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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Sparrows and spiders and aggression, oh my!

One of the major goals of evolutionary biology is to link phenotypic variation with specific genetic variation, yet for behavioral phenotypes in non-model species, this task remains daunting and generally elusive. Although behaviors are heritable and clearly acted upon by evolutionary forces, they are generally polygenic, flexibly expressed, and context-dependent. Two recent papers, however, accomplished this very thing, in white-throated sparrows (Zonotrichia albicolis; Merritt et al. 2020) and in a species of jumping spider from southeastern Asia (Portia labiata; Chang et al. 2020)!

Top left: Dr. Jennifer Merritt. Top Right: Dr. Chia-Chen Chang
Bottom left: White-striped and tan-striped morphs of the white-throated sparrow, Photo Credit Jennifer Merritt
Bottom right: White-mustached Portia Jumping Spider, Photo Credit Richard Ong on Project Noah
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Posted in association genetics, birds, insects, next generation sequencing, RNAseq | Tagged , , , , | Leave a comment

A genomic march of the penguins

It’s undeniable that penguins are a marine representative of the charismatic megafauna group. I have an affinity for stuff we need microscopes to see, BUT I agree that penguins are cute (just LOOK at these National Geographic photos…they’re even in comics). I’m guessing that many of us have also watched “March of the Penguins”, although maybe you also were today years old when you learned the original French version was narrated in first-penguin by the stars of the show themselves in “La Marche de l’Empereur”.

Our hearts all melt a tiny bit when we see a fluffy baby chick waddle around on the ice. But. Have you ever contemplated how many different penguin species there are, where exactly they’re found on the globe and how they ended up where they currently reside? If you’re like me, (and don’t work on anything remotely related to penguins), you might not be well versed in the diversity of these flightless diving birds.

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Urban ecology, evolution, and racism

Occasionally, while reading the literature, you stumble across a paper that is so eloquent and beautiful that you are awestruck. Since that happened to me this weekend, today’s post is a call to you to go read the incredible synthesis and call to action written by Schell et al. in Science (2020) – The ecological and evolutionary consequences of systemic racism in urban environments. In this paper, the authors affirm that biologists working in urban environments must consider how racial oppression affects the biological change they study.

Lead author Dr. Christopher Schell.
For more info, visit his webpage – https://faculty.washington.edu/cjschell/wordpress/people/

Evolutionary biologists have increasingly become interested in how the environmental change due to urbanization leads to changes in the phenotypic, genetic, and species make-up of urban ecosystems. Indeed, between 1965 and 1989, only 124 papers with the words “Urban ecology” in the abstract were published according to a quick non-exhaustive search of Web of Science (mean = 5.0 papers per year; performed 8-31-2020). However, from 1990 until 2019, the rate of publication increased exponentially to over 1,000 papers in 2019 alone.

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A decade of The Molecular Ecologist

Conveniently, I made a montage-header for The Molecular Ecologist back when we took a stab at crowdfunding in 2016.

I recently took a look through the “Archives by month” drop-down in our right-hand sidebar and discovered that it goes all the way back to July 2010. Which means The Molecular Ecologist had its tenth anniversary this very month — specifically back on July 11, an even decade since Brant Faircloth kicked off the blog with a rundown of essential (Python-centric) bioinformatic tools.

Given that it snuck up on us, and in the middle of the summer, and in the middle of this summer, we don’t have any kind of big event planned. But I didn’t want to let the month close out without marking the occasion. So here’s a rundown of some major events in the history of this fine blog:

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Serendipitous history in the microbial making

It’s been over 100 years since the Dutch Microbiologist Martinus Willem Beijerinck theorized that microbes could oxidize manganese to generate energy for growth. Last week, the first evidence for this theory was published, and you might be surprised about from where these fascinating microbes hail.

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The Molecular Ecologist Podcast: Rivers and rabbit resistance

(Flickr: Leandra Fallis)

A new episode of The Molecular Ecologist Podcast is now out on Anchor.fm. In this episode,

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Posted in Action Item, career, community ecology, conservation, howto, microbiology, TME Podcast | Tagged , , , | Leave a comment