feed.xml

<?xml version="1.0" encoding="utf-8"?>
<feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en">
<title type="text">phyletica</title>
<generator uri="https://github.com/jekyll/jekyll">Jekyll</generator>
<link rel="self" type="application/atom+xml" href="http://phyletica.org/feed.xml" />
<link rel="alternate" type="text/html" href="http://phyletica.org" />
<updated>2026-03-30T13:40:40-05:00</updated>
<id>http://phyletica.org/</id>
<author>
  <name>Jamie Oaks</name>
  <uri>http://phyletica.org/</uri>
  <email>phyletica@auburn.edu</email>
</author>


<entry>
  <title type="html"><![CDATA[Visiting Duke Center for Genomic and Computational Biology]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/duke-visit/" />
  <id>http://phyletica.org/duke-visit</id>
  <published>2022-11-09T00:00:00-06:00</published>
  <updated>2022-11-09T00:00:00-06:00</updated>
  <author>
    <name>Jamie Oaks</name>
    <uri>http://phyletica.org</uri>
    <email>joaks@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;I just got back to Auburn after a fun visit to the
&lt;a href=&quot;https://biostat.duke.edu/research/duke-center-genomic-and-computational-biology&quot;&gt;Center for Genomic and Computational Biology&lt;/a&gt;
at
&lt;a href=&quot;https://duke.edu/&quot;&gt;Duke University&lt;/a&gt;
to give a seminar.
One of the highlights of the visit was spending time with the graduate students
of the Computational Biology &amp;amp; Bionformatics Program.
They asked great questions after the seminar and at our lunch together.&lt;/p&gt;

&lt;p&gt;Many thanks to CBB Ph.D. student &lt;a href=&quot;https://www.devangthakkar.com/&quot;&gt;Devang Thakkar&lt;/a&gt;
for inviting me to speak and organizing my visit.&lt;/p&gt;

&lt;p&gt;Here are the slides from my talk:&lt;/p&gt;

&lt;iframe src=&quot;//www.slideshare.net/slideshow/embed_code/key/8dwx5Mfs8EdeP1&quot; width=&quot;595&quot; height=&quot;485&quot; frameborder=&quot;0&quot; marginwidth=&quot;0&quot; marginheight=&quot;0&quot; scrolling=&quot;no&quot; style=&quot;border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;&quot; allowfullscreen=&quot;&quot;&gt; &lt;/iframe&gt;
&lt;div style=&quot;margin-bottom:5px&quot;&gt; &lt;strong&gt; &lt;a href=&quot;//www.slideshare.net/jamieoaks7/generalizing-phylogenetics-to-infer-patterns-predicted-by-processes-of-diversification-254039437&quot; title=&quot;Generalizing phylogenetics to infer patterns predicted by processes of diversification&quot; target=&quot;_blank&quot;&gt;Generalizing phylogenetics to infer patterns predicted by processes of diversification&lt;/a&gt; &lt;/strong&gt; from &lt;strong&gt;&lt;a href=&quot;//www.slideshare.net/jamieoaks7&quot; target=&quot;_blank&quot;&gt;Jamie Oaks&lt;/a&gt;&lt;/strong&gt; &lt;/div&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/duke-visit/&quot;&gt;Visiting Duke Center for Genomic and Computational Biology&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on November 09, 2022.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Tanner receives SSB GSRA award!]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/tanner-ssb-award/" />
  <id>http://phyletica.org/tanner-ssb-award</id>
  <published>2022-05-27T00:00:00-05:00</published>
  <updated>2022-05-27T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congrats-tanner&quot;&gt;Congrats, Tanner!&lt;/h2&gt;

&lt;p&gt;Congratulations to
Ph.D. student
Tanner Myers
for receiving the
&lt;a href=&quot;https://www.systbio.org/graduate-student-research-awards.html&quot;&gt;Graduate Student Research Award&lt;/a&gt;
from the
&lt;a href=&quot;https://www.systbio.org/&quot;&gt;Society of Systematic Biologists&lt;/a&gt;
to study (among other things) if a large chromosomal inversion reduces gene
flow along a hybrid zone between two lineages of fence lizards.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/tanner-ssb-award/&quot;&gt;Tanner receives SSB GSRA award!&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on May 27, 2022.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Claire receives STRI Fellowship!]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/claire-stri-fellowship/" />
  <id>http://phyletica.org/claire-stri-fellowship</id>
  <published>2022-01-25T00:00:00-06:00</published>
  <updated>2022-01-25T00:00:00-06:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congratulations-claire&quot;&gt;Congratulations, Claire!&lt;/h2&gt;

&lt;p&gt;Congratulations to
&lt;a href=&quot;https://www.linkedin.com/in/claire-tracy-01a8a2225/&quot;&gt;Claire Tracy&lt;/a&gt;
for receiving a Short-Term Fellowship from the
&lt;a href=&quot;https://stri.si.edu/&quot;&gt;Smithsonian Tropical Research Institute&lt;/a&gt;.
This will help support her research into the evolution of
tolerance to temperature fluctuations in damselfish.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/claire-stri-fellowship/&quot;&gt;Claire receives STRI Fellowship!&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on January 25, 2022.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Generalizing Bayesian phylogenetics to model shared divergences]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/generalized-phylo-preprint/" />
  <id>http://phyletica.org/generalized-phylo-preprint</id>
  <published>2021-10-18T00:00:00-05:00</published>
  <updated>2021-10-18T00:00:00-05:00</updated>
  <author>
    <name>Jamie Oaks</name>
    <uri>http://phyletica.org</uri>
    <email>joaks@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;We are excited about some new work out of lab that relaxes an important
assumption in phylogenetics.
&lt;a href=&quot;https://doi.org/10.1101/2021.07.23.453597&quot;&gt;In a new bioRxiv preprint&lt;/a&gt;,
&lt;a href=&quot;https://perryleewoodjr.com/&quot;&gt;Perry Wood, Jr.&lt;/a&gt;,
&lt;a href=&quot;https://cameronsiler.com/&quot;&gt;Cam Siler&lt;/a&gt;,
&lt;a href=&quot;https://biodiversity.ku.edu/herpetology/people/brown&quot;&gt;Rafe Brown&lt;/a&gt;,
and I
describe how we generalize the space of trees in Bayesian phylogenetics to
avoid assuming divergences are independent across a phylogeny, and allow us to
infer shared divergences among multiple clades.
We have released
&lt;a href=&quot;http://phyletica.org/ecoevolity&quot;&gt;a new version of ecoevolity (Version 1.0.0)&lt;/a&gt;
that implements this fully phylogenetic approach to inferring shared divergence
events across phylogenetic trees.&lt;/p&gt;

&lt;h2 id=&quot;the-assumption&quot;&gt;The assumption&lt;/h2&gt;

&lt;p&gt;In phylogenetics, we assume lineages diverge independently (conditional on the
topology) and only leave two descendant lineages (i.e., bifurcate).
Put another way, we assume all processes of diversification cause only a single
lineage to bifurcate, and have no affect on any of the other extant lineages
across the phylogeny.
Across the tree of life, there are likely many exceptions to this assumption.
For example, we can imagine rising sea levels fragmenting an island and
causing co-distributed species of lizards to diverge at the same time.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/slides-bifurcating.gif&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/slides-bifurcating.gif&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                Island fragmenetaion causing bouts of shared divergences.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;Instead of lizards on islands, let’s imagine three members of a gene family
residing along a region of a chromosome that gets duplicated.
This would create shared divergences across the phylogenetic history of the
gene family.
When multiple infected individuals spread a pathogen to others at a social
gathering, this will create shared divergences in the “transmission tree” of
the pathogen.
In fields as diverse as biogeography, genome evolution, and epidemiology, there
are interesting processes that violate the assumption of independent
divergences and cause shared divergences.&lt;/p&gt;

&lt;p&gt;Back to our insular lizard example, we can also imagine
the rising sea levels fragmenting the island into more than
two islands, like in the animation below.
This will cause multifurcations
(a lineage diverging into three or more descendants)
in addition to shared divergences.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/slides-multifurcating.gif&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/slides-multifurcating.gif&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                Island fragmenetaion causing multifurcating, shared
                divergences.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;Similarly, in epidemiology, when an infected individual spreads a pathogen to
two or more others at a social gathering, this will create a multifurcating
divergence in the transmission tree.&lt;/p&gt;

&lt;p&gt;Current phylogenetic methods for inferring rooted trees assume all divergences
are independent and bifurcating.
More formally, if we have \(N\) tips, current methods only consider
trees with \(N-1\) independent, bifurcating divergences.
When shared or multifurcating divergences were common in the evolutionary
history of the system we want to study, such tree models are over-parameterized
as illustrated below.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/gecko-trees-flipped-cropped.svg&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/gecko-trees-flipped-cropped.svg&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                When shared or multifurcating divergences have occurred, current
                phylogenetic models are over-parameterized.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;More importantly, by assuming all divergences are independent and bifurcating,
current phylogenetic methods do not allow us to test for patterns of shared or
multifurcating divergences predicted by processes of diversification that are
of interest across fields like biogeography, genome evolution, and
epidemiology.&lt;/p&gt;

&lt;h2 id=&quot;our-approach&quot;&gt;Our approach&lt;/h2&gt;

&lt;p&gt;To relax this assumption, we developed a Bayesian approach to generalizing the
space of tree models to allow for shared and multifurcating divergences
&lt;a class=&quot;citation&quot; href=&quot;#Oaks2021phycoeval&quot;&gt;(Oaks &lt;span style=&quot;font-style: normal&quot;&gt;et al.&lt;/span&gt;, 2022)&lt;/a&gt;.
Under our generalized tree distribution,
trees with \(N - 1\) bifurcating divergences
are
only one class of tree models in a greater space of trees
with anywhere from from 1 to \(N - 1\) potentially shared
or multifurcating divergences.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/four-leaf-labeled-trees-boxed-highlight-shared-grid-cropped.png&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/four-leaf-labeled-trees-boxed-highlight-shared-grid-cropped.png&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                The rooted topologies considered by current phylogenetic methods (within
                box) and the additional tree models considered by phycoeval's generalized
                tree model.
                The tree models with nonindependent (shared) divergences are highlighted in
                orange.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;We developed reversible-jump Markov chain Monte Carlo algorithms to perform
inference across this generalized space of trees.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/phycoeval-rj-cartoon.png&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/phycoeval-rj-cartoon.png&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
&lt;/figure&gt;

&lt;p&gt;This allows us to jointly infer relationships, shared and multifurcating
divergences, and divergence times.&lt;/p&gt;

&lt;p&gt;We coupled the generalized tree model with the “SNAPP likelihood”
&lt;a class=&quot;citation&quot; href=&quot;#Bryant2012&quot;&gt;(Bryant &lt;span style=&quot;font-style: normal&quot;&gt;et al.&lt;/span&gt;, 2012)&lt;/a&gt;
for directly
calculating the probability of biallelic characters given a population (or
species) phylogeny, while analytically integrating over all possible gene trees
under a coalescent model and all possible mutational histories along those gene
trees under a finite-sites model of character evolution.
This allows us to tackle biogeographic questions by jointly inferring a species
tree and shared divergences from genomic data
&lt;a class=&quot;citation&quot; href=&quot;#Oaks2021phycoeval&quot;&gt;(Oaks &lt;span style=&quot;font-style: normal&quot;&gt;et al.&lt;/span&gt;, 2022)&lt;/a&gt;.
However, the generalized tree distribution and associated algorithms are
independent of the likelihood function, and so can be used with other data
types and likelihood models (i.e., lots of room for future work and
applications!).&lt;/p&gt;

&lt;p&gt;Using simulations, we found this approach consistently inferred shared and
multifurcating divergences with high support with moderately sized data sets.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/gecko-generalized-tree-pp-hist-cropped.svg&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/gecko-generalized-tree-pp-hist-cropped.svg&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                We simulated 100 data sets on the tree above. The histograms
                show the posterior probabilities of correctly inferring the
                shared and multifurcating divergences when analyzing all the
                data sets under the generalized tree model.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;We applied this new approach to genomic data from two genera of geckos
co-distributed across the Philippines.
Fragmentations of the islands caused by interglacial rises in sea level predict
shared and multifurcating divergences over the last 5 million years.
Our results show support for this predicted pattern.&lt;/p&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/gekko-phycoeval-cam-tree.svg&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/gekko-phycoeval-cam-tree.svg&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                Shared and multifurcating divergences inferred during the evolutionary history of
                &lt;i&gt;Gekko&lt;/i&gt; lizards across the Philippines.
                From &lt;a class=&quot;citation&quot; href=&quot;#Oaks2021phycoeval&quot;&gt;(Oaks &lt;span style=&quot;font-style: normal&quot;&gt;et al.&lt;/span&gt;, 2022)&lt;/a&gt;.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;figure&gt;
    &lt;a href=&quot;/images/phycoeval-preprint/cyrt-phycoeval-cam-tree.svg&quot;&gt;&lt;img src=&quot;/images/phycoeval-preprint/cyrt-phycoeval-cam-tree.svg&quot; width=&quot;100%&quot; /&gt;&lt;/a&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                Shared and multifurcating divergences inferred during the evolutionary history of
                &lt;i&gt;Cyrtodactylus&lt;/i&gt; lizards across the Philippines.
                From &lt;a class=&quot;citation&quot; href=&quot;#Oaks2021phycoeval&quot;&gt;(Oaks &lt;span style=&quot;font-style: normal&quot;&gt;et al.&lt;/span&gt;, 2022)&lt;/a&gt;.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;If you want to learn more, here’s a talk I gave at the Evolution Meetings this summer:&lt;/p&gt;

&lt;iframe width=&quot;560&quot; height=&quot;315&quot; src=&quot;https://www.youtube.com/embed/1PX5Yz-Vgec&quot; title=&quot;YouTube video player&quot; frameborder=&quot;0&quot; allow=&quot;accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture&quot; allowfullscreen=&quot;&quot;&gt;&lt;/iframe&gt;

&lt;p&gt;And you can read our &lt;a href=&quot;https://doi.org/10.1101/2021.07.23.453597&quot;&gt;preprint here&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;This work was a lot of fun, but we have only scratched the surface with the
generalized tree distribution.
If you are interested in this work, please reach out; there’s so much more to
do!&lt;/p&gt;

&lt;h2 id=&quot;references&quot;&gt;References&lt;/h2&gt;

&lt;ol class=&quot;bibliography&quot;&gt;&lt;li&gt;&lt;span id=&quot;Oaks2021phycoeval&quot;&gt;Oaks JR, Wood, Jr. PL, Siler CD, Brown RM. 2022. Generalizing Bayesian phylogenetics to infer shared evolutionary events. &lt;i&gt;Proceedings of the National Academy of Sciences&lt;/i&gt; &lt;span style=&quot;font-weight: normal&quot;&gt;119&lt;/span&gt;:e2121036119. DOI: 10.1073/pnas.2121036119.&lt;/span&gt;

&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.2121036119&quot;&gt;Link.&lt;/a&gt; 

&lt;/li&gt;
&lt;li&gt;&lt;span id=&quot;Bryant2012&quot;&gt;Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, Roychoudhury A. 2012. Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis. &lt;i&gt;Molecular Biology and Evolution&lt;/i&gt; &lt;span style=&quot;font-weight: normal&quot;&gt;29&lt;/span&gt;:1917–1932. DOI: 10.1093/molbev/mss086.&lt;/span&gt;

&lt;a href=&quot;http://dx.doi.org/10.1093/molbev/mss086&quot;&gt;Link.&lt;/a&gt; 

&lt;/li&gt;&lt;/ol&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/generalized-phylo-preprint/&quot;&gt;Generalizing Bayesian phylogenetics to model shared divergences&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on October 18, 2021.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Gen-Phy at MIC-Phy]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/mic-phy/" />
  <id>http://phyletica.org/mic-phy</id>
  <published>2021-02-26T00:00:00-06:00</published>
  <updated>2021-02-26T00:00:00-06:00</updated>
  <author>
    <name>Jamie Oaks</name>
    <uri>http://phyletica.org</uri>
    <email>joaks@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;The 2021 Mathematical, Inferential, and Computational Phylogenomics (MIC-Phy)
meeting was great. Lots of great
&lt;a href=&quot;https://mrborges23.github.io/micphy2021/posters&quot;&gt;posters&lt;/a&gt;,
&lt;a href=&quot;https://mrborges23.github.io/micphy2021/talks&quot;&gt;talks&lt;/a&gt;
and
&lt;a href=&quot;https://mrborges23.github.io/micphy2021/workshop&quot;&gt;workshops&lt;/a&gt;.
I was only bummed about the talks I missed due to the difference in time zones.
But, luckily, most of the
&lt;a href=&quot;https://mrborges23.github.io/micphy2021/program&quot;&gt;talks are now up online&lt;/a&gt;,
so I’m eager to catch up on what I missed.&lt;/p&gt;

&lt;p&gt;I presented some new work by
&lt;a href=&quot;https://perryleewoodjr.com/&quot;&gt;JR&lt;/a&gt;
and I,
where we generalized the space of trees explored during Bayesian phylogenetic
inference in order to infer shared and multifurcating divergences.
Based on simulations, the new approach can accurately infer such
branching patterns from genomic data.
Equally important, it does not spuriously support such patterns when
divergences are independent and bifurcating.
Using this approach, we found evidence for the signature of interglacial rises
in sea levels fragmenting the Philippine Islands in the phylogenies of two
genera of geckos.&lt;/p&gt;

&lt;p&gt;You can find our
&lt;a href=&quot;/slides/mic-phy-2021.pdf&quot;&gt;slides here&lt;/a&gt;
and the video below.&lt;/p&gt;

&lt;iframe width=&quot;560&quot; height=&quot;315&quot; src=&quot;https://www.youtube.com/embed/4xzcrkYyriU&quot; title=&quot;YouTube video player&quot; frameborder=&quot;0&quot; allow=&quot;accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture&quot; allowfullscreen=&quot;&quot;&gt;&lt;/iframe&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/mic-phy/&quot;&gt;Gen-Phy at MIC-Phy&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on February 26, 2021.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Holden joining the USGS]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/holden-usgs/" />
  <id>http://phyletica.org/holden-usgs</id>
  <published>2020-09-01T00:00:00-05:00</published>
  <updated>2020-09-01T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;holden-moving-on-to-the-usgs&quot;&gt;Holden moving on to the USGS&lt;/h2&gt;

&lt;p&gt;Congratulations to undergraduate
Holden Smith
for accepting a position at the United States Geological Survey.
Holden will be working as a Hydrologic Technician out of he Lower Mississippi
Gulf Water Science Center in Tuscaloosa, Alabama.
He will be collecting important hydrologic data from extremely diverse
drainages, such as the Tennessee, Alabama, Tombigbee, and Mobile Rivers.
We will miss him in the lab, but we are glad to know he will be looking out for
the diverse waterways of the southeast.
Congrats Holden!&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/holden-usgs/&quot;&gt;Holden joining the USGS&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on September 01, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Morgan joins the Phyleticians]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/welcome-morgan/" />
  <id>http://phyletica.org/welcome-morgan</id>
  <published>2020-08-23T00:00:00-05:00</published>
  <updated>2020-08-23T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;welcome-morgan&quot;&gt;Welcome Morgan!&lt;/h2&gt;

&lt;p&gt;The Phyletical Lab is happy to welcome new Ph.D. student,
&lt;a href=&quot;https://morganmuell.wixsite.com/home&quot;&gt;Morgan Muell&lt;/a&gt;.
Morgan joins us from the lab of
&lt;a href=&quot;https://www.jasonleebrown.org/&quot;&gt;Jason Brown&lt;/a&gt;
at
&lt;a href=&quot;https://siu.edu/&quot;&gt;Southern Illinois University&lt;/a&gt;,
where she did her master’s work on the phylogenomics and color pattern
evolution in poison frogs.
Morgan will be coadvised by
&lt;a href=&quot;https://warnerlab.weebly.com/&quot;&gt;Dan Warner&lt;/a&gt;,
and is interested in taking a comparative approach to the evolution of
phenotypic plasticity.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/welcome-morgan/&quot;&gt;Morgan joins the Phyleticians&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on August 23, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Ryan heading to Villanova this Fall]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/ryan-villanova/" />
  <id>http://phyletica.org/ryan-villanova</id>
  <published>2020-07-11T00:00:00-05:00</published>
  <updated>2020-07-11T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;ryan-is-philadelphia-bound&quot;&gt;Ryan is Philadelphia bound&lt;/h2&gt;

&lt;p&gt;Congratulations to
undergraduate
Ryan Cook
for being accepted into the graduate program at
&lt;a href=&quot;https://www1.villanova.edu/university.html&quot;&gt;Villanova University&lt;/a&gt;.
Ryan will be working with
&lt;a href=&quot;https://www1.villanova.edu/villanova/artsci/biology/facstaff.html?mail=aaron.bauer@villanova.edu&amp;amp;xsl=bio&quot;&gt;Aaron Bauer&lt;/a&gt;
and
&lt;a href=&quot;http://www87.homepage.villanova.edu/todd.jackman/&quot;&gt;Todd Jackman&lt;/a&gt;
on the diversification of reptiles and amphibians.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/ryan-villanova/&quot;&gt;Ryan heading to Villanova this Fall&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on July 11, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Paper: Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/codemog-paper/" />
  <id>http://phyletica.org/codemog-paper</id>
  <published>2020-07-04T00:00:00-05:00</published>
  <updated>2020-07-04T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;While we avoid mass-infection events this 4th of July, here’s a 
piece of good news out of the Phyletica Lab.
The work by 
Nadia L’Bahy (our 2018 Comp Bio REU student from UMass Amherst)
and Kerry that introduces a new, full-likelihood, Bayesian approach
to estimating simultaneous changes in effective population sizes
across populations is now published in the journal
&lt;a href=&quot;https://onlinelibrary.wiley.com/doi/abs/10.1111/evo.14052&quot;&gt;Evolution&lt;/a&gt;.
It turns out that, even when you use all the information from genomic data,
estimating shared demographic events across populations is still super hard.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/codemog-paper/&quot;&gt;Paper: Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on July 04, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Paper: Rivers of Indochina as potential drivers of diversification in flying lizards]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/draco-paper/" />
  <id>http://phyletica.org/draco-paper</id>
  <published>2020-06-10T00:00:00-05:00</published>
  <updated>2020-06-10T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;&lt;a href=&quot;http://randyklabacka.com/&quot;&gt;Randy’s&lt;/a&gt;
paper on the diversification of flying lizards across Indochina is now
&lt;a href=&quot;https://doi.org/10.1016/j.ympev.2020.106861&quot;&gt;published in Molecular Phylogenetics and Evolution&lt;/a&gt;.
Randy found that a model of diversification demarcated by the major rivers of
Indochina best explained variation in sequence data from across the
distribution of the &lt;em&gt;Draco maculatus&lt;/em&gt; species complex.
Randy did a ton of work to compare the marginal likelihoods of a large number
of diversification models to reach this conclusion.
Congrats Randy!&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/draco-paper/&quot;&gt;Paper: Rivers of Indochina as potential drivers of diversification in flying lizards&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on June 10, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Randy gets AGA EECG award!]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/randy-aga-award/" />
  <id>http://phyletica.org/randy-aga-award</id>
  <published>2020-03-15T00:00:00-05:00</published>
  <updated>2020-03-15T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congrats-randy&quot;&gt;Congrats Randy!&lt;/h2&gt;

&lt;p&gt;Congratulations to
&lt;a href=&quot;http://randyklabacka.com/&quot;&gt;Randy Klabacka&lt;/a&gt;
for being awarded $8,000 from the
&lt;a href=&quot;https://www.theaga.org/eecg-awards.php&quot;&gt;American Genetics Association&lt;/a&gt;
to study the genomic and bioenergetic costs of asexuality
in whiptail lizards.
We are interested in whether a non-recombining nuclear genome can adequately
coevolve with the mitochondria.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/randy-aga-award/&quot;&gt;Randy gets AGA EECG award!&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on March 15, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Paper: The why, when, and how of computing in biology classrooms]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/comp-bio-ed/" />
  <id>http://phyletica.org/comp-bio-ed</id>
  <published>2020-03-05T00:00:00-06:00</published>
  <updated>2020-03-05T00:00:00-06:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;We have published an
&lt;a href=&quot;https://f1000research.com/articles/8-1854/v2&quot;&gt;opinion article about the ins-and-outs of
teaching computational biology&lt;/a&gt;
in
&lt;a href=&quot;https://f1000research.com/&quot;&gt;F1000 Research&lt;/a&gt;.
This work was born from a fantastic
&lt;a href=&quot;https://www.ievobio.org/&quot;&gt;iEvoBio&lt;/a&gt; Meeting in Providence,
Rhode Island last Summer.
The meeting was organized by
&lt;a href=&quot;https://paleantology.com/the-wright-lab/&quot;&gt;April Wright&lt;/a&gt;
and focused on “enabling the next generation of computational biologists”.
The paper was a lot of fun to work on, thanks to great collaborators
&lt;a href=&quot;https://paleantology.com/the-wright-lab/&quot;&gt;April Wright&lt;/a&gt;,
&lt;a href=&quot;https://schwartzlaburi.github.io/&quot;&gt;Rachel Schwartz&lt;/a&gt;,
&lt;a href=&quot;https://www.catherinenewman.org/&quot;&gt;Catherine Newman&lt;/a&gt;,
and
&lt;a href=&quot;https://www.canterbury.ac.nz/science/schools-and-departments/biological-sciences/contact-us/academic-staff/sarah-flanagan.html&quot;&gt;Sarah Flanagan&lt;/a&gt;.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/comp-bio-ed/&quot;&gt;Paper: The why, when, and how of computing in biology classrooms&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on March 05, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Paper: Comparative phylogeography of West African amphibians and reptiles]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/west-african-phylogeography/" />
  <id>http://phyletica.org/west-african-phylogeography</id>
  <published>2020-02-20T00:00:00-06:00</published>
  <updated>2020-02-20T00:00:00-06:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;Recent work in collaboration with
&lt;a href=&quot;http://faculty.washington.edu/leache/wordpress/&quot;&gt;Adam Leache&lt;/a&gt;,
&lt;a href=&quot;https://csir-forig.org.gh/senior-members-profiles/309-caleb-ofori-boateng-phd&quot;&gt;Caleb Ofori-Boateng&lt;/a&gt;,
and
&lt;a href=&quot;https://fujitalab.com/&quot;&gt;Matt Fujita&lt;/a&gt;
is out in
&lt;a href=&quot;https://onlinelibrary.wiley.com/doi/abs/10.1111/evo.13941&quot;&gt;Evolution&lt;/a&gt;
on the comparative phylogeography of a diverse set of reptiles and amphibians
from West Africa.
We used computational methods developed in the Phyletica Lab to infer the
temporal distribution of divergences among 20 species across the Dahomey Gap.
We found a lot of variation in divergence times, suggesting that species
responded differently to past aridification across West Africa.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/west-african-phylogeography/&quot;&gt;Paper: Comparative phylogeography of West African amphibians and reptiles&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on February 20, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Charlotte gets Hyman Scholarship!]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/charlotte-hyman-award/" />
  <id>http://phyletica.org/charlotte-hyman-award</id>
  <published>2020-02-17T00:00:00-06:00</published>
  <updated>2020-02-17T00:00:00-06:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congrats-charlotte-again&quot;&gt;Congrats Charlotte (again)!&lt;/h2&gt;

&lt;p&gt;Congratulations to
undergraduate
Charlotte Benedict
for being awarded the
&lt;a href=&quot;https://sicb.burkclients.com/grants/hyman/&quot;&gt;Libbie H. Hyman Memorial Scholarship&lt;/a&gt;
from the Societiy for Integrative and Comparative Biology.
This award provides Charlotte $3,000 to participate in the Marine
Invertebrate Zoology course at the University of Washington Friday Harbor Lab.
It’s been a good week for Charlotte!&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/charlotte-hyman-award/&quot;&gt;Charlotte gets Hyman Scholarship!&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on February 17, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Charlotte gets graduate fellowship!]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/charlotte-osu-fellowship/" />
  <id>http://phyletica.org/charlotte-osu-fellowship</id>
  <published>2020-02-15T00:00:00-06:00</published>
  <updated>2020-02-15T00:00:00-06:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congrats-charlotte&quot;&gt;Congrats Charlotte!&lt;/h2&gt;

&lt;p&gt;Congratulations to
undergraduate
Charlotte Benedict
for being awarded a
&lt;a href=&quot;https://gradsch.osu.edu/pursuing-your-degree/graduate-fellows/university-fellowship&quot;&gt;University Fellowship from the Ohio State University&lt;/a&gt;.
Charlotte will begin her graduate work at the OSU in the lab of
&lt;a href=&quot;https://www.facebook.com/OSU-Lab-of-Marine-Invertebrate-Diversity-169688986441907/&quot;&gt;Meg Daly&lt;/a&gt;.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/charlotte-osu-fellowship/&quot;&gt;Charlotte gets graduate fellowship!&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on February 15, 2020.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Randy gets the Henri Seibert Award!]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/randy-seibert-award/" />
  <id>http://phyletica.org/randy-seibert-award</id>
  <published>2019-08-20T00:00:00-05:00</published>
  <updated>2019-08-20T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congrats-to-randy&quot;&gt;Congrats to Randy!&lt;/h2&gt;

&lt;p&gt;Congratulations to Randy Klabacka for
&lt;a href=&quot;https://www.auburn.edu/cosam/news/articles/2019/08/auburn_student_honored_with_research_award_on_reptile_study.htm&quot;&gt;winning the prestigious Henri Seibert Award&lt;/a&gt;
at the
&lt;a href=&quot;https://conferences.k-state.edu/jmih/&quot;&gt;Joint Meeting of Ichthyologists and Herpetologists&lt;/a&gt;.
This award from the
&lt;a href=&quot;https://ssarherps.org/&quot;&gt;Society for the Study of Amphibians and Reptiles&lt;/a&gt;
recognizes the student with the best talk in one of four research categories.
Randy was awarded the best talk in Evolution/Systematics for his presentation
on “Riverine barriers as potential drivers of biodiversification in the &lt;em&gt;Draco
maculatus&lt;/em&gt; species complex of Indochina.”
This project started out as a relatively simple exploration into this species
complex of gliding lizards.
However, Randy has done a great job transforming this work
into an in-depth comparison of
a large number of biogeographic models to determine the best explanation for
the current geographic distribution of this group’s genetic diversity across
Indochina.
Auburn University published
&lt;a href=&quot;https://www.auburn.edu/cosam/news/articles/2019/08/auburn_student_honored_with_research_award_on_reptile_study.htm&quot;&gt;a nice story&lt;/a&gt;
about Randy’s accomplishment.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/randy-seibert-award/&quot;&gt;Randy gets the Henri Seibert Award!&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on August 20, 2019.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Claire and Tanner awarded AU fellowships]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/au-fellows/" />
  <id>http://phyletica.org/au-fellows</id>
  <published>2019-08-19T00:00:00-05:00</published>
  <updated>2019-08-19T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;congrats-to-claire-and-tanner&quot;&gt;Congrats to Claire and Tanner!&lt;/h2&gt;

&lt;p&gt;New Phyletica Lab members, Claire Tracy and Tanner Myers, were awarded the
&lt;a href=&quot;http://graduate.auburn.edu/au-presidential-graduate-research-fellowships/&quot;&gt;Auburn University Presidential Graduate Research Fellowship&lt;/a&gt;,
which includes three years of funding for their dissertation work.
Claire was also awarded the Allsup Fellowship for her first year at AU.
Congratulations, Claire and Tanner!&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/au-fellows/&quot;&gt;Claire and Tanner awarded AU fellowships&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on August 19, 2019.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[The Phyletica Lab welcomes 4 new PhD students]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/new-grad-students/" />
  <id>http://phyletica.org/new-grad-students</id>
  <published>2019-08-15T00:00:00-05:00</published>
  <updated>2019-08-15T00:00:00-05:00</updated>
  <author>
    <name>Phyletica</name>
    <uri>http://phyletica.org</uri>
    <email>phyletica@auburn.edu</email>
  </author>
  <content type="html">
    &lt;h2 id=&quot;welcome-tashitso-claire-matt-and-tanner&quot;&gt;Welcome Tashitso, Claire, Matt, and Tanner!&lt;/h2&gt;

&lt;p&gt;The Phyletica lab is welcoming four new Ph.D. students this week.
Tashitso Anamza joins us from Tibet, where she is from;
she also spent time in Lawrence, Kansas earning her bachelor’s and master’s
degrees from the University of Kansas.
Claire Tracy and Matt Buehler are joining us from
&lt;a href=&quot;https://www1.villanova.edu&quot;&gt;Villanova University&lt;/a&gt;
where they are
finishing up their master’s work in
&lt;a href=&quot;https://www1.villanova.edu/villanova/artsci/biology.html&quot;&gt;Biology&lt;/a&gt;.
Tanner Myers comes to us after finishing his B.Sc. at the University of Kansas
while working in the Herpetology Division of the
&lt;a href=&quot;https://biodiversity.ku.edu/&quot;&gt;KU Biodiversity Institute&lt;/a&gt;.
Welcome, new phyleticians!&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/new-grad-students/&quot;&gt;The Phyletica Lab welcomes 4 new PhD students&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on August 15, 2019.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Phyleticians in Providence for Evolution 2019]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/evolution-recap/" />
  <id>http://phyletica.org/evolution-recap</id>
  <published>2019-07-01T00:00:00-05:00</published>
  <updated>2019-07-01T00:00:00-05:00</updated>
  <author>
    <name>Jamie Oaks</name>
    <uri>http://phyletica.org</uri>
    <email>joaks@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;Charlotte Benedict, Kerry Cobb, and I had a great time at
&lt;a href=&quot;https://www.evolutionmeetings.org/evolution-2019---providence.html&quot;&gt;Evolution 2019&lt;/a&gt;
in Providence, RI.
Charlotte presented a great poster on the independent evolution of clownfish
symbiosis among sea anemones.
Kerry gave a poster about our work showing the difficulty of estimating
simultaneous demographic changes among populations
(see
&lt;a href=&quot;/codemog-preprint/&quot;&gt;post here&lt;/a&gt;
and
&lt;a href=&quot;https://www.biorxiv.org/content/10.1101/679878v1&quot;&gt;preprint here&lt;/a&gt;).
I talked about our
&lt;a href=&quot;https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13754&quot;&gt;recent paper&lt;/a&gt;
on the comparative biogeography of Philippine geckos.
The slides from my talk are available for
&lt;a href=&quot;/slides/evol2019.pdf&quot;&gt;download here&lt;/a&gt;
and can be viewed via 
&lt;a href=&quot;https://www.slideshare.net/jamieoaks7/full-bayesian-comparative-biogeography-of-philippine-geckos-challenges-predictions-of-climatedriven-vicariant-speciation&quot;&gt;SlideShare&lt;/a&gt;
here:&lt;/p&gt;

&lt;figure&gt;
&lt;iframe src=&quot;//www.slideshare.net/slideshow/embed_code/key/LPkpqnD9GjO2IA&quot; width=&quot;595&quot; height=&quot;485&quot; frameborder=&quot;0&quot; marginwidth=&quot;0&quot; marginheight=&quot;0&quot; scrolling=&quot;no&quot; style=&quot;border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;&quot; allowfullscreen=&quot;&quot;&gt; &lt;/iframe&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                &lt;strong&gt; &lt;a href=&quot;//www.slideshare.net/jamieoaks7/full-bayesian-comparative-biogeography-of-philippine-geckos-challenges-predictions-of-climatedriven-vicariant-speciation&quot; title=&quot;Full Bayesian comparative biogeography of Philippine geckos challenges predictions of climate-driven vicariant speciation&quot; target=&quot;_blank&quot;&gt;Full Bayesian comparative biogeography of Philippine geckos challenges predictions of climate-driven vicariant speciation&lt;/a&gt; &lt;/strong&gt; from &lt;strong&gt;&lt;a href=&quot;https://www.slideshare.net/jamieoaks7&quot; target=&quot;_blank&quot;&gt;Jamie Oaks&lt;/a&gt;&lt;/strong&gt;
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;The recording of my talk is also
&lt;a href=&quot;https://www.youtube.com/watch?v=gULtPGdAQME&quot;&gt;up on YouTube&lt;/a&gt;:&lt;/p&gt;

&lt;figure&gt;
&lt;iframe width=&quot;560&quot; height=&quot;315&quot; src=&quot;https://www.youtube.com/embed/gULtPGdAQME&quot; frameborder=&quot;0&quot; allow=&quot;accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture&quot; allowfullscreen=&quot;&quot;&gt;&lt;/iframe&gt;
    &lt;figcaption&gt;
        &lt;p class=&quot;figure-caption-box&quot;&gt;
            &lt;span class=&quot;center-if-single-line&quot;&gt;
                Recording of Jamie's talk about the comparative biogeography of Philippine gekkonids.
            &lt;/span&gt;
        &lt;/p&gt;
    &lt;/figcaption&gt;
&lt;/figure&gt;

&lt;p&gt;Kerry and I also attended the
&lt;a href=&quot;https://ievobio2019.github.io/2019-iEvoBio/index.html&quot;&gt;iEvoBio Conference&lt;/a&gt;
the day after evolution, for
which I was a member of a panel on computational biology education.
The slides from my iEvoBio presentation can be
&lt;a href=&quot;/slides/ievobio-2019&quot;&gt;viewed here&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;We enjoyed our time in Providence and learned a ton from all the amazing talks
and posters we attended.
A huge thanks to the
&lt;a href=&quot;https://www.amnat.org/home.html&quot;&gt;ASN&lt;/a&gt;,
&lt;a href=&quot;https://www.systbio.org/&quot;&gt;SSB&lt;/a&gt;,
&lt;a href=&quot;https://www.evolutionsociety.org/&quot;&gt;SSE&lt;/a&gt;,
and all the conference organizers for a wonderful event.&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/evolution-recap/&quot;&gt;Phyleticians in Providence for Evolution 2019&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on July 01, 2019.&lt;/p&gt;

  </content>
</entry>


<entry>
  <title type="html"><![CDATA[Preprint: Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data]]></title>
  <link rel="alternate" type="text/html" href="http://phyletica.org/codemog-preprint/" />
  <id>http://phyletica.org/codemog-preprint</id>
  <published>2019-06-22T00:00:00-05:00</published>
  <updated>2019-06-22T00:00:00-05:00</updated>
  <author>
    <name>Jamie Oaks</name>
    <uri>http://phyletica.org</uri>
    <email>joaks@auburn.edu</email>
  </author>
  <content type="html">
    &lt;p&gt;A
&lt;a href=&quot;https://www.biorxiv.org/content/10.1101/679878v1&quot;&gt;new preprint&lt;/a&gt;
out of the lab demostrates the difficulties in estimating simultaneous changes
in effective population sizes across taxa.
REU Nadia L’Bahy (our 2018 Comp Bio REU student from UMass Amherst) and Kerry
Cobb contributed to this work.
Feedback is welcome!&lt;/p&gt;

    &lt;p&gt;&lt;a href=&quot;http://phyletica.org/codemog-preprint/&quot;&gt;Preprint: Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data&lt;/a&gt; was originally published by Jamie Oaks at &lt;a href=&quot;http://phyletica.org&quot;&gt;phyletica&lt;/a&gt; on June 22, 2019.&lt;/p&gt;

  </content>
</entry>

</feed>