...Dynamic Science, 2nd edition by Russell, Hertz, and McMillan. **It would greatly benefit you to read the “Constructing Cladogram” example in your text on pg. 514 -515 Goals: 1. Understand how to interpret a phylogeny 2. Understand how to construct a phylogenetic tree using cladistics Background Information: A phylogeny represents the evolutionary history of a group of organisms. Phylogenies are illustrated as phylogenetic trees. Phylogenetic trees are hypotheses that identify likely relationships among species or higher taxonomic groups (Kingdom, Phylum, Class, Order, Family, Genus). Like all hypotheses, they are constantly revised by scientist as they gather new data. Look at the phylogeny of vertebrates provided for you on your lab bench (and also on blackboard in a separate file). Notice that some of the lines are dashed representing a part of the phylogeny where there is not enough information to get a good idea about the evolutionary history of that particular group and how they fit into the overall phylogeny. Phylogenetic trees are often drawn along a time line and can be depicted either vertically or horizontally. If the phylogeny is vertical (like the example provided), the most ancient organisms and evolutionary events are at the bottom of the tree. Some phylogenies have explicit time scales meaning that length of each branch represents how long a group persisted before it diversified. However, many phylogentic trees used in textbooks (and those we will build today) do...
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...BREVIA Recently Formed Polyploid Plants Diversify at Lower Rates Itay Mayrose,1* Shing H. Zhan,1 Carl J. Rothfels,2 Karen Magnuson-Ford,1 Michael S. Barker,3 Loren H. Rieseberg,1,4 Sarah P. Otto1 olyploidy (or whole-genome duplication) is a widespread feature of plant genomes, but its importance to evolution has long been debated. Polyploids have been postulated to be evolutionary dead ends because of the inefficiency of selection when genes are masked by multiple copies (1). However, most plant species have experienced at least one genome doubling early in their history (2), suggesting that rather than being an evolutionary dead end, polyploidy is a route to evolutionary success. A recent study (3) confirmed the ubiquity of polyploidy, with about 35% of vascular plant species being recent polyploids (“neopolyploids,” having formed since their genus arose), representing 15% of speciation events in flowering plants and 31% in ferns. It remains unknown, however, whether the abundance of polyploids is a consequence of higher diversification rates following polyploidy or of frequent polyploid formation. We estimated diversification rates of neopolyploids relative to their diploid congeners. We compiled a data set of angiosperm (n = 49) and seed-free vascular plant (SFVP, including ferns and lycophytes; n = 14) generic-level groups in which ploidy levels could be estimated from cytological and phylogenetic data (4). Over 500 ploidy shifts were inferred with a probabilistic model of...
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...modification", what does that mean? (this will be explained more fully in class, but give it your best shot). Refers to the passing on of traits from a parent to an offspring. The passing of genes is not always exact. 2. What is a phylogeny, and what do each of the branching points represent? A phylogeny is used to represent a “family tree” of groups of closely related species. 3. What is a clade? A clade is a group of organisms that includes all the descendants of a common ancestor and that ancestor. 4. How does looking at the history of life as a tree differ from looking at it as a ladder? When looking at the history of life, a tree is the most correct way to read the information from. If reading it in a ladder form, the data will be slightly skewed because they stack on top of each other even when a few subjects should be on the same line. We would read it as them evolving at different times. 5. What does a Shared Derived Trait mean, and how are they used with Phylogenies? A shared derived trait meant in terms of categorizing organisms into groups of shared characters, which is where two lineages have in common, and a derived character is one that evolved in the lineage leading up to a clade. They are used within phylogenies to group together into less inclusive clades. 6. When did the following events occur: * First fish 500 millions of years ago * First dinosaurs 500 million of years ago * Extinction of the dinosaurs ...
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...“Substitution Model” heading we changed the Model/Method section from “Maximum Composite Likelihood” to “Kimura 2-parameter model.” A table was created that provided a measure of genetic distance for analysis. The final steps were in regard to generating a phylogenetic tree. Going back to the main page of Mega6, “phylogeny“ was selected, followed by “Construct/Test Neighbor-Joining Tree.” Under the “Phylogeny Test” heading, the Test of Phylogeny was changed from “None” to “Bootstrap Method.” Congruently, “p-distance” was selected under “Model/Method” in the Substitution Model heading. Pressing, “compute”, a neighbor-joining phylogenetic tree was produced containing our 9 organisms with Skunk as the “anchor.” We clicked on the “Bootstrap Consensus Tree” tab and change the value to 50, which allowed us to collapse nodes that have a bootstrap value less than 50 because they are unreliable (Baldauf, 2003) (Nydam, O’Quin, and Wooten, 2015). . Finally, we returned to the main Mega6 page to construct a maximum parsimony tree. Selecting “phylogeny” followed by, “Construct/Test Maximum Parsimony Tree” and changing “None” to “Bootstrap Method” under the “Test of Phylogeny” found in the “Phylogeny Test” heading. Clicking on compute, a maximum parsimony tree was produced, followed by collapsing nodes less than 50 with the same steps as laid out in the previous phylogenetic tree. Results The panda bear and the spectacled bear had the fewest number of unmatched base pairs, with a value of 0.157 seen...
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...more closely related to a bird than to a lizard c) A crocodile is equally related to a lizard and a bird d) A crocodile is related to a lizard, but is not related to a bird 3) By reference to the tree above, which of the following is an accurate statement of relationships? a) A seal is more closely related to a horse than to a whale b) A seal is more closely related to a whale than to a horse c) A seal is equally related to a horse and a whale d) A seal is related to a whale, but is not related to a horse 4) Which of the five marks in the tree above corresponds to the most recent common ancestor of a mushroom and a sponge? 5) If you were to add a trout to the phylogeny shown above, where would its lineage attach to the rest of the tree? 6) Which of trees below is false given the larger phylogeny above? 7) Which of the four trees above depicts a different pattern of relationships than the others? 8) Which of the four trees above depicts a different pattern of relationships...
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...University of St Andrews, St Andrews, Scotland. Goldman, N., Anderson, J.P. and Rodrigo, A.G. 2000. Likelihood-Based Tests of Topologies in Phylogenetics. Systematic Biology, 49(4), pp.652-670. Goodman, M. and Moore, W. 1973. Phylogeny of Hemoglobin. Syste matic Zoology, 32, pp.508-532. Hardison, R. 1998. Hemoglobins from bacteria to man: evolution of different patterns of gene expression. Journal of Experimental Biology, 201(8), pp.1099-1117. Hardison, R.C. 2012. Evolution of Hemoglobin and Its Genes. Cold Spring Harbor Laboratory Press, pp.1-18 Paradis E., Claude J. and Strimmer K. 2004. APE: analyses of phylog enetics and evolution in R language. Bioinformatics 20: 289 290. R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/. Roesner, A., Fuchs, C., Hankeln T. and Burmester, T. 2004. A Globin Gene of Ancient Evolutionary Origin in Lower Vertebrates:...
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...The Historicity of Adam A hotly debated topic among evolutionists, creation scientists, and evangelicals is the historicity of Adam. These people’s views can be summarized into four basic positions [1]. The most liberal view, evolutionary creationism, holds that there was no historical Adam. This view has been expounded upon by Denis Lamoureux, a well-known professor who has lectured widely on the topic of evolutionary creationism. Evolutionary creationism posits that God used evolution to create man and used ancient views of science to impart specific inerrant truths [2]. This idea of using ancient science to give truth is called the “Message-Incident Principle” [3]. The second position is the archetypal view. Those who hold this view, such as John Walton, an influential scholar who has written several books on the topic, believe that Adam was a real man, but was used biblically as an archetype, or a representation of humanity as a whole. According to this view, Adam may or may not have been the father of mankind, and that the Bible should not be used as an argument against scientific evidence about human origins [4]. The third position, old-earth creationism, suggests that Adam was the real “[headwater] of humankind” but argues that the Bible does not limit the timeline of history to a young-earth perspective. This view has been vocally promoted by a seminary professor named C. John Collins, who has also written a famous book on the subject entitled Did Adam and Eve Really...
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...The phenotype is determined by the relationship between the two parental alleles. For example. if someone has the genotype "Bb" for brown eyes (B) and blue eyes (b), their phenotype would be brown eyes, because the brown allele dominates over the blue eyes allele. * A gene is a piece of DNA that contains the instructions for a protein. It is a unit that is hereditary from a parent to offspring an is supposed to determine some characteristic of the child. For example, a child could inherit one dominant gene from the father for brown hair and one dominant gene from the mother for brown hair, resulting in the child having brown hair. * Phylogeny is the evolutionary history of a group of organisms. Phylogenies are created by using several lines of evidence, including both molecular data and morphology. An example of phylogeny would be like a family tree. A family tree is a diagram of the descending ancestors and who they came from. * A SNP is the most common type of genetic mutation among people. Each SNP represents a mutation is a single DNA building block called a nucleotide. A SNP can occur when a single base is either eliminated from the DNA strand or when it is replaced with a completely different base. For example, one single base from the DNA strand is deleted, this type of mutation causes the pairs to be different leaving an incomplete codon at the end leading to a completely different amino acid and creating a different polypeptide. This simple form of deletion...
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...Answer the following questions as you proceed through the activity slides. 1. Briefly explain how scientists draw relationships between organisms based on shared anatomical features. The more anatomical features organisms share the more likely they are to be closely related. 2. How are DNA sequences used to deduce evolutionary relationships? Scientists look for similarities and differences in the dna sequences to determine relationships. 3. What is one advantage of building phylogenetic trees using DNA comparisons rather than anatomical features? It is more objective to use DNA comparisons. 4. Watch the video clip on slide 3 and then draw a simple tree illustrating the evolutionary relationships between gorillas, chimpanzees, humans, and orangutans. 5. Watch the short video on slide 4. How has biotechnology affected the process of building phylogenetic trees from DNA sequences? It has made it possible to see everything as sequence and therefore draw the parallels between related organisms. 6. What do evolutionarily related organisms share? They share a common ancestor with an ancestral DNA sequence. 7. What are two common types of mutations? SNPs and indels 8. Explain the difference between distantly related and closely related organisms in terms of their DNA sequences. Closely related organisms have less differences in their DNA sequences than distantly related ones because of the amount of time it...
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...Chapter 17 Study Guide We will focus on only a few key concepts from this chapter. You should already be familiar with many of these concepts from other courses. 1. It is believed that the first organisms appeared on Earth around 3.8 billion years ago. What evidence do each of the following for this occurrence? • Stromatolites -the earliest forms of lfe for which we have clear fossil evidence -a bulbous mass of sedimentary layers of limestone accreted by microbes over years -within the outer layers, microbes grow as a microbial mat (sort of like a biofilm) -outer laters of mat contain oxygenic phototrips that exude bubbles of oxygen -a few mm below surface, red light supports bacteria photolyzing H2S to sulfate which is then reduced by lowe layers of sulface reducing bacteria -fossils formed as layers of phototropic microbial communities grew and died their form filled in by calcium carbonate or silica -accepted to date as eatly as 3.4 Gyr ago -too deformed to reveal the detailed structure of cells and the biological origin of such fossils is questioned by some researchers -mainly in isolated pools whose high salt concentration exclude predators • Microfossils -the most convincing evidence for ealy microbial life is the visua appearance of microfossils which are microscopic fossils in which minerals have precipitated and filled in the form of ancient microbial cells -dated bythe age of the rock formation in which they are found, which is based...
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...Biological classification Biological classification is the arrangement of organisms into categories that express their PHYLOGENY, or line of descent, based on information such as structure, development, biochemical or physiological functions, and evolutionary history of organisms. The purpose of such a classification is to provide a clear and practical way to organize and communicate information about organisms. Classification can show relationships between different ancient and modern groups, indicate the evolutionary pathways along which present-day organisms may have developed, and provide a basis for comparing experimental data about different plant and animal groups. Organisms included in a group share a common genetic heritage in their DNA, and they must be more closely related to each other than they are to the members of other groups of the same rank. However, classifications of organisms are modified as ideas of their phylogeny change. Taxonomy is the theory and practice of classifying organisms. It is a branch of systematics, the study of the diversity of organisms. The first scheme for classifying animals into logical groupings may have been proposed by Aristotle more than 2,000 years ago. Since that time, many new classification systems have been proposed; none, however, has succeeded in fitting all plants, animals, and microorganisms into a single, completely satisfactory scheme. For example, some taxonomists classify algae with the protista or consider them plants...
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...ts are mammals of the order Chiroptera (/kaɪˈrɒptərə/; from the Greek χείρ - cheir, "hand"[2] and πτερόν - pteron, "wing"[3]) whose forelimbs form webbed wings, making them the only mammals naturally capable of true and sustained flight. By contrast, other mammals said to fly, such as flying squirrels, gliding possums, and colugos, can only glide for short distances. Bats do not flap their entire forelimbs, as birds do, but instead flap their spread-out digits,[4] which are very long and covered with a thin membrane or patagium. Bats are the second largest group of mammals, representing about 20% of all classified mammal species worldwide, with about 1,240 bat species divided into two suborders: the less specialized and largely fruit-eating megabats, or flying foxes, and the highly specialized and echolocating microbats.[5] About 70% of bat species are insectivores. Most of the rest are frugivores, or fruit eaters. A few species, such as the fish-eating bat, feed from animals other than insects, with the vampire bats being hematophagous, or feeding on blood. Bats are present throughout most of the world, performing vital ecological roles of pollinating flowers and dispersing fruit seeds. Many tropical plant species depend entirely on bats for the distribution of their seeds. Bats are important, as they consume insect pests, reducing the need for pesticides. The smallest bat is the Kitti's hog-nosed bat, measuring 29–34 mm (1.14–1.34 in) in length, 15 cm (5.91 in) across...
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...By looking on the history of a company, we can know more about the company’s background and phylogeny, so that we can find out the secret of success. Justin is going to find out how McDonald’s become the market leader for many years, and why McDonald’s has continued to be successful in the competitive environment base on the company’s history, annual report, and financial statement. Angelo is going to do the SWOT analysis to evaluate the strengths, weaknesses, opportunities, and threats for McDonald’s. SWOT analysis can identify the internal and external factors, so that we can set achievable goals on the investment. Also, Angelo will compare McDonald’s with the other international fast food restaurant, The Burger King, and see why choosing McDonald’s as the new investment. ( I think we should add the reason why we are doing this, but I cannot think of any reason, so please help me to write this part, thanks.) After we finish the SWOT analysis, we should have enough data and sources to set achievable future goals for McDonald’s. Berret is looking at the future trends for the company. McDonald’s, as an international fast food corporation, it has a lot to do to take a good care for different markets. In the other hand, McDonald’s needs to have a better image when facing a lot of competitors in America, Berret is going to analyze does McDonald’s has an optimistic outlook, and is it worth the investment. Wing is going to look at McDonalds’ stock for the last 10 years to make sure...
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...has no place in the evolution syllabus. If not there, where? There are risks in leaving this issue unattended, as shown by the infamous 2004 statement by Dover High School in Pennsylvania that "Intelligent Design is an explanation of the origin of life that differs from Darwin's view ... The school leaves the discussion of Origins of Life to individual students and their families." Equally disturbing is Moore's questioning of the scientific maturity of origin-of-life studies, which he describes as "far from sound evolutionary theory". How life appeared is not known, but a better understanding of the prebiotic environment and the recognition of the RNA world as an early evolutionary stage have provided important insights. As molecular phylogeny cannot be extended to an evolutionary period before the emergence of ribosome-mediated protein...
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...Influenza B viruses have similar viral structures, genome organization, and epidemiology as influenza A viruses. However, there are many important differences. Influenza B mainly infects humans, whilst influenza A infects many species of vertebrates. Additionally, influenza B viruses are usually less prevalent and less severe than influenza A viruses, and they exhibit lower rates of evolutionary change. Influenza B strains are separated into two distinct lineages, whereas influenza A strains continually evolve into new clusters. This article describes evolutionary and epidemiological forces that shape the genetic diversity of influenza B viruses. Information will be used to predict future impact of influenza B and how to control future outbreaks....
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