8) Your textbook states that under optimal conditions, all of the methods discus

Question

8) Your textbook states that under optimal conditions, all of the methods discussed (parsimony of the phylogeny in question with accuracies approaching 100%. However, real phylogenies are ximum likelihood, neighbor joining, and Bayesian inference reveal the true branching pattern ly inferred under ideal circumstances. Explain, using examples, why this is so. valuate the merits and limits of parsimony, maximum likelihood, and Bayesian inference as tools for evaluating alternative phylogenies. 10) Convergence and reversal are two complications that can interfere with accurate strategies used to overcome them. onstruction of phylogenies. Describe each one, using examples, and explain the common 1 1) Biogeographers study the spatial distribution of living things, and how they came to be ere they are. Explain, using examples, how phylogeography can be used to answer the questions of biogeographers.

Explanation / Answer

Ans 8: Phylogenetic trees present evolutionary relationships. Systematics describes the pattern of relationships among taxa but history is not something we can see it has happened once and leaves only clues as to the actual events.

Phylogeny is the evolutionary history of relationships among organisms or their genes. It is portrayed in a diagram called a phylogenetic tree. Each split or node represents the point at which lineages diverged. The common ancestor of all organisms in the tree is the root. In phylogenetic studies, the most convenient way of visually presenting evolutionary relationships among a group of organisms is through illustrations called phylogenetic trees.

Phylogenetic methods can be used for reconstructing character evolution are parsimony, likelihood and bayesian methods can be used for reconstruction of character evolution. Phylogenesis is the the evolutionary development and diversification of a species or group of organisms or of a particular feature of an organism.

The steps involved in the determination of the age of the species from molecular phylogeny involves:

1 . Fossil record or known geological event, divide the molecular distance between two taxa in a phylogeny by their own divergence time based on fossils or relatives ancestors

2. Build a regression line whose slope is a function of substitution rate - do this for several nodes

3 interpolate divergence times on the regression line.

Maximum parsimony predicts the evolutionary tree or trees that minimize the number of steps required to generate the observed variation in the sequences from common ancestral sequences. Likelihood ratio test is a general hypothesis-testing method that uses the likelihood to compare two nested hypotheses (e.g. 100 dice in a bag, 90 biased and 10 unbiased. Likelihood for biased diced increases with higher numbers. When roll a 4 and a 6 with the same die. Then compare the likelihood of rolling a 4 and a 6 given that the die is biased or if it is unbiased. The term gives the result that is most likely from the two possibilities). Maximum likelihood is used to estimate the tree that is the most likely to have occurred given the observed data and the assumed model of evolution (substitution model)

Neighbour joining is a distance matrix method that uses a cluster algorithm to successively join pairs of taxa, until a fully resolved tree is obtained. Taxa are joined in order to minimise an estimate of tree length. Neighbor joining has a conversion step so it does not assume that all taxa evolve at a constant rate. Star decomposition joins all taxa onto single node and progressively decomposes tree similar to UPGMA

Bayesian analysis tells that what is the probability that the parameters are correct given observed data
Pr(parameters/data)=pr(data/parameters) * pr(parameters) all divided by Pr(data)

Ans 9: The advantages of molecular data when compared to morphological characters are:

1.Comparisons among all species possible, from unicellular to vertebrates
2.Generate virtually unlimited amounts of data in a relatively short time
3.Molecular clock - common yardstick of measuring divergence

The two main limitations of parsimony methods tree reconstruction includes underestimate branch lengths (different branch spans different lengths of time ) and it can be positively misleading or more data accumulated the more convinced that data is right even its we are wrong

Maximum likelihood differ from maximum parsimony methods of free reconstruction as maximum likelihood is the probability of change along a branch is a function of branch length in maximum likelihood while maximum parsimony performs best when probability of change is equal on all the branches. And bot are similar as they use discrete tax on by characters data matrix

Maximum likelihood analysis: each tree is assigned a likelihood score that is the combination of infinitesimally small scores given by the reconstruction of all possible ancestral states at all the nodes between all branches. Allows branches to have there own length.

The three advantage of Bayesian bases analysis over traditional likelihood methods involves posterior probability cannot be estimated analytically. Maximum likelihood offers the means to approximate posterior probabilities by sampling trees from the posterior probability distribution and use a hill climb algorithms. Bayesian methods are much faster and bayesian method can incorporate prior information

The three advantages of maximum likelihood methods of character reconstruction over parsimony based methods. Parsimony does not consider branch length information in character reconstruction, it does not allow the calculation of support for character states at ancestral nodes. Maximum Likelihood assumes that every character evolves at a constant rate across the tree, considers branch length (changes are less likely on shorter branches then Longer ones), estimates ancestral state probabilities (uncertainty of ancestral state is considered when testing a hypotheses about character evolution).

Ans 10: Similar features can evolve in unrelated groups of organisms. Convergent evolution independently evolved traits subjected to similar selection pressures may become superficially similar. Similar traits generated by convergent evolution and evolutionary reversals are called homoplastic traits or homoplasies. A character may revert from a derived state back to an ancestral state. This is evolutionary reversal. Homologous traits features shared by two or more species that were inherited from a common ancestor.

Convergent evolution features that independently evolved became superficially similar due to similar selection pressures. Convergent evolution example includes the wings of bats and birds

Evolutionary reversal occur when a character reverts from a derived state back to the ancestral state over many generations. Evolutionary reversal example: When most frogs do not have lower teeth (derived trait), but the ancestor of frogs did (ancestral trait). One frog genus has regained teeth in the lower jaw. This frog genus superficially resembles ancestor frogs although there is no recent common ancestry. Another example involves a relative to the Tetrapods (vertebrates with four walking limbs), snakes underwent an evolutionary reversal, losing their legs and reverting to a condition resembling ancestors of Tetrapods.

Ans 11: Biogeography is the study of historical changes in the geographic distribution of organisms, including those that affect their present distribution; ecological biogeography addresses current factors that affect present distributions.

Modern historical biogeography:

1) explicitly incorporate possibility of long-distance dispersal into phylogenetic hypotheses
2) allow for range shifts following isolatin that could obscure area-clade relationships
3) allow for incorrect phylogenetic reconstruction, including incongruence in gene and species trees

Phylogenetic niche conservatism slow evolution of the ecological requirements of a group of organisms, resulting in long-continued dependence of related species on similar resources and environmental conditions.Phylogrography description and analysis of the history and processes that govern the geographic distribution of genes within species and among closely related species, analysis that may shed light on the history of the populations.

Conclusions about historical ecological and evolutionary biogeography:

1. key is sythesis of data across disciplines to test hypotheses
2. major advances from:
-dated molecular phylogenetic and phylogeographic approaches
-ability to make predictions about current and historical species distributions.

Related Questions

Navigate

• Browse (All)
• Browse 8
• Subjects

---

---

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.