1/28/15Principles in Biological DiversityNotes from reference pages for January 28 and 30 Pages 107-114 of Campbell Biology Second Custom Edition for University of MontanaChapter 5: Phylogeny and the Tree of LifeKey Concepts5.1 Phylogenes show evolutionary relationships5.2 Phylogenes are inferred from morphological and molecular data5.3 Shared characters are used to construct phylogenetic trees5.4 An organism’s evolutionary history is documented in its genome5.5 Molecular clocks help track evolutionary time5.6 Our understanding of the Tree of Life continues to change based on new dataInvestigating the Tree of LifeA species is placed into a category by comparing its traits with its potential close relatives. The unit will be surveying diversities and describing hypotheses regarding how an organism evolved. Emphasis will shift from the process of evolution to its pattern.Biologists trace an organism’s phylogeny, or the evolutionary history of a species or group of species, in order to survey life’s diversity.Phylogenies are reconstructed and interpreted by biologists using systematics, or a discipline focuses on classifying organisms and determining their evolutionary relationships.Phylogenies show Evolutionary RelationshipsOrganisms that share characteristics share common ancestry. Organisms can share genes, metabolic pathways, and structural proteins with close relatives.The scientific discipline of taxonomy is used to name and classify organisms.Binomial NomenclatureThe reason why biologists refer to organisms by their Latin scientific names is to avoid ambiguity. A binomial is used, meaning the two-part format of the Latin scientific name of the organism. This was instituted by Carolus Linneaus in the 18th century. The first part of the binomial is the name of the genus and the second part is the specific Latin epithet that is unique for the species. The first letter of the binomial is capitalized and the entire binomial is either italicized or underlined. An example of a binomial is Panthera pardus, which is the binomial for the leopard. The binomial for human beings is Homo sapiens, which translates to “Wise man”.Hierarchical ClassificationThe Hierarchical Classification was also created by Linneaus. Each separate category within the classification is called are taxa (singular, taxon).The taxa of the Hierarchical Classification or the Linnaean Classification include:- Species- Genus- Family- Order- Class- Phylum- Kingdom- DomainSpecies → Genus → Family → Order → Class → Phylum → Kingdom → DomainThere are three Domains which include: Archaea, Bacteria, and Eukarya.These classifications give a structure of the human view of the organisms that roam the world.Linking Classification and PhylogenyThe way the evolutionary history of a group of organisms is represented is through a phylogenetic tree. It is a branching diagram that matches groups of organisms nested within moreinclusive groups.Phylogenetic trees contain branch points. Branch points are the representation of the divergence of two or more taxa from a common ancestor. It is usually shown as a dichotomy in which a branch representing the ancestral lineage splits into two branches, one for each of the two descendant lineages.Sister taxa are groups of organisms that share an immediate common ancestry and are each other’s closest relatives. Most phylogenetic trees are rooted, which means that a branch point within the tree represents the most recent common ancestor of all the taxa in the tree. Somephylogenetic trees contain a basal taxon, or a lineage that diverges early in the history of thegroup of taxa. Phylogenetic trees may also include a polytomy, which is a branch point from which more than to descendant groups emerge and signifies that that the evolutionary relationships among the taxa are not yet clear.What We Can and Cannot Learn from Phylogenetic TreesPhylogenetic trees are intended to show patterns of descent not phenotypic similarity. Branching in the tree does not indicate the actual or absolute ages of the particular species.The diagram is interpreted solely in terms of patterns of decent. No assumptions about time and the amount of changes that had occurred. No assumptions that a taxon evolved from thetaxon next to it. They have a common ancestor. Extant: livingApplying PhylogeniesPhylogenetic trees can be used to infer species identities by analyzing the relatedness of DNA sequences from different organisms.Phylogenies are inferred from Morphological and Molecular DataThe information about morphology, genes, and biochemistry of the relevant organisms must be gathered. Features of the organisms reflect evolutionary relationships.Morphological and Molecular HomologiesHomologies are shared ancestry that causes phenotypic and genetic similarities.Morphological divergence between species can be large and their genetic divergence can be small or vice versa. Sorting Homology from AnalogyAnalogy is the similarity between two species that is due to a common ancestor with the same trait, while the term homology is just shared ancestry.Convergent evolution occurs when similar environmental pressures and natural selection produce similar adaptations in organisms from different evolutionary lineages.Homoplasies is a similar structure or molecular sequence that has evolved independently in two species. The Geek translation for this term is “To mold in some way”.Genes: sequences of thousands of nucleotides, each of which represents an inherited character in form of one of the four DNA bases.The Four DNA bases: A (adenine), G (guanine), C (cytosine), T (thymine).The genes are most likely homologous if they share many portions of their nucleotide sequences.Evaluating Molecular HomologiesComparing DNA molecules:The molecules are sequenced and aligned sequences are compared from the species beingstudied. If the species are closely related, the sequences probably differ at only one or a few sites.Petition and insertion of DNA sequences causes a shift of what matched between the two species.An example of aligning segments of DNA:Two identical species:Species 1. CCATCAGAGTCCSpecies 2: CCATCAGAGTCCDeletion and insertion mutationsSpecies 1. CCATCAAGTCCSpecies 2. CCATGTACAGAGTCCThe species no longer align because of deleted and inserted mutationsA computer program adds gaps so then the mutations alignSpecies 1. CCAT CA AGTCCSpecies 2. CCATGTACAGAGTCCMolecular Homoplasies: Organisms that