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

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.

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New faces: Bryan McLean

(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

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!

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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

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

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

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.

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Genomics of Hybridization – Part 1

In a series of articles, I will discuss recent advances in hybridization genomics – the fundamentals of adaptive introgression, “islands of speciation”, differential gene flow, and linked selection have been discussed in my previous posts (here, here, and also at the Social Evolution Forum). I will focus this series on applications/support/fallibilities of theories in recent literature, and incidentally, also the focus of a new special issue of Molecular Ecology. Hybridization following secondary contact in Myzomela honeyeaters – Sardell and Uy, 2016, Evolution

Clockwise from left, Myzomela cardinalis, M. tristrami and a putative hybrid (note red feathers on nape/collar) of Makira. Image courtesy: Uy Lab @ http://www.bio.miami.edu/uy/Research/Myzo.jpg

Studying a hybrid zone of Myzomela honeyeater songbirds (M. tristrami – sexually monochromatic, black, and M. cardinalis – sexually dichromatic, black and red) in the Solomon Islands, Sardell and Uy (2016) reveal a scenario of incomplete reproductive isolation, recent secondary contact, and their evolutionary consequences through analyses of nuclear and mitochondrial haplotypes of >200 birds sampled across six sites. One mitochondrial and six nuclear markers were then amplified, sequenced, and phased. Divergence time between the two species was then estimated using BEAST to be around 5.8 mya (95% CI: 3.1-9.3 mya). Hybridization was quantified by comparing identifying haplotypes present exclusively in allopatry in sympatric heterospecifics – showing exclusive mitochondrial introgression (sex biased), and nuclear introgression from M. cardinalis into M. tristrami. Both mitochondrial and nuclear diversities were larger in M. tristrami, indicative of larger effective population sizes. Similar admixture patterns were also determined using estimation of population structure. Further characterization of hybridization using more markers, and population genetic models in the species will reveal a better understanding of the genomics of hybrid zones

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Posted in adaptation, evolution, genomics, methods, natural history, next generation sequencing, pedigree, phylogenetics, plants, population genetics, RNAseq, software, speciation, species delimitation, STRUCTURE, theory, transcriptomics | Tagged , , , , , , | Leave a comment

Threat down! Data accessibility in long-term studies

I’m coming for your long-term study’s data!

It way past Halloween, but something is still out there… and it’s coming for your long-term data. At least that’s what a string of recent opinions and replies in TREE might lead you to believe. But I think that the fears are misguided (and I’m not alone).

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An evolutionary cycle …

Rescan, Lenormand and Roze (2016) recently published new models on the evolution of life cycles in The American Naturalist.

An evolutionary cycle - A bicycle emerges from the water after evolving from two amoeba

Most animals and protists have diploid life cycles in which the haploid stage is reduced to a single-celled gamete.

Other organisms, such as charophytes and dinoflagellates, have a haploid life cycle in which the diploid phase is reduced to the zygote and meiosis occurs before any mitotic development.

There’s a third type of life cycle, that regular TME readers may have stumbled across with my posts: haploid-diploidy in which somatic development occurs in both haploid and diploid stages. In seed plants, the haploid stage is rather limited, but in fungi, mosses and macroalgae, the haploid stage is much more important.

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Top three of 2015 – Rob Denton

combine_images

We had a great 2015 at The Molecular Ecologist. The blog’s contributors provided more than 200 posts last year. Maybe you’ve read a few or maybe you’ve read them all. Either way, things are getting even better in 2016.

As we start this year with new ideas for content and new directions for how to deliver it, we are all looking back on what worked (and didn’t) last year. As part of looking back, we want to share our best posts (by pageviews) from 2015. Whether you missed them, read them, or forgot all about them, here are my top three:

1. The unforeseen genomic consequences of domestication

This post from August 26th discussed a new paper that showed how the accumulation of deleterious mutations in domestic crops varied depending on how those crops were domesticated. The extensive dataset, established authors, and well-written paper made this post a favorite from 2015.

 

2. Don’t trust your data: reviewing Bioinformatics Data Skills

Vince Buffalo was nice enough to send me a preliminary version of his new book Bioinformatics Data Skills early in 2015, and the resultant review appeared on the blog on April 8th. This book certainly deserved the attention and has been a frequent link sent to colleagues as a recommendation.

 

3. Reviewing the reviews: Twelve years of Landscape Genetics

The idea for this post was very straightforward: if the demand for literature reviews about landscape genetics was great enough to have multiple of them in just a few years, then a summary of those reviews might be helpful for a general audience.

 

BONUS

4. Should we use Mantel tests in molecular ecology?

I’m adding my fourth-highest viewed post to this list, because it was probably my favorite. I remember when I first read Jeremy Fox’s ideas about “Zombie Ideas in Ecology”, ideas that stick around in a field despite significant refutation. Using Mantel tests for spatial statistics seemingly fits this definition, so I loved this paper by Legendre et al.  that succinctly shows when Mantel tests are useful and when they should be avoided. I was happy to see how many TME readers agreed and shared this post accordingly.

 

 

Posted in blogging, linkfest, Molecular Ecology views | Tagged | 1 Comment