Transcript Powerpoint
CHAPTER 5 The Tree of Life Classification and Phylogeny Taxonomic Practices • Taxonomy – Naming and classification of organisms • Binomial System of Nomenclature – Developed by Linnaeus – Either composed of Latin or Latinized (conjugation and gender specific endings from latin) Taxonomic Practices • No two species can have the same Binomial name – Can have the same genus name for different organisms only for a single plant and single animal lineage • Priority – the valid name of a taxon is the oldest available name proposed – If it is found that what is considered 2 species actually is just one, the oldest name must be used, and the newer name is considered a junior synonym Taxonomic Revision • Species placed in different genera and are shown to • • • • be closely related may be shifted to the same genus, yet retain their species epithets A species may be removed from a genus and placed into a different one if it is shown not to be closely related Forms originally described as different species may prove to be the same species and be synonymized New species may be described These general rules also apply to higher taxa above the level of genus (families, orders, etc.) Phylogeny • Hypothesis of evolutionary relationships • Phylogenetic tree = graphical summary of evolutionary history • We have been using trees throughout the semester – Now we will examine how to construct them – Remember: Phylogenies, in almost all cases, are only estimates Phylogenetics • Under Darwin’s hypothesis of common descent Species in the same genus stem from a recent ancestor • Hierarchical classification reflects not a mystical ordering of the universe, but rather a real historical process Phylogenetics Terms • Monophyletic Group – All members are believed to stem from a single common ancestor, and the group includes this common ancestor • Paraphyletic Group – Group that is monophyletic except that some descendents of the common ancestor have been removed • Polyphyletic Group – consisting of unrelated lineages, each more closely related to other lineages not placed in the taxon Paraphyletic Groups Birds Lizards Crocodilians Snakes Turtles Mammals Reptiles are paraphyletic Class Reptilia should include Class Aves Polyphyletic Groups Wasps Reptiles Birds Spiders Protists Bacteria Winged organisms are polyphyletic Phenetics • Also called Numerical Taxonomy • Mostly developed by Charles Michener & Robert Sokal • Looks at the overall similarity of species based on all characters • Trees reconstructed with this method are called PHENOGRAMS • A phenogram does not necessarily represent phylogenetic relationships Phenetics • The problem with phenetics is that similarity in itself is not a reliable guide to phylogenetic relationships 1. Shared derived characters due to common ancestry 2. Shared ancestral characters relative to same species 3. Share similar feature but they are not homologous HOMOPLASY Phenetics • Thus, if shared ancestral characters or homoplasious characters outnumber similarities due to shared derived characters the phenogram will not often portray the true phylogeny Cladistics • Willi Hennig (1950), published in US in 1966 • Argued that classification should rigorously reflect phylogenetic relationships and NOT the degree of adaptive divergence or overall similarity Cladistics • Contends that only 1 type of evidence provide information about phylogenetic relationships – Homoplasious characters DO NOT – Simlarities based on shared ancestral characters DO NOT – Characters unique to a single taxon (autapomorphies) DO NOT – Shared derived characters DO Cladistics • Evidence that species share a more recent ancestor with each other than either do with other species is provided only by shared derived characters Synapomorphies • These are assumed to be evidence of this character evolving in the common ancestor of these two species Cladistics • Remember: a shared derived character provides evidence that species are a monophyletic group only if it is UNIQUELY derived – ie. Only evolved once within the group you are studying as a whole! • The Cladistic Principle – Monophyly is defined by the presence of shared uniquely derived character states Vocabulary of Cladistics • PLESIOMORPHY – ancestral or • • • • primitive character state SYMPLESIOMORPHY – shared ancestral character state APOMORPHY – derived or ‘advanced’ character state SYNAPOMORPHY – shared derived character state AUTAPOMORPHY – derived character not shared (unique to species or group) Cladistic Methods • Techniques that identify monophyletic groups based on synapomorphies • Synapomorphies define evolutionary branching points • Autapomorphies and ancestral characters do not • Must be able to identify homology of traits and direction of change through time Cladistic Methods • Several methods used to identify polarity – Most commonly used is the outgroup method – The character state of the target taxa is compared with that of a relative that diverged earlier – Outgroup represents the ancestral state – Identify outgroup from other phylogenetic studies or fossil data – Good to use several outgroups at once Cladistic Methods • When no convergence, parallelism, or reversal occurs all synapomorphies are congruent • When all nodes are not congruent try to minimize homoplasy • Tree made using synapomorphies is a cladogram – Clade is a monophyletic group Cladograms VS. Phylograms • Cladogram – Only shows you the relationships between taxa – Branch lengths provide no data! • Phylogram – Shows you relationships AND the amount of change (evolution) inferred along each branch – Therefore, branch lengths are very important! Cladograms VS. Phylograms Species A Species A Species B Species B Species C Species C Species D Species E Species D Species E Species F Species F 5 changes Cladistics Parsimony • Parsimony – explanation requiring the fewest • undocumented assumptions should be preferred over more complicated hypotheses that require more assumptions for which evidence is lacking Cladistic Tree or Most Parsimonious Tree ‘the best estimate of phylogeny is the one that requires the least number of steps (or character state changes) to explain the observed variation Parsimony: Preliminary Information • Generally the ancestral character state is • • assumed to be the one that is most widely distributed among taxa outside the group of interest Outgroups invaluable information for inferring relationships among the members of the monophyletic ‘ingoup’ under study Allows inferences about plesiomorphic and apomorphic characters We can infer the directional trends or Polarity of Evolution Parsimony and Phylogeny • Most closely related taxa should have the most traits in common – Assume that traits are independent, heritable, and variable in target taxa – Traits may be DNA sequence, presence or absence of skeletal elements or floral parts, mode of embryonic development, etc. – Traits scored in different taxa must be homologous Parsimony and Phylogeny • Evolutionary relationships should only be reconstructed from traits that are similar because they are derived from a common ancestor = Homology – Shared derived characters of all members of a group – Synapomorphy • Synapomorphies are used to decide where branches should be on a phylogeny Homology • Homologous features are derived from a common ancestor – Organs of 2 organisms are homologous if they have been inherited (& perhaps modified) from a single organ of a common ancestor • A character may be homologous among species but a character state may not – 5 toed state is homologous in humans and lizards but the 3 toed state is not homologous in Guinea pigs and Sloths – The wings of birds and those of bats are not homologous, although their forelimbs in general are homologous structures Homology • The features of organisms almost always evolve from pre-existing features of their ancestors – Unlikely that features arise de novo from nothing Examples of Synapomorphies which define groups of Fossil Birds Parsimony and Phylogeny • There are also traits that are derived along a single lineage – Autapomorphy – The same traits may be independently derived in different lineages • Seal and penguin flippers • Natural selection favors similar adaptations in similar habitats • Convergent evolution Parsimony and Phylogeny • Traits may revert to ancestral form because of mutation or selection – This may destroy phylogenetic signal and lead to reconstruction of misleading relationships • Convergence and Reversal and collectively known as Homoplasy Parsimony and Phylogeny • Homoplasy – Creates noise in the data – Some characters give conflicting information about relationships – Systematists try to minimize homoplasy in a data set – Choose characters that evolve slowly relative to age of taxa Parsimony and Phylogeny • Parsimony minimizes total amount of evolutionary change in a tree • Synapomorphies are usually more common than convergence and reversal • Most parsimonious trees minimize homoplasy to give best estimate of phylogeny Phylogeny of Whales • Whales and dolphins are in order Cetacea • Synapomorphy is loss of posterior limbs • Because whales are highly evolved for • aquatic life, assigning relationships with other mammals is difficult Phylogenetic studies have found that whales are closely related to artiodactyls – and... Guess what.... We have whale fossils with hind limbs!!!!! Whales as the “sister” taxon or clade to a monophyletic clade of Artiodactyls Phylogeny of Whales • Recent molecular studies suggest that traditional cetacean + hippo clade is more likely than artiodactyl + cetacean clade • Suggests that some traits for aquatic life shared among hippos and whales are not convergent but homologous Synapomorphies • Must test which phylogeny is more likely to be true Phylogeny of Whales • Which characters should be used to reconstruct the phylogeny? – Morphological characters • Skeleton – Molecular characters • Allozymes, DNA sequences, etc... – For fossils only morphological characters can be used – Morphological characters difficult to use because taxonomic expert needed Phylogeny of Whales • Which characters should be used to reconstruct the correct phylogeny? – Many molecular characters can be scored rapidly – Homoplasy difficult to identify • Only four bases: G, A, T, C so reversals or homoplasy is likely to occur • Often best to use both types of characters Phylogeny of Whales • Astragalus – Small bone towards rear of the foot (proximally positioned in the hind limb) – Important character in mammal systematics – Its shape and characteristics divides artiodactyls from perissodactyls – If whales are sister to all artiodactyls specialized astragalus evolved only once – If whales are sister to hippos, two evolutionary steps are needed • Whales lack an astragalus – Whale + hippo is less parsimonious Phylogeny of Whales • Extinct whales with legs have features of astragalus similar to artiodactyls • Support for whales as artiodactyls • Systematists use more than one character when reconstructing trees – Must minimize homoplasy over all characters – Gatesy used DNA sequence data • Also found support for whale + hippo clade Phylogeny of Whales • In the molecular data set some characters are parsimony informative, some are autapomorphic and some are invariant – Only synapomorphies used – Most synapomorphies support the overall phylogeny but one does not – One synapomorphy supports whale + hippo clade – Let’s find the most parsimonious solution for entire tree Patterns of Speciation That Make Reconstructing Phylogenies Difficult Phylogeny of Whales • How do we find the best tree? – With a small number of taxa you can evaluate all possible trees • Exhaustive search – With more taxa the amount of possible trees increase exponentially – For 8 taxa in artiodactyl tree there are 10,395 possibilities!!! – Must use a shortcut method to evaluate trees – Although faster, such shortcut methods open the possibility of not actually finding the best tree... Exhaustive Search Sequences Number of unrooted, binary trees 4 3 5 15 6 105 7 945 8 10,395 9 135,135 PAUP* can evaluate approx. 108,000 trees/s using parsimony for a problem with 21 sequences each about 900 nt long. 10 2,027,025 11 34,459,425 12 654,729,075 13 13,749,310,575 14 316,234,143,225 15 7,905,853,580,625 16 213,458,046,676,875 17 6,190,283,353,629,375 18 191,898,783,962,510,625 19 6,332,659,870,762,850,625 20 221,643,095,476,699,771,875 This run would just about be finished had we started it at the time prokaryotes diverged from eukaryotes (about 2.5 billion years ago!) Phylogeny of Whales • How do we evaluate confidence in a tree? – Is whale + hippo tree substantially better than whale + artiodactyl tree? – Can view slightly suboptimal trees (less parsimonious) to see how much difference there is – Bootstrapping statistically evaluates how much support data contains for nodes • Repeated sampling to see if tree differs from chance Phylogeny of Whales • How do we evaluate confidence in a tree? – Bootstrap values are percentages of the number of times the same branch arose after repeated sampling – Bootstrap support over 70% indicates that the correct relationship was probably found – Investigators usually report any bootstrap value over 50% Phylogeny of Whales • Other reconstruction methods – Parsimony is not the only criterion for reconstructing phylogenies – Maximum likelihood assumes a particular model of sequence evolution and estimates the most likely tree given the model of evolution and the dataset • Uses all data, even autapomorphies and invariant sites • Can only be used for molecular data – Morphological data cannot be modeled Phylogeny of Whales • Other reconstruction methods – Distance methods (=Phenetic) • Neighbor joining and UPGMA • Based on clustering technique • Based on overall similarity • Not a cladistic method • Uses differences (distances) among character states to group taxa Example of Distance Methods The % difference is calculated between all DNA sequences then used to make the tree by connecting pairs of species with the lowest distances NOTICE, this appears to be a Phylogram, although they did not give a scale bar for changes... Phylogeny of Whales • It is useful to use a variety of tree reconstruction methods • If methods are congruent you have more confidence in your reconstructions Using Phylogenies to Answer Questions • Phylogenies can be useful tools to answer important evolutionary questions • One must always question the methods used to reconstruct the phylogeny to be confident in the results Using Phylogenies to Answer Questions • Once a phylogeny is reconstructed with confidence, it can be used to answer evolutionary questions • Hawaiian fruit flies – Very high diversity – Must have radiated quickly to produce 500+ species in only 5-6 million years • Age of oldest island Kauai • Molecular clock dates species as older Using Phylogenies to Answer Questions • Molecular Clock – It is hypothesized that molecular change happens at a steady rate – If this is so, you should be able to use know dates to calibrate a molecular clock and be able to discern the ages of branching events • Calibrate with fossils or geologic events Using Phylogenies to Answer Questions • Molecular Clock – Clocks for a variety of taxa (especially mammals and birds) have been estimated to ‘tick’ at a rate of 2% sequence divergence per million years for mitochondrial genes • However, Different genes evolve at different rates – Other scientists have challenged the clock and found that molecular change does not always happen in a clocklike fashion Using Phylogenies to Answer Questions • Hawaiian fruit flies – Beverly and Wilson estimated a molecular clock for Hawaiian fruit flies – Found that some species are 42 million years old – How is this possible? – Hawaiian Islands are dynamic • Islands rise and subside • Have been islands over that geologic hot spot for a long time Using Phylogenies to Answer Questions • Mesozoic Birds – Because of branching order some extinct birds must have lived much earlier than fossils depict – Paleontologists predicted several fossil species would be found – Xu found an early Cretaceous dromaeosaurid bird from the dates predicted Using Phylogenies to Answer Questions • Phylogenetic systematics can aid in classification of taxa • Phylogenetic and evolutionary species concepts require that taxa be monophyletic • Many traditional classifications are not based on monophyly – Order Artiodactyla is not monophyletic • Order Cetacea should be sunk to family level Using Phylogenies to Answer Questions • Paraphyly example – The true phylogeny of reptiles includes birds – Birds are autapomorphic reptiles – Birds are the sister group to crocodilians – To fix the classification to contain only monophyletic groups: • Reduce class Aves to order • Or raise other orders of reptiles to classes – Turtles, crocdilians + birds, squamates, tuataras Paraphyletic Groups Birds Lizards Crocodilians Snakes Turtles Mammals Reptiles are paraphyletic Class Reptilia should include Class Aves Current Taxonomy of Great Apes and Humans -Family Pongidae – Gorillas, Chimps, Orangutans -Family Hominidae – Humans Is this really a valid taxonomy??? Proposed Classification (that no-one ever started using!!!) Using Phylogenies to Answer Questions • Coevolution – Leaf-cutting ants and fungi they farm • Leaf cutters grow fungus on leaves that they cut for food • 200 ant species of tribe Attini each farm a different fungus species • Did the two groups cospeciate? – Phylogenies should be congruent • Hinkle found congruence on all branches but one • Fungi were domesticated more than once Using Phylogenies to Answer Questions • Spread of AIDS – Suspicion that a Florida dentist infected his patients with HIV in 1990 – Difficult to know because some patients had other risk factors – Reconstructed a phylogeny of the HIV of all his patients and other local people – Phylogeny proved that dentist had infected several of his patients but not others Testing Biogeographic Hypotheses The two primary hypotheses of the spread of Homo around the world reduce to phylogenetic hypotheses •Clear from fossil evidence that the genus arose in Africa, but how did modern humans get to every other continent? •Was it a single exodus from Africa that replaced existing lineages (either through competition or direct combat) - the African replacement hypothesis •Or was it multiple origins of modern humans from the ancient lineages that had originally colonized each part of the globe? The multi-regional hypothesis Phylogenies to Identify Parallel Speciation and Adaptive Radiations Trunkdweller Twigdweller Trunkdweller Twigdweller tree-top tree-top Island 1 Island 2 Common Ancestor Using Phylogenies to Examine Evolution of Female Choice & Intersexual Selection Water Mites – Net-stance must have evolved first and then male trembling after for the sensory exploitation hypothesis to be true – Examine phylogeny to see probable order of evolution of the trait