Seminar 22/11: Daniel Field

posted Nov 16, 2017, 5:16 AM by Allison Hsiang

Our next SPG talk will be next Wednesday (Nov. 22) and given by Daniel Field, who is a 50th Anniversary Prize Fellow in the Department of Biology and Biochemistry at Bath. Daniel will speak about phylogenetic and biogeographic applications to understanding avian palaeobiology.

Please note that this seminar will be held in the Vintergatan conference room, rather than in the usual location.

Title: Birds, Fossils, and Lingering Question Marks: New Frontiers in Avian Phylogenetic Palaeobiology
Date: November 22, 2017
Time: 15:00-16:00
Place: Vintergatan conference room (map; upper level meeting rooms)

Abstract: Birds are among the most diverse and ubiquitously distributed tetrapod clades; they inhabit a myriad of different environments, and exhibit incredible disparity in their forms and lifestyles. Unraveling how, when, and why this diversity has arisen demands an appeal to the fossil record of crown birds (Neornithes), as fossils provide us with the only direct evidence of neornithine evolutionary history. Additionally, understanding the origins of the features that make birds unique—such as feather-assisted flight—forces us to look outside of Neornithes to the avian stem lineage, where the nature, timing, and order of character transformations are only accessible through fossils. I will discuss recent macroevolutionary advances related to crown birds and their close relatives among non-avian dinosaurs, covering questions like “How did the ancestors of modern birds survive the end-Cretaceous mass extinction event that eliminated their stem-group relatives?”, and “How and why have the biogeographic distributions of modern bird groups changed throughout their evolutionary history?”, with an appeal for the development of analytical methods suited to accommodating the complexity of macroevolutionary patterns revealed by the fossil record.

Seminar 15/11: Simon Whelan

posted Nov 16, 2017, 5:16 AM by Allison Hsiang

Our next SPG seminar will be given by Simon Whelan, researcher at the Department of Ecology and Genetics at Uppsala University. Simon will be speaking about sequence alignment and its impact on phylogenetic inference. 

Title: The problem of sequence alignment in phylogenetics
Date: November 15, 2017
Time: 15:00-16:00
Place: KÖL Lunch Room (Frescativägen 54)

Abstract: Inferring evolutionary histories and processes from sets of homologous sequences is a joint problem of sequence alignment and phylogenetic inference. Computational convenience led to the widespread adoption of the two-step process, whereby those problems are separated and solved in succession. Nearly all research in molecular evolution has focussed on the final phylogenetic inference problem, where models of substitution and tree shape have the potential to provide insights into natural selection and population structures. All of this progress rests upon the assumption that the sequence alignment step is correct. 

This talk discusses the gap between the perceived and real accuracy of the solutions to the sequence alignment problem and their impact on phylogenetics. I will explore first some of the evidence that errors in sequence alignment are real and have a demonstrable effect on downstream phylogenetic analyses, introducing systematic biases and affecting the biological conclusions drawn from these studies. Next I will discuss approaches that take existing alignments and try to identify and remove errors in them. These include existing alignment filtering approaches and some new approaches to processing alignments currently under development in my research group. Finally I will present an alternative to the two-step approach that can directly estimate evolutionary parameters, including the phylogenetic tree and selection, directly from sequences without assuming a fixed alignment. 

Seminar 25/10: Ajith Harish

posted Oct 18, 2017, 5:30 AM by Allison Hsiang

Our next SPG seminar will take place on next Wednesday, October 25th, from 10:00-11:00 (note the time is different from usual). Ajith Harish from Uppsala University will give a talk on building phylogenies using genomes. 

Title: The tree of life: What genomes tell (and what genes cannot!)
Date: October 25, 2017
Time: 10:00-11:00
Place: KÖL Lunch Room (Frescativägen 54)

Abstract: Evolution as viewed through genome trees brings into question the founding operational assumptions of the traditional gene-tree culture. The four assumptions of the gene tree culture that are singularly important to evolutionary interpretations of the tree of life (ToL) are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the ToL is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between sequence alignment-based gene trees are due to horizontal transfer (HT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from protein structural-domains does not support any one of the four principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HT including endosymbiosis is a negligible player in genome evolution from UCA to the present.

Seminar 4/10: Ashish Tomar

posted Sep 28, 2017, 5:34 AM by Allison Hsiang

Please join us for our first fall 2017 SPG seminar, to be presented by Ashish Tomar. Ashish is an Early Stage Researcher at Era7 Bioinformatics, Spain, and is co-supervised by Niklas Wahlberg and Fredrik Ronquist as part of the BIG4 consortium.

Title: Graph-based storage and visualization of Phylogenomics and Taxonomic information
Date: October 4, 2017
Time: 15:00-16:00
Place: KÖL Lunch Room (Frescativägen 54)

The talk is mainly focused on the use of latest technologies for storage and visual representation of the biological big data. Graph-based storage is better suited for representing the biological information which is often highly complex and connected. This talk also focuses on the different ways to visualize the hierarchical biological data especially the information represented as a tree. 

Seminar 31/5: Sequential Monte Carlo Mini-Symposium

posted May 22, 2017, 2:12 AM by Allison Hsiang

On Wednesday, May 31, we will be hosting a mini-symposium on Sequential Monte Carlo (SMC) at the museum. We will have two speakers, Fredrik Lindsten and Lawrence Murray, both from the Department of Information Technology at Uppsala University. The talks will take place in the morning, followed by lunch and afternoon discussion for all interested parties.


Title: Divide-and-Conquer Sequential Monte Carlo for Inference in Probabilistic Graphical Models
Speaker: Fredrik Lindsten
Date: May 31, 2017
Time: 10:00-11:00
Place: Naturhistoriska riksmuseet, Vintergatan conference room, 5th floor (near Cosmonova)

Abstract: Probabilistic graphical models (PGMs) are widely used to represent and to reason about underlying structure in high-dimensional probability distributions. We develop a framework for using sequential Monte Carlo
(SMC) methods for inference and learning in general PGMs. Structural information from the PGM is used to decompose the graph into a collection of subgraphs that can be organized in a tree. Based on this we develop a
new class of SMC samplers, Divide-and-Conquer SMC, for performing inference over the tree. We will see how this method extends the standard chain-based SMC framework to a method that naturally runs on trees. We
illustrate empirically that these approaches can outperform standard methods in terms of estimation accuracy. They also open up novel parallel implementation options and the possibility of concentrating the computational effort on the most challenging parts of the problem at hand.


Title: Software and Sequential Monte Carlo
Speaker: Lawrence Murray
Date: May 31, 2017
Time: 11:00-12:00
Place: Naturhistoriska riksmuseet, Vintergatan conference room, 5th floor (near Cosmonova)

Abstract: I will give a brief introduction to two software projects: LibBi and Birch. LibBi is used for state-space modelling on parallel and distributed computing hardware, such as multicore CPUs, GPUs and clusters, using Sequential Monte Carlo (SMC) and particle Markov chain Monte Carlo (PMCMC) methods. It is particularly effective for models with complex nonlinear dynamics, including continuous-time dynamics. Birch is its newer incarnation, currently in development. The idea of Birch is to broaden the class of models and inference methods that can be supported, beyond state-space models and SMC, moving from a model specification language to a general-purpose probabilistic programming language. I will focus in particular on the ability of Birch to solve analytically-tractable substructure in complex models.


Afternoon Discussion Session
Date: May 31, 2017
Time: 13:00-16:00
Place: Naturhistoriska riksmuseet, Sirius conference room, 5th floor (near Cosmonova)

Seminar 12/4: Gene transfers, like fossils, can date the tree of life (G. Szöllösi)

posted Apr 7, 2017, 2:51 AM by Johan Nylander

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.

Seminar 23/2: Michael Landis

posted Feb 14, 2017, 7:08 AM by Allison Hsiang   [ updated Feb 14, 2017, 7:23 AM ]

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
Time: 15:00-16:00
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.

Seminar 9/2: Chi Zhang

posted Feb 2, 2017, 5:52 AM by Allison Hsiang

Our first 2017 SPG seminar will be given by Chi Zhang, former postdoc with Fredrik Ronquist and current postdoc with Tanja Stadler at D-BSSE, ETH Zürich.

All are invited and encouraged to attend!

Title:  Bayesian inference of species networks from multilocus data
Date:  February 9, 2017
Time:  15:00-16:00
Place:  KÖL Lunch Room (Frescativägen 54)

Abstract:  Hybridization plays an important role during speciation in certain animals and plants. The process leaves “fingerprints” in the genomic data, yet there is a lack of models and tools for analyzing such data.  We developed a Bayesian method to infer species networks from multilocus sequence data. The method applied the multispecies network coalescent (MSNC) model for the gene trees embedded in the species network, which accounts for gene tree discordance due to incomplete lineage sorting and reticulate species evolution such as hybridization or introgression. We also applied novel MCMC operators to sample the species networks and gene trees along with other parameters.
The method will be available as package for BEAST2.

PhD Defence: Probabilistic Modelling of Domain and Gene Evolution

posted Sep 22, 2016, 2:16 AM by Johan Nylander

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

Date: 2016-09-26

Jens Lagergren

Course: Phylogenetics, Phylogenomics, Citizen science and Entrepreneurship

posted Sep 19, 2016, 12:27 AM by Johan Nylander

BIG 4 Fall Workshop 2016

Phylogenetics, Phylogenomics, Citizen science and Entrepreneurship

Dates: Mon Oct 10 - Tue Oct 18, 2016

Venue: Tovetorp research station (


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.

Course registration and fee

Register for the course no later than September 28 using the form at this web site: 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.

Schedule Overview

Monday October 10
Fredrik Ronquist. Introduction to statistical inference. Bayesian phylogenetic inference and Markov chain Monte Carlo simulation.
Fredrik Ronquist. Stochastic models of evolution. Introduction to MrBayes. Exercises using MrBayes.

Tuesday October 11
Fredrik Ronquist. Divergence time estimation: node dating and total-evidence dating. Statistical biogeography. Model testing, model averaging and other special topics.
Fredrik Ronquist. Phylogenetic graphical models. Introduction to RevBayes. Exercises using MrBayes and RevBayes.

Wednesday October 12
Erik Gobbo. De novo genome sequencing: next generation sequencing and genome assembly.
Chris Wheat. Gene finding, genome annotation and phylogenomic inference.
Chris Wheat, Erik Gobbo. Genome assembly, gene finding, genome annotation and phylogenomics exercises. Questions, discussion.

Thursday October 13
Rodrigo Esparza-Salas. Introduction to metabarcoding.
Daniel Marquina. Metabarcoding: special topics.
Rodrigo Esparza-Salas, Daniel Marquina. Metabarcoding exercises.

Friday October 14
BIG 4 Midterm Review [Only BIG 4 participants].
BIG 4 Midterm Review [Only BIG 4 participants].

Saturday October 15
Johan Nylander. Handling bioinformatics data in a unix environment. Bioinformatics exercises. Bring your own data and questions!

Sunday October 16
Free day for social activities. Food will be served as usual.

Monday October 17
Inga von Sydow. Why you should become an entrepreneur.
Inga von Sydow, Lyubomir Penev, Eduardo Pareja, Karin Carlsson. Round table discussion on entrepreneurship in biosystematics, informatics and genetics.
Karin Karlsson (Savantic AB). Training session: Steps in the entrepreneurship process.

Tuesday October 18
Karoly Makonyi. A personal view on citizen science.
Karin Carlsson. Gamification and viral effects: a case study.
Jakob Jönsson. Citizen science in cosmology.
Devin Sullivan. [Title TBA].
Erik Thorelli. Bionote - A citizen science platform for logging and sharing species sightings
Miroslav Valan. A brief history of citizen science and its potential in the era of big data. 
Miroslav Valan, Karoly Makonyi. Roundtable discussion on citizen

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