We are soliciting nominations for the annual Molecular Ecology Prize.
The field of molecular ecology is young and inherently interdisciplinary. As a consequence, research in molecular ecology is not currently represented by a single scientific society, so there is no body that actively promotes the discipline or recognizes its pioneers. The editorial board of the journal Molecular Ecology therefore created the Molecular Ecology Prize in order to fill this void, and recognize significant contributions to this area of research. The prize selection committee is independent of the journal and its editorial board.
So you’ve decided it’s time to finally get around to starting that sequencing project. But before you aimlessly leap into it and generate terabytes of sequencing data, just STOP.
It’s far too tempting to rush into sequencing projects for a number of reasons. Maybe you need to get it done quickly to spend some left-over grant money or use up some reagents. Isn’t everyone doing genomics these days? How hard can it be? But trust me on this one – before breaking out the Qiagen columns (if you’re loaded), lung melting organic solvents (if you’re not), or partaking in the world’s most annoying game of -80 hide-and-seek with your new least favourite sample, take a step back.
This article will be the first in a series that will take you from planning your genomics project all the way through to analysing your sequence data and plotting some nice figures. One thing to bear in mind for this series is that as you might have already found out if you have spent any time on Biostars or stackoverflow, there are hundreds of ways to do even the most basic of genomics projects. What I hope to cover in this series is by no means the ‘best’ ways of doing things (not that this even exists), but rather one way of doing things, with the aim of pointing you in the right direction to finding something that works for your project.
Rather shockingly, sexual reproduction remains an enigma – despite over a century of study. Theory has identified the costs and benefits of sex, illustrating why almost all* eukaryotes go to the trouble, at least occasionally.
* Even supposedly obligate asexuals have been found to dabble in “cryptic sex” (e.g., Boyer et al. 2021)
While we have a rich literature from which to describe the genetic processes that maintain sexual reproduction, we lack ecological context. What happens in nature? There are abiotic and biotic interactions that result in complex sexual/asexual dynamics in actual populations.
There are some impediments to studying the ‘ecology of sex’. For example, many asexual lineages arise from hybridization events and are polyploid. How to separate diploid vs. polyploid or the effects of hybridization?
Like many universities and learned societies around the world, the University of Alabama at Birmingham hosts Darwin Day events on or around 12 February each year. The UAB Darwin Day and celebration of science dates back to 2013 and we’ve had speakers from Joe Palca to Briana Pobiner.
Usually events happen live and in person – each lab presents a poster on the latest research highlighting the students and post-docs giving us a chance to showcase what we’ve been doing to the local community. In 2020, we were able to have our regular Darwin Day events just before everyone went into lockdown.
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.
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.
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).
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.
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!
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.