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.

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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.

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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.  

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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.

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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

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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?

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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.

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Snapshots of Biodiversity: eDNA as a methodology for species detection

Nicole Conner wrote this post as a project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham.  She is a Master’s student in Dr. Thane Wibbels’ lab where she is developing new protocol to detect diamondback terrapins off the coast of Alabama using eDNA. This will allow for an accurate and streamlined process for evaluating the distribution of the species in Alabama. Nicole completed a B.S. in Marine Science and Biology at the University of Alabama and participated in an REU internship through the Duke University Marine Lab in 2017. Throughout her life she has been passionate about the conservation of marine species and hopes to continue participating in research that improves conservation management approaches.

How do we detect an organism that can’t be seen? Or how can we reliably identify a species’ geographic range if it spends its life underwater?

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Genetics of Returning Turtles

Amy Bonka wrote this post as a project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham. Amy grew up in Florida, completed a BS in Biology with a concentration in Marine Science and Chemistry as well as an MS in Biology from UAB. She is currently pursuing her PhD as a student in Dr. Thane Wibbels’ lab where her research is focused on early lifehistory behaviors of hatchling sea turtles and the dynamics of arribada nesting in the Kemp’s ridley sea turtle. 

How many come home? 

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What next for DNA barcoding?

I’m a late adopter of DNA barcoding. As a botanist it has often felt that DNA barcoding wasn’t really for me. Unlike in animals, where the mitochondrial gene CO1 often tracks species boundaries, in plants, there is rarely an exact match between DNA barcode sequence and plant species identity. A more general issue is that the use of one or a few regions of non-recombining organellar DNA just doesn’t cut it for answering the population genetic questions I’m most interested in.

But it’s now becoming clear that the scalability of DNA barcoding that allows it to be used on hundreds or thousands of specimens at a reasonable cost may make it a primary tool to accelerate species discovery and to describe biodiversity patterns in the face of massive species extinctions. Perhaps equally important to me is that the plant DNA barcode isn’t set in stone and new sequencing technologies will allow us to find better options for using DNA to tell plant species apart (Hollingsworth et al., 2016).  

Given my new-found enthusiasm for DNA barcoding, last month I went to the 8thInternational Barcoding of Life Conference in Trondheim, Norway, to find out the new developments in this field. Here’s what I learnt:

DNA barcoding has found its place in the genomics era. What’s the point of sequencing a few genes when we can now sequence whole genomes? That’s the question on my mind when I arrive, and I was pleased to see many good answers at the meeting. The most convincing one is that DNA barcoding is perfectly well-suited for discovering species in some of the most neglected animal groups. Dan Janzen gave a superb example of how DNA barcoding is being used to discover Costa Rica’s insect diversity on a massive scale, while many speakers highlighted the use of DNA barcoding for unearthing new species in the marine realm. In these environments, complete genome sequencing would be overkill, too expensive, and often poorly suited to very small samples. The scalability and applicability of DNA barcoding for species discovery and documenting and monitoring biodiversity are part of the motivation behind BIOSCAN, a major new initiative launched at the meeting. BIOSCAN’s three research themes will employ DNA barcodes to speed species discovery, to probe species interactions, and to track species dynamics. At a cost of $180 million and involving hundreds of research scientists, the project will not only build a more comprehensive reference library of DNA barcode sequences, but tackle major research questions about complex and cryptic species interactions, and the spatial scale that biodiversity is partitioned (including in often overlooked aquatic and soil systems). I’m excited to see what they find.

There’s exciting new technology. I love a new gadget or an exciting piece of technology. Paul Herbert showcased the remarkable LabCyte Echo 525—which is every lab scientists dream: a liquid handling system that eliminates plastic waste and pipetting. It uses acoustic energy to dispense reagents rather than pipetting. The motivation behind using this was to put a stop to the mountain of plastic waste produced in highly multiplexed DNA barcoding. This is good for the environment and for reducing costs, particular now that plasticware is a bigger cost than sequencing for multiplexed DNA barcoding on the PacBio Sequel 2. My other favourite bit of kit on show at the main meeting was the Bento Lab, a beautiful portable piece of equipment combining a centrifuge, PCR machine, and gel visualisation in one portable box. This goes a long way towards portable genomics, especially if used in conjunction with the various portable sequencers produced by Oxford Nanopore Technologies, such as the forthcoming smartphone sequencer the SmidgION. However, for my purposes, I’d still struggle to get good quality DNA extractions for plant samples using current protocols and the Bento Lab, and I’m waiting for someone to come up with an easy field protocol for high molecular weight DNA extraction from plant samples. 

The Bento Lab. A mini mobile lab for (nearly) all your DNA extraction and PCR needs.

DNA barcoding has gone (mega)genomic. It comes as no surprise that every aspect of DNA barcoding has gone genomic. But what did surprise me is that it’s gone genomic in a range of smart ways where it’s now more reliable to infer biodiversity patterns. For example, Pierre Taberlet showed that the plummeting costs of sequencing allow metabarcoding studies to have high replication and multiple positive and negative controls (Zinger et al., 2019). Inger Greve Alsos showed how genome skimming can be used to generate complete plastid genomes for thousands of plant samples from Scandinavia, giving greatly improved taxonomic resolution over the current plant DNA barcodes. Linda Neaves showed how high-throughput sequencing of panda faecal samples can be used to detect rare components of their diet. Overall, there were numerous good examples where masses of genomic data have helped the study of biodiversity in interesting ways. 

Quantifying species diversity in mixtures remains difficult. There is real interest in quantifying the abundance of different organisms in mixed samples. Phylogeographers would like to know the abundance of different pollen types in ancient sediments, clinicians need to know the exact composition of natural medicinal compounds, and ecologist would like to trace diet composition of herbivores over space and time. But quantifying DNA in mixed sample is fraught with difficulties. Different species and tissue types often persist differently in a given environment (e.g. DNA of certain resilient plant material may remain more intact than other species in a faecal sample), while the representation of different species in a sequencing library will be affected by differential template amplification. I had hoped that someone may have found a solution to some of these problems but my impression is that people are presenting relative read count and using this as a proxy for relative abundance. There is good work going on in this area, and I was interested to see research where people give herbivores a known diet, then estimate diet composition from sequence data generated from the faecal samples, to calibrate quantification from DNA barcode data. But in general it seems that reliable quantification remains a major challenge and there’s lots still to do.

There’s a gap between DNA barcoding and ecological and evolutionary research. The only disappointment at the meeting was that, in general, the big data being generated isn’t being placed in the broad conceptual framework of ecological and evolutionary research. For example, throughout the meeting there were many cases of researchers generating large DNA barcode datasets and then comparing diversity between geographic sites. There are real opportunities to do this in an ecological or evolutionary context, building on classic theory, and using well-developed statistical approaches. But unfortunately I didn’t see much of that. Instead, most scientists presented descriptive findings of species counts and new taxa. My hope is that as the datasets (and replication in metabarcoding) grow there’ll be more connected thinking and interaction with ecological and evolutionary researchers.


Hollingsworth, P. M., Li, D.-Z., van der Bank, M., & Twyford, A. D. (2016). Telling plant species apart with DNA: from barcodes to genomes. Phil. Trans. R. Soc. B, 371(1702), 20150338. 

Zinger, L., Bonin, A., Alsos, I. G., Bálint, M., Bik, H., Boyer, F., Deagle, B. E… Taberlet, P (2019). DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology, 28(8), 1857-1862. 

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