Abstracts For Presentations By Nicholas J Matzke
Table of Contents

Botany Society of America 2016: Bayesian estimation of the global biogeographic history of the Solanaceae

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Dupin, Julia; Matzke, Nicholas J.; Saarkinen, Tiina; Knapp, Sandra; Olmstead, Richard G.; Bohs, Lynn; Smith, Stacey D. (2016). "Bayesian estimation of the global biogeographic history of the Solanaceae." Botany Society of America 2016. July 3-August 3, Savannah, Georgia. http://2016.botanyconference.org/engine/search/533.html

Abstract: Aim. The tomato family Solanaceae is distributed on all major continents except Antarctica and has its center of diversity in South America. Its worldwide distribution suggests multiple long distance dispersals within and between the New and Old Worlds. Here we apply maximum likelihood (ML) methods and newly developed biogeographic stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Methods. Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model-fitting of a range of biogeographic models with the program BioGeoBEARS. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographic events. Results. Our best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America. Conclusions. For Solanaceae, South America is not only the family's current center of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build-up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction, and timing of biogeographic events in a statistically rigorous framework.

Keywords: BioGeoBEARS, directionality, long-distance dispersal, historical biogeography, Biogeographic Stochastic Mapping (BSM), Solanaceae

SSB Special Symposium at Evolution 2016: Putting evolution into ecological niche modeling: Building the connection between phylogenies, paleobiology, and species distribution models

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Symposium: SSB1
Title: Putting evolution into ecological niche modeling: Building the connection between phylogenies, paleobiology, and species distribution models
Co-organizers: Nicholas J. Matzke and Dan Warren
Date: Sunday, June 19 (morning)
Time: 8:15 am-9:45 am, 10:15-11:45 am (12 slots at 15 minutes each)
Room: Ballroom C, Theater
Summary website: http://www.evolutionmeetings.org/special-talks.html
Organizational website: http://phylo.wikidot.com/putting-evolution-into-ecological-niche-modeling

Meeting: Evolution 2016
Location: Austin, TX
Venue: Austin Convention Center
Dates: June 17-21, 2016
Website: http://www.evolutionmeetings.org/evolution-2016---austin-texas.html

Summary: Species Distribution Models (SDMs) are increasingly popular tools in ecology, conservation biology, and climate change research. They have been used in hundreds of publications (Figure 1). The most common SDM methods correlate occurrence data with environmental variables, estimating an ecological or environmental niche model (ENM). This niche model is then projected onto a map to predict species distribution (or suitable habitat). Despite their immense popularity, SDM results are often limited by several common problems. Large data sets allow complex correlational models to be fit, but these models are often over-fit, extrapolating poorly to changed environments in the past 1,2 (when predicting paleo-distributions) or present 3 (when predicting species invasions). This lowers confidence in SDMs predicted under future climate change scenarios. Also, SDMs typically assume that geographic range is wholly determined by environment, ignoring dispersal limitation and other historical biogeography processes 4,5, as well as species interactions. This means that ENMs may include some environmental variables as predictors when they are only "accidental" correlates of some other spatial process, further contributing to the overfitting problem.

The fundamental issue underlying the above difficulties is that the SDMs are typically estimated one-species-at-a-time, at one time point (the Recent). This ignores any information that might be gained from the phylogenetic relationships of species, even though phylogenetic niche conservatism appears to be common 4. It also ignores any information that might be gained from time-series data on distributions and climate. As evolutionary biologists, we should be seeking ways to make evolutionary methods and models useful to the wider scientific community, and it seems likely that by combining information on present-day niches distributions, and how niches and distributions evolved on the phylogeny, will provide both evolutionary insight and improved niche models that more robust and do better at capturing the true predictors of species ranges 4. Therefore Symposium will be devoted to "building the connection" between SDMs and phylogenies. How can we integrate phylogenetic models of niche evolution and trait evolution into the SDM estimation process? How can we better integrate paleoclimate and paleo-range data, and historical biogeography? The Symposium will solicit contributions from researchers at the forefront of relevant areas, whether or not they consider themselves "species distribution modelers" per se. For example, workers in phylogenetic comparative methods and evolutionary morphometrics will have much to contribute to the question of how niche evolution should be modeled and estimated, as do conservation biologists who take into phylogenetic relatedness and diversity 6,7, and paleobiologists who have examined the congruence of SDM predictions and fossil occurrences 1,2,8-11. All symposium speakers will be asked to connect their research to the overall question, "How can we connect phylogeny, paleobiology, and species distribution modeling?"

The Skeptic Zone Podcast: The evolution of antievolutionism

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Matzke, Nicholas J. (2016). The Evolution of Antievolutionism. Podcast, "Maynard's Spooky Action" segment of The Skeptic Zone, April 10, 2016. Starts at 0:05:15. http://skepticzone.libsyn.com/the-skeptic-zone-390-10april2016

Maynard Interviews Dr Nick Matzke, a postdoctoral scientist at ANU, holding a Discovery Early Career Researcher Award (DECRA) from the Australian Research Council.

Australian Skeptics: The Evolution of Anti-evolutionism. Dinner Presentation

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Matzke, Nicholas J. (2016). The Evolution of Anti-evolutionism. Dinner Presentation for Australian Skeptics, April 9, 2016. http://www.skeptics.com.au/2016/03/06/sydney-dinner-april-9-the-evolution-of-antievolutionism/ PDF of presentation: http://phylo.wikidot.com/local--files/abstracts-for-presentations-by-nicholas-j-matzke/2016-04-09_Australian_Skeptics_v8.pdf

AUSTRALIAN SKEPTICS DINNER

SATURDAY April 9, 2016
Heritage Function Centre (upstairs),
Ryde-Eastwood Leagues Club, 117 Ryedale Road, West Ryde
6.30pm for 7.15pm $50 per person (includes buffet dinner)

You might have thought creationism was dead, done and dusted. But far from it. We're kicking off our new year of Skeptics dinners in Sydney with a bit of an eye-opener - the evolution of the anti-evolution movement.

Professor Graham Oppy, head of the School of Philosophical, Historical & International Studies at Monash University says that, since 2000, the teaching of creationism in science classes has become "more prevalent".

"Groups like CSF (Christian Science Foundation), Answers in Genesis, Creation Ministries, and Creation Research … work hard to get their materials into schools", he says, and this includes giving creationist 'showbags' to students in NSW.

Who better, then, to speak on this topic than someone involved in the infamous US Kitzmiller v Dover trial in 2005 over a policy that required the teaching of 'intelligent design' in biology classes.

Dr Nick Matzke is a postdoctoral scientist at ANU, holding a Discovery Early Career Researcher Award (DECRA) from the Australian Research Council. He is located in the Moritz Lab in ANU's Division of Evolution, Ecology, and Genetics, and is working in evolutionary biogeography & phylogenetics. From 2004-2007, Nick worked for the US National Centre for Science Education, which combats attempts to insert creationism and other anti-science topics into public schools. In December 2015, he published an article in Science magazine, "The Evolution of Anti-evolution Policies after //Kitzmiller v. Dover//," that presented a phylogenetic tree of anti-evolution legislation in the US.

So what's the latest on creationism, intelligent design, evolution and anti-evolution? How is the anti-evolution movement 'evolving' to spread its message? All of this … and food … at the Skeptics dinner on April 9 at the Ryde-Eastwood Leagues Club.

Molecular Paleobiology of Australia’s Terrestrial Vertebrates: Ground-truthing tip-dating methods and models using fossil Canidae reveals major differences in performance

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Matzke, Nicholas J. Ground-truthing tip-dating methods and models using fossil Canidae reveals major differences in performance. Molecular Paleobiology of Australia’s Terrestrial Vertebrates Conference. Melbourne, Victoria, Australia. Melbourne Museum, 11-11:15 a.m., Tuesday, April 5, 2016. http://www.australianmolecularpaleobiology.org/p/program.html

Abstract: Tip-dating methods - methods where the ages of fossil OTUs (operational taxonomic units/terminal taxa) are directly used as the primary source of dating information - are becoming popular alternatives to traditional "node-dating." However, they have not been extensively tested. Here, I "ground-truth" the most popular methods against a dated tree (~1-2 my resolution) of fossil Canidae. This "ground truth" tree was constructed in monographs by Canidae experts Wang and Tedford, who combined parsimony analysis with detailed knowledge of species stratigraphy and morphological gradations. The term "ground truth" is taken from accuracy assessment in remote sensing, and although the big picture of canid phylogeny and dating seems to be secure, I have no objection to interpretation of the study as a test of Bayesian methods to reproduce expert opinion, rather than literal "truth." Using a revised canid morphology dataset from Slater (PNAS, 2015), I compare MrBayes 3.2.5 (released April 2015) to Beast 2.3 combined with BEASTmasteR (phylo.wikidot.com/beastmaster), an R package that automates the conversion of dates, priors, and NEXUS character matrices into the complex Beast2 XML format. I find that unconstrained MrBayes analysis under the uniform tree prior fails to retrieve reasonable results, exhibiting extremely high uncertainty in dates. On the other hand, Beast2 inference matches the ground-truth well, under both birth-death serially sampled (BDSS, disallowing direct ancestors) and sampled ancestor (SABD) tree models, as does MrBayes using BDSS. MrBayes using SABD seems to have difficulty converging in some runs. These results, on a very high quality fossil dataset, indicate that while tip-dating is very promising, methodological issues in tip-dating can have drastic effects, and require close attention, especially on more typical datasets where the distinction between "method problems" and "data problems" will be more difficult to detect.

Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS

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Matzke, N.J. (2016). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. ANU Research School of Biology. Poster at Early-and Mid-Career Conference (Follow on Twitter at #RSBEMCR16). R. N. Robertson Lecture Theatre, Bldg. 46. Feb. 11th, 2016, 4:45 pm.

Link: http://phylo.wikidot.com/local--files/abstracts-for-presentations-by-nicholas-j-matzke/2016-02-11_ANU_trait-based_dispersal_v2.pdf

When Darwin Visited Valparaiso (Chile). Darwin Day Lecture at Valparaiso University

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Matzke, Nicholas J. (2016). When Darwin Visited Valparaiso (Chile). Darwin Day Lecture at Valparaiso University, Friday, Jan. 15, 3:30-4:30 pm, Christopher Center Library. Sponsor: Robert Swanson.

The Evolution of Antievolutionism before and after Kitzmiller v. Dover (2005)

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The Evolution of Antievolutionism before and after Kitzmiller v. Dover (2005)

by Nicholas J. Matzke, DECRA Fellow, Research School of Biology, ANU.
ua.ude.una|ekztam.kcin#ua.ude.una|ekztam.kcin
http://phylo.wikidot.com/nicholas-j-matzke

Date: 2016 (TBA)
Time: ???
Room: ???
Sponsor: Lindell Bromham, Tempo and Mode Seminar

Abstract: Antievolutionist creationism has had a number of major waves, focused in the U.S. but spreading internationally. The last major wave was "intelligent design" creationism, which received its greatest defeat in the Federal court case Kitzmiller v. Dover, decided December 20, 2005. This case challenged the constitutionality of an "intelligent design" policy required in high school biology classrooms in Dover, Pennsylvania. I worked on this case while at the National Center for Science Education (NCSE), a nonprofit watchdog group devoted to defending classroom coverage of evolution, global warming, and other allegedly "controversial" topics. I will discuss the case and its background, and also present a new study conducting a phylogenetic analysis of "crypto-creationist" proposals in the decade since Kitzmiller.

Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS

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Matzke, Nicholas J. (2016). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. Speciation and Biogeography session, Society of Integrative and Comparative Biology Annual Meeting, Jan. 3-8, 2016. Wednesday, January 6, 3:30-4:30 pm. 3:30 pm, Wed. Jan. 6, Poster P3-12.

Link: http://phylo.wikidot.com/local--files/abstracts-for-presentations-by-nicholas-j-matzke/2016-01-06_SICB_trait-based_dispersal_v2.pdf

Abstract: Organism traits must be important in historical biogeography. In particular, rates of dispersal (both range-expansion dispersal, and jump dispersal leading to founder-event speciation) must depend to some degree on traits such as flight and its loss, and seed dispersal mechanisms and the dispersal abilities of animals that transport seeds. However, to date no probabilistic historical biogeographical models have been available that allow geographic range and traits to co-evolve on the phylogeny, with traits influencing dispersal ability. In purely continuous-time Markov models, adding a trait is just a matter of doubling the size of the rate matrix; however, biogeographical models also include a much more complex discrete-time model describing how geographic range can change during cladogenesis. Traits might also influence this process. I present an addition to the R package BioGeoBEARS that enables an evolving discrete trait to influence dispersal ability for both anagenetic and cladogenetic range change. This model can be freely combined with models adding jump dispersal (e.g., DEC+J), distance as a predictor of dispersal (+x models, with dispersal rate multiplied by distance^x), and other variants. I test the model against simulations and datasets where large evolutionary changes in dispersal ability are highly likely (e.g., Pacific rails, which have repeatedly lost flight).

Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS

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Matzke, N. (2015). Trait-dependent dispersal models for phylogenetic biogeography, in the R package BioGeoBEARS. Annual Meeting of the Society of Australian Systematic Biologists, 2015. Tuesday, December 8, 2015. Sirius Room: From R to ecology, 3:50-4:10.

Abstract: Organism traits must be important in historical biogeography. In particular, rates of dispersal (both range-expansion dispersal, and jump dispersal leading to founder-event speciation) must depend to some degree on traits such as flight and its loss, and seed dispersal mechanisms and the dispersal abilities of animals that transport seeds. However, to date no probabilistic historical biogeographical models have been available that allow geographic range and traits to co-evolve on the phylogeny, with traits influencing dispersal ability. In purely continuous-time Markov models, adding a trait is just a matter of doubling the size of the rate matrix; however, biogeographical models also include a much more complex discrete-time model describing how geographic range can change during cladogenesis. Traits might also influence this process. I present an addition to the R package BioGeoBEARS that enables an evolving discrete trait to influence dispersal ability for both anagenetic and cladogenetic range change. This model can be freely combined with models adding jump dispersal (e.g., DEC+J), distance as a predictor of dispersal (+x models, with dispersal rate multiplied by distance^x), and other variants. I test the model against simulations/datasets where large evolutionary changes in dispersal ability are highly likely (e.g., Pacific rails).

Univ. Tasmania, Stochastic Modelling Meets Phylogenetics 2015 (#SMMP2015)

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Matzke, Nicholas J. (2015). Putting Evolution Into Ecological Niche Modelling (And: Statistical model choice in phylogenentic biogeography more generally). At: Stochastic Modelling meets Phylogenetics (SMMP), collaborative workshop November 16-18, University of Tasmania, Hobart. November 16, 2015, 12:30 pm. Mathematics & Physics Building, University of Tasmania. (#SMMP2015) http://www.maths.utas.edu.au/People/oreilly/SMMP/smmp2015.html
http://phylo.wikidot.com/local--files/abstracts-for-presentations-by-nicholas-j-matzke/2015-11-16_Matzke_UTas_v1_putting_evo_into_ENM.pdf

ANU - intro talk for Craig Moritz Lab Group

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Title: Biogeographical Stochastic Mapping: Bayesian estimation of the history and timing of biogeographical events on phylogenies

Nicholas Matzke (2015). "Biogeographical Stochastic Mapping: Bayesian estimation of the history and timing of biogeographical events on phylogenies." Craig Moritz Lab Group, Gould Meeting Room, 2 pm, August 5, 2015

Date: August 5, 2015
Time: 2-3 pm

Link: NA

Summary: Traditional likelihood methods in historical biogeography estimate the probability of each geographic range at each node. Usually the most-probable range at each node is plotted, and this is taken to be the approximate history. This is not technically accurate and might be badly misleading in some cases. A solution is stochastic mapping of possible histories on the phylogeny. This has been widely applied in phylogenetics for sequence data and discrete characters, but these character models are inappropriate in historical biogeography, where the state space is much more complex, and geographic range changes through both anagenetic and cladogenetic events. I present a novel algorithm that enables stochastic mapping on any biogeographic model available in BioGeoBEARS, as well as graphical display and statistical summary of the timing and frequency of dispersal and vicariance events. An animation of realizations of possible histories under the DEC and DEC+J models is demonstrated for Hawaiian Psychotria shrubs. R functions and an example script performing stochastic mapping are available at http://phylo.wikidot.com/biogeobears . The functions build upon on the R package BioGeoBEARS, available for all platforms at CRAN.

Contact: ua.ude.una|ekztamkcin#ua.ude.una|ekztamkcin

Supplementary Information: R source code is also archived in this article’s online Supplementary Data. (And here: http://phylo.wikidot.com/biogeobears#stochastic_mapping )

Society of Vertebrate Paleontology 2015

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SVP 75th Annual Meeting
October 14-17, 2015
Hyatt Regency Dallas
Dallas, Texas, USA

Submission Number: 891
Abstract Title: Bayesian tip-dating with continuous characters using BEASTmasteR
First Author: Nicholas Matzke
Session: Technical Session V
Session Title: Histology and Methods
Session Date: Wednesday, October 14, 2015
Session Time: 1:45 PM - 4:15 PM

Bayesian "tip-dating" is a method for simultaneously inferring the topology and dating of a phylogeny by including fossils as dated tips and conducting a total-evidence analysis, for example in the program BEAST2. Tip-dating is being actively explored, but all work to date has only used discrete (qualitative) characters for fossil tips. However, continuous (quantitative) characters are often available for fossil specimens, and ideally tip-dating analyses would include these as well. To enable such analyses, continuous-data capabilities were added to the R package BEASTmasteR. BEASTmasteR takes a data table of continuous traits and converts them into BEAST2 XML format, adding these characters to any DNA, amino acid, and/or discrete morphological data that is available. The likelihood of continuous traits on the tree is calculated using the Brownian motion model available in BEAST2 through modification of BEAST2's 2-dimensional continuous phylogeography model into a 1-dimensional model for any trait. Each trait is given a separate rate parameter which is also estimated. To test the validity of the model, continuous characters were simulated on an assumed tree (derived from a dated canid tree) with 22 tips (both fossil and living) under a Brownian motion model. Sets of 10, 25, or 100 continuous characters were generated and BEAST2 XML files were constructed using BEASTmasteR. Each BEAST2 inference was run for 50,000,000 generations. Inference on 10- or 25-character datasets converged quickly on the true tree, with the 25-character dataset showing higher posterior probabilities for many clades (only 4 branches with <50% posterior probability, PP) than the 10-character dataset (10 branches with <50% PP). Dating uncertainty also decreased by about 30%. However, the 100-character dataset failed to converge, perhaps because of the difficulty of jointly searching tree space and 100 rate parameters. The implications for practical analysis will be discussed, including the importance of the assumptions of independence between characters and independent rates. BEASTmasteR performance indicates that it should be helpful to researchers exploring continuous data: BEAST2 XML setup with continuous data takes <1 minute in BEASTmasteR, but at least 4 hours for an experienced user constructing the XML input by hand.

Evolution 2015

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Matzke, Nicholas J. (2015). Historical biogeography models with dispersal probability as a function of distance

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Matzke, Nicholas J. (2015). "Historical biogeography models with dispersal probability as a function of distance(s)." SSE symposium: Frontiers in Parametric Biogeography, Presentations for the SSB Biogeography Symposium in Guarujá, Brasil, Evolution 2015. 10:45-11:15 a.m.

PDF of presentation: http://phylo.wikidot.com/local--files/abstracts-for-presentations-by-nicholas-j-matzke/2015-06-30_Matzke_DEC%2BJ%2Bx_Evo2015_v3.pdf

Massana et al. (2015). Non-null effects of a null range: Exploring parameter estimation in the dispersal-extinction-cladogenesis model.

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Massana, Kathryn; Beaulieu, Jeremy; Matzke, Nicholas J.; O'Meara, Brian (2015). "Non-null effects of a null range: Exploring parameter estimation in the dispersal-extinction-cladogenesis model." SSE symposium: Frontiers in Parametric Biogeography, Presentations for the SSB Biogeography Symposium in Guarujá, Brasil, Evolution 2015. 8:45-9:15 a.m.

Dupin et al. (2015). Solanaceae biogeography: dispersal patterns over space and time.

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Dupin, Julia; Matzke, Nicholas; Knapp, Sandra; Bohs, Lynn; Olmstead, Richard; Särkinen, Tiina; Smith, Stacey D. (2015). "Solanaceae biogeography: dispersal patterns over space and time." Poster session, 7 p.m., Sala de exposições room, at Evolution 2015 in Guarujá, Brasil.

Society for Systematic Biologists Standalone Meeting 2015, Ann Arbor, Michigan

Zhang et al. (2015), Biogeography of Caribbean weevils highlights the importance of founder-event speciation

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Zhang, Guanyang; Barashat, Usmaan; Matzke, Nicholas J.; Franz, Nico (2015). Biogeography of Caribbean weevils highlights the importance of founder-event speciation. Society for Systematic Biologists Standalone Meeting 2015 (SSB2015), Ann Arbor, Michigan, May 21, 2015. http://ssb2015standalone.weebly.com/program.html http://www.slideshare.net/GYZhang1/b-100-zhang

Matzke (2015), BEASTmasteR: Tip-dating with fossils in Beast2, using R to convert NEXUS data files to XML input

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Matzke, Nicholas J. (2015). "BEASTmasteR: Tip-dating with fossils in Beast2, using R to convert NEXUS data files to XML input." Lightning Talk, Society of Systematic Biology Standalone Meeting 2015 (SSB2015), Ann Arbor, Michigan. 1:30 pm, session C, Michigan Union, Pendleton room. http://ssb2015standalone.weebly.com/program.html http://phylo.wdfiles.com/local--files/beastmaster/2015-05-21_Matzke_SSB2015_BEASTmasteR_v1.pdf

Dating dinos by putting fossils in trees: simultaneous estimation of evolutionary relationships and phylogenetic divergence times of dinosaurs (and other groups) with Bayesian MCMC techniques, February 27, 2015

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Title: Dating dinos by putting fossils in trees: simultaneous estimation of evolutionary relationships and phylogenetic divergence times of dinosaurs (and other groups) with Bayesian MCMC techniques

Date: Friday, February 27, 2015
Time: 4 pm
Location: Room 213 Academic Support Building B. Department of Math, Howard University: http://www.coas.howard.edu/mathematics/colloquia&seminars.html

Room: Room 213 Academic Support Building B
Host: Alex Burstein

SUMMARY:

Fossil data are crucial to correct estimation of phylogeny and divergence times. However, most traditional methods artificially separate the analysis of fossil relationships and divergence time analysis. For example, it is common for paleontologists to estimate the topological position of fossils using cladistic or Bayesian methods, either in a morphology-only or “total evidence” analysis. This tree, which is undated, may then be used by molecular biologists to supply calibration distributions for dating a molecules-only tree of living taxa, using a Bayesian MCMC program such as BEAST ("Bayesian Evolutionary Analysis by Sampling Trees"). Such trees form the starting point for various comparative methods which require dated phylogenies, e.g., model-based ancestral state analyses, diversification analyses, or historical biogeography.

Such procedures “throw away” most of the fossil data, treating paleontology as merely a source of calibration points for molecular analyses, and separate the questions of estimating relationships and dating, when in fact they may be linked. However, increasing collaboration between paleontologists, biologists, statisticians and computer scientists has been fruitful in yielding new technologies and techniques that attempt to combine fossil and living morphology, fossil dates, and molecular data in joint analyses, also known as "tip-dating" as the dated fossils are included as tips in the phylogenetic tree.

I discuss BEASTmasteR, an R package that can combine fossil, DNA, and dating information into the complex XML input required by BEAST. BEASTmasteR also produces XML Bayesian hierarchical models encoding absolute or relative dating information, including: (1) fossil tips with uncertain dates (e.g., date-ranges based on stratigraphic bins, or distributions derived from radiometric dates); (2) relative dating information for tips (e.g., in some cases two fossils from the same deposit have approximately the same date, despite their absolute date being uncertain; or one fossil may be known to be older than another); and (3) relative dating information for nodes with linked dates. These approaches are demonstrated on several invertebrate and vertebrate datasets. In assassin spiders, inclusion of amber-preserved fossils as tips supports divergences consistent with ancient Gondwanan vicariance. In salmonids, inclusion of Eosalmo as a tip suggests that genome duplication preceded the evolution of anadromy by 45-60 My. In hominids, linking nodes of a gene tree/species tree analysis to a fossil tip-dated phylogeny inferred a human-chimp divergence at 4.38-5.54 Ma, while a morphology-only analysis yielded 4.5-8.95 Ma. With theropod dinosaurs, Bayesian joint estimation supports traditional views about the relationships of Archaeopteryx to other dinosaurs.

http://phylo.wikidot.com/beastmaster

Bavaria State Botanical Garden and Herbarium, January 2015

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Title: Model Selection in Historical Biogeography: when is Founder-event Speciation important?

Date: Friday, January 26, 2015
Time: 11 am
Location: Botanische Staatssammlung München
(Bavarian State Collection for Botany, Munich, Bavaria, Germany)
http://www.snsb.mwn.de/index.php/en/institutionen-2?id=60

The Bavarian Natural History Collections (Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB)
http://www.snsb.mwn.de/index.php/en/

Room: TBA
Host: Susanne Renner, Ludwig-Maximilians-Universität, Munich (LMU Munich), Germany; Director of the Botanical Gardens of Munich, Director of the Herbaria in Munich
http://www.sysbot.biologie.uni-muenchen.de/en/people/renner/

SUMMARY:

New Biogeography Model: Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC+J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. Both models are shown to be special cases of the "claSSE" model.

Simulation tests: The identifiability of DEC and DEC+J is tested on datasets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC+J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes +J.

Empirical tests: DEC and DEC+J are compared on 13 empirical datasets drawn from studies of island clades. Likelihood ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC+J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC+J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.

Further applications: Probabilistic modeling in biogeography opens up many possible research applications, including biogeographical stochastic mapping, biogeographical dating, and inclusion of phylogenetic information in species distribution modeling (SDM).

BioGeoBEARS: Help, tutorials and updates on the BioGeoBEARS R package are available at:

http://phylo.wikidot.com/biogeobears

University of Helsinki, January 2015

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Title: Model Selection in Historical Biogeography: when is Founder-event Speciation important?

Date: Friday, January 16, 2015: Lecture 2 pm
Time: 2 pm - 2:45 pm
Location: Geosciences Department, University of Helsinki, Finland
Room: TBA
Host: Laura K Säilä, Dept. of Geosciences, University of Helsinki, Finland

SUMMARY:

New Biogeography Model: Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC+J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. Both models are shown to be special cases of the "claSSE" model.

Simulation tests: The identifiability of DEC and DEC+J is tested on datasets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC+J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes +J.

Empirical tests: DEC and DEC+J are compared on 13 empirical datasets drawn from studies of island clades. Likelihood ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC+J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC+J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.

Further applications: Probabilistic modeling in biogeography opens up many possible research applications, including biogeographical stochastic mapping, biogeographical dating, and inclusion of phylogenetic information in species distribution modeling (SDM).

BioGeoBEARS: Help, tutorials and updates on the BioGeoBEARS R package are available at:

http://phylo.wikidot.com/biogeobears

IBS 2015, Bayreuth, Germany

(link to this section)

Title: Biogeographical Stochastic Mapping: Bayesian estimation of the history and timing of biogeographical events on phylogenies

Nicholas Matzke (2015). "Biogeographical Stochastic Mapping: Bayesian estimation of the history and timing of biogeographical events on phylogenies." Talk at the 2015 Biannual Meeting of the International Biogeography Society. Session: Historical and Paleo-Biogeography. January 10, 2015, 13:30-13:45, H 22, RW II.

Date: Saturday, January 10, 2015
Time: 1:30-1:45 pm

Link: http://www.bayceer.uni-bayreuth.de/ibs2015/en/prog/bayconf/beitrag_detail.php?id_obj=12643

Summary: Traditional likelihood methods in historical biogeography estimate the probability of each geographic range at each node. Usually the most-probable range at each node is plotted, and this is taken to be the approximate history. This is not technically accurate and might be badly misleading in some cases. A solution is stochastic mapping of possible histories on the phylogeny. This has been widely applied in phylogenetics for sequence data and discrete characters, but these character models are inappropriate in historical biogeography, where the state space is much more complex, and geographic range changes through both anagenetic and cladogenetic events. I present a novel algorithm that enables stochastic mapping on any biogeographic model available in BioGeoBEARS, as well as graphical display and statistical summary of the timing and frequency of dispersal and vicariance events. An animation of realizations of possible histories under the DEC and DEC+J models is demonstrated for Hawaiian Psychotria shrubs. R functions and an example script performing stochastic mapping are available at http://phylo.wikidot.com/biogeobears . The functions build upon on the R package BioGeoBEARS, available for all platforms at CRAN.

Contact: gro.soibmin|ekztam#gro.soibmin|ekztam

Supplementary Information: R source code is also archived in this article’s online Supplementary Data. (And here: http://phylo.wikidot.com/biogeobears#stochastic_mapping )

SVP 2014, Berlin: Putting fossils in trees: new methods for combining morphology, time, and molecules to estimate phylogenetic position and divergence times of living and fossil taxa

(link to this section)

Note 1: See the Abstracts for "Putting Fossils in Trees Symposium"
Note 2: See the BEASTmasteR code and example scripts!

Putting fossils in trees: new methods for combining morphology, time, and molecules to estimate phylogenetic position and divergence times of living and fossil taxa

Co-Convenors: Nicholas J. Matzke, April Wright, Graeme Lloyd, David W. Bapst

Fossil data are crucial to correct estimation of phylogeny and divergence times. However, most traditional methods artificially separate the analysis of fossil relationships and divergence time analysis. For example, it is common for paleontologists to estimate the topological position of fossils using cladistic or Bayesian methods, either in a morphology-only or “total evidence” analysis. This tree, which is undated, may then be used by molecular biologists to supply calibration distributions for dating a molecules-only tree of living taxa. Such trees form the starting point for various comparative methods which require dated phylogenies, e.g., model-based ancestral state analyses, diversification analyses, or historical biogeography.

Such procedures “throw away” most of the fossil data, treating paleontology as merely a source of calibration points for molecular analyses, and separate the questions of estimating relationships and dating, when in fact they may be linked. However, increasing collaboration between paleontologists, biologists, statisticians and computer scientists has been fruitful in yielding new technologies and techniques that attempt to combine fossil and living morphology, fossil dates, and molecular data in joint analyses. This symposium will be devoted to reviewing, discussing, and critiquing new methods and models for estimating phylogenetic trees and for incorporating fossils in the derivation of divergence times.

The three foci of the symposium are: 1. "Model-based methods: advantages and limitations." This will focus on the assumptions behind the current probabilistic models for morphological and fossil data, the resulting advantages and limitations, and suggestions for improvements. 2. "Fossils as terminal taxa in dating analyses: prospects and challenges." Methods using fossils as terminal taxa in dating analyses are new and mostly unevaluated, so participants will present case studies that give insight into the practical benefits and problems encountered in the use of such methods. 3. "Fossils as dual information sources: morphology and stratigraphy." The stratigraphic range and sampling frequency of clades also gives important information about the timing of clade origins. Stratocladistics was an early attempt to take this information into account, but was not widely adopted. Probabilistic methods, as well as advances in fossil databases, may allow improved approaches. Participants will review and critique recent developments in this area.

EvMorph series, University of Chicago, October 2014

(link to this section)

Evolutionary Morphology Seminar: Nicholas Matzke, University of Tennessee

When: Thursday, October 9, 2014 7:30–8:30 p.m.

Where: Henry Hinds Laboratory, Room 176

5734 South Ellis Avenue, Chicago, IL

Description: Model Selection in Historical Biogeography: When is Founder-Event Speciation Important?

Contact: Geophysical Sciences
773-834-0695

Tag: Seminars

Notes: Persons with disabilities who need an accommodation in order to participate in this event should contact the event sponsor for assistance. For events on the Student Events Calendar, please contact ORCSA at (773) 702-8787.

http://events.uchicago.edu/cal/event/eventView.do?b=de&amp%3BcalPath=%2Fpublic%2Fcals%2FMainCal&amp%3Bguid=CAL-ff808081-48cb3bcf-0148-cc0715b7-00001ab4eventscalendar%40uchicago.edu&amp%3BrecurrenceId=#.VDYcSFTIq6g.gmail

SMBE 2014, Puerto Rico

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins

Monday 9th June: Life Technologies Lunchtime Symposium / Posters 1001 - 1278 - 9th June 13.00 - 15.30

P-86

Nicholas Matzke 1 ,2, Patrick Shih3 ,4

1 National Institute of Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA,

2 Department of Integrative Biology, University of California, Berkeley, CA, USA,

3 Joint Bioenergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA, 4Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA

Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the α and β subunits of ATP synthase and its relatives, and the EF-Tu. The methods yield reductions in dating uncertainty of 14–26% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred ~900 Mya and mitochondrial endosymbiosis occurred ~1,200 Mya.

See poster:

PDF of poster for SMBE 2014

This work is based on:

Shih, Patrick M.; Matzke, Nicholas J. (2013). "Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins." Proceedings of the National Academy of Sciences, 110(30), 12355-12360. (Scholar | DOI | Journal)

Also, see writeup of this article by:

Zhaxybayeva, Olga (2013). "Anciently duplicated genes reduce uncertainty in molecular clock estimates." Proceedings of the National Academy of Sciences, 110(30), 12168–12169. (Scholar | DOI | Journal)

Evolution 2014, Raleigh, NC

Simulation tests of probabilistic models for historical biogeography: DEC and DEC+J

PDF of draft talk

2C_306B Methodology
Date: Sunday, June 22, 2014
Time: 1:30 PM - 2:45 PM
Location: 306 B
Chair: Mario dos Reis

2:00 PM - 2:15 PM

18

Nicholas Matzke, NIMBioS, gro.soibmin|ekztam#gro.soibmin|ekztam (Presenter)

Contributed Presentation

Simulation tests of probabilistic models for historical biogeography: DEC and DEC+J

Several phylogenetic models for historical biogeography are in widespread use, e.g. character mapping, Dispersal-Vicariance Analysis (DIVA), and Dispersal-Extinction-Cladogenesis (DEC). In addition, new models have become available: BayArea, and the variety of models implemented in the R package BioGeoBEARS. These include DEC+J (which adds founder-event speciation to DEC) and DIVALIKE (a likelihood interpretation of DIVA; a DIVALIKE+J model is also available). There has been very little testing of biogeographical models against simulated data in the situation when the true model is substantially different than the assumed inference model. Also, all of the above models assume that the observed tree is the true tree, ignoring possible missing speciation/extinction events, and dependence of speciation/extinction rates on geographic range. These possibilities are taken into account by the GeoSSE and ClaSSE models, but at the cost of many more free parameters, which may strain typically small biogeographic datasets. To test the accuracy of DEC and DEC+J inference on datasets simulated under different biogeographical and SSE models, I jointly simulated phylogenies and geographic range under 6 macroevolutionary models. The first three assumed speciation/extinction were independent of geographic range: (1) Yule process (pure-birth, no extinction); (2) Birth-Death (BD) process with extinction rate 1/3 of the speciation rate; (3) BD process with extinction equal to speciation. The next three assumed an SSE model where the base speciation rate was multiplied by the number of areas occupied, and base extinction rate was divided by the number of areas occupied. This produced (4) SSE with speciation but zero extinction rate; (5) SSE with with the base extinction rate 1/3 of the speciation rate; and (6) SSE with base rates of speciation and extinction equal. For each of the 6 macroevolutionary models, all combinations of low/middle/high values were used for these biogeographic parameters: d (rate of range-expansion), e (rate of range-contraction), and j (relative weight of founder-events versus traditional DEC cladogenesis events at speciation). The datasets (138 parameter combinations, 100 simulations each with 50 living species) were subjected to inference under DEC and DEC+J. DEC and DEC+J were distinguishable under all 6 models, except when j was very small and d very high. DEC artificially raises d and e when DEC+J is the true model, and shows significantly reduced accuracy in inferring ancestral range. These results indicate that the fact that DEC+J is favored over DEC by many empirical datasets is not likely to be an artefact of missing SSE processes.

Non-null effects of a null range: Exploring parameter estimation in the dispersal-extinction-cladogenesis model

1324

Non-null effects of a null range: Exploring parameter estimation in the dispersal-extinction-cladogenesis model

3A_301A Phylogenetic Methods
Date: Monday, June 23, 2014
Time: 8:30 AM - 9:45 AM

Location: 301 A
Chair: Elizabeth Wade
9:15 AM - 9:30 AM

Kathryn Massana, University of Tennessee, Knoxville, ude.ktu|anassamk#ude.ktu|anassamk (Presenter)
Jeremy Beaulieu, NIMBios, gro.soibmin|ueiluaebj#gro.soibmin|ueiluaebj
Brian O'Meara, ude.ktu|araemob#ude.ktu|araemob
Nicholas Matzke, NIMBioS, gro.soibmin|ekztam#gro.soibmin|ekztam

Parametric models in historical biogeography that integrate geographic ranges and phylogenies have shown to be extremely informative in understanding the geographic range evolution of taxa. One such approach is the dispersal-extinction-cladogenesis (DEC) model, which has been widely used in empirical analyses of the evolution of geographic range using discrete area states. However, local extinction rates are difficult to estimate well in this model. We explore the cause of this as well as a potential solution.

rexpokit and cladoRcpp: R packages integrating FORTRAN and C++ for faster matrix exponentiation and likelihood calculations in historical biogeography

PDF of draft talk

ievobioE_402 iEvoBio software bazaar

Open-source software demos and reception for iEvoBio

Date: Tuesday, June 24, 2014

Time: 3:15 PM - 5:00 PM

Location: 402

rexpokit and cladoRcpp: R packages integrating FORTRAN and C++ for faster matrix exponentiation and likelihood calculations in historical biogeography (1219)
Nicholas Matzke, NIMBioS (United States)
Drew Schmidt, University of Tennessee

1219

Drew Schmidt, University of Tennessee, ude.ktu.htam|tdimhcs#ude.ktu.htam|tdimhcs
Nicholas Matzke, NIMBioS, gro.soibmin|ekztam#gro.soibmin|ekztam (Presenter)

iEvoBio Software Demo

rexpokit and cladoRcpp: R packages integrating FORTRAN and C++ for faster matrix exponentiation and likelihood calculations in historical biogeography

Probabilistic models for phylogeny-based inference of historical biogeography face several computational challenges, especially when programmed in R. The first is large state spaces: for example, an analysis using 10 discrete geography areas has 2^10=1024 possible combinations of presence/absence in each region, and a transition matrix that is 1024x1024. Exponentiating this matrix is extremely slow in standard R matrix exponentiation routines. The R package "rexpokit" integrates the FORTRAN EXPOKIT library, making exponentiation of such large matrices feasible, although not rapid. Further speed improvements are made by parallel processing. A second challenge is enumerating and assigning probabilities to different biogeographical events at cladogenesis. Here, a naive implementation would have to examine every possible combination of ancestor state, left descendant state, and right descendant state, which would be 1023^3, or over 1 billion combinations. Here I made great improvements in speed with algorithms that eliminate impossible combinations a priori, and use of Rcpp for all for-loops. This is implemented in the R package cladoRcpp. I will present quick demonstrations of these calculations, the resulting speedups, and suggest that these packages can serve as relatively simple examples for researchers wishing to integrate FORTRAN or C++ into their R programming.

Rexpokit: http://cran.r-project.org/web/packages/rexpokit/index.html CladoRcpp: http://cran.r-project.org/web/packages/cladoRcpp/index.html Used for historical biogeography by: BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts http://cran.r-project.org/web/packages/BioGeoBEARS/index.html Examples, updates, and help listserv are at PhyloWiki: http://phylo.wikidot.com/biogeobears

GNU General Public License version 3.0 (GPL-3.0) http://opensource.org/licenses/GPL-3.0

SVP 2014, Berlin: Tip-Dating: Estimating Dated Phylogenies Using Fossils as Terminal Taxa

(link to this section)

Note: See the BEASTmasteR code and example scripts!

Tip-Dating: Estimating Dated Phylogenies Using Fossils as Terminal Taxa - FULL

This workshop will introduce participants to new computational methods that allow joint inference of phylogenetic relationships and divergence times. In older dating methods, fossil relationships were estimated with an undated cladistic or Bayesian analysis, and then these fossils were converted, usually subjectively, into prior probability distributions on the dates of certain nodes. These calibrations were then used in molecular clock analyses to date molecular trees. This procedure essentially “threw away” hard-won fossil data (and any living morphology data as well) once the dating calibration was produced.

However, in the last two years, several methods have become available that allow the addition of fossil and living morphology, as well as fossil dates, to dating analyses. In these methods, the phylogenetic relationships of the fossils and living taxa are estimated simultaneously with the dating of the tree. These methods have the potential to revolutionary for paleontologists. First, because character and dating data from fossil specimens are a requirement for the method, paleontologists and morphologists will have an increased role to play in future divergence time analyses, previously the domain of molecular biologists. Second, the joint estimation of fossil relationships and the divergence times of fossil taxa is of intrinsic interest, and many phylogenetic comparative methods can be applied to fossil data once statistically-estimated, time-scaled trees of fossil taxa are available.

The two main methods in use currently are BEAST (Pyron 2011; Wood, Matzke et al. 2013; Alexandrous et al. 2013) and MrBayes 3.3 (Ronquist et al. 2012). Both take more skill and background than traditional phylogeny-estimation and dating methods. Therefore we will guide participants through tutorials and then help them to set up analyses of their own data.

Date: Tuesday, November 4

Time: 10:00am - 4:00pm

Location: The Leibniz Headquarters (Chausseestr. 111, 150 meters away from the Museum für Naturkunde and next to the UBahn station Naturkundemuseum)

Cost: Free (FULL!)
Minimum Number of Participants: 10
Maximum Number of Participants: 40

Leaders:

Nicholas J. Matzke
National Institute for Mathematical and Biological Synthesis
University of Tennessee
gro.soibmin|ekztam#gro.soibmin|ekztam

April Wright
Univeristy of Texas, Austin
moc.liamg|mlirpa.thgirw#moc.liamg|mlirpa.thgirw

Society for Molecular Biology and Evolution (SMBE) 2014 Poster

Title: "Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins."

Society for Molecular Biology and Evolution (SMBE) 2013 Poster

Title: "Tighter estimation of hominoid divergence times by hierarchical Bayesian analysis of dated fossil morphology and incompletely sorted genes."

International Biogeography Society 2013 Poster

Link to the poster PDF and poster abstract. Title: "Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses."

References also included

Animation Of The Geographical History Of The Hawaiian Islands

Animation Of The Geographical History Of The Hawaiian Islands, based on Clague (1996), R code by Nick Matzke.

R-based Labs for IB200B - Phylogenetics - Ecology & Evolution, spring 2011, U.C. Berkeley Dept. of Integrative Biology

R-based Labs for IB200B - Phylogenetics - Ecology & Evolution, spring 2011, U.C. Berkeley Dept. of Integrative Biology

WORKSHOP: Methodological Workshop on Biodiversity Dynamics

Methodological Workshop on Biodiversity Dynamics — for: "Evolution of Life on Pacific Islands and Reefs: Past, present, and future", May 26, 2011

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