Phylogenetic relationships and classification of the major lineages of Apoidea (Hymenoptera) : with emphasis on the crabronid wasps / by Gabriel A. R. Melo.

no.14

The Compleat cladist : a primer of phylogenetic procedures / E.O. Wiley [et al.]

no.19 (1991)

Restricted walks in regular trees

Let T be the Cayley graph of a finitely generated free group F. Given two vertices in T consider all the walks of a given length between these vertices that at a certain time must follow a number of predetermined steps. We give formulas for the number of such walks by expressing the problem in terms of equations in F and solving the corresponding equations.

Generating trees for permutations avoiding generalized patterns

We construct generating trees with with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation, which allows us to incorporate the adjacency condition about some entries in an occurrence of a generalized pattern. We use these trees to find functional equations for the generating functions enumerating these classes of permutations with respect to different parameters. In several cases we solve them using the kernel method and some ideas of Bousquet-Mélou [2]. We obtain refinements of known enumerative results and find new ones.

The equation xpyq=zr and groups that act freely on Λ-trees

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Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe.

Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.

Polynomial functors and trees

We explore the relationship between polynomial functors and trees. In the first part we characterise trees as certain polynomial functors and obtain a completely formal but at the same time conceptual and explicit construction of two categories of rooted trees, whose main properties we describe in terms of some factorisation systems. The second category is the category Ω of Moerdijk and Weiss. Although the constructions are motivated and explained in terms of polynomial functors, they all amount to elementary manipulations with finite sets. Included in Part 1 is also an explicit construction of the free monad on a polynomial endofunctor, given in terms of trees. In the second part we describe polynomial endofunctors and monads as structures built from trees, characterising the images of several nerve functors from polynomial endofunctors and monads into presheaves on categories of trees. Polynomial endofunctors and monads over a base are characterised by a sheaf condition on categories of decorated trees. In the absolute case, one further condition is needed, a projectivity condition, which serves also to characterise polynomial endofunctors and monads among (coloured) collections and operads.

Climate change effects on animal and plant phylogenetic diversity in southern Africa

Much attention has been paid to the effects of climate change on species' range reductions and extinctions. There is however surprisingly little information on how climate change driven threat may impact the tree of life and result in loss of phylogenetic diversity (PD). Some plant families and mammalian orders reveal nonrandom extinction patterns, but many other plant families do not. Do these discrepancies reflect different speciation histories and does climate induced extinction result in the same discrepancies among different groups? Answers to these questions require representative taxon sampling. Here, we combine phylogenetic analyses, species distribution modeling, and climate change projections on two of the largest plant families in the Cape Floristic Region (Proteaceae and Restionaceae), as well as the second most diverse mammalian order in Southern Africa (Chiroptera), and an herbivorous insect genus (Platypleura) in the family Cicadidae to answer this question. We model current and future species distributions to assess species threat levels over the next 70years, and then compare projected with random PD survival. Results for these animal and plant clades reveal congruence. PD losses are not significantly higher under predicted extinction than under random extinction simulations. So far the evidence suggests that focusing resources on climate threatened species alone may not result in disproportionate benefits for the preservation of evolutionary history.

Level-wise node size distribution of randomly generated regular trees

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The use of classification and regression trees to predict the likelihood of seasonal influenza.

Background Individual signs and symptoms are of limited value for the diagnosis of influenza. Objective To develop a decision tree for the diagnosis of influenza based on a classification and regression tree (CART) analysis. Methods Data from two previous similar cohort studies were assembled into a single dataset. The data were randomly divided into a development set (70%) and a validation set (30%). We used CART analysis to develop three models that maximize the number of patients who do not require diagnostic testing prior to treatment decisions. The validation set was used to evaluate overfitting of the model to the training set. Results Model 1 has seven terminal nodes based on temperature, the onset of symptoms and the presence of chills, cough and myalgia. Model 2 was a simpler tree with only two splits based on temperature and the presence of chills. Model 3 was developed with temperature as a dichotomous variable (≥38°C) and had only two splits based on the presence of fever and myalgia. The area under the receiver operating characteristic curves (AUROCC) for the development and validation sets, respectively, were 0.82 and 0.80 for Model 1, 0.75 and 0.76 for Model 2 and 0.76 and 0.77 for Model 3. Model 2 classified 67% of patients in the validation group into a high- or low-risk group compared with only 38% for Model 1 and 54% for Model 3. Conclusions A simple decision tree (Model 2) classified two-thirds of patients as low or high risk and had an AUROCC of 0.76. After further validation in an independent population, this CART model could support clinical decision making regarding influenza, with low-risk patients requiring no further evaluation for influenza and high-risk patients being candidates for empiric symptomatic or drug therapy.