Beetles’ diversity was driven by coevolution with plants — and a little help from some microbial friends

A green immigrant leaf weevil, Polydrusus sericeus, one of tens of thousands of species in the family Curculionidae (Flickr, Dann Thrombs)

Beetles have long had a special place, if not in the heart of the Creator, in the imaginations of evolutionary biologists. They’re widely considered the most diverse single clade of animals, something upwards of 400,000 species that share a common ancestor — when the explosive diversification of that ancient lineage began, how it proceeded, and what caused it have been the subject of a lot of research. Many of those questions are addressed in a paper published in Proceedings of the National Academy of Sciences last month, which uses an unprecedented genomic dataset to figure out when beetles began their epic diversification, and tests one major hypothesis for the reason behind that diversification.

Continue reading

Posted in insects, next generation sequencing, phylogenetics, plants, RNAseq | Tagged , , | Leave a comment

Molecular ecology highlights at the American Naturalist 2020 meeting

A great blue heron keeps watch over the dunes of Asilomar State Beach.

Even-numbered years are distinguished by Olympic Games (summer or winter), U.S. Congressional elections, and the American Society of Naturalists biennial meeting at Asilomar, a retreat center embedded in a California state park near the northern tip of the Monterey Peninsula. AmNat2020, which took place over the first weekend of the decade, featured the full range of biological research represented by the American Society of Naturalists and the U.S. scientific journal with the longest continuous publication history, but genetic and genomic data were key to many of the meeting’s highlights.

Continue reading

Posted in community, conferences, evolution, genomics | Tagged | Leave a comment

New Kids on the Blog: Katie E. Grogan & R. Shawn Abrahams

 Name: Katie E. Grogan

Current Position, Institution, & Department: Postdoctoral fellow in the Departments of Anthropology & Biology at Pennsylvania State University

Contact information (if you want people to be able to reach you):

What is your elevator pitch? AKA what do you do/study?

My research uses human and non-human primates to ask how genetic and epigenetic variation impacts inter-individual differences in fitness across environmental conditions. With the effects of human-induced climate change becoming more pronounced, understanding the interplay of the environment, evolutionary genomics, and individual fitness is critical to our ability to conserve biodiversity and understand humanity’s ability to adapt to climate change.

What is your background & When/how did you know you wanted to get into the world of scientific research?

I decided I wanted to study animals at the age of 8 after giving up on being an Olympic figure skater. I grew up in Kentucky surrounded by animals of all kinds (e.g., dogs, lizards, turtles, snakes, birds, fish, etc), watching tv shows about elephants and wolves on the Discovery Channel, and they fascinated me. As I got older, I focused more on becoming a scientist who studied animals. During my undergraduate studies at Vanderbilt, I started doing research in a molecular ecology lab and fell in love with genetics. Since then, I’ve been refining the questions I’m interested in and adding humans to the list of organisms I’ve studied. That list now includes aphids, marmots, howler monkeys, ring-tailed lemurs, white-throated sparrows, and humans!

What is the funniest or most memorable thing that has happened to you while working in science?

I once walked around Toliara, Madagascar with a stranger’s poop on the back of my pant calf for 24 hours without realizing it. I had to fly to South Africa with it still on my pants. 

What do you do when you’re not working?

Walk or run with my dog. Read voraciously. Hike. Be with friends. Watch Kentucky basketball with my dad. Drink cider or cocktails. 

What are your hopes for 2020?

Get a faculty job & a second dog. Submit my ‘leftover’ papers from my PhD and first postdoc (N=3) and run >350 miles. 

Image may contain: R Shawn Abrahams, smiling

 Name: R. Shawn Abrahams (They/Them)

Current Position, Institution, & Department: PhD Candidate in the Department of Biological Sciences at the University of Missouri, Columbia.

Contact information (if you want people to be able to reach you):

What is your elevator pitch? AKA what do you do/study?

I study the the evolution of plant metabolism. My dissertation research focuses on the specialized metabolites called glucosinolates (Mustard oils) and how they have become such a diverse and complex group of defense metabolites. To that end, I utilize insights from comparative genomics, phylogenomics, and plant-insect interactions. Did I mention polyploidy? That’s in there too.

What is something that fascinates you from another field?

Physics and astrophysics have recently caught my interest. Specifically when it comes to time, relativity, quantum theory, and how that relates to biology. For example there is a great interview with the physicist Carlo Rovelli on one of my favorite podcasts “On Being”, where he describes everything in existence as interactions, or “happenings”, at different time scales as opposed to static things. Both a dirt clog and a stone of the same size are collections of sediment and rock, but one will be gone in a day and the other may last hundreds of years. A kiss is a happening made up of all of the same things the individuals kissing are, but it only last for a moment. Whereas the happening of a person, that is to say the cells and molecules that make up an individual, can go on for a lifetime. Physics is a broad field, but understanding it can change how we perceive our world.

Top 3 favorite organisms?

Not counting any humans: 1) My cat Zsa Zsa (Below, she’ a feisty Cornish Rex) 2) The Zilla macroptera that I planted my first year of grad school and that finally flowered after 4 years of growth. 3) The Putranjiva roxburghii that sat in the back of our greenhouse for those same 4 years until I only recently realized it was there! It represents a convergent evolution of mustard oils outside of the Brassicaceae (Mustard family). Basically, it is a tree where the leaves taste like radishes. 

No photo description available.

When/how did you know you wanted to get into the world of science research? 

As a kid I loved plants, they surprised me. Specifically, while watching the Private Life of Plants with David Attenborough, there is a time lapse scene of a bramble crawling across the forest floor. I knew plants were alive as a fact, but I hadn’t internalized it until that moment. I was hooked. I had heard the word botanist somewhere and decided that would be my career. At the same time other kids my age wanted to be sensible things like astronauts so my parents were a little confused. They suggested I become a doctor and have a garden instead, little did they know I could be both! It wasn’t until high school where I was entered into a magnet program for environmental science and Everglades restoration, that I really started to take the idea of scientific research seriously. One of my teachers had her masters in plant biology and mentored me. I was our student herbarium curator for the school’s Everglades flora collection and I participated in several science projects associated with Fairchild Tropical gardens, in Miami Fl. It’s hard to believe that I would be doing what I’m doing today without that experience.  

What was the biggest obstacle that you had to overcome?

My first fall semester of graduate school was particularly rough. It had all of the normal characters you might expect: imposter syndrome, anxiety, loneliness. But that semester my campus had also made national news for protests headed by black students of the “Concerned Students 1950” organization and the Mizzou football team. Racist acts on campuses in the US are common enough that I had experienced my fair share by then, either directly or indirectly.  This was different. A lack of sufficient action on the part of the administration to racially charged events (A swastika displayed on a campus dorm, harassment of the campus’s first black student body president) led to wide spread protests. The events on campus became tangled up in emotions from the then recent murder of Michael Brown, the unarmed teenager shot by police not two hours away in a neighborhood that was similar if not the same as many undergraduate students attending the University. 

As these kinds of things are, it wasn’t neat. Some members of the campus were in open support of the protests demanding action, others actively upset. I remember one graduate student going on a rant about how the protests were damaging their degree and that the students should be forced to stop. The worst of it, for me, came with a shooting threat posted to social media, saying that they would “shoot every black person [they saw]”. It was easy to not show up on campus that day, but there was at least one professor who refused to cancel their exam suggesting that students should stand up to the “bullies” that made the shooting threat. Even just recalling it all now feels like a fever dream. It probably says a lot that I haven’t mentioned yet the university administration abruptly canceling graduate student health insurance at the start of that semester, days before renewal. They used a change in IRS federal policy to justify the action, but have since reevaluated with protest pressure and a lawsuit by the graduate student union. 

My friends and family worried for me, and I worried that I had made the wrong decision going to graduate school. What good would my study of evolution be for people around me suffering? If I was smart and capable surely I should be doing something more than indulging my interests in the mysteries of life. I don’t think I so much overcame that semester as much as survived it. In the end, I decided to stay the course. I decided I needed to be here, in science, particularly for times like those, for students who would have to go through what I had to go through.

Posted in housekeeping, introduction | Tagged , | Leave a comment

Genomic data reveal links between demography and adaptation in experimental host-virus coevolution

Phase-contrast image of Chlorella algal cells
Phase-contrast image of Chlorella algal cells. (Wikimedia)

Coevolution between hosts and symbionts is fundamentally asymmetric. Symbiotic mutualists or parasites can adapt to their hosts faster than hosts can adapt in response because the symbionts usually have shorter generation times — and they also generally have the benefit of much larger population sizes, providing a bigger pool of potentially useful mutations and reduced influence of genetic drift. This latter advantage, though, can be lost to the ecological consequences of coevolution with hosts. If hosts evolve resistance to a parasite, the parasite population will collapse, until a new counter-resistance mutation emerges.

How this kind of ecological feedback affects the coevolution of hosts and symbionts is a challenging thing to track, but a paper published recently in Science Advances manages to do it with a genomics-enabled experimental model of host-parasite coevolution. Tracking the population sizes and genomic diversity of the unicellular alga Chlorella variabilis and a DNA virus that attacks it, the authors identify how host and parasite population dynamics shape host-parasite coevolution.

Continue reading

Posted in adaptation, Coevolution, ecology, evolution, genomics | Tagged , , | Leave a comment

We’re seeking new molecular ecologists for 2019 and 2020!

The Molecular Ecologist is seeking two new regular contributors for 2019 and 2020! Join us in blogging about “ecology, evolution, and everything in between.”

Ideal candidates should have expertise and experience in the use of genetic data to understand the past and future of the living world. We’re particularly interested in senior graduate students, postdoctoral researchers, and other working scientists who can discuss basic science on a level that engages research biologists as well as the general public. New contributors should be ready to commit to posting multiple times a month for their first year on the blog. In addition, the two contributors recruited in this cohort will be asked to help manage social media for the blog — either overseeing our Twitter account or reviving our presence on Facebook.

New contributors will receive a stipend for their first year, and may continue on a voluntary basis after that. Blogging for The Molecular Ecologist can be an excellent way to hone familiarity with current research, establish connections within the scientific community, and build a portfolio of science writing for a broader audience. In light of this, we are particularly interested in applications from candidates whose racial, ethnic, sexual, or gender identities are underrepresented in science careers.

To apply, please use our application form to tell us about yourself and why you want to write for The Molecular Ecologist. Applications should be received by the end of the day on 31 October, 2019 to ensure consideration.

Posted in blogging, community, housekeeping | Tagged | Leave a comment

In defense of hatcheries: a response to the “Artifishal” documentary

A month or so ago, I had opportunity to screen the documentary, “Artifishal” (admittedly, a pretty clever title), in a room full of fish biologists, geneticists, and hatchery managers.  The premise of the film is that both hatcheries and open pen aquaculture of salmonids are directly responsible for the decline of natural runs and if allowed to continue, will lead to extirpation of these species. Hoo boy. Talk about the air being sucked out of a room.

The conclusion the documentary comes to is extreme, but it does beg the question of the current consensus  of how salmonid hatcheries impact their wild counterparts. Of course, the answer is “it’s complicated”, mostly because hatcheries are species-, ecosystem-, and goal-specific.  Lumping all hatcheries into a monolithic group (and in the documentary, hatcheries were conflated with oceanic, open net pen aquaculture practices as well) fails to capture the nuances that exist between hatchery programs.  

Continue reading

Posted in conservation, domestication | Tagged , , | Leave a comment

Even in the ocean, geography shapes how species cope with changing climates

A green sea turtle, Chelonia mydas, in the Caribbean near Bonaire. (Wikimedia: Kris Mikael Krister)

This year, for the first "real" lecture of my evolutionary biology class, I gave an overview of the history of the Earth, from the Big Bang to the present. It went fast, and I only had a couple of slides at the end for one of the geological processes most responsible for current patterns of biodiversity: the climate cycles of the Pleistocene. Periods of warming and cooling, and accompanying changes in sea level and glacial coverage, were engines of diversification, subdividing species’ ranges into refugia, then allowing species pushed towards the equator by advancing ice sheets to expand towards the poles again. These patterns are evident all over terrestrial temperate regions today, and a paper published over the summer in The Molecular Ecologist shows how the impacts of Pleistocene climate change extended beyond land, into marine communities.

Continue reading

Posted in conservation, demography, population genetics | Tagged | Leave a comment

Conference catch-up: Seventh European Phycological Congress Zagreb, Croatia – algae and abominable life cycles!

The first European Phycological Congress was held in Cologne, Germany in 1996. In the last 20-odd years, the meeting has been held every four years since then in Italy, Northern Ireland, Spain, Greece, and then in London in 2015 (see posts from this last EPC here and here).

This year, the Seventh EPC was held in Zagreb, Croatia from 25-30 August. Each day began with a plenary lecture followed by symposia and poster sessions, as well as a silent auction and a banquet. All presentations and events occurred at the Esplanade Hotel, a hotel that was a stop over on the Orient Express. I’ve recapped a selection of talks from each day below.

Participants of EPC 7 in Zagreb, Croatia. Apparently, our assembly by the hotel resulted in a police action as we had a huge group with no announcement of a public gathering! Not bad for a group of phycologists. © EPC 7

Continue reading

Posted in blogging, career, community, conferences, ecology, evolution, just for fun, Science Communication | Tagged , , , | Leave a comment

Loki and behold: one microbial culture that brings us one leap closer to understanding the origins of eukaryotic cells

What were you doing 10 years ago? Can you remember? Were you, perhaps, trying to sort out the origins of eukaryotic life?

A pre-print (yet to be peer-reviewed) was released earlier this month by Imachi et al., describing a 12 year long effort to isolate what the authors refer to as a “Lokiarchaeota-related Asgard archaeon from deep marine sediments”. The results presented in this study have been widely covered in articles see here, here, here, or over here for just a few examples. So…what’s the big deal?

Continue reading

Posted in ecology, evolution, genomics, metagenomics, microbiology | Tagged , , | Leave a comment

The Research Coordinated Network for Evolution in Changing Seas (RCN-ECS)

The Molecular Ecologist contributors Reid Brennan, Laetitia Wilkins, and I (Stacy Krueger-Hadfield) were invited to attend the Research Coordinated Network for Evolution in Changing Seas synthesis workshop at the Shoals Marine Lab this past week (19-23 August).

Stacy, Reid, and Laetitia

Evolving Seas is a global network of marine scientists and evolutionary biologists.

Continue reading

Posted in blogging, career, chat, community, ecology, evolution, funding, just for fun | Tagged , , , | Leave a comment