BIOS 1715 - Lab 7 Phylogenetics & Invertebrate Diversity I Phylogeny is the evolutionary history of life. Groups of species are descended from a common ancestor, which, over evolutionary time, split into two species. These descendants split again and so on over vast stretches of time resulting in large groups of evolutionarily related species. Visually, the phylogeny of a group is a tree that shows the evolutionary relationships of the species within the group. Figure 1 shows the relationship between humans, gorillas and chimpanzees. All 3 species share a common ancestor at node 1, while humans and chimps share a common ancestor at node 2. Figure 1: The relationship between speciation and a phylogenetic tree. Figure from, Morris J et al. Biology How Live Works (2016) W.H. Freeman and Company Figure 2, showing the relationship among primates, illustrates types of groups commonly discussed in phylogenetics. Monophyletic - A group of species sharing a single common ancestor and ALL its descendants. The entire primate group is monophyletic, and it contains several monophyletic groups, for example the simians, colored in yellow. Paraphyletic - A group that contains some, but not all of the descendants of a common ancestor. For example the prosimians, in blue. Figure 2: Phylogenetic tree of primates. polyphyletic - A group that shares a particular character, but doesn’t include the last common ancestor. For example the lorises and tarsiers, colored in red. The shared character that this group possesses is that these are the only primates that are nocturnal. A shared character that is not derived from a common ancestor is called a homoplasy (Figure 3). What do we mean by character? In phylogenetics, characters include anatomical, physiological, behavioral or molecular features that make up an organism. And character states refer to several observable states of any particular character. A derived character is a character found in a group of organisms that is not found in their ancestral group. Thus, it separates the group from their ancestors. A derived character that is found in the most recent common ancestor and all its descendants is known as a synapomorphy (Figure 3). Figure 3 So let’s construct a simple tree from 4 organisms – a gorilla, lion, toad and a sea urchin using anatomical characters. From these 4 organisms you could select a lot of characters, but it’s best to limit the number to a few noticeable traits. To keep this simple we’ll do 4 traits: backbone, fur, bilateral symmetry and spines. Next we construct a character matrix and insert a zero, 0, or “no” if the character is absent and a one, 1, or “yes” if it is present. As you’ll see later, sometimes you have to use other notations for characters in more complex trees. character / species backbone fur bilateral symmetry spines Sea urchin 0 0 1 1 toad 1 0 1 0 lion 1 1 1 0 gorilla 1 1 1 0 So, if we analyze the matrix we see: All 4 species have bilateral symmetry, so that is a character of the common ancestor of them all, so it is the first node in the tree, next to the root. Since each node has to bifurcate (i.e. split in 2), and since bilateral symmetry is the only character the sea urchin shares with the others, and it has a character that none of the others have, then it will be on one line leading from the node and the other 3 species will be on the other. The toad, lion and gorilla all share a backbone in common, so the common ancestor of these 3 must have had a backbone, so it becomes the next node in our “3 species” line. Finally, the lion and the gorilla have fur, a character not possessed by the toad, so the toad goes on one of the bifurcations from the backbone node and lion and gorilla go on the other. Voila! A simple phylogenetic tree! Now you are ready to construct a phylogenetic tree…a little bit more complex! As you go through the exercises; remember there is no one correct phylogenetic tree – they are all hypotheses! Activity 1 – Filling in a Phylogenetic Tree Examine the simplified phylogenetic tree of vertebrates shown on your worksheet and to the right. Several character traits are shown at positions where they might be proposed to have evolved. 1. Match the organism from the list on your worksheet to the number at the end of the branch where it belongs. 2. Answer the questions on your worksheet. Activity 2 – Phylogeny of the Roundoids 1 2 3 4 5 6 Allow us to introduce you to the Roundoids – a group of species invented for your phylogenetic pleasure! The cartoons above represent a group of species for which you are trying to reconstruct phylogeny. Assume that the open circle (1) is the ancestral condition. Develop a character matrix for the roundoids on your worksheet and then use the matrix to develop a phylogenetic hypothesis (tree) for these taxa (sing. taxon) mapping the evolutionary events described in the character matrix. It will be obvious to you that you can’t use the 0 and 1, or “yes and no” system for everything here – think up succinct descriptors for the same trait that has different forms, such as the nose, mouth and some others. Construct your tree on the Worksheet (it can be on its side like in your book or vertical, like a tree) and answer the questions on the worksheet. Make sure you label on the tree where you are hypothesizing each trait arose and possibly changed. Activity 3 – Molecular Phylogeny of a Pseudogene On your worksheet are four gene sequences. These are taken from four animals that are believed to be closely related – that is they have a “recent shared ancestry”. The gene sequences are from a so-called “broken gene” or pseudogene, the evolutionary remnant of a gene which is now nonfunctional in a given species or group of related species. In this case, the gene is called GULO (L-gulonolactone oxidase), which codes for the enzyme that catalyzes a key step in the synthesis of ascorbic acid - more commonly known as vitamin C. Along the way, some animals have lost the function of this gene (by random mutation) and must consume vitamin C in their diet. 1. Examine the four gene sequences and mark any differences among the sequences that you can find. If there is only one nucleotide difference in any column, just highlight the one nucleotide. If there are more than one, highlight the column. 2. Do you notice any specific pattern that helps reveal ancestry? Below sequence #4 mark with an asterisk the columns you think help reveal ancestry. What could this pattern mean regarding the ancestry/relatedness of the four species? 3. Make a hypothesis about the ancestry of these four species in the form of a phylogenetic tree. Draw this tree on the Worksheet (last page) and make a few notes explaining why you drew it this way. You can either print the worksheet, draw the tree and submit a picture of it on Blackboard, or use the drawing tools in Word to draw the tree on your computer. Hint: Think of nucleotides in a given position as characters and differences in nucleotides at that position as different character states. credits Fig 1 from Morris et al. Biology: How Life Works. © 2017 W.H Freeman and Co. Fig. 2 fromPrimate phylogenetic tree: Petter Bøckman, Author. Source: http://commons.wikimedia.org/wiki/File:Monophyly-paraphyly-polyphyly.jpg. This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license. Image is in original form Phylogeny of the Roundoids activity: Dr. Willem Roosenberg, Ohio University Fig. 3 By Ferahgo the Assassin - Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=12056326 Activity 3 was adapted for use from “Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part InquiryBased Exercise” Nathan H. Lents, Oscar E. Cifuentes, and Anthony Carpi. 2010. ©2010 N. H. Lents et al. CBE—Life Sciences Education©2010 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/bync-sa/3.0). The wording and formatting was modified from the original. INVERTEBRATE DIVERSITY I Mammone, Gurien, Van Brocklyn 2016, 2017 Animals as a group are characterized as being eukaryotic, heterotrophic, multicellular organisms. Invertebrates are animals without a vertebral column (backbone) that are estimated to make up more than 98% of known animals species, yet if you were asked to name an animal it is unlikely that you would name an invertebrate. Invertebrates are a very diverse group that includes animals such as sponges, jellyfish, corals, worms of many forms, insects, lobsters, crabs, clams, octopuses, snails and sea stars. Invertebrates play invaluable roles in ecosystems in food webs and bring about many ecosystems services such as pollination, decomposition and nutrient availability among many other services. Some may refer to invertebrates as spineless and sometimes small, but they might actually rule the world. Biologists use the classification (taxonomy) of organisms to help place animals in groups often based on their phylogeny. Animals are currently placed into 34 or so phyla (plural for phylum) of which invertebrates are included in all phyla, yet vertebrates are only a portion of one phylum. In the next 3 labs you will be introduced to just a small subset of the invertebrate phyla and learn about some of their shared characteristics. phylum examples Porifera sponges Cnidaria corals, jellyfish Mollusca snails, squid, clams Platyhelminthes flatworms Annelida earthworms Nematoda Roundworms (C. elegans) Arthropoda crustaceans, insects, spiders Echinodermata Sea stars, sea urchins Chordata Some invertebrates and all vertebrates no true tissues radial symmetry tissues protostomes bilateral symmetry deuterostomes Figure 1. Phylogenetic tree showing the evolutionary relationship of several major animal phyla that we will be studying in this and the next 2 labs. Pictures and examples show commonly known animals within each phylum. Some important characteristics of animals are labeled on the tree showing at what point in evolution they originated. Important characteristics of animals Figure 1 shows a phylogenetic tree of several major animal phyla. The first division in this tree separates Phylum Porifera, the sponges, from other animal phyla. Sponges have several different cell types, however they do not have true tissues or organs. The other animal phyla possess true tissues which are derived from embryonic germ layers. While Cnidaria have tissues derived from only two embryonic germ layers, the outer ectoderm and inner endoderm, the other phyla that we will examine in this lab have a third, middle layer called the mesoderm. Having a mesoderm allows many of the organisms we will study to develop of a structure called the coelom, a body cavity between the body wall and the gut. The coelom allows for greater complexity of the body plan as internal organs can develop, acts to cushion internal organs, and allows muscles and the outer body wall to move independently of the gut. Another important aspect of the body plan of most animals is body symmetry. Sponges do not possess body symmetry. Cnidarians are symmetrical in multiple directions around a central axis. This is called radial symmetry. The remaining phyla shown in Figure 1 have bilateral symmetry, meaning they have a left and right half which are essentially mirror images of each other. Bilaterally symmetrical animals often display cephalization, the development of a head, which is useful as it allows for the concentration of nervous system tissue at one end and the integration of information from sensory organs. As we will see when we get to echinoderms they possess bilateral symmetry as larvae, but show a return to radial symmetry as adults. Also indicated on Figure 1 is the spilt between two groups of animal phyla that show different patterns of embryonic development, the protostomes and deuterostomes. Among several other differences in early embryonic development, the defining characteristic of protostomes versus deuterostomes is in the developmental fate of the blastopore, the first opening formed in the developing embryo. In protostomes the blastopore eventually develops into the mouth, while in deuterostomes, it develops into the anus. Phylum Chordata, which contains all the vertebrates and some invertebrates, and Phylum Echinodermata are deuterostomes, indicating their closer evolutionary relationship. Another aspect of animals is their ability to move. We commonly picture animals as being mobile, and all animals are mobile at some point in their life cycle, however several animals have a phase of their life cycle in which they are attached to the ground and immobile. The term we use for this is sessile. In lab today we will observe specimens of animals from these phyla in order to learn about the different characteristics of these animals. PHYLUM PORIFERA (Sponges) Tissue layers: No true tissues Symmetry: None (a few are radial) Coelom: acoelomate (have no body cavity) Defining characteristics: No true tissues or organs, pore-bearing Sponges lack true tissues and organs but have a number of different cell types that perform specific functions. For this reason they are often considered to be the most primitive animals, and to be on the first branch off the phylogenetic tree (Notice their position on the tree in Figure 1). All sponges are aquatic, and most are found in marine systems. They are sessile as adults. Some have radial symmetry, but most sponges lack body symmetry. They are porous and have a current of water flowing through the pores. The current is created by cells with flagella, called choanocytes, that line the inside of the sponge. The sponge cells filter food particles and extract oxygen from the water flowing through them. The body is supported by skeletal elements consisting of hard spicules and/or flexible spongin fibers and as adults they are sessile (permanently attached to the substrate). Many of the cells can change from one type to another and as a result a whole sponge can be regenerated from a few separated cells, as you will see in the reaggregation experiment. Sponges have been overharvested for use as bath sponges and more recently we are beginning to learn about their unique cellular and biochemical properties, which may have implications for medical research. PHYLUM CNIDARIA Tissue layers: ectoderm and endoderm Symmetry: radial Coelom: acoelomate (have no body cavity) Defining Characteristics: tentacles with stinging cells called nematocysts If you have ever snorkeled or been diving on a living coral reef you saw a virtual jungle of cnidarians. The phylum includes the familiar jellyfish, sea anemones and corals, as well as a diversity of other animals. Most cnidarian species are marine, but there are a few freshwater species which may be found in local ponds and small lakes in Ohio. The phylum gets its name from the presence of cnidocytes, cells containing stinging threads called nematocysts located on the tentacles which surround the mouth. They are used to inject toxins into prey to immobilize them for feeding. A secondary function of nematocysts is for protection. The cnidarians exhibit an increase in body complexity compared to sponges. Cnidarians are the first phylum to have a tissue level of organization characterized by an outer epidermis, an inner gastrodermis (derived from the embryonic ectoderm and endoderm respectively) and a layer of non-living jelly-like mesoglea sandwiched in between. In addition they all exhibit radial symmetry, where all body parts are arranged around a central axis, with multiple planes of symmetry. Many species exhibit polymorphism in which their life cycles involve an POLYP MEDUSA alternation between the polyp and medusa forms. The polyp form is generally sessile with tentacles and mouth Fig. 2 The polyp and medusa forms found in cnidarians. pointing upward, and the medusa is free-floating with tentacles and mouth pointing downward (Figure 2). PHYLUM PLATYHELMINTHES (Flatworms) Tissue layers: ectoderm, endoderm and mesoderm Symmetry: bilateral Coelom: acoelomate (have no body cavity) Development: protostome Defining characteristics: Dorso-ventrally flattened worms Phylum Platyhelminthes consists of soft, wormlike animals with bodies that are elongated and dorso-ventrally flattened. This group is made up of many parasites such as flukes and tapeworms, as well as free-living planarians and the colorful marine flatworms. Members of this phylum and the rest of the phyla, the we will consider next week, have three distinct tissue layers: an outer ectoderm and an inner endoderm (as in the cnidarians), and also a middle mesoderm layer. However, flatworms are acoelomate, indicating that they do not possess the body cavity known as a coelom. Platyhelminthes exhibit, bilateral symmetry, in which one plane divides the animal into distinct left and right sides with a head end typically loaded with sensory structures (cephalization).
