In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

Th. État--Sci. nat.--Paris 11, 1987. / Bibliogr. p. 133-141.

Origin-Destination (O-D) matrices are required in order to model traffic routing behavior in networks. Direct techniques for collecting O-D information from home and roadside interviews have historically been utilized to estimate O-D tables. However, these techniques are not only very costly, labor intensive, and disruptive to trip makers, but traditionally also do not capture traffic peaking behavior, which is often required for traffic operational purposes. Consequently, more cost-effective indirect or synthetic O-D estimation techniques have been developed, and continue to be developed. They utilize readily available traffic volume counts to estimate the most likely O-D tables that may have generated the observed link counts. This thesis describes the basic formulations that have been proposed to formulate and solve the static O-D problem synthetically using link flow observations based on Maximum Entropy techniques. As is the case with many mathematical solutions to engineering problems, a number of simplifying assumptions have been made in order to solve the synthetic O-D problem. Unfortunately, the descriptions of these simplifying assumptions are often not fully described in the literature, and in some cases, these assumptions are not mentioned at all. Furthermore, the literature fails to systematically demonstrate what impact these assumptions have on the final O-D table estimate. Therefore, this thesis utilizes simple hypothetical networks to; 1. Demonstrate and compare the two main types of synthetic O-D formulations, namely the trip and volume based formulations. 2. Track the O-D estimation procedure from its initial formulation to its final formulation, demonstrating all significant assumptions that have been made and the implications of these assumptions on the final solution. 3. Demonstrate to what extent the final O-D estimation formulation remains valid when these assumptions are invoked. 4. Test the applicability of some packages which implement the various formulations and solution techniques that are available. / Master of Science

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Phylogenetic analysis is used in all branches of biology by inferring evolutionary trees. Applications include designing more effective drugs, tracing the transmission of deadly viruses, and guiding conservation and biodiversity efforts. Most analyses rely on effective heuristics for obtaining accurate trees. However, relatively little work has been done to analyze quantitatively the behavior of phylogenetic heuristics in tree space. This is important, because a better understanding of local search behavior can facilitate the design of better heuristics, which ultimately leads to more accurate depictions of the true evolutionary relationships. In order to access and analyze the tree search space, we implement an effec- tive local search heuristic. Having an effective heuristic that can open the space is important, since no search heuristic in this field can effectively provide data collec- tion control. So we have implemented and estimated a search heuristic, Simple Local Search or SLS, that works reasonably well in the space. Our investigations led to several interesting observations about the behavior of a search heuristic and the tree search space. We studied the correlation of tree features of search path trees, where tree features refer to the parsimony score, the Robinson- Foulds distance and the homoplasy measure. Most importantly from the results, parsimony score was highly correlated with Robinson-Foulds distance only in trees that lie on the search path to a local optimum. We also note that the scores of neighborhoods along search paths improve together, as a local search progresses. Correlations of tree features of search path trees are particularly useful in char- acterizing and controlling a search path. This paper proposes one possible stopping criterion to maximize the tree search results while minimizing computational time tested on three biological datasets using the correlation between the parsimony score and the RF distance value of search path trees. Also, the observation that scores of a neighborhood on a search path improve together gives us a significant amount of flexibility in selecting the next pivot of a search without losing performance. Eventually, our long-term goal is developing an effective search heuristic that can deal with large scale tree space in reasonable time. Improved knowledge about the tree search space and the search heuristic can provide a reasonable starting point toward the goal.

Thèse--Sc. nat.--Paris XI, 1981. / Bibliogr. p. 143-151.

München, Techn. University, Diss., 2004.

Berlin, Humboldt-Universiẗat, Diss., 2002.