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In a recent study, Bryant, Francis and Steel investigated the concept of enquote{future-proofing} consensus methods in phylogenetics. That is, they investigated if such methods can be robust against the introduction of additional data like extra trees or new species. In the present manuscript, we analyze consensus methods under a different aspect of introducing new data, namely concerning the discovery of new clades. In evolutionary biology, often formerly unresolved clades get resolved by refined reconstruction methods or new genetic data analyses. In our manuscript we investigate which properties of consensus methods can guarantee that such new insights do not disagree with previously found consensus trees but merely refine them. We call consensus methods with this property emph{refinement-stable}. Along these lines, we also study two famous super tree methods, namely Matrix Representation with Parsimony (MRP) and Matrix Representation with Compatibility (MRC), which have also been suggested as consensus methods in the literature. While we (just like Bryant, Francis and Steel in their recent study) unfortunately have to conclude some negative answers concerning general consensus methods, we also state some relevant and positive results concerning the majority rule (MR) and strict consensus methods, which are amongst the most frequently used consensus methods. Moreover, we show that there exist infinitely many consensus methods which are refinement-stable and have some other desirable properties.
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Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when restricted to the original set of taxa. However, if the new trees, restricted to the original set of taxa, were to agree exactly with the earlier trees, then we might hope that their consensus would either agree with or resolve the original consensus tree. In this paper, we ask under what conditions consensus methods exist that are future proof in this sense. While we show that some methods (e.g. Adams consensus) have this property for specific types of input, we also establish a rather surprising `no-go theorem: there is no reasonable consensus method that satisfies the future-proofing property in general. We then investigate a second notion of future proofing for consensus methods, in which trees (rather than taxa) are added, and establish some positive and negative results. We end with some questions for future work.
We propose a game-theoretic dynamics of a population of replicating individuals. It consists of two parts: the standard replicator one and a migration between two different habitats. We consider symmetric two-player games with two evolutionarily stable strategies: the efficient one in which the population is in a state with a maximal payoff and the risk-dominant one where players are averse to risk. We show that for a large range of parameters of our dynamics, even if the initial conditions in both habitats are in the basin of attraction of the risk-dominant equilibrium (with respect to the standard replication dynamics without migration), in the long run most individuals play the efficient strategy.
Species diversity in ecosystems is often accompanied by the self-organisation of the population into fascinating spatio-temporal patterns. Here, we consider a two-dimensional three-species population model and study the spiralling patterns arising from the combined effects of generic cyclic dominance, mutation, pair-exchange and hopping of the individuals. The dynamics is characterised by nonlinear mobility and a Hopf bifurcation around which the systems phase diagram is inferred from the underlying complex Ginzburg-Landau equation derived using a perturbative multiscale expansion. While the dynamics is generally characterised by spiralling patterns, we show that spiral waves are stable in only one of the four phases. Furthermore, we characterise a phase where nonlinearity leads to the annihilation of spirals and to the spatially uniform dominance of each species in turn. Away from the Hopf bifurcation, when the coexistence fixed point is unstable, the spiralling patterns are also affected by nonlinear diffusion.
Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R (recombinations without mutations) and Model RM (recombinations with mutations). For these models, we ask an identifiability question: is it possible to construct a pedigree from the joint probability distribution of extant sequences? We present partial identifiability results for general pedigrees: we show that when the crossover probabilities are sufficiently small, certain spanning subgraph sequences can be counted from the joint distribution of extant sequences. We demonstrate how pedigrees that earlier seemed difficult to distinguish are distinguished by counting their spanning subgraph sequences.
Phylogenetic diversity indices provide a formal way to apportion evolutionary heritage across species. Two natural diversity indices are Fair Proportion (FP) and Equal Splits (ES). FP is also called evolutionary distinctiveness and, for rooted trees, is identical to the Shapley Value (SV), which arises from cooperative game theory. In this paper, we investigate the extent to which FP and ES can differ, characterise tree shapes on which the indices are identical, and study the equivalence of FP and SV and its implications in more detail. We also define and investigate analogues of these indices on unrooted trees (where SV was originally defined), including an index that is closely related to the Pauplin representation of phylogenetic diversity.
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