Objectives
1)
To understand the theoretical basis of phylogeny reconstruction, and to gain an understanding of how phylogenetic trees are constructed in practice 2) To gain an appreciation of the value of phylogenetic reconstruction for understanding evolutionary patterns and processes 3) To construct your own phylogenetic hypotheses
Introduction
The Tree of Life Perhaps the most important implication of the theory of evolution is that all species of organisms, including humans, are related to each other in a genealogical sense. Even organisms as distinct as fungi, humans, and bacteria have ancestors in common. Some species, such as chimps and humans, share a fairly recent common ancestor (less than 10 million years ago), while for others you have to go way back to find a common ancestor (e.g., the common ancestor of humans and jelly fish lived at least 600 million years ago). A very useful way of thinking about relationships among organisms is as a tree of life. Imagine that at the base of the tree is the original population of organisms. As they evolve through time, two things can happen: 1) This lineage of organisms can acquire new characteristics, and 2) the lineage of organisms can split into two separate lineages (speciation). These processes, repeated over and over, result in a “tree of life” that represents the relationship among organisms (see Figure 1). This tree of life is also referred to as a phylogeny or phylogenetic 1 tree.
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The situation isn’t always this simple. In some cases genes are shared across species (e.g., bacteria), or hybridization is common (e.g., oaks), and sometimes even very distantly related organisms merge to form a composite (e.g., eukaryotes). Each of these cases would cause the branches to rejoin. Fortunately, this doesn’t appear to be a major problem for higher organisms.
Today we will investigate the theory and practice of reconstructing the phylogeny of organisms. As you can imagine, reconstructing events that occurred millions, or even billions, of years ago is not an easy task. Fortunately, the last 30 years have produced astounding theoretical and technical breakthroughs in phylogenetic reconstruction. Phylogeny reconstruction (and the related field of systematics) now plays a central role in all of comparative and historical biology, and advances in systematic knowledge and theory have led to tremendous progress in understanding the patterns and processes of evolution.
Figure 1. Simplified cladogram of vertebrates Phylogenies—Why Are They Useful? Before we discuss how phylogenies are reconstructed, it’s worth asking the always relevant question “why bother?” Creating a non-arbitrary classification— Systematics has traditionally been concerned with the identification and naming of species, and the grouping of these species into a classification. Carolinus Linnaeus (1707–1778), an early and very influential taxonomist, developed the hierarchical classification system used today in which species are arranged into ever more inclusive groups. The complete Linnean classification for humans is at right ->
used for later experiments. This experiment involves the separation of benzoic acid from a more crude form, consisting of benzoic acid, methyl orange, a common acid/base indicator, and cellulose, a natural polymer of glucose (Huston, and Liu 17-24). The technique that is used to perform this separation is called extraction. Extraction is a systematic process of separating mixtures of compounds, taking advantage of the affinity differences of compounds to separate them (Padias 128-37). This technique…
Fruit DNA Extraction Introduction: All living things come with a set of instructions stored in their deoxyribonucleic acid (DNA), that determine the way you look and how your body functions. Whether you are a human, cat, strawberry, or bacteria, each cell has DNA contained in it (with some extremely rare exceptions), and is located in the cell nucleus. DNA contains the instructions needed for an organism to develop, survive and reproduce. It is the blueprint for everything that happens inside…
use of perfume began during religious ceremonies in the ancient times but soon was used to improve people’s overall smell. The Egyptians used the earliest known extraction method called expression. In this technique, plants are squeezed and compressed until the oils come out of them. Although the Egyptians used this as a primary extraction method, it is only used today for extracting essential oils from the rimes of citrus fruits. King Louis XIV of France bathed in perfume since bathing in water wasn’t…
Saadi Wafae Liquid-Liquid extraction: Extraction is the drawing or pulling out off something from something else, Liquid-Liquid Extraction used to remove unwanted components from a mixture according to the two different solubilities of the two immiscible liquids to separate with the unwanted components. In this experiment we are going to purify a sample of benzoic acid contaminated with sodium chloride through liquid liquid extraction techniques. Results: The next step was to shake the…
Objective: The objective of this experiment is to use acid-base extraction techniques to separate a mixture of organic compounds based on acidity and/or basicity. After the three compounds are separated we will recover them into their salt forms and then purify them by recrystallization and identify them by their melting points. Procedure: Extraction of Carboxylic Acid A pre-weighed (0.315g) mixture of Carboxylic acid, a phenol, and neutral substance was placed into a reaction tube (tube 1)…
composed of MoO3 and residual solution. Molybdenum was separated with alkylphosphonic acid PC-88A by solvent extraction method, from the leach liquor containing copper, rhenium and iron among other impurities. The extraction efficiency of molybdenum was about 96% at pH 0.8 with zero co-extraction of other metals. The loaded organic was stripped with ammonia aqueous solution. One extraction stage and two stripping stages were required for the enrichment of Mo…
Exercise DNA Extraction 10/30/13 DNA in all organisms is found primarily in chromosomes. Eukaryotic cells, like those found in humans, contain several linear chromosomes. Prokaryotic cells, such as bacteria, contain one large circular chromosome. DNA is composed of building blocks called nucleotides, each made up of a five-carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base. The four kinds of nucleotides differ only in their nitrogenous bases. It is the nucleotides…
was done using extraction, solubility, crystallization and vacuum filtration. The experiment was carried out two times, both of which were successful. Background Information: This experiment combined all the knowledge of the previous labs performed throughout the semester. An unknown mixture containing an organic acid or base and an organic neutral compound in nearly equal amounts needs to be separated to its separate components. An understanding of solubility, extraction, crystallization…
2013, pg. 552). A decision support database is a specialized database management system tailored to provide fast answers to complex queries. There are three main requirements for a decision support database, which are the database schema, data extraction and filtering, and the size of the database. The decision support database schema must support complex data representations and must be able to extract multidimensional time slices (Coronel, Morris, and Rob, 2013, pg. 553). The schema must also…
DNA Extraction: Genomic DNA is found in the nucleus of eukaryotic cells. Mitochondria contain singlestranded DNA from our mother. Reagents Used in Lab: ● Lysis Buffer: Disolves the cells’ nuclear membranes and the phospholipid bilayer, allowing for the DNA to be released ● Protease: Breaks down cellular proteins. We used protease to DESTROY DNAses and the histones. ● Cold Alcohol: to precipitate the DNA out of the solution. The DNA is less soluble in alcohol, so it WILL become visible…