One of the most recognized and distributed photographs ever is of the earth taken by the crew of the Apollo 17 spacecraft 28,000 miles above where you’re reading this, and was named “The Blue Marble“. As the photo implies, our earth is indeed blue, with about 70% of it covered by water.
Underneath all that blue is the seafloor, one of the most abundant ecosystems on the planet and among the most challenging to study. Across the seabed, gasses rise through sediments along with fluids. One of these gasses is methane, an important greenhouse gas. It is key to understand how changes to the seafloor (both natural and human driven), impact and alter this unique environment, as it can have global implications.
Last December, we posed the question Should journals solicit submissions from preprint archives?and solicited feedback from the community on whether this was a promising path forward for the field. First off, thank you to the 145 people who responded to our survey! Here is the quick summary, before diving deeper into the results:
Our sample is predominantly composed of people who already use preprint servers or plan to do so in the future – so keep this in mind.
Most people would respond positively to journal solicitations and are willing to wait up to 2 weeks after submitting to a preprint server to receive a solicitation.
Most people see journal solicitations as beneficial to the field in general.
There are concerns about the need for accountability and transparency in the solicitation process to avoid bias, and preprint solicitation potentially enabling predatory journals.
Sabrina Heiser wrote this post as a project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham. Sabrina grew up in Germany, completed a BSc (Hons) in Marine Biology at Plymouth University (UK) and then lived in Antarctica for 2.5 years working for the British Antarctic Survey (see more about her story here. Now, as a PhD student in Dr. Chuck Amsler’s lab at UAB, she is finally able to combine her love for macroalgae and the Frozen Continent, where she is investigating algal population structure and how gene flow shapes the distribution of geographic patterns in physiological traits. Sabrina tweets at @sabrinaheiser and you can find out about her research on her website.
Alice and the Red Queen, from John Tenniel’s illustrations of Through the Looking-Glass (Wikimedia)
One of the most fundamental observations of evolution is that it never seems to stop. This is particularly true in host-pathogen coevolution, in which each species must adapt in response to the other. This constant evolution is the process biologists refer to as the Red Queen’s race, after the character in Lewis Carroll’s Through the Looking-Glass who declares that “it takes all the running you can do, to keep in the same place.”
Across many species, the sequences of genes that interact with hosts and/or pathogens change faster over time than many other parts of the genome. A nifty new study recently released in PNAS examines the rapid changes of a Red Queen’s race directly, by experimentally coevolving hosts with a pathogen and sampling the genetic diversity of their populations over time.
Aisha O’ Connor wrote this post as a project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham. She sat in on lectures while she was at UAB as part of a British Phycological Society Student Bursary project. Aisha grew up in Ireland and completed a BSc (HONs) in Marine Science at the National University of Ireland Galway from which she graduated in October 2018. Currently, Aisha is in the middle of a research project looking at the genetic structure of kelp forests in Ireland. She is hoping to pursue further algal research, is looking into funding opportunities, and is applying to graduate programs. Aisha tweets at @Aisha_MOC.
When the opportunity arose to participate in a collaborative research study, with Dr. Stacy Krueger-Hadfield (University of Alabama at Birmingham) and Dr. Kathryn Schoenrock (National University of Ireland Galway), I jumped at the chance to study the population genetic structure of Laminaria hyperboreaforests along the west coast of Ireland. For part of August and September 2018, I was a visiting student in the Krueger-Hadfield Evolutionary Ecology lab dipping my toes into the molecular ecology sea.
Last week I was whining about gaps in our
understanding of evolutionary processes in the ocean. The universe heard me,
and today I am satisfied to write about the published genome of Euprymna scolopes – the Hawaiian bobtail
squid and the implications this genome has for the study of (marine)
animal-microbial symbioses.
The Hawaiian bobtail squid Chris Frazee and Margaret McFall-Ngai via Wikimedia Commons
E. scolopes presents a very potent model species for understanding how symbioses between animals and bacteria form and evolve (Nyholm and McFall-Ngai 2004). It has two specialized organs to host bacterial symbionts, the light organ and the accessory nidamental gland. The former maintains a monoculture of bioluminescent bacteria (Vibrio fischeri). During the night when the squid is active, it can glow with the help of its symbiont bacteria. From below, its glowing silhouette will disappear in the surrounding moon light and this provides camouflage from predators. Check out a video on nature’s cutest symbiosis here! (This is a must see.) The latter specialized organ is important for reproduction and only found in females (Collins et al. 2012; Kerwin and Nyholm 2017). It hosts a microbial consortium that has been hypothesized to protect developing embryos from fouling and infection. Colonization of these two symbiotic organs has been studied in great detail leveraging a plethora of articles on microscopic structures in the host tissue, biochemical pathways, microbial genomics, gene expression patterns, and ultimately the evolution of symbiosis in this system. Microbial comparative genomics has been especially helpful in identifying elements important for the bacterial symbiont. For example, microbial biofilm formation, which was eloquently summarized by Julian Jackson. Yet, so far, most insight about the evolutionary trajectory of this symbiosis came from studies of the bacterial symbiont. Now, with the public availability of the host genome, we can learn about the evolutionary history from the host’s perspective. Once more, the charismatic little shallow water creature from Hawai’i is opening new avenues for exciting research.
The current American administration is excited about its space program on extraterrestrial exploration and discovery. A mission to the moon, several ones to Mars, and perhaps others someday to other planets are part of the current funding plan. NASA has chosen Jezero Crater as the landing site for its upcoming Mars 2020 rover mission after almost six years of scrutinizing and debating which location might be optimal. This rover mission will include rock and soil collections to find signs of habitable conditions and microbial life. Jazero Crater is located just north of the Martian equator. The 45 kilometers wide crater had most probably been a huge river delta in ancient Mars times more than 3 billion years ago. The explorers hope to find preserved ancient organic molecules in the delta’s sediment and learn about any type of previous and current life on Mars.
Since August 2018, we also know about liquid water under Mars’ southern ice cap thanks to a study published in Science by Roberto Orosei et al. (2018). These authors detected a 20 kilometer wide lake of liquid water underneath solid ice, similar to an aquifer, using a MARSIS (Mars Advanced Radar for Subsurface and Ionosphere Sounding). ‘The presence of liquid water on Mars has implications for astrobiology, evolution and future human exploration’ (as the authors state). Now I can understand why Jeremy Y. is watching First Contact on a Sunday night. The idea of finding water sources on other planets, studying extraterrestrial molecules, and learning about Martian ecology is so romantic! How exciting it would be if we could just take off and start human settlements on other planets?! Now that we have officially entered theAnthropocene and humankind has heralded Earth’s sixth major extinction event, it only makes sense to consider migration as an option.
If you’ve ever had to explain how all the elements of a big, multi-part project come together, you’ve probably at least considered making something like a Gantt chart. A Gantt chart is a horizontal bar plot with time as the x-axis, illustrating the time required for different activities within a larger project. The basic design is named for turn-of-the-20th-Century American engineer and management consultant Henry Gantt, though examples from Poland and Germany predate Gantt’s original charts.
A Gantt chart for a purely hypothetical project
I’ve just spent more time than I care to admit squinting at draft Gantt charts for a proposal that’s going in soonish, and I’m happy to report that actually making the chart, and making it look nice, was not the hardest part of the process. (That would be, um, figuring out how to fit everything in the proposed project into the allotted funding period.) As you might expect, I did it in R, taking full advantage of the tidyverse packages — as you might not expect, I also used that ancient nemesis of modern data science, Microsoft Excel.
I’ve recently made a career change. Actually, I’m not even sure whether to call it that, or the next step of a natural, if meandering progression of a scientist not on the academic career path. Even though I see more and more articles and social media threads showcasing the career opportunities outside of academics and the need to emphasize those opportunities, it can still feel like a walk in the wilderness to someone with a non-medical, non-human, non-microbial genetics background. With genetics and genomics data gathering and analysis skills, it SEEMS like it would be easy to slide into a biomedical lab, either with the government, or private industry, though the job applications tend to require clinical lab experience as well as expertise with data and analyses on a scale much larger than what the typical ecological geneticist is used to. On my job seeking journey, I worried that I would have to give up “interesting” science in favor of drug testing and humanGWAS data analysis or continue to look for the unicorn research position whereI had job stability and could work on projects with a more conservation and ecological slant.
Luckily, I managed to land at Eagle Fish Genetics Lab (EFGL) in Eagle, Idaho where resources and funding are available to power large scale genetics projects that inform management decisions affecting endangered and threatened fish species along with the management of non-native and invasive species. There are several conservation genetics labs across the country that have created a similar niche where applied and pure research is being conducted (see Robin Waple’s illustrious career at NOAA’s Northwest Fisheries Science Center, for one example). The projects here at EFGL fall into three major categories: Genetic Stock Identification (GSI), Parentage Based Tagging (PBT), and Sex Marker Discovery. Every year, juvenile and adult steelhead and Chinook salmon return to the Lower Granite Dam on the Snake River. These fish are genotyped using a species-specific SNP panel consisting of several hundred markers. The genotypes are compared to baseline genetic data of known stocks in the region to ascertain the stock composition of the returning fish.
The number of preprints published on bioRxiv per month, November 2013 to November 2018.
The use of preprints has increased drastically in the life sciences over the past few years. Preprints are manuscripts submitted to open access servers prior to, or in some cases instead of, formal publication. One popular preprint server is bioRxiv (although there are an increasing number of servers to choose from). Since bioRxiv came online in 2013 the number of preprints posted there each month has increased dramatically, from 39 in November of 2013 to 2,241 in November of 2018 (Figure 1; bioRxiv). This trend is not limited to the life sciences, and other fields, particularly physics, have embraced preprints for decades (Kaiser 2017). While supporters of preprints argue that preprint servers will accelerate the pace of science by allowing researchers to rapidly disseminate and get feedback on their work, others worry that preprints will lead to stolen ideas and a large volume of un-reviewed literature (Kaiser 2017).
Where are preprints leading us?
The future of preprints is unclear. Some have suggested that preprint servers will replace journals altogether (Kaiser 2017). Others see preprints as a step to take prior to publication in a peer-reviewed journal, rather than a replacement. It is also possible that the two could play off of each other. What if journals solicited preprints?
Imagine: you post your paper on bioRxiv. A few weeks later, you receive an email from an Associate Editor inviting you to submit your paper to a particular journal. How would you respond, and how would this change your attitude towards preprint servers? How could this change the fields of evolutionary biology and ecology? The Junior Editorial Board of Molecular Ecology and Molecular Ecology Resources wants your feedback on this subject. Please take this short survey (~3 minutes) to let us know how you feel about preprints and the idea of journals soliciting promising preprints for submission. Thanks in advance for your valuable feedback.
–The Junior Editorial Board
Megan L. Smith
Luke Browne
Nick Fountain-Jones
References
Kaiser, J. “Are preprints the future of biology? A survival guide for scientists.” Science 397 (2017). doi: 10.1126/science.aaq0747
