BIO1130 2nd Part Lecture Notes PDF

Welcome to the 2nd part of BIO1130! A few words on the 2nd part of the course All lectures are in-person No lecture videos to watch prior to class Learning activities during class Lectures are recorded and will be posted on BrightSpace Additional Wooclap practice quizzes are available fo...

Welcome to the 2nd part of BIO1130! A few words on the 2nd part of the course All lectures are in-person No lecture videos to watch prior to class Learning activities during class Lectures are recorded and will be posted on BrightSpace Additional Wooclap practice quizzes are available for Topic 8-16. They are not graded! Midterm 2 will cover Topic 8-12 (from Pr. Delcourt) Pr. Delcourt's office hours will be in person - BSC 108 on... Monday 1pm-2pm Tuesday 10am-11am 2  Topic 7 Systematics Learning Outcomes Define systematics and its two components (taxonomy and phylogenetics). Write genus and species names of an organism following the Linnaean nomenclature. Distinguish between homologous vs. analogous traits and explain why it is important to do so. Explain how analogous traits can evolve. Interpreting phylogenetic trees and infer the evolutionary relationships based on its branching patterns. Define common terminology used in phylogenetic tree reconstruction (e.g., root, branch, tip, common ancestor, clade, mono/para/polyphyletic, taxon/taxa, sister taxa, ingroup/outgroup, etc.). Explain the basic principle of cladistics. Explain the use of morphology or molecular data in the construction of phylogenetic trees. Distinguish ingroups and outgroups Distinguish shared derived vs. shared ancestral characters. Define parsimony and explain how it is used in the construction of phylogenetic trees. Reconstruct a simple phylogenetic tree based on molecular data and following the principle of parsimony. Discuss the difference between a cladogram and a phylogram. Explain two methods by which dates can be added to trees. 4 https://www.wooclap.com/BIO1130 5  Topic 7 Systematics 7.1 – Definitions and taxonomy Definitions Systematics: the science of classifying organisms and determining their evolutionary relationships Two components: 1. Taxonomy: the scientific discipline of naming and classifying organisms. 2. Phylogenetics: the study of evolutionary relationships. Phylogenetic tree: a diagrammatic hypothesis of the evolutionary relationships of a group of organisms that results from a phylogenetic analysis 7 Definitions Systematics: the science of classifying organisms and determining their evolutionary relationships Two components: 1. Taxonomy: the scientific discipline of naming and classifying organisms. 2. Phylogenetics: the study of evolutionary relationships. Phylogenetic tree: a diagrammatic hypothesis of the evolutionary relationships of a group of organisms that results from a phylogenetic analysis Phylogenetic trees vary in their support – some are well resolved and others less so; in fact, individual ‘nodes’ (branching points) within a phylogenetic tree can each have their own level of support reflecting our confidence in that particular evolutionary relationship. 8 Classification/taxonomy Carl Linnaeus (created taxonomy) and described over 12,000 plant and animal species. Carl Linnaeus (1775) The Linnaean system groups species in a hierarchy of increasingly inclusive categories based on shared characters Taxon (plural, taxa): a group at any level of the classification hierarchy (e.g., species, genera, families, oders, classes, phyla, etc.). Different taxa are not necessarily comparable. (e.g., genetic differences among families of snails are substantially greater than among families of mammals). A key aspect of the Linnaean system is the use of binomial nomenclature: à combination of a genus and species name which provides a unique identifier for every species: e.g., Homo sapiens (H. sapiens), Castor canadensis (C. canadensis) à Only the genus name uses a capital letter, not the species name! à Both Genus and species names are italicized! If hand-written they are simply underlined! 9 Classification/taxonomy Linnaeus built his scheme on morphological/structural similarities of organisms These similarities are called homologous traits or homology: similarities due to shared ancestry 10 Classification/taxonomy But convergent evolution can give rise to analogous traits Marsupial (or analogy): similarities that are not due to shared ancestry but rather by shared environment (or independent identical mutations). Rodent Species can secondarily lose a homologous trait shared by close relatives (e.g., hair in whales). Grouping by only a few specific shared traits can therefore result in Linnaean classifications that do not reflect the true evolutionary history (i.e. the phylogeny). After the widespread acceptance of evolution following the publication of The Origin of Species by Darwin, it was generally accepted that classification should reflect evolutionary history (i.e. the phylogeny), an approach known as cladistics. 11 Linnean nomenclature reflecting phylogeny 12  Topic 7 Systematics 7.2 – Phylogenetic trees Phylogenetics Phylogenetics: the study of evolutionary relationships Originally done via morphological similarity (and still done largely this way for fossils). Standard approaches now compare molecular sequences like DNA, RNA, and proteins (all more accurate). Results phylogenetic analyses are depicted as phylogenetic trees: a hypothesis of the evolutionary relationships among a set of taxa. 14 Phylogenetic trees Sister taxa tips Time root University of California Museum of Paleontology's Understanding Evolution 15 Phylogenetic trees Equivalent trees can be drawn in differ ways: Trees can be rotated around any branch point (node)… which means that physical proximity of taxa at the tips does not indicate relatedness. 16 Phylogenetic trees Evolution produces patterns of relatedness that are tree-like, not ladder-like: Aristotle’s ‘Great Chain of Being’ is incorrect No taxa is ‘higher’ or ‘lower’, or more or less advanced than another: 17 Phylogenetic trees Taxa are not more or less ‘evolved’! All species alive today (also called extant species) share a common ancestor that lived >3.5 billion years ago called L.U.C.A (Last Universal Common Ancestor)… and therefore do not differ in the length of their evolutionary history. Species at the tips do not have an ancestor/descendant relationship; rather they are evolutionary ‘relatives’. 18 Phylogenetic trees Beware: phylogenetic trees can look different because of ‘pruning’ and/or ‘collapsing’ parts: Or because extinct taxa are included or excluded: à Not including all species within a taxon can be misleading and may suggest an artificially less diverse taxon! 19 Phylogenetic trees Relatedness is indicated by how recently two taxa share a common ancestor. Taxa that share a more recent common ancestor are more closely related than taxa that share an older common ancestor. Relatedness is NOT indicated by the number of nodes between two taxa. à This is because the number of nodes depends on what other taxa are included or not in the phylogeny) 20 Phylogenetic trees A monophyletic group (= a clade) is composed of an ancestral species and ALL of its descendants. A paraphyletic group contains an ancestor and only some of its descendants, not all. A polyphyletic group lacks the common ancestor of all its members (and does not accurately reflect the group’s evolutionary history). 21  Topic 7 Systematics 7.3 – Constructing phylogenies Cladistics An approach to systematics in which common ancestry is the primary basis for classifying organisms. à Uses homologies to define clades (= monophyletic groups). Implications: Taxonomy (i.e. classification) should reflect this evolutionary history In phylogenetics studies, organisms should be organised into nested series of monophyletic groups (i.e., clades) that reflect their shared evolutionary history. Evidence for common ancestry comes from the study of shared derived characters: characters possessed by, and unique to, all members of a group, due to descent from a common ancestor. 23 Cladistics A clade is a group that includes a common ancestor and all its descendants (living and extinct). By definition, clades are monophyletic: Clades are nested within one another: 24 Cladistics Many existing taxonomic groups are not monophyletic; e.g. the class Reptilia is paraphyletic and the clade Dinosauria is only monophyletic if you include birds. Reptiles Aves 25 Cladistics Fish (paraphyletic) 26 Constructing phylogenies Can be built from morphological or molecular data (more accurate). Evidence for common ancestry comes from homologous traits (i.e. shared characters due to common descent). Analogous traits (i.e. characters that are similar due to causes others than shared ancestry, like convergent evolution) can be misleading. Homologous characters can be further divided into ancestral vs. derived: backbones are an ancestral character of mammals; all mammals have backbones, but so do other species of vertebrates (so backbones don’t distinguish mammals from other vertebrates). backbones are a derived character of vertebrates because they are present in all vertebrates but are absent in the ancestor that is common to their closest relatives. Backbones are shared only among vertebrates (a shared derived character). Phylogenies are inferred by forming clades based on shared derived characters. 27 Convergent evolution Convergent evolution: independent evolution of similar traits in different lineages. Creates analogies (similarities that are not due to shared ancestry, but rather by shared environment or independent identical mutations). C ! ev olution Not an 28 Constructing phylogenies Shared derived characters are, by definition, unique to some group and must have arisen from a common ancestor in which this trait first appeared. Species outside the clade will lack the trait, so by sampling species, including an outgroup (one or more species outside the group of interest – the ingroup), evolutionary relationships can be inferred. Systematists compare ingroup species among themselves and with the outgroup to differentiate between shared derived vs. ancestral characteristics, grouping species with shared derived characters together, thereby determining which characters were derived at various branch points. More info on building a tree (worth reading!): https://evolution.berkeley.edu/the-tree-room/how-to-build-a-tree/building-trees-using-parsimony/ 29 Constructing phylogenies Principle of parsimony: the most likely phylogenetic tree is the one that involves the fewest number of evolutionary transitions (e.g., gains or losses of a trait or change in character state). 9 evolutionary steps 6 evolutionary steps The phylogeny on the right is further supported by a detailed examination of the hearts of birds and mammals which reveals clear differences in structure, supporting their independent evolution (i.e., the fact they both have four chambers is a superficial similarity that is not due to inheritance from a common ancestor). 30 Adding time to trees 2 types of trees Cladograms: show only the branching pattern with no information about timing or amount of change (i.e., branch lengths are arbitrary) Phylograms: show branching patterns AND branch lengths are proportional to either the amount of genetic change or the times of the various branching points 31 Dating of branching points (nodes) Can be done via: Fossils in combination with radiometric dating and/or stratigraphy (the study of rock layers and layering). Molecular clock: assumes the rate of nucleotide substitutions per unit of time is roughly constant for a given gene. 32 Molecular clock Molecular clocks are calibrated against branches whose dates are known from the fossil record. Individual genes vary in how clock-like they are (i.e., some mutate faster than others). Population genetic theory shows that, if most of the evolutionary changes in genes have no effect on fitness, then the rate of molecular change should be roughly constant, like the ticking of a clock. Differences in molecular clock rate for different gene are a function of the importance of the gene or its parts (i.e., selective constraints). Each dot is a pair of sister taxa. A pair of species with 45 base pair differences in that gene shared a common ancestor about 74 Mya. 33