BIOL 1030 Topic One Notes
BIOL 1030 Topic One Notes BIOL 1031 - 001
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This 6 page Class Notes was uploaded by Kassandra Balsters on Monday February 15, 2016. The Class Notes belongs to BIOL 1031 - 001 at Auburn University taught by Scott Anthony Bowling in Fall 2015. Since its upload, it has received 42 views. For similar materials see Organismal Biology Laboratory in Biology at Auburn University.
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Date Created: 02/15/16
BIOL 1030: Organismal Biology Topic One Notes Biologists use a hierarchical binomial system for classifying organism o Taxonomy- the science of classifying and naming organisms o Carolus Linnaeus-18 century Swedish botanist; 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 two words Names are Latin Same language used universally in biology Dead language—not changing Names of people can be “Latinized” for use in naming Species- basic unit of classification or taxonomy o If sexual, a group of organisms that can interbreed and produce fertile offspring o If asexual, grouped based on similarities (DNA sequence is best) Genus- a group of closely related species Species name- together the genus and specific epithet names make up the binomial name used to name a species o The genus name is always capitalized, and the specific epithet is never capitalized o The genus and specific epithet are always together, and italicized (or underlined) o May abbreviate genus name is used already and context is clear Taxonomic classification is hierarchical A group of related genera make up a Family Related families make up an Order Related orders make up a Class Related classes make up a Phylum or Division Related phyla or divisions make up a Kingdom Related kingdoms make up a Domain, the highest level of classification in the modern system 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) 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 o Not always clear-cut, because some can interbreed under “artificial” conditions but don’t appear to do so in nature o Sometimes, “race” and “subspecies” designations are used, but often different specific epithets are used when there are clear morphological difference involved Asexual species-definition based on biochemical (think DNA sequence) and morphological differences; no solid rules o Also includes use of “race,” “subspecies,” and “strain” designations o In asexual species, microevolution over time directly leads to macroevolution (speciation) Evolutional Species Concept- o A single line of descent (lineage) that maintains its distinctive identity from other lineages o Works for all species, but it can be hard to clearly define “distinctive identity” So how many species are there? o No one knows for sure, best guess is about 10 million, but only about 1.8 million have been described by humans o Most are tropical o Human activities (particularly in the tropics) are certainly destroying many species before they can even be described; we are undergoing the sixth mass extinction event in the history of life on earth (and the first one driven by the activities of man) Classification is largely based on inferred evolutionary relationships between organisms; the two major approaches to this are cladistics and traditional taxonomy o Phylogeny- evolutionary tree; explanation of evolutionary relationships among groups (what evolved from what, in what order, and when) o Systematics- study and reconstruction of phylogenies Groups of organisms may be: o Monophyletic (includes most recent common ancestor and all descendants)- synonymous with a “clade”; sometimes called holophyletic o Paraphyletic (includes most recent common ancestor BUT not all descendants) o Polyphyletic (does not include most recent common ancestor) Both cladistics and traditional taxonomy avoid polyphyletic groups; cladistics also avoids paraphyletic groups Cladistics groups organisms on the basis of unique shared characters inherited from common ancestor, or derived character o Clade- group of organisms related by descent o Synapomorphy- a derived character that is unique to and thus defines a particular clade o Cladogram- branching diagram based on cladistics analysis that represents a phylogeny Cladograms are based on comparative analysis, so each cladogram must have an outgroup and an ingroup o Outgroup- organism that is different from all others in the cladogram (but not too different) It is expected to have split with the others from a common ancestor before any of the rest (the ingroup) split from each other Often different cladograms can be produced for a given set of organisms depending on how the analysis is done o Usually a choice has to be made for which cladogram is the most likely reflection of evolutionary history o Usually the most parsimonious one, the one that requires the simplest explanation, is chosen Cladograms are always open to refinement as more data becomes available Naming based on cladograms only allows for monophyletic groups Traditional taxonomy weighs characters according to presumed biological or evolutionary significance o Line of descent is considered as well (and may incorporate cladograms), but naming allows for some paraphyletic groups o Example: classifying birds Traditional taxonomists view feathers as being so important that birds are placed in their own Class (thus making Reptilia paraphyletic in their taxonomies) Cladists put birds with reptiles to make Reptilia monophyletic “Right” is in the eye of the beholder here, and is an area of much debate—both ways are still used If you are after phylogeny, cladistics is clearly the way to go— any traditional taxonomy that is at major odds with phylogeny is likely to lose out Most biologists use traditional taxonomy informed (and often revised by) cladistics; that is what we will use in this course Traditional taxonomy is the old way and is being replaced in many cases with cladistics Characteristics useful for classification o Morphology (form, such as unicellular or multicellular, etc.) o Nutrition mode (autotroph or heterotroph) o Cell structure (presence or absence of a nucleus; presence or absence of a cell well, etc) o Chemistry (cell wall makeup, protein sequences, DNA sequences, etc) o Reproductive traits (sexual, asexual, etc) o Many others THREE DOMAINS and SIX KINGDOMS Two domains consist of prokaryotes o Organisms with no internal membrane-bound organelles o Thus with no true cellular nucleus o These domains are Archaea and Bacteria Domain Archaea—Kingdom Archaebacteria o Bacteria typically found in extreme environments o Distinguished from other bacteria mainly by ribosomal RNA sequence and lack of peptidoglycan in their cell walls o Include methanogens, extreme halophiles, and extreme thermophiles o Some nonextreme archaebacteria exist—distinguished from eubacteria by signature sequences in their DNA Domain Bacteria—Kingdom Eubacteria o Very diverse group of bacteria; defined best as prokaryotes that are not archaebacteria o Examples: blue-green algae, Escherichia coli Prokaryotes are abundant and important organisms o More in your mouth than mammals on Earth! o 5 million per square cm of your skin o 1 gram of soil has 2.5 billion bacteria o More biomass than rest of life on Earth combined! o 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 o Now we will proceed to essentially ignore prokaryotes for the rest of this course One domain, Eukarya, consists of eukaryotes, organisms with a discrete cellular nucleus (and other internal membrane-bound organelles); it is divided into four kingdoms o Kingdom Protista—protists o Kingdom Fungi—fungi o Kingdom Plantae—plants o Kingdom Animalia—animals A phylogeny from r RNA 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 In this course, we will focus on eukaryotes Kingdom Protista—protists o Single celled and simple multicellular organisms having nuclei o Includes protozoa, algae, water molds, and slime molds o Where everything that doesn’t fit another eukaryotic kingdom is put o A paraphyletic group at best Kingdom Fungi—fungi o Organisms with cell walls consisting of chitin o Most are multicellular o Includes molds and yeasts o Probably monophyletic Kingdom Plantae—plants o Complex multicellular organisms having tissues and organs o Plant cells have walls containing cellulose o Most (but not all) contain chlorophyll in chloroplasts, and carry on the process of photosynthesis o Apparently monophyletic Kingdom Animalia—animal o Complex multicellular organisms that must eat other organisms for nourishment o Typically contain cells lacking walls, and have organs and organ systems o Most (but not all) forms are motile o Probably monophyletic Evolution of eukaryotes involved endosymbiosis, incorporation of Eubacteria cells into eukaryotes as mitochondria and chloroplasts 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 Sexual reproduction by syngamy is a trait not found in any prokaryotes, but found in many eukaryotes A major consideration will be eukaryotic life cycles for sexually reproducing species o 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 The three major types of life cycles are o Zygotic meiosis o Gametic meiosis, and o Alternation of generations with Sporic meiosis Zygotic meiosis o Zygote immediately undergoes meiosis o Diploid zygote never undergoes mitosis; mitosis only in haploid cells, making haploid individuals o Found in most fungi (sometimes modified) and in many protists Gametic meiosis o Meiosis produces gametes that never undergo mitosis o Zygote undergoes mitosis, making diploid individuals o Found in most animals Alternation of Generations with sporic meiosis o Zygote undergoes mitosis, making diploid individuals o Some diploid cells undergo meiosis to make haploid spores (sporic meiosis) o Mitosis in haploid spores, making haploid individuals o Some spores develop into gametes, which undergo syngamy to make a diploid zygote o Thus, two bodies in one life cycle—two instances of mitosis in one life cycle o Found in plants and some protists (algae)
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