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?
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!
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.
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.
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 Ecologytherefore 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.
Male (left) and female eastern bluebirds, Sialia sialis. In birds, males are homogametic (with two Z chromosomes) and females are heterogametic (with one Z and one W) — and this means that, all things being equal, he has a slightly longer life expectancy than she does. (Flickr: Vicki DeLoach)
Sex chromosomes are one of evolution’s stranger inventions, when you think about it. Many sexually dimorphic species, including most reptiles and amphibians and lots of plants have sex determination via gene complexes on otherwise conventional chromosomes, or even as a response to environmental variation; and those that do have sex chromosomes don’t all have the same kind.
In mammals, most of us learned in high school biology (or possibly via dusty sitcom jokes), individuals carrying two X chromosomes typically develop as female, while those with one X and one Y chromosome typically develop as male. But, as you find out if you stick around for university-level biology or do the right kind of extracurricular reading, a number of non-mammalian taxa, like birds, do it the other way around, with males carrying two Z chromosomes and females carrying a Z and a W chromosome. It’s a classic evolutionary kluge: there’s more than one way to genetically encode separate features for males and females, and which solution is in use within a given group of species depends largely on the happenstance of their shared ancestry. And, like all kludges, it comes with a downside — recessive deleterious mutations on the X or Z create a genetic burden borne only by XY or ZW individuals — and a paper recently published in Biology Letters finds that, across a wide range of animal taxa, this is indeed the case.
With the increasingly pressing matter of populations being threatened by fragmentation and isolation, and with progressively more efficient sequencing technologies and analytical tools at hand, conservation genetics is starting to turn the spotlight on the topic of genetic load. It has become clear that population survival is not only about population sizes and estimates of genetic diversity. Some populations thrive despite extremely low genome-wide diversity, while others go extinct despite seemingly much better prospects.
The buzzword that keeps coming up in recent publications, is purging. Purging is defined as the “increased purifying selection facilitated by inbreeding as it increases the homozygosity of partially recessive deleterious variants” (Hedrick and Garcia-Dorado 2016). In other words, in small populations, where the inbreeding usually increases homozygosity, more of the really nasty stuff [aka highly deleterious mutations] is revealed in homozygous state, which makes it easier for purifying selection to act upon.
The problem
is that studies examining bottlenecked natural populations are not conclusive
on how much mutational load accumulates in small populations and how much is
purged by selection. Remember that in small populations, selection is assumed
to be overshadowed by the effects of genetic drift, therefore it is not clear
how much power it has for eliminating deleterious mutations.
While some
studies found empirical evidence of accumulation of genetic load in a
population with low effective population size, for instance in the woolly
mammoth (Rogers and
Slatkin 2017) and the crested ibis (Feng et al.
2019), others showed that purging of
highly deleterious mutations does take place in populations of extremely
bottlenecked species, for example in the Channel Island foxes (Robinson et al.
2018) and mountain gorillas (Xue et al.
2015).
The new study by Christine Grossen and colleagues (Grossen et al. 2020) looked at the problem in a beautiful model system of the once near-extinct Alpine ibex. Back at the beginning of the 19th century, there were less than 100 individuals left in a single population in Gran Paradiso, Italy. After recolonizations, the Alpine ibex is now at a census size of 50,000 individuals. Interestingly, the successful recolonized populations were used to found other populations, and thus, the extant populations experienced two to four bottlenecks, which are also well documented in the records.
When an organism is exposed to a pathogen, what determines their ability to resist or recover from infection? Mounting an effective immune response is a complex dance with multiple partners, changing tempos, and maybe even a costume change or two: An adaptive immune response results from the interplay of the surrounding environment and the specific individual, that individual’s (and sometimes the parents!) history of infection, and the genetic make-up of the individual, just to name a few of the partners. Scientists have been investigating the effects of immunogenetic diversity and genotype on immune system functionality for decades. Among the most studied immune system genes are those of the Major Histocompatibility Complex (MHC), which encode the cell-surface proteins responsible for distinguishing between ‘self’ and ‘non-self’ peptides (Piertney & Oliver 2006). Thus, MHC genes control, in part, an organism’s ability to respond to pathogens through the adaptive immune system. I did my Ph.D. on MHC genes, so I still have a soft spot in my heart for this set of genes; Also, I really love a paper that makes tasty lemonade out of lemons, as a recent paper by Arnaud Gaigher and colleagues (2019) did.
This week, some of my favorite #scicomm games on Twitter are teaming up with March Mammal Madness to reveal this year’s #2020MMM contestants in my favorite “battle of the fittest.” Specifically, today (2/21/2020) at 12:30 pm EST, Dr. Michelle LaRue (@drmichellelarue) will be dropping an image for her #CougarOrNot science communication game with the big combatant reveal at 2:30 pm EST.
Photo provided by National Parks Service via Wikimedia
The timing is appropriate because the genome of the cougar (Puma concolor; also called mountain lion or puma) was published at the end of last year, providing insights into the divergence between North and South American cougars, as well as some interesting findings regarding genomic diversity that have conservation implications for the puma (Saremi & Supple et al. 2019). Continue reading for some cool cougar insights to prepare you to fill your #2020MMM bracket!
Two Northwestern crows (Corvus caurinus), or maybe two American crows (Corvus brachyrynchos) — Wikipedia’s caption can’t make up its mind.
If you are a moderately bird-interested person who’s spent much time in Seattle or Vancouver, you’ve probably had a version of the following conversation with a less bird-interested friend or family member from out of town, after one of you spots a midsized black bird perched on the rail of the Burrard Street Bridge or scavenging in Pike Place Market:
The less-bird-interested person: “Hey, a crow!”
You: “Yeah, there’s a different species of crow around here. The Northwestern crow.”
