Atomic Evolution and Reconstruction of Evolutionary Trees

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Layout. Developmental/Phylogenetic Tree Reconstruction

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Atomic Evolution and Reconstruction of Evolutionary Trees

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Outline Evolutionary/Phylogenetic Tree Reconstruction "Out of Africa" theory Did we advance from Neanderthals? Remove Based Phylogeny Neighbor Joining Algorithm Additive Phylogeny Least Squares Distance Phylogeny UPGMA Character Based Phylogeny Small Parsimony Problem Fitch and Sankoff Algorithms Large Parsimony Problem Maximum Likelihood Method Evolution of Wings HIV Evolution of Human Repeats

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Early Evolutionary Studies Anatomical components were the overwhelming criteria used to infer transformative connections between species since Darwin till mid 1960s The developmental connections got from these moderately subjective perceptions were frequently uncertain. Some of them were later demonstrated inaccurate 47 million year old primate fossil discovered 5/17/09

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Evolution and DNA Sequence Analysis: the Giant Panda Riddle For approximately 100 years researchers were not able make sense of which family the mammoth panda has a place with Giant pandas look like bears however have highlights that are uncommon for bears and commonplace for raccoons, e.g., they don't rest In 1985, Steven O'Brien and partners tackled the monster panda grouping issue utilizing DNA arrangements and calculations

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Evolutionary Tree of Bears and Raccoons

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Out of Africa Hypothesis Around the time the goliath panda question was illuminated, a DNA-based recreation of the human developmental tree prompted to the Out of Africa Hypothesis that c laims our most antiquated predecessor lived in Africa about 200,000 years back

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Human Evolutionary Tree (cont'd)

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The Origin of Humans: "Out of Africa" versus Multiregional Hypothesis Out of Africa: Humans advanced in Africa ~150,000 years prior Humans moved out of Africa, supplanting different humanoids around the world There is no immediate descendence from Neanderthals Multiregional: Humans moved out of Africa blending with different humanoids in transit There is a hereditary progression from Neanderthals to people Humans developed in the last two million years as a solitary animal varieties. Autonomous appearance of present day qualities in various territories

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mtDNA examination underpins "Out of Africa" Hypothesis African cause of people deduced from: African populace was the most differing (sub-populaces had more opportunity to wander) The developmental tree isolated one gathering of Africans from a gathering containing each of the five populaces. Tree was established on branch between gatherings of most noteworthy distinction.

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Evolutionary Tree of Humans (mtDNA) The transformative tree isolates one gathering of Africans from a gathering containing every one of the five populaces. Careful, Stoneking, Harpending, Hawkes, and Wilson (1991)

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Evolutionary Tree of Humans: (microsatellites) Neighbor joining tree for 14 human populaces genotyped with 30 microsatellite loci.

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Human Migration Out of Africa 1. Yorubans 2. Western Pygmies 3. Eastern Pygmies 4. Hadza 5. !Kung 1 2 3 4 5

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Two Neanderthal Discoveries Feldhofer, Germany Mezmaiskaya, Caucasus Distance: 25,000km

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Two Neanderthal Discoveries Is there an association amongst Neanderthals and today's Europeans? On the off chance that people did not develop from Neanderthals, whom did we advance from?

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Multiregional Hypothesis? May foresee some hereditary coherence from the Neanderthals through to the Cro-Magnons up to today's Europeans Can clarify the event of shifting local qualities

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Sequencing Neanderthal's mtDNA from the bone of Neanderthal is utilized on the grounds that it is up to 1,000x more bounteous than atomic DNA rot extra time and just a little measure of antiquated DNA can be recuperated (maximum farthest point: 100,000 years) PCR of mtDNA (pieces are too short, human DNA might be blended in)

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Neanderthals versus Humans: Surprisingly extensive dissimilarity AMH versus Neanderthal: 22 substitutions and 6 indels in 357 bp district AMH versus AMH just 8 substitutions However, a draft Neanderthal genome was sequenced in 2010, recommending 1% - 4% commitment to non-African human genomes and some proof of interbreeding

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Evolutionary Trees How are these trees worked from DNA groupings?

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Evolutionary Trees How are these trees worked from DNA successions? In a transformative (or phylogenetic ) tree , leaves speak to existing species (or taxa ) inside vertices speak to predecessors (and speciation occasions) root speaks to the most seasoned developmental progenitor edges are some of the time called heredities

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Rooted and Unrooted Trees In an unrooted tree, the position of the root ("most seasoned precursor") is obscure. Else, they resemble established trees. We are particularly inspired by degree-3 (unrooted) trees since they relate to paired phyolegenies.

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Distances in Trees Edges may have weights reflecting: Number of changes in the transformative procedure starting with one animal categories then onto the next Time evaluate for advancement from one animal groups into another In a tree T , we frequently register d ij (T) - the length of the way between leaves i and j d ij (T) is known as the tree separate amongst i and j

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j i Distance in Trees: an Example d 1,4 = 12 + 13 + 14 + 17 + 12 = 68

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Distance Matrix Given n species, we can process a n x n remove lattice D ij D ij might be characterized as the alter separate between a quality in animal categories i and species j , where the quality of intrigue is sequenced for all n species. D ij – alter separate amongst i and j (min number of alter operations to change one grouping into the other) An arrangement showcases how to alter one succession into the other utilizing operations addition, cancellation, and substitutions . The biggest score suggests the littlest altering cost. Thus, the alter separation is the supplement of the ideal arrangement score. A C T G GA T A G T GA C T

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Edit Distance versus Tree Distance Given n species, we can process the n x n remove lattice D ij D ij might be characterized as the alter separate between a quality in animal groups i and species j , where the quality of intrigue is sequenced for all n species. D ij – alter separate amongst i and j Note the distinction with d ij (T) – tree remove amongst i and j

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Fitting Distance Matrix Given n species, we can figure the n x n separate framework D ij Evolution of these qualities is depicted by a tree that we don't know . We require a calculation to develop a tree that best fits the separation lattice D ij

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Fitting Distance Matrix Fitting means D ij = d ij ( T ) Lengths of way in a ( obscure ) tree T Edit remove between species ( known )

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Tree recreation for any 3x3 framework is direct We have 3 leaves i, j, k and an inside vertex c Reconstructing a 3 Leaved Tree Observe: d ic + d jc = D ij d ic + d kc = D ik d jc + d kc = D jk

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d ic + d jc = D ij + d ic + d kc = D ik 2d ic + d jc + d kc = D ij + D ik 2d ic + D jk = D ij + D ik d ic = (D ij + D ik – D jk )/2 Similarly, d jc = (D ij + D jk – D ik )/2 d kc = (D ki + D kj – D ij )/2 Reconstructing a 3 Leaved Tree (cont'd)

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Trees with > 3 Leaves A degree-3 tree with n leaves has 2n-3 edges This implies fitting an offered tree to a separation grid D requires settling an arrangement of "n pick 2" conditions with 2n-3 factors This is not generally conceivable to fathom for n > 3

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Additive Distance Matrices Matrix D is ADDITIVE if there exists a tree T with d ij ( T ) = D ij NON-ADDITIVE generally

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Distance Based Phylogenetic Reconstruction Goal : Reconstruct a transformative tree from a separation network Input : n x n separate grid D ij Output : weighted tree T with n leaves fitting D If D is added substance, this issue has an answer and there is a straightforward calculation to understand it

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Find neighboring leaves i and j with parent k Remove the lines and sections of i and j Add another line and segment relating to k , where the separation from k to some other leaf m can be registered as: Using Neighboring Leaves to Construct the Tree D km = (D im + D jm – D ij )/2 Compress i and j into k , and repeat calculation for rest of tree

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Finding Neighboring Leaves To discover neighboring leaves we could basically choose a couple of nearest takes off.

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Finding Neighboring Leaves To discover neighboring leaves we could essentially choose a couple of nearest clears out. WRONG

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Finding Neighboring Leaves Closest leaves aren't really neighbors i and j are neighbors, however ( d ij = 13) > ( d jk = 12) Finding a couple of neighboring leaves is a nontrivial issue!

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Neighbor Joining Algorithm In 1987, Naruya Saitou and Masatoshi Nei built up a neighbor joining calculation (NJ) for phylogenetic tree reproduction Finds a couple of leaves that are near each other yet a long way from alternate leaves: verifiably finds a couple of neighboring leaves Advantage: functions admirably for added substance and other non-added substance lattices, it doesn't have the imperfect atomic check suspicion More points of interest in the old slides

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Degenerate Triples A deteriorate triple is an arrangement of three unmistakable components/taxa 1≤i,j,k≤n where D ij + D jk = D ik Element j in a worsen triple i,j,k lies on the developmental way from i to k (or is appended to this way by an edge of length 0).

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Looking for Degenerate Triples If separate network D has a decline triple i,j,k then j can be "expelled" from D subsequently diminishing the span of the issue. On the off chance that separation framework D does not have a decline triple i,j,k, one can "make"