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BACKGROUND Determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, 'rocks' and 'clocks'), have appeared irreconcilable; the fossil record supports a Cenozoic origin for most modern lineages,(More)
SUMMARY Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger(More)
BACKGROUND Stramenopiles constitute a large and diverse eukaryotic clade that is currently poorly characterized from both phylogenetic and temporal perspectives at deeper taxonomic levels. To better understand this group, and in particular the photosynthetic stramenopiles (Ochrophyta), we analyzed sequence data from 135 taxa representing most major(More)
Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally,(More)
Understanding the rate at which new species form is a key question in studying the evolution of life on earth. Here we review our current understanding of speciation rates, focusing on studies based on the fossil record, phylogenies, and mathematical models. We find that speciation rates estimated from these different studies can be dramatically different:(More)
OBJECTIVES There is limited knowledge concerning how the effects of socioeconomic status (SES) on mortality interact with gender and age. In addition, current studies are largely based on data from the Western nations. The validity of prior observations needs to be further evaluated. This research examines socioeconomic inequalities in old age mortality in(More)
OBJECTIVE This research evaluates the hypothesis that poor health triggers a change in living arrangements among elderly adults in Japan. METHODS Data came from a national probability sample of 2,200 Japanese people aged 60 or older. Four surveys of this sample were conducted over a period of 9 years, from 1987 to 1996. Multinomial logit regression(More)
Scientists rarely reuse expert knowledge of phylogeny, in spite of years ofeffort to assemble a great “Tree of Life” (ToL). A notableexception involves the use of Phylomatic, which provides tools togenerate custom phylogenies from a large, pre-computed, expert phylogeny ofplant taxa. This suggests great potential for a more generalized systemthat, starting(More)
MOTIVATION Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve(More)