Animal and Plant Diversity Study Guide 2024 PDF

BLG1502/001/4/2024 MO001/4/2024 Animal and Plant Diversity BLG1502 Semesters 1 & 2 Department of Life and Consumer Sciences IMPORTANT INFORMATION...

BLG1502/001/4/2024 MO001/4/2024 Animal and Plant Diversity BLG1502 Semesters 1 & 2 Department of Life and Consumer Sciences IMPORTANT INFORMATION Please register on myUnisa and activate your myLife e-mail address and ensure that you have regular access to the myUnisa module site BLG1502-24-S1 OR BLG1502-24-S2, depending on which semester you are registered for, as well as your group site. Note: This is an online module; therefore your module is available on myUnisa. However, to support you in your studies, you will also receive certain study material in print format.  BLG1502/001/4/2024 Content Page Preface…………………………………………………………………………………………………………………………3 Learning unit 0: Welcome and introduction ……………………………………………………………………………….4 Learning unit 1: Phylogeny and systematics……………………………………………………………………………..15 Learning unit 2: Prokaryotes and the origins of metabolic diversity……………………………………………………23 Learning unit 3: How plants colonised land………………………………………………………………………………31 Learning unit 4: Plant diversity II: the evolution of seed plants…………………………………………………………37 Learning unit 5: Fungi………………………………………………….……………………………………………………42 Learning unit 6: Plant structure, growth and development………………………………………………………...……48 Learning unit 7: Photosynthesis……………………………………………………………………………………….…..56 Learning unit 8: Animal reproduction……………….……………………………………………………………………..63 Learning unit 9: Animal nutrition…………………………………………………………………………………..……….72 Learning unit 10: Circulation and gas exchange…………………………………………………………………………76 Learning unit 11: The body's defences……………………………………………………………………………….…..83 Learning unit 12: Regulating the internal environment………………………………………………………………….89 2|Page  BLG1502/001/4/2024 Preface Welcome to Animal and Plant Diversity (BLG1502). This module is online, but you can also use this document for your studies. It is a convenient document that you can consult at any time, and you can make notes on it. I would nevertheless encourage you to also make use of the module site, because it has several advantages. You can access any part of the study material by clicking on the links in the table of contents of the study units (learning units), and you can communicate with your lecturer and fellow students on the course website's discussion forum. This document contains the text of the Animal and Plant Diversity module learning units. You must definitely read learning unit 0 because it contains important information about the module. Remember to read Tutorial Letter 101, where you will find essential information about the module and the assignments. I wish you all the best in your studies. Your lecturer M H Mkhombo 3|Page  BLG1502/001/4/2024 Learning Learning unit 0: Welcome and introduction Units Contents Module site 0.1 Getting started Things to 0.2 Lecturer and contact details remember 0.2.1 Lecturer and department 0.2.2 University 0.2.3 Student support services 0.3 Purpose and outcomes of this module 0.4 How the content of this module is structured 0.5 Learning resources 0.6 Study plan 0.7 How should you go about studying this module? 0.7.1 Learning strategies you can apply: the SSS method 0.7.1.1 Skimming 0.7.1.2 Scanning and outlining 0.7.1.3 Study-reading and active learning 0.7.2 Managing your self-paced study time 0.7.3 Finding research/scientific articles 0.7.4 Avoiding plagiarism 0.8 Using myUnisa 0.8.1 The myUnisa menu options 0.8.2 myUnisa etiquette 0.8.3 Activity 0.1: Introduce yourself 0.9 Assessment in this module 0.1 Getting started Welcome to Animal and Plant Diversity (BLG1502). This module is offered by Unisa's Department of Life and Consumer Sciences. This is an online module, which means that you will find everything you need to complete the module on the module site. Check this site regularly for updates, posted announcements and additional resources uploaded throughout the semester. The university's online platform, myUnisa, allows you to submit assignments (I recommend that you submit your assignment online, as this will ensure that you receive rapid feedback and comments) 4|Page  BLG1502/001/4/2024 access your official study material access the Unisa Library functions "chat" to your lecturer or to fellow students and participate in online discussion forums access a variety of learning resources Please take some time to familiarise yourself with the site so that you get to know where the different options and resources are. I will give you more information about this later in this learning unit. Although I really encourage you to study this module online, I realise that some of you don't have online access at all, while others may have online access only from time to time. For this reason, Unisa has provided a printed study pack for this module. Your study material for this module consists of your prescribed textbook these learning units Tutorial Letter 101 any other tutorial letters you may receive throughout the year Details of your prescribed book are given in the Prescribed Books menu option, which you can access on the left-hand side of this screen, and also in Tutorial Letter 101. Tutorial Letter 101 will be posted to you, but you can also access it on this site. Do this by clicking on Official study material in the menu on the left. Once there, select Tutorial Letter 101. Tutorial Letter 101 is just one of the tutorial letters you will be receiving during the semester. Please read it carefully. You will also receive further tutorial letters shortly after the due dates for submission of the assignments; these will contain suggested solutions to the assignments. In this learning unit, I will give you an overview of and some general information about this module. I will also tell you more about possible study strategies, how to use myUnisa and about the assessment in the module. Click on "Next" to go to the next screen, where you will find more information about contact details. 0.2 Lecturer and contact details In this section I will give you my own contact details, as well as details of the Department of Life and Consumer Sciences at Unisa, which is the academic department that offers this module. I will also give you the university's contact details, as well as some information about the student support services at Unisa, which you are welcome to use. Whenever you contact the university, whether in writing or by phone, always provide the module code and your student number. If you write to Unisa, you may enclose more than one letter in an envelope, but do not direct enquiries to different departments (e.g. Despatch and Library Services) in the same letter as this will cause a delay in the replies to your enquiries. Please write a separate letter to each department and mark each letter clearly for the attention of that department. You may not include letters to lecturers together with assignments. 0.2.1 Lecturer and department Lecturer: Dr Mfana Henry Mkhombo Telephone number: +27 11 471 2237 (during office hours 8:00 – 16:00) E-mail address: [email protected] Postal address: 5|Page  BLG1502/001/4/2024 The Lecturer (BLG1502) Department of Life and Consumer Sciences Private Bag X6 Florida 1710 The department offering this module is the Department of Life and Consumer Sciences. Telephone number (departmental secretary): +27 11 471 2230 Fax number: +27 11 471 2796 0.2.2 University If you need to contact the university about matters not related to the content of this module, consult my Studies @ Unisa. This brochure contains information on how to contact the university (e.g. to whom you can write for different queries, important telephone and fax numbers, addresses and details of the opening and closing times of particular facilities). You may access this site at www.unisa.ac.za/contents/study2012/docs/myStudies-Unisa-2014.pdf You can also use the following contact routes: Unisa website: http://www.unisa.ac.za & http://mobi.unisa.ac.za E-mail (general enquiries): [email protected]. International students can also use the e-mail address [email protected] [email protected] for enquiries related to application and registration [email protected] for assignment enquiries [email protected] for examination enquiries [email protected] for study material enquiries [email protected] for student account enquiries [email protected] for assistance with myUnisa [email protected] for assistance with myLife e-mail accounts SMS 32695 – South Africa only You will receive an auto response SMS with the various SMS options. The cost per SMS is R1,00. Fax 012 429 4150 0.2.3 Student support services For information about the various student support systems and services available at Unisa (e.g. student counselling, tutorial classes, language support), consult my Studies @ Unisa at www.unisa.ac.za/contents/study2012/docs/myStudies-Unisa-2014.pdf Fellow students 6|Page  BLG1502/001/4/2024 It's always a good idea to have contact with fellow students. You can do this using the Discussion menu option on myUnisa. You can also use the Discussion forum to find out whether there are students in your area who would like to form study groups. Library my Studies @ Unisa lists all the services offered by the Unisa Library at the site www.unisa.ac.za/contents/study2012/docs/myStudies-Unisa-2014.pdf To log in to the Library website, you need to provide your login details, i.e. your student number and your myUnisa password, in order to access the Library's online resources and services. This will enable you to request library material view and renew your library material use the Library's e-resources Unisa Directorate for Counselling and Career Development (DCCD) DCCD supports prospective and registered students before, during and after their Unisa studies. There are resources on its website (http://www.unisa.ac.za/Default.asp?Cmd=ViewContent&ContentID=15974), and also printed booklets available to assist you with career advice and how to develop your employability skills study skills academic literacy (reading, writing and quantitative skills) assignment submission exam preparation Advocacy and Resource Centre for Students with Disabilities (ARCSWiD) You will find more information about this centre on its web page at http://www.unisa.ac.za/default.asp?Cmd=ViewContent&ContentID=19553. You can also contact Ms Vukati Ndlovu on 012 441 5470. 0.3 Purpose and outcomes of this module This module forms part of the BSc Life Sciences. It will focus on the fundamental concepts and theory relating to the biology of plants and animals in the field of biological sciences. Students who complete this module can also explain the origins of diversity and can justify the ecological importance of plants and animals in an interrelated ecosystem. More specifically, after completing the module, you should be able to describe the structure, composition and function of prokaryotic cell walls draw a flow diagram of the life cycles, indicating the gamete and sporophyte generation identify and discuss the structure of the three basic organs of a plant body, namely the stems, leaves and roots describe the characteristics of three tissue systems that the organs are composed of, namely dermal, vascular and ground tissue define and name the classes of essential nutrients explain the major functions of the organs that make up the mammalian digestive system The next section will give you a better idea of how the content of the module is structured and how the various ideas expressed in the learning outcomes are related. 0.4 How the content of this module is structured? 7|Page  BLG1502/001/4/2024 This module covers a wide range of subject areas. We will start with learning unit 1. This unit traces the phylogeny or evolutionary history of a species or a group of species. It will teach you the principles of studying biological diversity and also how this is done. Learning unit 2 focuses on the aspects of prokaryotes. Prokaryotes were the earliest organisms. They have continued to adapt and evolve and have helped change the earth. In this unit we will show you their morphology and environmental importance. In learning unit 3 you will learn about the history of the plant kingdom, which is a story of adaptation and changing terrestrial conditions. This unit concentrates on the development of different groups of plants to live exclusively on land. Then we will look at basic patterns of plant growth. Learning unit 4 continues with the theme of how plants have adapted to life on land. It deals with the development of seed plants and the importance of seed plants to humans. In learning unit 5, you will learn about fungi, which are responsible for recycling the organic (dead) material back to the environment in forms that other organisms can use. This unit concentrates on the general morphology of fungi and investigates two groups of fungi in particular. In learning unit 6, we focus on a group of plants known as angiosperms. Angiosperms are the most widespread and economically important plants on earth. This unit introduces the structural organisation of flowering plants and their development from a single cell. Plants have the ability to use the energy from sunlight together with CO2 and to convert it to chemical energy stored in sugar. In learning unit 7, we will explain the process of this conversion, namely photosynthesis. Animal form and function are major themes in biology and, to understand both, we will be examining body plans and the external environment in learning unit 8. After you have worked through this unit, you will have a basic knowledge of animal structure and function that will enable you to understand the more complex bodily functions of animals. In learning unit 9, you will learn that every mealtime is a reminder that we are heterotrophs who depend on a regular supply of food derived from other organisms. A balanced diet provides fuel for cellular work, as well as all the materials the body needs to construct its own organic molecules. In this unit we will examine the nutritiona l requirements of animals and look at some of the diverse adaptations used by animals to obtain and process food. In learning unit 10, you will realise that every organism must exchange materials and energy with its environment and that this exchange ultimately occurs at cellular level. In this unit you will learn about the mechanisms of internal transport in animals. Learning unit 11 deals with an animal’s defences. An animal has to defend itself against a variety of pathogens. There are three cooperative lines of defence that counter the threat of pathogens. The first line of non-specific (innate) defence is external, and consists of epithelial tissues that cover and line our bodies. The second, which is triggered by chemical signals, involves phagocytic cells and antimicrobial proteins that indiscriminately attack invaders. The third line of defence is the immune system, which comes into play simultaneously with the second line of defence. In this unit we examine how an animal’s non-specific and specific defences work together to protect the body from invaders. In learning unit 12, you will see that one of the most remarkable characteristics of animals is that they can maintain physiologically favourable internal environments even when external conditions undergo dramatic shifts that would be lethal to individual cells. Animals' ability to regulate their internal environment is called homeostasis. In this unit, we focus on thermoregulation, water balance and excretion. Now that you have a better idea of how the module is structured, let's look at what your studies will involve. 0.5 Learning resources Your main learning resources for this module will be your prescribed textbook and the learning units. These resources will be supported by tutorial letters. The prescribed textbook that you need to use in conjunction with the online material is as follows: Biology: a global approach, 11th edition, 2017, by NA Campbell, JB Reece, LS Urry, ML Cain, SA Wasserman, PV Minorsky & RB Jackson, published by Pearson Benjamin Cummings (San Francisco). ISBN-10:1-292-17043- 3 or ISBN-13: 978-1-292-17043-5. If you cannot get hold of the 11th edition, you can buy the 9th or 10th edition. The two editions are very close to the 11th edition. 8|Page  BLG1502/001/4/2024 You will find more details about the textbook in the menu option Prescribed books to the left of this screen, and also in Tutorial Letter 101. The textbook is a comprehensive guide that covers a large scope in the field of plants and animals, such as plant anatomy and physiology, taxonomy, plant systematics, invertebrates, animal structure and function, animal nutrition, circulation and gas exchange. You don't have to learn everything in the textbook, so please follow the guidelines I will be giving you in terms of what to study. Also, use the online learning material to guide you in what you need to learn. You will need to study the chapters listed at the beginning of each learning unit and any recommended reading sections. If you find a topic particularly interesting, you're very welcome to do further reading about it. For the sake of convenience, in the learning units I will refer to the textbook as "Campbell et al (2017)". 0.6 Study plan Consult my Studies @ Unisa for suggestions on general time management and planning skills. Access this at www.unisa.ac.za/contents/study2012/docs/myStudies-Unisa-2014.pdf. This is a semester module offered over 15 weeks and requires at least 120 hours of study time. This means that you will have to study at least 8 hours per week for this module. Here is a suggested schedule that you could use as a guideline for studying this module. ACTIVITY HOURS Reading and rereading Tutorial Letter 101 and learning unit 0 3 Skimming learning units and textbook, forming a thorough general impression of 5 the whole module First reading of learning units 1–12 and textbook (2 hours per learning unit) 16 In-depth study of learning units 1–12: making mind maps and summaries, and 64 doing learning activities (10 hours per learning unit) Completing two assignments (Note: Assignment 01 should take less time than 14 Assignment 02) Revising for the examination 16 Writing the examination 2 Total 120 This schedule is an example of how you could structure your study plan. Week Activity (each week represents 8 hours of study time) 1 Read and reread Tutorial Letter 101 and learning unit (LU) 0 (January/July) Skim the learning units and textbook, forming a thorough general impression of the whole module 2 Read through the learning units and textbook and identify all key areas 3 4 Study LU 1-6 in depth (make mind maps and summaries and do learning activities) 5 9|Page  BLG1502/001/4/2024 6 Complete and submit Assignment 01 (depending on how you will submit the completed assignment, allow sufficient time for the assignment to reach Unisa on or before the due date) 7 In-depth study of LU 6-8 (make mind maps and summaries and do learning activities) 8 If possible, participate in the online discussion activities 9 10 Complete and submit Assignment 02 (depending on how you will submit the completed assignment, allow sufficient time for the assignment to reach Unisa on or before the due date) 11 Study LU 8-12 in depth (make mind maps and summaries and do learning activities) 12 If possible, participate in the online discussion activities 13 14 Revise and prepare for exam 15 (April/October) 0.7 How should you go about studying this module? Distance studies are unique, with particular requirements for success that you should not underestimate. Once you have received your study material, plan how you will approach and complete this module. You can use the study plan in the previous section as a guideline to draw up a reasonable study schedule to guide you through the module. Remember to take into consideration the due dates for the assignments, which I supplied in Tutorial Letter 101 for this module. A crucial phase in the process of understanding and learning the basics of botany, ethnobotany, biology and plant taxonomy is to articulate your ideas about the principles you are learning, both orally and in writing. Only when you have tried this process for yourself will you understand the full value of this exercise. The assignments in this module will take the form of written work, and they should give you an idea of how well you are progressing in terms of achieving the learning outcomes. Work through the learning units, using the learning strategies explained in the sections that follow. In each case skim through the unit and draw your own basic mind map of the content, and then expand this map as your knowledge and understanding of the unit increase make your own summary of every unit do a reflection exercise at the end of every unit (I will explain this in more detail in a later section) As you work through the units, build up your own study and exam preparation portfolio. This portfolio won't be assessed, but it will be an extremely valuable tool as you complete your assignments and revise for th e examination. What is a portfolio? A portfolio is a folder/file in which you gather and compile additional and/or summarised information during the year as you work through the learning material. Your portfolio should comprise answers to each activity in each learning unit a mind map/summary of each learning unit your marked assignments (or a copy you made prior to submitting your assignment) 10 | P a g e  BLG1502/001/4/2024 your reflections on each learning unit extra reading material taken from the internet, additional books and medical and/or scientific journals a new vocabulary of words or glossary of new terms in your own words To ensure that you achieve the learning outcomes for this module, you can use the learning strategies explained in the following section. After explaining these, I will also say more about managing your study time, finding articles for further reading and avoiding plagiarism. 0.7.1 Learning strategies you can apply: the SSS method There are a number of strategies that can help you study, one of which is the SSS strategy. The three techniques in the SSS strategy are skimming scanning and outlining study-reading and active learning To help you understand what these steps involve, I will give you more detail in the sections that follow. 0.7.1.1 Skimming Skimming involves moving your eyes quickly over a piece of text to get a general overview of what the text is about. 1. Page through and explore. First, read the section quickly, forming a rough idea of what it is about. Concentrate on headings and subheadings, any words or phrases that are in bold or italic type, text in boxes, tables and illustrations, and – in the case of a chapter or learning unit – introductions and summaries. The outcomes for a learning unit are important. (Think of how you would page through a magazine. When starting a new learning unit, scan it and concentrate on the concepts that catch your eye.) 2. Make a cursory survey. As you read, ask yourself: What key terms occur in this learning unit or chapter? Stop when you identify a key term, and carefully read what is said about it. Mark it in the book or in your printed study text. What you are trying to do is help yourself to remember the location of important information so that you can draw on it later. The key question is: Where is it? 0.7.1.2 Scanning and outlining Scanning also involves moving your eyes quickly over a text, but in this case you are doing it to find specific key words or specific items of information. 1. Basing yourself on the key concepts you identified during skimming, scan the chapter, learning unit or section. If you have internet access, you can find more information on skimming and scanning here: https://www.aacc.edu/tutoring/file/skimming.pdf 2. Outline the section by starting a mind map (for the whole learning unit or chapter or for parts of it, as in starting a summary). You are looking for items and concepts while reading the information in the section or chapter in a more evaluative way. Reflect on relationships between concepts. The question now is: What is the main topic of this section/unit? What are the key concepts, and how do they relate to the topic? If you have access to the internet, you can find a great deal of information about drawing mind maps, and also see examples. Some good sites to start with are http://www.wikihow.com/Make-a-Mind-Map http://www.mind-mapping.co.uk/make-mind-map.htm 3. Extend your outline. Start by giving your mind map a structure. As you work through the prescribed activities of the section or chapter, keep returning to the mind map to fill in the detail. Think about the value and meaning of categories, concepts and key terms. 0.7.1.3 Study-reading and active learning 1. Study-reading and completing activities. This follows directly from what you have done so far, and you need to be careful, thorough and thoughtful. You have to make connections between the key terms and concepts you have identified, and here the mind map and summaries are important. (Remember to include your detailed mind 11 | P a g e  BLG1502/001/4/2024 map in your portfolio.) Pause while reading, consolidate what you remember, and consider how new information fits in with the information you already have. This will give you a good representation of the whole. Your learning will be enhanced if you are active throughout this process. Whenever you get to an activity in your study guide, complete it in full on loose pages which you then insert in your portfolio, grouped together according to section and learning unit. Supplement this with your own notes from your portfolio. (You don 't need to submit activities or the portfolio to me, but these are essential for exam preparation.) Take time to understand what you read. Note new vocabulary words. Consult a dictionary to understand the meaning of new words, or use Google to find definitions. You could compile a page of new words and terms and their definitions for each learning unit, and add it to your portfolio. 2. Communicate. If you have access to the internet, use the Discussions option to raise any issues you find difficult, or even just interesting. If you cannot find help from your fellow students, feel free to contact me. Also respond to other students' postings by means of the Discussions option. Communicating with others about what you are learning is an important part of the learning process. 3. Reflect. At the end of every learning unit, reflect on what you have learnt. This involves asking yourself questions such as these: What are the main new insights I gained in this learning unit? (Write down two or three.) What did I already know and find quite easy? What did I find difficult? Why might I have found this difficult? What can I do to resolve these difficulties? Has the new knowledge I gained perhaps changed my thinking about issues such as how the body functions, how my own health is or should be maintained and what the uses of biological knowledge might be in my life or career? (Either write down your thoughts on this, or share them with fellow students by means of the Discussions option.) Reflection has enormous potential to enhance your learning by making you aware of your individual learning strategies and progress, of the wider context in which you can apply your learning, and also of the impact of your learning process on yourself and your circumstances. 0.7.2 Managing your self-paced study time As I mentioned in an earlier section, to achieve the outcomes for this module you need to devote at least 120 hours to your studies (although some of you may need a bit more time, and some slightly less). As you will have about 15 weeks to complete a semester module, you should plan to devote at least 8 study hours per week to a module. Remember that if you have registered for more than one module, you need to plan time for each module. I recommend that you draw up a study schedule or keep a diary so that you have a clear idea of the time you have available for study. This will help you to manage your studies within the time you have available and balance your studies with work and family life. In Tutorial Letter 101 and on myUnisa you will find a list of due dates for various assignments. Record these in your diary. Divide the large assignments into a series of smaller, manageable tasks, and then complete these one at a time. 0.7.3 Finding research/scientific articles One of the easiest ways to find scientific and scholarly articles is to use the site Google Scholar, which you can access at http://scholar.google.com. On this site, you will see that there is a down arrow within the search bar where you are to enter your search terms. If you click on this arrow, you will get a menu, "Advanced Search", which will allow you to make your search much more specific. When you have entered your search terms and clicked on "search" (or on the icon representing this, which is a magnifying glass), a number of websites relating to your query will appear. The advantage of using this portal is that you can access most journal references in this way. Certain journals, such as Science Direct, however, can only be accessed through a tertiary academic institution such as Unisa. To access this journal, you need to do the following: 1. Go to Unisa online at http://www.unisa.ac.za/ 2. Click on "Library" at the top of the page. 12 | P a g e  BLG1502/001/4/2024 3. In the menu on the left-hand side of the screen, click on "Search library resources". 4. Follow the guidelines if you are a first-time user. 5. Click on the option "Find e-resources". 6. Now click on "A–Z list of electronic resources". 7. Various links for databases will now be on your screen. Click on any database to do a search. For molecular biology/biochemistry we recommend clicking on Science Direct, Nature or SpringerLink. (Remember, to find Science Direct, select S at the top and a list of all the databases starting with s will appear; if you want to go to Nature, select N, etc.) 8. When you have entered one of these databases, you can search for scientific articles by typing in the relevant keywords in the "search" box. Be very specific in terms of the keywords you use. If you type in just one very general word, this will usually result in too much information that does not relate to the specific topic you are looking for. 9. You will need to do some independent searches yourself, as part of your portfolio, assignments and exam preparation. This is especially true because this is a distance education course, which needs to be supplemented with information from internet sources. Contact the Unisa Library if you have any difficulties or for assistance: +27 12 429 3206 or see the Library website for the local branch library's telephone number. 0.7.4 Avoiding plagiarism Never try to pass off other people's work (or our learning units and study material) as your own. If you want to incorporate other people's words and ideas or our notes in your own answers, enclose these in quotation marks if you are quoting directly, and always acknowledge your source. Use the Harvard referencing method. You can search for more information on this method online; a good source is http://www.staffs.ac.uk/assets/harvard_quick_guide_tcm44-47797.pdf. If you are unsure about the correct way to acknowledge sources, contact Unisa's Library Information Desk. Students who do not acknowledge quotations, or who plagiarise from lecture notes and outside sources, or who copy someone else's answers may be refused permission to write the examination, or may be penalised in the assignment. 0.8 Using myUnisa I explained the advantages of online learning in section 0.1 of this learning unit. In the sections that follow, I will give you an orientation to using myUnisa. You will see how the Unisa menu options work, and I will draw your attention to the "rules" or "etiquette" of online communications. Finally, you will have the opportunity to try using one of the most important tools on myUnisa, the Discussions options. 0.8.1 The myUnisa menu options You need to be able to use the various menu options on this course site, as they will enable you to participate actively in the learning process. Click on the links that follow to see where the various options are located. Learning Units: The learning units are your main learning resource in this module. They contain the content and learning activities that you need to work through to achieve the module outcomes. Official Study Material: A copy of Tutorial Letter 101 as well as past examination papers will be stored as printable PDF versions under this option. Announcements: From time to time I will use this facility to give you important information about this module. You should receive e-mail notification of new announcements posted on myUnisa. 13 | P a g e  BLG1502/001/4/2024 Schedule: This option gives you access to important dates and details about events, such as examination dates and deadlines for your assignments. You will need this information to help you manage your time and plan your own schedule. Course Contact: If you want to send me e-mails in connection with this module, use this option to communicate with me. Additional Resources: A copy of the learning units will be stored as printable PDF versions under this option. This option allows you to access any additional learning support material that might help you in your studies for this module. I will send an e-mail alert or announcement to inform you if I add anything to this folder. Discussions: This option allows us to hold discussions as if we were in a contact setting, and I hope that this will give you clarity on many of the issues that students tend to struggle with. I will set up a number of discussion forums that you can visit to discuss specific topics. There will also be a forum for students, where you can discuss issues among yourselves, or just support one another. Assignments: This option allows you to submit your assignments electronically, and to monitor your results. If you can, please submit your assignments via myUnisa. If you don't know how to do this, consult Tutorial Letter 101. 0.8.2 myUnisa etiquette myUnisa is the university's online platform, where lecturers and students meet, interact and participate in an ongoing process of learning and teaching. In interacting online, always remember to be respectful towards your fellow students and your lecturers. The rules of polite behaviour on the internet are referred to as netiquette – a term that means "online manners". You can access these websites to learn more about netiquette: http://networketiquette.net/ http://www.studygs.net/netiquette.htm http://www.carnegiecyberacademy.com/facultyPages/communication/netiquette.html Please observe the rules of netiquette during your normal, everyday online communication with colleagues, lecturers and friends. In particular, remember to be courteous to your fellow students when using the Discussions option. 0.8.3 Activity 0.1: Introduce yourself At this point, I would like you to do an activity called an icebreaker. What is an icebreaker? An icebreaker helps you to get to know the myUnisa online environment get to know and connect with your fellow students To do the activity, click on the Discussions option in the menu on the left-hand side of the screen. From here, click on the forum Module-related discussions, and then on the topic "Introducing yourself". Once inside the topic, post a short entry in which you tell us who you are and where you live share what the subject area you are studying means to you, and why you chose to study it Also respond to at least one posting by one of your fellow students. 0.9 Assessment in this module Your work in this module will be assessed by the following: 14 | P a g e  BLG1502/001/4/2024 two written assignments, which will be used to calculate a year mark that will count 30% towards your final mark one written examination of 2 hours, which will count 70% towards your final mark Please consult Tutorial Letter 101 for details about the assessment in this module. Be sure to read the following information in the tutorial letter: how your assignment and exam marks will be calculated the due dates for and unique numbers of your assignments how to submit your assignments examination periods, admission and marks Tutorial Letter 101 also contains the actual assignment questions. Remember that although Tutorial Letter 101 will be sent to you, you can also access an electronic version by using the link on this page, or else going to Official Study Material. I wish you well in your studies. Enjoy the course! Learning Phylogeny and systematics unit 1 Contents 1.1 Introduction 1.2 Learning outcomes 1.3 Phylogenies show evolutionary relationships 1.3.1 Binomial nomenclature 1.3.1.1 Activity 1.1 1.3.1.2 Feedback on activity 1.1 1.3.2 Hierarchical classification 1.3.2.1 Activity 1.2 1.3.2.2 Feedback on activity 1.2 1.3.3 Linking classification and phylogeny 1.4 Construction of phylogeny trees 1.5 An organism's evolutionary history is documented in its genome 1.6 Molecular clocks help track evolutionary time 1.7 Activity 1.3 1.8 Feedback on activity 1.3 1.9 Summary 1.1 Introduction To complete the learning unit, you will need to refer to pages 523–542 of chapter 22 in Campbell et al (2015) You may wonder why and how biologists distinguish between and categorise the millions of species on earth. In this unit we will focus on how biologists trace phylogeny, the evolutionary history of a species or group of species. A phylogeny of snakes and lizards, for example, shows that both eastern glass lizards and snakes evolved from lizards with legs – but they evolved from different lineages of legged lizards. This is demonstrated in figure 22.2 in your prescribed textbook. So it appears that their legless condition evolved independently. We will look at how biologists reconstruct and interpret phylogenies using systematics. Systematics is a discipline focused on 15 | P a g e  BLG1502/001/4/2024 classifying organisms and determining their evolutionary relationships. We then focus on how systematists develop hypotheses about the evolutionary relationship of all the branches, twigs and leaves on the tree of life. 1.2 Learning outcomes By the end of this learning unit, you should be able to explain the determination of phylogeny from common ancestries describe the binomial nomenclature system explain the hierarchical system of classification list the different hierarchical classification groupings discuss cladistic analysis on which systematics is based discuss the principle of parsimony and maximum likelihood construct the phylogeny tree 1.3 Phylogenies show evolutionary relationships Recommended reading: pages 524–527 of chapter 22 in Campbell et al (2015) Organisms share many characteristics because of common ancestry. As a result, you can learn a great deal about a species if you have explored its evolutionary history. For example, an organism is likely to share many of its genes, metabolic pathways and structural proteins with its close relatives (figure 1.1). We will consider practical applications of this information later in this unit, but first we will examine how organisms are named and classified, the scientific discipline taxonomy. We will also look at how we can interpret and use diagrams that represent evolutionary history. Figure 1.1: Relationships between wolf-like canids (Canis species) capable of hybridising (https://commons.wikimedia.org/wiki/File:Wolf-like_canids_phylogeny_(ita).jpg) 1.3.1 Binomial nomenclature Born in Sweden, Carl von Linné (1707-1778), better known as the Latinised name, Carolus Linnaeus, was the first modern practitioner of taxonomy, the science that identifies, names and classifies new species. Linnaeus invented the system of binomial nomenclature, in which species are assigned a Latinised two-part name, or binomial. The first part of a binomial is the name of the genus (plural, genera) to which the species belongs. Note that genus is a group of species with similar characteristics. The first letter of the genus is capitalised. The second part of the binomial is called the specific epithet, and is unique for each species within the genus. It is always written in small letters. Both genus and specific epithet are always underlined or italicised. For biologists to avoid ambiguity and confusion when communicating about their research, Latin scientific names are used. There are many binomial names today, for example Panthera pardus and Homo sapiens are the scientific names of the leopard and humans, respectively. 16 | P a g e  BLG1502/001/4/2024 1.3.1.1 Activity 1.1 Do this activity and add it to your portfolio. Remember, this could serve as part of your summary to use in preparing for the exam! Refer to your textbook, and answer the following questions: a) How does the system of binomial nomenclature minimise ambiguity in the naming and identification of species? b) Are the following scientific names correct? Give reasons. 1. Acacia aerioloba 2. Panthera pardus 3. Ophisaurus ventralis 4. Homo sapie 1.3.1.2 Feedback on activity 1.1 a) The system of binomial nomenclature avoids ambiguity in the naming of species because it assigns a unique two-part name to each species. b) Were you able to easily recognise the rules of binomial nomenclature before you attempted any of these scientific names? If yes, keep up the good work! If not, make sure that you go back to the binomial nomenclature section and revise the simple rules on scientific names. The answers to the questions are as follows: 1. Yes, because the scientific name is written correctly and the first letter of the genus has been written with a capital letter, and both the genus and specific epithet are underlined. 2. No, though the name has been correctly spelt, both genus and specific epithet should be either underlined or italicised. 3. Yes, all the rules have been followed. 4. No, the scientific name must always be spelt correctly. The correct way is Homo sapiens. 1.3.2 Hierarchical classification In addition to naming species, Linnaeus also grouped living organisms into a hierarchy of increasingly inclusive categories. Linnaeus's classification, called the taxonomic hierarchy, includes a nested series of formal categories which are domain, kingdom, phylum, class, order, family, genus, species and lastly, subspecies. The biological classification of a particular organism is like a postal address identifying a person in a particular flat, in a building with many flats, on a street with many buildings of flats, in a city with many streets, and so on. Note that the organisms included within any category of the taxonomic hierarchy comprise a taxon (plural, taxa). Leopard, for example, is a taxon (Felidae) at family level, and Panthera is a taxon at genus level (refer to figure 22.4 in your textbook). Species that are included in the same taxon at the bottom of the hierarchy (that is, in the same genus or family) generally share many characteristics. By contrast, species that are included in the same taxon only near the top of the hierarchy (that is, the same kingdom or phylum) generally share fewer traits. Very important, in the Linnaean system, taxa broader than the genus are not italicised or underlined, though they are capitalised. 1.3.2.1 Activity 1.2 Do this activity and add it to your portfolio. Refer to your textbook and answer the following questions: a) How does the taxonomic hierarchy help biologists organise information about different species? b) List the major taxonomic categories from most to least inclusive. 1.3.2.2 Feedback on activity 1.2 a) The taxonomic hierarchy helps biologists organise information about different species because it categorises them into increasingly inclusive groups. Species that are included in a lower taxonomic 17 | P a g e  BLG1502/001/4/2024 category share many characteristics, whereas those included only in the same higher category share fewer characteristics. b) kingdom, phylum, class, order, family, genus, species 1.3.3 Linking classification and phylogeny Systematists explore phylogeny by examining various characteristics in living and fossil organisms. They construct branching diagrams called phylogenetic trees to depict their hypotheses about evolutionary relationships. The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups. Methods for tracing phylogeny began with Darwin, who realised the evolutionary implications of Linnaean hierarchy. Darwin introduced phylogenetic systematics in On the origin of species when he wrote: "Our classifications will come to be, as far as they can be so made, genealogies." 1.4 Construction of phylogeny trees Recommended reading: pages 529–535 of chapter 22 in Campbell et al (2015) Patterns of shared characteristics can be drawn in a cladogram. If shared characteristics are homologous and therefore explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree. A clade is defined as a group of species that includes an ancestral species and all its descendants. The study of resemblances among clades is called cladistics. Each branch, or clade, can be nested within larger clades. A valid clade is monophyletic, consisting of an ancestral species and all its descendants. When we lack information about some members of a clade, the result is a paraphyletic grouping that consists of some, but not all, of the descendants. The result may also be several polyphyletic groupings that lack a common ancestor. These situations need further reconstruction to uncover species that tie these groupings together into monophyletic clades. It is difficult to determine which similarities between species are relevant to grouping the species in a clade. It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy. Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters. A "character" refers to any feature that a particular taxon has. A shared derived character is unique to a particular clade. A shared primitive character is found not only in the clade being analysed, but also in older clades. For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods. It is a shared derived character that uniquely identifies mammals. However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals. Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates. Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not. The status of a shared derived character versus a shared primitive character may depend on the level at which the analysis is being performed. A key step in cladistic analysis is outgroup comparison, which is used to differentiate shared primitive characters from shared derived ones. To do this, we need to identify an outgroup, a species or group of species that is closely related to the species that we are studying, but known to be less closely related than any members of the study group are to one another. To study the relationships between an ingroup of five vertebrates (a leopard, a turtle, a salamander, a tuna and a lamprey) on a cladogram, let’s use the example of an animal called the lancelet. The lancelet is a small member of the phylum Chordata that lacks a backbone. The species making up the ingroup display a mixture of shared primitive and shared derived characters. In an outgroup analysis, the assumption is that any homologies shared by the ingroup and outgroup are primitive characters that were present in the common ancestor of both groups. Homologies present in some or all of the ingroup taxa are assumed to have evolved after the divergence of the ingroup and outgroup taxa. In our example, a notochord, present in lancelets and in the embryos of the ingroup, is a shared primitive character and therefore not useful for sorting out relationships between members of the ingroup. The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup. The presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram. 18 | P a g e  BLG1502/001/4/2024 Analysing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny. A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms. However, this chronology does not indicate the time of origin of the species that we are comparing, only the groups to which they belong. For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group. A cladogram is not a phylogenetic tree. To convert it to a phylogenetic tree, we need more information from sources such as the fossil record, which can indicate when and in which groups the characters first appeared. Any chronology represented by the branching pattern of a phylogenetic tree is relative (earlier versus later) rather than absolute (so many millions of years ago). Some kinds of tree diagrams can be used to provide more specific information about timing. In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in a lineage. Even though the branches in a phylogram may have different lengths, all the different lineages that descend from a common ancestor have survived for the same number of years. Humans and bacteria had a common ancestor that lived more than 3 billion years ago. This ancestor was a single-celled prokaryote and was more like a modern bacterium than a human. Even though bacteria have apparently changed little in structure since that common ancestor, there have nonetheless been 3 billion years of evolution in both the bacterial and eukaryotic lineages. These equal amounts of chronological time are represented in an ultrameric tree. In an ultrameric tree, the branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal lengths. Ultrameric trees do not contain the information about different evolutionary rates that can be found in phylograms. However, they draw on data from the fossil record to place certain branch points in the context of geological time. The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny According to the principle of maximum parsimony, we look for the simplest explanation that is consistent with the facts. In the case of a tree based on morphological characters, the most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters. For phylograms based on DNA sequences, the most parsimonious tree requires the fewest base changes in DNA. The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree should reflect the most likely sequence of evolutionary events. Maximum likelihood methods are designed to use as much information as possible. Many computer programs have been developed to search for trees that are parsimonious and likely: "distance" methods minimise the total of all the percentage differences among all the sequences. More complex "character-state" methods minimise the total number of base changes or search for the most likely pattern of base changes among all the sequences. Although we can never be certain precisely which tree truly reflects phylogeny, if they are based on a large amount of accurate data, the various methods usually yield similar trees. Phylogenetic trees are hypotheses Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related. The best hypothesis is the one that best fits all the available data. A hypothesis may be modified when new evidence compels systematists to revise their trees. Many older phylogenetic hypotheses have been changed or rejected since the introduction of molecular methods for comparing species and tracing phylogeny. Often, in the absence of conflicting information, the most parsimonious tree is also the most likely. Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious. Nature does not always take the simplest course. In some cases, the particular morphological or molecular character we are using to sort taxa actually did evolve multiple times. For example, the most parsimonious assumption would be that the four-chambered heart evolved only once in an ancestor common to birds and mammals but not to lizards, snakes, turtles and crocodiles. But 19 | P a g e  BLG1502/001/4/2024 abundant evidence indicated that birds and mammals evolved from different reptilian ancestors. The hearts of birds and mammals develop differently, supporting the hypothesis that they evolved independently. The most parsimonious tree is not consistent with the above facts, and must be rejected in favour of a less parsimonious tree. The four-chambered hearts of birds and mammals are analogous, not homologous. Occasionally misjudging an analogous similarity in morphology or gene sequence as a shared derived homology is less likely to distort a phylogenetic tree if several derived characters define each clade in the tree. The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence. 1.5 An organism's evolutionary history is documented in its genome Recommended reading: pages 535–536 of chapter 22 in Campbell et al (2015) Molecular systematics is a valuable tool for tracing an organism's evolutionary history. The molecular approach helps us to understand phylogenetic relationships that cannot be measured by comparative anatomy and other non-molecular methods. For example, molecular systematics helps us uncover evolutionary relationships between groups that have no grounds for morphological comparison, such as mammals and bacteria. Molecular systematics enables scientists to compare genetic divergence within a species. Molecular biology has helped to extend systematics to evolutionary relationships far above and below the species level. Its findings are sometimes inconclusive, as in cases where a number of taxa diverged at nearly the same time. The ability of molecular trees to encompass both short and long periods of time is based on the fact that different genes evolve at different rates, even in the same evolutionary lineage. For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively slowly, so comparisons of DNA sequences in these genes can be used to sort out relationships between taxa that diverged hundreds of millions of years ago. In contrast, mitochondrial DNA (mtDNA) evolved relatively recently and can be used to explore recent evolutionary events, such as relationships between groups within a species. Gene duplication has provided opportunities for evolutionary change Gene duplication increases the number of genes in the genome, providing opportunities for further evolutionary change. Gene duplication has resulted in gene families, which are groups of related genes within an organism's genome. Like homologous genes in different species, these duplicated genes have a common genetic ancestor. There are two types of homologous genes: orthologous genes and paralogous genes. The term “orthologous” refers to homologous genes that are found in different gene pools because of speciation. The ß haemoglobin genes in humans and mice are orthologous. Paralogous genes result from gene duplication and are found in more than one copy in the same genome Olfactory receptor genes have undergone many gene duplications in vertebrates. Humans and mice each have huge families of more than 1 000 of these paralogous genes. Now that we have compared entire genomes of different organisms, two remarkable facts have emerged. Orthologous genes are widespread and can extend over enormous evolutionary distances. Approximately 99% of the genes of humans and mice are demonstrably orthologous, and 50% of human genes are orthologous with those of yeast. All living things share many biochemical and development pathways. The number of genes does not seem to have increased at the same rate as phenotypic complexity. Humans have only five times as many genes as yeast, a simple unicellular eukaryote, although we have a large, complex brain and a body that contains more than 200 different types of tissues. Many human genes are more versatile than yeast and can carry out a wide variety of tasks in various body tissues. 1.6 Molecular clocks help track evolutionary time Recommended reading: pages 536–540 of chapter 22 in Campbell et al (2015) In the past, the timing of evolutionary events has rested primarily on the fossil record. One of the goals of evolutionary biology is to understand the relationships between all living organisms, including those for which there is no fossil record. Molecular clocks serve as yardsticks for measuring the absolute time of evolutionary change. They are based on the observation that some regions of the genome evolve at constant rates. For these 20 | P a g e  BLG1502/001/4/2024 regions, the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the two species last shared a common ancestor. In the case of paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated. We can calibrate the molecular clock of a gene by graphing the number of nucleotide differences against the timing of a series of evolutionary branch points that are known from the fossil record. The slope of the best line through these points represents the evolution rate of that molecular clock. This rate can be used to estimate the absolute date of evolutionary events that have no fossil record. No molecular clock is completely accurate. Genes that make good molecular clocks have fairly smooth average rates of change. No genes mark time with precise accuracy in the rate of base changes. Over time there may be chance deviations above and below the average rate. Rates of change of various genes vary greatly. Some genes evolve a million times faster than others. The molecular clock approach assumes that much of the change in DNA sequences is due to genetic drift and is selectively neutral. Neutral theory suggests that a great deal of evolutionary change in genes and proteins has no effect on fitness and is therefore not influenced by Darwinian selection. Researchers supporting this theory point out that many new mutations are harmful and are removed quickly. However, if most of the rest are neutral and have little or no effect on fitness, the rate of molecular change should be clocklike in their regularity. Differences in the rates of change of specific genes are a function of the importance of the gene. If the exact sequence of amino acids specified by a gene is essential to survival, most mutations will be harmful and will be removed by natural selection. If the sequence of genes is less critical, more mutations will be neutral, and mutations will accumulate more rapidly. Some DNA changes are favoured by natural selection. This leads some scientists to question the accuracy and utility of molecular clocks for timing evolution. Evidence suggests that almost 50% of the amino acid differences in proteins of two Drosophila species have resulted from directional natural selection. Over very long periods, fluctuations in the rate of accumulation of mutations caused by natural selection may even out. Even genes with irregular clocks can mark elapsed time approximately. Biologists are sceptical of conclusions derived from molecular clocks that have been extrapolated to time spans beyond the calibration in the fossil record. Few fossils are older than 550 million years old. Estimates for evolutionary divergences prior to that time may assume that molecular clocks have been constant over billions of years. These estimates have a high degree of uncertainty. The molecular clock approach has been used to date the jump of HIV from related simian immunodeficiency viruses (SIVs) that infect chimpanzees and other primates to humans. SIV has spread to humans more than once. The multiple origins of HIV are reflected in the variety of strains of the virus. HIV-1 M is the most common HIV strain. Investigators have calibrated the molecular clock for the virus by comparing samples of the virus collected at various times. From their analysis, they project that the HIV-1 M strain invaded humans in the 1930s. There is a universal tree of life The genetic code is universal in all forms of life. From this, researchers infer that all living things have a c ommon ancestor. Researchers are working to link all organisms into a universal tree of life. Two criteria identify regions of DNA that can be used to reconstruct the branching pattern of this tree. The regions must be able to be sequenced. They must have evolved slowly, so that even distantly related organisms show evidence of homologies in these regions. Ribosomal-RNA genes, coding for the RNA component of ribosomes, meet these criteria. Two points have emerged from this effort: i) The tree of life consists of three great domains: Bacteria, Archaea and Eukarya. Most prokaryotes belong to Bacteria. Archaea includes a diverse group of prokaryotes that inhabit many different habitats. Eukarya includes all organisms with true nuclei, including many unicellular organisms as well as the multicellular kingdoms. 21 | P a g e  BLG1502/001/4/2024 ii) The early history of these domains is not yet clear. Early in the history of life, there were many interchanges of genes between organisms in the different domains. One mechanism for these interchanges was horizontal gene transfer, in which genes are transferred from one genome to another by mechanisms such as transposable elements. Different organisms fused to produce new, hybrid organisms. It is likely that the first eukaryote arose through fusion between an ancestral bacterium and an ancestral archaean. 1.7 Activity 1.3 Do this activity and add it to your portfolio. Refer to your textbook and answer the following questions: a) Distinguish between phylogeny and systematics. b) In the following cladogram, which node occurred earliest in time? c) In the cladogram for question (b), which node represents the most recent common ancestor of terminal taxa B and C? d) In the cladogram for question (b), which terminal taxon is B more closely related to, A or C? e) Explain how shared derived characteristics can be used to construct a phylogenetic diagram. f) Describe the evidence that suggests that there is a universal tree of life. 1.8 Feedback on activity 1.3 a) Phylogeny is the evolutionary history of a species or group of related species. Systematics is the study of biological diversity in an environmental context, encompassing taxonomy and involving the reconstruction of phylogenetic history. b) Since the common ancestor is located at the base, your answer should be node 1. c) Node 2. d) Terminal taxon C. e) Biologists hypothesise that all of the chromosomes were inherited from the same ancestor. It's possible that in one of the descendants, one chromosome became two or two chromosomes became one; therefore, they can conclude that there is evolutionary history between the two species. f) The tree of life is based on ribosomal RNA sequences. All life on earth can be placed in one of the three major categories, leading biologists to believe that all life started from a common ancestor. 1.9 Summary Linnaeus's binomial classification system gives organisms two-part names: a genus and specific epithet. Species are grouped in increasingly broad taxa. Related genera are placed in the same family, families in orders, orders in classes, classes in phyla, phyla in kingdoms and, lastly, kingdoms in domains. Systematics depicts evolutionary relationships as branching phylogenetic trees. However, many systematists propose that classification be based entirely on evolutionary relationships. A clade is a monophyletic grouping that includes an ancestral species and all of its descendants. Clades can be distinguished by their shared derived characters. Among phylogenies, the most parsimonious tree is the one that requires the fewest evolutionary changes. Orthologous genes are homologous genes found in different species as a result of speciation. Paralogous genes are homologous genes within a species that result from gene duplication. Distantly related species often have many 22 | P a g e  BLG1502/001/4/2024 orthologous genes. Some regions of DNA change at a rate consistent enough to serve as a molecular clock, in which the number of genetic changes are used to estimate the date of past evolutionary events. Molecular clock analyses suggest that the most common strain of HIV transmitted from primates to humans in the early 1900s. Learning Prokaryotes and the origins of metabolic diversity unit 2 Contents 2.1 Introduction 2.2 Learning outcomes 2.3 Structure, function and reproduction of bacteria 2.3.1 Activity 2.1 2.3.2 Feedback on activity 2.1 2.4 Nutritional and metabolic adaptations 2.4.1 Activity 2.2 2.4.2 Feedback on activity 2.2 2.5 Prokaryotes have radiated into a diverse set of lineages 2.5.1 Activity 2.3 2.5.2 Feedback on activity 2.3 2.6 Prokaryotes play crucial roles in the biosphere 2.6.1 Chemical recycling 2.6.2 Ecological interactions 2.6.3 Pathogenic bacteria 2.6.4 Prokaryotes in research and technology 2.6.5 Activity 2.4 2.6.6 Feedback on activity 2.4 2.7 Summary 2.1 Introduction To complete the learning unit, you will need to refer to pages 629–648 of chapter 27 in Campbell et al (2015) Organisms informally called prokaryotes have inhabited planet earth for more than 3.5 billion years. They have existed for much longer than eukaryotes, which evolved at least 2.2 billion years ago. Although prokaryotes are microscopic, they are so numerous that they probably account for more than half of earth's biomass. Prokaryotes can tolerate extreme conditions, such as very low pH, too cold and/or too hot, and some have even been found living within rocks 3.2 km below the earth's surface. Their ability to adapt to a broad range of habitats helps scientists to explain why prokaryotes are the most abundant organisms on earth. Members of the domains Bacteria and Archaea cause many diseases, such as tuberculosis, tetanus, respiratory infections and food poisoning in humans. However, both Bacteria and Archaea play essential roles in the biosphere. As decomposers they break down organic molecules into their components. Without these remarkable microorganisms, certain elements such as carbon, nitrogen and phosphorus would remain locked up in the wastes and dead bodies of plants and animals. 23 | P a g e  BLG1502/001/4/2024 In this learning unit, we will describe the structure of bacteria and archaea. We will also examine the adaptations, diversity and enormous ecological impact of these remarkable organisms. 2.2 Learning outcomes By the end of this learning unit, you should be able to name the two main branches of prokaryotic evolution describe the structure, function and reproduction of bacteria discuss the ecological impact of bacteria describe the organisation and specialisation of a bacterial cell describe the structure, composition and function of prokaryotic cell walls distinguish between the staining properties of gram-positive and gram-negative bacteria explain how the genetic organisation of the prokaryotic genome differs from that of eukaryotic cells 2.3 Structure, function and reproduction of bacteria Recommended reading: pages 630–636 of chapter 27 in Campbell et al (2015) Prokaryotes seem to be found everywhere. Collective prokaryote biomass outweighs all eukaryotes combined by at least tenfold. They exist almost everywhere, including places where eukaryotes cannot. Most prokaryotes are beneficial; humans could not live without them, for example nitrogen-fixing bacteria. There are approximately 5 000 species of prokaryotes that have been identified, but estimations of prokaryote diversity range from 400 000 to 4 000 000 species. Bacteria and Archaea are the two main branches of prokaryote evolution. Archaea are thought to be more closely related to eukaryotes than to Bacteria. Most prokaryotes are unicellular. Although, they are unicellular and small, prokaryotes are well organised, achieving all of an organism's life functions within a single cell (figure 2.1). Some species form aggregates of two or more individuals. Prokaryotes are typically 0.5 -5 μm in diameter, but some can be seen with the naked eye. Eukaryotic cells are typically 10-100 μm in diameter. Almost all prokaryotes have cell walls external to the plasma membrane. 24 | P a g e  BLG1502/001/4/2024 Figure 2.1: Prokaryotic cell (https://commons.wikimedia.org/wiki/File:Average_prokaryote_cell-_en.svg) A key feature of nearly all prokaryotic cells is the cell wall, which maintains cell shape, protects the cell and prevents it from bursting in a hypotonic environment. There are three common shapes: cocci (round), bacilli (rod) and helical (spiral). Refer to your textbook, page 630, figure 27.2. Cell walls are composed of peptidoglycan. There are two types of cell walls. Bacteria are grouped according to cell wall type, and that is gram-positive bacteria and gram- negative bacteria. Gram-positive bacteria have simple, thick cell walls. Their cell walls are composed of a relatively large amount of peptidoglycan. Gram-negative bacteria have less peptidoglycan and are more complex. They have a peptidoglycan layer surrounded by the plasma membrane and an outer membrane. Gram-negative bacteria are typically more resistant to host immune defence and antibiotics. Note that the two types of bacteria can be stained to determine which is gram-negative (pink) and gram-positive (purple) using a gram stain. Most prokaryotes secrete sticky substances that form a protective layer and enable them to adhere to substrates. The sticky protective layer secreted by prokaryotes is called the capsule. Endospores are resistant cells formed by certain bacteria as a way to withstand harsh conditions. The cell replicates its chromosome and wraps it in a durable wall that can protect the chromosome from adverse conditions, e.g. boiling water, desiccation. When the environment is good again, the cell will revive to a new vegetative (growing) spore. Some prokaryotes adhere to substrates using pili (singular, pilus). Some pili are specialised for DNA transfer. This process is called conjugation. Many prokaryotes are motile. Moreover, some exceed speeds 100 times their body length per second. The mode of movement is executed by three types, namely flagellum - basal apparatus rotates the flagellum and propels the cell; corkscrew movement of spirochetes (helical) and, finally, some prokaryotes glide over jets of slimy secretions. 25 | P a g e  BLG1502/001/4/2024 Many prokaryotes move towards or away from stimulus-taxis. Chemotaxis is the movement towards or away from a chemical. Neither mitosis nor meiosis occur in the prokaryotes. Reproduction is asexual by binary fission. DNA synthesis is almost continuous. Prokaryotes grow and adapt rapidly. The doubling time for E. coli is 20 minutes. If you started with one E. coli cell, after 48 hours of doubling every 20 minutes, the mass of E. coli would be 10 000 times the mass of the earth. Bacteria do not have gene transfer by sexual reproduction, but do transfer genes. Why? This is an aid in adapting (evolving). There are three ways for genes to be transferred between cells: Transformation – cell takes up genes from the surrounding environment. Conjugation – direct transfer of genes from one prokaryote to another; use the sex pilus to conjugate. Transduction – viruses transfer genes between prokaryotes. 2.3.1 Activity 2.1 Do this activity and add it to your portfolio. Refer to your textbook and answer the following questions: a) Describe the differences between eukaryotic cells and prokaryotic cells. b) Discuss the structure of the prokaryotic cell wall and explain how the structure could be of medical value. c) What is a Gram stain and why is it important to doctors? 2.3.2 Feedback on activity 2.1 You may answer a) in the form of table like this: Eukaryotic cell Prokaryotic cell Nucleus Present Absent Number of chromosomes More than one One, but not true chromosome Cell type Usually multicellular Usually unicellular Mitochondria Present Absent Chloroplasts Present (in plants) Absent Cell size Large (10-100 um) Small (1-10 um) Structural complexity Complex Much simpler DNA found in the region Nucleus Nucleoid Membrane-enclosed Present Absent organelles Lysosomes and peroxisomes Present Absent Endoplasmic reticulum Present Absent Golgi apparatus Present Absent 26 | P a g e  BLG1502/001/4/2024 Permeability of nuclear Selective Not present membrane Plasma membrane Present Present Cytosol Present Present Cell division Mitosis Binary fission Ribosomes Present (larger) Present (smaller) b) A cell wall is a layer located outside the cell membrane found in plants, fungi, bacteria, algae and archaea. A peptidoglycan cell wall composed of disaccharides and amino acids gives bacteria structural support. The bacterial cell wall is often a target for antibiotic treatment. c) A Gram stain is a method of staining bacteria using a dye called crystal violet. It is important in that it helps distinguish between different types of bacteria. 2.4 Nutritional and metabolic adaptations Recommended reading: pages 637-638 of chapter 27 in Campbell et al (2015) All prokaryotes (as well as eukaryotic species) are grouped into four categories according to how they obtain energy and carbon. Refer to your textbook, table 27.1, page 638. Species that use light energy are phototrophs. Species that obtain energy from chemicals in their environment are chemotrophs. Organisms that need only CO2 as a carbon source are autotrophs. Organisms that require at least one organic nutrient as a carbon source are heterotrophs. These categories of energy source and carbon source can be combined to group prokaryotes according to four major modes of nutrition. Mode Energy source Carbon source Types of organisms Autotroph Photoautotrophs Since they are CO2, HCO3‒, or related Cyanobacteria; plants photosynthetic compound is the (eukaryotic) species, they use light carbon source as the energy source Chemoautotrophs Energy from oxidation CO2 is the carbon Sulfolobus, Beggiatoa of inorganic source substances (e.g. NH4, and S) Heterotroph Photoheterotrophs Light as energy source Organic compounds Unique to certain are source of carbon aquatic and salt-loving prokaryotes (e.g. Rhodobacter, Chloroflexus) Chemoheterotrophs Organic compounds Organic compounds Many prokaryotes are energy source are source of carbon (Clostridium), animals (this includes humans) and fungi (eukaryotic); some plants The role of oxygen in metabolism 27 | P a g e  BLG1502/001/4/2024 Prokaryotic metabolism also varies with regard to oxygen (O2). The following are the three different groups: Obligate aerobes - Use O2 for respiration; cannot grow without it. (Humans are obligate aerobes.) Facultative aerobes - Use O2 when available; ferment when O2 is not available. Obligate anaerobes - Poisoned by O2; use fermentation or live by anaerobic respiration. In anaerobic respiration, inorganic molecules like SO42‒, NO3, and Fe3+ are used instead of oxygen. Note that photosynthesis evolved early in prokaryotic life. Cyanobacteria started to produce O 2 about 2.7 billion years ago. There are contrasting hypotheses for the taxonomic distribution of photosynthesis among prokaryotes. 2.4.1 Activity 2.2 Do this activity and add it to your portfolio. Refer to your textbook and answer the following questions: a) Describe the differences between photoautotrophs and photoheterotrophs. b) List and describe the three groups of prokaryotes with regard to oxygen. 2.4.2 Feedback on activity 2.2 a) Photoautotrophs convert inorganic materials into organic materials for use in cellular functions such as biosynthesis and respiration and provide nutrition for many other forms of life. Photoheterotrophs depend on light for their source of energy and mostly organic compounds from the environment for their source of carbon. b) You should be able to name obligate aerobes, facultative aerobes and obligate anaerobes. You should also describe how they differ from one another. 2.5 Prokaryotes have radiated into a diverse set of lineages Recommended reading: pages 639–643 of chapter 27 in Campbell et al (2015) Since their origin 3.5 billion years ago, prokaryotic populations have radiated extensively as a wide range of structural and metabolic adaptations have evolved in them. Collectively, these adaptations have enabled prokaryotes to inhabit every environment known to support life. In recent decades, advances in genomics are beginning to reveal the extent of prokaryotic diversity. Early on, prokaryotes diverged into two lineages, the domains Archaea and Bacteria. A comparison of the three domains -- Archaea, Bacteria, and Eukarya -- demonstrates that Archaea have at least as much in common with eukaryotes as with Bacteria (refer to your textbook, page 642, table 27.2). Archaea also have many unique characteristics. Most species of archaea have been sorted into the kingdom Euryarchaeota or the kingdom Crenarchaeota. However, much of the research on archaea has focused not on phylogeny, but on their ecology - their ability to live where no other life can. Archaea are extremophiles, "lovers" of extreme environments. Based on environmental criteria, archaea can be classified into methanogens, extreme halophiles and extreme thermophiles. Methanogens obtain energy by using CO2 to oxidise H2, replacing methane as a waste. Methanogens are among the strictest anaerobes. They live in swamps and marshes where other microbes have consumed all the oxygen. Methanogens are important decomposers in sewage treatment. Other methanogens live in the anaerobic guts of herbivorous animals, playing an important role in their nutrition. They may contribute to the greenhouse effect, through the production of methane. Extreme halophiles live in saline places such as the Great Salt Lake and the Dead Sea. Some species merely tolerate elevated salinity; others require an extremely salty environment to grow. Colonies of halophiles form a purple-red scum from bacteriorhodopsin, a photosynthetic pigment very similar to the visual pigment in the human retina. Extreme thermophiles thrive in hot environments. The optimum temperatures for most thermophiles are 60 °C - 80 °C. Sulfolobus oxidises sulphur in hot sulphur springs in Yellowstone National Park. Another sulphur-metabolising thermophile lives at 105 °C water near deep-sea hydrothermal vents. If the earliest prokaryotes evolved in extremely hot environments like deep-sea vents, then it would be more accurate to consider most life as "cold-adapted" rather than viewing thermophilic archaea as "extreme". Recently, scientists have discovered an abundance of marine archaea among other life forms in more moderate habitats. 2.5.1 Activity 2.3 Do this activity and add it to your portfolio. 28 | P a g e  BLG1502/001/4/2024 Refer to your textbook and answer the following questions: a) Describe the difference between extreme halophiles and extreme thermophiles. b) In your understanding, what makes archaea "lovers" of extreme environments? 2.5.2 Feedback on activity 2.3 a) Did you note that the major difference is that halophiles live in environments with plenty of salt concentration and thermophiles live in geothermal areas where there is plenty of heat? b) Don’t forget to consider their physiological aspects and their extreme tolerance. 2.6 Prokaryotes play crucial roles in the biosphere Recommended reading: pages 643–646 of chapter 27 in Campbell et al (2015) If people were to disappear from the planet tomorrow, life on earth would change for many species, but few would become extinct. In contrast, prokaryotes are so important to the biosphere that if they were to disappear, the prospects of survival for many other species would be dim. 2.6.1 Chemical recycling Ongoing life depends on the recycling of chemical elements between the biological and chemical components of ecosystems. If it were not for decomposers, especially prokaryotes, carbon, nitrogen and other elements essential for life would become locked in the organic molecules of corpses and waste products. Prokaryotes also mediate