Exploring the genomic diversity of tubeworm endosymbionts

Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how nifty these creatures are, you could check out this educational video by Ed Yong published last November, and then read this recently published article by Reveillaud and colleagues.

In this study, the authors report the characterization of the endosymbionts from the giant tube worm genera Lamellibrachia and Escarpia from the Caribbean Sea. This study is the first to take a swing at characterizing the endosymbionts from tubeworms outside of the Pacific Ocean as well as from these two lesser studied genera.

Escarpia sp. tubeworms. Image credit: The Chemo III project, BOEM and NOAA OER

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Posted in bioinformatics, Coevolution, community ecology, evolution, genomics, metagenomics, microbiology | Tagged , , | Leave a comment

How Molecular Ecologists Work: Sean Hoban on Google Docs and time-per-task calculations

Welcome to “How Molecular Ecologists Work”, the interview series that asks scientists how they get stuff done. In the final installment of this second season of interviews, we welcome Dr. Sean Hoban from The Morton Arboretum.

Location: The Morton Arboretum, a botanical institute in Lisle Illinois (30 minutes west of Chicago)

Current Position: Tree Conservation Biologist, Department: Center for Tree Science (equivalent to Assistant Professor)

Current mobile device(s): iPhone SE (remarkably, my first smart phone!)

Current computer(s): custom built workstation from Puget Systems– 32 core Xeon processors with 128 GB RAM, 8 TB HD, running Kubuntu; a Toshiba laptop; a basic Windows desktop

What kind of research do you?

I like empirical, applied, and theoretical work, so my research program spans three elements. (1) Interpreting genetic data to understand population ecology, in particular contemporary dispersal and mating patterns as well as longer time-scale (Quaternary) changes in species’ distributions.  I also investigate the evolutionary impact of disease and fragmentation; adaptation in new environments; and hybridization.  (2) Conservation of rare species via planning ex situ seed collections and in situ population prioritization, primarily using genetic data but increasingly using non-genetic data.  The goal is to ensure the long term survival of species with effective intervention (such as our current IMLS funded project).  (3) Developing and improving statistical methods and software in population genetics and conservation; I particularly like to test methods in situations for which they weren’t designed as well as evaluate sampling strategies.  This area of work is crucial because misapplication of methods or misinterpretation of results can lead an entire field in the wrong direction.

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Retrieving a million sequences and avoiding primer bias, a new method that might have it all

We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA gene sequences were reported directly from environmental samples. As Soren M Karst and colleagues point out in a recent article in Nature Biotechnology, we are now in an era where sequencing has become an integral part of microbial ecology centered research.

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Posted in bioinformatics, evolution, metagenomics, methods, microbiology, next generation sequencing | Tagged , , | Leave a comment

How Molecular Ecologists Work: Hanna Kokko on tending her literature garden and learning by reviewing

Location: University of Zurich

Current Position: professor of evolutionary ecology

What kind of research do you?

Evolutionary ecology

Can you use one word to describe the way you work?

Multitaskingly. Is that a word?

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How Molecular Ecologists Work: Kathryn Hodgins on one liners and the beautiful drone of construction work

Welcome to “How Molecular Ecologists Work”, the interview series that asks scientists how they get stuff done.

This week, we are headed to Australia to talk to Dr. Kathryn Hodgins. Her work focuses on understanding rapid local adaptation, especially in the context of invasive/weedy plants. I asked her how she gets it done.

Location: Monash University, Melbourne Australia

Current Position: Lecturer (Teaching and Research position)

Current mobile device(s): Samsung S8, iPad

Current computer(s): MacBook Pro, iMac

What kind of research do you?

I study the genetic basis of adaptation in invasive and foundation plant species. I am interested in how species evolve during colonization and invasion. I am also particularly concerned with the factors that facilitate gene reuse during adaptation to similar environments. My research involves a mix of genomic data analysis, common garden experiments and field work.

Can you use one word to describe the way you work?

Tenacious

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Notes from Asilomar: 150 years of the American Naturalist

View from Asilomar State Beach (jby)

My 2018 academic year started with a drive north. Asilomar Conference Grounds, on the Monterey Peninsula, is a half-day trip north of Los Angeles, so when the American Society of Naturalists announced it as the site for the society’s meeting celebrating the 150th anniversary of the American Naturalist, its scientific journal, I registered almost immediately. Asilomar’s rustic-luxury architecture, set amidst Monterey pines on the edge of the ocean, was an appropriate venue for a conference celebrating the impact of the oldest continuously publishing scientific journal in North America.

I’m cribbing that factoid from the introductory presentation by Dan Bolnick, the incoming editor-in-chief of Am Nat, who opened the meeting with a walk through the journal’s history. Founded in 1867 by a quartet of disgruntled Harvard graduate students, Am Nat grew into the turn-of-the-twentieth-century version of Science under editor/owner Edward Drinker “yes that” Cope. Worried that Am Nat had become a dumping ground for papers rejected by more specialized journals, a later editor re-focused on biology, and Am Nat became a major venue for research underlying the Modern Synthesis of Mendelian genetics and Darwinian evolutionary theory, then for the growth of theoretical ecology — and as the millennium turned it emerged as a nexus for ecology, evolution, and behavioral research. Bolnick nicely balanced stories about individual papers and contributors to the journal with a quantitative look at how its content has changed over time.

(Twitter: @DanielBolnick)

(I hope he’ll be posting the full slide show somewhere. Update: He has!)

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Climate change and genomic vulnerability

As the world burns and we barrel heedlessly into an ever-smaller and uglier future, predicting how species will respond to climate change will be critical for conservation planning. Intuition suggests most organisms will shift their ranges up in latitude or elevation in an attempt to track their thermal niche and its ecological covariates. Yet because other abiotic and biotic factors may be decoupled from mean temperature — e.g., precipitation, the presence of competitors, or habitat modification — “downslope” range shifts have also been observed. Moreover (and to the surprise of no one reading this website), the occurrence or severity of range shifts can be mediated by evolutionary responses. As a result, the amount and character of genetic variation in regions of the genome associated with climatic variables can help predict whether species will adapt quickly enough to track global warming.

Yellow Warbler. Flickr: tessa nickels

In a paper published this week in Science, Rachel Bay and coauthors explored the link between adaptive potential and documented population trends in a migratory songbird (Yellow Warbler Setophaga petechia; hereafter “YEWA”). Using genome-wide SNP data from 229 individuals and 21 populations spanning YEWA’s breeding range, Bay et al. first asked if geographic and environmental distance predicted genetic variation. While variation was largely shaped through isolation-by-distance, a machine-learning approach found that smaller subsets of the genome are explained by environment, and that significant differences in environmentally-associated genetic variation are found across the species’ range.

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Posted in conservation, evolution, genomics | Tagged | 1 Comment