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Home , Taxonomy (biology)

BIOL 1030 – TOPIC 1 LECTURE NOTES Topic 1: Classification and the Diversity of (Chapters 25, 26.6)

I. Backgroun d review ( 1020 material)

A. 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 . • 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 : The Modern Synthesis 1. Evolutionary relationships between provides the theoretical framework for modern classification systems; as such, it is the organizing principle underlying the structure of most of course 2. In POPULATIONS, new (random) and recombination of current variations (random) occurs. 3. Populations encounter EVOLUTIONARY MECHANISMS: • (greater by the “fittest”) • (random, greater for small populations) • (genetic exchange with other populations) • mutations (new changes in genetic material) 4. Evolutionary mechanisms cause : changes in population genotype and allele frequencies for the next generation. 5. Adding any REPRODUCTIVE ISOLATION MECHANISM allows (). • Examples of reproductive isolation mechanisms include physical separation, selective mating, and sterile offspring. 6. Speciation can be rapid () or gradual; relative amounts of these are debated but both appear to occur.

1 of 7 BIOL 1030 – TOPIC 1 LECTURE NOTES II. Classi fication of organisms

A. use a binomial system for classifying organisms. 1. - the science of classifying and naming organisms. 2. Linnaeus (18th century ) developed a system of classification that is the basis of what is used today • binomial system: today each ’ official scientific name is made of 2 words (bi=“2” nomen=“name”) • names are Latin . same 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. - 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: sapiens or Homo sapiens B. Taxonomic classification is hierarchical. 1. A group of related genera make up a . 2. Related families make up an . 3. Related orders are grouped into a . 4. Related classes are grouped into a or . 5. Related or divisions are grouped into a . 6. Related kingdoms are grouped into a , 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 (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 • sometimes, “” and “” 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 2. asexual species – definition based on biochemical (think DNA sequence) and morphological differences; no solid rules • also includes use of “race,” “subspecies,” and “” designations • in asexual species, microevolution over time directly leads to macroevolution (speciation) 3. evolutionary species concept – a single line of descent () that maintains its distinctive identity from other lineages; works for all species, but it can be hard to clearly define “distinctive identity” D. So how many species are there? 1. no one knows for sure, best guess is about 10 million, but only about 1.8 million have been described by 2. most are tropical 3. activities (particularly in the tropics) are certainly destroying many species before they can even be described; we are undergoing the sixth mass event in the on earth (and the first one driven by the activities of man)

IV. Classi fication: constructing phylogenies

A. classification is largely based on inferred evolutionary relationships between organisms; the two major approaches to this are and traditional taxonomy 1. phylogeny – evolutionary ; explanation of evolutionary relationships among groups (what evolved from what, in what order, and when) 2. – study and reconstruction of phylogenies 3. groups of organisms may be: • monophyletic (includes most recent common ancestor and all descendants) • paraphyletic (includes most recent common ancestor BUT not all descendants) • polyphyletic (does not include most recent common ancestor) 4. both cladistics and traditional taxonomy avoid polyphyletic groups; cladistics also avoids paraphyletic groups

EXPLANATION What do terms monophyletic, paraphyletic and polyphyletic mean?

These terms are used to describe groupings of organisms, and indicate the extent to which they can be considered as ``natural groups''. They are best explained using examples, so consider the following family-tree diagram: Aves / / / Mammalia \ Dinosauria \ \ / \ \ / \ \ / Synapsida Reptilia \ / \ / \ / Amniota

Here are examples of all three types of group:

3 of 7 BIOL 1030 – TOPIC 1 LECTURE NOTES • Consider the group consisting of all the in this diagram - that is, Amniota. This group is monophyletic because it consists of a single together with all of its descendants. The Dinosauria, including the modern , is another monophyletic group, sometimes defined as the most recent common ancestor of Igunanodon and together with all its descendants. Monophyletic groups are also called , and are generally considered as the only ``natural'' kind of group. They are very important in phylogenetic classification. • Now consider the group consisting of the non-avian (which is what people usually mean by the informal term ``dinosaurs''). This is a paraphyletic group, because it can't be defined simply as ``this animal plus all its descendants'', but must be described as one minus another: in this case, Dinosauria minus Aves. The ``non-avian dinosaurs'' make up a singly paraphyletic group because only one clade need be omitted from its base definition. Groups may also be doubly paraphyletic, thrice paraphyletic, etc., depending on how many sub-clades they omit. • Finally, consider the group of ``warm-blooded animals'', which consists of Mammalia and Aves. This is a polyphyletic group - a totally unnatural assemblage - because it can't even be expressed as a paraphyletic group, that is, a clade minus one or more of its subclades. Such groups are not used at all in phylogenetic work since they are a purely artificial construct. In terms of , a ``warm-blooded animals'' grouping makes no more sense than a Synapsida-plus-Crocodilia group - though this is not to say the notion of a warm-blooded group may not be useful in some informal discussions. So far, so straightforward. The only wrinkle in this scheme is that some workers use the word ``monophyletic'' in a sense that includes what we have described here as paraphyletic groups. These people then use ``holophyletic'' to describe what are usually called monophyletic groups. It's tempting in the face of this ambiguity just to abandon the word ``monophyletic'' and use a holophyletic/paraphyletic dichotomy, but this terminological abuse is probably not widespread enough to merit such extreme measures. It's just something to be on the watch for.

Exercise: Determine which of these groupings are mono, para and polyphyletic (Refer Textbook for more details).

B. cladistics groups organisms on the basis of unique shared characters inherited from common ancestor, or derived character 1. clade – group of organisms related by descent 2. synapomorphy – a derived character that is unique to and thus defines a particular clade 3. – branching diagram based on cladistic analysis that represents a phylogeny • are based on comparative analysis, so each cladogram must have an and ingroup • outgroup – 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 4. often different cladograms can be produced for a given set of organisms depending on how the analysis is done; usually a choice has to be made for which cladogram is the most likely reflection of evolutionary history (usually the most 4 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 ) • cladists put birds with 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. (, such as unicellular or multicellular, etc.) 2. mode (autotroph or heterotroph, etc.) 3. cell structure (presence or absence of a nucleus; presence or absence of a , 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 , organisms with no internal membrane-bound organelles (and thus no true cellular nucleus) 1. Domain – Kingdom Archaebacteria • 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 , coli 3. prokaryotes are abundant and important organisms • more in your mouth than 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 , organisms with a discrete cellular nucleus (and other internal membrane- bound organelles); it is divided into four kingdoms 1. Kingdom Protista - • single celled and simple multicellular organisms having nuclei • includes , algae, water , 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 3. Kingdom Plantae – • complex multicellular organisms having tissues and organs • cells have walls containing cellulose • most (but not all) contain in , and carry on the process of . 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

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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 (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

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