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| | Population Thinking and Tree Thinking in Systematics |
 | | Don’t worry if your tree is not perfect or if you can’t remember technical terminology; this is not a graded exercise, and you should not even put your name on the page.” Most trees the students produced have as their longest branches the ones leading humans or to mammals or vertebrates generally. | | | Tree thinking may be contrasted with two other ways of thinking about systematics and large-scale evolutionary phenomena. | | | There is another aspect of group thinking that tree thinking is supplanting, and that is the traditional inclination to regard taxa of equal rank within certain large groups as equivalent and comparable in some sense. |
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http://rjohara.net/cv/1997Scripta.html
(3698 words)
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| | Telling the Tree: Narrative Representation and the Study of Evolutionary History |
| | If evolutionary biologists are concerned that not only students but also their colleagues in other disciplines learn these principles correctly—and I believe they should be so concerned—then they need to give attention to the processes by which their research results are simplified. | | | Conclusions about evolutionary processes that are based on the structure of trees that have been, by selective simplification, brought into alignment with preexisting nomenclature probably say less about evolution than they do about the narrative character of the preexisting nomenclature. | | | Those of us who work in the historical sciences of systematics and evolutionary biology often think of ourselves as being more aware of the historicity of nature—more aware of the natural past—than are our colleagues in the physical and functional sciences. |
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http://rjohara.net/cv/1992BP.html
(8443 words)
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| | Bioinformatics and Genomics - Week 14 |
| | The primary assumption in all phylogenetic analyses is that all organisms are actually related, and that the real problem is that of determining just how close or distant the relationship is, and what evolutionary tree describes how the current organisms evolved (the "true" tree). | | | The primary assumption in all phylogenetic analyses is that all organisms are actually related, and that the real problem is that of determining just how close or distant the relationship is, and via what evolutionary tree the current organisms evolved and by what process. | | | UPGMA stands for Unweighted Pair Group Method with Arithmetic Mean) depend on this notion in their construction of the tree. |
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http://www.library.csi.cuny.edu/~davis/Bio_326/lectures/lect14/lect_14.html
(4517 words)
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| | Problems of Building a Consistent Evolutionary Tree -- Evolution or Creation? -- Faith Facts |
| | While hair comes in different varieties—from quills in porcupine to soft fur of a kitten-no structures are known which can be considered in any sense transitional between any other vertebrate structure and hair. | | | But these different methods lead to different conclusions about taxonomy, suggesting that life forms are non-branching—a problem for the evolutionist. | | | As an example, Denton discusses mammalian hair, and points out that there is no evolutionary pre-cursor. |
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http://faithfacts.gospelcom.net/ev_origins_b.html
(2492 words)
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| | Evolutionary Threads |
| | Given this position, the politics of evolutionary psychology still seems a little of a fence-saving compromise, avoiding the issue of individual genetic differences by claiming essentially a 'group selectionist' position that individual differences are not significant in evolutionary psychology, but only characteristics shared by society or the human species. | | | Possibly, but there is a fundamentally deeper problem, to do with the famous myth of evolutionary progress, decried by neo-Darwinists and Stephen Jay Gould's ilk alike, perhaps their only point of agreement - the opposition to the idea that evolution means inevitable progress of types in some teleological or utopian sense. | | | On the other hand it is clear that sociobiology, genes, culture, individual effort and ethical choice all play a role in individual decision-making and the actions we take, so attempting to reduce freedom of choice to genetic determinism is clearly another kind of mechanistic fallacy. |
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http://www.dhushara.com/book/evol/evol.htm
(5136 words)
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| | HHMI News: Molecular Biologists Prune Branches from the Animal Family Tree |
| | The data on jellyfish and sponges-organisms which are radially symmetric, like a tire-are incomplete and therefore difficult to interpret, Grenier says. | | | For example, investigators may need to reexamine their choices of model species for basic research. | | | The new understanding should also prompt changes in the way students are taught, Grenier says. |
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http://www.hhmi.org/news/carroll.html
(774 words)
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| | Field Museum plays key role in massive project to map Tree of Life |
| | These relationships will serve as a comparative framework with which to organize and understand the vast amount of information already available on avian ecology, evolution, physiology and behavior. | | | Field Museum scientists will help lead three of the seven grants recently awarded to researchers around the world to construct a new framework for understanding the evolutionary relationships between all species, extinct and living. | | | This project will attempt to uncover the evolutionary patterns among archosaurs, focusing on theropods. |
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http://www.eurekalert.org/pub_releases/2002-10/fm-fmp103002.php
(1193 words)
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| | Phylogeny |
| | The final goal of such an analysis is to prepare an evolutionary tree describing the relationship of the various taxa with respect to each other. | | | LDH_L for mouse and LDH_M for rat) is available and isoenzyme data are missing, then the resulting phylogeny would suggest a much earlier separation of mouse and rat. | | | Keep in mind that in the case of bootstrap analysis only nodes that occur in more than 95% of the cases are reliable. |
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http://www.icp.ucl.ac.be/~opperd/private/phylogeny.html
(1346 words)
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| | "Evidence of Evolutionary Transitions" by Michael J. Benton, Ph.D. |
| | Summary: This lesson focuses on applying evidence for evolutionary transitions to the general theory of evolution. | | | The role of missing links is most difficult to understand. | | | All life is related on the tree of life. |
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http://www.actionbioscience.org/evolution/benton2.html
(2127 words)
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| | Evolution - Wikipedia, the free encyclopedia |
| | Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems. | | | The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of ecology. | | | Evolutionary biology is a kind of meta field because it includes scientists from many traditional taxonomically oriented disciplines. |
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http://en.wikipedia.org/wiki/Evolution
(3641 words)
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| | Science News Online (2/6/99): DNA's Evolutionary Dilemma |
| | Similarities in facial characteristics and skin tone between Africans and Melanesians probably represent common human adaptations to life in a tropical climate, Templeton says. | | | One after another, investigators concluded that modern humans probably arose in Africa around 200,000 years ago and then spread elsewhere, replacing Neandertals and any other species in our evolutionary past. | | | According to the theory, they therefore have existed as a relatively separate population for a longer time. |
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http://www.sciencenews.org/sn_arc99/2_6_99/bob1.htm
(2227 words)
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| | Tree of Life Help |
| | Instruction on how you can locate the ToL page for a particular group of organisms. | | | Each ToL page focuses on one particular group. | | | The Tree of Life is a collection of WWW pages illustrating the phylogenetic (or evolutionary) tree of organisms, and presenting information about the characteristics of thousands of different groups of organisms. |
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http://tolweb.org/tree/home.pages/treehelp.html
(257 words)
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| | human evolution: The Evolutionary Tree |
| | Feeling humans and social animals: Theological considerations for an evolutionary account of human emotion. | | | EVOLUTIONARY BIOLOGY: Preparing the Ground for a Modern 'Tree of Life' (Science) | | | EVOLUTION: Evolutionary Pulse Found, But Complexity as Well (Science) |
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http://www.infoplease.com/ce6/society/A0858697.html
(322 words)
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| | PHYLOGENETIC ANALYSIS |
| | Stochastic processes may model evolutionary changes where each "position" evolves independently. | | | Phylogenetic analysis is the study of these evolutionary relationships. | | | The other major approach for constructing evolutionary tree is the character-based approach. |
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http://www.msci.memphis.edu/~giri/compbio/f99/hari/hari.html
(1070 words)
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| | Fungi Classficatiom - Evolutionary Tree |
| | As further research continues, their position within the evolutionary tree can change. | | | Fungi of this Subdivision lack a sexual stage and are consequently called the Fungi Imperfecti because their life cycles are "imperfect". | | | For more detail try some of these links, and hopefully not become as confused as I in trying to make some sense of it all. |
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http://www.hiddenforest.co.nz/fungi/class/tree.htm
(205 words)
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| | Bioinformatics Research at the University of Waterloo |
| | The results of a simulation study that strongly support the practicality, efficiency and effectiveness of hypercleaning are also presented. | | | This technique is a substantial improvement over previous algorithms in its ability to recover edges of the evolutionary tree. | | | More precisely, the hypercleaning technique computes from sequence data a small subset of edges that is likely to contain most edges of the correct tree. |
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http://monod.uwaterloo.ca/papers/expanded.php?paper=2000002
(264 words)
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| | Man’s Social Evolutionary Tree |
| | This rather rude sort of behavior soon invoked much peer pressure, which soon turned into evolutionary pressure. | | | Now women, by virtue of their growing power and influence, took charge of the evolutionary tree, and selected men who were sensitive, considerate, had tiny little testicles, and who looked like either Alan Alda or Phil Donahue. | | | However, the most intelligent women were too busy creating their own little castles to find time to mate, and pretty soon the world was filled with the offspring of sensitive men and stupid women. |
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http://www.homestead.com/flowstate/files/zevoltree.htm
(971 words)
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| | Evolutionary Tree of Fishes |
| | Some of the traits that distinguish evolutionary groups are not as easily observed as these, and have been discovered by studying DNA. | | | A chart on the floor of the display demonstrates that a graphic representation of the relationships revealed by examining shared traits looks like a branching tree rather than the straight line that many have envisioned evolution to resemble. | | | Thus as a group they have an ancestry distinct from that of rays. |
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http://www.amnh.org/exhibitions/expeditions/treasure_fossil/Treasures/Evolutionary_Tree_of_Fish/fish.html?sea
(232 words)
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| | Cornell Lab of Ornithology |
| | One of the most direct is in clarifying our understanding of evolutionary relationships. | | | Each of these research groups is responsible for providing DNA information on one subgroup within the larger Emberizine radiation. | | | For example, our research has already shown that a number of species of birds long considered to be warblers are not closely related to the “true” warblers. |
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http://birds.cornell.edu/evb/Projects_WarblerTree.htm
(441 words)
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| | Molecular Cytogenetics and Genome Organization - Pat Heslop-Harrison |
| | The various patterns of the tandem array internal structure is likely to have resulted from the evolutionary interplay, array homogenization and the generation of heterogeneity mediated by double-strand breaks (DSBs) and associated repair mechanisms. | | | The results suggest that the mantled phenotype is not caused by major rearrangements of transposable elements but may relate to changes in the methylation pattern of other genomic components. | | | It is concluded that many of the protective features form a prophylactic shield and are key components of the angiosperms in general, which may have contributed to their evolutionary success as a group. |
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http://www.le.ac.uk/biology/phh4/titleabst.htm
(13464 words)
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| | An Effective Approach for Constructing the Phylogenetic Tree on a Grid-Based Architecture |
| | The quantitative nature of species relationships therefore requires the development of more rigorous methods for tree construction. | | | Reconstructing evolutionary tree is a major research problem in biology, and this problem is often known as phylogeny problem. | | | In biological research, scientists often need to use the information of the species to infer the evolutionary relationship among them. |
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http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/bibe/2004/2173/00/2173toc.xml&DOI=10.1109/BIBE.2004.1317335
(330 words)
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| | Chapter 22 Comments |
| | For our understanding of evolutionary biology the word survival means "successful in reproduction" only! | | | one might wonder what the figure legend means when it says "Ancient forms are low on the tree." Perhaps this really means that extant organisms thought to be most-similar to common ancestors are nearer to the base of the tree. | | | As variants become isolated into the areas where they are most successful, additional changes lead to speciation. |
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http://koning.ecsu.ctstateu.edu/Plant_biology/ch22.html
(1171 words)
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| | Microbiology: Discovering the 3 Domains of Life |
| | Archaea means "ancient" because use ancient energy mechanisms | | | Organisms that differ by only a few bases have diverged more recently in evolutionary time than organisms that differ by many bases. | | | Exercise: Constructing an evolutionary tree by error analysis |
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http://mmedia.ucc.uconn.edu/~terry/Common/3domains.html
(1093 words)
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| | Mapping individual gene data on an evolutionary tree |
| | Evolutionary trees are an important instrument in inter-genome analysis. | | | Resulting gene histories will be interpreted as histories of different pathogenic functions for further analysis and use. | | | This project is devoted to a related problem - developing methods of interpretation of various types of data on the extant species by mapping them in a biologically meaningful way onto an evolutionary tree and annotating the tree nodes with relevant evolutionary events. |
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http://www.dcs.bbk.ac.uk/~mirkin/Mapp2.html
(705 words)
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| | Der Stammbaum des Menschen |
| | The "genealogical tree" of Haeckel is set forth in its original form in Haeckel's General Morphology and developed in his later writings. |
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http://genome.imb-jena.de/stammbaum.html
(135 words)
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| | Evolutionary tree - Encyclopedia.WorldSearch |
| | Hypothetically taxonomy would follow the tree whenever possible, but in many places it does not at present. | | | Most of the tree was based on ideas from cladistics; where more than two groups are shown in a single branch, there is disagreement about how they diverged. | | | Evolutionary relationships of casque-headed tree frogs with co-ossified skulls (family Hylidae) (University of Kansas publications, Museum of Natural History, v. |
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http://encyclopedia.worldsearch.com/evolutionary_tree.htm
(222 words)
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| | Evolutionary Trees and Multiple Alignment |
| | Nevertheless it is a reasonable approach when the strings are similar and a prototype program of this kind has been written for the 1-state model. | | | A theory is a house made of hypotheses. | | | The value of DAGs is that in sections where there is consensus between the strings, the effective number of neighbours of a cell in the DPA "matrix" is much reduced. |
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http://www.csse.monash.edu.au/~lloyd/tildeStrings/Multiple/92.HICSS_25
(6485 words)
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| | Discovering Biodiversity |
| | Ecologists and evolutionary biologists are of course within our intended audience, but the course is also of relevance to students throughout the life sciences, because the genetic structure of life's history has broad-reaching implications and applications throughout biology. | | | A travelogue through highlights in the Tree of Life, from archaeans and bacteria through the eukaryotes (protists, plants, fungi, and animals), with portraits of interesting organisms and their evolutionary stories. | | | Phylogeny &; Phylogeny, which is the evolutionary tree linking all species genetically, is a fundamental part of the structure of life's history. |
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http://salticidae.org/2005Bio448G
(695 words)
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| | EVOLUTIONARY TREE OF BIOLOGICAL VISION |
| | Return to the Phylogenic Tree page describing the species frequently used in vision research and the primates in particular. | | | The tree is formed based on the presence of retinol (Vitamin A) in their systems. | | | Three distinct types of Vitamin A have found that relate to the visual system. |
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http://www.4colorvision.com/files/evoltree.htm
(290 words)
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| | [No title] |
| | The problem can be formally expressed as a PAC-learning problem. | | | I will spend some time describing the model and explaining concepts and then give some of the ideas we used to design the algorithm and prove its correctness. | | | In this model, an evolutionary tree is a tree with n leaves: each leaf represents a species, and each edge represents a period of evolutionary change induced by the stochastic process for that edge. |
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http://www.cs.ucd.ie/events/seminars/abstracts/cryan09_11_01.txt
(286 words)
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| | Tree Set Visualization Project |
| | Systematitists can collect molecular data, such as nucleotide or amino acids, or they can use morphological or behavioral information to construct an evolutionary tree. | | | A set of trees may include several optimal or near-optimal parsimony trees or the set of trees may be the trees sampled during a Bayesian analysis. | | | This research project is supported by a grant from the National Science Foundation, NSF-ITR 0121651/0121682: "Collaborative Research: Exploring the Tree of Life." |
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http://comet.lehman.cuny.edu/treeviz
(217 words)
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| | The New Evolutionary Tree: Five Kingdoms of Life |
| | This older view recognized two or at most three kingdoms of life (plants, animals, unicells), each of which was also pictured as a tree. | | | Such a model equalizes the evolutionary status of all five major life kingdoms, each of which still continues with its particular adaptation to this day. | | | The mutual interaction between microbes which cycle sulfur gases, methane and amonia, plants which release oxygen, absorbing carbon dioxide, and animals which excrete CO2 and breathe oxygen, is the fundamental, metabolic energy exchange of the biosphere. |
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http://www.svn.net/rmetzner/geo_kingdoms.html
(1237 words)
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| | Wildlife News: Squirrels' evolutionary 'family tree' reveals major influence of climate |
| | The first-ever genetic delineation of nearly all existing squirrel groups suggests not only some surprising branchings in the squirrels' family tree. | | | The study also reveals strong evidence that geological and climatic change influenced how their ancestors evolved and spread over 36 million years from just one part of ancient North America to nearly all of today's world. | | | The exception among South American tree squirrels is a pygmy variety that the researchers' evidence suggests diverged from other squirrels as long as 35 million years ago, when South America was still presumably isolated. |
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http://www.naturalworldtours.co.uk/articles2003/feb/feb2203a.htm
(1107 words)
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| | Portsmouth Herald World/National News: Fossil found in Kenya could redefine evolutionary tree |
| | That means anthropologists may have to rethink the human evolutionary tree. | | | Leakey said the species represented by the new skull could have been an ancestor of modern humans, or it could have been an evolutionary dead end. | | | But he said it also adds to evidence that there were several human-like species between 2 million and 3.5 million years ago that adapted well to different environments. |
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http://www.seacoastonline.com/2001news/3_22_w1.htm
(687 words)
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| | UCI biologist proposes pruning human evolutionary tree 06/26/03 |
| | Homo species are characterized by larger brains and increased bipedal activity. | | | There are as many as seven recognized groups or branches to the Hominid tree, which encompass the entire human lineage. | | | Its species are notable for distinct differences from the Hominids that evolved into human beings, such as having thin molar enamel, similar to that of the African great apes. |
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http://www.irvineworldnews.com/Astories/june26/ucievolve.html
(609 words)
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| | Fossils cited as missing branch of evolutionary tree - 3/15/00 |
| | The finding was reported in the science journal Nature. | | | Scientists from the Carnegie Museum of Natural History in Pittsburgh, Northwestern University Medical School in Chicago and the Institute of Vertebrate Paleontology & Paleoanthropology in Beijing contributed to the study. | | | Much of the debate in the field has been to figure out which of those early prosimian fossil primates gave rise to anthropoids," he said. |
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http://www.detnews.com/2000/religion/0003/15/03160010.htm
(376 words)
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| | Life on Earth |
| | Unless you are a Tree of Life developer, you really shouldn't be here. | | | This page is part of our beta test site, where we develop new features for the ToL, often messing up a thing or two in the process. | | | Each ToL branch page provides a synopsis of the characteristics of a group of organisms representing a branch of the Tree of Life. |
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http://tolweb.org/tree?group=Life_on_Earth&contgroup=
(175 words)
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| | Kids.net.au - Encyclopedia Phylogenetic tree - |
| | is a tree of several life forms and their relations. | | | Kids.net.au - Search engine for kids, children, educators and teachers - Searching sites designed for kids that are child safe and clean. |
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http://www.kids.net.au/encyclopedia-wiki/ph/Phylogenetic_tree
(42 words)
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| | [No title] |
| | This method is demonstrated on SH2-domain containing proteins, resulting in a change in the SwissProt subfamily assignment for Src2_drome, and a suggested evolutionary relationship between Nck_human and Drk_drome, Sem5_caeel, Grb2_human and Grb2_chick. | | | Bete is also computationally efficient in the number of taxa (n^2 log(n), where n=the number of taxa), so that large numbers of sequences (in the hundreds) may be used as input to the tree-estimation process. | | | It is robust with respect to differing evolutionary clocks among taxa, differing mutation rates at sites in the molecule, handles deletions of portions of the molecule among taxa, and produces tree topologies that agree more closely with accepted phylogenies and functional subgroups within the data. |
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http://alumni.cse.ucsc.edu/~kimmen/papers.html
(1246 words)
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| | How to read an evolutionary family tree |
| | However, these explanatory tools can also be confusing, and in some cases misleading, when the illustrations and their implications are not fully explained. | | | The dotted lines reinforce the fact that there is no evidence to prove the existence of a common ancestor for the insects shown. | | | Charts and diagrams can be wonderful aids in giving clarity and visual reinforcement to a point, or lesson, one is trying to make. |
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http://www.answersingenesis.org/docs/1274.asp
(307 words)
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| | Creation Moments - Radio |
| | It is supposed to depict how life began as a single-celled organism and over immense periods of time mutated into all the various forms of life we see today. | | | We have offered several Creation Moments programs recently that explained how new genetic studies simply don't support this evolutionary tree. | | | New genetic information shows that there is not one trunk to the tree of life. |
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http://www.creationmoments.com/radio/transcript.asp?track_id=786
(294 words)
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| | Biological Complexity - Evolutionary Tree of Life |
| | The story of terrestrial evolution is about continual variation in the genetic make-up of species and the ecological effects of those variations. | | | Genetic change is the basis of biological evolution &; an ever-developing pattern of species in interacting ecosystems distributed across the globe. | | | The historical record of the genetic changes that have taken place during the last four billion years is rather like a web, especially because of occasional "horizontal gene transfer" between species, but it is often presented as a tree or star diagram. |
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http://www.phy.auckland.ac.nz/staff/prw/biocomplexity/evolutionary_tree.htm
(382 words)
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| | The Cockroach Home Page |
| | Why are the Cockroaches a good group in which to study... | | | Where are some of your favorite cockroaches on the above tree? | | | Go to the 'Tree of Life' Web Site to see where the cockroaches have been fit into the scheme of animal evolution. |
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http://www.bio.umass.edu/biology/kunkel/cockroach.html
(183 words)
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| | Using Traveling Salesman Problem Algorithms for Evolutionary Tree Construction |
| | To do this, the problem of tree construction is reduced to the Traveling Salesman Problem (TSP). | | | We present a new tree construction method that constructs a tree with minimum score for a given set of sequences. | | | For data sets with large errors, a dynamic programming approach is used to reconstruct the tree. |
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http://www.inf.ethz.ch/personal/gonnet/papers/Construction/Construction.html
(170 words)
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| | Tree of Life Web Project Home |
| | Though their skulls are not uncommon, there is little yet known about their postcrania..."read more | | | Each page contains information about a particular group of organisms (e.g., echinoderms, tyrannosaurs, phlox flowers, cephalopods, club fungi, or the salamanderfish of Western Australia). | | | On more than 4000 World Wide Web pages, the project provides information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics. |
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http://tolweb.org/tree/phylogeny.html
(229 words)
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| | Evolutionary Relationships of Archosaurs |
| | The cladogram depicts the evolutionary relationships between some major groups of archosaurs ("ruling reptiles") and their relatives. | | | Near the base of the tree are the Champsosauridae — there is no page on this group as yet, but it includes a bizarre menagerie of aquatic reptiles that survived the extinction of the giant dinosaurs at the end of the Cretaceous. | | | Those boxes which are a lighter blue (or lighter gray) are groups which do not belong to the Archosauria proper, but are close relatives. |
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http://www.ucmp.berkeley.edu/diapsids/archosy.html
(408 words)
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| | Mammalian Phylogeny |
| | This last work was based on the analysis of both nuclear and mitochondrial genes and verifies mammalian groupings suggested by previous molecular analysis. | | | An interesting variant of this tree, based on a large number of mitochondrial genomes, was published in 2002 (PNAS, 11 June). | | | Mammalian mitogenomic relationships and the root of the eutherian tree |
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http://whozoo.org/mammals/mammalianphylo.htm
(232 words)
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