Bio 503

explain what the following are and what they can be incorporated into systematic studies: discrete character states, additive binary coding, and mixed coding.

-Discrete character states: usually coded with a number or letter -Additive binary coding: an alternative way of ordering a linear multistate character that preserves specific hypotheses of character transformation by segregating each transformation into a separate column. - Coding: used to compare relationships among states that are hypothesized to have a nonlinear relationship -Mixed coding: space saving technique that eliminates at least one extra data column to capture the hypotheses of transformation.

explain what "special" or "intrinsic" similarity, and conjunction are and what they can tell us about taxa

-it seems that if the observed homologs are analyzed and not found to be statistically similar they are considered special or intrinsically similar, my interpretation is that it is similar to anecdotal similarities? W&L pg 129

list and explain the basic principles of parsimony

1. There is only one correct tree out of the many possible trees. 2. Characters can develop and be passed on to descendants 3. Shared characters between species signifies that those species are related unless otherwise proven 4. Once a character appears and is fixed, there is no reason to think that it will change 5. Characters are treated as independent 6. The result of the analysis places character states on a tree in the order they are thought to have originated 7. The tree with the fewest steps is the preferred tree

10 aspects of a publication

1. Title - informative, not overly long. Should be easily searchable for access to content. 2. Authors name and address - Address should be the address researcher was at during the investigation to give credit to the instituion 3. Key words - effective electronic searches depend on solid key words 4. Abstract 5. Introduction 6. Materials and methods 7. Body of the text 8. Acknowledgments 9. References cited 10. Appendices

What year were the Darwin and Wallace papers published?

1858

How long ago did life begin on earth

3.5 to 4 billion years ago

Define, provide examples of lateral gene transfer, and explain how it can affect systematic studies.

Gene transfer between unrelated groups. In addition to normal gene transfer from parent of offspring (vertical transfer) genes are also transmitted between distinct evolutionary lineages (Horizontal gene transfer Importance of lateral gene transfer to the evolution of bacteria was recognized by the end of the 20th century. Bacteria poses several mechanisms for transmission of genes between unrelated groups. Horizontal gene transfer is the primary mechanism of the spread of antiobiotic resistance in bacteria. The malaria pathogen Plasmodium vivax acquired genetic material from humans that might help facilitate its long stay in the body. Contradicted the notion of species and a hierarchial view of evolution in bacterial groups

define and provide examples of: homology, analogy

Homolog: same structure different function (forearm of human fore arm of bird) - could infer shared ancestry Analog: different structure same function (bat wing bird wing) - could infer similar niche or environment

- explain and explain what the following can tell us: strict consensus, and majority-rule consensus trees

Strict Consensus: trees contain only those monophyletic groups that are common to all of the trees. A form of the Majority-rule consensus tree. Majority-rule consensus trees: 50% majority rule consensus tree reports all clades that appear in more than 50% of the trees.

Explain how biogeographic studies can assist us in decreasing the effects of our current loss of biodiversity due to human actions

Subjective, but I would say something along the lines of: One of the ways biogeographic studies can assist us in decreasing biodiversity loss is by identifying habitat characteristics that are the most critical for certain endangered or threatened species. By determining these characteristics, we can determine the most effective and efficient way to try and conserve them.

explain different ways character evolution can be represented on trees

A) Across Leaves- modified versions of such diagrams move the character bars down the tree to make the groupings more explicit and easier to read. Edges bisected by character bars connect known taxa that have the character, and thus bisection of two edges denotes sharing of the same character. (Almost never used! So why is it in the book?!) B) Edges and leaves, more often used. Claim that can be made is that it is hypothesized that the characters in question were fixed as autapomorphies (a distinctive trait, or derived trait) somewhere along the ancestral edge, between the two known speciation events C) On nodes, same as B but all information is at the nodes

- list the various methods used to determine polarity of a character; state some pros and cons are for each

Outgroup Comparison - Using an outgroup to determine which characters evolved first. Involves deductive reasoning but depends on assumptions that the characters evolved once. Also requires the assumption of a single monophyletic origin of species. This is the best, most common method for determining polarity.

explain what parsimony is and why it is essential to phylogenetics

Parsimony is the concept that the simplest explanation is most likely the most accurate explanation. In phylogenetics this means that the shortest phylogenetic tree with the fewest steps is most likely the most accurate one.

explain why parsimony is "nonparametric" as opposed to parametric analyses (ML and Bayesian analyses)

Parsimony searches for the shortest tree and does not assume that trees are normally distributed. ML and Bayesian on the other hand assume that trees are normally distributed in order to determine the best tree.

List and explain 3 ways you can use analytic methods in performing a historical biogeographic study

Phylogenetic analysis aims to determine area/biotic relationships and relies on having phylogenies of clades available, and also information about where the taxa in theses clades are distributed Three ways you can use analytic methods in preforming a historical biogeographic study are: evaluating congruence among competing characters, to analyze how similar or different geographic distribution patterns are with phylogenetic histories, and to determine how much these geographical distributions have changed during cladogenesis.

List and explain 2 alternative biogeographic methods and what are the benefits of using that method

Phylogenetic analysis for comparing trees (PACT): uses an initial input tree to build a template tree from this and compares where it agrees and disagrees with other area cladograms. Benefits: doesn't require generation of a data matrix from area cladograms; doesn't presuppose that all diversification follows the vicariance model and instead allows diversification to be driven by range expansion. Brooks parsimony analysis (BPA): a biogeographic method that takes information from area cladograms and converts that information into a data matrix. Benefits: can be used to consider geological evolution and coevolution to find a pattern of vicariance, as well as determining other patterns between biogeography and phylogenetic analysis.

Explain how phylogenetic classification differs from classifying via the Linnaean hierarchy

Phylogenetic classification names groups of organisms according to their evolutionary history. Linnaean classification classifies organisms in a hierarchal order and has rules for naming and the use of names of organisms. They are similar in the fact that they produce a nested hierarchy where an organism is assigned a series of names. They are different in the fact that phylogenetic classification only names clades and does not assign ranks to hierarchical levels.

explain what the general ideas behind algorithmic approaches and optimality approaches are for systematics; state some pros and cons are for each method type

Algorithmic approaches: the algorithm defines the selection criteria and combines the inference and the criteria to create a preferred tree. They are fast and are likely to find trees close to optimal. Great for creating hypotheses but can get stuck on more local analyses. They produce a tree but not all trees which could result in the investigator missing a tree that is just as good. Optimality approaches: an objective function is specified and then uses an algorithm to compute that function for a particular tree topology. Then computes the function for another tree and compares the two. Slower but can return all of the trees that fit the function.

Explain why ribosomal RNA sequences are appropriate for looking at bacterial relationships

All cells need rRNA's to construct proteins, their similarities and differences could be used to track lineages of anything with a cell. rRNA is abundant in cells and easily extracted. Woese hypothesized that rRNA molecular sequences would change very slowly over an evolutionary time scale. They would be the most conserved elements within organisms and therefore would make excellent recorders of life's long evolutionary past.

explain what a posteriori character argumentation is and how you can use it in analyses

All characters are freely reversible. With this assumption we can create an unrooted tree without polarization. There is no phylogenetic interpretation on an unrooted tree. But we can root the tree by creating a starting point. This creates a bridge between the newer computer assisted analysis method and the traditional phylogenetic methods. A posteriori character argumentation basically involves creating an unrooted tree then from analyzing that tree rooting it to create a rooted tree.

Explain how understanding the "history" of biogeographic studies can improve our current studies

Also subjective, but I would say something about how understanding the history of biogeographic studies allows us to better understand what data we need to collect to most efficiently test our hypotheses about biogeography for our organism(s) of study and which analysis is best suited for that data.

Explain how within-species studies might differ from between-species studies of biogeography

Both search for congruence among the phylogenetic and biogeographic patterns of different clades, but within-species studies focus on an individual species and between-species studies focus on multiple species in a given area.

- list 2 lines of evidence Woese had to support his proposed realignment of systematics and taxonomy

The data they used were fossil records: photosynthetic eubacteria were already present 3-4 billion years ago which led them to the conclusion that the evolutionary events that transformed the common ancestor must have occurred rapidly Hairpin loop criteria. They back this up with molecular evidence that shows that eubacteria have a hairpin loop of 6 nucleotides and everything else has 7 nucleotides in the hairpin loop.

Linnaeus:

The father of modern taxonomy. Published Systema Naturae in 1758 for the naming of animals and Species Plantarum in 1753 for the naming of plants.

Molecular clock

The molecular clock hypothesis states that DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms. A direct consequence of this constancy is that the genetic difference between any two species is proportional to the time since these species last shared a common ancestor. Therefore, if the molecular clock hypothesis holds true, this hypothesis serves as an extremely useful method for estimating evolutionary timescales.

Neutral Evolution

The neutral theory of molecular evolution suggests that most of the genetic variation in populations is the result of mutation and genetic drift and not selection. According to this theory, if a population carries several different alleles of a particular gene, odds are that each of those alleles is equally good at performing its job — in other words, that variation is neutral

explain how we can determine whether a given trait is truly homologous or not

Through statistical analysis comparing different sets of homologues characteristics. Often researcher build matrices then run analysis to compare each column and every row to see differences and similarities.

define and explain what the following can tell you about a given resultant tree from analyses: tree length, consistency indices (ci vs CI), rescaled consistency index, retention index, consistency index (ci vs CI),

Tree Length: The number of steps it takes to get from point A to point B Consistency indices: (CI Measures of the performance of both individual characters and entire matrices relative to particular tree topologies. If there are no instances of homoplasy then it is considered to be perfect. Consistency index of a single transformation series: (ci) ratio of the minimum number of steps or changes it might undergo and the number of steps it actually undergoes. Rescaled consistency index: product of the original consistency index and the retention index. Retention index: measures the fraction of apparent synapomorphy to actual synapomorphy

- state what "tree length" is and why there are multiple "types" of methods to do this

Tree length is the number of steps it takes from the origin point to the termination point. There are multiple different methods of determining this because there are many different ways creating a tree depending on assumed relationships and whether characters are reversible or not. It is necessary to have different criteria for tree length because there are different methods and types of parsimony. One tree length of criteria does not explain or work for both ordered and unordered parsimony. If it is ordered then there will be a set amount of steps. If it is unordered parsimony then it could skip some steps present in the ordered tree and the tree could be shorter. It would be nearly impossible to make comparisons if you were using the same tree length calculations for completely different methods of creating trees.

explain what synonyms and homonyms are in scientific names and how you can avoid generating them

Two published and available names for the same taxon are synonyms. Homonyms are the same name applied to two taxa. Do your research, follow the codes.

List and explain 2 considerations that extinction can affect a given biogeographic analysis

Two ways that extinction can affect biogeographic analysis: (1) incorporating additional taxa into phylogenetic studies, especially extant, fossil taxa can increase phylogenetic accuracy and (2) extant taxa can also decrease the ability to detect biogeographic congruence among representatives of the extant taxa.

Law

describes a phenomenon that occurs constantly

Classification tree-

diagram of classification made for the purpose of checking the logical consistency between a proposed phylogeny and a formal classification.

What is the precambrian explosion and why was it important for life

explosion and radiation of plant and animal life in the fossil record 495 to 560 million years ago. Complexity of organisms increased greatly showing the first insights of complex lifeforms much like those we see on earth today.

Consensus tree

graphs that summarize the common knowledge claims of different phylogenetic trees (W&L). Way to summarize the agreement between two or more trees (Wiki). Network- refer to cyclic graphs, that is, graphs where there are two distinct pathways to one or more taxa (W&L). A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species (Wiki).

Genetic Code

he genetic code is a set of rules defining how the four-letter code of DNA is translated into the 20-letter code of amino acids, which are the building blocks of proteins. The genetic code is a set of three-letter combinations of nucleotides called codons, each of which corresponds to a specific amino acid or stop signal. The concept of codons was first described by Francis Crick and his colleagues in 1961. The DNA in our genome is sometimes likened to a blueprint or a recipe book, as it contains the instructions needed to build an organism.

Node rotation

leaves and edges can be rotated freely without changing the hypothesis of relationships. This free rotation can cause students and others unfamiliar with trees to misinterpret relationships

Wagner tree-

parsimony tree resulting from Wagner analysis Maximum parsimony tree- results from a maximum parsimony optimality criterion and may be referred to as Wagner tree (WTF?).

Phylogram

phylogenetic tree in which the length of the edges is proportional to the amount of relative change along the edge (W&L). a phylogenetic tree that has branch spans proportional to the amount of character change (Wiki)

Network

refer to cyclic graphs, that is, graphs where there are two distinct pathways to one or more taxa (W&L). A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species (Wiki).

Maximum likelihood tree-

result from an analysis using maximum likelihood optimality criterion Bayesian tree- results from a Bayesian analysis.

Explain some similarities and some differences between ecological and phylogenetic biogeography

Ecological biogeography: focuses on organisms and processes in the economic or ecological hierarchy. Interested in studying patterns in ecological groups such as populations or communities while testing for the role of processes like population dynamics an, competition, niche partitioning, and dispersal relative to the biotic context of communities and the abiotic environment. Phylogenetic biogeography: focuses on organisms and processes in the genealogical hierarchy like species and clades and testing how processes such as geological and climatic change influence speciation, extinction, and geodispersal. They both focus on organisms and processes in a hierarchy, but look at different processes to create that hierarchy.

Define: historical biogeography

the study of animal distributions emphasizing evolution and over evolutionary time scales, using a combination of phylogenetic and distributional data

Darwin:

wrote "On The Origin of Species" published in 1858, which was one of the first descriptions of the theory of evolution and still stands today.

- list and state the 3 major ways to analyze a data matrix for phylogenetics; state some pros and cons are for each

Exhaustive search is used for fewer than 12 taxa. It is the most beneficial to use on smaller phylogenies given it is more likely to contain all of the information available and determine the shortest tree possible. Branch and Bound can be used for up to 22 taxa. It groups different taxa together and determines the trees for those groups then combines those groups into a final tree. Heuristic Search is used for above 22 taxa or where the data is not very organized or well understood. It is used because it is no longer possible to determine the exact solution. This method is used because it will provide many possibilities.

Woese:

Famous for defining Archaea as a new domain of life.

explain what a "character" is, and what aspects of a character make it an informative one

- A character is a property (feature, expression, part) of an organism that is a quasi-independent (might evolve separately from other features) from other properties of the organism. - A character state is an interpretation of the character of an organism that is used to compare the character of that organism with another organism. - Typically researchers look for independent, heritable traits that are unique for that individual or clade. - Character as a feature of one organism that differentiates it from another organism

30. explain what cladograms and gene trees are, in general terms

- A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed; many evolutionary trees can be inferred from a single cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a groups of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it - Gene tree is a phylogenetic tree that has been constructed from information from alleles of one or a few genes. Do NOT assume that gene trees are that same as species trees since they are constructed from different information. It is standard however to analyze differences and similarities between species trees and gene trees.

27. explain what tree diagrams are and what information we can express with them

- A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities their phylogeny based upon similarities and differences in their physical or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor. Phylogenetic trees are central to the field of phylogenetics. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of the descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetic comparative methods. Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred.

explain what "character states" are and what makes an informative one

- Attribute or features of entities and thus seem intuitively to be properties of the entities. - Same as above heritable, independent traits unique to individual or clade.

explain similarities and differences between stem-based and node-based phylogenetic trees

- By the term stem-based tree, it is a tree that models (hypothesized) phylogenetic relationships among taxa by depicting taxa as edges and speciation events as vertices - In a node-based tree, taxa are represented by vertices, not by edges. An edge of a node-based tree does not represent a lineage or anything else occurring in nature. Rather, an edge simply represents a relationship among two vertices, or, in phylogenetic parlance, the hypothesis of a relationship.

explain what historical and ahistorical characters are and what they can and cannot tell us about taxa

- Historical character state properties are contingent, spatiotemporally restricted properties that have a relationship among themselves or part-whole relationships with larger individuals. The relationship is relative to a reference point, the entity with which that character property shares the relationship. - Ahistorical (non-historical traits) kinds, properties of kinds, and members of kinds and how these instantiate the properties enumerated. The properties of kinds are not spatiotemporally limited. W&L pg 112

explain which do you think is more important to evolution of species: cooperation or competition

- No correct answer: Cooperation within a species assists the success of species as a whole. Cooperation among species can increase diversity, filling of multiple niches, encouraging specialization. - Competition within a species ensures only the strongest survive encouraging vigor within the species. Competition among species encourages the persistence of strong species potentially encouraging resilience and forcing the remaining species to be stronger and persist long enough to diverge/speciate creating diversity.

26. explain whether you think evolution acts mainly on genes, organisms, or populations

- No correct answer: Genes are what are being changed during evolution, could be argued genes are the mechanism for evolution. - Organisms are the ones who are being tested by their environment. If they possess new traits and survive it is the organism that is passing the genes down to their offspring. - Populations are where large changes can be observed, some could argue that is isn't considered an evolved trait (rather than a mutation) till a portion of the population possesses said trait.

explain what a transformation series is and what it can tell us about taxa

- a series is a constructed hypothesis essentially stating that two different homologs are different in function but one was transformed from the other.

explain what historical groups and natural kinds are and what they can tell us about taxa

- both are important to science because they are not arbitrary like nominal kinds, historical groups function significantly in science because they are the result of the operation of natural processes on their parts. Natural kinds function significantly in science when they can predict or explain how individuals will behave while undergoing natural processes. They differ because the character properties of historical groups are historical, not necessary, and not significant. W&L pg 113

explain what some similarities and differences are between trees based on individuals versus those based on groups of individuals

- looking at the section in W&L all they say is: "We do not work with all characters, or even all apomorphic characters; instead, we work with a selected set of characters. However, we should not confuse the way we study a thing, an epistemological issue, with the ontology of the thing itself. Just because we work with sets does not mean that speciesare sets. Just because our set of specimens has a set of studied characteristics, does not mean the characters are sets." - My thought is W&L are stating that all trees are based on sets of information (sets of characteristics of an individual or a group of individuals). But the take away from both scenarios is that; we never as scientists are able to collect all information, we only study "sets" of information or "sets" of characteristics. I think they are stating that it is important for the researcher to understand we are using information from a "set" to give us insight pertaining to the "whole". - AKA complicated circular thought by W&L impossible to have a definitive answer.

explain what shared character states can and cannot tell us about taxa

- two or more organisms share the same character state when this character property is truly and simultaneously instantiated in both organisms at the same time. Could indicate a direct historical relationship, indirect historical relationship, or an indirect ahistorical relationship.

Theory

A generalization that explains and makes sense of laws, hypotheses, and observations.

Hypothesis

A predicative statement about the outcome of a study or event.

State the definition of evolution

A process by which living organisms are thought to have changed and diversified through natural selection.

Explain what were some of the arguments against the current arrangement of the 3 domains, and how these arguments have been overcome

Archaebacteria and eubacteria had many genes in common, Ernst Mayr stated that one could not make inferences on the differentiation of domains based solely on rRNA phylogenies. Dobzhansky and Simpson were opposed to any molecular approach to classification. The swift rise of molecular biology was perceived to be in direct competition with the interests of evolutionary biologists and their traditional evolutionary studies. Mayrs 1998 offensive against rRNA phylogenies came just as the three domain proposal was getting into biology textbooks and microbial evolutionists were reporting that bacteria contained a diversity that rivaled and surpassed that of all the macrobiological world. Mayr insisted that "all archeabacteria are nearly indistinguishable" and cannot posess a degree of diversity even close to the eukaryotic world. Using a combination of molecular and morphological traits when reconstructing phylogenies and trees will render the most scientifically sound results.

List and explain some considerations of "areas and biotas" you must consider for any biogeographic analysis

Areas: geological area is an area individuated by geological processes and that the area forms a part-whole relationship with the Earth and shares relationships with other parts of the Earth. In biogeographic analysis, areas are treated as individuals and thus each has a history with a unique birth and death point, and some spatiotemporal localization throughout its history. Biota: the sum of all individual organisms of all species living in an area, can be nominal or geologic. Examples of this are the biota of a national park or nominal areas of a soil community. In biogeographic analysis, biotas can be studied at many levels. Both allow you to determine how congruent or incongruent phylogenies are with the history of the areas/biota.

Explain how the classification of bacteria has changed over time.

Bacteria were based on morphology throughout most of the 20th century. Attempts at constructing a natural classification of bacteria were largely unsuccessful due to the low amount of morphological differences between bacteria. Present day classifications are based upon DNA, RNA and protien sequencing which displays much more differentaition between protiens than morphological measures and gives a more accurate idea of the evolutionary timescale of bacteria evolution.

Explain what the following are, and state why each is important to historical biogeography: congruence, hierarchies of climate, vicariance, and dispersal

Congruence: agreement or harmony. Importance to historical biogeography: congruence in the biogeographic patterns among diverse assemblages of taxa indicates uniformity in the historical determinants of biotic distributions. Hierarchies of climate: a numerical representation of the climate system based on the physical, chemical, and biological properties of its components, their interactions and feedback processes, and accounting for some of its known properties. Importance to historical biogeography: these climatic changes can powerfully influence the geographic distributions of organisms and their patterns of evolution and extinction. Vicariance: geographical separation of a population, typically by a physical barrier, resulting in a pair of closely related species. Importance to historical biogeography: studying these patterns of distribution lead us to methods that can discriminate between congruent and incongruent patterns of distribution that form the basis for subsequent evolutionary studies. Dispersal: the process of species distributing over a wide area. Importance to historical biogeography: similar to vicariance, allows use to determine congruent and incongruent patterns of distribution that aid in subsequent evolutionary studies.

explain how we can avoid choosing "poor" or "vague" characters when doing a systematic study

Continuous, qualitative character data could be more fully used, especially when looking for phylogenetic signal within a species or among closely related species.

state what some of the "evaluating support" for trees: counting/evaluating synapomorphies, Bremer support, bootstrapping, jackknifing, permutation tests, and measure of skewness

Counting/ evaluating synapomorphies: qualitative assessment of the number of synapomorphies. Monophyletic groups supported by synapomorphies with high individual ci-values are considered robust Bremer support: difference in the length of a tree where it appeared as a monophyletic group and the tree where it did not. Jackknife: rerun the analysis a predetermined amount of times while deleting one or more observations without replacement. The resulting trees are saved and the frequency of appearance of each clade over all the trees constitutes its jackknife frequency. Bootstrapping: a way to simulate the variability in the underlying pattern of character distribution by using known empirical data. Permutation tests: designed to test for hierarchical structure. It works by shuffling characters in each data column and assigning them randomly to species. We assume that any random shuffling would result in an analysis worse than the original analysis Measure of skewness: If all possible trees are plotted based on length in a histogram it would be normally distributed. If this is skewed to short or long trees then this is a relatively strong signal indicating it is one way or another.

explain some considerations you must consider when deciding whether a complex character was truly a complex character or should be separate characters

Deciding between complex characters and separate characters can alter the type of analysis you choose to do and alter your results. When characters are determined to be separate characters you use reductive coding and when they are determined to be complex characters you use composite coding. Both of these methods of coding for characters can produce different results.

Wallace

Independently came to similar conclusion on evolution as Darwin. Collected specimens to sell and came to conclusions of evolution through his observations of different species in different areas.

explain what the Codes of Nomenclature are, what their purpose(s) is/are, and where can you access them

International Code of Nomenclature for algae, fungi and plants (ICN), International Code of Nomenclature of Bacteria (ICNB), International Code of Nomenclature for Cultivated Plants (ICNCP), International Code of Phytosociological Nomenclature (ICPN), International Code of Zoological Nomenclature (ICNCP) - Sets of rules and recommendations dealing with the formal names that are given to taxa. These rules may be difficult to abide by but it reduces homonyms and provides an official record of organisms discovered and named along with who discovered the organisms. - These codes can be found in libraries in hard copy or online.

Carl Woese

Led new era of studies on bacterial evolution research Developed an emperical framework for a natural classification of microbes based on comparisons of ribosomal RNA sequences. Proposed the new domain archea Developed the early workings of genetic code.

Explain some limitations of classifying with the Linnaean hierarchy

Linnaean classification does not tell you everything about the evolutionary history of the organism you are studying. Additionally, the Linnaean classification system "ranks" groups of organisms artificially into kingdoms, phyla, orders, etc. These "ranks" can be misleading because they suggest that different groupings with the same rank are equivalent. For example, cats (Felidae) and orchids (Orchidaceae) are both family level groups in Linnaean classification, but the two groups are not comparable.

- For plants and animals, determine what the starting point(s) are for naming organisms, as per your Code of Nomenclature. Be able to state the names, author(s), and years of these starting points for any and all quizzes and exams

Linnaeus, C. 1753. Species plantarum. Laurentius Salvius, Sweden. 1200 pages. Linnaeus, C. 1758. Systema naturae 10th edition. Laurentius Salvius, Sweden. 532 pages.

explain why ML and Bayesian analyses are considered "parametric"

ML and Bayesian analyses use the most common character or size of character which is present at the peak of the normal distribution curve to perform the analyses.

explain in general terms how ML and Bayesian analyses are performed

Maximum likelihood analysis is based on finding the tree that has the highest probability of being observed. Through many calculations on many different trees the most likely tree is revealed. It determines the probability of the data given the model and topology. It tests multiple models for how well it predicts future relationships. It is based on how well it can predict these relationships and not on how accurate it is. By using this method you can determine likely relationships that may not be accurate but based on the evidence they are the most likely. This could end poorly if you are using observed characteristics or characters that observed independently in convergent evolution. The parameters used are very important and can lead to vastly different results. This method is evaluating the likelihood of the data given a particular model of evolution. Phylogenetic analysis is searching for the best topology. You calculate the likelihood of each character arising at each node and then add all of the likelihoods on a tree together to determine the most likely tree given the information provided. Bayesian analysis is based on determining the probability based on the data and the model instead of the probability of the data based on the model. This analysis allows for the ranking of data and allows the investigator to determine what they believe is possible and what is not. Bayesian analyses look to determine the likelihood that the model is correct based on the data, the opposite of maximum likelihood. These analyses are complex and are much easier on a computer. This is best used when you have reliable data and many possible models to use. If you collect data reliably and don't have any doubts about it but aren't sure of the best way to model it then you can develop several potential models and run a Bayesian analysis to determine the best model to use.

explain some considerations and how we can handle missing data in a systematic study

Missing data can result in multiple equally parsimonious trees. For proper analyses it is important to include as much information as possible. Fossil records are very important to include as they often contain character states not present in extant species. 99.9% or species have already gone extinct which means that the existing taxa are not representative of the overall phylogenetic tree. Missing data can result in low quality trees and clades with a lot of missing data may be placed in a wide range of locations on the tree depending on how the missing data is interpreted versus the available data. The most important thing in a phylogenetic analysis when it comes to missing data is to use characters for which there is information for all species. Missing columns are less damaging than incomplete columns.

Explain what Brooks modified parsimony analysis is; explain 2 benefits and 2 limitations to using it

Modified brooks parsimony analysis (MBPA) is an extension of brooks parsimony analysis that takes information from area cladograms and converts that information into a data matrix. Benefits: allows you to analyze the relationships of biotas or geologic areas using the relationships of taxa and a criterion; allows you to decide among competing biogeographic hypotheses by using parsimony criterion. Limitations: when using this method for analysis, the characters are the taxa themselves and their ancestral nodes, which doesn't always make sense evolutionarily; this method only focuses on recovering congruent episodes of vicariance and thus could not identify congruent episodes of geodispersal.

Explain what kinds of DNA sequences we can use to determine molecular clocks

Nucleotide sequences for DNA, Amino acid sequences for protiens. Allow us to look at differences between species due to the slow rate of change of rRNA. Gives us a perspective on the timescale of species divergence.

explain why homology is essential in systematics

Often homology is the starting point or springboard for phylogenetic research. It is very typical to develop hypotheses on morphological homologies and build a study around that.

define polarization, and explain why it is essential to phylogenetics

Polarizing means to determine which traits originated first. This is important to determine because if you do not know in which way these traits developed your trees will be incorrect and show something completely different. If you don't polarize the character states, you will likely end up with some traits evolving multiple times when it is likely that they evolved once in a common ancestor. Without polarizing character states there is no order and it will result in a tree that is chaos and shows no accurate relationships.

List 2 benefits and 2 limitations for using numerical prefix schemes for classification

Prefix schemes denote hierarchical rank with a prefix that is unique to each taxon and fixes the hierarchical level of each taxon relative to others. Advantages: fossil species can be inserted anywhere in the system without changing the hierarchical level of recent taxa; preadapted to work well with computer languages; hierarchical levels are self sustaining in that there is no need to create new rank categories as these are made "on the fly" as a consequence of adding taxa. Disadvantages: numerical prefixes are not the language of humans and are foreign to our efforts to communicate; prefixes are unique and therefore there are as many prefixes as there are branches in the tree (ranks can't be reused).

explain what "presence-absence" coding can tell us in a systematic study

Presence-absence coding uses 0 and 1 to display whether a particular individual or species has a certain character. This helps in determining homologous characters across species. This method of coding does not necessarily mean that 0 does not have that character and 1 does it can be better be explained using a and b to show that it is just highlighting that they are 2 different morphs.

explain what the principle of priority is, why it is important, and how you can determine it

Priority is a fundamental principle of modern botanical nomenclature and zoological nomenclature. Essentially, it is the principle of recognizing the first valid application of a name to a plant or animal. There are two aspects to this: 1 The first formal scientific name given to a plant or animal taxon shall be the name that is to be used, called the valid name in zoology and correct name in botany. 2 Once a name has been used, no subsequent publication of that name for another taxon shall be valid (zoology) or validly published (botany).

- explain why you might want to include random addition searches and rearrange tree topology in your phylogenetic analyses

Random addition searches involves running the analysis many times varying the original tree randomly to produce different results and determine the most parsimonious tree. Rearranging the tree topology helps in determining the most parsimonious tree as well. It may reduce the number of steps if a section of the tree originates in a different location. These can be combined to help find the most parsimonious tree in your phylogenetic analyses.

Explain how important or unimportant symbioses are to the evolution of organisms, and why you think so.

Symbiosis is recognized to have played an important role in the evolution of eukaryotes. Conflicts with the central tenants of the evolutionary synthesis of the 1930's -40's and therefore may have or currently received less funding and interest than natural selection. Symbiosis often has a role in many of the evolutionary phenomenon's that cannot be explained using natural selection. Organelles, cells, individuals, and species to develop symbiotic relationships with other biological lifeforms and results in changes to the ecology of both individuals and can lead to morphological or genetic changes as the relationship evolves.

define: classification; explain how it differs from systematics

Systems of names organized to show relationships among the entities named. Classification is the actual naming of the species where systematics is determining the relationships.

Hennig:

Taxonomist that specialized in dipterans. Considered the founder of phylogenetic systematics (aka cladistics). Published the theory of cladistics in 1950. His works on evolution and systematics revolutionized the view of the natural order of beings.

Explain why the NSF does not get directly involved in the publications of grants/projects

The NSF focuses on identifying and funding important scientific research. Scientific journals currently saturate the wide breath of scientific work. Without the added workload of the peer review and publishing process, the NSF is allowed to focus on funding of important research. If there is no problem with the current publication system, why change it.

Explain the purpose of the NSF

The NSF is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. "to promote the progress of science; [and] to advance the national health, prosperity, and welfare by supporting research and education in all fields of science and engineering."

Explain why the addition of oxygen to the atmosphere was important, how did it happen?

The addition of oxygen to the atmosphere allowed for the evolution of more complex organisms, Oxygen is one of the defining elements resulting in the existence of eukaryotic life forms. Cyanobacteria created the first oxygen on planer earth using the same photosynthetic apparatus as plants. They synthesized oxygen from abundant carbon dioxide in the atmosphere.

Explain what the phylocode is; state 2 benefits and 2 limitations of using it for classification

The phylocode aims to produce classifications that are logically consistent and fully informative concerning the relationships among organisms Advantages: there are not categorical levels, especially within the genus group of the Linnaean classification system, to serve the needs of some practicing phylogeneticists; it eliminates a major source of instability under the rank based codes - changes in clade names due solely to shifts in rank. Disadvantages: the stability of names relative to specifiers is given precedence to the stability of the total content of the clades named; to achieve stability of names relative to specifiers, taxa must be treated as kinds and not as individuals.

Explain what evidence Lynn Margulies observed that lead her to hypothesize that so many eukaryotic organelles were the result of endosymbiosis.

The venerable notion that eukaryotic cytoplasmic organelles had evolved as bacterial symbionts in the remote past was championed by Margulies. She revitalized symbiosis theory with contemporary data from molecular biology and genetics. The deployment of the electron microscope in the late 1960's revealed structures of cell organelles and their structures. The image of cytoplasmic organelles as quasi-independent organisms subsequently reemerged. Margulis told the story of how the eukaryotic cell may have originated eons ago by a series of events in which bacteria indicated a primitive "ameboid microbe" and how mutual aggression eventually evolved to tolerance as the indicating bacteria served useful functions to their host. Margus offered a far-reaching symbiosis theory to account for what was considered to be the greatest of all discontinuities in nature, that between bacteria and eukaryotes.

Explain why there are different types of classification in biology

There are different types of classification in biology because there are many different things (organisms, stars, elements, etc.) in the world that need to be classified. Not all things are similar to each other and therefore cannot be classified the same way. Having different classification types provides scientists with several ways to classify a given object/organism according to their goals or objectives.

explain why there are various kinds of parsimony (don't memorize all the different types)

There are other types of parsimony analyses because there are many different ways of thinking about evolution and how it occurs. Some models believe that each trait is considered to be one step while others count a single step as multiple traits that originated at the same time. Some models say that evolution only occurs in one direction and once a trait is gained it cannot be lost while others say that all traits can be gained and lost. Because there are so many different ways of thinking about evolution and the development of characteristics there needs to be different models that can display each of these different methods. Evolution is still widely debated and misunderstood which means that there are many explanations and many methods for achieving each goal. Many of these did not originate or were not heavily discussed until computer analyses became a significant part of parsimony analysis.

explain why this proposal by Woese was so important to Biology and systematics

They want to add a higher classification to further separate eukaryotes and prokaryotes as the fossil record clearly indicates that They originated at similar times from a common ancestor. They suggest that prokaryotes should not be classified at the same level as groups of eukaryotes like plants and animals. They propose the addition of a higher classification called the domain to further separate these groups from later evolved kingdoms.

explain what weighting is and why we might want to do it; list the various types of weighting you can do and provide some pros and cons for each

When there is more information available on a certain characteristic this should be weighted. If you do not weight anything you are making the assumption that everything is equal, and nothing developed prior to anything else. In most cases we know this is not true. If we know that a given trait is present in the outgroup and have additional evidence that this trait was developed before another trait then this should be weighted as so. If we do not weight this then it could result in an incorrect phylogeny that does not represent the data that we have available. It could result in the development of more recent traits prior to more distant traits and the distant traits could develop independently instead of in a common ancestor.

Explain how dealing with ancestors and hybridization pose issues for any classification attempt

You many not always know all the ancestors for a given organism because some of these ancestors may be extinct. When ancestral organisms are extinct, you must rely either museum specimens or fossil evidence to determine how they are related to an organism of interest. However, this information may not always be available, which can cause some issues when classifying organisms. Hybrids also cause issues when classifying an organism because hybrids make it difficult to determine the ancestral species of that organism. Additionally, hybrids often share the traits of two different organisms, which can make it difficult to determine where hybrids fall on the evolutionary timeline.

state some situations you might encounter where you might want to analyze data via ML or Bayesian analysis instead of using phylogenetics/parsimony

You would choose maximum likelihood if you have a reliable model but are unsure of how the data fit in. This analysis is used to determine the most likely way that the data fit given the model used. You would use Bayesian analysis if you have reliable data but are not sure how to model the data. This analysis determines the best model given the data provided. In theory both of these methods could be used in conjunction with each other to determine the overall best relationships with the best model. They each have specific instances where they are more valuable and because of this they also can benefit each

Cladogram

a parsimony tree where the weight of the edges is not relevant (W&L). a branching diagram showing the cladistic (method of classification of animals and plants according to the proportion of measurable characteristics that they have in common) relationships between a number of species. (Wiki)

Unrooted trees

are acyclic graphs (not possessing cycles or complete circles) that specify a particular number of possible routes one might follow to get from one taxon to another, but they restrict the number of routes taken