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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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?


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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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How Molecular Ecologists Work: Daniel Cadena on the eclectic approach and getting the country view

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

This week, I’m interviewing Carlos Daniel Cadena, Professor at Universidad de los Andes in Colombia. Daniel’s work cuts across a broad swath of evolution and ecology, but mostly focuses on the evolution and systematics of neotropical birds. I asked him how he gets it done.

Location: Universidad de los Andes, Bogotá, Colombia

Current Position: Professor in the Departamento de Ciencias Biológicas

Current mobile device(s): iPhone 6.

Current computer(s):Macbook Pro

What kind of research do you?

Broadly speaking, I am interested in and work on evolutionary biology of birds and (occasionally) other vertebrates. Over the years, I have worked on a broad range of topics, from genetics, physiology and behavior all the way up to diversification and broad-scale patterns of diversity, with a little bit of everything in between. I am most interested in questions in biogeography and I am especially intrigued about the causes of high tropical diversity at various levels. I like to pursue my interests in tropical diversity from a wide variety of perspectives combining field, lab, museum, and computational work.

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


What specific strategies do you recommend for running (or establishing) a lab?

My approach to running a lab has been rather different to that of many other researchers in our field. When I first landed my faculty job I often wondered whether I should focus on a single study system in which to address questions at great depth from multiple perspectives and really get to know the system in detail, or rather pursue my curiosity (and allow for student freedom in developing their independent projects) by spreading out quite thinly working on multiple topics and various systems at the same time, moving on from one project/system to the next after learning a few things. I somehow ended up picking the latter option and although I sometimes suffer of the “impostor syndrome” by thinking that much the specifics of my work are rather superficial relative to careful in-depth work done by many colleagues, I believe that knowing relatively little about many different things has been a great career path, if only to maintain my excitement with regards to answering new questions and learning new things.

I say all this only to explain why I believe a strategy that has worked for me is to be open and flexible, and willing to learn from students and colleagues. This has allowed me to mentor a great diversity of students and to collaborate with colleagues with various interests and backgrounds. I also think that being in a lab where people might be working on a bunch of (seemingly) unrelated topics is especially valuable for graduate students, who I think should be exposed to a broad spectrum of ideas and tools. I like to think my students will appreciate my somewhat eclectic approach in the long run.

Where do you work with data (personal computer, lab computers, cluster, etc.)?

Honestly, I am not a big data cruncher these days. Because I have had a rather heavy teaching and administrative burden, over the past few years much of the research I have done has been conducted by supervising students, and it’s really them doing the hard–and fun–work. For the few projects I am currently analyzing data myself, I mostly use my personal computer. In terms of where do I physically work, now that I am relatively free of meetings, etc., I have been exploring working in various places aside from my office including other spots on campus, cafes, and at home. I recently rented a house out in the country outside of the city and working there has been especially fun and productive. I guess the views help.

Besides your phone and computer, what gadget can’t you live without and why?

It’s not really a gadget, but I rely heavily on Slack for communication with members of my team. When I was department chair, my email was total chaos and important and fun things would often get lost, so I basically abolished communication via email with my students and lab associates. Slack allows me to respond quickly and to have all the important communications related to people and projects in the lab properly organized.

What part of your job do you spend the most time on in a week? What part do you wish you had more time for?

Teaching, including preparing and giving lectures, but also reading even if my readings do not immediately get incorporated into classes. Although it is increasingly hard to keep up with the literature, I believe that you really need to know where various fields are going in order to be a good educator. Like almost everyone else, I would like to have more time for research and especially to think about long-term research plans. However, I should say that I was on sabbatical leave recently and while I honestly did not miss teaching a whole lot while I was away, getting back to my classes has been quite enjoyable; I like teaching a lot.

How do you stay organized (to-do lists, digital reminders, etc.)?

I don’t know! I hardly ever write down a to-do list (except when things are getting out of control) and I don’t use a calendar to schedule appointments, etc.. This is probably not good advice for many people, but I guess I (sort of) remember the important things I need to do and they somehow get done. Well, most of the time.

What do you do to recharge outside of science?

Definitively, sports are my escape valve. I started running more than six years ago and very quickly got really into it and became a long-distance runner. I’ve run nine marathons so far and train very hard for this with a team, typically 5-6 days a week. I also picked up road cycling a little over a year ago and have already done a couple of century-mile events. More recently, I started swimming and a few weeks ago completed my first short triathlon; I am now training for my first long-distance event. It will take time, but I think I will end up running ultramarathons and likely ironman triathlons, that’s the kind of person I am.

Some people say they have great ideas for work while running or cycling, but I hardly ever think about work while training. This is my time to get totally disconnected from work and I think this gives me great energy to get me through the day and work effectively. I recently gave what I thought was a quite smooth lecture on a relatively difficult topic at 9 am; my students probably did not notice my day had started very early and I had already run 30 km before showing up to class.

What are you currently reading?

Research manuscripts and thesis drafts! Also, I am little-by-little reading Andrea Wulf’s “The Invention of Nature” on Alexander von Humboldt’s fascinating story.

What is your sleep routine like?

I’m definitively a morning person. I usually go to bed quite early and wake up very early to train. Some of my triathlete friends think I am too much of a wimp because I am not willing to wake up at 3 am to go for a long bike ride, but I am fine with starting my day at 4:30 am to go swim, ride, or run.

Fill in the blank: I’d like to see _______ answer these questions.

Bob Ricklefs. I had the fortune to work with him, but I still do not get how he does it all.

Thanks Daniel! Next week: Dr. Kathryn Hodgins…..

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Molecular ecology, the flowchart

Towards the end of last semester my department’s evolutionary genetics journal club read Rasmus Nielsen’s terrific 2005 review of tests for recent natural selection in genetic data. Nielsen provides figures illustrating the effects of a recent selective sweep and the shape of the site frequency spectrum that you’ve probably seen reproduced in a score of research seminars, and tables that neatly categorize (1) how different evolutionary processes affect diversity within and among species and (2) a selection of widely used test statistics, the patterns they test for, and the kind of data they need. It’s now more than a dozen years old, but it holds up mighty well as an introduction to what we can learn from genetic samples of a population, in no small part because the tests Nielsen describes in human data have only recently become widely accessible for non-human, non-model organisms.

Re-reading the paper and thinking about how I’d approach it as a new grad student, though, it occurred to me that precisely because he was writing in an era when a handful of species were the focus of most real “genomic” research, Nielsen doesn’t really account for the wide variation of genomic research infrastructure we cope with today. Anyone can collect genome-wide SNP data from a tube-rack-full of tissue samples and a RADseq protocol, but what you can do with that data afterwards depends a lot on the species you sampled, the set of individuals in the sample, what other kinds of data you can connect to the samples, and the existence of resources like a reference genome, a linkage map, or “annotations” that might be anything from the results of functional genetic experiments to algorithmic identification of hypothetical gene sequences.

In that journal club discussion we started talking through some of these possibilities in terms of if-then links: if you have SNPs and they’re placed within larger contigs or a whole reference genome then you can look for runs of homozygosity or extended linkage disequilibrium or islands of differentiation … Or if you have SNPs and they’re from multiple species you can estimate a phylogeny and then do ancestral state reconstruction and if you know codon positions you can estimate dN/dS … And so on. I started sketching on the whiteboard, and the result is below:

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Posted in association genetics, bioinformatics, genomics, howto, infographic, linkage mapping, next generation sequencing, phylogenetics, phylogeography, population genetics, selection | Leave a comment