Phylogenetics and Fossils PDF

How do we classify all these forms of life? In the 1700s, a system for species classification was developed. This system is based on the presence of common/similar physical traits between species. Carolus Linneaus 1707-1778 In the last few decades, DNA sequencing of whole genomes now provides a way...

How do we classify all these forms of life? In the 1700s, a system for species classification was developed. This system is based on the presence of common/similar physical traits between species. Carolus Linneaus 1707-1778 In the last few decades, DNA sequencing of whole genomes now provides a way to genetically determine relatedness amongst species independent of their physical traits. Taxonomy: A system for classifying organisms Most general set of traits Most specific set of traits Each taxonomic level is defined by a specific set of traits. The set of traits becomes more specific at each level. 1 Scientific Names and Binomial Nomenclature: A functional system for naming to species Every organism has an 8-part taxonomic name. For the black bear it is: Eukarya Animalia Chordata Mammalia Carnivora Ursidae Ursus americanus We use a shortened form of a taxonomic name to refer to specific organisms. Scientific Names and Binomial Nomenclature: A functional system for naming to species Circle the part of this taxonomic name is most specific to the black bear? Eukarya Animalia Chordata Mammalia Carnivora Usidae Ursus americanus 2 Scientific Names and Binomial Nomenclature: A functional system for naming to species Scientific names of organisms are their genus and species. Scientific names are always written in italics. The Genus name is always capitalized The species name is always written in all lower case. Ex: Ursus americanus Phylogeny Phylogeny: the relatedness between species that came to be through a history of descent with branching Phylogenies are a product of the Process of Speciation The Nature of Phylogenetic trees Phylogenies are hypotheses of evolutionary relationships. They are based on the current data Phylogenies are often updated as we learn more and develop new techniques 3 Phylogenies include Last Common Ancestors Last common ancestor: most recent species that all the organisms in a phylogeny descended from Reading a Phylogenetic Tree Root: The bottom/beginning of the tree. It represents the last common ancestor of all groups in the tree Nodes: branch points in the tree that represent the last common ancestor of two species Branches: the path of decent between taxa longer branches = more evolutionary time Groups: taxonomical groups of related organisms at the ends of branches Chapter 22 Active Lecture Slide 7 Sister Groups Two groups that are each other’s closest relatives are called sister groups. Sister groups on a phylogenetic tree are two groups that are more closely related to each other than either is to anything else on the tree. Phylogenetic trees can reflect Linnaean classification Organisms are classified into taxonomic groups (taxa): Domains, kingdoms, phyla, classes, orders, families, genera, and species. The relationship between these taxa are often reflected in phylogenetic trees Chapter 22 Active Lecture Slide 12 Phylogenetic trees can reflect Linnaean classification. Organisms are classified into taxonomic groups (taxa): Domains, kingdoms, phyla, classes, orders, families, genera, and species. The relationship between these taxa are often reflected in phylogenetic trees Phylogenies are based on Organisms’ Characteristics When constructing a phylogenetic tree, morphological, physiological, or molecular features can be used. These “features” are called characters. Chapter 22 Active Lecture Slide 15 Homologous vs Analogous Features Homologous characters are present in groups that descended from a common ancestor. Analogous characters are those that arose separately because of similar selective environments. Which would you guess are useful for building phylogenies? A. Homologous characters B. Analogous Characters Constructing a Phylogenetic Tree Presence or absence of characters helps us define groups that are descended from a common ancestor. Numerous characteristics are used together to construct a tree Outgroups help with tree construction Outgroup: a group of organisms not belonging to the group whose evolutionary relationships are being modeled in a tree Determining the Best Solution for a Phylogeny Trees with the fewest character changes are preferred, as character changes are relatively rare in the process of evolution Choosing the simpler of two or more hypotheses is called parsimony. Using Molecular Data to Build Phylogenetic Trees Variation in DNA and RNA sequences can be used as character states to construct phylogenetic trees. In using molecular data, we compare species to an outgroup and generate a phylogeny on the basis of synapomorphies. This approach works by using the concept of molecular clocks. Mutations accumulate at a relatively constant rate. The more genetic differences between groups, the longer they have been separated in evolutionary time. Molecular Phylogeny and Human Evolution Mitochondrial Eve: The last female common ancestor of all living people based on DNA sequences from mitochondria Y-chromosome Adam: The last male common ancestor of all living people based on DNA sequences from the Y chromosome What are Fossils? Fossils: remains or impression of a prehistoric organism preserved in petrified form or as a mold or cast in rock Most fossils preserve the hard parts of organisms, as these are slowest to decay Formation of the Fossils 1. An organism dies and is rapidly buried in sediment before it can decay 2. Over time, bone or hard tissues are replaced by rock through mineralization 3. The patterns of mineralization preserve the anatomy of the organism over very long periods of time Geology and The Fossil Record Over millions and billions of years, many layers of sediment accumulate and become rock The rock layers have unique chemical properties that can tell us about the environment and geological activity on the earth at the time of their formation These layers create a chronological set of rock that contains fossils of different ages Geology and The Fossil Record Geological processes such as to plate tectonics and erosion move deeply buried sediment layers to the surface where they are accessible to paleontologists The fossil record is not complete Only a small subset of organisms are fossilized when they die. The fossil record contains a small fraction of all organisms Not all organisms fossilize well We have to physically unearth fossils in order to gain information from them Not all fossils come from mineralized bone Organisms that lack hard parts can leave a fossil record in two other ways: Trace fossils Molecular fossils Trace Fossils Trace fossils are preserved evidence of an organism’s presence or activity. Tracks and Trails Coprolites Burrows Molecular Fossils Molecular fossils occur when a dead organism leaves behind some of its biomolecules even if the rest organism itself is decayed DNA RNA Protein Phylogeny and Fossils Together Phylogenies can predict the when different groups diverged from on another in relative time The Fossil Record provides absolute dates for divergence events and includes transitional fossils of common ancestors Molecular Fossils and Denisovans Denisovans are a species closely related to humans Fossil record includes mainly small finger bone fragments and a few teeth Full genome was sequenced in 2012 Denisovans, Neanderthals, and Humans Three species lived at the same time Genetic evidence from modern humans indicate that these three species could produce hybrid offspring