Similarity. Difference. Classification. Taxonomy

Transcription

1 EVOLUTION

2 PHYLOGENY

3 Similarity Difference Classification Taxonomy

4

5 Common origin Descent with modifications Selection

6 Figure 22.10

7 Figure (a) A flower mantid in Malaysia (b) A leaf mantid in Borneo

8 Figure 23.3 (a) (b)

9 Figure 24.2b (b) Diversity within a species

10 Evolution and Phylogeny The definition---- Evolution Biological evolution, simply put, is descent with modification. This definition encompasses small-scale evolution (changes in gene frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations). Evolution helps us to understand the history of life.

11 Chapter 22 (pp ) Descent with Modification: A Darwinian View of Life Chapter 26 (pp ) Phylogeny and Tree of Life

12 LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 26 Phylogeny and the Tree of Life Lectures by Erin Barley Kathleen Fitzpatrick

13 Overview: Endless Forms Most Beautiful A new era of biology began in 1859 when Charles Darwin published The Origin of Species The Origin of Species focused biologists attention on the great diversity of organisms

14 Darwin noted that current species are descendants of ancestral species Evolution can be defined by Darwin s phrase descent with modification Evolution can be viewed as both a pattern and a process

15 Figure Lamarck publishes his hypothesis of evolution Malthus publishes Essay on the Principle of Population Hutton proposes his principle of gradualism Cuvier publishes his extensive studies of vertebrate fossils Lyell publishes Principles of Geology While studying species in the Malay Archipelago, Wallace sends Darwin his hypothesis of natural selection Charles Darwin Darwin travels around is born. the world on HMS Beagle On the Origin of Species is published Darwin writes his essay on descent with modification. The Galápagos Islands

16 Figure 22.5 Darwin in 1840, after his return from the voyage Great Britain EUROPE HMS Beagle in port NORTH AMERICA ATLANTIC OCEAN The Galápagos Islands Fernandina Isabela Kilometers Pinta Marchena Santiago Pinzón Santa Cruz Florenza Santa Fe PACIFIC OCEAN Genovesa Equator Daphne Islands San Cristobal Española Chile PACIFIC OCEAN SOUTH AMERICA Andes Mtns. Brazil Argentina Cape Horn Cape of Good Hope AFRICA Equator Malay Archipelago AUSTRALIA PACIFIC OCEAN Tasmania New Zealand

17 Figure 22.5c The Galápagos Islands Fernandina Pinta Marchena Santiago Pinzón PACIFIC OCEAN Genovesa Equator Daphne Islands Isabela Kilometers Santa Cruz Florenza Santa Fe San Cristobal Española

18 Darwin s Focus on Adaptation In reassessing his observations, Darwin perceived adaptation to the environment and the origin of new species as closely related processes From studies made years after Darwin s voyage, biologists have concluded that this is what happened to the Galápagos finches

19 Figure 22.6 (a) Cactus-eater (b) Insect-eater (c) Seed-eater

20 In 1844, Darwin wrote an essay on natural selection as the mechanism of descent with modification, but did not introduce his theory publicly Natural selection is a process in which individuals with favorable inherited traits are more likely to survive and reproduce In June 1858, Darwin received a manuscript from Alfred Russell Wallace, who had developed a theory of natural selection similar to Darwin s Darwin quickly finished The Origin of

21 The Origin of Species Darwin explained three broad observations: The unity of life The diversity of life The match between organisms and their environment

22 Descent with Modification Darwin never used the word evolution in the first edition of The Origin of Species The phrase descent with modification summarized Darwin s perception of the unity of life The phrase refers to the view that all organisms are related through descent from an ancestor that lived in the remote past

23 In the Darwinian view, the history of life is like a tree with branches representing life s diversity Darwin s theory meshed well with the hierarchy of Linnaeus

24 Figure 22.7

25 Figure 22.8 Hyracoidea (Hyraxes) Moeritherium Sirenia (Manatees and relatives) Barytherium Deinotherium Mammut Platybelodon Stegodon Mammuthus Elephas maximus (Asia) Loxodonta africana (Africa) Loxodonta cyclotis (Africa) Millions of years ago Years ago

26 Artificial Selection, Natural Selection, and Adaptation Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a process called artificial selection Darwin drew two inferences from two observations

27 Figure 22.9 Selection for apical (tip) bud Cabbage Brussels sprouts Selection for axillary (side) buds Broccoli Selection for flowers and stems Kale Selection for leaves Wild mustard Selection for stems Kohlrabi

28 The Evolution of Drug-Resistant Bacteria The bacterium Staphylococcus aureus is commonly found on people One strain, methicillin-resistant S. aureus (MRSA) is a dangerous pathogen S. aureus became resistant to penicillin in 1945, two years after it was first widely used S. aureus became resistant to methicillin in 1961, two years after it was first widely used

29 Methicillin works by inhibiting a protein used by bacteria in their cell walls MRSA bacteria use a different protein in their cell walls When exposed to methicillin, MRSA strains are more likely to survive and reproduce than nonresistant S. aureus strains MRSA strains are now resistant to many antibiotics

30 Figure ,750, ,000 base pairs 2,500,000 Chromosome map of S. aureus clone USA ,000 2,250,000 2,000,000 Key to adaptations Methicillin resistance Ability to colonize hosts Increased disease severity Increased gene exchange (within species) and toxin production 750,000 1,000,000 1,750,000 1,500,000 1,250,000

31 Natural selection does not create new traits, but edits or selects for traits already present in the population The local environment determines which traits will be selected for or selected against in any specific population

32 Homology Homology is similarity resulting from common ancestry

33 Anatomical and Molecular Homologies Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor

34 Figure Humerus Radius Ulna Carpals Metacarpals Phalanges Human Cat Whale Bat

35 Comparative embryology reveals anatomical homologies not visible in adult organisms

36 Figure Pharyngeal pouches Post-anal tail Chick embryo (LM) Human embryo

37 Vestigial structures are remnants of features that served important functions in the organism s ancestors Examples of homologies at the molecular level are genes shared among organisms inherited from a common ancestor

38 Homologies and Tree Thinking Evolutionary trees are hypotheses about the relationships among different groups Homologies form nested patterns in evolutionary trees Evolutionary trees can be made using different types of data, for example, anatomical and DNA sequence data

39 Figure Branch point Lungfishes 1 Digitbearing 2 limbs Amnion 3 Amphibians Mammals Lizards and snakes Amniotes Tetrapods Homologous characteristic 4 5 Feathers 6 Crocodiles Ostriches Hawks and other birds Birds

40 A Different Cause of Resemblance: Convergent Evolution Convergent evolution is the evolution of similar, or analogous, features in distantly related groups Analogous traits arise when groups independently adapt to similar environments in similar ways Convergent evolution does not provide information about ancestry

41 The Fossil Record The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time

42 Biogeography Biogeography, the geographic distribution of species, provides evidence of evolution Earth s continents were formerly united in a single large continent called Pangaea, but have since separated by continental drift An understanding of continent movement and modern distribution of species allows us to predict when and where different groups evolved

43 Endemic species are species that are not found anywhere else in the world Islands have many endemic species that are often closely related to species on the nearest mainland or island Darwin explained that species on islands gave rise to new species as they adapted to new environments

44 What Is Theoretical About Darwin s View of Life? In science, a theory accounts for many observations and data and attempts to explain and integrate a great variety of phenomena Darwin s theory of evolution by natural selection integrates diverse areas of biological study and stimulates many new research questions Ongoing research adds to our understanding of evolution

45 Figure (a) Gibbon LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION (b) Orangutan Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson (c) Gorilla (d) Chimpanzees (e) Bonobos Lectures by Erin Barley Kathleen Fitzpatrick

46 Figure LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Paranthropus Peter V. Homo Minorsky, Robert HomoB. Jackson robustus ergaster neanderthalensis Homo sapiens? Paranthropus boisei Australopithecus africanus Millions of years ago Kenyanthropus platyops Australopithecus anamensis Australopithecus garhi Homo habilis Homo rudolfensis Homo erectus Australopithecus afarensis Orrorin tugensis Ardipithecus ramidus Sahelanthropus tchadensis Lectures by Erin Barley Kathleen Fitzpatrick

47 Figure 24.2b (b) Diversity within a species

48 Phylogeny is the evolutionary history of a species or group of related species The discipline of systematics classifies organisms and determines their evolutionary relationships Systematists use fossil, molecular, and genetic data to infer evolutionary relationships

49 Figure 26.2a

50 Figure 26.2b

51 Figure 26.2c

52 Figure 26.2

53 Concept 26.1: Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms

54 Binomial Nomenclature In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances Two key features of his system remain useful today: two-part names for species and hierarchical classification

55 The two-part scientific name of a species is called a binomial The first part of the name is the genus The second part, called the specific epithet, is unique for each species within the genus The first letter of the genus is capitalized, and the entire species name is italicized Both parts together name the species (not the specific epithet alone)

56 Hierarchical Classification Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species A taxonomic unit at any level of hierarchy is called a taxon The broader taxa are not comparable between lineages For example, an order of snails has less genetic diversity than an order of mammals

57 Figure 26.3 Domain: Bacteria Kingdom: Animalia Domain: Eukarya Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Domain: Archaea Phylum: Chordata

58 Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees

59 Figure 26.4 Order Family Genus Species Carnivora Felidae Mustelidae Panthera Taxidea Lutra Panthera pardus (leopard) Taxidea taxus (American badger) Lutra lutra (European otter) Canidae Canis Canis latrans (coyote) Canis lupus (gray wolf)

60 Linnaean classification and phylogeny can differ from each other Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents

61 A phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point represents the divergence of two species Sister taxa are groups that share an immediate common ancestor

62 A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree A basal taxon diverges early in the history of a group and originates near the common ancestor of the group A polytomy is a branch from which more than two groups emerge

63 What We Can and Cannot Learn from Phylogenetic Trees Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage It should not be assumed that a taxon evolved from the taxon next to it

64 Concept 26.2: Phylogenies are inferred from morphological and molecular data To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms

65 Morphological and Molecular Homologies Phenotypic and genetic similarities due to shared ancestry are called homologies Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

66 Sorting Homology from Analogy When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution

67 Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

68 Figure 26.7

69 Bat and bird wings are homologous as forelimbs, but analogous as functional wings Analogous structures or molecular sequences that evolved independently are also called homoplasies Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity The more complex two similar structures are, the more likely it is that they are homologous

70 Evaluating Molecular Homologies Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

71 Figure

72 Figure Insertion Deletion

73 Figure Insertion Deletion 3 1 2

74 Figure Insertion Deletion

75 It is also important to distinguish homology from analogy in molecular similarities Mathematical tools help to identify molecular homoplasies, or coincidences Molecular systematics uses DNA and other molecular data to determine evolutionary relationships

76 Figure 26.9

77 Concept 26.3: Shared characters are used to construct phylogenetic trees Once homologous characters have been identified, they can be used to infer a phylogeny

78 Cladistics Cladistics groups organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants Clades can be nested in larger clades, but not all groupings of organisms qualify as clades

79 A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

80 Figure (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A A A B C Group B C B C Group D D D E E Group E F F F G G G

81 Figure 26.10a (a) Monophyletic group (clade) A B Group C D E F G

82 A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

83 Figure 26.10b (b) Paraphyletic group A B C D E Group F G

84 A polyphyletic grouping consists of various species with different ancestors

85 Figure 26.10c (c) Polyphyletic group A B C Group D E F G

86 Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organism has both shared and different characteristics

87 A shared ancestral character is a character that originated in an ancestor of the taxon A shared derived character is an evolutionary novelty unique to a particular clade A character can be both ancestral and derived, depending on the context

88 Inferring Phylogenies Using Derived Characters When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

89 Figure CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amnion Lancelet (outgroup) Lamprey TAXA Bass Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey Bass Frog Turtle Hair Amnion Hair Leopard (a) Character table (b) Phylogenetic tree

90 Figure 26.11a TAXA Lancelet (outgroup) Lamprey Bass Frog Turtle Leopard Vertebral column (backbone) CHARACTERS Hinged jaws Four walking legs Amnion Hair (a) Character table

91 Figure 26.11b Lancelet (outgroup) Lamprey Vertebral column Hinged jaws Bass Frog Four walking legs Turtle (b) Phylogenetic tree Amnion Hair Leopard

92 An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied The outgroup is a group that has diverged before the ingroup Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics

93 Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor

94 Phylogenetic Trees with Proportional Branch Lengths In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage

95 Figure Drosophila Lancelet Frog Zebrafish Chicken Human Mouse

96 In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record

97 Figure Drosophila Lancelet Zebrafish Frog Chicken Human PALEOZOIC MESOZOIC Millions of years ago CENOZOIC Present Mouse

98 Maximum Parsimony and Maximum Likelihood Systematists can never be sure of finding the best tree in a large data set They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood

99 Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely 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

100 Figure Human Mushroom Tulip Human 0 30% 40% Mushroom 0 40% Tulip 0 (a) Percentage differences between sequences 15% 5% 5% 15% 15% 10% 20% 25% Tree 1: More likely (b) Comparison of possible trees Tree 2: Less likely

101 Computer programs are used to search for trees that are parsimonious and likely

102 Figure TECHNIQUE 1 Species Species Species Three phylogenetic hypotheses: 2 Species Species Species Ancestral sequence Site C T A T C A A T G G T A T C C T 3 1/C 1/C 1/C 1/C 1/C 4 2/T 3/A 3/A 2/T 4/C 3/A 4/C 3/A4/C 4/C 2/T4/C 2/T 2/T3/A RESULTS 6 events 7 events 7 events

103 Figure 26.15a TECHNIQUE Species Species Species 1 Three phylogenetic hypotheses:

104 Figure 26.15b TECHNIQUE 2 Species Species Species Ancestral sequence Site C C A A T T G G A T A T T C C T

105 Figure 26.15c TECHNIQUE 3 1/C 1/C 1/C 1/C 1/C 4 2/T 3/A 3/A 2/T 4/C 3/A 4/C 3/A4/C 4/C 2/T 4/C 2/T 2/T 3/A RESULTS 6 events 7 events 7 events

106 Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs

107 Figure Lizards and snakes Crocodilians Common ancestor of crocodilians, dinosaurs, and birds Ornithischian dinosaurs Saurischian dinosaurs Birds

108 Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding These characteristics likely evolved in a common ancestor and were shared by all of its descendents, including dinosaurs The fossil record supports nest building and brooding in dinosaurs Animation: The Geologic Record

109 Figure Front limb Hind limb Eggs (a) Fossil remains of Oviraptor and eggs (b) Artist s reconstruction of the dinosaur s posture based on the fossil findings

110 Concept 26.4: An organism s evolutionary history is documented in its genome Comparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms evolutionary history DNA that codes for rrna changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago mtdna evolves rapidly and can be used to explore recent evolutionary events

111 Gene Duplications and Gene Families Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes Repeated gene duplications result in gene families Like homologous genes, duplicated genes can be traced to a common ancestor

112 Orthologous genes are found in a single copy in the genome and are homologous between species They can diverge only after speciation occurs

113 Figure Formation of orthologous genes: a product of speciation Ancestral gene Formation of paralogous genes: within a species Ancestral gene Ancestral species Species C Speciation with divergence of gene Gene duplication and divergence Orthologous genes Paralogous genes Species A Species B Species C after many generations

114 Paralogous genes result from gene duplication, so are found in more than one copy in the genome They can diverge within the clade that carries them and often evolve new functions

115 Genome Evolution Orthologous genes are widespread and extend across many widely varied species For example, humans and mice diverged about 65 million years ago, and 99% of our genes are orthologous

116 Gene number and the complexity of an organism are not strongly linked For example, humans have only four times as many genes as yeast, a single-celled eukaryote Genes in complex organisms appear to be very versatile, and each gene can perform many functions

117 Concept 26.5: Molecular clocks help track evolutionary time To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

118 Molecular Clocks A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated

119 Molecular clocks are calibrated against branches whose dates are known from the fossil record Individual genes vary in how clocklike they are

120 Figure Number of mutations Divergence time (millions of years)

121 Problems with Molecular Clocks The molecular clock does not run as smoothly as neutral theory predicts Irregularities result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty The use of multiple genes may improve estimates

122 Applying a Molecular Clock: The Origin of HIV Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates HIV spread to humans more than once Comparison of HIV samples shows that the virus evolved in a very clocklike way Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

123 Figure Index of base changes between HIV gene sequences HIV Range Adjusted best-fit line (accounts for uncertain dates of HIV sequences) Year

124 Concept 26.6: New information continues to revise our understanding of the tree of life Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics

125 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 The three-domain system is supported by data from many sequenced genomes Animation: Classification Schemes

126 Figure Eukarya Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Cellular slime molds Amoebas Animals Fungi Euglena Trypanosomes Leishmania Thermophiles Sulfolobus Green nonsulfur bacteria (Mitochondrion) Spirochetes Halophiles Methanobacterium Archaea COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria Chlamydia Cyanobacteria (Plastids, including chloroplasts) Bacteria

127 A Simple Tree of All Life The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria The tree of life is based largely on rrna genes, as these have evolved slowly

128 There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Horizontal gene transfer complicates efforts to build a tree of life

129 Figure Bacteria Eukarya Archaea Billions of years ago

130 Is the Tree of Life Really a Ring? Some researchers suggest that eukaryotes arose as an fusion between a bacterium and archaean If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

131 Figure Archaea Eukarya Bacteria