GEOME is putting genetic data in its place

Records for sequenced mollusk samples along the southern California coast (GEOME)

Infrastructure to make genetic data widely available for research beyond its initial publication has been a theme of the genomics revolution, from GenBank to the Sequence Read Archive. For molecular ecologists, though, genetic data is only half of our field — the other half is the ecological context in which that data is collected. This month, Molecular Ecology Resources highlights an initiative to bring that ecological context to genetic data archiving: the Genomic Observatories Metadatabase, or GEOME.

Led by Cynthia Riginos at the University of Queensland, Eric Crandall at Penn State, Libby Liggins at Massey University, and Michelle Gaither at the University of Central Florida, the GEOME collaborators present the case for creating yet another data deposition service: although there are a number of established databases for public deposition of genetic and ecological data, no one repository linked both types together. GEOME, which launched in 2017, offers a single metadata framework to link DNA sequence or marker data to sample locality and ecological measurements.

GEOME allows researchers to create records linked to sequence data they’ve already posted to a public repository — or, now, to upload samples to the International Nucleotide Sequence Data Collaboration SRA alongside ecological data through a single unified portal. Datasets are then searchable through the GEOME website, which includes multiple levels of search control alongside a useful map visualization, or through a new R package that interacts with the GEOME API.

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Fieldwork in the time of COVID

Life as we knew it came to a screeching halt back in March. Almost a year ago, how is that possible??? Yet, at the same time it feels like several lifetimes have passed …

At a recent editorial meeting, we were talking about TME posts and in the past, I’ve written about fieldwork. I always felt fortunate to be able to travel to far flung places, but I don’t think I truly appreciated how much being out in the field really meant to me. In between bouts of existential dread and complete overwhelmed-ness over the last 9-odd months, I’ve realized how much I took for granted. Fieldwork was one thing that was simply part of the fabric of my life.

Our time in the field entails long days of driving hither and yon, sampling (often in hot, humid weather or the freezing rain – we like extremes I guess), and then processing late into the night. At some point Cher, Céline, or some other guilty pleasure musician make an appearance to get us through the slog – whether in the lab or on the road. Sometimes, we’re processing samples in a nice lab. Other times, we’re sitting backwards on a toilet in a Motel6 using the tank lid as a makeshift bench. We eat too much McDonald’s, go back for more and regret it immediately. Yet, these are the times of the year I find myself anxiously awaiting, counting down the days on my calendar until we are on the road.

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Posted in blogging, career, chat, ecology, evolution, fieldwork, haploid-diploid, just for fun, mating system, natural history, population genetics, postdoc, Science Communication | Tagged , , , , , , , , , | Leave a comment

Join the Molecular Ecologist team in 2021!

Blue skies and white clouds mirrored in a broad bay
One of Kelle Freel’s fieldwork nostalgia photos, from Kāneʻohe Bay, Oʻahu, Hawaiʻi

The Molecular Ecologist is seeking two new regular contributors for 2021! Join us in blogging about “ecology, evolution, and everything in between.”

Ideal candidates should have expertise and experience in our core topic, the use of genetic data to understand the past and future of the living world. We’re particularly interested in senior graduate students, postdoctoral researchers, and other working scientists who can discuss basic science on a level that engages research biologists, as well as explaining fundamental molecular ecology concepts to the general public. The two contributors in the 2021 cohort will receive small stipends for their first year with the blog, in exchange for committing to posting on a monthly basis, helping to manage social media for TME — either our Twitter account or our presence on Facebook — and contributing to the Molecular Ecologist Podcast.

In addition to the direct compensation, blogging for The Molecular Ecologist can be an excellent way to hone familiarity with current molecular ecology research, establish connections within the scientific community, and build a portfolio of science writing for a broader audience. In light of this, we are particularly interested in applications from candidates whose racial, ethnic, sexual, or gender identities are underrepresented in science careers.

To apply, please e-mail Jeremy Yoder at jbyoder@gmail.com with a brief cover letter explaining (1) why you want to write for The Molecular Ecologist and (2) what topics you would write about for the site, along with (3) an appropriate sample of your writing. Applications should be received by the end of the day on 11 December, 2020 to ensure consideration.

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Hosts select symbionts for greater mutual benefit, an evolutionary experiment shows

The roots of a barrel medick plant, with pink nodules housing rhizobia. (Wikimedia Commons: Ninjatacoshell)

Who’s in charge of a symbiotic mutualism? You might think the host organism, whose body is the venue for an exchange of nutrients or services with a microbial symbiont, is running the show, able to evict or punish symbionts that don’t play nice. However, there are many examples of hosts making do with symbionts that aren’t particularly good partners, and some evolutionary theory has suggested that competing symbionts can gain the upper hand. Results from an evolutionary experiment recently reported in the journal Science lend support to the host-in-the-driver-seat view, though — bacterial symbionts selected by five generations of hosts evolved to be better mutualists.

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Take the Molecular Ecologist reader survey!

Following up on this being our tenth year of blogging operations, we thought it was past time to check in with you, our readers. To that end, we’ve put together a brief survey about how you read The Molecular Ecologist, what kinds of posts you follow us for and what you’d like to see more of, and who you are — in terms of career stage and scientific interests. There’s also an open-ended suggestion box, to tell us what we should have asked about but didn’t think to.

In total it should take less than ten minutes, and if you’ve got the time to spare, it’ll be very helpful. You can fill the survey form in right here on the blog, or follow this link to the Google Form. Thanks in advance!

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Marmots, seasons, and climate change

I love when nostalgia for a project, place, or species intersects with a current interest, as happened this week for me with a paper by Cordes et al. 2020, about the contrasting effects of climate change on the seasonal survival of yellow-bellied marmots in the Colorado Rocky Mountains.

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Simple rules for organizing data in a spreadsheet

Most scientists collect and organize at least some data in spreadsheets, usually Excel or Google Sheets, despite the potential pitfalls of using such products (there are even archives of spreadsheet horror stories). The most commonly bemoaned problem in Biology, that of Excel converting some gene names to dates, even caused the HGNC (HUGO Gene Nomenclature Committee) to change the names of at least 27 gene this year to avoid this issue. No matter your feelings about spreadsheets, they are generally the first program students learn to use for creating a database of samples, recording data, or doing simple calculations. Furthermore, for people without extensive coding or experience, spreadsheets are the default. Fortunately, by following some simple guidelines, we can avoid most of the hassles as well as countless hours re-formatting data tables for analysis and endless confusion trying to decipher color-codes from 10 years ago.

This paper by Broman & Wu is from 2018, but it came to my attention this week and I have now added it to my canon of “Must read” literature for future students.

Karl W. Broman, lead author

Many of these tips seem obvious, but I’m guessing if you think back, you will recall an instance(s) where you (or a co-author) violated each of these tips and in retrospect knew you had erred. These days you are wiser but could probably use a refresher. This paper prevents the re-invention of the wheel during every PhD. I urge you to read the full paper, but here I’m providing the lightly edited (I combined some tips and re-arranged them a bit) cliffs notes. These guidelines, if implemented across the lab, also allow for easy hand-off and transfer of data between students and colleagues.

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Molecular Ecology and Molecular Ecology Resources are recruiting new Associate Editors

Molecular Ecology and Molecular Ecology Resources are looking for new Editorial Board members to join the journals as Associate Editors in the key subject areas below:

  • Eco-immunology/emerging diseases/disease resistance
  • Proteomics/protein evolution
  • Computer programs/statistical approaches
  • Environmental DNA/metabarcoding

Experience with genome assemblies would also be advantageous.  

Nominations and personal applications are welcome, and whilst scientific qualifications are paramount, we would particularly appreciate nominations and applications from suitably qualified researchers in underrepresented groups, including women, ethnic minority scientists, and scientists with disabilities, among others. Please email nominations/applications by October 15th, 2020 to manager.molecol@wiley.com with the following items:

  • Cover letter stating the reasons for your nomination, of if applying for yourself, your interest in the role and familiarity with the journals,
  • Abbreviated CV (Education, Publications, Outreach) if you have it.
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Genetic Rescue – Fitness and genomic consequences

Dr. Sarah Fitzpatrick, lead author.
Photo Credit:
https://www.kbs.msu.edu/people/sarah-fitzpatrick/

As a PhD student studying the effects of genetic diversity overall and immunogenetic diversity specifically on survival and reproductive success in an endangered primate in captive and wild populations, I thought a lot about the potential effects of inbreeding and outbreeding depression. I read literally 100s of papers on the topic. Inbreeding depression describes the negative fitness effects that can occur in small populations when relatives breed with each other for multiple generations, thus genetic diversity is lost through genetic drift and negative alleles are expressed. Outbreeding depression, by contrast, is the negative consequence of breeding two genetically distinct populations leading to a loss of local adaptation. Concerns about outbreeding depression are one of the major theoretical limitations to re-introductions and attempts at ‘genetic rescues’ when small populations and/or endangered species might be suffering from inbreeding depression. For the most part, however, evidence of outbreeding depression has mostly been limited to plants and captive or laboratory studies. Earlier this year, however, Dr. Sarah Fitzpatrick and her co-authors documented an extremely cool example of genetic rescue in populations of wild Trinidadian guppies, contradicting the hypothesis about the potential for maladaptive gene flow in population introductions (Fitzpatrick et al. 2020).

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The Molecular Ecologist Podcast: What do you look for in a journal?

The Boston Public Library (Flickr: Little Koshka)

A new episode of The Molecular Ecologist Podcast is now out on Anchor.fm. In this episode, we turn to a question that every academic scientist has to answer at some point: How do you choose a scientific journal to receive your paper? Kelle Freel, Shawn Abrahams, Katie Grogan and Jeremy Yoder chat about what they like in a journal, what they consider when picking a publication venue for a new paper, and the various meanings of an “impact factor.”

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