{"id":295,"date":"2016-07-10T20:51:57","date_gmt":"2016-07-10T20:51:57","guid":{"rendered":"http:\/\/blogs.vsb.bc.ca\/mcarmichae\/?p=295"},"modified":"2016-07-10T20:51:57","modified_gmt":"2016-07-10T20:51:57","slug":"phylogeny-and-systemics-notes","status":"publish","type":"post","link":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/2016\/07\/10\/phylogeny-and-systemics-notes\/","title":{"rendered":"Phylogeny and Systemics Notes"},"content":{"rendered":"
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Biology 11 Outline Notes<\/p>\n

Classification of Organisms<\/p>\n

Overview
\nPhylogeny and Systematics<\/p>\n

    \n
  • Evolutionary biology is about both process and history.\n
      \n
    • \u00b0 \u00a0The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species.<\/li>\n
    • \u00b0 \u00a0A major goal of evolutionary biology is to reconstruct the history of life on earth.<\/li>\n<\/ul>\n<\/li>\n
    • In this chapter, we will consider how scientists trace phylogeny, the evolutionary history of a group of organisms.<\/li>\n
    • To reconstruct phylogeny, scientists use systematics, an analytical approach to understanding the diversity and relationships of living and extinct organisms.\n
        \n
      • \u00b0 \u00a0Evidence used to reconstruct phylogenies can be obtained from the fossil record and from morphological and biochemical similarities between organisms.<\/li>\n
      • \u00b0 \u00a0In recent decades, systematists have gained a powerful new tool in molecular systematics, which uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships between individual genes or even entire genomes.<\/li>\n<\/ul>\n<\/li>\n
      • Scientists are working to construct a universal tree of life, which will be refined as the database of DNA and RNA sequences grows.\n

        A. Phylogenies Are Based on Common Ancestries<\/p>\n

        1. Sedimentary rocks are the richest source of fossils.<\/li>\n<\/ul>\n

          \n
        • Fossils are the preserved remnants or impressions left by organisms that lived in the past.<\/li>\n
        • In essence, they are the historical documents of biology.<\/li>\n
        • Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms.\n
            \n
          • \u00b0 \u00a0As deposits pile up, they compress older sediments below them into layers called strata.<\/li>\n
          • \u00b0 \u00a0The fossil record is the ordered array in which fossils appear within sedimentary rock strata.\n

            \uf0a7 These rocks record the passing of geological time.<\/li>\n

          • \u00b0 \u00a0Fossils can be used to construct phylogenies only if we\n

            can determine their ages.<\/li>\n

          • \u00b0 \u00a0The fossil record is a substantial, but incomplete, chronicle of evolutionary change.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n
            \n

            See Chapter 17<\/p>\n<\/div>\n<\/div>\n

            \n
            \n

            Notes<\/p>\n

            Review: Genetics
            \nRead text chp 10 \u201cDNA, RNA, and<\/p>\n

            Protein Synthesis.\u201d This content is also required for Biology 12.<\/p>\n<\/div>\n<\/div>\n

            \n
            \n

            Conserved Sequences<\/p>\n

            are similar or identical sequences that may occur within nucleic acids (e.g., DNA), proteins or polymeric carbohydrates within multiple species of organism or within different molecules produced by the same organism. In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be.<\/p>\n

            Sequence similarities serve as evidence for structural and functional conservation, as well as of evolutionary relationships between the sequences.<\/p>\n<\/div>\n<\/div>\n

            \n
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            Evolution: Taxonomy<\/p>\n<\/div>\n

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            8\/5\/07<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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            Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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            Notes<\/p>\n<\/div>\n<\/div>\n

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              \n
            • \u00b0 \u00a0The majority of living things were not captured as fossils upon their death.\n

              \uf0a7 Of those that formed fossils, later geological processes destroyed many.<\/p>\n

              \uf0a7 Only a fraction of existing fossils have been discovered.<\/li>\n

            • \u00b0 \u00a0The fossil record is biased in favor of species that existed for a long time, were abundant and widespread, and had hard shells or skeletons that fossilized readily.\n

              2. Morphological and molecular similarities may provide clues to phylogeny.<\/li>\n<\/ul>\n

                \n
              • Similarities due to shared ancestry are called homologies.<\/li>\n
              • Organisms that share similar morphologies or DNA sequences are likely to be more closely related than organisms without such similarities.<\/li>\n
              • Morphological divergence between closely related species can be small or great.<\/li>\n<\/ul>\n

                \u00b0 Morphological diversity may be controlled by relatively few genetic differences.<\/p>\n

                  \n
                • Similarity due to convergent evolution is called analogy.\n
                    \n
                  • \u00b0 \u00a0When two organisms from different evolutionary lineages experience similar environmental pressures, natural selection may result in convergent evolution.\n

                    \uf0a7 Similar analogous adaptations may evolve in such organisms.<\/li>\n

                  • \u00b0 \u00a0Analogies are not due to shared ancestry.<\/li>\n<\/ul>\n<\/li>\n
                  • Distinguishing homology from analogy is critical in the\n

                    reconstruction of phylogeny.<\/p>\n

                      \n
                    • \u00b0 \u00a0For example, both birds and bats have adaptations that allow them to fly.<\/li>\n
                    • \u00b0 \u00a0However, a close examination of a bat\u2019s wing shows a greater similarity to a cat\u2019s forelimb that to a bird\u2019s wing.<\/li>\n
                    • \u00b0 \u00a0Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors.<\/li>\n
                    • \u00b0 \u00a0Thus a bat\u2019s wing is homologous to other mammalian forelimbs but is analogous in function to a bird\u2019s wing.<\/li>\n<\/ul>\n<\/li>\n
                    • Analogous structures that have evolved independently are also called homoplasies.<\/li>\n
                    • In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently.<\/li>\n<\/ul>\n

                      \u00b0 For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones.<\/p>\n<\/div>\n<\/div>\n

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                      Evolution: Taxonomy<\/p>\n<\/div>\n

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                      2<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                      Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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                      Notes<\/p>\n<\/div>\n<\/div>\n

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                      • \u00b0 \u00a0The two skulls match almost perfectly, bone for bone.<\/li>\n
                      • \u00b0 \u00a0It is highly unlikely that such complex structures have\n

                        separate origins.<\/li>\n

                      • \u00b0 \u00a0More likely, the genes involved in the development of both skulls were inherited from a common ancestor.<\/li>\n<\/ul>\n
                          \n
                        • The same argument applies to comparing genes, which are sequences of nucleotides.<\/li>\n
                        • Systematists compare long stretches of DNA and even entire genomes to assess relationships between species.<\/li>\n<\/ul>\n

                          \u00b0 If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.<\/p>\n

                            \n
                          • It may be difficult to carry out molecular comparisons of nucleic acids.\n
                              \n
                            • \u00b0 \u00a0The first step is to align nucleic acid sequences from the two species being studied.<\/li>\n
                            • \u00b0 \u00a0In closely related species, sequences may differ at only one or a few sites.<\/li>\n
                            • \u00b0 \u00a0Distantly related species may have many differences or sequences of different length.\n

                              \uf0a7 Over evolutionary time, insertions and deletions accumulate, altering the lengths of the gene sequences.<\/li>\n<\/ul>\n<\/li>\n

                            • Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.<\/li>\n<\/ul>\n

                              \u00b0 To deal with this, systematists use computer programs to analyze comparable DNA sequences of differing lengths and align them appropriately.<\/p>\n

                              \u2022 The fact that molecules have diverged between species does not tell us how long ago their common ancestor lived.<\/p>\n

                              \u00b0 Molecular divergences between lineages with reasonably complete fossil records can serve as a molecular yardstick to measure the appropriate time span of various degrees of divergence.<\/p>\n

                                \n
                              • As with morphological characters, it is necessary to distinguish homology from analogy to determine the usefulness of molecular similarities for reconstruction of phylogenies.\n
                                  \n
                                • \u00b0 \u00a0Closely similar sequences are most likely homologies.<\/li>\n
                                • \u00b0 \u00a0In distantly related organisms, identical bases in otherwise different sequences may simply be coincidental matches or molecular homoplasies.<\/li>\n<\/ul>\n<\/li>\n
                                • Scientists have developed mathematical tools that can distinguish \u201cdistant\u201d homologies from coincidental matches in extremely divergent sequences.<\/li>\n<\/ul>\n<\/div>\n<\/div>\n
                                  \n
                                  \n

                                  Evolution: Taxonomy<\/p>\n<\/div>\n

                                  \n

                                  3<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                                  \n

                                  Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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                                  Notes<\/p>\n<\/div>\n<\/div>\n

                                  \n
                                  \n

                                  \u00b0 For example, such molecular analysis has provided evidence that humans share a distant common ancestor with bacteria.<\/p>\n

                                  \u2022 Scientists have sequenced more than 20 billion bases worth of nucleic acid data from thousands of species.<\/p>\n

                                  B. Phylogenetic Systematics: Connecting Classification with Evolutionary History<\/p>\n

                                    \n
                                  • In 1748, Carolus Linnaeus published Systema naturae, his classification of all plants and animals known at the time.<\/li>\n
                                  • Taxonomy is an ordered division of organisms into categories based on similarities and differences.<\/li>\n
                                  • Linneaus\u2019s classification was not based on evolutionary relationships but simply on resemblances between organisms.<\/li>\n<\/ul>\n

                                    \u00b0 Despite this, many features of his system remain useful in phylogenetic systematics.<\/p>\n

                                    1. Taxonomy employs a hierarchical system of classification.<\/p>\n

                                      \n
                                    • The Linnaean system, first formally proposed by Linnaeus in Systema naturae in the 18th century, has two main characteristics.\n
                                        \n
                                      • Each species has a two-part name.<\/li>\n
                                      • Species are organized hierarchically into broader and\n

                                        broader groups of organisms.<\/li>\n<\/ul>\n<\/li>\n

                                      • Under the binomial system, each species is assigned a two-\n

                                        part Latinized name, a binomial.<\/p>\n

                                          \n
                                        • \u00b0 \u00a0The first part, the genus, is the closest group to which a\n

                                          species belongs.<\/li>\n

                                        • \u00b0 \u00a0The second part, the specific epithet, refers to one\n

                                          species within each genus.<\/li>\n

                                        • \u00b0 \u00a0The first letter of the genus is capitalized and both names\n

                                          are italicized and Latinized.<\/li>\n

                                        • \u00b0 \u00a0For example, Linnaeus assigned to humans the optimistic scientific name Homo sapiens, which means \u201cwise man.\u201d<\/li>\n<\/ul>\n<\/li>\n
                                        • A hierarchical classification groups species into increasingly broad taxonomic categories.<\/li>\n
                                        • Species that appear to be closely related are grouped into the same genus.<\/li>\n<\/ul>\n

                                          \u00b0 For example, the leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris).<\/p>\n

                                          \u2022 Genera are grouped into progressively broader categories: family, order, class, phylum, kingdom, and domain.<\/p>\n<\/div>\n<\/div>\n

                                          \n
                                          \n

                                          Evolution: Taxonomy<\/p>\n<\/div>\n

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                                          4<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                                          Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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                                          Notes<\/p>\n<\/div>\n<\/div>\n

                                          \n
                                          \n

                                          \u2022 Each taxonomic level is more comprehensive than the previous one.<\/p>\n

                                          \u00b0 As an example, all species of cats are mammals, but not all mammals are cats.<\/p>\n

                                          \u2022 The named taxonomic unit at any level is called a taxon.<\/p>\n

                                          \u00b0 Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all of the many orders of mammals.<\/p>\n

                                            \n
                                          • Higher classification levels are not defined by some measurable characteristic, such as the reproductive isolation that separates biological species.<\/li>\n
                                          • As a result, the larger categories are not comparable between lineages.<\/li>\n<\/ul>\n

                                            \u00b0 An order of snails does not necessarily exhibit the same degree of morphological or genetic diversity as an order of mammals.<\/p>\n

                                            2. Classification and phylogeny are linked.<\/p>\n

                                              \n
                                            • Systematists explore phylogeny by examining various characteristics in living and fossil organisms.<\/li>\n
                                            • They construct branching diagrams called phylogenetic trees to depict their hypotheses about evolutionary relationships.<\/li>\n
                                            • The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups.<\/li>\n
                                            • Methods for tracing phylogeny began with Darwin, who realized the evolutionary implications of Linnaean hierarchy.<\/li>\n
                                            • Darwin introduced phylogenetic systematics in On the Origin of Species when he wrote: \u201cOur classifications will come to be, as far as they can be so made, genealogies.\u201d\n

                                              3. Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters.<\/li>\n<\/ul>\n

                                                \n
                                              • Patterns of shared characteristics can be depicted in a diagram called a cladogram.<\/li>\n
                                              • If shared characteristics are homologous and, thus, explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree.<\/li>\n<\/ul>\n

                                                \u00b0 A clade is defined as a group of species that includes an ancestral species and all its descendents.<\/p>\n

                                                \u2022 The study of resemblances among clades is called cladistics. \u00b0 Each branch, or clade, can be nested within larger<\/p>\n

                                                clades.<\/p>\n

                                                \u2022 A valid clade is monophyletic, consisting of an ancestral species and all its descendents.<\/p>\n<\/div>\n<\/div>\n

                                                \n
                                                \n

                                                Evolution: Taxonomy<\/p>\n<\/div>\n

                                                \n

                                                5<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                                                Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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                                                Notes<\/p>\n<\/div>\n<\/div>\n

                                                \n
                                                \n
                                                  \n
                                                • \u00b0 \u00a0When we lack information about some members of a clade, the result is a paraphyletic grouping that consists of some, but not all, of the descendents.<\/li>\n
                                                • \u00b0 \u00a0The result may also be several polyphyletic groupings that lack a common ancestor.<\/li>\n
                                                • \u00b0 \u00a0Such situations call for further reconstruction to uncover species that tie these groupings together into monophyletic clades.<\/li>\n<\/ul>\n
                                                    \n
                                                  • Determining which similarities between species are relevant to grouping the species in a clade is a challenge.<\/li>\n
                                                  • 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.<\/li>\n
                                                  • Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters.\n

                                                    \u00b0 A \u201ccharacter\u201d refers to any feature that a particular taxon possesses.<\/p>\n

                                                    \u00b0 A shared derived character is unique to a particular clade.<\/p>\n

                                                    \u00b0 A shared primitive character is found not only in the clade being analyzed, but also in older clades.<\/li>\n

                                                  • For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.<\/li>\n<\/ul>\n

                                                    \u00b0 It is a shared derived character that uniquely identifies mammals.<\/p>\n

                                                    \u2022 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.<\/p>\n

                                                    \u00b0 Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.<\/p>\n

                                                    \u2022 Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.<\/p>\n

                                                    \u00b0 The status of a character shared derived versus shared primitive may depend on the level at which the analysis is being performed.<\/p>\n

                                                      \n
                                                    • A key step in cladistic analysis is outgroup comparison, which is used to differentiate shared primitive characters from shared derived ones.<\/li>\n
                                                    • 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 each other.<\/li>\n
                                                    • To study the relationships among an ingroup of five vertebrates (a leopard, a turtle, a salamander, a tuna, and a<\/li>\n<\/ul>\n<\/div>\n<\/div>\n
                                                      \n
                                                      \n

                                                      Evolution: Taxonomy<\/p>\n<\/div>\n

                                                      \n

                                                      6<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                                                      Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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                                                      Notes<\/p>\n<\/div>\n<\/div>\n

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                                                      lamprey) on a cladogram, an animal called the lancelet is a good choice.<\/p>\n

                                                      \u00b0 The lancelet is a small member of the Phylum Chordata that lacks a backbone.<\/p>\n

                                                        \n
                                                      • The species making up the ingroup display a mixture of shared primitive and shared derived characters.<\/li>\n
                                                      • 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.<\/li>\n
                                                      • Homologies present in some or all of the ingroup taxa are assumed to have evolved after the divergence of the ingroup and outgroup taxa.<\/li>\n
                                                      • In our example, a notochord, present in lancelets and in the embryos of the ingroup, is a shared primitive character and, thus, not useful for sorting out relationships between members of the ingroup.\n
                                                          \n
                                                        • \u00b0 \u00a0The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup.<\/li>\n
                                                        • \u00b0 \u00a0The presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram.<\/li>\n<\/ul>\n<\/li>\n
                                                        • Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.<\/li>\n
                                                        • A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.\n
                                                            \n
                                                          • \u00b0 \u00a0However, this chronology does not indicate the time of origin of the species that we are comparing, only the groups to which they belong.<\/li>\n
                                                          • \u00b0 \u00a0For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group.<\/li>\n<\/ul>\n<\/li>\n
                                                          • A cladogram is not a phylogenetic tree.<\/li>\n<\/ul>\n

                                                            \u00b0 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.<\/p>\n

                                                              \n
                                                            • 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).<\/li>\n
                                                            • Some kinds of tree diagrams can be used to provide more specific information about timing.<\/li>\n<\/ul>\n<\/div>\n<\/div>\n
                                                              \n
                                                              \n

                                                              Evolution: Taxonomy<\/p>\n<\/div>\n

                                                              \n

                                                              7<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                                                              Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

                                                              \n
                                                              \n

                                                              Notes<\/p>\n<\/div>\n<\/div>\n

                                                              \n
                                                              \n
                                                                \n
                                                              • 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.<\/li>\n
                                                              • 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.\n
                                                                  \n
                                                                • \u00b0 \u00a0Humans and bacteria had a common ancestor that lived more than 3 billion years ago.<\/li>\n
                                                                • \u00b0 \u00a0This ancestor was a single-celled prokaryote and was more like a modern bacterium than like a human.<\/li>\n
                                                                • \u00b0 \u00a0Even 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.<\/li>\n<\/ul>\n<\/li>\n
                                                                • These equal amounts of chronological time are represented in an ultrameric tree.<\/li>\n
                                                                • 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.<\/li>\n
                                                                • Ultrameric trees do not contain the information about different evolutionary rates that can be found in phylograms.<\/li>\n<\/ul>\n

                                                                  \u00b0 However, they draw on data from the fossil record to place certain branch points in the context of geological time.<\/p>\n

                                                                  4. The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny.<\/p>\n

                                                                  \u2022 As available data about DNA sequences increase, it becomes more difficult to draw the phylogenetic tree that best describes evolutionary history.<\/p>\n

                                                                  \u00b0 If you are analyzing data for 50 species, there are 3 \u00d7 1076 different ways to form a tree.<\/p>\n

                                                                    \n
                                                                  • According to the principle of maximum parsimony, we look for the simplest explanation that is consistent with the facts.\n
                                                                      \n
                                                                    • \u00b0 \u00a0In 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.<\/li>\n
                                                                    • \u00b0 \u00a0For phylograms based on DNA sequences, the most parsimonious tree requires the fewest base changes in DNA.<\/li>\n<\/ul>\n<\/li>\n
                                                                    • 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.<\/li>\n<\/ul>\n<\/div>\n
                                                                      \n

                                                                      Parsimony<\/p>\n

                                                                      In science, parsimony is to prefer least complicated explanation for an observation. This is generally regarded as good when judging hypotheses. Ockham’s Razor also states this idea<\/p>\n<\/div>\n<\/div>\n

                                                                      \n
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                                                                      Evolution: Taxonomy<\/p>\n<\/div>\n

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                                                                      8<\/p>\n<\/div>\n<\/div>\n<\/div>\n

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                                                                      Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

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                                                                      Notes<\/p>\n<\/div>\n<\/div>\n

                                                                      \n
                                                                      \n

                                                                      \u00b0 Maximum likelihood methods are designed to use as much information as possible.<\/p>\n

                                                                        \n
                                                                      • Many computer programs have been developed to search for trees that are parsimonious and likely:\n
                                                                          \n
                                                                        • \u00b0 \u00a0\u201cDistance\u201d methods minimize the total of all the percentage differences among all the sequences.<\/li>\n
                                                                        • \u00b0 \u00a0More complex \u201ccharacter-state\u201d methods minimize the total number of base changes or search for the most likely pattern of base changes among all the sequences.<\/li>\n<\/ul>\n<\/li>\n
                                                                        • 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.\n

                                                                          5. Phylogenetic trees are hypotheses.<\/li>\n<\/ul>\n

                                                                          \u2022 Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related.<\/p>\n

                                                                          \u00b0 The best hypothesis is the one that best fits all the available data.<\/p>\n

                                                                          \u2022 A hypothesis may be modified when new evidence compels systematists to revise their trees.<\/p>\n

                                                                          \u00b0 Many older phylogenetic hypotheses have been changed or rejected since the introduction of molecular methods for comparing species and tracing phylogeny.<\/p>\n

                                                                            \n
                                                                          • Often, in the absence of conflicting information, the most parsimonious tree is also the most likely.\n

                                                                            \u00b0 Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious.<\/p>\n

                                                                            \u00b0 Nature does not always take the simplest course.<\/p>\n

                                                                            \u00b0 In some cases, the particular morphological or molecular character we are using to sort taxa actually did evolve multiple times.<\/li>\n

                                                                          • 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.<\/li>\n
                                                                          • But abundant evidence indicated that birds and mammals evolved from different reptilian ancestors.\n
                                                                              \n
                                                                            • \u00b0 \u00a0The hearts of birds and mammals develop differently, supporting the hypothesis that they evolved independently.<\/li>\n
                                                                            • \u00b0 \u00a0The most parsimonious tree is not consistent with the above facts, and must be rejected in favor of a less parsimonious tree.<\/li>\n<\/ul>\n<\/li>\n
                                                                            • The four-chambered hearts of birds and mammals are analogous, not homologous.<\/li>\n<\/ul>\n<\/div>\n<\/div>\n
                                                                              \n
                                                                              \n

                                                                              Evolution: Taxonomy<\/p>\n<\/div>\n

                                                                              \n

                                                                              9<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                              \n
                                                                              \n
                                                                              \n

                                                                              Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

                                                                              \n
                                                                              \n

                                                                              Notes<\/p>\n<\/div>\n<\/div>\n

                                                                              \n
                                                                              \n

                                                                              \u2022 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.<\/p>\n

                                                                              \u00b0 The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence.<\/p>\n

                                                                              6. An organism\u2019s evolutionary history is documented in its genome.<\/p>\n

                                                                                \n
                                                                              • Molecular systematics is a valuable tool for tracing an organism\u2019s evolutionary history.<\/li>\n
                                                                              • The molecular approach helps us to understand phylogenetic relationships that cannot be measured by comparative anatomy and other nonmolecular methods.<\/li>\n<\/ul>\n

                                                                                \u00b0 For example, molecular systematics helps us uncover evolutionary relationships between groups that have no grounds for morphological comparison, such as mammals and bacteria.<\/p>\n

                                                                                \u2022 Molecular systematics enables scientists to compare genetic divergence within a species.<\/p>\n

                                                                                \u00b0 Molecular biology has helped to extend systematics to evolutionary relationships far above and below the species level.<\/p>\n

                                                                                  \n
                                                                                • Its findings are sometimes inconclusive, as in cases where a number of taxa diverged at nearly the same time.<\/li>\n
                                                                                • 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.<\/li>\n<\/ul>\n

                                                                                  \u00b0 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.<\/p>\n

                                                                                  \u2022 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.<\/p>\n

                                                                                  7. Gene duplication has provided opportunities for evolutionary change.<\/p>\n

                                                                                    \n
                                                                                  • Gene duplication increases the number of genes in the genome, providing opportunities for further evolutionary change.<\/li>\n
                                                                                  • Gene duplication has resulted in gene families, which are groups of related genes within an organism\u2019s genome.<\/li>\n<\/ul>\n<\/div>\n
                                                                                    \n

                                                                                    Introns & Exons (grade 10 review)<\/p>\n

                                                                                    Introns are sections of DNA within a gene that do not encode part of the protein that the gene produces, and are spliced out of the mRNA that is transcribed from the gene before it is exported from the cell nucleus. Introns exist mainly (but not only) in eukaryotic cells. The regions of a gene that remain in the spliced mRNA are called exons.<\/p>\n

                                                                                    Source: Wikipedia<\/p>\n

                                                                                    Introns = interruptions in the DNA Exons = expressed DNA code<\/p>\n<\/div>\n<\/div>\n

                                                                                    \n
                                                                                    \n

                                                                                    Evolution: Taxonomy<\/p>\n<\/div>\n

                                                                                    \n

                                                                                    10<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                    \n
                                                                                    \n
                                                                                    \n

                                                                                    Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

                                                                                    \n
                                                                                    \n

                                                                                    Notes<\/p>\n<\/div>\n<\/div>\n

                                                                                    \n
                                                                                    \n
                                                                                      \n
                                                                                    • Like homologous genes in different species, these duplicated genes have a common genetic ancestor.<\/li>\n
                                                                                    • There are two types of homologous genes: orthologous genes and paralogous genes.<\/li>\n
                                                                                    • The term orthologous refers to homologous genes that are found in different gene pools because of speciation.<\/li>\n<\/ul>\n

                                                                                      \u00b0 The \u00df hemoglobin genes in humans and mice are orthologous.<\/p>\n

                                                                                        \n
                                                                                      • Paralogous genes result from gene duplication and are found in more than one copy in the same genome.\n
                                                                                          \n
                                                                                        • \u00b0 \u00a0Olfactory receptor genes have undergone many gene duplications in vertebrates.<\/li>\n
                                                                                        • \u00b0 \u00a0Humans and mice each have huge families of more than 1,000 of these paralogous genes.<\/li>\n<\/ul>\n<\/li>\n
                                                                                        • Now that we have compared entire genomes of different organisms, two remarkable facts have emerged.<\/li>\n
                                                                                        • Orthologous genes are widespread and can extend over enormous evolutionary distances.\n
                                                                                            \n
                                                                                          • \u00b0 \u00a0Approximately 99% of the genes of humans and mice are demonstrably orthologous, and 50% of human genes are orthologous with those of yeast.<\/li>\n
                                                                                          • \u00b0 \u00a0All living things share many biochemical and development pathways.<\/li>\n<\/ul>\n<\/li>\n
                                                                                          • The number of genes seems not to have increased at the same rate as phenotypic complexity.\n
                                                                                              \n
                                                                                            • \u00b0 \u00a0Humans 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.<\/li>\n
                                                                                            • \u00b0 \u00a0Many human genes are more versatile than yeast and can carry out a wide variety of tasks in various body tissues.\n

                                                                                              8. Molecular clocks may keep track of evolutionary time.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n

                                                                                                \n
                                                                                              • In the past, the timing of evolutionary events has rested primarily on the fossil record.<\/li>\n
                                                                                              • One of the goals of evolutionary biology is to understand the relationship among all living organisms, including those for which there is no fossil record.<\/li>\n
                                                                                              • Molecular clocks serve as yardsticks for measuring the absolute time of evolutionary change.\n
                                                                                                  \n
                                                                                                • \u00b0 \u00a0They are based on the observation that some regions of the genome evolve at constant rates.<\/li>\n
                                                                                                • \u00b0 \u00a0For these 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.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n
                                                                                                  \n

                                                                                                  Homologous genes – genes having similar structures and functions.<\/p>\n

                                                                                                  Paralogous – two genes or clusters of genes at different chromosomal locations in the same organism that have structural similarities indicating that they derived from a common ancestral gene.<\/p>\n

                                                                                                  Orthologous – homologous genes that originated through speciation, i.e., genes in different species, that are similar to each other because they originated from a common ancestor (for example, human and mouse, e.g., globin (transport) protein).<\/p>\n

                                                                                                  Source: Wikipedia<\/p>\n

                                                                                                  Gene Duplication<\/p>\n

                                                                                                  Gene duplication occurs when an error in DNA replication leads to the duplication of a region of DNA containing a (generally functional) gene. The significance of this process for evolutionary biology is that if a gene is under natural selection, most mutations will lead to the death of the organism. When a gene is duplicated selection may be removed from one copy and now the other gene locus is free to mutate and discover new functions.<\/p>\n

                                                                                                  The two genes that exist after a gene duplication event are called paralogs and usually code for proteins with a different function and\/or structure. By contrast, orthologous genes are ones which code for proteins with similar functions but exist in different species, and are created from a speciation event.<\/p>\n

                                                                                                  Source: Wikipedia<\/p>\n<\/div>\n<\/div>\n

                                                                                                  \n
                                                                                                  \n

                                                                                                  Evolution: Taxonomy<\/p>\n<\/div>\n

                                                                                                  \n

                                                                                                  11<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                  \n
                                                                                                  \n
                                                                                                  \n

                                                                                                  Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

                                                                                                  \n
                                                                                                  \n

                                                                                                  Notes<\/p>\n<\/div>\n<\/div>\n

                                                                                                  \n
                                                                                                  \n

                                                                                                  \u00b0 In the case of paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated.<\/p>\n

                                                                                                    \n
                                                                                                  • 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.\n
                                                                                                      \n
                                                                                                    • \u00b0 \u00a0The slope of the best line through these points represents the evolution rate of that molecular clock.<\/li>\n
                                                                                                    • \u00b0 \u00a0This rate can be used to estimate the absolute date of evolutionary events that have no fossil record.<\/li>\n<\/ul>\n<\/li>\n
                                                                                                    • No molecular clock is completely accurate.\n
                                                                                                        \n
                                                                                                      • \u00b0 \u00a0Genes that make good molecular clocks have fairly\n

                                                                                                        smooth average rates of change.<\/li>\n

                                                                                                      • \u00b0 \u00a0No genes mark time with a precise tick-tock accuracy in\n

                                                                                                        the rate of base changes.<\/li>\n

                                                                                                      • \u00b0 \u00a0Over time there may be chance deviations above and below the average rate.<\/li>\n<\/ul>\n<\/li>\n
                                                                                                      • Rates of change of various genes vary greatly.<\/li>\n<\/ul>\n

                                                                                                        \u00b0 Some genes evolve a million times faster than others.<\/p>\n

                                                                                                          \n
                                                                                                        • The molecular clock approach assumes that much of the change in DNA sequences is due to genetic drift and is selectively neutral.\n
                                                                                                            \n
                                                                                                          • \u00b0 \u00a0The neutral theory suggests that much evolutionary change in genes and proteins has no effect on fitness and, therefore, is not influenced by Darwinian selection.<\/li>\n
                                                                                                          • \u00b0 \u00a0Researchers supporting this theory point out that many new mutations are harmful and are removed quickly.<\/li>\n
                                                                                                          • \u00b0 \u00a0However, 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.<\/li>\n<\/ul>\n<\/li>\n
                                                                                                          • Differences in the rates of change of specific genes are a function of the importance of the gene.\n
                                                                                                              \n
                                                                                                            • \u00b0 \u00a0If 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.<\/li>\n
                                                                                                            • \u00b0 \u00a0If the sequence of genes is less critical, more mutations will be neutral, and mutations will accumulate more rapidly.<\/li>\n<\/ul>\n<\/li>\n
                                                                                                            • Some DNA changes are favored by natural selection.<\/li>\n<\/ul>\n

                                                                                                              \u00b0 This leads some scientists to question the accuracy and<\/p>\n

                                                                                                              utility of molecular clocks for timing evolution.<\/p>\n

                                                                                                              \u2022 Evidence suggests that almost 50% of the amino acid differences in proteins of two Drosophila species have resulted from directional natural selection.<\/p>\n<\/div>\n<\/div>\n

                                                                                                              \n
                                                                                                              \n

                                                                                                              Evolution: Taxonomy<\/p>\n<\/div>\n

                                                                                                              \n

                                                                                                              12<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                              \n
                                                                                                              \n
                                                                                                              \n

                                                                                                              Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

                                                                                                              \n
                                                                                                              \n

                                                                                                              Notes<\/p>\n<\/div>\n<\/div>\n

                                                                                                              \n
                                                                                                              \n

                                                                                                              \u2022 Over very long periods of time, fluctuations in the rate of accumulation of mutations due to natural selection may even out.<\/p>\n

                                                                                                              \u00b0 Even genes with irregular clocks can mark elapsed time approximately.<\/p>\n

                                                                                                                \n
                                                                                                              • Biologists are skeptical of conclusions derived from molecular clocks that have been extrapolated to time spans beyond the calibration in the fossil record\n
                                                                                                                  \n
                                                                                                                • \u00b0 \u00a0Few fossils are older than 550 million years old.<\/li>\n
                                                                                                                • \u00b0 \u00a0Estimates for evolutionary divergences prior to that time may assume that molecular clocks have been constant over billions of years.<\/li>\n
                                                                                                                • \u00b0 \u00a0Such estimates have a high degree of uncertainty.<\/li>\n<\/ul>\n<\/li>\n
                                                                                                                • The molecular clock approach has been used to date the jump of the HIV virus from related SIV viruses that infect chimpanzees and other primates to humans.\n
                                                                                                                    \n
                                                                                                                  • \u00b0 \u00a0The virus has spread to humans more than once.<\/li>\n
                                                                                                                  • \u00b0 \u00a0The multiple origins of HIV are reflected in the variety\n

                                                                                                                    of strains of the virus.<\/li>\n<\/ul>\n<\/li>\n

                                                                                                                  • HIV-1 M is the most common HIV strain.\n
                                                                                                                      \n
                                                                                                                    • \u00b0 \u00a0Investigators have calibrated the molecular clock for the virus by comparing samples of the virus collected at various times.<\/li>\n
                                                                                                                    • \u00b0 \u00a0From their analysis, they project that the HIV-1 M strain invaded humans in the 1930s.\n

                                                                                                                      9. There is a universal tree of life.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n

                                                                                                                      \u2022 The genetic code is universal in all forms of life.
                                                                                                                      \n\u00b0 From this, researchers infer that all living things have a<\/p>\n

                                                                                                                      common ancestor.<\/p>\n

                                                                                                                        \n
                                                                                                                      • Researchers are working to link all organisms into a universal tree of life.<\/li>\n
                                                                                                                      • Two criteria identify regions of DNA that can be used to reconstruct the branching pattern of this tree.\n
                                                                                                                          \n
                                                                                                                        • \u00b0 \u00a0The regions must be able to be sequenced.<\/li>\n
                                                                                                                        • \u00b0 \u00a0They must have evolved slowly, so that even distantly related organisms show evidence of homologies in these regions.<\/li>\n<\/ul>\n<\/li>\n
                                                                                                                        • rRNA genes, coding for the RNA component of ribosomes, meet these criteria.<\/li>\n
                                                                                                                        • Two points have emerged from this effort:<\/li>\n<\/ul>\n

                                                                                                                          1. The tree of life consists of three great domains: Bacteria,<\/p>\n

                                                                                                                          Archaea, and Eukarya.<\/p>\n

                                                                                                                          \u00b0 Most prokaryotes belong to Bacteria.<\/p>\n<\/div>\n<\/div>\n

                                                                                                                          \n
                                                                                                                          \n

                                                                                                                          Evolution: Taxonomy<\/p>\n<\/div>\n

                                                                                                                          \n

                                                                                                                          13<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                                          \n
                                                                                                                          \n
                                                                                                                          \n

                                                                                                                          Classification of Organisms<\/p>\n<\/div>\n<\/div>\n

                                                                                                                          \n
                                                                                                                          \n
                                                                                                                            \n
                                                                                                                          • \u00b0 \u00a0Archaea includes a diverse group of prokaryotes that inhabit many different habitats.<\/li>\n
                                                                                                                          • \u00b0 \u00a0Eukarya includes all organisms with true nuclei, including many unicellular organisms as well as the multicellular kingdoms.<\/li>\n<\/ul>\n

                                                                                                                            2. The early history of these domains is not yet clear.<\/p>\n

                                                                                                                              \n
                                                                                                                            • \u00b0 \u00a0Early in the history of life, there were many interchanges\n

                                                                                                                              of genes between organisms in the different domains.<\/li>\n

                                                                                                                            • \u00b0 \u00a0One mechanism for these interchanges was horizontal gene transfer, in which genes are transferred from one genome to another by mechanisms such as transposable elements.<\/li>\n
                                                                                                                            • \u00b0 \u00a0Different organisms fused to produce new, hybrid organisms.<\/li>\n
                                                                                                                            • \u00b0 \u00a0It is likely that the first eukaryote arose through fusion between an ancestral bacterium and an ancestral archaean.<\/li>\n<\/ul>\n<\/div>\n
                                                                                                                              \n

                                                                                                                              Horizontal gene transfer –
                                                                                                                              \nhinders clarification of the deepest branchings in a phylogenetic tree that depicts the origins of the three domains.<\/p>\n

                                                                                                                              Source:
                                                                                                                              \nBiology 7th ed, Campbell Joan Sharp, SFU<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Notes<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Evolution: Taxonomy<\/p>\n<\/div>\n

                                                                                                                              \n

                                                                                                                              14<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Biology 11 Review Notes<\/p>\n

                                                                                                                              Classification of Organisms Appendix See Chapter 17<\/p>\n

                                                                                                                              Vocabulary List for Chapter 17 \u2013 Classification of Organisms<\/p>\n<\/div>\n<\/div>\n\n\n\n\n<\/colgroup>\n\n\n
                                                                                                                              \n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              B
                                                                                                                              \n\uf071 binomial nomenclature \uf071 blastopore
                                                                                                                              \n\uf071 blastula<\/p>\n

                                                                                                                              C
                                                                                                                              \n\uf071 cladistics \uf071 cladogram \uf071 class<\/p>\n

                                                                                                                              D
                                                                                                                              \n\uf071 derived character \uf071 division
                                                                                                                              \n\uf071 domain
                                                                                                                              \n\uf071 domain Archaea<\/p>\n

                                                                                                                              \uf071 domain Bacteria \uf071 domain Eukarya<\/p>\n<\/div>\n<\/div>\n<\/td>\n

                                                                                                                              		\n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              E
                                                                                                                              \n\uf071 echinoderm \uf071 eubacteria<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              F
                                                                                                                              \n\uf071 family<\/p>\n

                                                                                                                              G
                                                                                                                              \n\uf071 genus<\/p>\n

                                                                                                                              K
                                                                                                                              \n\uf071 kingdom \uf071 kingdom \uf071 kingdom \uf071 kingdom \uf071 kingdom<\/p>\n

                                                                                                                              \uf071 kingdom \uf071 kingdom<\/p>\n<\/div>\n

                                                                                                                              \n

                                                                                                                              Animalia Archaebacteria Eubacteria Fungi<\/p>\n

                                                                                                                              Plantae Protista<\/p>\n<\/div>\n<\/div>\n<\/td>\n

                                                                                                                              		\n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              O
                                                                                                                              \n\uf071 order<\/p>\n

                                                                                                                              P
                                                                                                                              \n\uf071 phylogenetic tree \uf071 phylogeny
                                                                                                                              \n\uf071 phylum
                                                                                                                              \n\uf071 protist<\/p>\n

                                                                                                                              S
                                                                                                                              \n\uf071 species
                                                                                                                              \n\uf071 species identifier \uf071 species name
                                                                                                                              \n\uf071 subspecies
                                                                                                                              \n\uf071 systematics<\/p>\n

                                                                                                                              T
                                                                                                                              \n\uf071 taxonomy<\/p>\n

                                                                                                                              V
                                                                                                                              \n\uf071 variety<\/p>\n<\/div>\n<\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Some of these terms are used for the online Crossword review.<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Evolution: Taxonomy 15<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Classification of Organisms Appendix<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Vocabulary List by Topic (with additional terms)<\/p>\n

                                                                                                                              Overview<\/p>\n

                                                                                                                              Phyogeny and Systematics \uf071 phylogeny
                                                                                                                              \n\uf071 systematics,
                                                                                                                              \n\uf071 molecular systematics,<\/p>\n

                                                                                                                              A. Phylogenies Are Based on Common Ancestries<\/p>\n

                                                                                                                              1. Sedimentary rocks are the richest source of fossils.<\/p>\n

                                                                                                                              fossil record<\/p>\n

                                                                                                                              2. Morphological and molecular similarities may provide clues to phylogeny.
                                                                                                                              \n\uf071 analogy.
                                                                                                                              \n\uf071 homoplasies.<\/p>\n

                                                                                                                              B. Phylogenetic Systematics: Connecting Classification with Evolutionary History<\/p>\n

                                                                                                                              1. Taxonomy employs a hierarchical system of classification.
                                                                                                                              \n\uf071 binomial.
                                                                                                                              \n\uf071 genus,<\/p>\n

                                                                                                                              \uf071 specific epithet,
                                                                                                                              \n\uf071 species
                                                                                                                              \n\uf071 hierarchical classification
                                                                                                                              \n\uf071 family, order, class, phylum, kingdom, \uf071 domain.
                                                                                                                              \n\uf071 taxon.<\/p>\n

                                                                                                                              2. Classification and phylogeny are linked.<\/p>\n

                                                                                                                              Etymologies<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              3. Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters.
                                                                                                                              \n\uf071 clade
                                                                                                                              \n\uf071 cladistics.<\/p>\n

                                                                                                                              \uf071 monophyletic,
                                                                                                                              \n\uf071 paraphyletic
                                                                                                                              \n\uf071 polyphyletic
                                                                                                                              \n\uf071 shared derived character \uf071 shared primitive character \uf071 outgroup,<\/p>\n

                                                                                                                              \uf071 ingroup
                                                                                                                              \n\uf071 phylogram,
                                                                                                                              \n\uf071 ultrameric tree.<\/p>\n

                                                                                                                              4. The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny.
                                                                                                                              \n\uf071 maximum parsimony,<\/p>\n

                                                                                                                              \uf071 maximum likelihood
                                                                                                                              \n5. Phylogenetic trees are hypotheses.<\/p>\n

                                                                                                                              6. An organism\u2019s evolutionary history is documented in its genome.<\/p>\n

                                                                                                                              7. Gene duplication has provided opportunities for evolutionary change.
                                                                                                                              \n\uf071 orthologous<\/p>\n

                                                                                                                              \uf071 Paralogous<\/p>\n

                                                                                                                              8. Molecular clocks may keep track of evolutionary time.
                                                                                                                              \n\uf071 Molecular clocks
                                                                                                                              \n\uf071 neutral theory<\/p>\n

                                                                                                                              9. There is a universal tree of life.<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              analog- = proportion (analogy: similarity due to convergence)<\/p>\n

                                                                                                                              bi- = two; nom- = name (binomial: a two-part latinized name of a species)<\/p>\n

                                                                                                                              clado- = branch (cladogram: a dichotomous phylogenetic tree that branches repeatedly)<\/p>\n

                                                                                                                              homo- = like, resembling (homology: similarity in characteristics resulting from a shared ancestry)<\/p>\n

                                                                                                                              mono- = one (monophyletic: pertaining to a taxon derived from a single ancestral species that gave rise to no species in any other taxa)<\/p>\n

                                                                                                                              parsi- = few (principle of parsimony: the premise that a theory about nature should be the simplest explanation that is consistent with the facts)<\/p>\n

                                                                                                                              phylo- = tribe; -geny = origin (phylogeny: the evolutionary history of a taxon)<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Evolution: Taxonomy 16<\/p>\n<\/div>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Classification of Organisms Appendix<\/p>\n<\/div>\n<\/div>\n

                                                                                                                              \n
                                                                                                                              \n

                                                                                                                              Evolution: Taxonomy 17<\/p>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

                                                                                                                              Biology 11 Outline Notes Classification of Organisms Overview Phylogeny and Systematics Evolutionary biology is about both process and history. \u00b0 \u00a0The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species. \u00b0 \u00a0A major goal of evolutionary biology is to […]<\/p>\n","protected":false},"author":245,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5,6],"tags":[],"class_list":["post-295","post","type-post","status-publish","format-standard","hentry","category-biology-eleven","category-biology-eleven-notes"],"_links":{"self":[{"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/posts\/295","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/users\/245"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/comments?post=295"}],"version-history":[{"count":1,"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/posts\/295\/revisions"}],"predecessor-version":[{"id":296,"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/posts\/295\/revisions\/296"}],"wp:attachment":[{"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/media?parent=295"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/categories?post=295"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.vsb.bc.ca\/mcarmichae\/wp-json\/wp\/v2\/tags?post=295"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}