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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. |
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| Introduction to Bayesian Phylogenetics |
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| 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. |
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| Reducing
Bias in Dating the Origins of Avian Lineages |
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Joshua Rest, Jaime García-Moreno, Michael Sorenson, and David Mindell |
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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.
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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.  |
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| Nuclear
DNA Does Not Reconcile ‘Rocks and Clocks’ in Neoaves |
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Robert Payne and David Mindell |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| Systematics and Bottleneck Appraisal of
Peregrine Falcons |
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Peter van Coeverden de Groot, Tim Birt, Gilles Seutin, Peter Boag,
and Vicki Friesen |
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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. |
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| 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. (COVER ARTICLE) |
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| I discussed
this research recently with Bob MacDonald on the popular science radio
show Quirks and Quarks on
CBC Radio One. Visit the story here
or download the mp3. |
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Photo by Dr. Gordon
Court |
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| Data Partitioning for Phylogenetic Inference |
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David Mindell |
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| 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.
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| Population Connectivity in Species of
Concern in Canada |
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| with
Briar Howes, Lisle Gibbs, Pat Weatherhead, Steve Mockford, Tom Herman,
and Kent Prior |
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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. |
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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
online early. |
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| Effective Population Size in a Stable
Peregrine Falcon Population |
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| with
Peter van Coeverden de Groot, Tim Birt, Gilles Seutin, Peter Boag,
and Vicki Friesen |
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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. |
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Photo
by Dr. Gordon Court |
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| Phylogenetic Systematics of Cathartidae |
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Jeff Johnson and David Mindell |
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| The
New World Vultures (family Cathartidae) comprise a small (6 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
Molecular Phylogenetics and Evolution. |
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| Genetic Relationships of Peregrine Falcon
Subspecies |
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| with
Jeff Johnson, Sandra Talbot, and David Mindell |
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| This
study, lead by Jeff Johnson, is aimed at investigating the genetic
relationships amongst subspecies of Peregrine Falcons. Using microsatellite
data from both published studies and newly processed samples, we hope
to discern phylogeographic patterns that could suggest historical
processes that lead to the contemporary distribution. |
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Photo
by Dr. Gordon Court |
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