BIOL 3300

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BIOL 3300
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2015-10-29 03:25:34
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Evolution biolog midterm
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BIOL 3300 - Evolutionary Biology midterm
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  1. Biological diversity
    • Enormous variation in morphology and ecology
    • This diversity is ordered: Groups of similar ind. (species); species may be similar or very distinct -> classification
  2. Interpretations of diversity:
    Special creation
    • Species were created recently (4004 B.C.)
    • Species are unchanging
    • variation = imperfection
    • (Linnaean classification)
  3. Interpretation of diversity:
    Evolution
    • Living species arose from a common ancestor over millions of years
    • Species have been modified (evolved) through time
    • variation = opportunity
  4. Evolution: Descent with modification
    Anagenesis
    Cladogenesis
    • Anagenesis = change through time
    • Cladogenesis = (speciation) from common ancestor
  5. Evolution - the beginning
    • Proposed in late 1700's - early 1800's 
    • - Comte du Buffon
    • - Jean-Baptiste Lamarck
    • - Eramus Darwin

    No compelling mechanism
  6. Evolution important people
    • C. Darwin, A.R. Wallace, 1858
    • C. Darwin: Origin of species, 1859

    • Volume of evidence
    • Natural selection as mechanism

    Darwin introduced the metaphor of the "Tree of Life"
  7. Evolutionary Biology (Futuyma 1998)
    Two grand questions
    • What are the causes of evolution?
    • What has been the history of life?
  8. Popular perceptions
    • Fact of evolution widely accepted
    • Human evolutionary past often invoked to explain modern human behaviour or physical ailments
    • - Feet, back, or knee problems
    • - Obesity
    • - Type 2 diabetes

    • Extreme is the "paleofantasy" perspective:
    • - Modern humans evolved in Paleolithic (2.6 mya - 12,000 ya)
    • - Cultural chance has since outpaced evolutionary change, leading to a "gene-culture mismatch"
    • - e.g. sugar cravings
  9. Popular perceptions: Paleosolutions
    Anagenesis and stasis
    • Run barefoot; eat raw food; and cut out wheat
    • ...But how much evolution since Paleolithic

    • stasis = stability through time
    • Anagenesis = change through time
  10. L2 Evidence for evolution
    • Micro-evolution - changes within species
    • Speciation
    • macro-evolution - large evolutionary change, usually between genera or higher order taxa
    • Common ancestry
  11. Micro-evolution
    • Domesticated species e.g. dogs
    • Natural or artificial selection experiments e.g. Mice selected for breeding based on distance ran on exercise wheel
    • Microbial evolution: antibiotic/pesticide resistance; host switches (1918 influenza epidemic H1N1), evolution within hosts (HIV)
  12. Micro-evolution of HIV - human immunodeficiency virus
    • Several strains of HIV-1
    • Each originated from a chimpanzee
    • Group M (most common strain) transfer was ca. 1930
    • HIV-1 group M has diverged rapidly since transfer (hinders vaccine development:
    • HIV also evolves within hosts (leads to collapse of immune systems)
  13. Other evidence of micro-evolution
    • Vestigial organs
    • eyes in cave fish
    • limbs in snakes
    • wings in flightless birds
    • tailbone in humans
  14. Speciation and ring species
    • Cladogenesis: from common ancestor
    • in action. Adjacent populations of the salamander look similar and mate with one another — but where the two ends of the loop overlap in Southern California, the two populations look quite different and behave as distinct species. The idea is that this continuum of salamanders — called a ring species — represents the evolutionary history of the lineage as it split into two.
    • e.g. ring species:
    • Greenish warbler
    • Gulls across northern hemisphere
    • Salamander
  15. Macro-evolution
    large phenotypic change usually between genera or higher order taxa
  16. Macro-evolution 3#
    • Extinct species
    • Law of succession
    • Transitional forms
  17. Macro-evolution (Paleontology)
    Extinct species: dinosaurs, pleiostocene megafauna

    George Curvier: Listed 23 extinct species in 1801. Proved Irish Elk extinct in 1812
  18. Macro-evolution - Law of succession
    Fossil and living organisms from the same region are related, and are distinct from those in other regions
  19. Macro-evolution: Transitional forms
    • Dinosaurs -> birds (Archaeopteryx)
    • Land mammals -> whales (Basilosaurus, Dorudon)
    • Ferns -> seed plants (Archaeopteris)
  20. Evidence of Common ancestry
    • Biogeography: similar species in geographic proximity
    • e.g. Galapagos' finches; birds of paradise (New Guinea); honeycreepers (Hawaii), silverswords and tarweeds, Hawaii; and anole lizards Carribean
    • Biogeography: different groups fill same niche on different continents 
    • e.g. Cactaceae - New World; Euphorbiaceae - Old World
    • Homology = similarity in form, despite difference in function, similarity due to common ancestry
    • Evidence from: morphology, embryology, molecular biology
  21. Homology in molecular biology
    • genetic code
    • gene sequences
    • biochemical pathways

    -> utility of model organisms
  22. L3 History of Evolutionary Theory: Theory of Natural Selection 5#
    • 1. Significance and necessary conditions
    • 2. Fitness
    • 3. Examples (polymorphic and continuous traits)
    • 4. Properties of natural selection
    • 5. Conceptual changes
  23. 1a Significance
    • 2 major hypotheses in the Origin of Species
    • Provided organizing principles for biology
    • "Nothing in biology makes sense, except in the light of evolution" Dobzhansky
  24. Conditions for evolution by natural selection:
    • Variation in phenotypes
    • Inheritance of variation
    • Variation in fitness
    • Association between phenotype and fitness
    • --> Testable hypothese
  25. Darwinian Fitness
    Major components
    • Survival (viability)
    • Number of offspring (fecundity)
    • Fitness = viability x fecundity
    • Fitness = lifetime contribution of genes to next generation
    • Relative measure
  26. Darwinian Fitness
    • Malthus and reproduction
    • Every organism produces:
    • more gametes than offspring
    • more offspring than survive ("Struggle for survival")
    • Small variations in phenotypes may affect survival and reproduction
  27. Fitness (sub) components
    • 1. Viability
    • 2. Mating success
    • 3. Gamete number and quality
    • 4. Fertilization success
  28. 3a Evolution of polymorphic traits (discrete phenotypes)
    • -> shifts in trait distribution between generations
    • e.g. white and yellow snapdragons
  29. 3b Continuous traits
    • -> Shifts in trait distributions between generations
    • e.g. Galapagos finches
  30. 4 Properties of natural selection
    • 1) acts on individuals, affects populations
    • 2) acts on phenotypes, changes allele freq.
    • 3) is not random, but not progressive/goal directed (e.g. no higher vs lower forms)
    • 4) existing variants + new mutants -> novel phenotypes
    • e.g. the blind watchmaker and the vertebrate eye
    • 5) not perfect e.g. bipedalism in humans
    • 6: acts on individuals, not for the good of the species
  31. 5. Conceptual changes with Darwinism
    • Tree thinking
    • Population thinking:
    • Variation = opportunity
    • Small changes accumulate to generate large scale patterns
  32. 6. Conceptual changes
    • Natural selection explains speciation, change within species and extinction
    • Speciation is gradual:
    • Varieties -> subspecies -> species
    • Difficulty in species definitions explained
  33. L4 Why Darwin?
    • Naturalist
    • Theoretical leanings - geology, math
    • Experimentalist - breeding pigeons, measuring survival in birds
    • Right time (age of exploration), right place
  34. The path to an idea
    • Fact 1: Potential exponential increase of populations (Paley, Mathus, and others)
    • Fact 2: Stability of populations (universal observations)
    • Fact 3: Limited resources (obsevations, Mathus)
    • Leads to:
    • - Inference 1: Struggle for existence (Mathus)
    • - Fact 4: Uniqueness of individual (breeders, taxonomists)
    • - Facts 5: Heritability of individual (breeders)
    • Leads to:
    • Inference 2: Differential survival (Darwin)
    • Inference 3: Evolution (Darwin)
  35. Five sub-theories in The Origin of Species
    • Evolution
    • Common descent
    • Multiplication of species
    • Gradualism
    • Natural Selection
    • (Increasing controversy)
  36. 2. Controversy about Natural Selection
    • a) Religious beliefs
    • 1constant world
    • 2unique position of man
    • 3created world
    • 4wise and benign creator
    • (first two refuted by fossil record, homology, the realization the earth changes (tetonic plates))
    • b) Secular beliefs
    • Essentialism
    • Physics envy
    • Teleology
    • Political ideology
  37. Controversy (Politics)
    • Nazi Germany: 
    • Favoured Eugenics
    • Firm belief in teleology
    • Pre-soviet Russia a leader in genetics
    • Stalin and communist leaders:
    • Denounced and jailed geneticists
    • Based agricultural policies in Russia and China on Lamarckian beliefs
  38. Controversy (Politics) - Why do genetics and natural selection conflict with communist ideals?
    • Nikolai Vavilov, bourgeois geneticist
    • Established worlds first seed bank (1920s)
    • President, international Congress of Genetics 1939
    • Youngest member of USSR academy of Science
    • Died in prison, 1945

    • Crop breeding under Comrade Lysenko
    • Used Lamarckian logic to breed for cold tolerance and fudged data
    • Disastrous crop improvement programs
    • Crop failures, food shortages, and starvation in USSR and China
  39. Controversy
    • Missing/incorrect Data
    • Origin of variation
    • inheritance of variation, particularly for continuous traits
    • age of earth
  40. Alternatives to NS
    • a) Neo-lamarckism
    • combined elements of NS and lamarckism
    • "soft" inheritance
    • very widespread
    • (even Darwin)
  41. Alternative #2
    • b) Orthogenesis
    • mostly paleontologists
    • variation internally generated
    • fixed direction of change
    • could explain extinct forms
  42. Alternative #3
    • c)Mutationism
    • 1900 Mendel's work rediscovered
    • spontaneous variants defined as mutants
    • discrete variation
    • mutations of large effects
    • *(last two points = define new species)

    Richard Goldschmidt: Hopeful monster also known as the hopeful monsters hypothesis is a biological theory which suggests that major evolutionary transformations have occured in large leaps between species due to macromutations.
  43. 4. Foundations for consensus
    1900-1030's
    • a) "Hard" inheritance
    • - Mendel
    • - Weismann: mousetails (separation of germ-line and soma cells)
    • b) Revised calculationsof the earth's age
    • c) Contributions by geneticists
    • Chromosomal recombination
    • most mutations of small effect
    • inheritance of continuous (polygenic) traits
    • theory of population genetics
    • d) Contributions by "naturalists"
    • systematics and paleontology
    • macro-evolutionary patterns in the fossil record
    • geographic variation among populations
    • individual variation within populations
  44. Evolutionary Synthesis
    1930's - 40s
    • "Second Darwinian revolution"
    • Mutual education between geneticists and naturalists
    • T. Dobzhansky:
    • - Drosophila genetics and cytology at Cal. Tech.
    • - genetic variants in wild pop.
    • - ardent naturalist
    • - familiar with population genetic theory
  45. Synthesis
    • Jessup lectures, Columbia University -> 4 books
    • Incorporated mathematical theory of population genetics - Fisher, Haldane, Wright
    • Genetics, natural selection, and chance events combine to cause adaptive evolution
    • data from many different fields
    • 1946
    • - Society for scientific exploration (SSE) founded
    • --> Journal "Evolution"
  46. Phylogeny
    evolutionary history of a species or group of species
  47. Why is phylogeny important?
    • 1. Useful for classification
    • For manageability
    • To convey info
    • Helps us organize and communicate info about millions of sp.
    • Helps us predict properties of organisms (e.g. according to properties of closest relatives)

    • 2. Helps us elucidate mechanisms of evolution
    • Look at evolution of traits in phylogenetic context
    • To see way in which characters change over time (e.g. direction and frequency of change)
    • - e.g. secondary return of aquatic habitats in vertebrates
    • - e.g. loss of limbsoccurring independently in multiple vertebrate lineages
  48. Species grouped hierarchically
    • Nested into more and more inclusive taxa
    • Higher levels of classification more inclusive
    • Lower levels more exclusive
  49. Binomial nomenclature
    scientific naming of species, standardized by Linnaeaus
  50. Taxon
    named taxonomic unit at any level 

    Classification should reflect degree of relatedness = how recently they last shared an ancestor
  51. Phylogenetic trees show...
    relative order of branching since common ancestors

    Evolutionary relationships defined by how recently taxa last shared a common ancestor (not necessarily how similar they appear)
  52. Sister taxa
    each other's closest relatives: shared an ancestor most recently
  53. Evolutionary trees are hypotheses
    • Evolutionary history rarely directly observed
    • We can only estimate or infer evolutionary history using "clue" left behind
    • If classification intended to reflect evolutionary relationships
    • Classifications will change as hypotheses re" these relationships change (e.g. WHIPPO)
    • Branching order hypothesized based on inferences re: order in which evolutionary modifications (transitions) occurred
  54. Logic of inferring evol. trees
    • Descent with modification from a common ancestor
    • Modifications = evolutionary novelties = derived characters
    • Infer evolutionary history of a group of species from nested sets of shared evolutionary innovations = synapomorphies
  55. Apomorphy
    evolutionary innovation = derived character
  56. Plesiomorphy
    Pre-existing or ancestral character
  57. Synapomorphy
    shared derived character

    Presence of synapomorphies (rather than retention of ancestral characters) tells us about branch order
  58. Cladistics
    hierarchical classification of species based on evolutionary ancestry
  59. Clade
    monophyletic group = an ancestor and all of its descendants
  60. Monophyly
    • Cladistics recognizes only taxonomic groups that are monophyletic
    • Where same ancestor gives rise to all species in that taxon and to no species in any other taxon
  61. Polyphyletic taxa
    Members are derived from two or more distantly related lineages (excluding their common ancestor)
  62. Paraphyletic taxa
    Which include common ancestor but don't include all descendants of this ancestor
  63. Polytomy or polychotomy
    nodes where lineage splits into more than two descendant lineages simultaneously

    Either because evolutionary relationships cannot be fully resolved to dichotomies (due to insufficient information)

    Or maybe because of an adaptive radiation = an event in which an ancestor gave rise to more than two daughter species at the same time
  64. Phylogeny inference in non-ideal cases
    • 1.Characteristics of common ancestor often unknown
    • 2.Similar characteristics sometimes evolve independently indifferent lineages (convergent evolution)
    • 3. Sometimes evolutionary novelties secondarily load (reversals)

    • Use out group anaylsis to infer charcteristics of common ancestor
    • Use multiple characters and parsimony analysis to distinguish homology from homoplasy
  65. Outgroup analysis
    • To identify synapomorphies, we have to know what is ancestral (plesiomorphic) and what is derived (apomorphic)
    • i.e. direction of change or polarity
    • In some cases,we may know from:
    • * Fossil record - e.g. leglessness in whales is derived
    • * Embryological studies - e.g. 2 humps in camels is ancestral

    Or by comparing to character state in outgroup
  66. Outgroup
    Species that branched off earlier from taxa being compared (ingroup)

    • Therefore involves "borrowing conclusions" from other phylogenetic analyses
    • Use uncontroversial outgroup
    • Close enough to allow inference from sequence or trait data

    Assumes no evolutionary change in outgroup's lineage since divergence with ingroup
  67. Convergence and Reversal
    • Only homologous characters (likeness due to shared ancestry) say something meaningful about evolutionary history
    • Similar characters that evolved independently (i.e. are homoplasious) would be misleading
  68. Causes of homoplasy
    • Similar characters evolve independently ("convergently" or"in parallel") in separate lineages
    • Evolutionary reversal

    Independent evolution of trait - i.e., not indicative of ancestry
  69. Homologies are thus:
    • hypotheses about the singular evolutionary origin of certain similarities
    • Not always obvious - e.g. identical skin toxin caerulein produced by both magnificant tree frog and African clawed frog encoded by different genes
    • Convergence can lead to misleading inference, if homoplasies are undetected
    • And pronounced adaptation and modification can obscure homologies - e.g. Homology of ear ossicles of mammals and jaw elements of reptiles
  70. How do we distinguish homology from homoplasy?
    • 1. Comparative embryology
    • - Before extensive modification during subsequent development obscures homologies
    • e.g. Gill pouches - become Eustachian tubes in humans
    • 2. Fossil record
    • - Transitional fossils linking past and present
    • e.g. Homology between mammalian ear ossicles and jaw elements of reptiles
    • e.g. Whale fossils with hindlimbs demonstrate that body shape in whales and sharks homoplasious
    • - Fossils also useful for determining ages of taxa and polarity of characters states
    • 3. Agreement with other phylogenetic hypotheses
    • - Homoplasy rather than homology if "stronger" evidence indicates groups are not sister taxa
  71. Agreement with other phylogenetic hypotheses
    • a) Number of features
    • - Inconsistent character most likely homoplasious
    • - Assume that the most parsimonious trees = those using fewest changes to illustrate evolutionary relationships
    • Are most likely to be correct

    • b) Complexity of features
    • - If two similar structures are very complex
    • - And match in so many details
    • - It is unlikely that they evolved independently
    • - And gain of similar complex traits more unlikely than loss
    • - Complex characters may be given more weight
    • - Important to use multiple characters in phylogeny reconstruction
  72. L7 Characters used in phylogeny reconstruction
    • Morphological characters
    • Comparative physiology, histology, or ethology
    • Molecular characters
  73. Morphological characters
    • In animals, outer form and inner structure, such as:
    • Number, structure and position of bones in vert. forelimb, skull
    • Number and shape of teeth
    • Presence or absence of feathers
    • Number of Chambers in heart, number of aortic arches
    • Presence or absence of placenta
    • Presence or absence of ruminant stomach

    In plants, leaf venation, pollen structure, arrangement of sepals, petals, bracts, cone scales, etc.
  74. Comparative physiology, histology, or ethology
    • e.g. Body temperature regulation
    • e.g. Cellular types and organization
    • e.g. Animal social systems
  75. Character and character states
    • Character = structure or feature
    • Character states = variant conditions of the character
    • e.g. character = toe number
    • character stsate = 5(human) or 3 (guinea pigs)
    • Character = leaf venation
    • Character state = parallel or net veined
  76. Molecular characters
    • Molecular data (e.g. nucleic acids, proteins)
    • Mutations accumulate as species diverge
    • DNA "document of evolutionary history"
    • - Most sensitive, especially among closely-related taxa
    • - Includes silent mutations that would not result in any phenotypic change
    • Although observed DNA sequence differences aren't necessarily basis of phenotypic differences = neutral genetic markers
    • Independent indicator of common ancestry
  77. DNA
    • Made up of 4 nucleotides or base pairs: A,C,G,T
    • Some regions (genes) code for proteins (e.g. subunits of hemoglobin, various enzymes)
    • But many regions do not (e.g. rRNA, introns, 'junk' DNA;)
    • Difference in sequence referred to as substitutions
  78. Genes are translated into proteins using the genetic code
    • DNA transcribed into mRNA (where U replaces T)
    • Translated into proteins at ribosomes using genetic code
    • Nucleotides grouped into triplets called codons
    • 'Degenerate' genetic code = 64 codons for only 20 amino acids
    • Multiple codons for same amino acid
    • Permits mutations (at 3rd, and sometimes 1st positions)
    • They are 'silent" or 'synonymous'. 
  79. Genome
    • the whole hereditary information of an organism that is encoded in the DNA (gene + chromosome)
    • Includes genes and noncoding sequences
  80. Types of DNA used in phylogeny reconstruction
    • Nuclear genome
    • Chloroplast Genome
    • Mitochondrial genome
  81. Nuclear genome
    • DNA in the nucleus on chromosomes
    • Inherited from both parents
    • Approximately 3.2 billion bp in humans
    • Encodes most traits that vary among taxa
  82. But Nuclear DNA
    • Is large and complex in eukaryotes
    • Complete genomes being sequenced in dozens of model organism
    • But annotation (identifying actual gene regions) only starting
    • Gene content varies considerably
    • Contains large amount of noncoding DNA
    • Not easy to work with (sequence genes, interpret results) in non model organisms
  83. Chloroplast genome
    • In cytoplasm of plants and protists
    • Chloroplast thought to have originated as endosymbiotic cyanobacteria
    • Own small genome, originally bacterial genome
    • Reduced in size compared to free-living cyanobacteria
    • Approximaely 120-217 kb (vs. 1.7-4.7 Mb in most cyanobacteria)
    • But still clear similarities (circular, gene sequence) 
    • Many 'missing' genes now in nucleus
  84. Mitochondrial genome
    • In cytoplasm of most eukaryotes
    • Also derived from endosymbiotic bacteria
    • Own circular genome
    • And with own 'machinery' for protein synthesis (ribosomes, tRNAs)
    • Which uses different genetic code than nuclear genome (some codons resemble those of purple nonsulfur)
  85. Mitochondrial gnome very compact
    • Approx. 16-17 kb in vertebrates
    • Contains very little noncoding DNA
    • - Many genes transferred to nucleus, no longer self-sufficient
    • Gene content and gene order of remaining genes highly conserved
    • But bigger (e.g. 196 kb in common liverwort) and more variable in plants
  86. mtDNA consists of?
    • a) 13 protein-coding genes
    • - Enzymes involved in oxidative phosphorylation
    • e.g. cytochrome b
    • e.g. cytochrome c oxidase subunits I, II, and III

    • b) 22 tRNAs 
    • Code for RNA (74-93 bp) that transfers amino acids during translation
    • But not protein-coding
    • Not 'junk' DNA
    • RNA used directly, not translated into amino acids using triplet genetic code

    • c) 2 rRNAs
    • 12S and 16S ribosomal RNA
    • Small and large subunits of mitochondrial ribosomes

    • d) Control region
    • D-loop, displacement loop, origin of replication
  87. Advantages of mtDNA
    • a)Well-characterized in 1000s of organisms
    • b) mtDNA evolves rapidly
  88. a) Well-characterized in 1000s of organisms
    • Permits design of conserved primers that amplify and sequence homologous regions in wide range of taxa
    • Using PCR, polymerase chain reaction
    • Amplifies millionfold any stretch of DNA that is flanked by synthetic oligonucleotide primers
    • Only limitation is that DNA sequence of flanking region must be known to design primers
  89. b) mtDNA evolves rapidly
    • Often allowing even recently-diverged species to be distinguished
    • DNA 'barcoding' project
    • Generally evolves 5-10 times faster than single-copy nuclear genes
    • 1000s mitochondria per cell
    • Less stringent proofreading required during transcription
  90. c) And some regions more or less conserved than others
    • Conserved regions for comparing distantly-related species
    • Rapidly evolving regions for recently-diverged taxa

    • e.g. protein-coding genes
    • Less variable than D-loop
    • But much easier to align!
  91. Disadvantages of mtDNA
    • a) Maternally inherited without recombination
    • b) Represents very small portion of organism's genome
  92. Maternally inherited without recombination
    • Cytoplasm from egg only
    • Not combined genetic information about maternal and paternal lineages
    • Problem detecting hybridization using mtDNA alone 
    • Divergent mtDNA sequences even if introgression in nuclear genome
    • But when used with nuclear DNA, can tell you direction of hybridization (which species was the mother)
    • Therefore, mtDNA haploid
    • Different mtDNA sequences = different haplotypes (equivalent to 'alleles')
  93. Represents very small portion of organism's genome
    • Difference in mtDNA rarely actual cause of phenotypic differences
    • But 'neutral' indicator that species have diverged
    • Degree to which mt genome of two organisms differ is an independent measure of their evolutionary distance
  94. A) Homology still essential with molecular characters
    • i) Same gene
    • Some genes similar (e.g. from same gene family)
    • Especially in taxa with polyploidization in history
    • Conserved primers may not always amplify homologous genes
    • And sometimes similar "pseudogenes"
    • e.g. "Numts" (nuclear copies of mitochondrial genes)
    • ii)Same gene position Must align sequence to make sure comparing same position of each gene Using programs such as ClustalW
  95. Aligning protein-coding regions
    Due to 3-nucleotide codons, insertions or deletions must be in multiples of 3 to maintain reading frame
  96. Aligning non-protein coding sequences
    e.g. D-loop (displacement loop, control region) Indels of any number of bases More variable Therefore, especially good for intraspecific comparisons But sequences among distantly-related taxa can be so different, no match looks good
  97. B) Character state must be homologous
    Same nucleotide at given position due to descent from common ancestor Or convergent evolution? E.g. independent mutations in divergent lineages just happened to both produce a C or T at a particular site?

    Only 4 character states (nucleotides)

    • Good chance that independent mutations will occur
    • And multiple substitutions at same site: Therefore, distinguish homology from homoplasy by "preponderance of evidence"
  98. Preponderance of evidence
    Compare large number of characters (sites): Wouldn't base conclusions on similarities or differences at only a few sites Consider "complexity" of characters:  Some mutations more common than others (=less complex morphological traits) e.g. transitions and third-position mutations Receive less weight Most common substitutions lose their phylogenetic signal at saturation
  99. 2nd position substitutions uncommon
    e.g. in cytochrome b, 1:2:3 position substitutions occur 10:1:33 ratio Same 2nd codon position substitution less likely to have arisen independently
  100. Growing literature re: evolution of DNA
    • -Models, computer programs meant to improve objectivity of molecular phylogenetic analysis
    • -e.g. Kimura's two-parameter model  -Corrects for multiple substitutions at the same time
    • -And differences in frequency of transitions to transversions
  101. e.g. in MEGA
    • Closely-related species
    • - Nucleotide difference = 16/924 = 1.73%
    • - K2P = 1.76% K2P
    • More distantly-related species
    • - Nucleotide difference = 144/924 = 15.58%
    • - K2P = 17.67%K2P

    • Multiple substitutions at same site increase with time since divergence due to convergent evolution and reversals
    • Difference between sequences saturates at approx. 75%
  102. L8 Parsimony Analysis
    Looking for the simplest evolutionary scenario that can explain distribution of character states in descendant species (i.e., the fewest number of evolutionary changes)
  103. Tree-building approaches
    A. Phenetic Approach
    • Estimates taxonomic affinities from overall
    • similarity
    • Compares as many characters as possible
    • With no weighting or phylogenetic assumptions (e.g., regarding homology or polarity of character states)
    • Assumes that contribution of homology to overall similarity should be swamped by degree of homology if enough characters compared

    • But critics argue that overall similarity not reliable index of relatedness
    • More closely related if shared ancestor more recently
  104. Neighbour-joining method
    • e.g. using Kimura's 2-parameter model
    • Length of branch indicates genetic distance
    • Distance method
    • Represents phenetic approach
    • Clusters taxa so that themost similar forms are grouped together
    • Rooting with outgroup can allow inferences about direction of change
    • Many possible trees but preferred one minimizes the total distance among taxa
    • Not the most accurate method, but reasonably good, and has advantage of being fast, even with large data sets
  105. Cladistic approah
    • Argues that degree of relatedness ≠degree of similarity
    • Classifies organisms according to order that branches arose along a dichotomous phylogenetic tree

    • Parsimony analysis of synapomorphies determines which phylogeny would require fewest changes to illustrate evolutionary relationships
    • Therefore, only shared, derived characters (synapomorphies) are informative
    • Parsimony informative characters are shared by two or more taxa
    • Characters unique to one lineage are parsimony uniformative
  106. Parsimony analysis
    • Need outgroup to identify synapomorphies
    • i.e. to know what is ancestral (plesiomorphic) and what is derived (apomorphic)

    • Only branch order important
    • Length of branch not important
    • Trees dichtomous

    • e.g. Maximum parsimony analysis in MEGA
    • Computerprograms compare all possible trees
    • Computationally more challenging than Neighbour joining tree
    • Even with 8 species, more than 10,000 possible trees
  107. Evaluating reliability of the trees
    • How much confidence should we place in any particular branch point?
    • Evalutae statistically using bootstrapping

    • Builds replicate trees by creating new data sets from existing one by repeated sampling ("pseudoreplication")
    • Generates artificial data sets by random sampling, with replacement, from the ctual data set
    • e.g. if 300 bp in sequence, randomly selects one site and uses it
    • as first entry in new data set
    • Randomly selects second site etc., up to 300 sites
  108. Bootstrapping
    • New sequence random subset of original
    • Used to estimate phylogeny
    • Repeated 1000 times
    • i.e. 1000 different trees built with differnt subset of data

    • Generates consensus tree indicating in what percentage of the trees each particular branch occurred
    • If results are being biased by a few nucleotide sites, branch values will be low
  109. Molecular clocks
    • Can the rate at which DNA mutations accumulate be used to date when major events occurred?
    • e.g. when two taxa diverged (i.e. last shared an ancestor) based on degree of genetic differentiation between them

    • Yes: if we can calibrate this 'molecular clock'
    • Measure geneti distance between two taxa whose divergence is known from:
    •  Fossil record
    • Geological record e.g. divergence between marine organisms on wither side of Isthmus of Panama
  110. Molecular clock with mito genome
    • Brown et al. - estimated 2% sequence divergence per million years in mammals using fossil record across mt genome
    • Bermingham and Lessios - estimated divergence in sister species of sea urchins found on either side of Isthmus of Panama (1.8%-2.2% per million years)

    • Similar in butterflies (Brower)
    • And Birds (Shields and Wilson; Weir and Schluter)
  111. But some exception to molecular clock
    Suggestions that mutation rate faster in organisms with: Short generation times; warm-blooded vs. cold-blooded organisms

    • And different rates at which substitutions become fixed lead to differences within mt genome (across genes)
    • - Some genes and gene regions more conserved than others

    • And estimates not necessarily applicable across all time scales (for both closely and distantly related taxa)
    • - e.g. due to saturation
    • - If rate is underestimated, divergence times will be overestimated
  112. L9 Molecular phylogeny inference and the Origin of Whales (Cetaceans)
    • Closest living relative of cetaceans difficult to determine since they are so specialized for aquatic life
    • Relationship  between cetaceans and ungulates, suggested by structure of internal organs and skeletal characters

    • Based on dentitions, perhaps sister group to artiodactyls?
    • Which would make ungulates paraphyletic
    • i.e. whales are in the ungulate clade
  113. Cetacea: Molecular data goes even further
    • Whale (cetaceans) not just within ungulate clade
    • But also within artiodactyl clade
    • Suggests cetaceans are sister taxon to hippos (Gatesy et al.)
    • i.e. that whales are artiodactyls
  114. Whale and hippo hypothesis
    • Suggests that traits of hippos and whales 
    • That were thought to be convergent adaptations for aquatic life (hippo = river horse)
    • Might actually be synapomorphies
  115. How do we resolve these conflicting hypotheses?
    • Additional fossil data:
    • Several synapomorphies identify Artiodactyla as descendants of common ancestor
    • Notably smooth, pulley-shaped astragalus
  116. Living Whales have no ankles!
    • But fossil whales (with hindlimbs) found
    • With pulley-shaped astragalus (Thewissen and Madar, Thewissen et al.)

    In first fossils, not conclusive that ankle bone found didn't belong to some other artiodactyla in same deposit

    • But second, conclusive fossil find
    • Two species where size and shape of ear bones clearly identified them as whales
    • And pulleylike astragalus marked them as artiodactyls
  117. Also additional molecular data
    Presence or absence of homologous SINEs and LINEs (short or long interspersed elements)

    • Convergence unlikely:
    • Unlikely that inserted into two independent host lineages at exactly same location
    • Reversal detectable:
    • When lost, usually lose part of host genome too
    • Therefore, extremely reliable characters(="complex")

    • Support whale and hippo as sister taxa (Nikaido et al.) 
    • Now order Cetartiodactyla generally recognized
  118. Early whales gave birth on land
    • 47.5 million-year-old fossils discovered in Pakistan
    • Male and female of new species (Maiacetus inuus)
    • With four flippers like limbs modified for foot-powered swimming; could support their weight but probably couldn't travel far on land
    • Female with fetus positioned for head-first delivery, like land mammals but unlike modern whales = indicating birth on land
    • Size difference of male and female only moderate - suggesting that males didn't control territories or command harems
    • of females
  119. Rafflesia Giant Flower with fetid odor
    Classified at last
    • 200 year old mystery of world's biggest yuckiest flower solved using molecular phylogeny
    • The Rafflesiaceae have giant blooms, which look and smell like decomposing meat to attract carrion flies that pollinate them
    • Are also parasitic (gaining nutrients from tissue of the tropical grape vine rather than photosynthesis)

    Previously difficult to place phylogenetically because of lack of roots, leaves, and stems

    • Using DNA analysis, found to belong to the Euphorbiaceae family
    • Which includes the rubber tree, castor oil plant, and the cassava schrub
    • They fall in the middle of this group with minute flowers
    • Big, odour flowers likely evolved because these plants occur in dimly-lit tropical rainforest understoreys
    • Davis et al.
  120. Using Phylogenies to answer other questions
    • Can tumor cells move from patient to patient?
    • Canine transmissible venereal tumor (CTVT)
    • Question:
    • a) Are the tumor cells transmitted from dog to dog?
    • b) or is each tumor an obnormal growth of each dog's own cells (caused perhaps by a virus that is transmitted)?

    • If a), genetic analysis will show tumor cells to be monophyletic
    • If b), the dogs and their tumors will each be monophyletic
    • Stong support for (a)
  121. Using Phylogenies to answer other questions - When did humans start wearing clothes?
    • To answer, Kittler et al reasoned thatbody lice (which lives in clothing) arose from head lice around the time humans started wearing clothing
    • Therefore, estimated when body lice arose by estimating genetic distance between body lice and head lice in humans from aroundt the world.
    • - To convert genetic divergence into chronological divergence, needed to "calibrate" molecular clock
    • - Reasoned that head lice that parasitized humans and lice that parasitized chimps diverged when their host species diverged (approx. 5.5 million years ago, according to fossil record) to calculate "conversion factor"
    • Therefore, estimated that body lice (and therefore clothing) originated approx. 72,000 yrs ago
    • Associated with spread of early humans outof Africa?
  122. L10 In theory,species =
    • smallest evolutionarily independent unit
    • Essence of speciation is lack of gene flow
    • Separate gene pools
    • But practical criteria for identifying when populations are evolving independently?
  123. Morphospecies Concept
    • Assumes reproductively isloated populations will accumulate morphological differences
    • But not all differences are species-level differences
    • - Sexual dimorphism
    • - Life cycle differences
    • - Environmental effects
    • - Intraspecific polymorphisms (e.g. eye colout) and polyphenisms (e.g. queen, worker, solder ants)

    • And some species may be cryptic
    • DNA barcoding uncovering many cryptic species
  124. Phylogenetic species concept
    • Species are smallest identifiable units that are diagnostic and monphyletic
    • Many possible monophyletic groups

    • Different criterion than BSC to establish whether lack of gene flow
    • PSC detects species tat have been evolutionarily independent long enough for diagnostic traits to emerge
  125. Advantages of PSC
    • Can be based on numerous characters (not just morphological - but not just genetic characters)
    • Any type of organisms
    • Testable

    Requirement for monophyly means that species that appear similar due to convergent evolution are recognized as separate species (e.g. benthic and limnetic sticklebacks)
  126. BSC
    • Criterion is reproductive isloation
    • Separate species if they do not hybridize regularly in nature or if they fail to prodcue viable fertile offspring whenthey do

    • Widely accepted since Ernst Mayr "championed it" in 1942 e.g. legal definition used in U.S.Endangered Species Act 1973
    • Lack of gene flow "litmus test" for evolutionary independence

    But is demonstration of current reproductive isolation sufficient?
  127. And hybridization between "good" species
    • More common than previously thought
    • - Hard to detect prior to use of genetic methods, especially with backcrossing
    • Many well-known hybrids are generally sterile
    • - But not always (e.g."beefalo")

    • Particularly common in plants (more later)
    • Hybridization in wild often result of anthropogenic change
    • - introduction of non-natives
    • - removal of isolating barriers
    • - range shifts
    • e.g. Hybrid grizzly-polar bears a worrisome sign of the North's changing climate
  128. Biological species concept (BSC)
    • And difficult totest and apply:
    • - In populations that don't co-occur
    • - In fossil forms
    • - Irrelevant in asexual organisms

    • Have to make inferences (based on morphological, genetic, or behavioural differeces) about whether they might be reproductively isolated
    • -> Have to understand causes of reproductive isloation
  129. Comparing species concepts
    1. Copepods

    • Morphologically, single species
    • Molecular phylogeny showed at least 8 species
    • Different phylogenies species unable to produce fertile offspring (even where they overlap in distribution)
    • At least 8 cryptic species by both BSC, PSC

    • 2. Elephants
    • Traditionally African and Asian elephants
    • Two African types (forest and grasslan) but don't interact to test BSC
    • PSC showed them to be distinct species

    3. Cryptic species in marine phytoplankton

    • Diatoms responsible for harmful algal blooms (genus Pseudo-nitzchia)
    • Two morphological species using light microscopy
    • But TEM (transmission electron microscopy) and phylogenetic analysis using DNA sequence data revealed 8 spp.
    • Mating trials agreed

    • Production of neurotoxin during algal blooms variable
    • Perhaps due to different species compositions at different times

    • 4. Cryptic skate species
    • Generally considered single species (common skate)
    • Molecular phylogenetic analysis revealed two distinct species (blue skate and flapper skate)
    • - Which weren't even sister species
    • Further investigation showed species:
    • - Could be morphological distinguished (by tooth shape)
    • - Had different geographicaldistributions
    • Important for conservation purposes
  130. L11 Mechanisms of isolation
    • Classically, speciation in 3 steps:
    • 1. Isolation
    • 2. Divergence
    • 3. Reproductive isolation (RI)
  131. A. Physical isolation as barrier to gene flow
    • a) Allopatric speciation (geographic speciation)
    • Evolutionary independence begins with cessation of gene flow due to physical separation of populations
    • Populations then develop intrinsic genetic differences especially if conditions different on each side of barrier)
    • RI if secondary contact
  132. Geographic isolation through?
    • Dispersal and colonization
    • Vicariance
  133. Geographic isolation through dispersal and colonization
    Divergence begins after the founding event, resulting from genetic drift and natural selection

    • e.g. Hawaiian Drosophila
    • >1000 spp. (Many island endemics)
    • Each island likely founded by small number of individuals or even single gravid female
    • - Genetic drift and natural selection on genes responsible for courtship displays and habitat use
    • Supported by phylogenetic evidence: suggests that islands were colonized in sequence ("island hopping")
  134. Dispersal to and colonization of novel environments
    • Considered general mechanism for initiating speciation
    • Especially in motile animals (or with resting stages)
    • e.g. invasive species in ballast water of ships

    • and plants
    • e.g. small number of seeds to new habitats by wind or water currents or by the feet, feathers, and digestive tracts of birds and other mammals

    Founding by small population of colonists results in drift and selection
  135. Geographic isolation through Vicariance
    • Can be slow process (e.g. rise of moutain range, glaciers) or rapid (e.g. lava flow)
    • - Includes human-caused habitat fragmentation
    • - Whether barrier to gene flow depends on species

    • e.g. Snapping shrimp
    • On either side of isthmus of Panama (Land bridge closed approx. 3 mya)
    • Morphological sister species on either side of isthmus
    • Confirmed phylogenetically (DNA)
    • And mating study showed pairs no longer capable of interbreeding
    • Speciation complete
  136. B. Divergence with Gene flow
    Parapatric speciation

    When a population enters new habitat within range of parent species

    No physical separation between populations (i.e. no extrinsic barrier)

    Instead, speciation results from evolution of other mechanisms that reduce gene flow between populations
  137. Parapatric speciation
    e.g. banded and unbanded water snakes: mainland banded; many on islands unbanded

    • Allopatric speciation if water currents completely prevented migration
    • But parapatric because frequent migration from mainland and hybridization
    • - With selection against banded on islands
    • Outcome dependent on balance between gene flow and selection
    • Speciation most likely in small populations when gene flow is low, selection for divergence is strong (intrinsic barriers)
  138. Sympatric speciation
    • Occurs entirely within range of parent species
    • Therefore, must be intrinsic barriers to gene flow

    (Polyploidy and other chromosome changes as barrier to gene flow; and other mechanisms of isolation)

    • i) Polyploidy and other chromosome changes as barrier to gene flow
    • - Whole genome duplication 
    • - Largest scale of mutation possible
    • Error in meiosis produces diploid (unreduced) gametes
    • Gametes with different chromosome numbers normally incompatible (3N low fertility)
    • Immediate reproductive isolation between parental and daughter populations
  139. Speciation through polyploidization
    • Polyploidy common in plants since capable of self-fertilization
    • 70% angiosperms, 95% ferns with polypoidy in history

    • Polyploidization in animals relatively rare, although self-fertilization and parthenogenesis in many groups
    • e.g. whiptail lizards: polyploidy produced by hybridization between species (allopolyploidy)
    • e.g. Each species may arise independently multiple times
  140. Other changes in chromosomes
    • Not whole genome duplication
    • But any differences in chromosome number still usually prevent formation of fertile offspring

    • e.g. butterfly genus Agrodiaetus
    • Species with chromosome number ranging from 10 to 134
    • - Sympatric species with same number of chromosomes rare, suggesting that differences are important in maintaining isolation

    But unknown whether chromosome differences were initial isolating step or arose after speciation
  141. Other mechanisms of isolation
    Other intrinsic barriers to gene flow in sympatry include temporal reproductive isolation (e.g. differences in flowering time), host or pollinator specilization, or anatomical or behavioural isolation

    • e.g. Japanese winter moth
    • - In N. Japan (where deep snow and extreme cold preclude reproduction in midwinter), one species reproduces late fall/early winter and other reproduces late winter/early spring
    • Species are genetically divergent despite geographic overlap
    • But in S. Japan (where reproduction possible throughout winter), no temporal isolation and single interbreeding population

    • e.g. two species of monkeyflowers: one pollinated by bees, other by hummingbirds
    • - No opportunity for hybridization even where they co-occur

    • e.g. Japanese land snail (genus Euhadra)
    • - Single gene controls whether shell shows left-handed or right-handed coiling
    • - Mutation producing other handedness results in immediate reproductive isolation "due to anatomical reproductive incompatibility
    • - Phylogeny suggests right-handedness has arisen multiple times

    Divergence leading to isolation
  142. Mechanisms of Divergence
    • Natural selection becoming recognized as most important factor promoting divergence
    • Different selection pressures on each population in different habitats, using different resources

    • e.g. Apple and hawthorn maggot flies
    • - Incipient speciation in sympatry
    • - Species first observed on apples in mid-1800s
    • - Host trees occur together and flies search widely for host 
    • - Not morphologically distinct
    • But strong host preference
    • Therefore, assortative mating since they mate on host
  143. Adaptation to different habitats (Ecological Speciation) in Apple and Hawthorn maggot flies
    Divergence just result of genetic drift due to reproductive isolation?

    • Or two "races" exposed to different selection pressures?
    • Evdence suggests selection driven by difference in when fruit from each host ripens
    • - Apples ripen 3-4 weeks before hawthorns
    • - Therefore, still warm when apple fly larvar pupate vs. cool (prewinter) temperature for hawthorn larvae

    Ecological speciation - can be rapid if selection is strong
  144. Mutation followed by rapid selection led to beige mice on sand dunes
    • Deer mice from Sand Hills in Nebraska
    • Light colour coded by a single gene (agouti)
    • Estimated that gene appeared approx. 4,000 years ago (few thousand years after colonization by dark mice)
    • New gene has since become very common
    • Used owl predation experiments to estimate strength of selection pressure: paler mice have 0.5% survival advantage
    • Linnen et al.
  145. Other examples of speciation by natural selection
    • 1. Sticklebacks
    • - Independent armour loss in isolated lakes
    • - Reduced ion availability and lower predation intensity

    Parallel patterns of phenotypic differentiation accompanied by similar ecological shifts suggest that deterministic factors (i.e. natural selection) rather than random processes (e.g. drift, mutation) have been important in shaping diversity in these species

    Likewise, parallel divergence of benthic and limnetic pairs (Rundle et al.)

    • 2. Walking stick insects
    • Unstriped morph more common on host plant with broad leaves
    • Striped morph more common on host with thin, needle-like leaves

    • Predation by birds and lizards
    • Divergence in body size, shape, host preference, behaviour
    • Driven by intense divergent selection for crypsis (Nosil et al.)
    • Not genetic drift

    Assortative mating by-product of ecological selection
  146. Sexual selection
    • Special type of natural selection acting on phenotypes involved in mate choice
    • Assortative mating due to direct mate choice (not by-product of ecological selection)
    • Can contribute to reproductive isolation that may lead to speciation

    • e.g. Hawaiian cricket genus  Laupala
    • - Females choose males of their species based on song pulse rate
    • - Differences important in maintaining RI among 38 species
    • - Genetic basis not known but male song and female preference tightly linked

    • e.g. Cichlids
    • >500 species in Lake Malawi alone
    • Can direct mate choice (based on differences in male colour) prevent interbredding or is RI result of habitat segregation?
    • Yes: complete assortative mating, even in lab
    • Highly significant genetic differences indicate RI

    • In some situations, mating preferences and environmental factors interact
    • In Lake Victoria, where water clarity poor, males of both species have similar colour patterns and are less genetically divergent
  147. L12 hybridization and gene flow between species
    • Two general mechanisms reduce interbreeding and hybridization:
    • 1) Prezygotic isolation
    • Mostly premating isolation  - temporal isolation (e.g. Japanese winter moth), host or pollinator specialization, anatomical reproductive incompatibility (Japanese land snails), mate choice (e.g. assortative mating in cichlids, crickets)
    • Also gametic isolation (e.g. Drosophila)

    2) Postzygotic isolation - hybrid or backcross inferiority (inviability, sterility, or reduced fitness)
  148. Hybridization and gene flow between species CONT'D
    • Expect RI between good species (according to BSC)
    • But hybridization between recently-diverged species not uncommon (e.g. following secondary contact)
    • - e.g. over 700 introduced plant species in British Isles hybridize with native species
    • - And at least half of these produce fertile hybrids

    Fate of hybrids will determine course of speciation
  149. Fate of hybrids will determine course of speciation
    • If hybrids completely inviable
    • Already distinct gene pools

    1. If hybrids less fit, reinforcement of prezygotic isolation

    • 2. When equally fit, divergence between parental populations erased 
    • 3. Higher fitness (e.g. in intermediate or new habitat)
    • - Creating a distinct population of their own
    • - Either stable hybrid zone (higher fitness at boundary of parental ranges) or new species (in novel habitats)
  150. Reinforcement
    Evolution of mechanisms that prevent interbreeding between newly interacting incipient species (prezygotic)

    • If hybrids are less fit: (postzygotic)
    • Parental populations under different selection pressures
    • Changes in mating systems
    • Or if fixation of alleles that don't work well together when heterozygous

    • Selection against hybrids should reinforce selection  for assortative mating (prezygotic RI)
    • And finalize the speciation process 
    • Minimizes "gamete" wastage
  151. Predicts that RI mechanisms should be stronger where species are sympatric vs. allopatric
    • e.g. Drosophila santomea and D. yacuba 
    • Should be selection for evolution of prezygotic isolation in sympatry since hybrid males are sterile

    • In allopatric populations, females produce about equal numbers of offspring sired by males of each species
    • But in sympatric populations, females produce mostly eggs sired by males of own species, even if mated first with male of other species = gametic isolation
  152. e.g., Pheromones in Drosophila (Higgins et al.)
    • Pheromones in 2 species chemically different when sympatric
    • But not when allopatric

    • BUT: in allopatric populations brought together in lab
    • Pheromones diverged to resemble those found in sympatric species
    • In 9 generations

    Selection for pheromones that permitted RI
  153. e.g. Reinforcement in green-eyed tree frogs in Australia
    Hoskin et al.
    • Two divergent lineages isolated in N and S rainforest refugia during Pliocene and Pleistocene
    • Reconnected ca. 6500 years ago in contact zone

    • Selection against hybridization through mate choice greater in contact zones than in allopatric area = reproductive character displacement
    • Post-mating reproductive isolation:
    • - S females x N males inviable
    • - N females x S males viable but with slower development
    • Greater "penalty" if S female choose wrong male
    • Led to pre-mating reproductive isolation (reinforcement):
    • - S females better than N females at choosing own males
  154. 2. Hybridization erasing divergence
    • If hybrids are equally fit
    • Especially in young (or incipient) species

    Decreased prezygotic RI

    • e.g. One stickleback population
    • Breakdown of benthic-limnetic species pair into hybrid swarm (Gow et al. 2006)
    • Likely due to environmental change in lake
    • Exotic crayfish introduced in early 1990s (Taylor et al)

    • e.g. cichlids in Lake Victoria
    • Increased turbidity causing breakdown of pre-mating reproductive barriers (Seehausen et al)
  155. Despeciation due to decreased selection against hybrids
    • Hendry et al - possible human impacts on adaptive radiation: beak size bimodality in Darwin's finches
    • Divergence with respect to beak size and shape within medium ground finch Geospiza fortis
  156. Hendry et al. cont'd
    • Biomodal distribution evident in 1940s-1960s
    • Few with intermediate beak size
    • No intrinsic genetic incompatibility
    • Presumably disruptive selection due to selection against hybrids
    • Insufficient supply of seeds with intermediate size/hardness

    Dcreased postzygotic RI

    • Site with increased human presence after 1960
    • Finch feeders with rice that can be cracked by birds having wide range of beak sizes
    • No longer selection against intermediate beaks
  157. 3.Hybrids create a distinct population/species
    a) Stable hybrid zones
    • e.g. big sagebush in Utah
    • 2 subspecies, basin, and mountain, hybridize at intermediate elevations
    • Hybrid zone relatively narrow by stable over time

    • Reciprocal transplant experiments showed that each subspecies did best at its own elevation
    • Hybrids superior in transitional habitat
    • Continue to hybridize at interface

    • e.g. two wildflower species in Colorado
    • Hybrids grew as well or better in transitional habitats
  158. 3 b) Creation of new species through hybridization
    • Sunflower Helianthus anomalous thought to have been created by hybridization between two other species (H.annuus  and H. petiolaris)
    • Reproductive isolation from parental species

    • DNA evidence supports previous hypothesis that Aubodon's warbler (D. auduboni) is a hybrid between two other species (D. coronata and D. nigrifrons)
    • Homoploid hybrid speciation otherwise thought to be rare in tetrapods
  159. Hybrid origin for Butterfly species supported
    • Researchers recreated Heliconius heurippa in the lab by crossing Heliconius cydno and Heliconius melpomene 
    • And natural hybrids show wing patterns very similar to H. heurippa 
    • Wing pattern of H. heurippa leads to reproductive isolation from parent species

    • Growing circumstantial evidence for hybrid speciation in Ragoletis fruit flies, swordtail fish and African cichlids
    • And some suspect American red wolf could be product of hybridization between coyotes and gray wolves
  160. L13
  161. Genetics of speciation
    • Hot topic in evolutionary biology research now
    • Including identification of actual genes and mutations

    • e.g. "blonde" deer mice on Sand Hills in Nebraska (Linnen et al. 2009)
    • e.g. "reinforcement" gee in flycatchers (Sether et al)
  162. Birds of a feather prefer to breed together
    • Pied and collared flycatchers
    • Speciation occurred during last ice age; reunited when glaciers receded
    • Closely related, look similar, share same territory, but rarely breed together and hybrids are sterile

    • Females prefer conspecific males but about 2% hybridize
    • Studied hybrids to determine if preference genetic or learned through exposure: mechanism of pre-mating RI?
    • Hybrid females prefer males of same species as genetic father; hybrid males showed no preference

    • Genes found on sex chromosome (Z) of females (from father)
    • Saether et al. 2007
  163. What degree of genetic differentiation is required to create a new species?
    • Previously thought that radical reorganization required = "genetic revolution"
    • RI due to genome-wide divergence in allopatry
    • Sequential fixation of large number of genetic changes, each with very small effect (Fisher's geometric model)

    • But recent research shows speciation can also result from: Few large-effect changes 
    • - Crickets, cichlids: few genes related to mate choice
    • Phlox: few genes related to flower colour

    • And speciation can result from both:
    • New mutations:
    • e.g. deer mice from Sand Hills in Nebraska (Linnen et al)
    • e.g. Pelvic reduction in stickbacks  (Chan et al.)
    • and Standing variation:
    • e.g. reduced plates in FW sticklebacks (Colosimo et al.)

    Helps predict ability of organisms to adapt to rapid environmental change
  164. Same or different genes where parallel evolution?
    Examples from Arendt and Reznick (2008)
    • e.g.1: Beach mice on Florida Gulf Coast
    • Single nucleotide difference in melanocortin-1 receptor gene accounts for up to 36% of the lighter coat colour
    • Same mutation not present in light-coloured Altantic coast mice, suggesting convergent phenotypic evolution 
    • Agouti gene involved in blonde deer mice from Sand Hills in Nebraska
    • Hoekstra et al.

    • e.g.2: Dark pigmentation in rock pocket mice invading lava flows in Arizona vs. New Mexico
    • "Clearly, in nature, independent populations can have different genetic solutions to similar ecological" problems

    • e.g.3 Complete loss of pigment in Mexican cavefish
    • Two populations with different deletions in the ocular albinism 2 gene
    • Other populations show full complementation; different gene likely involved
  165. Scientists restore sight to blind fish (CBC news)
    • Crossing blind cavefish (Astyanax mexicanus) from distant caves can restore some sight
    • Supports idea that blindness evolved convergently in distantly related cavefish populations
    • Mutations in different genes responsible for loss of sight in separate lineages

    "Does this change your view of the value of PSC vs. BSC in cases of "parallel evolution"?
  166. Examples of distantly-related taxa using same genes/pathways
    e.g.1: Exact same amino acid polymorphism in Mc1r in blonde beach mice and woolly mammoths

    • e.g.2: Pitx1 gene involved in pelvic reduction in threespine and ninespine sticklebacks
    • Suspected involvement in manatees
  167. L14 Evolution and the fossil record
    • First metazoans in fossil record approx. 565 Ma
    • e.g. multicellular butsmall and morphologically simple jellyfshes and sponges

    • Then Cambrian "explosion" (545-505 Ma)
    • In time, Cambrian represents <1% of Earth's history
    • But with appearance of most living animal phyla
    • e.g. arthropods, annelids, molluscs, chordates

    Considered one of the great events in history of life

    Start of Phanerozoic (= visible life) eon
  168. Fossil
    any trace left by a past organism
  169. Nature of the fossil record.
    Is the fossil record an accurate record of evolution?
    The fossilization process and types of fossils
    • 1. Amber and freezing
    • Least altered remains but rare
    • e.g. insects preserved in hardened plant resins
    • e.g. woolly mammoth in permafrost
    • Other environments without weathering, scavenging animals, decomposition
    • e.g. human remains in peat bogs

    • 2. Permineralization and replacement
    • Where dissolved minerals (e.g. calcite, silica, gypsum) replace original mineral content or precipitate in and around it
    • Can preserve 3D details of internal structure

    • 3. Molds and casts
    • Remains decay after being buried in sediment
    • Casts = new material fills space and hardens into rock
    • Molds = unfilled spaces
    • Preserves 3D information about surface shape

    • 4. Compression and impression fossils
    • Organic matter is buried in sediment before it decomposes
    • Under weight of sediment, leaves 2D impression in material below

    • 5. Trace fossils
    • Trackways or burrows (e.g. Tyndall stone)
    • Coprolites (e.g. sloth dung in desert caves)
  170. Fossilization depends on:
    • 1. Durability of specimen or protection
    • 2. Burial
    • 3. Lack of oxygen

    • Therefore:
    • Fossils mostly hard structures left where sediments are deposited
    • e.g. river deltas, beaches, floodplains,marshe, sea floors
    • Also anaerobic swamps

    Common fossils are marine bivalves (hard structures and already buried) and teeth
  171. Therefore biases in fossil record
    • 1. Habitat bias
    • Sedimentary deposits accumulate mostly in coastal marine areas
    • - Composed of material eroded from landmasses
    • Therefore, mostly marine organisms
    • - To lesser extent, other coastal or floodplain organisms

    • 2. Taxonomic bias
    • Bias towards organisms with mineralized structures (shell or bone)
    • >60% of animal phyla without hard structures are under-repressented
    • Critical plant parts (e.g. flowers) rarely fossilize

    • 3. Temporal bias
    • Old rocks rarer than new rocks as mountains erode and tectonic plates subduct
    • Fidelity of the fossil record better for more recent fossils

    • 4. Collection bias
    • e.g. certain groups of fossils are preferentially collected
  172. Geological time scale
    • Hierarchy divided into eons, eras, periods, epochs, and stages
    • early 1800s, intervals arranged by relative ages onlyAbsolute times assigned with development of dating techniques
  173. Overview of the Phanerozoic eon
    • Three eras: Paleozoic, Mesozoic, Cenozoic
    • Within Cenozoic, either:
    • Three periods: Paleogene, Neogene, and Holocene (5th ed.)
  174. Life on an Evolving Earth
    • Life evolved on a world that was itself changing (Freeman and Herron)
    • Rearrangement of continents and oceans due to plate tectonics
    • Resulted in major climatic changes:
    • e.g. climate patterns extreme when continents came together because smaller relative amount of coastline (with its moderating effect on climate)

    • Collision of plates can cause also increased mountain building -> rock weathering -> decreased CO2 -> decreased temperatures and glaciation
    • During times of high CO2, poles free from glaciation
  175. L15 Ediacaran biota (precambrian)
    • Dated 565-544 Ma
    • Discovered in 1940s
    • Named for Ediacara hills, Australia
    • But similar fossil at 20 sites around world

    • Mostly compression and impression fossils or traces
    • Organisms without shells or other hard parts
    • Small sponges, jelyfishes, comb jellies
    • Morphologically simple
  176. Ediacaran Fauna
    • Asymmetrical or with radial symmetry
    • But were more complex bilaterally symmetric animals present this early?
    • Argument that linear burrows and tracks were made by organism with head and tail

    • Fossilized embryos also suggest bilateral symmetry
    • - e.g. resembling larval sponges
    • - e.g. resembling cleaving arthropod embryos
    • Strong fossil evidence for bilaterally symmetric animals in late Precambrian
    • e.g. mollusc-like Kimberella
    • Together suggests bilaterians small but present
  177. Burgess Shale Fauna (Cambrian)
    • Dated 505 Ma
    • Discovered 1909 near Field, BC
    • Described in Stephen Jay Gould's "Wonderful life"

    Similar to Chenjiang biota (525-520 Ma)

    • Mostly compression and impression fossils
    • Variety of large, complex bilaterally symmetric forms
    • Little overlap with Ediacaran fossils

    • Well-developed segmentation, heads, appendages
    • Complex arthropods (e.g. trilobites)

    • Segmented worms, wormlike priapulids, molluscs
    • Several chordates with segmented trunk muscles, notochord that resemble hagfishes and lampreys

    • Also unusual organisms not obviously related to any extant phyla
    • Sometimes grouped together as "Problematica"
    • Some of which might represent new phyla
    • If so, Cambrian explosion resulted in even greater morphological diversity than realized
    • Many major groups later extinct

    • However, further studies suggest "Problematica" probably member s or close relatives of living phyla
    • e.g. Opabina
    • e.g. Wiwaxia

    A lot happened between 544 and 520 Ma
  178. Still...
    • Something unusual happened during the Cambrian
    • That led to earliest members of virtually all major animal lineages appearing relatively suddenly
    • At same time, in many parts of the world

    • Diversification in terms of Morphological innovations
    • Locomotion
    • Feeding
  179. Progression in development and body plan organization
    Major divergences shown between Ediacaran fauna and Burgess Shale Fauna

    • 1. Radially or asymmetric (diploblastic) e.g. Jellyfishes, comb jellies
    • vs.
    • Bilaterally-symmetric (triploblastic) = Bilatera e.g. arthropods, nematodes, molluscs, chordates

    Within Bliatera, animals evolved two different processes for producing multicellular body with 3 types of ambryonic tissues

    • 2. Protostome vs. deuterostome
    • Protostome: 
    • Gastrulation forms mouth first
    • e.g. arthropods, nematodes, molluscs, annelids, flatworms
    • vs.
    • Deuterostome: first opening becomes anus 
    • e.g. echinoderms, chordates
  180. Was the cambrian explosion really explosive?
    • How long did these traits exist before appearing in fossil record?
    • Use molecular clock to date events not dated in fossil record

    Runnegar (1982) dated origin of bilaterians at 900 Ma (using hemoglobin amino acid sequence)

    • Wray et al. used 7 different genes, all independently calibrated
    • Estimated that chordates and echinoderms diverged 1000 Ma
    • Protostomes and deuterostomes diverged 1200 Ma

    • i.e. divergences occurred hundreds of millions of years before first appearance in fossil record
    • If so, fossils of bilaterians, protostomes, and deuterostomes should eventually be found in Proterozoic rocks

    With few exceptions, such fossils haven't been found
  181. Did the cambrian explosion have a long fuse?
    • Cooper and Fortey, Smith
    • Suggested that the lineages leading to the living Bilatera diverged over prolonged period in Proterozoic
    • But most were small organisms that left no fossil trace

    • If so, what lit the fuse?
    • What aused dramatic change in body size in multiple lineages, during same brief time?
    • May have been connected with ecological changes (e.g. in atmosphere or oceanic geochemistry)
    • Especially rising oxygen concentrations in seawater due to increase in photosynthetic algae during Proterozoic
  182. Cambrian trigger
    • Knoll and Carroll suggested mass extinction of much Ediacaran fauna just before Cambrian
    • At same time as rise in atmospheric oxygen
    • Allowed tiny bilaterians to evolve in response to changed conditions

    • Geological evidence for rise in oxygen (e.g. Knoll and Carroll)
    • But additional predictions still untested:
    • No fossil evidence of small-bodied protostomes and deuterostomes in Proterozoic
    • No evidence of mass extinction of Ediacaran fauna
  183. Microevolution
    Changes in gene frequencies and trait distributions within species and populations
  184. Macroevolution
    Large evolutionary change

    Fossil record shows composition of biota has changed "radically" over time
  185. Adaptive radiation
    • Single or small group of ancestral species rapidly diversifies into large number of descendant species
    • Usually occupy wide variety of niches
  186. What factors trigger adaptive radiations?
    • Ecological opportunity
    • Establishment of key innovation
  187. Ecological opportunity
    • Lack of competitors permits diversification to fill unoccupied niches
    • a) Following colonization of new, depauperate environment
    • e.g. Galapagos finches; Fish in postglacial lakes
    • b) Extinction of other taxa
    • e.g. diversification of mammals after dinosaurs became extinct at end of Cretaceous period
    • e.g. Diversification of Bilatera after extinction of many Ediacaran fauna
  188. Estblishment of key innovation
    • e.g. diversification of arthopods due to jointed limbs
    • e.g. adaptive radiation among land plants
    • 1. Radiation of terrestrial plants from aquatic ancestors (400 Ma)
    • - Key morphological features (e.g. waxy cuticles, stomata)
    • 2. Radiation of angiosperms (110 Ma)
    • - Flower key innovation since it made pollination so efficient
  189. Adaptive radiation vs. Statsis
    • Absence of evolutionary changein one or more characters for some period of evolutionary time
    • New morphospecies appear suddenly in fossil record
    • Then persist for millions of years without apparent change

    • Contrary to Phyletic gradualism
  190. Phyletic gradualism
    • Darwin emphasized gradual nature of evolution by natural selection to contrast instantaneous creation of new forms presented in Theory of Special Creation
    • Attributed lack of transitional forms to incompletedness of fossil record
    • Gradualism accepted patternfor next century
  191. Punctuated Eq'm
    • Gradualism opposed by Eldredge and Gould
    • Claimed stasis is real pattern in fossil record

    • Morphology is static within species
    • And morphological variation occurs at time of speciation (cladogenesis)
  192. e.g. Demonstrating Stasis: Is it real?
    • Tested in bryozoans 
    • Abundant in fossil record for past 100 my
    • Phylogeny well known
    • Confident that morphospecies designations reflect phylogent

    • Cheetham, Jackson and Cheetham
    • Caribbean bryozoans from 20 my -present
    • 19 extinct and living species in two genera
    • Estimated phylogeny for each genus

    • None of the populations showed traits intermediate between species
    • Characteristics of species were stable through time

    • i.e. Shows unequivocal patterns of stasis
    • - Punctuated by rapid morphological change
  193. What is the relative frequency of stasis and gradualism?
    • Erwin and Anstey reviewed 58 studies for evidence of punctuated equilibrium
    • Wide variety of taxa and period
    • Varied in ability to meet criteria for testing stasis
    • But number of studies may compensate for this

    Conclusion: "Paleontological evidence overwhelmingly supports a view that speciation is sometimes gradual and sometimes punctuated, and that no one mode characterizes this very complicated process in the history of life"
  194. Why does stasis occur?
    e.g. Why would morphology of bryozoans remain unchanged for 5-10 million years?

    Address using so-called "living fossil"

    • Species or clades that show little or no measurable change over millions of years
    • Although don't necessarily retain all of the "primitive" features of ancestral lineage
  195. Living fossils
    • 1. Ginkgo biloba
    • Single extant species with no close living relatives
    • Leaves similar to 40 Ma impression fossils
    • Thought for centuries to be extinct in wild but is now known to grow wild in at least two small areas in eastern China

    • 2. Horsetail
    • Approx. 15% extant species in genus Equisetum with no close living relatives
    • Much larger and more diverse group 350-300 Ma before seed plants became dominant

    • 3. Coelacanth
    • Prehistoric fish believed extinct for 65 million years
    • Until live specimen was found off east coast of South Africa in 1938
    • Once successful group with many genera and species
    • Abundant fossil record from 400-65 Ma

    • 4. Horseshoe Crab
    • Extant species in genus Limulus virtually identical to fossil species from 150 Ma
  196. Why have these living fossils not changed?
    • Is it due to a lack of genetic variation?
    • No, according to Avise et al:
    • Compared mtDNA variation in horseshoe crabs to that of king hermit crab clade
    • Same (or more) genetic variation within horseshoe

    • Instead, likely due to relatively stable environment
    • Stabilizing selection around an optimal phenotype
  197. L17 Mass extinctions
    • 5 major extinction episodes during Phanerozoic
    • ca. 20-55% families went extinct
    • ca. 60-95% species went extinct in 1 million year span

    • Global in extent
    • Involved wide range of organisms
    • Rapid relative to expected life span of taxa

    • Although "The Big Five" responsible for only 4% of all extinctions during Phanerozoic
    • Other 96% extinctions occurred at normal or background rates:
    • - Taxa with restricted ranges and limited dispersal more likely to go extinct
  198. Mass extinctions
    "The Big Five"
    • 5 mass extinction events recognized in early 1800s
    • 1. Terminal-Ordovician (ca. 440 Ma)
    • 2. Late-Devonian (ca. 365 Ma)
    • 3. Permian-Triassic (252 Ma)
    • 4. End-Triassic Extinction(215 Ma)
    • 5. Cretaceous-Paleogene (65 Ma)
  199. Terminal-Ordovician
    • 440 Ma
    • Extinction of >100 families of marine inverts
    • e.g. brachiopods, bryozoans, reef-building fauna

    • Probably caused by glaciation of southern supercontinent Gondwana
    • Glacial deposits from this period found in Sahara Desert
    • Glaciation also caused lowering of sea level and reduced availability of continental shelf habitat
  200. Late-Devonian
    • 365 Ma
    • Mostly affected warmwater marine species (e.g. rugose corals, brachiopods, trilobites)

    • Perhaps caused by another episode of global cooling
    • With accompanying lowering of sea level
    • Glacial deposits of this age in northern Brazil

    • Meteorite impacts also suggested
    • But evidence inconclusive
  201. Permian-Triassic
    • 252 Ma
    • End of Paleozoic
    • Biggest of big five
    • Mother of mass extinctions (Erwin 1993)
    • Extinction of 90-95% of marine species

    • Primarily affcted marine inverts
    • e.g. foraminifera, trilobites, bryozoans, brachiopods, echinoderms

    • And also vertebrates such as pelycosaurs
    • - Mammal-like reptiles e.g. Dimetrodon
    • Fossils found many places worldwide
    • Especially Texas and Oklahoma
    • Where much of oil derived from Permian fossils
  202. Causes of Permian-Triassic extinction?
    • Still debated bytnumerous theories
    • 1. Glaciation on Gondwana
    • 2. Reduction of shallow continental shelf habitat due to formation of supercontinent Pangea
    • - Which occurred in early and middle Permian

    • 3. Large volanic eruptions in Siberia
    • - evidence of silica-rich lava flows dated to this time

    likely driven by multitude of interacting factors
  203. End-Triassic extinction
    • 215 Ma
    • Particularly severe in the oceans
    • e.g. brachiopods, gastropods, molluscs severely affected
    • Some terrestrial groups affected
    • e.g. some reptile and amphibian groups

    • Precise cause not known
    • But huge volcanic eruptions occurred ca. 208-213 Ma as supercontinent Pangea began to break apart
    • Triassic extinctions allowed dinosaurs to become dominant
  204. Cretaceous-Paleogene (K-Pg)
    • 65 Ma
    • End of the Mesozoic
    • Marine plankton and invert affected
    • And (non-avian) dinosaurs, pterosaurs, large-bodied marine reptiles (ichthyosaurs, plesiosaurs) wiped out
  205. Causes of K-Pg?Evidence
    • Evidence that huge asteroid hit the earth
    • - High concentration of iridium at K-Pg boundary
    • - Iridium rare in Earth's crust but abundant in extra-terrestrial objects
    • Amount of iridium suggests asteroid 10-15 km wide
  206. Evidence for the impact event
    • Also presence of two other minerals at K-Pg bounday:
    • - Shocked quartz particles
    • - Microtektites (tiny glass particles melted by heat of an impact)
    • Known from other well-documented meteorite crash sites

    • Shocked quatz and microtektitea at K-Pg boundary in Caribbean
    • Site of impact found in early 1990s from magnetic and gravitational anomalies in Yucatan peninsula
    • Crater 180 km in diameter
    • Dater 65 Ma
  207. K-Pg boundary killing mechanisms
    10 km asteroid striking ocean would have produced series of events affecting climate, atmosphere, and oceanic chemistry worldwide

    • Material ejected considerable distances from site
    • Sig. amounts melted or vapourized
    • Water vapour and SO2 (from anhydrite in ocean floor) into atmosphere
    • Forming sulfuric acid, causing acid rain

    • SO2 also scatters solar radiation
    • Leading to global cooling and darkening

    • Soot at K-Pg boundary also suggests widespread wildfires
    • Force of impact prob. sufficient to trigger massive earthquakes and set off volcanes
    • And tidal wave in Atlantic - estimated as high as 4 km

    • Fern spike in pollen and spore deposits suggest forest communities replaced by ferns
    • More than 35% of land plants at some NA sites wiped out (probably in "splash zone")

    • Global reduction in primary productivity of phytoplankton
    • Changes in temp. and chemical gradient in Atlantic
    • Many organisms wiped out within days or months
    • Plus decline of other groups over 500,000 years due to disruption of:
    • Ecological processes
    • Biogeochemical cycles of nutrients
    • Interactions among species

    Debate re: whether dinosaurs already in decline before impct (e.g. as a result of volcanic eruptions from Deccan traps in India)
  208. Equivalent mass extinction in plants?
    Willis and McElwain
    • Disagreement among studies re: extent of extinction in plants
    • Generally decrease in plant diversity after "Big Five"
    • But less so than in animal taxa
    • and more gradual and rarely global

    Major reorganization of plant communities and evolution of new species instead of sudden extinctions
  209. Persistence in Plants
    • Why difference in levels of extinctions between animal and plant kingdoms?
    • Due to greater ability of plants to withstand major ecological trauma

    • Not as sensitive to small population sizes
    • Mechanisms for coping with environmental stress
    • e.g. leaves or whole branch systems that can wilt or be shed during period of drought
    • e.g. ability to die back to the ground and survive from one growing season to next as underground stems or rhizomes
    • e.g. lie dormant during periods of adverse weather, survive for long period of time in seed banks
    • e.g. reproduce vegetatively

    Not exclusive to plants (e.g. rotifers, microsporean parasittes) but more common
  210. The sixth mass extinction?
    the human meteorite?
    • Polynesian Avifauna
    • Steadman estimated that 200 bird species went extinct in past 200 years as result of human colonization

    • e.g. Tonga
    • Of 27 spp. in prehuman fossil record,only 6 still extant
    • Charred bird bones suggest direct predation by humans
    • And pigs, dogs, rats, imported by colonists
    • - Extinction of many ground-nesting or flightless birds since most islands previously lacked mammalian predators

    Also habitat destruction
  211. Other examples of human caused extinctions
    • Extinction of 60 spp. endemic to Hawaii
    • After arrival of settlers 1500 years ago
    • Species began dropping out of fossil record soon after appearance of first fire pits, etc.

    • And extinction of 44 spp. in New Zealan
    • Including 8 spp. of moas
    • Since human arrival ca. 1280 CE (AD)

    • cf. Galapagos islands
    • Without permanent human settlement until 1535
    • Only 3 populations lost in 4000-8000 years before humans
    • 20 taxa since
  212. Megafaunal extinctions in Late Pleistocene
    • Dozens of genera of large mammals went extinct throughout Western Hemisphere in last 1-2 million years
    • NA lost 35 genera of large mammals ca. 14,000-11,000 ago:
    • Giant Beaver
    • Glyptodont
    • Ground sloths
    • Florida cave bear
    • Dire wolf
    • American cheetah and other large cats
    • Capybaras
    • Tapirs, peccaries, camel, llamas
    • Pronghorns, elk-moose
    • America mastodon
    • Mammoths
  213. Megafunal extinctions in Late Pleistocene Cont'd
    • Extinction synchronous andcorrresponds with evidence for humans (e.g. Clovis hunter-gatherers) in NA
    • But also with Younger Dryas cold interval and extraterrestrial impact

    • Therefore, various hypotheses for extinction:
    • Overkill
    • Climate change
    • Extraterrestial impact
    • Hyperdisease

    Possibly the result from a intersection of these events
  214. Giant Irish Deer victim of ancient climate change
    • Isotopes in teeth suggest starvation
    • Went extinct in reland ca. 10,600 years ago
    • - Likely before humans arrivedin ireland
    • Isotope analysis showed that the ecosystem in which the deer lived became stressed by drought
    • - Changing from forest to more open and tundra-like
    • Also colder

    • Other populations across Europe and Western Asia
    • Remains found in Siberia from ca. 7,000 years ago
    • Mainland giant deer were able to move to better environment ("glacial refugium") and survive longer
  215. The sixth mass extinction? Is a mass extinction event currently underway?
    • 50-90% taxa went extinct during the Big Five
    • Overall percent extinct since 1600 <1%
    • Although threatened species as high as 11% in birds and mammals
    • And >30% gymnosperms and palm species threatened

    • Most past losses due to colonization (NA, Caribbean, Australasia, islands of Pacific Ocean)
    • Many susceptible species already lost in these areas
    • Already put though an "extinction filter"?
  216. Current extinction rates
    • But most current concerns re: habitat loss due to expanding human populations
    • At current rate of growth, population 13 billion by 2050
    • Current extinction rate estimated at 100-1000 times background rate

    • But still uncertainties, especially in unexplored areas
    • And with poorly studied taxa

    • Smith et al. (1993) argues that human-cased mass extinction not yet occurring
    • But could if current extinction rates continue

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