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My research interests are, admittedly, quite diffuse, and bridge the fields of population genetics (population genetic structure/connectivity; effective population size; coalescent theory; etc.) and phylogenetics (model-based phylogenetic reconstruction; model selection/sensitivity; phylogenetic dating; rate heterogeneity; data partitioning; etc.). The common link among these interests is that they are all require analytically intensive approaches (MCMCMC; genetic algorithms; parametric bootstrapping; maximum likelihood and Bayesian probabilistic approaches; etc.). From my tenure as a graduate student it has become apparent that I am at least as interested in the validity and mechanics of the analytical process as I am with the actual biological question at hand. I am therefore currently working on a number of varied projects with equally varied collaborators.

 
     
       
Introduction to Bayesian Phylogenetics   
Here is a paper I wrote as an Introduction to Bayesian Phylogenetics for neophytes. After reading the primary literature I was certain that there was an easier way to learn this exciting new field. The paper is a little antiquated now, but still useful (I think) to some. If you like it/hate it then I would love to hear your comments (josephwb(at)umich.edu). Better yet, if you know of a better forum in which I could circulate it (after some serious updating) I would be very thankful.
 
TimeTree of Life
with David Mindell
TimeTree      
 

I recently contributed three chapters (Falconiformes, Strigiformes, and Apodiformes) to the hugely collaborative TimeTree of Life project, lead by Blair Hedges and Sudhir Kumar of Penn State. The goal of this project was twofold: 1) summarize the up-to-date taxonomic status of major groups (families and above), and 2) produce a time-calibrated phylogeny (chronogram) synthesized from relevant papers in the field. It was certainly a privilege to be a part of a project that includes some of the worlds greatest systematic biologists, and encompasses all known branches of the tree of life.

     
  The book has been published by Oxford University Press, and chapters can be downloaded for free from the TimeTree of Life website.
 
Reducing Bias in Dating the Origins of Avian Lineages
with Joshua Rest, Jaime García-Moreno, Michael Sorenson, and David Mindell
Rock-Clock

There often exists a large gulf between divergence date estimates derived from the fossil record and genetic data – the so-called 'rock-clock' gap. This gap is particularly wide for the origins of modern avian lineages, where genetic-based dates can sometimes double analogous estimates from the fossil record. In this study, I pay close attention to: i) adequate taxon/character sampling; ii) valid calibration points; iii) allowing for lineage-specific rate heterogeneity; and iv) accommodating uncertainty in tree topology. Despite these efforts, the age estimates generated are consistent with previous molecular studies, and indicate that Neornithes underwent extensive diversification in the Cretaceous, contra to the fossil record.

 
Joseph W. Brown, Joshua S. Rest, Jaime García-Moreno, Michael D. Sorenson, and David P. Mindell. 2008. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biology 6:6. highly_accessed Citations
 
Nuclear DNA Does Not Reconcile ‘Rocks and Clocks’ in Neoaves  
Neoaves Timeline
with Robert Payne and David Mindell
 
Ericson et al. (2006) recently generated a significant neoavian genetic data set and report the youngest genetic divergence time estimates yet published. These authors conclude that there is no reliable molecular support for extensive diversification of Neoaves in the Cretaceous. While an increased agreement with the fossil record is encouraging (and, indeed, sought after), we find a number of problems with their study that calls this conclusion into question. These concerns include inappropriate fossil calibrations, the reliance upon an untested dating method, and the total absence of error intervals on these estimates. Ericson et al. reply to our comment here. Our paper is discussed (favourably!) in a recent News and Views article in Nature by Penny and Phillips here.
An additional problem with the study not mentioned in our critique is that the inferred age of Pandionidae at ~29 Ma is significantly younger than the oldest known Pandionidae fossil at ~37 Ma, a fossil that was supposedly used as a minimum age constraint in their dating analyses.
Joseph W. Brown, Robert B. Payne, and David P. Mindell. 2007. Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al. Biology Letters 3 (3): 257-259. Citations
Here is a NEXUS chronogram file that is formatted for reading in the program FigTree. This format allows the incorporation of error intervals (I used this to generate the figure in the paper), however typical programs like TreeView do not like these. If you want to use TreeView you can simply delete any information within square brackets.
 
Systematics and Bottleneck Appraisal of Peregrine Falcons  
Molecular_Ecology_Cover
with Peter van Coeverden de Groot, Tim Birt, Gilles Seutin, Peter Boag, and Vicki Friesen
My Masters research (thesis pdf) entailed a genetic survey of the entire range of Canadian peregrine falcons, and was a joint project between Queen's University and Parks Canada. We were firstly interested in the validity of sub-species designations (anatum, tundrius, pealei) by determining levels of structure/differentiation based on genetic markers (mitochondrial control region and a suite of nuclear microsatellites). Next we looked into the effects of the massive bottleneck that culminated in the early 1970s with the near range-wide extirpation of the anatum subspecies, both by assessing current levels of genetic polymorphism relative to species with similar changes in population size and by comparing extant individuals with pre-crash museum specimens. Lastly, we were interested in quantifying the effects of introduced (stocked) individuals on the genetic landscape by performing population genetic surveys.
 

Joseph W. Brown, Peter J. van Coeverden de Groot, Tim P. Birt, Gilles Seutin, Peter T. Boag, and Vicki L. Friesen. 2007. Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus. Molecular Ecology 16 (2): 327-343. Citations

I discussed this research with Bob MacDonald on the popular science radio show Quirks and Quarks on CBC Radio One. Visit the story here or download the mp3.
Photo: Dr. Gordon Court
 
Data Partitioning for Phylogenetic Inference
mtDNA
The legitimacy of inferences made using maximum likelihood or Bayesian methodologies ultimately rely on the suitability of the underlying model assumed. While standard nucleotide substitution models are routinely tested for fit to the data at hand (e.g. using the Akaike Information Criterion), various partitioning schemes, which themselves represent different models of molecular evolution, are not. Here I evaluate the fit of models of varying complexity (number of partitions) to a multi-gene mitochondrial DNA data set from paleognathous birds to determine the optimal partitioning strategy for protein-coding mtDNA sequences. Partitioned models are evaluated by fit (in both Bayesian and maximum likelihood frameworks), performance, and predictive abilities. This manuscript is in preparation for Systematic Biology.  
 
Population Connectivity in Species of Concern in Canada  
Blanding's Turtle
with Briar Howes, H. Lisle Gibbs, Pat Weatherhead, Steve Mockford, Tom Herman, and Kent Prior
     

This study, lead by Briar Howes, seeks to index effective population sizes and connectivity patterns amongst populations of two species of concern in Canada, the Black Rat Snake and the Blanding's turtle. Of primary interest is comparing and contrasting historic versus contemporary levels of gene flow. Knowledge of the connectivity of populations within each species is imperative for devising management initiatives. My role in this project is very minor, and is restricted to data analysis.

 
Black Rat Snake Briar J. Howes, Joseph W. Brown, H. Lisle Gibbs, Tom B. Herman, Stephen W. Mockford, Kent A. Prior and Patrick J. Weatherhead. 2008. Directional gene flow patterns in disjunct populations of the black ratsnake (Pantheropis obsoletus) and the Blanding’s turtle (Emydoidea blandingii). Conservation Genetics 10 (2): 407-417.
 
Temporal Assessment of North American Peregrine Falcons     PEFA
with Jeff Johnson, Sandra Talbot, George K. Sage, Kurt K. Burnham, Tom L. Maechtle, William S. Seegar, Michael A. Yates, Bud Anderson, and David Mindell
   
Lead by Jeff Johnson. Genetic measures from temporally-spaced samples reflect the overall stability of populations as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (FST and DEST), and effective population size (Ne). Temporal samples collected at Padre Island Texas (1985-2007) detect no significant differences in genetic diversity or population differentiation in allele frequencies between time periods were observed for North American migratory peregrines. Estimates of harmonic mean Ne were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. Our empirical and simulation results suggest a stable population consistent with data from field-based monitoring. This paper is currently in revision at PLoS ONE.
Photo by Dr. Gordon Court
Effective Population Size in a Stable Peregrine Falcon Population     Peregrine with prey
with Jeff Johnson, Peter van Coeverden de Groot, Tim Birt, Gilles Seutin, and Vicki Friesen
   
Effective population size, Ne, is a fundamental parameter in population genetics, and is critical in conservation biology as it provides a context for interpreting direct census counts (generally expressed as Ne/N). To date, no estimate of Ne has been generated for a stable population of Peregrine Falcons. Here we generate various temporal estimates of Ne using three serial temporal samples from a stable Peregrine Falcon population in Rankin Inlet, Nunavut. We find, consistent with Ne estimates from other birds of prey, that peregrines have a small Ne/N ratio. Knowledge of this ratio can influence future management/survey policies. A manuscript is currently in revision at Conservation Genetics.
 
Photo by Dr. Gordon Court
Phylogenetic Systematics of Cathartidae      
with Jeff Johnson and David Mindell Turkey Vulture
The New World Vultures (family Cathartidae) comprise a small (7 species) specialized group of carrion feeders, ecologically very similar to the unrelated Old World Vultures (family Accipitridae). Using a suite of mitochondrial genes and nuclear introns, we investigate the phylogenetic relationships of extant cathartid taxa, and put these diversification patterns in a temporal framework. A manuscript is in preparation for Systematic Biology.  
Timescale of Land Plant Evolution  
with Yin-Long Qiu
Gingko_fossil    
  This study, spearheaded by Yin-Long Qiu, is aimed at producing a molecular genetic timescale for early land plant evolution. Utilizing multiple genes from cpDNA, mtDNA, and nucDNA genomes for all major branches of the land plant phylogeny, we reconstructed the temporal diversification pattern of this important group considering multiple "relaxed clock" approaches. A manuscript is in preparation for Proceedings of the National Academy of Sciences USA.
   
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