Explaining Evolution via Constrained Persistent Perfect Phylogeny

BACKGROUND: The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. RESULTS: We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. CONCLUSIONS: A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model

Understanding the evolutionary history of the papillomaviruses

This thesis focuses on the evolutionary history of the papillomaviruses (PVs) using phylogenetic approaches. Two aspects have been examined: the first is the level of phylogenetic compatibility among PV genes and the second is determining the ancestral diversification mechanisms of the PVs in order to explain the origin of the observed associations with host species. Bayesian phylogenetic analysis has been used to make evolutionary inferences. The existence of phylogenetic compatibility among genes was examined by estimating constrained and unconstrained phylogenies for pairs of PV genes. The Bayes' factor statistic derived from comparison of the constrained and unconstrained models indicated significant evidence against identical phylogenies between any of the 6 PV genes investigated and may indicate the existence of ancestral recombination events. The formation of new host-virus associations can occur via a process of 'codivergence', where, following host speciation, the ancestral virus association is effectively inherited by the descendant host species; 'prior divergence' of the virus, which results in multiple virus associations with the host; and 'host transfer', in which the virus lineage is transferred between contemporaneous host species. To distinguish between these mechanisms of virus diversification, an approach based on temporal comparisons of host and virus divergence times was devised. Difficulties associated with the direct estimation of PV divergence times led to the incorporation of a biased sampling approach into Bayesian phylogenetic estimation. This allowed for viral divergence events to be biased in favour of codivergence but allowed sampling of times that violate this assumption and therefore indicate either prior divergence or host transfer. Statistical evaluation of the proportion of violations at each viral divergence identified significant evidence of prior divergence events behind many of the observed PV-host associations and one ancestral host transfer event

Organisational phylogenesis : Developing and evaluating a memetic methodology.

This research evaluates the unorthodox proposition that organisational development proceeds through the Darwinian processes of variation, selection and inheritance acting upon a non-genetic replicating code. This new replicator represents the fundamental unit of cultural transmission and was termed by evolutionist, Richard Dawkins, as the meme. The memetic position re-introduces many often neglected, sometimes shunned, evolutionary arguments into social and organisational debate by providing a naturalistic and plausible hereditary element upon which socio-cultural adaptation operates. The popularity of the neologism 'meme' initially grew through rather ad-hoc non-scientific usage on the Internet. For some time, this geekish tendency has tarnished the idea of memetics and impeded serious academic investigation into the subject. A more rigorous philosophical treatment has been provided by Daniel Dennett who has argued that, while a science of memetic cladistics may be both desirable and feasible, it remains unlikely. On the other hand one of Dawkins' most famous critics, Mary Midgley, heralds dark forebodings that one-day memes may be given actual credence. The present study necessitated the adaptation of conventional genealogical and taxonomic methods, for novel application in confirming congruence between actual organisational phylogeny and hereditary traits. One specific requirement was to develop a means of identifying, capturing and codifying such traits as meme strips for phenetic analysis. In order to handle the computational complexity inherent in the phenetic reconstruction algorithms, proprietary software had to be produced. This was extensively tested upon meme strips generated through simulated evolution. Western Christian denominational families provided a source of empirical evidence and demonstrated that the methods could be successfully applied to real organisational forms. A theological phylogeny was reliably reconstructed thereby upholding the hypothesis of cultural descent with modification based on a memetic replication. Further support for the claim was made in conjunction with the rendering of a facilities management market landscape. More importantly however, the results coming from this research suggest that the potential for formulating a science of memetics may be significantly greater than in Dennett original consideration

Systematics of the macrourid fishes

The systematics of rattail fishes (Teleostei: Gadiformes, Macrouridae) is reexamined focussing on the $\textit{Coryphaenoides}$ group of genera, including $\textit{Albatrossia, Lionurus, Chalinura and Nematonurus}$. The data matrix consists of 69 osteological characters based on personal observations, 17 characters, generally of the soft anatomy, from various published sources and 34 characters reported from peptide mapping of muscle-type lactate dehydrogenase. An evolutionary systematics of morphology requires, firstly, a historical concept of homology and secondly, a scientific basis for the recognition of patterns. Viewing the organism as a hierarchy of constraint, homology is a relationship of development constraint inherited by parts of organisms. Taxa are types, relationships of constraint inherited by organisms. If, from the morphological perspective, taxa are relationships not groups, conventional concepts of monophyly and related terms cannot apply to them. In practice they describe comparisons between trees. The creation/discovery of patterns is embedded in the practice of systematics and has its basis in the intelligent abilities of human beings. Morphology deals with the linguistic aspect of evolution, rather than with its dynamic genetic aspect. Dynamic and linguistic aspects are complementary yet incompatible. The scientific status of morphology is shown to rest on this principle of complementarity. Through cladistic analysis of a large number of published characters, I investigate the scenarios and relationships of gadiform fishes that have recently been proposed. The results of the rattail analysis are thus placed within the broader context of gadiform ecology and evolution. In cladistics, parsimony plays the role of Popper's-empirical concept of simplicity, as a method of estimating the hypothesis of highest empirical support. Assumptions are made about the likely pathways of evolution in the way the characters are coded. Original classifications of the Gadiformes and the Macrouridae are proposed. Within the gadiforms there is a general trend from jaw precision to jaw protrusion. An index of protrusion/precision shows a negative correlation with depth. Rattails show low values of the index indicating high jaw protrusion. However, within the family the trend is towards higher jaw precision, and the precision/protrusion index is positively correlated with maximum depth. The discovery of cartilage in the exoskeleton of rattail fishes was an unforeseen result of the method of preparation. In rattails alcian blue reveals hyaline cell cartilage at the margins of certain dermal elements where it is gradually replaced by bone

Evolutionary novelty: a philosophical and historical investigation

Evolutionary novelty, the origin of new characters such as the turtle shell or the flower, is a fundamental problem for an evolutionary view of life. Accordingly, it is a central research topic in contemporary biology involving input from several biological disciplines and explanations at several levels of organization. As such it raises questions relative to scientific collaboration and multi-level explanations. Novelty is also involved in theoretical debates in evolutionary biology. It has been appropriated by evo-devo, a scientific synthesis linking research on evolution and development. Thanks to its focus on development, evo-devo claims to explain the mechanistic origin of novelties as new forms, while the Modern Synthesis can only provide statistical explanation of evolutionary change. The origin of an evolutionary novelty is a historical emergence of a new character involving form and function. I focus on three neglected dimensions of the problem of novelty, the functional-historical approach to the problem, research on novelty in the Modern Synthesis era and novelty in plants. I compare the evo-devo approach to novelty to a functional-historical approach of novelty. I focus on its origin in Darwin and its presence in the Modern Synthesis. The comparison of the two approaches reveals distance between conceptual frameworks and proximity in explanatory practices. This is partly related to unwarranted conceptual opposition. In particular, I list several ways of distinguishing novelty and adaptation, some of which are not conceptually sound. I then focus on the relation between novelty and adaptation in the Modern Synthesis era, and on the relation of novelty to other fundamental biological problems (speciation, origin of higher taxa, complexity). Pushing this approach further, I challenge the view that the Modern Synthesis excluded development and reached a hardened consensus. Finally, I analyse how Günter Wagner’s developmental theory of novelty applies to novelties in plant.European Commissio