Biology taxonomy for first year students, Lecture notes of Plant Taxonomy and Evolution

Download Biology taxonomy for first year students and more Lecture notes Plant Taxonomy and Evolution in PDF only on Docsity! BIOL 1030 – TOPIC 1 LECTURE NOTES Topic 1: Classification and the Diversity of Life (Chapters 25, 26.6) I. Background review (Biology 1020 material) A. Scientific Method 1. observations 2. scientific model • explains observations • makes testable predictions 3. test predictions (can confirm predictions) 4. reject, revise, or tentatively accept scientific model 5. caveats: • Scientific models can only be proven false, never proven true. • Correlation does not equal causation. • Testable predictions cannot include the supernatural (the supernatural cannot, by definition, be tested scientifically); thus, the supernatural is outside the realm of science. • The term “theory” has a very different meaning in science than in most everyday conversations. 6. terms: • hypothesis – model that has not been tested or has only been tested some • theory – model that has been tested extensively and is accepted by most scientists in that field • law – usually a very well-established theory that explains a wide body of observations B. Theory of Evolution: The Modern Synthesis 1. Evolutionary relationships between organisms provides the theoretical framework for modern classification systems; as such, it is the major organizing principle underlying the structure of most of this course 2. In POPULATIONS, new mutations (random) and recombination of current variations (random) occurs. 3. Populations encounter EVOLUTIONARY MECHANISMS: • natural selection (greater reproduction by the “fittest”) • genetic drift (random, greater for small populations) • gene flow (genetic exchange with other populations) • mutations (new changes in genetic material) 4. Evolutionary mechanisms cause MICROEVOLUTION: changes in population genotype and allele frequencies for the next generation. 5. Adding any REPRODUCTIVE ISOLATION MECHANISM allows MACROEVOLUTION (speciation). • Examples of reproductive isolation mechanisms include physical separation, selective mating, and sterile offspring. 6. Speciation can be rapid (punctuated equilibrium) or gradual; relative amounts of these are debated but both appear to occur. 1 of 7 BIOL 1030 – TOPIC 1 LECTURE NOTES II. Classification of organisms A. Biologists use a binomial system for classifying organisms. 1. taxonomy - the science of classifying and naming organisms. 2. Carolus Linnaeus (18th century biologist) developed a system of classification that is the basis of what is used today • binomial system: today each species’ official scientific name is made of 2 words (bi=“2” nomen=“name”) • names are Latin  same language used universally in biology  dead language – not changing  names of people can be “Latinized” for use in naming 3. species - basic unit of classification or taxonomy (more on this later) • if sexual, a group of organisms that can interbreed and produce fertile offspring • if asexual, grouped based on similarities (DNA sequence is best) • about 1.8 million living species have been described, likely millions more 4. genus - a group of closely related species. 5. together the genus and specific epithet names make up the binomial name used to name a species • the Genus name is always capitalized, and the specific epithet is never capitalized. • the Genus and specific epithet are always together, and italicized (or underlined). • example: Homo sapiens or Homo sapiens B. Taxonomic classification is hierarchical. 1. A group of related genera make up a Family. 2. Related families make up an Order. 3. Related orders are grouped into a Class. 4. Related classes are grouped into a Phylum or Division. 5. Related phyla or divisions are grouped into a Kingdom. 6. Related kingdoms are grouped into a Domain, the highest level of classification in the modern system. 7. The gold standard for “related” is based on DNA sequence similarities, but other criteria are used as well (we don’t have the complete DNA sequence of all known species) III. What is a species? A. Species: “Kind of living thing” B. Word “species” is both plural and singular C. relatively easy to define for sexual organisms, hard for asexual organisms and extinct species 1. biological species concept (for sexual organisms) – one or more populations whose members are capable of interbreeding and producing fertile offspring, and whose members are reproductively isolated from other such groups • not always clear-cut, because some can interbreed under “artificial” conditions but don’t appear to do so in nature • sometimes, “race” and “subspecies” designations are used, but often different specific epithets are used when there are clear morphological differences involved 2 of 7 BIOL 1030 – TOPIC 1 LECTURE NOTES parsimonious one, the one that requires the simplest explanation) 5. cladograms are always open to refinement as more date become available 6. naming based on cladograms only allows for monophyletic groups C. traditional taxonomy weighs characters according to presumed biological or evolutionary significance 1. line of descent is considered as well (and may incorporate cladograms), but naming allows for some paraphyletic groups 2. example: classifying birds. • traditional taxonomists view feathers as being so important that birds are placed in own Class (thus making Reptilia paraphyletic in their taxonomies) • cladists put birds with reptiles to make Reptilia monophyletic D. So who is right? How the heck do we classify birds? 1. right is in the eye of the beholder, and is an area of much debate – both ways are still used 2. if you are after phylogeny, cladistics is clearly the way to go – any traditional taxonomy that is at majors odds with phylogeny is likely to lose out 3. most biologists use traditional taxonomy informed (and often revised by) cladistics; that is what we will use in this course 4. traditional taxonomy is the old way and is being replaced in many cases with cladistics E. characters useful for classification 1. morphology (form, such as unicellular or multicellular, etc.) 2. nutrition mode (autotroph or heterotroph, etc.) 3. cell structure (presence or absence of a nucleus; presence or absence of a cell wall, etc.) 4. chemistry (cell wall makeup, protein sequences, DNA sequences, etc.) 5. reproductive traits (sexual, asexual, etc.) 6. many others V. The most widely accepted classification system today includes three domains and six kingdoms A. Two domains consist of prokaryotes, organisms with no internal membrane-bound organelles (and thus no true cellular nucleus) 1. Domain Archaea – Kingdom Archaebacteria • bacteria typically found in extreme environments; • distinguished from other bacteria mainly by ribosomal RNA sequence and lack of peptidoglycan in their cell walls • include methanogens, extreme halophiles, and extreme thermophiles • some nonextreme archaebacteria exist – distinguished from eubacteria by signature sequences in their DNA 2. Domain Bacteria – Kingdom Eubacteria • very diverse group of bacteria; defined best as prokaryotes that are not archaebacteria • examples: blue-green algae, Escherichia coli 3. prokaryotes are abundant and important organisms • more in your mouth than mammals on Earth! • 5 million per square cm of your skin • 1 gram of soil has 2.5 billion bacteria 5 of 7 BIOL 1030 – TOPIC 1 LECTURE NOTES • more biomass than rest of life on Earth combined! • Play important roles in life:  Some are photosynthetic (vital for putting energy into ecosystems)  Some are decomposers (vital for recycling matter in ecosystems)  Some cause disease B. One domain, Eukarya, consists of eukaryotes, organisms with a discrete cellular nucleus (and other internal membrane- bound organelles); it is divided into four kingdoms 1. Kingdom Protista - protists • single celled and simple multicellular organisms having nuclei • includes protozoa, algae, water molds, and slime molds • where everything that doesn’t fit another eukaryotic kingdom is put 2. Kingdom Fungi - fungi • organisms with cell walls consisting of chitin • most are multicellular • includes molds and yeasts 3. Kingdom Plantae – plants • complex multicellular organisms having tissues and organs • plant cells have walls containing cellulose • most (but not all) contain chlorophyll in chloroplasts, and carry on the process of photosynthesis. 4. Kingdom Animalia – animals • complex multicellular organisms that must eat other organisms for nourishment • typically contain cells lacking walls, and have organs and organ systems • most (but not all) forms are motile 6 of 7 BIOL 1030 – TOPIC 1 LECTURE NOTES C. a phylogeny from rRNA analysis indicates that Eubacteria are the most ancient group or an outgroup to the domains Archaea and Eukarya – but some analyses of complete genome sequences give cladograms that contradict this D. in this course we will focus on eukaryotes; key characteristics of eukaryotes include: 1. evolution of eukaryotes involved endosymbiosis, incorporation of Eubacteria cells into eukaryotes as mitochondria and chloroplasts 2. true multicellularity (a body formed of cells which are in contact and coordinate activities) is a trait not found in any prokaryotes, but found in many eukaryotes 3. sexual reproduction by syngamy is a trait not found in any prokaryotes, but found in many eukaryotes E. a major consideration will be eukaryotic life cycles for sexually reproducing species 1. these life cycles always involve: • meiosis (reduction division)  diploid (2N) cell produces one or more haploid (1N) cells  chromosome number halved • gametes: cells that must join to another cell before a new organism is produced • fertilization (syngamy): fusion of gametes to form a zygote, first diploid cell for a diploid organism 2. the three major types of life cycles are zygotic meiosis, gametic meiosis, and alternation of generations with sporic meiosis • zygotic meiosis  zygote immediately undergoes meiosis  diploid zygote never undergoes mitosis; mitosis only in haploid cells, making haploid individuals  found in many protists • gametic meiosis  meiosis produces gametes that never undergo mitosis  zygote undergoes mitosis, making diploid individuals  found in most animals • alternation of generations with sporic meiosis  zygote undergoes mitosis, making diploid individuals  some diploid cells undergo meiosis to make haploid spores (sporic meiosis)  mitosis in haploid spores, making haploid individuals  some spores develop into gametes, which undergo syngamy to make a diploid zygote  thus, two bodies in one life cycle – two instances of mitosis in one life cycle  found in plants and some algae 7 of 7