Digging for Knowledge … and Nematodes

Hannah Oswalt wrote this post as a part Dr. Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Hannah is working towards her PhD in Dr. Chuck Amsler’s lab where she is investigating the effects of ocean acidification on macroalgae and amphipods around the western Antarctic Peninsula.

In early spring, a farmer prepares their field for the season’s planting. They till, then fertilize the soil. It’s easy to imagine how tilling and fertilizing, often referred to as soil management, affects the organisms that can be seen above ground. But, have you ever considered how tillage and fertilizer affect animals beneath the surface? 

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For population genetics, continuous space might be the final frontier

Real landscapes rarely have tidy patches. (Flickr: Martin Hefner)

"All models are wrong, but some are useful," is a basic operational principle of population genetics. The aphorism is attributed to George Box, who cited the ideal gas law as an example, but it crops up in every attempt we make to relate on-the-ground biology and ecology to observed patterns of diversity in DNA sequences.

My first exposure to this issue was probably reading Whitlock and McCauley’s 1999 review of the tricky relationship between pairwise genetic differentiation and actual migration rates. Classic theory by none other than Sewall Wright related the differentiation index FST to the effective migration rate as FST ≈ 1/(4Nm+1) — but for that relationship to hold, every population of a sampled species needed to be the same effective size, and individuals needed to move between all pairs of populations at exactly the same rate. It is, to put it mildly, rather unlikely that any naturally distributed species might meet those conditions.

In the years since Whitlock and McCauley (1999), population genetics has accumulated a wealth of methods to provide more realistic models of population structure. But most of these still rely on treating populations as discrete patches linked by a web of migration — and while there are taxa that really are distributed in patches, environmental variation in the real world is much less tidy. A new paper published online ahead of print in Genetics takes a dive into the effects of modeling patchy distributions when your data comes from a continuously distributed world, and it suggests that this particular wrong model may be less useful than we’ve assumed.

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Raising boys – Not for the faint of heart

According to all of my parent friends, raising girls is quite different from raising boys, from the toys to the tantrums, the clothes to the bathroom habits, even for the most liberal, gender-neutral of my friends. In most sexually dimorphic species, raising boys is actually physically more costly than raising girls because males are larger than females. This trend usually begins at birth and continues into adulthood. In sexually dimorphic species, males generally fight amongst themselves for access to females during mating season, so size is an important factor for male reproductive success. The bigger a male baby is when he’s born or weaned, the bigger he is likely to be as an adult. Male offspring are therefore more energetically expensive to raise than females. In fact, raising sons versus daughters early in life can influence how quickly the mother ages later in life!

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“Of all the Islands in all the Seas in all the World…”

Ashley Jones wrote this post as a part of Dr. Stacy Krueger-Hadfield’s Scientific Communication course at the University of Alabama at Birmingham. She earned a B.S. in Animal Science from Auburn University where she also spent several years working at the Auburn University College of Veterinary Medicine. This past semester, she completed her M.S. in Biology at UAB with a focus on infectious diseases under the mentorship of Dr. Stephen Watts. Her graduate research project centered on the epidemiology of Lyme Disease in the United States. She is currently employed as a PCR technician in the virology laboratory at Takeda Pharmaceuticals where she is also enrolled in an MT certification program. In her free time, Ashley volunteers for local animal rescues and the Wildlife Resources and Education Network (WREN).

The study of genomic diversity lends itself to conservation efforts for threatened populations by providing information on which species may need intervention more urgently than others. For instance, when faced with a particularly harsh environment – such as in times of drought, famine, or disease – a population with high genetic diversity is more likely to have at least a few survivors due to their better-suited alleles. The survivors will then be able to pass along their “advantageous” alleles to future offspring. Et voilà!

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Posted in birds, blogging, Coevolution, conservation, Science Communication | Tagged , , , | Leave a comment

Co-opting responses for old enemies

On Friday, Shelby Gantt introduced us to an unusual type of parasite, the brood parasite! As Shelby eloquently described, brood parasitism is when an individual’s offspring are raised by someone else who incurs a cost to raising these offspring. The most well-known examples of bird brood parasitism are the cuckoo and the cowbird, but at least 100 species of birds (nearly 1% of all bird species) are obligate parasites on the nests of at least 950 or >10% other species of birds (Abolins-Abols & Hauber 2018). The costs to the foster parents include a reduction in the size and fledging success of the foster parents’ biological offspring and a potential decrease in future reproductive success due to the energetic costs of feeding the foster chick.

On the left is a red-chested cuckoo chick being fed by its much smaller foster parent, a cape robin-chat on the right.
Alandmanson/Wikimedia Commons (CC BY-SA 4.0)

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Brood Parasitism or Adoption? Mixed Parentage of Brooding Damselfishes

Shelby Gantt wrote this post for Dr. Stacy Krueger-Hadfield’s Scientific Communication course at the University of Alabama at Birmingham. Long enamored with coral reef communities, Shelby completed a B.S. in Biology with a certificate in Marine Biology at the Georgia Institute of Technology and a M.S. in Marine Biology from the University of North Carolina at Wilmington where she studied sponge microbial communities and nutrient cycling on coral reefs. She is currently working towards her PhD in Dr. Dustin Kemp’s lab where she is exploring the relationships between climate change and coral microbial and algal symbiont associations. Shelby tweets at @GanttShelby.

When thinking about parasites, things like tapeworms or malaria probably come to mind. Brood parasites, such as birds (Davies, 2010), the Mochokid (Cuckoo) Catfish (Blažek et al., 2018; Sato, 1986), or even coral reef fish, probably do not come to mind. 

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Posted in blogging, Coevolution, DNA barcoding, fieldwork | Tagged , , , | 1 Comment

#NewPI chat: Headed for lockdown edition

We’re bringing back #NewPI chats, where Molecular Ecologist contributors who are in our junior years on faculty convene on Slack to talk about that #NewPI life for an hour. What follows is a transcript of our recent chat (3/16/2020), lightly edited for clarity and grammar and with the odd hyperlink added for context. Enjoy!

— Rob

Who’s here?

  • Stacy Krueger-Hadfield (SKH) – Assistant Professor at the University of Alabama Birmingham since 2016
  • Jeremy Yoder (JY) – Assistant Professor at California State University, Northridge since 2017
  • Rob Denton (RD) – Assistant Professor at the University of Minnesota Morris since 2018

RD: While we are chatting right now, we are also in the midst of a national health crisis that is drastically influencing everyone’s work and personal life. In academia, that means campus closures, on-line learning, and research schedules that are suddenly up in the air. What’s your situation right now?

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Introducing The Molecular Ecologist Podcast

The Molecular Ecologist is trying out a new medium for the first time since we launched: audio! That’s right, TME contributors, talking about the science we’ve been reading and writing about, recorded for easy listening on any internet-capable device. As a starting point for material, we’ll recap and discuss some of our favorite recent posts to the blog — if this turns out to be something folks like, we may branch out into podcast-only content like interviews.

We’re distributing over the hosting service Anchor.fm, which makes a lot of the backend logistics very simple, including hooking up the RSS feed to standard podcast subscription services like Spotify and Apple Podcasts (coming soon) — we’ll also post new episodes to the blog as they come out.

Take a listen below, and let us know what you think!

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Posted in community, housekeeping, microbiology, modest proposals, natural history, Science Communication, Science History, TME Podcast | Tagged , , | Leave a comment

FISHing for molecules, a link between form and function in animal–bacteria symbioses

I am posting a blog post that was written by Benedikt Geier, a Ph.D. candidate who just handed in his Ph.D. thesis at the Max Planck Institute for Marine Microbiology in Bremen, Germany. In my eyes, these last couple of months before submitting a doctoral thesis are the hardest, and that’s why I am even more impressed with Benedikt’s summary of one of his Ph.D. chapters that was recently published. When I received the first draft of this post, I literally got goosebumps and was holding my breath while reading it. So spectacular. Enjoy!

Naturalists like Amalie Dietrich, Marian Farquharson, Alfred R. Wallace, or Charles Darwin visualized the form and function of animals, plants, and environments by drawing the organisms and their behaviour. Today, we know that the natural world consists of far more organisms and processes than that we can see by eye and that must be considered to understand biological systems. A perfect example is bacteria. Every animal and plant is not only in physical contact with bacteria but also interacts with them through a hidden chemical language. The aim of our study and my PhD in general was to develop approaches to visualize and understand the molecular interactions between animals and almost every animal or plant on our planet.

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Posted in Coevolution, community ecology, ecology, evolution, genomics, methods, microbiology, natural history, Symbiosis, transcriptomics | Tagged , , , , , , , | Leave a comment


I just submitted my four year review and in so doing listed out the students that had published blogs on The Molecular Ecologist. Seventeen students have not only received course credit, but also have a non-peer reviewed publication on their CVs.

Starting a week from today, the next batch of student posts will go live on our new #StudentSciComm post series. Students wrote posts as part of my Evolution and Sci Comm courses this past autumn.

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Posted in blogging, career, chat, community, ecology, evolution, howto, methods, Molecular Ecology, the journal, Science Communication, science publishing | Tagged , , , , , | 1 Comment