Is taxonomy still relevant to innovative science?

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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The (silent) thunder down under: mud volcanoes and the microbes that love them

“The Blue Marble”

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.

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Survey results: Journal solicitations from preprint servers

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.

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“Through endurance we conquer.”* Are humans really the only ones who can make it across Drake’s Passage?

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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“It takes all the sequencing you can do, just to keep up with coevolution”

Alice and the Red Queen
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.

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Kelp forests: the underwater woodlands

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. 

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Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

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 article I am referring to was published yesterday in PNAS by Mahdi Belcaid et al.

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Posted in Coevolution, evolution, genomics, microbiology, next generation sequencing, Symbiosis | Tagged , , , , | 1 Comment

Do we need to get to Mars first before we start understanding change in our oceans?

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 the Anthropocene and humankind has heralded Earth’s sixth major extinction event, it only makes sense to consider migration as an option.

Mars Valles Marineris – Wikimedia commons

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Posted in adaptation, evolution, journal club, population genetics, Science Communication, Uncategorized | Tagged , , , , | 1 Comment

Simple Gantt charts in R with ggplot2 … and Microsoft Excel

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.

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.

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A Highlight of Molecular Ecology outside of Academia

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.

In addition, hatchery supplementation of several species is employed throughout the Columbia River and Snake River Basin. Several hatcheries rear smolts to be released at various places throughout the river systems in order to decrease fishing pressure on the natural populations.  The broodstock generating the smolts are replaced annually. Since 2008, there has been a concerted effort to genotype every broodstock fish at every hatchery facility (~17,000 fish per year), so that any hatchery-generated fish collected in the system can be traced back to their broodstock parents using genetic pedigree information. The success of PBT relies upon the thorough genotyping of the broodstock annually.  This is accomplished using the Genotyping-in-Thousands by sequencing (GTseq) methodology.  Beyond yearly monitoring of hatchery and wild populations, the data generated can be used to assess the most effective hatchery practices, salmonid life history harvest patterns, and trait heritability.

A taste of the management effort via hatchery supplementation that goes
into steelhead and Chinook in Idaho. Map by Dylan Kovis

Another focus of EFGL work is finding genetic markers to determine the sex of various fish species as a way to track the success of Trojan Y invasive species control.  In this scenario, males are exposed to estradiol, a female hormone, which causes some to produce eggs. These feminized males are mated with untreated males, which results in ~25% YY “super” or “Trojan” males. Any subsequent cross with the resultant YY fish will result in male progeny.  The hope is to extirpate the non-native population with continued releases of Trojan males.  A codominant, genetic marker that can distinguish XY males from YY males helps to track the efficacy and efficiency of the technique. We employ the modified RadSeq protocol, BestRAD, to a mixture of phenotypically male and female samples, then use Stacks (see previous TME posts here and here for an overview and interview with the author, Julian Catchen) and Python scripts to sort putative SNPs into piles that segregate with sex. Though steelhead and Chinook salmon are the main species of interest, other projects involve carp, burbot, sculpins, and other species of salmonids.

It takes a village to collect, inventory, extract, genotype, and analyze these samples annually. The jobs here at this facility include technicians, biologists (including geneticists), a data manager, and a supervisor and we work in close proximity to a fish health lab, a wildlife forensics lab, and many personnel tasked with maintaining the on-site Sockeye salmon hatchery.  At EFGL, the technicians are well versed in DNA extraction (often performing several hundred to thousands of them per project), SNP genotyping, and RadSeq to name a few.  There are also ample opportunities to help with fish sampling throughout the state and spawning events within hatcheries.The biologists/geneticists coordinate the various projects and analyze the data for reports and manuscripts.  The data manager is the gate keeper making sure that all samples sent to the facility have all the required labeling and metadata and those in the field taking samples across the region are adequately briefed and prepared. The data manager also runs QC scripts on sequencing runs and maintains a gigantic database of sampling, pedigree, and genotype information on every fish that we’ve sampled.  The database system we use is Progeny (designed for human disease pedigree data, of course) and it ain’t cheap (naturally), but considering the enormity of the task at hand, and the fact that it’s built for storing metadata AND genotypes, it does a great job.

My motivation for providing this brief overview of the facility here is to pique the interest of  beginning researchers thinking about their future career paths and assuage some doubts about opportunities for those not interested in the academic career eight-lane highway (that may end in a brick wall with a tunnel painted on it). If you are in the early stages of your career, and you want some experience in a lab generating and analyzing genomic data for a project likely to have a beginning and end during your tenure, I suggest you seek out these types of programs.  Furthermore, if the thought of relentless and never ending grant writing (and the stress of running out of funding) leaves you cold, a well-funded wildlife genetics lab with multiple long-term, ongoing projects on species people love to hunt/fish/photograph/eat may be the niche you are looking for. Not to say that opportunities are not available for securing your own funding and/or pursuing a pet project, necessarily, though that would be lab specific. Collaborations within the agency, with other non-profits and governmental agencies, and academic labs are common as well.

Another motivation of mine is to put these types of labs on the radar of researchers that are attempting to ramp up their program to larger scale/higher throughput pipelines.  If you are overwhelmed with data and sample tracking and organization or concerned about tailoring protocols and/or scripts to fit your needs, it may be that wildlife genetics labs have already done the tweaking and QC for you and some of those resources can be found outside of the primary literature (e.g agency reports,  Reaching out to your fellow scientists at wildlife labs would surely be mutually beneficial. Lastly, and most importantly, tell your students interested in wildlife genetics and bioinformatics about these  jobs!  Sure, they’re rare, but so are tenure track positions.

For a little more detail about our little corner of the world, click here.

Sockeye salmon in the Snake River basin are endangered.  Therefore, every wild fish is brought into the hatchery to spawn.  Every female is crossed with two males and vice versa. The left photo shows the deft harvesting of milt from a male. The center photo is of eggs harvested from a single female.  EVERY SINGLE EGG is accounted for throughout the process.  Finally, in the right photo, a marriage betwixt the two. Photo by Katharine Coykendall

Posted in career, conservation, ecology, funding, pedigree, population genetics, quantitative genetics, Uncategorized | Tagged , , , , , | Leave a comment