SYSTEMATICS REVIEWER.pdf

SYSTEMATICS REVIEWER 3. The taxon’s content. For example... All members of this lab class are in the taxon Homo Systematics and Taxonomy sapie...

SYSTEMATICS REVIEWER 3. The taxon’s content. For example... All members of this lab class are in the taxon Homo Systematics and Taxonomy sapiens (we hope) The taxon Canis familiaris All domestic dogs are Biodiversity included in the taxon Canis familiaris One of the important steps one must take in The taxon Chordata includes all animals that have understanding the diversity of life around us is to (at some point) CLASSIFY IT Dorsal, hollow nerve tube Notochord Taxonomy & Systematics Tail posterior to the anus - Taxonomy is the science of naming living Pharyngeal gill slits organisms and placing them into a nested hierarchy of classification groups called taxa (singular = The Taxonomic Key taxon) - Tool for identifying organisms - Systematics is the study of evolutionary - Organized as dichotomous (two-way) choices relationships among organisms, both extant and extinct. Example: You have four birds One is yellow with a crest of feathers Taxonomic Key – a tool used to identify One is black with a crest of feathers unknown organisms in your possession One is blue with red legs Phylogenetic Tree – a diagrammatic One is blue with yellow legs representation of the evolutionary history of a group of ⮚ Your first dichotomy might be: related organisms 1a. Feathers are blue.........................................go to 2 Taxonomy 1b. Feathers are not blue..................................go to 3 A taxon is a group of organisms considered by taxonomists to form a related unit. ⮚ Next dichotomies: In modern systematics, taxa are assembled on the 2a. Legs are yellow..................................Phoenecius azuli basis of recency of descent from common ancestors. 2b. Legs are red..................................Phoenecius erythrism Biological nomenclature is the application of 3a. Feathers are black.......................Phoenecius obscurus names to organisms recognized as part of a 3b. Feathers are yellow..................Phoeneceius aureus particular taxon. Taxa are organized in a nested hierarchy of - By taking each bird through the dichotomy, you taxonomic ranks, from largest (most inclusive) to should be able to identify it to its scientific name. smallest (least inclusive). Phylogenetic systematics (Cladistics) is the biological discipline whose practitioners reconstruct evolutionary history and study the patterns of relationships among organisms. Data can come from various sources Morphology Ontogeny (embryo development) Molecular Studies (DNA, RNA, protein sequence) Constructing Phylogenies - The biological definition of a species: Three aspects of a taxon - A group of similar organisms that can interbreed 1. The taxon’s name. For example... under natural conditions to produce fertile, viable Mammalia offspring. Chordata - The species is the only taxonomic rank with Fungi biological significance. Homo sapiens - But even the species is sometimes difficult to Rodentia define, and not everyone agrees on how to define a - The taxon’s name has no real biological significance. It is species. a tool we use to group similar things, and serves the same - We do know that, over generations, one species can functions as names like “hats” and “flying monkeys”. change into a new species via the various processes of evolution. 2. The taxon’s rank. For example... Domain (rank) – Eukarya (name) The systematist uses various traits (a.k.a., characters) to Kingdom (rank) – Animalia (name) establish evolutionary links. Phylum (rank) – Chordata (name) - Morphological Class (rank) – Mammalia (name) - Ontogenetic Order (rank) – Primates (name) - Molecular Family (rank) – Hominidae (name) Genus (rank) – Homo (name) The condition, or state, of the character gives important Species (rank) – sapiens (name) information about recency of common descent. - Every species is nested in a sequentially more primitive character (plesiomorphy) shows little inclusive set of taxonomic ranks, as shown above or no change from the same character in an for our own species. ancestor  symplesiomorphy (literally "shared primitive character") is a primitive character shared between two or more taxa For example, all Chordates have pharyngeal gill slits and a tail posterior to the anus at some point in development. These are symplesiomorphies with respect to all Chordates. The Phylogenetic Tree - Initial character analysis usually yields an UNROOTED TREE. - No common ancestor is indicated. derived character (apomorphy) has changed in appearance and/or function relative to the same character in an ancestor synapomorphy (literally "shared derived character") is a derived character shared between two or more taxa For example, the same pharyngeal pouches that become - To root the tree, one must use an OUTGROUP. gills in a fish will develop into structures of the middle ear - This is a taxon related to, but not included in, the in a mammal. group of interest (the ingroup). - The characters shared by both the outgroup and All mammals share the ingroup can be identified as this trait, which is symplesiomorphies. a synapomorphy - These are not useful for determining smaller, less of mammals with inclusive groups within the ingroup. respect to all other - The outgroup confers polarity to the tree. vertebrates. Beware analogous characters: - Traits that look the same or have the same function in two species but was NOT the product of inheritance from a common ancestor are called analogous characters or homoplasies. - These must not be confused with homologies, as this can lead to incorrect phylogenies. - The goal of phylogenetic systematics is to construct taxa descended from a single common ancestor. Such a taxon is said to be monophyletic. - A taxon constructed incorrectly that does not include all descendants of an ancestral taxon is said to be paraphyletic.  - A taxon incorrectly groups taxa descended from different common ancestors is said to be polyphyletic. You will now learn how to create a phylogenetic Phylogeny and Classification tree by employing CLADISTICS: USING SHARED, DERIVED CHARACTERS TO CONSTRUCT MONOPHYLETIC TAXA. “Our classifications You will use the Caminalcules as your Operational will come to be, as Taxonomic Units (OTUs) far as they can be We call them OTUs to avoid specifying at what so made, genealogies.” rank we are classifying them. - Charles Darwin, 1859 Phylogeny and the Tree of Life Phylogeny is the study of the Systematics: Connecting Classification to Phylogeny pattern of divergence history. Systematics, Taxonomy, and Phylogeny (as opposed to speciation, which Constructing cladograms addresses process.) ➔ Phylogenetic Classification ➔ Molecular Systematics Assembling a phylogeny ➔ Parsimony using cladistics, taxa are associated on the Systematics is the study of biological diversity basis of shared evolutionary in an evolutionary context. It includes innovations. speciation taxonomy phylogeny. One of the evolutionary innovations shared by birds is the Taxonomy is the branch of systematics concerned feather... with naming and classification. Homology, the sharing of an innovation (derived Scientific names are binomials character) because of its invention in a common ancestor Example: Acer saccharum - Acer is the genus name - it is a Latin noun - saccharum is the specific epithet - it is a Latin adjective Carolus Linnaeus 1707-1778 Biological classifications are hierarchical: each taxonomic group is nested within a more inclusive higher order group. DNA Evolution: stable and labile characters relate to function. Example: Homeobox genes, which govern variation in serial homologs. How to construct a cladogram: Choose a study group Choose an appropriate outgroup Compile data matrix The homeobox (in the gene) codes for a homeodomain (in Polarize characters the protein synthesized from the gene). The Use shared derived characters to associate study group homeodomain has a precise three-dimensional structure taxa and construct the cladogram related to its function. The outgroup is the group used to polarize character states in the study group. It should be the group most closely related (on the basis of other lines of evidence) to the study group that is not actually part of the study group. The primitive character is the one shared by the outgroup and some, but not all, of the study group. Kinds of Characters The nested relationship of clades is reflected in the nested Apomorphy - a derived character state relationship of taxa in the resultant classification. All are Synapomorphy - a shared derived character state monophyletic groups. Autapomorphy - a derived character state unique to one study group member Symplesiomorphy – a shared primitive character state Cladistic Analysis and Classification: Kinds of Groups From Two Kingdoms to Three Domains Early taxonomists classified all species as either plants or animals Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia More recently, the three domain system has been adopted: Bacteria, Archaea, and Eukarya For Phylogenetic Classification, taxa (taxonomic Phylogeny is the study of evolutionary relationships groups) should be natural groups, that is groups among organisms. reflecting phylogeny. In phylogenetic analysis, taxa are associated on the In a phylogenetic classification, only monophyletic groups basis of shared evolutionary innovations. are named. If a paraphyletic group bears a name, it will A cladogram is an evolutionary hypothesis: it summarizes be an informal one (e.g., ‘gymnosperms’) information about ancestor- descendent relationships. Branch points represent an inferred common ancestor. On the diagram, the red star denotes the common ancestor of leopard and turtle, while the yellow star indicates the common ancestor of tuna, salamander, turtle, and leopard. A cladogram is an evolutionary hypothesis. It can be revised as new evidence becomes available. Molecular Phylogenetics - In molecular phylogenetic studies, individual nucleotide positions are the characters, while the particular nucleotide occurring at that position Taxonomy & Phylogeny is the character state. Introduction - The practice of categorizing organisms according to similar features goes back to Aristotle. - The goal of Taxonomy today is to produce a formal system for naming and classifying species to illustrate their evolutionary relationships. Classification Using parsimony analysis to choose among competing - In classification, the taxonomist asks whether the cladograms. species being classified contains the defining feature of a certain taxonomic grouping. - Focus is on features. Systematization - In systematization, the taxonomist asks whether the characteristics of a species support the hypothesis that it descends from the most recent common ancestor of the taxonomic group. - Focus is on the evolutionary origin of those features. Linnaeus and Classification Shared Primitive Characteristics - A shared primitive character is a homologous In the 18th century, Carolus Linnaeus designed structure that is older than the branching of a the hierarchical classification system still in use particular clade from other members of that clade. today. - It is shared by more than just the taxon we are - Kingdom trying to define. - Phylum - Example – mammals all have a backbone, but so do - Class other vertebrates. - Order - Family Shared Derived Characteristics - Genus - A shared derived character is a new evolutionary - Species feature, unique to a particular group. - Example - all mammals have hair, and no other Taxa animals have hair. - Taxa (singular = taxon) are the major groups of organisms. ➔ These are the features that are most useful for - Each rank can be subdivided into additional levels determining evolutionary relationships! of taxa. - Superclass, suborder, etc. Ancestral Character States - The ancestral character state is the form of the Binomial Nomenclature character that was present in the common ancestor - Binomial nomenclature is the system Linnaeus of the group. developed for naming species. - Variations of the character that arose later are - The two-part scientific name includes the genus called derived character states. and species - Names are latinized and italicized, only the genus Polarity is capitalized. - Polarity (which version of the trait is ancestral) is - Sitta carolinensis determined by using outgroup comparison. - An outgroup is closely related, but not part of the Phylogeny group being examined (the ingroup). - The goal of systematics is to determine the - An ancestral character is one that is found in both phylogeny – the evolutionary history – of a species the study group and the outgroup. or group of related species. - Derived character groups are those found in the - Phylogenies are inferred by identifying organismal study groups but not the outgroups. features, characters, that vary among species. These characters can be: Clades Morphological - Clades are groups that share derived characters Chromosomal and form a subset within a larger group. Molecular - A clade is a unit of common evolutionary descent. Behavioral or ecological Synapomorphy Homology - A synapomorphy is a derived character that is - Homologous characters are shared characters that shared by all the members of the clade. result from common ancestry. - Using synapomorphies to define clades will result in a nested hierarchy of clades. Homoplasy - Homoplasies are shared characters that are not a Symplesiomorphy result of common ancestry, but of independent - Ancestral character states for a taxon are called evolution of similar characters (they are not plesiomorphic. homologous). - Symplesiomorphies are shared ancestral - Can result from convergent evolution. characters. - Symplesiomorphies do not provide useful Convergent Evolution information for forming a nested series of clades. - Convergent evolution occurs when natural selection, working under similar environmental Cladogram pressures, produces similar (analogous) - The nested hierarchy of clades can be shown as a adaptations in organisms from different cladogram that is based on synapomorphies. evolutionary lineages. Phylogeny - When trying to determine evolutionary relationships (inferring a phylogeny), we only want to consider homologous characters. - Homoplasies can create errors. Shared Primitive and Shared Derived Characteristics - Focusing on homologous structures, we need to determine when that character arose. - Newer characters tell us more! - Primitive (older) vs. derived (newer) characters Monophyletic - A valid clade is monophyletic, it consists of the Sister Groups ancestor species and all its descendants. - A sister group is a pair of taxa that are most closely related to each other. - Humans are most closely related to chimpanzees, so humans & chimpanzees form a sister group. - Gorillas form a sister group to the clade containing humans and chimpanzees. Paraphyletic Cladistics vs. Evolutionary Taxonomy - A paraphyletic clade consists of an ancestral - The important difference between these two species and some, but not all, of the descendants. theories of taxonomy is that traditional evolutionary taxonomy sometimes accepts paraphyletic clades, while cladistics does not. - Both accept monophyletic clades. - Both reject polyphyletic clades. Carl Linnaeus - developed the classification system including the Polyphyletic binomial scientific name - A polyphyletic clade includes many species that - Swedish scientists. lack a common ancestor. Homo sapiens - example of binomial nomenclature is formatted correctly Homology - associated with characters that share common ancestry. Shared derived characters = synapomorphies - when defining a clade, synapomorphies is what we should use. Cladistics - Cladistics, also called phylogenetic systematics, is a Cladogram - The branching diagram that illustrates taxonomic theory that is based on cladograms. the nesting hierarchy of clades. - All taxa must be monophyletic! - Since all groupings must be monophyletic in A monophyletic clade is one that contains An ancestor cladistics, the paraphyletic arrangement of ape and all of its descendants. families doesn’t work. A polyphyletic clade is one that contains Several species - Humans, chimpanzees, gorillas, and orangutans that lack a common ancestor. are now all included together in one monophyletic A paraphyletic clade is one that contains An ancestor and family - Hominidae. some of its descendants. This cladogram illustrates a Paraphyletic clade. The difference between cladistics and traditional Evolutionary Taxonomy evolutionary taxonomy - Traditional Evolutionary taxonomy is based on Both accept monophyletic clades common descent and the amount of evolutionary Cladistics reject paraphyletic clades, while change to rank higher taxa. evolutionary taxonomy sometimes accepts them. - Sometimes this type of classification includes Both reject polyphyletic clades. paraphyletic groupings. The following cladograms illustrates sister groups Phylogeny and Systematics Biologists draw on the fossil record - Which provides information about ancient organisms MORPHOLOGICAL and MOLECULAR HOMOLOGIES In addition to fossil organisms - Phylogenetic history can be inferred from certain morphological and molecular Biologists also use systematics similarities among living organisms - as an analytical approach to understanding In general, organisms that share very similar the diversity and rel;ationships of organisms, morphologies or similar DNA sequences both present-day and extinct - Are likely to be more closely related than Currently, systematists use organisms with vastly different structures or - Morphological, biochemical, and molecular sequences comparisons to infer evolutionary relationships Sorting Homology from Analogy A potential misconception in constructing a phylogeny - Is similarity due to convergent evolution, called analogy, rather than shared ancestry Convergent evolution occurs when similar environmental pressures and natural selection - produces similar (analogous) adaptations in organisms from diff. evolutionary lineages Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence THE FOSSIL RECORD Sedimentary rocks - are the richest source of fossils - are deposited layers called strata Analogous structures or molecular sequences that evolved independently - are also called homoplasies The fossil record- is based on the sequence in which fossils have accumulated in such data Fossil reveal- ancestral characteristics that may have been lost over time Concept 25.2: Phylogenetic systematics connects classification with evolutionary history Taxonomy - is the ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences Binomial Nomenclature Clades can be nested within larger clades, but not is the two-part of the scientific name of an all groupings or organisms qualify as clades organisms A valid clade is monophyletic developed by Carolus Linnaeus - signifying that it consists of the ancestor The binomial name of an organism or scientific species and all its descendants epithet wwwww Linking Classification and Phylogeny Systematists depict evolutionary relationships - in branching phylogenetic trees A paraphyletic clade - is a grouping that consists of an ancestral species and some, but not all, of the descendants Each branch point - represents the divergence of two species “Deeper” branch points - represent progressively greater amounts of A polyphyletic grouping divergence - Includes numerous types of organisms that lack a common ancestor. Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics A cladogram: In cladistic analysis - a depiction of patterns of shared – Clades are defined by their evolutionary novelties characteristics among taxa A clade within a cladogram A shared primitive character - is defined as a group of species that includes – Is a homologous structure that predates the branching of an ancestral species and all its descendants a particular clade from other members of that clade Cladistics – Is shared beyond the taxon we are trying to define - is the study of resemblances among clades A shared derived character Cladistics – Is an evolutionary novelty unique to a particular clade Outgroups Systematists use a method called outgroup comparison - To differentiate between shared derived and shared primitive characteristics As a basis of comparison we need to designate an outgroup - which is a species or group of species that is closely related to the ingroup, the various species we are studying Outgroup comparison - Is based on the assumption that homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor The outgroup comparison - enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade Maximum Parsimony and Maximum Likelihood Systematists - Can never be sure of finding the single best tree in a large data set - Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood Among phylogenetic hypotheses - The most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters Phylogenetic Trees and Timing Applying parsimony to a problem in molecular Any chronology represented by the branching systematics pattern of a phylogenetic tree - is relative rather than absolute in terms of representing the timing of divergences Phylograms In a phylogram - the length of a branch in a cladogram reflects the number of genetic changes that have taken place in a particular DNA or RNA sequences in that lineage Applying parsimony to a problem in molecular systematics The principle of maximum likelihood - States that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events Ultrametric Trees APPLICATION In considering possible phylogenies for a group of species, systematists In an ultrametric Tree compare molecular data for the species. The most efficient way to study the various phylogenetic hypotheses is to begin by first considering the most parsimonious—that is, - the branching pattern is the same as in a which hypothesis requires the fewest total evolutionary events (molecular changes) to phylogram, but all the branches that can be have occurred. traced from the common ancestor to the TECHNIQUE Follow the numbered steps as we apply the principle of parsimony to a present are of equal length hypothetical phylogenetic problem involving four closely related bird species.  ➔ First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here) ➔ Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases). ➔ Now focus on site 1 in the DNA sequence. A single base- change event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data Concept 25.4: Much of an organism’s evolutionary history is documented in its genome Comparing nucleic acids or other molecules to infer relatedness - is a valuable tool for tracing organisms’ revolutionary history Gene Duplications and Gene Families Gene Duplication - is one of the most important types of mutation in evolution because it increases the no. of genes in the genome, providing further opportunities for evolutionary changes Orthologous genes - Are genes found in a single copy in the genome - Can diverge only once speciation has taken place Figure 25.17a 4. 5. Paralogous Genes - Result from gene duplication, so they are 6. found in more than one copy in the genome - Can diverge within the clade that carries them, often adding new functions RESULTS To identify the most parsimonious tree, we total all the base-change events noted in steps 3–6 (don’t forget to include the changes for site 1, on the facing page). We conclude that the first tree is the most parsimonious of these three possible phylogenies. (But now we must complete our search by investigating the 12 other possible trees.) Genome Evolution Orthologous genes are widespread Phylogenetic Trees as Hypotheses - And extend across many widely varied The best hypotheses for phylogenetic trees species - are those that fit the most data: The widespread consistency in total gene number in morphological, molecular, and fossil organisms of varying complexity Sometimes there is compelling evidence - Indicates that genes in complex organisms - that the best hypothesis is not the most are extremely versatile and that each gene parsimonious can perform many functions Concept 25.5: Molecular clocks help track evolutionary time Molecular Clocks The molecular clock - Is a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates Neutral Theory Neutral theory states that - Much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection - And that the rate of molecular change in these genes and proteins should be regular like a clock Difficulties with Molecular Clocks The molecular clock - does not run as smoothly as neutral theory predicts Applying a Molecular Clock: The origin of HIV Phylogenetic analysis shows that HIV - is descended from viruses that infect chimpanzees and other primates A comparison of HIV samples from throughout the epidemic - has shown that the virus has evolved in a remarkably clocklike fashion The Universal Tree of Life The tree of life - Is divided into three great clades called domains: Bacteria, Archaea, and Eukarya The early history of these domains is not yet clear Figure 25.18