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      Random ultrametric trees and applications

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          Abstract

          Ultrametric trees are trees whose leaves lie at the same distance from the root. They are used to model the genealogy of a population of particles co-existing at the same point in time. We show how the boundary of an ultrametric tree, like any compact ultrametric space, can be represented in a simple way via the so-called comb metric. We display a variety of examples of random combs and explain how they can be used in applications. In particular, we review some old and recent results regarding the genetic structure of the population when throwing neutral mutations on the skeleton of the tree.

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          Most cited references18

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          The sampling theory of selectively neutral alleles.

          W.J. Ewens (1972)
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            Reconciling molecular phylogenies with the fossil record.

            Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ~10 Myr.
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              On the convergence of supercritical general (C-M-J) branching processes

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                Author and article information

                Journal
                2017-02-25
                Article
                1702.07916
                7dc96615-fcc0-4d69-93fd-3de8afb92e33

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

                History
                Custom metadata
                05C05, 60J80, secondary 54E45, 60G51, 60G55, 60G57, 60K15, 92D10
                20 pages, 7 figures, proceedings of MAS 2016, Grenoble, France (Stochastic modeling and Statistics Conference, French Society for Applied and Industrial Math, SMAI)
                math.PR q-bio.PE

                Evolutionary Biology,Probability
                Evolutionary Biology, Probability

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