Welcome to the following seminar.
Time and location: April 12, 15:00, in the Pascal room, Gamma 6, Science for Life Laboratory.
Speaker: Gergely J. Szöllösi, Eötvös University, Hungary
Gene transfers, like fossils, can date the tree of life
The geological record provides the only source of absolute time information to date the tree of life. But most life is microbial, and most microbes do not fossilize, leading to major uncertainties about the ages of microbial groups and the timing of some of the earliest and most important events in life's evolutionary history. I discuss our recent results, which show that patterns of lateral gene transfer deduced from analysis of modern genomes encode a novel and highly informative source of information about the temporal coexistence of lineages throughout the history of life. We use new phylogenetic methods to reconstruct the history of thousands of gene families and show that dates implied by gene transfers are strongly correlated with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukaryotes. A comparison with mammalian fossils shows that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.
Please join us for the next SPG seminar, which will be given by Michael Landis. Michael is a Donnelly Postdoctoral Fellow in the Department of Ecology and Evolutionary Biology at Yale University with Michael Donoghue.
Title: Inference of phylogenetic biogeography using models of range evolution
Date: February 23, 2017
Place: KÖL Lunch Room (Frescativägen 54)
Abstract: The spatial distribution of modern biodiversity was generated by evolutionary processes acting over deep time. Because these historical processes cannot be observed directly, phylogenetic models of biogeographic evolution have been employed to reconstruct ancestral species ranges. This family of models, however, is young and the limits of their usefulness and scalability are still being explored. First, to their usefulness, I will discuss how biogeographic processes may be used to date speciation times when conditioning on dated empirical models of paleogeography. Second, to their scalability, I will describe how the unusual features of biogeographic character evolution complicate the use of standard phylogenetic marginalization techniques--such as the pruning algorithm--and demonstrate how Markov chain Monte Carlo may be configured to numerically marginalize over the space of complex evolutionary histories.
Sayyed Auwn Muhammad's PhD defense, Monday, 26 September, in Air room at Scilifelab
Title: Probabilistic Modelling of Domain and Gene Evolution
Opponent: Bastien Boussau, Biometry and Evolutionary Biology Lab, CNRS, Lyon, France
Location: Conference room Air (Gamma building) SciLifeLab, Tomtebodavägen 23A, Solna
Starting Time: 9 AM
Dates: Mon Oct 10 - Tue Oct 18, 2016
Venue: Tovetorp research station (http://www.zoologi.su.se/tovetorp/)
The BIG4 fall workshop 2016 has two main themes. One theme is focused on phylogenetics, phylogenomics and bioinformatics, and is intended to provide students with an introduction to these topics, focused on skills that will be useful in their PhD research projects. There will be a mixture of lectures and practicals; students are encouraged to bring their own datasets and analysis problems. The other theme is citizen science and entrepreneurship, and this part of the course will provide broad introductions, exercises, and inspiration for students interested in pursuing these subjects as part of their current or future activities.
The workshop is primarily aimed at BIG 4 students but (except for the Friday morning session) is open to outside participants as well. We have room for up to 10 additional outside participants on a first come first served basis. Outside participants may choose to come for only part of the course, if they wish.
Register for the course no later than September 28 using the form at this web site: http://bit.ly/2c6i6v0. Outside student participation will be confirmed on September 29. If you cancel past that date, we may very well have to charge you the course fee anyway.
There will be a fee for course, accommodation and food. We expect the total cost to be approximately 2,000 SEK/day for students participating for part of the course, and approximately 15,000 SEK in total for those students taking the entire workshop. Students will receive an invoice after the course is finished.
Monday October 10
Tuesday October 11
Wednesday October 12
Thursday October 13
Friday October 14
Saturday October 15
Sunday October 16
Monday October 17
Tuesday October 18
Raja Hashim Ali will defend his thesis on Thursday 25 Feb at 14:00, in room “Fire”, bottom floor of the Gamma building at Science for Life Laboratory.
The title of the thesis is "From genomes to post-processing of Bayesian inference of phylogeny” and Dannie Durand from CMU is the opponent.
Life is extremely complex and amazingly diverse; it has taken billions of years of evolution to attain the level of complexity we observe in nature now and ranges from single-celled prokaryotes to multi-cellular human beings. With availability of molecular sequence data, algorithms inferring homology and gene families have emerged and similarity in gene content between two genes has been the major signal utilized for homology inference. Recently there has been a significant rise in number of species with fully sequenced genome, which provides an opportunity to investigate and infer homologs with greater accuracy and in a more informed way. Phylogeny analysis explains the relationship between member genes of a gene family in a simple, graphical and plausible way using a tree representation. Bayesian phylogenetic inference is a probabilistic method used to infer gene phylogenies and posteriors of other evolutionary parameters. Markov chain Monte Carlo (MCMC) algorithm, in particular using Metropolis-Hastings sampling scheme, is the most commonly employed algorithm to determine evolutionary history of genes. There are many softwares available that process results from each MCMC run, and explore the parameter posterior but there is a need for interactive software that can analyse both discrete and real-valued parameters, and which has convergence assessment and burnin estimation diagnostics specifically designed for Bayesian phylogenetic inference.
In this thesis, a synteny-aware approach for gene homology inference, called GenFamClust (GFC), is proposed that uses gene content and gene order conservation to infer homology. The feature which distinguishes GFC from earlier homology inference methods is that local synteny has been combined with gene similarity to infer homologs, without inferring homologous regions. GFC was validated for accuracy on a simulated dataset. Gene families were computed by applying clustering algorithms on homologs inferred from GFC, and compared for accuracy, dependence and similarity with gene families inferred from other popular gene family inference methods on a eukaryotic dataset. Gene families in fungi obtained from GFC were evaluated against pillars from Yeast Gene Order Browser. Genome-wide gene families for some eukaryotic species are computed using this approach.
Another topic focused in this thesis is the processing of MCMC traces for Bayesian phylogenetics inference. We introduce a new software VMCMC which simplifies post-processing of MCMC traces. VMCMC can be used both as a GUI-based application and as a convenient command-line tool. VMCMC supports interactive exploration, is suitable for automated pipelines and can handle both real-valued and discrete parameters observed in a MCMC trace. We propose and implement joint burnin estimators that are specifically applicable to Bayesian phylogenetics inference. These methods have been compared for similarity with some other popular convergence diagnostics. We show that Bayesian phylogenetic inference and VMCMC can be applied to infer valuable evolutionary information for a biological case – the evolutionary history of FERM domain.
Seminar 25/11: Understanding the History of Life Using Morphology and Fossils: New Computational Approaches
Seminar at the Swedish Museum of Natural History on Wednesday November 25, 16:15–17:00 in the lunch/seminar room of the KÖL building, level 2:
Understanding the History of Life Using Morphology and Fossils: New Computational Approaches
Postdoctoral Associate, Yale University
Abstract. Fossils represent a unique and indispensable source of data for studying macroevolutionary processes and dynamics, as they provide us with direct glimpses of how life actually evolved on Earth. Although stratigraphic data from fossils have been used extensively in divergence time calibration, morphology remains the primary type of data that can be extracted from fossils for use in phylogenetic inference. In general, however, molecular sequence data is more widely used and trusted for phylogenetic analyses (e.g., 106,255 vs. 33,473 publications matching the topic of “molecular phylogeny” vs. “morphological phylogeny” on the Web of Science between 2010-2015). This is due both to the relative ease of generating large amounts of genetic data as well as concerns about subjectivity and the acquisition of morphological data. As a result, when phylogenetic incongruence arises between morphological/paleontological and molecular datasets, the latter is often viewed as more robust, even when the divergences being inferred occurred in deep time. Molecular data, however, are not infallible, and the meaningful influence of fossil data in phylogeny estimation and comparative analyses is well established. Therefore, efforts directed towards improving the methodological process of generating and analyzing morphological data are a priority.
In this presentation, I will discuss computational approaches that illustrate that: 1) systematic biases and misleading signal may have a profound effect on molecular phylogenetic analyses; 2) the inclusion of phenomic-scale datasets in combined analyses can affect phylogenetic inference and comparative methods, even when morphological characters are vastly outnumbered; and 3) morphological data extraction can potentially be automated and scaled up effectively and efficiently. To demonstrate these points, I use three case studies, respectively: 1) the position of turtles within the amniote tree of life; 2) the evolutionary history and origin of snakes; and 3) the evolution of shape across North Atlantic communities in planktonic foraminifera. These studies set the groundwork for future work aiming to improve computational methods for analyzing morphological and paleontological data, both in terms of data extraction and data interpretation/analysis.
Molecular-Clock Dating Using MrBayes - Seminar and Workshop
22 April - Stockholm: 09:30-11:30, Rum 540, Institutionen för ekologi, miljö och botanik (Lilla Frescati), Stockholms universitet
23 April - Uppsala: 13:15-15:15, Lärosal 4, Evolutionsbiologiskt Centrum, Uppsala universitet
Chi Zhang*, Swedish Museum of Natural History, Stockholm
Johan Nylander, BILS/Swedish Museum of Natural History, Stockholm
MrBayes - the most often used software for Bayesian phylogenetic analysis - has
included many new features since version 3.2. In this seminar, we will
highlight some newly implemented functionality, with focus on the
molecular-clock dating capacities of the current version (v.3.2.4).
The seminar will consist of two parts, where following a presentation* giving
the necessary backrground information, there will be a hands-on tutorial where
participants are encouraged to bring their own data (and computers).
There are two approaches on dating using molecular data: node dating and
total-evidence dating. Node dating calibrates the internal nodes of the tree by
assigning distributions using information from external sources, such as the
fossil record. Total-evidence dating uses the morphological data from fossil
record and morphological and sequence data from recent organisms together to
infer the dates. Several steps involve in Bayesian dating analysis, including
data partitioning, node or fossil age calibration, and setting priors for the
tree and the molecular clock model. I will describe the available calibration
probability distributions, clock tree priors - especially the fossilized
birth-death prior for total-evidence dating, and relaxed clock models, through
a step-by-step tutorial of MrBayes.
The program (MrBayes v.3.2.5) is available from
Participants in the practical part are encouraged to bring their own computers
with the software installed from the above mentioned URL's.
Speakers: Alexandre Antonelli (University of Gothenburg),
Hannes Hettling and Rutger Vos (Naturalis Biodiversity Center,
Title: SUPERSMART: Ecology and evolution in the era of big data
Time: March 24 at 15:00-16:00
Venue: Room 525, Naturhistoriska riksmuseet, Stockholm
Host: Fredrik Ronquist
Abstract: Rapidly growing biological data volumes - including
molecular sequences and fossil records - hold an unprecedented
potential to reveal how evolutionary processes generate and
maintain biodiversity. However, most studies integrating these
data use an idiosyncratic step-by-step approach for the
reconstruction of time-calibrated phylogenies. We will present a
novel conceptual framework, termed SUPERSMART (Self-Updating
Platform for Estimating Rates of Speciation and Migration, Ages,
and Relationships of Taxa), and present our proof of concept for
dealing with the moving targets of biodiversity research. This
framework reconstructs dated phylogenies based on the assembly
of molecular and genomic datasets. The data handled for each step
are continuously updated as databases accumulate new records. We
believe that this emerging framework will provide an invaluable
tool for a wide range of hypothesis-driven research questions in
systematics and evolution. For more information please see
Speaker: William J. Murphy
Title: Genomic Prospects for Resolving Modes of Speciation Across the Mammal Tree of Life
Time: May 19 at 15:15-16:00
Venue: C8:301, BMC, Uppsala,
Host: Robert Ekblom
Recent advances in mammalian phylogenomics have converged on a well-resolved phylogeny at the family level, and even the generic level for some orders (e.g. Primates and carnivores). Despite these advances, the majority of species are not placed in a comprehensive phylogeny based on adequate genomic sampling that is conducive to divergence time estimation and studying patterns of character evolution. Most phylogenies in the literature are based on mitochondrial DNA that may not reflect the true species tree, therefore new tools and methods are needed for examining phylogenetic concordance across the nuclear genome to understand regional variation in signal that might highlight regions influenced by hybridization and reproductive isolation. Here I will present the results from two genomic approaches used to achieve well-resolved nuclear and mitochondrial phylogenies at the species level. The first approach describes the application of genome-wide SNP arrays to produce a comprehensive nuclear phylogeny of the cat family, and a preliminary characterization of regional chromosomal discordance in phylogenetic signal. The second approach highlights the application of low-coverage genome sequencing and capture hybridization approaches on DNAs extracted from archived museum specimens, with a focus on hidden biodiversity within Southeast Asian mammals, and the promise of applying museum-based sequencing to produce a fully resolved tree of life for mammals.
William Murphy is Associate Professor at the Texas A & M University. He has a broad interest in phylogenomics, molecular evolution and sex chromosome evolution and is working primarily with mammals (especially felines).