular phylogenetic tree provides an alternative hypothesis that may better explain the evolution of the character.
	www.mhhe.com /biosci/pae/zoology/animalphylogenetics/molecular.doc (17024 words)

	Applied Phylogenetics (Site not responding. Last check: 2007-10-12)
		Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at levels of organization ranging from molecules to ecosystems.
		The construction of phylogenetic trees is becoming a methodology that is well-defined, with broad agreement on the central issues and questions.
		On the other hand, applications of phylogenetic methods to interesting problems outside of systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely.
	ginger.ucdavis.edu /sandlab/ap.htm (424 words)

	Lect 2 overview of phylogenetics
		Phylogenetics attempts to uncover the branching pattern of the tree of life.
		A phylogenetic perspective is important to any of these kinds of questions, and many other very different sorts of questions.
		An unsettling aspect of phylogenetic analyses is their sensitivity to the number and nature (e.g., choice of outgroup) of the taxa included in the analysis.
	www.uwyo.edu /dbmcd/molmark/lect02/lect2.html (1876 words)

	SASB Introduction to Phylogenetics
		Phylogenetic analysis was originally developed by biological systematists who wanted to reconstruct evolutionary genealogies of species based on morphological similarities.
		The results of phylogenetic analysis may be depicted as a hierarchical branching diagram, a "cladogram" or "phylogenetic tree" (e.g.
		Swofford D.L., Olsen G.J., Waddell P.J. and Hillis D.M. Phylogenetic inference.
	www.science.uts.edu.au /sasb/WestonCrisp.html (1436 words)

	INI Programme PLG -
		Phylogenetics is the reconstruction and analysis of trees and networks to describe and understand the evolution of species, populations and individuals.
		Although the foundations of phylogenetics were laid down many decades ago, it is currently experiencing an exciting renaissance due to the wealth and types of biological data that are now becoming available.
		The main themes that will be worked on during this programme are new data types in phylogenetics; modelling reticulate evolution; constructing large trees; probabilistic models of evolution; and phylogenetic combinatorics.
	www.newton.cam.ac.uk /programmes/PLG/index.html (190 words)

	Phylogenetics Glossary (Site not responding. Last check: 2007-10-12)
		In phylogenetic analysis, the optimal tree under the maximum likelihood criterion is the tree that is the most likely to have occurred given the observed data and the assumed model of evolution.
		In phylogenetic analysis, the optimal tree under the maximum parsimony criterion is the tree that requires the fewest number of character-state changes (which may be differentially weighted across characters and/or character-states).
		Outgroup One or more taxa assumed to be phylogenetically outside the ingroup that are used as a rooting point of a phylogenetic tree and may be used to assign the direction of change to character-state transformations.
	www.bcu.ubc.ca /~otto/EvolDisc/Glossary.html (1155 words)

	Bonnie's Phylogenetics Reference
		The formal definition of phylogenetics from the Oxford University Press reads; "Phylogenetics is the taxonomical classification of organisms on the bases of their degree of evolutionary relatedness".
		TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers." Biologists may submit their data to this database as a way to make it available to the general community, especially if their publication didn't or couldn't give complete details as to what was done.
		Phylogenetics can be a powerful method of taxonomy when properly understood.
	homepage.usask.ca /~blc257/Cmpt857.html (1453 words)

	UCMP Glossary: Phylogenetics
		phylogenetics -- Field of biology that deals with the relationships between organisms.
		Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans.
		Systematics is usually divided into the two areas of phylogenetics and taxonomy.
	www.ucmp.berkeley.edu /glossary/gloss1phylo.html (1380 words)

	Principles of Phylogenetics: IB200A
		This project will be a phylogenetic analysis of the interrelationships among a set of taxa using all major available methodologies.
		In addition to a written report in the form of a professional journal publication, we will have a mini-symposium at the end of the term where students can give a short presentation of their results.
		IB 200B "Principles of Phylogenetics: Ecology and Evolution" (taught in odd-numbered years), Both are intended for graduate students and advanced undergraduates.
	ib.berkeley.edu /courses/ib200a (274 words)

	Rediscovering Biology - Online Textbook: Unit 3 Evolution and Phylogenetics
		Instead, he used the phrase "descent with modification." Evolutionary classification today is based on those two central features of evolution: groups of organisms descend from a common ancestor and, with the passage of time, acquire modifications.
		Cladistic analysis, also known as cladistics and phylogenetic systematics, is the main approach of classification used in contemporary evolutionary biology.
		The German taxonomist Willi Hennig developed cladistics in 1950, but his work was not widely known until it was translated into English in 1966.
	www.learner.org /channel/courses/biology/textbook/compev/compev_3.html (1087 words)

	Amazon.com: Molecular Evolution and Phylogenetics: Books: Masatoshi Nei,Sudhir Kumar (Site not responding. Last check: 2007-10-12)
		Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students.
		Accordingly, attention is shifted to reviewing many recent advances in methods of phylogenetic inference with an obvious bias towards distance methods, particularly those which the senior author devised.
		It stands as a unique contribution because the authors explain the mathematical and conceptual framework of a given topic in molecular evolution or phylogenetic analysis and give subsequent examples to show how various analytical methods can be applied to the study of that topic.
	www.amazon.com /Molecular-Evolution-Phylogenetics-Masatoshi-Nei/dp/0195135857 (1651 words)

	Phylogenetics - Wal-Mart
		'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics.
		The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species.
		This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics.
	www.walmart.com /catalog/product.gsp?product_id=2017049 (670 words)

	Introduction to Bayesian phylogenetics — Agapow.net site (Site not responding. Last check: 2007-10-12)
		(In phylogenetic terms, we would want to know what frequency particular clades and subtrees occur at.) So what we need is a way of sampling those solutions in a logical manner.
		In this case the data is snake-eyes and our model is the idea that the dice is fair, every side has the same chance of coming up and is independent of the other die and therefore the chance of rolling a 1 on either die is 1 in 6.
		There are a number of programs you can use for Bayesian phylogenetics, but in practice there are only three, and actually only one.
	www.agapow.net /teaching/kew2003_phylogenetics (3231 words)

	p4, a Python package for phylogenetics
		P4 is a Python package that does maximum likelihood and Bayesian phylogenetic analyses on molecular sequences.
		For those who like to tinker, p4 can be used as a phylogenetic toolkit, the elements of which you can string together in different ways depending on the job at hand.
		It is useful for programmatic manipulation of phylogenetic data and trees.
	www.nhm.ac.uk /research-curation/projects/software/p4.html (211 words)

	IB200 - Principles of Phylogenetics - UC Berkeley (Site not responding. Last check: 2007-10-12)
		This course covers applications of phylogenetics to ecology, evolution, development, functional morphology, populational genetics, conservation, biogeogeography, and speciation that are revolutionizing those fields.
		This project is an important practical experience; we allow (in fact, encourage) students to focus on questions that they are studying for their thesis or other research.
		IB 200A covers the core theory and methodology for comparative biology: phylogenetic analyses using morphology and molecules, and living and fossil organisms.
	ib.berkeley.edu /courses/ib200b (168 words)

	T. Collins: Advanced Phylogenetics
		The emphasis will be on bringing students up to speed on current methodological and conceptual issues in the literature of phylogenetic analysis, as well as sampling the range of biological problems that can be addressed.
		Farris, J. The logical basis of phylogenetic systematics, pp.7-36 in N.I. Platnick, and V. Funk (eds.) Advances in Cladistics.
		Krajewsji, C. Phylogenetic measures of biodiversity: A comparison and critique.
	www.fiu.edu /~collinst/courseinfo/advphylo.html (840 words)

	[No title]
		Itai Yanai Molecular Genetics Department Weizmann Institute of Science, Rehovot 76100, Israel itai.yanai@weizmann.ac.il http://bioinformatics.weizmann.ac.il/~iyanai Phylogenetics and the Tree of Life Evolution Trees are the icons of evolutionary biology, and not haphazardly.
		Haeckel is notorious today for misrepresentation of experimental results and biologically “based” racism, however he should be remembered also as the first person to seriously work towards Dawin’s vision of unraveling the history of life.
		Maximum parsimony as a character-state phylogeny method A drawback of the distance based methods such as UPGMA and NJ is that the sequences are summarized by a distance matrix, never to be examined in detail.
	bioportal.weizmann.ac.il /course/evogen/Phylogenetics/Phylogenetics.doc (3260 words)

	The Bibliography of Crocodilian Biology: Phylogenetics (Site not responding. Last check: 2007-10-12)
		Most of the references were provided by Chris Brochu, Univ. Texas at Austin, who studies the phylogenetic relationships of eusuchians.
		A reanalysis of Bernissartia fagesii, with comments on its phylogenetic position and its bearing on the origin and diagnosis of the Eusuchia.
		Willis, P.M.A. The phylogenetic systematics of Australian crocodilians, their bearing on the biostratigraphic relationships of Oligo-Miocene sites at Riversleigh, northwestern Queensland and the wider biocorrelations of those deposits with other Australian Oligo-Miocene deposits.
	utweb.ut.edu /faculty/mmeers/bcb/phylo.html (567 words)

	IB200 - Principles of Phylogenetics - UC Berkeley (Site not responding. Last check: 2007-10-12)
		This course covers the many applications of phylogenetics to ecology, behavior, development, functional morphology, populational genetics, conservation, biogeogeography, and speciation that are revolutionizing those fields.
		This project is an important practical experience; we allow (in fact, encourage) students to focus on organisms that they are studying for their thesis or other research.
		IB 200A covers the core theory and methodology for comparative biology: phylogenetic analysis with emphases on both morphology and molecules, and both living and fossil organisms--to be offered spring 2000!
	ucjeps.berkeley.edu /bryolab/ib200 (193 words)

	Phylogenetics (Site not responding. Last check: 2007-10-12)
		PHYLOGENETICS is a branch of evolutionary studies which deliberately tries to reconstruct evolutionary trees that show the relationships of existing and/or fossil species.
		Organisms that are more similar to each other are closer together on the tree, or have more recent common ancestors.
		Analyses of nucleotide composition showed that two of the lineages in the Carcharhinidae family differ significantly from the other members of the Carcharhinidae.
	www.science.mcmaster.ca /biology/CBCN/genetics/ply_phylogenetics.html (204 words)

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