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.
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.
Salmonid hatcheries are employed for different reasons
depending on the species and system: to provide harvest and so relieve fishing
pressure on wild stocks, to recover wild stocks, or a combination of the two. Furthermore,
hatchery fish often are managed as separate stocks from their wild counterparts
with the intention of keeping them genetically separate. These fish are tagged and either caught by
anglers or, upon returning, brought back into hatcheries to create the next
generation of hatchery fish. Alternatively, some programs integrate wild fish
into the production of hatchery stocks to prevent the propagation of a
domesticated phenotype. Different hatchery programs have decreased short-term
extinction risks for endangered populations, mitigated for habitat degradation
and impediments, provided demographic boosts to existing populations, and re-introduced
salmon into habitat from which they had been extirpated.
So what’s the latest
on salmonid hatcheries? Unsurprisingly, it depends on the hatchery and species.
The recent development of parentage-based tagging (PBT) whereby hatchery-origin fish are genotyped across generations will allow for tracking of quantitative traits like reproductive success, disease resistance, run timing, and age at maturity. Such studies are ramping up now, especially in steelhead, chinook, sockeye, and coho salmon fisheries in the Pacific Northwest. For example, Evans et al (2019) reconstructed pedigrees of three full cohorts of chinook salmon from two river systems in Oregon and estimated heritibilities and evolvabilities of several fitness traits in both wild and hatchery populations.
Janowitz-Koch et al (2018)
looked at a population of chinook salmon returning to Johnson Creek, Idaho over
16 years using pedigree information. They were able to track the reproductive
success of natural-origin fish and those originating from a supplementation
program. In this case, broodstock are
created every generation by bringing natural-origin fish into captivity to
spawn thereby preserving local adaptation.
The authors found that the hatchery supplementation program provided a
demographic boost to the population over two generations. When hatchery-origin fish spawned in the
wild, they had a lower reproductive success than natural-origin fish, but when
hatchery fish spawned with wild fish, the reproductive success of the offspring
was similar to those with both wild parents. Also, origin (hatchery vs wild),
return year, and body length were significant predictors of fitness.
Several studies over the past 30 years, mostly focused on Columbia river basin steelhead stocks, have suggested that natural-origin steelhead have a better survivorship than their hatchery counterparts and rivers with predominately hatchery-origin returns have a lower reproductive success than rivers dominated by wild returns. Studies on steelhead in the Hood River in Oregon from 2007 to 2012 showed that even a single generation of hatchery rearing could significantly reduce the survival and reproductive success of fish in the wild. Notably, other similar studies on chinook salmon failed to document such marked declines of reproductive success. However, even as hatcheries produced huge numbers of salmon, stocks continue to decline and the massive production efforts led to hatchery fish constituting the lion’s share of many stocks in the basin (over 90% of coho salmon, more than 70% each of spring and summer chinook salmon, and steelhead, and 50% of the fall chinook salmon, according to NOAA (Johnson et al 2019).
Sockeye salmon originating in Idaho waters travel the furthest of all migrating
salmonid species, traversing more than 900 miles with a 6500 foot elevation
gain, and over/around 8 dams before spawning in the Sawtooth Valley in the
headwaters of the Salmon River. In 1991, Idaho sockeye were listed under the
federal Endangered Species Act as only four adult natural-origin sockeye
returned to the Stanley Basin. The combined annual returns from 1991-99 were 23
fish, including the infamous “Lonesome Larry”, the single sockeye to return to
Redfish Lake in 1992. Because of these alarming trends, a captive broodstock
program began in the 1990’s using 11 males and five females taken into
captivity from 1991 to 1998. Thankfully, the program has been
able to retain about 95 percent of the species’ remaining genetic variability.
Fast forward to the end of August, 2019, and a mere 15 sockeye have returned to
their origin, including the first
and only return from the Springfield hatchery brought online in 2013.
Conservation and management of Idaho sockeye illustrates the degree of
difficulty and amount of resources it can take to maintain a severely
imperiled, anadromous species. Unequivocally,
however, if it weren’t for hatcheries, there would be no more sockeye salmon
returning to Idaho.
Bandied about in the fisheries world is the concept of the 4 H’s: Hydro, Habitat, Hatcheries, and Harvest. These are four main factors that affect freshwater migrating species. I’d like to highlight an important part of habitat that was glossed over (if mentioned at all?) in “Artifishal” – ocean conditions. Most likely, when we think about salmonids, we think about them struggling upstream to their spawning grounds. However, salmonids can spend more than half their lives, anywhere from 2 to 6+ years depending on the species, in the ocean where they feed and grow, but environmental conditions are often easier to monitor in rivers. We can observe when they begin their freshwater migrations and track water quality, flow regimes, and temperature. Obviously, this is more difficult in the ocean, especially if they head off-shore. Nevertheless, recovery of these species obviously depends on favorable oceanic conditions where they spend their time maturing, but at this point, the ocean is a big black box with regard to its measurable effect on salmonids. What we do know is that five years ago, an expanse of warm water, seven degrees Fahrenheit above average temperature (i.e. the “blob”), developed that stretched from Alaska down to California and corresponded with diminished salmon returns. And good news, everyone! The blob is back. As ocean monitoring progresses and time-series datasets become available, we may start to see direct associations between salmonid return abundance and ocean conditions. A recent study links oceanic indices associated with climate change – sea temperature, ice coverage, and phytoplankton blooms with juvenile chinook salmon growth (and by extension, survivability). The study included growth data of juvenile chinook salmon from 1974 to 2010 in two regions of the East Bering Sea (EBS) and showed that cooler temperatures and sea ice coverage meant that a lipid-rich prey item, capelin, were more abundant, which led to greater growth of salmon. Furthermore, in the southern EBS where temperatures were higher and fluctuated more and sea ice was less predictable, environmental variables were better predictors of salmon growth (or lack thereof) than in the more stable north EBS. If this trend continues, management of salmon fisheries and prediction of returns will become more challenging in the EBS if sea temperatures continue to rise and sea ice coverage continues to vary.
Some excellent points were raised in “Artifishal” about the complications around hatcheries (I saw the film a month ago so some details may be foggy.). For example, are large amounts of resources going into these programs? Yes. Is the return on investment slow to grow? Yes. But to lump open net pen aquaculture and all hatcheries together, and call for the disbandment of all hatcheries is woefully myopic. The documentary implied that hatcheries are THE factor causing the depressed returns without taking into account changing oceanic conditions. So let’s suppose we dismantle all hatchery programs and wild stocks continue to decline. Now we have no biological reserves. If we had taken this tack in the 1990’s sockeye salmon in Idaho would be gone. Therefore, I find the final message in the film to be overly reactionary and careless. There are improvements to be made but to jump to the conclusion that all hatcheries are detrimental to all wild fisheries is unreasonable and alienates a cadre of managers that have the same goal as activists: restoration of salmonid runs to sustainable, healthy numbers.
Evans, M.L., Hard, J.J., Black, A.N., Sard, N.M., O’Malley, K.G., 2019. A quantitative genetic analysis of life-history traits and lifetime reproductive success in reintroduced Chinook salmon. Conserv Genet 20, 781–799. https://doi.org/10.1007/s10592-019-01174-4
Janowitz‐Koch, I., Rabe, C., Kinzer, R., Nelson, D., Hess, M.A., Narum, S.R., 2019. Long‐term evaluation of fitness and demographic effects of a Chinook Salmon supplementation program. Evolutionary Applications 12, 456–469. https://doi.org/10.1111/eva.12725
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.
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.
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?
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?
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.
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.
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.
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.