Friday, February 15, 2013

LECTURE NOTE: Estimating Evolutionary Tree

BIO155: Estimating Evolutionary Tree
-        Phylogeny or phylogenic tree is a graphical summary of this history
-        Synapomorphy is a homologous trait that is shared among certain species and is similar because it was modified in a common ancestor (are shared, derived traits)
o   A type of homology
o   Group all of living organisms into a single lineage that descended from the same common ancestor
-        Any group that includes an ancestor and all of its descendants is called a monophyletic group (or clade or lineage)
o   Genetic code helps identify that bacteria and mammals as members of the same monophyletic group, but it does not help us distinguish bacteria from eukaryotes
o   Bacteria are identified by synapomorphies such as cell walls that contain a compound called peptidoglycan; eukaryotes have synapomorphies such as nuclear envelop
o   All synapomorphies are homologous traits, but not all homologous traits are synapomorphies.
o   Synapomorphies can be identified at whatever taxonomic level
§  Populations, species, genera, and phyla
o   To understand:
§  Synapomorphies identify evolutionary branch point
§  Synapomorphies are nested, meaning that you moved through time and trace a tree from its root to its tips, each branching event adds one or more shared, derived traits (hierarchy of branching events)
o   Phylogeny inference methods that use these principles are called cladistics methods (First determine what is ancient, and what is derived)
§  Outgroup analysis – the character state in the group of interest (the ingroup) is compared to the state in a very close relative that clearly branched off earlier (the outgroup) => confirm with the fossil record
§  A phylogenetic tree inferred by clustering synapomophies in this way is called cladogram
-        Morphological similarities like the eyes and skulls evolve independently in different lineages due to convergent evolution, which occurs when natural selection favors similar structures as solutions to problems posed by similar environment
-        Reversals are common in DNA data because there are only four possible states for each base in a sequence. Other things being equal, there is a 25% chance that a reversal to the previous state will occur each time a change occurs at a particular site in DNA
-        The most efficient way to distinguish homology from homoplasy is to analyze many traits in reconstructing evolutionary relationships instead of just one or a few
-        Under parsimony, biologists consider the hypothesis of convergence as the most likely. (Two changes occur, instead of 6 in the homologous theory)
o   Octopuses and vertebrates each have a layer of light sensitive cells in their eyes; but in octopuses these cells are oriented toward the opening where light enters the eye, while in vertebrates the light sensitive cells are oriented in the opposite direction (Octopus moves the eyes back and forth, change the shape of eyeball to focus, but vertebrate depends in the muscle that change the shape of the lens
o   When parsimony is applied to phylogeny inference, the preferred tree is the one that has the least total amount of evolutionary change (least subject to homoplasy, and more reliable source of synapomorphies)
-        The phylogeny of Whales
o   Lack of posterior limbs
o   Found a fossil of relative of whales (53.5 myr ago). These whales had hind limbs and reassemble and extinct group of amphibian mammals called mesonychains
o   Choosing character: Morphology and Molecules
§  First, choose character to use as data
·        Skeletal features and other morphological characteristics
·        DNA sequence and other molecular traits
o   Finding the best tree implied by the data
§  Parsimony with a single morphological character
§  Cetaceans are close relative to ungulates
·        Ungulates – Perissodactyls (horses/ rhinos), artiodactyls (cow, deer, pig)
·        Features found in angle bone called astragalus (in artiodactyl – both end of the bone are smooth and pulley shaped
o   Shows that hippos and whales are not related
o   Whales are descended from artiodactyl ancestor
§  Parsimony with multiple molecular character
·        Milk protein gene called beta-casein
·        Site 142, most organisms seem to have G at this position from common ancestor
·        Site 192, all taxa have C except the camel
·        Site 162, cows, whales, deer and hippo have a T at this site (other artiodactyl and outgroup has C)
·        Site 166 provides only synapomorphy in these 60 bases for monophyletic group consisting of whales and hippos
·        Site 177 provides a synapomorphy for a clade consisting of whales, hippos, pigs, and peccaries, which conflict with info from site 162
o   Reversal and convergence have resulted in homoplasy (either 162 or 177 does not reflect the actual evolutionary history of artiodactyl)
o   Artiodactyl implies total of 47 nucleotide changes while whale-hippo implies 41 changes.
§  In this case, Whale-Hippo is more parsimonious
§  60 characters and 8 taxa
·        When the number of taxa in a study is relatively low—fewer than 11—a computer program can evaluate all of the possible trees (Exhaustive Search) Because it guarantees that the optimal tree implied by a particular data set will be found, the approach is called an exact method
§  Evaluating the best tree
·        Use other methods besides Parsimony: Maximum likelihood (ML) and Bayesian Markov Chain Monte Carlo (BMCMC)
o   Maximum likelihood (ML) shows how likely it will match the hypothesis (deciding how good the data is)
o   Bayesian approaches are similar to likelihood methods, except that the principle is to ask what the probability is of particular tree being correct, given the data and a model of how the traits in question change over time
o   Later on is the introduction of distance methods
o   Produce consensus tree under parsimony
o   Using statistical test o evaluate the best tree under ML and BMCMC
o   Compare the best tree under parsimony, ML and BMCMC to see how consistence they are
·        Evaluating Particular Branch: Bootstrapping
o   Not every individual can represent the entire population (If variety in population is high then less confident that sample average is reliable)
o   With trees based on ML or BMCMC analyses, you can compare tree with and without a particular branch and compute which is more likely.
§  Bootstrapping process begins by randomly selecting one of the sites and using it as the first entry in a new data set. Then it randomly selects another site which becomes the second data point in the new data set.
§  Resampling until particular branches occur in 50%, 80% or 100% of the tree estimated from the resampled data sets
§  Aunder 50%, then polytomy, or a point of uncertainty
§  Strong support for whale-hippo clade
·        Resolving conflicts
o   Need larger data set and less homoplasy
o   The presence or absence of SINE or LINE at a homologous location in the genome of two different species can be used as a trait in phylogeny inference
o   Less likely that SINE will insert itself into two independent host lineages at exactly the same location (possible but not improbable)
o   Not likely a reversal because the loss of SINE or LINE is tracable
o   No homoplasy in data set, and thus no conflicts among characters when they are mapped onto the tree
o   Found fossils of semi-aquatic ancestor that lead back to the  link between whale and hippo
-        Using Phylogenies to Answer questions
o   Classification and Nomenclature: Is there such a thing as fish?
§  The effort to name and classify species is called systematics
§  Linnaean system starts with giving each species a unique genus and species name and then groups progressively more similar species into kingdoms, classes, orders, families, and genera (phonetic approach)
§  In contrast, naming schemes that are based on evolutionary relationships are referred to as phylogenetic or cladistics approaches (tree based and branching events).
·        More specifically, only monophyletic groups, which includes all descendants of common ancestors are named
·        Paraphyletic groups, which include some but not all descendants of a common ancestor, should not be named
o   Using molecular clock ( a hypothesis)
§  There are good theoretical reasons to expect that at least some types of DNA sequences change in a clocklike fashion
§  Instead of being favor or eliminated by natural selection, these “neutral change” responds to a random process called genetic drift
§  Neutral theory of molecular evolution predicts that neutral changes in DNA should accumulate in population as rate equal to mutation rate. If the mutation rate does not change much over time and if generation times remain similar, then the number of neutral molecular differences between two taxa should be proportional to the age of their most recent common ancestors
§  By documenting the number of different neutral mutations observed in two species and multiplying by a calibration rate, representing how frequently neutral changes occur per myrs, researchers can estimate when the species diverged
§  Mutation rate to neutral alleles will vary from gene to gene, and linkage to linkage and base to base
§  Third position of codons are much more neutral than the first and second, more like a clocklike rate
§  If alleles change through natural selection, then the mutations are likely to be working in clock fashion
§  Rate of change that are calibrated for a particular gene and lineage are unlikely to work for other groups, diff in generation time and selection histories
§  Determine by fossil and geological record
o   Analyzing Phylogeography: How did Chameleons Get from Africa to India?
§  The effort to understand where organisms live and how they came to be there is called biogeography
§  Broke up of Gondwana
§  Human cause
o   Co-speciation: When new species of Aphids Form, what happens to the Bacteria that live inside their cells?
§  When natural selection occurs during these interactions and produces adaptations in both species involved, coevolution is said to take place
§  Aphids and bacteria inside them have symbiotic relationship (endosymbiosis)


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