Sub-atomic Evolution

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Sub-atomic Evolution

Outline Evolutionary 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 Evolution of Wings HIV Evolution of Human Repeats

Early Evolutionary Studies Anatomical components were the prevailing criteria used to determine 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 erroneous

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

Evolutionary Tree of Bears and Raccoons

Evolutionary Trees: DNA-based Approach 40 years back: Emile Zuckerkandl and Linus Pauling carried recreating developmental associations with DNA into the spotlight In the initial couple of years after Zuckerkandl and Pauling proposed utilizing DNA for transformative reviews, the likelihood of remaking transformative trees by DNA examination was fervently Now it is a prevailing way to deal with study advancement.

Who are nearer?

Human-Chimpanzee Split?

Chimpanzee-Gorilla Split?

Three-way Split?

Out of Africa Hypothesis Around the time the goliath panda conundrum was comprehended, a DNA-based recreation of the human transformative tree prompted to the Out of Africa Hypothesis that c laims our most antiquated predecessor lived in Africa approximately 200,000 years prior

Human Evolutionary Tree (cont'd) http://www.mun.ca/science/scarr/Out_of_Africa2.htm

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

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

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

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

Human Migration Out of Africa 1. Yorubans 2. Western Pygmies 3. Eastern Pygmies 4. Hadza 5. !Kung 1 2 3 4 5 http://www.becominghuman.org

Evolutionary Trees How are these trees worked from DNA successions? leaves speak to existing species inward vertices speak to progenitors root speaks to the most seasoned developmental precursor

Rooted and Unrooted Trees In the unrooted tree the position of the root ("most seasoned predecessor") is obscure. Else, they resemble established trees

Distances in Trees Edges may have weights reflecting: Number of transformations on developmental way starting with one animal varieties then onto the next Time appraise for advancement of one animal groups into another In a tree T , we regularly figure d ij (T) - the length of a way between leaves i and j d ij (T) – tree remove amongst i and j

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

Distance Matrix Given n species, we can process the n x n separate lattice D ij D ij might be characterized as the alter remove between a quality in animal varieties i and species j , where the quality of intrigue is sequenced for all n species. D ij – alter remove amongst i and j

Edit Distance versus Tree Distance Given n species, we can process the n x n separate framework D ij D ij might be characterized as the alter remove between a quality in animal varieties 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

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

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

Tree reproduction for any 3x3 lattice 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

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)

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

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

Distance Based Phylogeny Problem Goal : Reconstruct a developmental tree from a separation grid Input : n x n separate lattice 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 tackle it

Find neighboring leaves i and j with parent k Remove the lines and segments of i and j Add another line and section 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 , emphasize calculation for rest of tree

Finding Neighboring Leaves To discover neighboring leaves we just select a couple of nearest takes off.

Finding Neighboring Leaves To discover neighboring leaves we just select a couple of nearest clears out. WRONG

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!

Neighbor Joining Algorithm In 1987 Naruya Saitou and Masatoshi Nei built up a neighbor joining calculation for phylogenetic tree remaking Finds a couple of leaves that are near each other however a long way from different leaves: verifiably finds a couple of neighboring leaves Advantages: functions admirably for added substance and other non-added substance networks, it doesn't have the imperfect atomic clock suspicion

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

Looking for Degenerate Triples If separate lattice D has a worsen triple i,j,k then j can be "expelled" from D subsequently diminishing the span of the issue. In the event that separation lattice D does not have a worsen triple i,j,k, one can "make" a degenerative triple in D by shortening all hanging edges (in the tree).

Shortening Hanging Edges to Produce Degenerate Triples Shorten all "hanging" (edges that associate leaves) until a worsen triple is discovered

Finding Degenerate Triples If there is no decline triple, all hanging edges are lessened by a similar sum δ , with the goal that all match insightful separations in the network are decreased by 2 δ . In the long run this procedure breakdown one of the leaves (when δ = length of most limited hanging edge), framing a worsen triple i,j,k and lessening the measure of the separation framework D. The connection point for j can be recuperated in the turn around changes by sparing D ij for each broken down leaf.

Reconstructing Trees for Additive Distance Matrices

Character-Based Tree Reconstruction Better strategy : Character-based reproduction calculations utilize the n x m arrangement lattice ( n = # species, m = #characters) straightforwardly as opposed to utilizing separation grid. Objective : figure out what character strings at inside hubs would best clarify the character strings for the n watched species

Character-Based Tree Reconstruction (cont'd) Characters might be nucleotides, where A, G, C, T are conditions of this character. Different characters might be the # of eyes or legs or the state of a snout or a balance. By setting the length of an edge in the tree to the Hamming separation, we may characterize the niggardliness score of