Shedding light on symbiotic relationships

Lots of critters glow in the dark, but most of them aren’t found in just any back yard…unless that back yard happens to be the beach. The ocean is full of bioluminescent critters that use light to attract prey (possibly like the “glowing sucker octopus” Stauroteuthis syrtensis), find mates (like Odontosyllis undecimonda, aka fireworms), or act as a defense mechanism. Organisms might produce a startling flash to scare off a potential predator or use bioluminescence for counterillumination, making it harder for a predator to clearly see the outline of its next snack. My favorite example is the absolutely ADORABLE Hawaiian bobtail squid, you can’t deny the cuteness…there are articles about it.

While it’s possible for animals to actually harbor the chemicals needed for a lovely glow, the light itself is often produced by symbiotic bioluminescent bacteria. Just five years ago, researchers determined that it has been at least 17 times (yes…that’s a lot!) that ray-finned fishes evolved symbioses with glowing bacteria buddies (Davis et al., 2016). However, a broader picture defining patterns across these symbioses had not yet been carefully defined, and I suppose it was time to find out.

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Can small populations benefit genetic rescue?

The core dogma of conservation biology is clear: small populations are bad for species’ persistence. If we observe a population of endangered vertebrates harboring abundant deleterious mutations but without any reduction in fitness, what is happening there? I would like to bring up the curious case of the Channel Island foxes that was posted in the Molecular Ecologist blog a while ago and an interesting debate about using a small population as a source for genetic rescue that have been happening up until now.

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Posted in conservation, genomics, mammals, mutation, population genetics, theory | Tagged , , , , , , , , , , , | 1 Comment

PopGroup – the small conference that packs a punch

First held in 1968 as a working group to discuss population genetics, the PopGroup conference is a yearly staple of UK-based evolutionary researchers (and increasingly researchers from further afield). However, this year there was to be no university student accommodation, no frigid lecture hall air-conditioning drama, and certainly no ceilidh dancing (although certain people – no comment – were perhaps not quite as devastated about this part), as the 54th ‘Liverpool’ edition of PopGroup was held online. 

Although PopGroup is a small conference and lasts only 2.5 days it packs a punch – but a friendly punch, maybe something more akin to a fist bump. The meeting typically has an attendance of around 150-200, but for this year’s edition this number grew to around 400, with four parallel zoom sessions in contrast to the usual two or three. In addition to the the increased attendance was a notable, and welcome, increase in geographic breadth of attendees, from a typically UK-centric attendance (also reinforced by the fact that PopGroup is always held around the Christmas/New Year period), to this year’s edition, which included speakers based in over twenty different countries. This year’s plenary talks spanned a variety of topics including the spatial patterns of genetic variation, longevity and anticancer mechanisms in mammals, the evolutionary ecology of host-defence, and the impact of drosophila seminal proteins on fertilisation and fitness (a list of plenary speakers can be seen HERE).

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How butterflies match their wings

A pair of butterflies, with black wings marked by bright red stripes on the forewings and white bars on the hindwings.
Heliconius melpomene, in the “postman” pattern (Flickr: alain01789)

The following is a guest post by Ornob Alam, a graduate student in Michael Purugganan’s lab at New York University. Ornob’s PhD projects examine the demographic and evolutionary history of domesticated Asian rice in the context of past climate change and human migrations.

In 1859, the English naturalist Henry Walter Bates emerged from the rainforests of Brazil after more than a decade of recording the natural history of the region. Among his many discoveries, the adaptive strategy of mimicry in butterflies has in particular become embedded as a key area of study in evolutionary biology.

Bates noted that some butterflies that were different enough to be classified as separate species (or subspecies) closely resembled each other in wing color patterns. He concluded that certain butterflies had evolved to mimic others that were poisonous and avoided by birds. Birds learn to interpret the wing color patterns of poisonous butterflies as warning signals to avoid eating them, and any non-poisonous species that resembles a poisonous one gains some protection from predation.

Bates, however, was not able to explain why different poisonous species living in proximity also sometimes resembled each other. In 1879 Fritz Müller, a German naturalist, finally explained this as a numbers game. Teaching birds to recognize warning patterns comes at a cost, in the form of a certain number of individuals being eaten. When two poisonous species evolve to share the same wing color pattern, they share this cost and reduce it for each individual species. If a bird learns to avoid one species, the other benefits, and vice versa.

All of that helps to explain the selection pressures that favor the evolution of these two types of mimicry. But how does one species come to resemble another? Does the mimicking species independently evolve genetic variants that produce similar wing color patterns to the mimicked species, or is there occasional interspecies mating and flow of genetic variants between different species? If they do independently evolve the same patterns, do the genetic variants underlying the patterns in the different species occur in the same regions of the genome? 

There are multiple answers to these questions, depending on the colors, patterns, or species being considered. Let us attempt to answer them in the specific context of Müllerian mimicry, where different poisonous species share similar wing color patterns, in Heliconius butterflies. We will look at two (relatively) recent studies that come away with interesting but seemingly contrasting conclusions.

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Meet the new molecular ecologists

With the new year, we’re bringing on some new contributors to the blog, as promised. Please give a warm Molecular Ecologist welcome to Sabrinha Gita Aninta and Rishi De-Kayne, introducing themselves below. Keep an eye out for their first posts soon!

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Our one thousandth post!

(Wikimedia Commons, with an edit by jby)

About six months after The Molecular Ecologist‘s tenth anniversary, we’ve hit another round-number milestone — this post is the one thousandth published on the site. I’ll refer you to that anniversary post for a rundown of highlights from the nine hundred and ninety nine that precede it. For this one, I thought I’d turn the focus outward — to our readers, and to what we’ve got to offer in the new year.

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Posted in housekeeping, just for fun | Tagged , | 1 Comment


Yikes. This year has been a doozy, and while we all know that the hand on the wall (if you have one of those old fashioned things) that strikes midnight on December 31st will not put out the dumpster fires that we are living amongst, we can hope that 2021 will (maybe….possibly) bring something good… yes, I’m knocking on wood.

I know I’m not alone, but I’ve recently heard a bunch about viruses. Maybe it’s fitting to end this chapter of what has turned out to be a completely wild year, by learning even more about viruses…of the giant variety.

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The Molecular Ecologist Podcast: Science and scholarship in the pandemic year

A new episode of The Molecular Ecologist Podcast is now out on In this episode, Stacy Krueger-Hadfield, R Shawn Abrahams, and Jeremy Yoder chat about their experiences managing research, teaching, and scientific conferences in the year of COVID-19.

(This episode was recorded back in October, but production’s been delayed because of, well, everything. It’s still a pretty good retrospective on a strange and challenging year!)

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Happy Thanksgiving: COVID-19 style

It was the Ides of March in 2020 when I moved from California to Europe. Thanksgiving marks March 271st. I was still a postdoc in Jonathan Eisen’s lab at UC Davis and my contract would have ended in the end of August 2020. In March 2020, my husband and I were in the process of booking a container to bring our belongings through the Panamá Canal to Europe. He was applying for jobs in Germany, I had already an offer, and we were looking at schools for our children. I was in the middle of analyzing my data I had collected during one of the many field trips to Central America in the months before, when my mom from Switzerland called and told us we have to come now. Switzerland is closing its borders in the next few days and many European countries are already closed!

Graphical abstract for Thanksgiving methods. Idea by Grace Ho @Gracegusta. Sorry Canadians, that this idea comes a bit too late!
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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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