Last week, a friend sent me this policy forum article published in Science. Fifty co-authors, mostly tenured and from prestigious universities, some of them among my dearest idols, have written this piece to call for publicly available genome data. What struck me the most is their request that data shall be immediately released after its generation.
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Elise Keister wrote this post as a final project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham. Elise studies the impact of climate change on corals as a PhD student in Dr. Dustin Kemp’s lab. Elise completed a B.S. in Biology and Marine Science at the University of Miami’s Rosenstiel School of Marine at Atmospheric Science (RSMAS) and is passionate about working with these susceptible invertebrates, which play such a foundational role in coral reef ecosystems. She hopes to aid in determining resilience mechanisms coral populations are already utilizing to withstand high temperatures, as this will only become more common in the decades to come. Elise tweets at @elise_keister.
Funding for taxonomic research has been waning for many decades in favor of ground-breaking research with tangible links to improving human interactions with our environment. Furthermore, taxonomic work is time intensive, which does not fit into the publish or perish academic world of today. Is there still a place for taxonomic research in this new era of science?
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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.
Continue readingLast 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:
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.
What makes Antarctica so interesting to study?
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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.
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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.
Continue readingLast 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.
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 article I am referring to was published yesterday in PNAS by Mahdi Belcaid et al.
Continue readingThe 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 the Anthropocene and humankind has heralded Earth’s sixth major extinction event, it only makes sense to consider migration as an option.
making Gantt charts is a form of self-care
— Colin J. Carlson (@ColinJCarlson) November 26, 2018
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.
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.
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