176 research outputs found
Bayesian total evidence dating reveals the recent crown radiation of penguins
The total-evidence approach to divergence-time dating uses molecular and
morphological data from extant and fossil species to infer phylogenetic
relationships, species divergence times, and macroevolutionary parameters in a
single coherent framework. Current model-based implementations of this approach
lack an appropriate model for the tree describing the diversification and
fossilization process and can produce estimates that lead to erroneous
conclusions. We address this shortcoming by providing a total-evidence method
implemented in a Bayesian framework. This approach uses a mechanistic tree
prior to describe the underlying diversification process that generated the
tree of extant and fossil taxa. Previous attempts to apply the total-evidence
approach have used tree priors that do not account for the possibility that
fossil samples may be direct ancestors of other samples. The fossilized
birth-death (FBD) process explicitly models the diversification, fossilization,
and sampling processes and naturally allows for sampled ancestors. This model
was recently applied to estimate divergence times based on molecular data and
fossil occurrence dates. We incorporate the FBD model and a model of
morphological trait evolution into a Bayesian total-evidence approach to dating
species phylogenies. We apply this method to extant and fossil penguins and
show that the modern penguins radiated much more recently than has been
previously estimated, with the basal divergence in the crown clade occurring at
~12.7 Ma and most splits leading to extant species occurring in the last 2
million years. Our results demonstrate that including stem-fossil diversity can
greatly improve the estimates of the divergence times of crown taxa. The method
is available in BEAST2 (v. 2.4) www.beast2.org with packages SA (v. at least
1.1.4) and morph-models (v. at least 1.0.4).Comment: 50 pages, 6 figure
Probabilistic Graphical Model Representation in Phylogenetics
Recent years have seen a rapid expansion of the model space explored in
statistical phylogenetics, emphasizing the need for new approaches to
statistical model representation and software development. Clear communication
and representation of the chosen model is crucial for: (1) reproducibility of
an analysis, (2) model development and (3) software design. Moreover, a
unified, clear and understandable framework for model representation lowers the
barrier for beginners and non-specialists to grasp complex phylogenetic models,
including their assumptions and parameter/variable dependencies.
Graphical modeling is a unifying framework that has gained in popularity in
the statistical literature in recent years. The core idea is to break complex
models into conditionally independent distributions. The strength lies in the
comprehensibility, flexibility, and adaptability of this formalism, and the
large body of computational work based on it. Graphical models are well-suited
to teach statistical models, to facilitate communication among phylogeneticists
and in the development of generic software for simulation and statistical
inference.
Here, we provide an introduction to graphical models for phylogeneticists and
extend the standard graphical model representation to the realm of
phylogenetics. We introduce a new graphical model component, tree plates, to
capture the changing structure of the subgraph corresponding to a phylogenetic
tree. We describe a range of phylogenetic models using the graphical model
framework and introduce modules to simplify the representation of standard
components in large and complex models. Phylogenetic model graphs can be
readily used in simulation, maximum likelihood inference, and Bayesian
inference using, for example, Metropolis-Hastings or Gibbs sampling of the
posterior distribution
Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates
Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events in a phylogenetic tree and sampled fossils were generated by the same underlying diversification process. A crucial advantage of this model is that it incorporates the possibility that some species may never be sampled. Here, we present an FBD model that estimates tree-wide diversification rates from stratigraphic range data when the underlying phylogeny of the fossil taxa may be unknown. The model can be applied when only occurrence data for taxonomically identified fossils are available, but still accounts for the incomplete phylogenetic structure of the data. We tested this new model using simulations and focused on how inferences are impacted by incomplete fossil recovery. We compared our approach with a phylogenetic model that does not incorporate incomplete species sampling and to three fossil-based alternatives for estimating diversification rates, including the widely implemented boundary-crosser and three-timer methods. The results of our simulations demonstrate that estimates under the FBD model are robust and more accurate than the alternative methods, particularly when fossil data are sparse, as the FBD model incorporates incomplete species sampling explicitly
Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient
Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science
Lessons learned from organizing and teaching virtual phylogenetics workshops
No abstract available
Interleukin-11 Is the Dominant IL-6 Family Cytokine during Gastrointestinal Tumorigenesis and Can Be Targeted Therapeutically
SummaryAmong the cytokines linked to inflammation-associated cancer, interleukin (IL)-6 drives many of the cancer “hallmarks” through downstream activation of the gp130/STAT3 signaling pathway. However, we show that the related cytokine IL-11 has a stronger correlation with elevated STAT3 activation in human gastrointestinal cancers. Using genetic mouse models, we reveal that IL-11 has a more prominent role compared to IL-6 during the progression of sporadic and inflammation-associated colon and gastric cancers. Accordingly, in these models and in human tumor cell line xenograft models, pharmacologic inhibition of IL-11 signaling alleviated STAT3 activation, suppressed tumor cell proliferation, and reduced the invasive capacity and growth of tumors. Our results identify IL-11 signaling as a potential therapeutic target for the treatment of gastrointestinal cancers
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An introduction to video methods in organizational research
Video has become a methodological tool of choice for many researchers in social science, but video methods are relatively new to the field of organization studies. This article is an introduction to video methods. First, we situate video methods relative to other kinds of research, suggesting that video recordings and analyses can be used to replace or supplement other approaches, not only observational studies but also retrospective methods such as interviews and surveys. Second, we describe and discuss various features of video data in relation to ontological assumptions that researchers may bring to their research design. Video involves both opportunities and pitfalls for researchers, who ought to use video methods in ways that are consistent with their assumptions about the world and human activity. Third, we take a critical look at video methods by reporting progress that has been made while acknowledging gaps and work that remains to be done. Our critical considerations point repeatedly at articles in this special issue, which represent recent and important advances in video method
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