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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Posted in bioinformatics, blogging, citizen science, community, conservation, DNA barcoding, ecology, evolution, fieldwork, metagenomics, natural history | Tagged , , , , | Leave a comment

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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Posted in blogging, citizen science, conservation, DNA barcoding, ecology, evolution, fieldwork, methods, natural history, Science Communication | Tagged , , , , | Leave a comment

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.

References

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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It’s all because of the holobiont

It’s conference season at the Molecular Ecologist. I went for the first time to a Gordon Research Conference (GRC). GRCs @GordonConf are well known for their efforts to foster an informal and inclusive atmosphere where frontier research in the biological, chemical, physical, and engineering sciences is discussed. Isolated venues and long breaks in the afternoons promote networking and give room for social activities and breakout sessions. Researchers are encouraged to present unpublished results and the contributions are off-record, that means that nobody is allowed to take photos, record sound or video, or share the presentations on social media. And here I am writing about it.

I attended the Animal-Microbe Symbioses Conference #GRCAnimalSymbioses. I went first and most of all because of the incredible line-up of presenters (almost 50% women). Second, I’ve heard that Gordon Research Conferences are especially family-friendly. I was not disappointed.

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Five years as a new PI

Life as a new Principal Investigator (PI) in science is full of surprises. On any given day you’ll be dealing with the past (finishing off manuscripts from your postdoc), present (helping current students) and anticipating the future (working on the next grant). I’ve heard various people say that it’s both the most exciting, and the most stressful, time in someone’s scientific career. The excitement comes from having the opportunity to steer science the way you want to, having well-developed skills to work with the data, and some time to do the analyses. The stress comes from wanting to build a successful new lab, and learning to balance new roles such as teaching and admin while doing the science we all love. In compiling a list of things I’ve learnt I wanted to look beyond the woes of grant writing and rejection, and challenges of work-life balance, which seem to get the most coverage. So, five years in, here are five things that I’ve learnt:

Obsessing about efficiency is not efficient. Time as a new PI seems precious. There are many things to juggle, and there’s no one breathing down your back as to when to do them. So, it’s natural to want to be efficient. We’ve all read lists of 10 tips on managing your time, or lifestyle posts on how ‘successful’ people live. The reality of it though is that a routine of getting up at 5am, going for a run, checking emails once, blocking out time for writing, and generally saying ‘no’ to every request, is going to make you miserable and unpopular. I’ve learnt that most efficiency tips aren’t helpful and end up being a distraction. I make sure that I write most days, and I always have a pet project on the go so that I’m always handling data, but beyond that I go with the flow. Letting go of efficiency targets has made me more productive, and leads to the occasional guilt-free long-lunch with colleagues or coffee break with a student, which can only be a good thing. I also think that giving research time to evolve, rather than pressing to publish as soon as possible, leads to better manuscripts in the end.

The Darwin Dance Hall at the Ashworth Laboratories in Edinburgh. Home to long-lunches and welcome distractions. Photo reproduced with permission from Laurence Winram.

Oppose unwanted scientific drift. I’ve always been open-minded to expanding my research to tackle new questions and to work on new study systems. While my primary research interest is in the population biology of natural plant populations, I’ve dabbled in all sorts of topics including phylogenetics, QTL mapping, taxonomy and cytology. Early on as a PI, it became clear to me that a single collaborative grant on a topic of tangential interest, or the (co-)supervision of a student in a new topic, could draw you in new directions. While this can be a good thing to expand horizons, it can also distract from your main research interests, or require you to read large amounts of new literature and work overtime to get up-to-speed. This is exactly what happened to me early on. I think I’ve finally learnt that there’s no harm working on a few interesting topics outside your core interests, but only if this is not at the expense of what you’re really passionate about. In practice, this means always having at least one student and trying to secure funding for at least one grant on a favourite topic. 

Collaborate with your mentors. In the some grant applications, academic independence is measured by the number of publications not involving your PhD advisors. Even without this criterion, many PIs want to be seen to be doing their own thing, or seem stubborn about working with their mentors. While I might have felt this way at the start, in the last couple of years I’ve started new projects with my PhD and postdoc advisors and I’m pleased that I have. I’ve always got on well with them and value their expertise, and in many ways its easier now as I’m not working “for” them but collaborating with them as equals. 

Students are diverse. As a community I like to think that we celebrate the diversity of students. But most PIs I know treat all their students in the same or similar way, and to start with I followed this model. I met with each student for an hour a week (and did this back-to-back to be more efficient, see point 1, above). But it’s now clear to me that this weekly schedule doesn’t work for everyone. I have one student who likes to go away and come back with substantial new results without being interrupted (who I meet every other week but for longer) and another who wants to speak briefly most days. The frequency and duration of meetings also changes over time. I think it’s an important to have the conversation about the frequency and style of meetings to make sure everyone is happy.

Be bold and buy big equipment. There’s a real temptation to save your hard-earned start-up funds and avoid big purchases. But for me buying my own server has been the best single purchase I’ve made since starting my research group. I was so indecisive about buying it—deciding whether it was a good idea, whether I had the expertise to manage it, what specification to get. Various academics warned me off buying one as I could use time on the University super computer, or that in five years’ time everyone will use cloud compute. This is simply not true. Having an easy-access computer server gives you immediate on-demand compute that cannot be matched by other resources. I’ve seen other people agonise about similar large purchases like walk-in growth chambers. But I haven’t known anyone who regrets investing in something so important for their research.

For anyone interested in reading more about life as a new PI, this article in Science is a good start, and there’s lots of useful information on Twitter (#NewPI). And of course, The Molecular Ecologist has many relevant articles (like this one).

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Molecular ecologists — and molecular ecology — at Evolution 2019

The Providence skyline. (Flickr: Timothy Burling)

June means summer is well underway in the northern hemisphere, and those of us tied to the academic calendar are off to fieldwork, buckling down for summer teaching or grant-writing or just writing — and planning for conferences. Evolution, the joint annual meeting of the American Society of Naturalists, Society of Systematic Biologists, and Society for the Study of Evolution, is a big one for molecular ecology and molecular ecologists, and as in many years multiple contributors to this very blog will be present and presenting in Providence, Rhode Island. Here’s a quick rundown of which TME contributors and alumni will be speaking at Evolution 2019, and what events on the program schedule have us excited. Look for our coverage of the conference itself when we converge on the [checks Wikipedia] "Ocean State" on Friday, June 21.

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The state of coral: A mini-review

Coral reefs are one of the main harbingers of the climate crisis.  As such, there have been numerous studies, TED talks, Blue Planet episodes, podcasts, et cetera, about the state of corals. I’ve condensed a select few research findings for a mini-review to highlight some of the most recent results. This is by no means a comprehensive review of the coral literature, obviously.  I will, no doubt, egregiously fail to mention some rock stars who are making great strides in coral biology and conservation.  It’s a big group – both of scientists and of species.

A quick background on coral endosymbionts

Shallow water corals are considered holobionts, comprised of the host coral, endosymbiotic dinoflagellates (often referred to colloquially as zooxanthellae), bacterial and archaea communities. The endosymbionts provide the fixed carbon for the coral via photosynthesis.  When water temperature increases above average for a prolonged time, the endosymbionts are expelled from the coral polyps, leaving bleached coral behind. Corals can rely upon heterotrophy to get their nutrients and fixed carbon, but this is not sustainable over long stretches of time. They can reuptake endosymbionts and recover if temperatures return to normal in a short enough time span.  Most corals obtain their endosymbionts from the environment (horizontally) either during their larval stage in the water column or shortly after settling. Others inherit endosymbionts vertically from their parents. The most reported and studied coral endosymbionts historically have belonged to the genus Symbiodinium, but a recent revision has split the several clades within the genus into seven distinct genera.

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Hybridization in the depths of the last glacial period created a world-conquering clover

White clover, Trifolium repens, in a Los Angeles city park, a hemisphere away from the glacial refugia where it originated. (jby)

Plants’ flexibility with the structure of their genome — able to cope with proliferating transposons, whole-genome duplications, or even acquisition of complete sets of chromosomes from another species — is a big source of evolutionary novelty. Duplication of a single gene allows the duplicate and its template to evolve new functions; adding a whole additional genome provides that much more raw material. That may be the secret of the success of one worldwide weed we’ve seen featured on this blog before, Trifolium repens, or common white clover. A new paper in The Plant Cell delineates two fairly intact progenitor genomes within the T. repens genome, and reconstructs the history of an evolutionary mashup that created a wildflower you can very likely find by simply stepping outside and walking to the nearest well-watered lawn.

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Introducing Molecular Ecology Spotlight

Today, the Molecular Ecology journals are launching a new venue for highlights and behind-the-scenes looks at the research they publish. Molecular Ecology Spotlight fills a niche as the official blog of Molecular Ecology and Molecular Ecology Resources, publishing author summaries and interviews linked to noteworthy new papers in the journals — and a Twitter feed that will broadcast all new papers as they’re published.

The new blog is a project of the Junior Editorial Board, formed last year with early-career researchers who were recognized in the Harry Smith Prize competition. The goal is that this will provide another way to follow research results from the journals, and context and background for papers of particular interest; where The Molecular Ecologist has always defined itself as a forum for the field of molecular ecology writ broadly, Molecular Ecology Spotlight will, as the name implies, shine a light on the best work in Molecular Ecology and Molecular Ecology Resources specifically.

You can find Molecular Ecology Spotlight at molecularecologyblog.com, and on Twitter at @molecology.

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Go north, young salamander

Plethodon shenandoah (Wikimedia Commons)

Shenandoah salamanders are a case study in restricted distributions, known only from three mountainsides in Shenandoah National Park, in the Appalachian Mountains of Virginia. What’s keeping them in such a restricted range? A new paper in the journal Ecology and Evolution aims to answer that question using population genetics.

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