New Faces: Christine Ewers-Saucedo

Posted on 3 Feb, 2016 by Jeremy Yoder

Christine, catching barnacle-ridden crabs with the Skidaway Institute for Oceanography. (Christine Ewers-Saucedo)

Christine, catching barnacle-ridden crabs with the Skidaway Institute for Oceanography. (Christine Ewers-Saucedo)


This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who am I?
My name is Christine Ewers-Saucedo. Originally from a small island in Germany, I moved to the United States in 2010 after receiving my Diplom in Biology at the Christian-Albrechts University of Kiel, Germany. A German Diplom is comparable to a masters degree.
Where am I?
I received my PhD from the University of Georgia, and just started a postdoc position at the University of California at Davis.
What do I study?
I am fascinated by the evolution of life histories, particularly larval and reproductive traits (think variation in egg size and mating system). My study system of choice are marine invertebrates, which exhibit an impressive diversity of life histories.
What do I do when I am not studying?
I began playing soccer when I began my PhD. Since then, I have played almost every week, always loving the game, even though the game didn’t always love me. I also like to read historical novels (I was close to becoming an archeologist once), and all kinds of creative hands-on work, such as sewing and woodwork. Last year, my husband and I adopted the best dog in the world (sorry, Lassie and Beethoven), and every day has been more fun ever since.

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New faces: Patrícia Pečnerová

Posted on 2 Feb, 2016 by Jeremy Yoder

(Patrícia Pečnerová)

(Patrícia Pečnerová)


This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who are you?
My name is Patrícia Pečnerová and I’m a PhD student.
Where are you?
I’m doing a PhD in Stockholm, Sweden. I study at Stockholm University and my office is situated at the Swedish Museum of Natural History.
Since my first visit to the Natural History Museum Vienna, I’ve always wanted to work at a museum of natural history, and now I’m fulfilling this dream.
I’m originally from Slovakia and I’ve done my pre-graduate studies in the Czech Republic before coming to Sweden.
What do you study?
My PhD research project is about using ancient DNA to trace changes of genetic diversity in the last population of the woolly mammoth before its extinction. My research is a combination of ancient DNA, next generation sequencing, bioinformatics, population and conservation genomics.
What do you do when you’re not studying it?
I travel and blog about it at thejourneyjournal.com. I have a sweet tooth and I like to bake, which is a terrible combination. I try to counterbalance the high sugar income by being a Les Mills fitness instructor. In general, I’m happiest when I’m having a good book in one hand and a cup of coffee in the other.

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New faces: Kelle Freel

Posted on 1 Feb, 2016 by Jeremy Yoder

(Kelle Freel)

(Kelle Freel)


This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who are you?
Kelle C. Freel
Where are you?
I am currently living in Santa Cruz, California where I was born and raised. I attended the University of California, San Diego, and then stuck around for grad school at Scripps Institution of Oceanography. After graduating, I decided to opt for an international postdoc and studied yeast population genomics in Strasbourg, France.
What do you study?
I study the phylogeny and biogeography of microbes and how distinct species fit into their ecological niche. I am interested in studying bacterial communities, and how members interact with each other as well as their environment.
What do you do when you’re not studying it?
When I’m not studying, I run, cycle, and (when I’m close to an ocean) go surfing. I also love to cook, travel, and generally have adventures.

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New faces: Ethan Linck

Posted on 29 Jan, 2016 by Jeremy Yoder

(Ethan Linck)

(Ethan Linck)


This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who are you?
Ethan Linck
Where are you?
I’m a Ph.D. student at the University of Washington and Burke Museum of Natural History & Culture, in Seattle.
What do you study?
I’m in John Klicka’s lab, where we’re broadly concerned with analyzing and archiving avian biodiversity using genomic data and natural history museum specimen collections. My (nascent) dissertation work is focused on the role of natural selection in driving divergence in a lineage of tropical kingfishers distributed along an elevational gradient. My more-realized research has focused on the contribution of ecology and geography in determining phylogeographic structure.
What do you do when you’re not studying it?
I spend a lot of time running, climbing, and ski touring in the Cascades, compulsively reading the news, and writing (most frequently at http://beyondtheranges.wordpress.com). I’m usually in search of my next cup of coffee.

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A race to the bottom with a new card from the coevolutionary deck

Posted on 29 Jan, 2016 by Stacy Krueger-Hadfield

I’m a sucker for a clever, amusing title, though I’ve recently read that amusing titles are cited less (see here). Alas, maybe a well placed metaphor can enliven a manuscript and also not get lost in a citation-less abyss?
In basic evolution courses, students are taught about the Red Queen Hypothesis or evolutionary “arms races.”

© Lewis Carroll Through the Looking Glass

© Lewis Carroll Through the Looking Glass


Taken from Lewis Carroll’s Through the Looking-Glass, the Red Queen says “it takes all the running you can do, to keep in the same place.” This has been used as a clever way to explain the interaction between hosts and pathogens. A parasite evolves a way to overcome a host’s defenses and the host evolves a new defense. In response, the parasite evolves a new mechanism to attack the host. And so on and so on.
Continue reading →

Posted in Coevolution, evolution, horizontal gene transfer, microbiology, selection | Tagged , , | Leave a comment

New faces: Bryan McLean

Posted on 28 Jan, 2016 by Jeremy Yoder

(Bryan McLean)

(Bryan McLean)


This week and next we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who are you?
Bryan McLean
Where are you?
PhD Candidate at University of New Mexico (Albuquerque, NM) and Predoctoral Fellow at National Museum of Natural History (Washington, DC; through March 2016)
What do you study?
I study mammalian phylogeny, morphology, ecology and macroevolution. I spend large amounts of time in both the field and the (molecular) lab. I work in, conduct research in, and am in general an appreciator of natural history museums.
What do you do when you’re not studying it?
When not doing those things, I’m often traveling, or exploring the great state of New Mexico, or checking items off my museum life list, or exploring the culinary universe.

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Genomics of Hybridization – Part II, Top three of 2015

Posted on 28 Jan, 2016 by Arun Sethuraman

Death Valley pupfishes (Cyprinodon) are among the most endangered vertebrates on earth, with small inbred populations, with heavy risks of extinction in extreme environments. Martin et al. (2016) in a recent publication quantify diversity and adaptability in a very small population of Cyprinodon diabolis (census size:35-548 in Devil’s Hole, Nevada).

Cyprinodon (pupfish) species across the Death Valley. Image courtesy: http://waynesword.palomar.edu/images2/pupfish2b.jpg


Using ddRADSeq to genotype 56 individuals across 13000 loci, Martin et al. determined that five populations of Cyprinodon are structured, and individual populations harbored up to 40-fold lower genetic diversity than coastal populations in the clade.
Dating their emergence to around 10,000 ybp, with the confidence interval centered around the last flooding of the Death Valley, their study also determined that a much more recent separation of the five populations (around 200 ybp), dating to the Great Flood of 1862. Interestingly, their study also reports recent gene flow between C. diabolis, C. amargose and C. pectoralis using analysis of admixture, and D-statistics. Significant gene flow between these populations was also estimated by TreeMix analyses.
With surprising levels of morphological diversification in C. diabolis (>5 times that of other Cyprinodon species in the Death Valley), Martin et al’s study points to how despite multiple extinction events, frequent dispersal over thousands of years from multiple populations
may have contributed to concurrent genomic diversity, phenotypic diversification, adaptation, and survival.

Combined with the 60 000 year age of Devils Hole, this suggests that pupfish extinction and gene flow may have happened many times before in this unique habitat and that diabolis may not be the first pupfish population to have survived there. Protecting the connectivity of this region will be essential for this cycle of rebirth to continue.

Reference:
Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth, Martin et al. (2016). Proceedings of the Royal Society B DOI:10.1098/rspb.2015.2334
Also, following Rob and Melissa‘s leads, here were my top 3 posts from 2015!
Continue reading →

Posted in bioinformatics, conservation, genomics, methods, natural history, next generation sequencing, population genetics, R, software, speciation, STRUCTURE, theory | Tagged , , , , | Leave a comment

New Faces: Katie Everson

Posted on 27 Jan, 2016 by Jeremy Yoder

Katie works with students at the University of Alaska Fairbanks Museum of the North Open House (via Katie Everson)

Katie works with students at the University of Alaska Fairbanks Museum of the North Open House (via Katie Everson)


This week and next we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who are you?
Kathryn M. (Katie) Everson
Where are you?
I’m an NSF Graduate Research Fellow in the University of Alaska Museum’s Mammals Collection. I’ve been in Fairbanks, Alaska since Fall 2012. I’m originally from Cincinnati, Ohio and I received my Bachelor’s degree from Ohio State.
What do you study?
I study species delimitation and phylogeography in Madagascar’s tenrecs using a combination of genetic, geographic, and morphological data.
What do you do when you’re not studying it?
I love graphic design — especially using design to make better scientific figures and posters. I also spend my time being a typical Alaskan: skiing, fishing, and wearing wool socks.

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Top three of 2015 – Melissa DeBiasse

Posted on 25 Jan, 2016 by Melissa DeBiasse

Following Rob’s lead, today I am sharing my top 3 posts of 2015 based on the number of pageviews they received. I’m also throwing in one of the posts I had the most fun researching and writing. Thank you to all the readers who have read, liked, shared, and commented The Molecular Ecologist posts last year. We have some exciting things planned for the blog in 2016, and hope y’all will continue to support the site!
1. Gene expression analyses- are we doing it wrong?


This post from June 29th, 2015 highlighted three preprints focused on potential problems with current RNA-seq/gene expression analyses. For an in-depth review on the dangers of batch effects, check out this post by my fellow TME contributor Noah Snyder-Mackler. Improvements to how we analyze transcriptomic data continue to roll out. One example is a new preprint by Soneson et al. on F1000Research showing gene-level rather than transcript-level analyses are superior in terms of performance and interpretation. Continue reading →

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Macroalgal miscellany

Posted on 22 Jan, 2016 by Stacy Krueger-Hadfield

It’s been a jam-packed week and I’ve found myself at Friday. Grandiose plans for a post continuing the series on clonality (see here and here) did not come to fruition.
But, I was saved with a new article that tumbled out of my Twitter feed this morning.
Coralline red algae are important components of marine ecosystems as bio-constructors. They consolidate coral reefs and other coralligenous structures that provide 3-D habitats that favor the development of other benthic organisms (see here).
Corallines also significantly contribute to the deposition of carbonate in shallow seas and as such are frequently used as models for understanding the effects of ocean acidification on carbon sequestration (see Brodie et al. 2014 for a review).
 

A truly freshwater (FW) representative has never been reported so far, either as a fossil or as a living species. Like other important marine lineages such as echinoderms, corallines have been considered restricted to marine water, never making the evolutionary step into FW.

Continue reading →

Posted in adaptation, DNA barcoding, evolution, genomics, haploid-diploid, speciation | Tagged , , , , | Leave a comment