A Highlight of Molecular Ecology outside of Academia

Posted on 21 Dec, 2018 by Katharine Coykendall

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.

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

Should journals solicit submissions from preprint archives?

Posted on 10 Dec, 2018 by Jeremy Yoder
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

“Advanced Search.” BioRxiv, Cold Spring Harbor Laboratory, www.biorxiv.org/search.

Posted in community, Molecular Ecology, the journal, science publishing | Tagged | 1 Comment

Earth BioGenome: The launch of biology’s moonshot

Posted on 7 Dec, 2018 by Alex Twyford

The Earth BioGenome Project aims to sequence all currently described ~1.5 million eukaryotic species on earth (Lewin et al., 2018; Figure 1). The scale and scope are enormous, and it is hard to imagine a more ambitious but exciting goal.

Last month, I attended the launch of the Earth BioGenome Project, held at the Wellcome Trust in London. From the first session you could sense the buzz and anticipation. Harris Lewin opened the meeting with his vision for the project. He sees Earth BioGenome as biology’s ‘moonshot’, as transformative for science as placing a man on the moon. The projected cost of $4.7bn is similar to the Human Genome Project ($2.7bn, equivalent to $5bn today), and is somewhat comparative in the need for collaborative effort from different research groups. The need for global collaboration is clear: to sequence earth’s diversity we need to use samples held in museum, zoo and botanic garden collections from across the globe; we need extensive new field collections (particularly in biodiversity hotspots); we need to develop new sequencing infrastructure and bioinformatic pipelines; and we need scientists to use these data for research, biodiversity monitoring and conservation. Lewin reminded us that not all the uses of the human genome were clear when the project was launched, and the same applies to Earth BioGenome data. But obvious uses are for benefitting human welfare (e.g. drug discovery and crop improvement), protecting biodiversity, and understanding ecosystems.

Figure 1 – Current state of sequencing the tree of life. Synthesis phylogeny from the Open Tree of Life. Available complete genomes marked in red in the inner circle. Figure from Lewin et al. (2018). 
Continue reading →
Posted in conservation, evolution, genomics, natural history, next generation sequencing, phylogenetics | Tagged , , | Leave a comment

Conference catch-up: The many colors of snow

Posted on 3 Dec, 2018 by Stacy Krueger-Hadfield

Red snow … watermelon snow … green snow … did you know that snow came in so many different colors?

I had never heard of watermelon ice (#🍉❄) until a talk given by Robin Kodner from Western Washington University at the Phycological Society of America meeting in Monterey in 2017. We both gave talks in the last session of the meeting. We chatted at the end of the session, a chance conversation that led to a collaboration that led to Potsdam, Germany and the 2nd Snow Algae Meeting.

I’ll confess I felt a little bit self conscious presenting life cycle theory when I have not seen a snow alga in person (or in situ), let alone worked on them yet (several grant applications didn’t quite reach the summit, pun intended), but the organizers and all participants were incredibly gracious. Though I was suffering from the worst jet lag I’ve ever experienced, this meeting was motivating and exciting, as well as incredibly welcoming to a #🍉❄ novice.

So … what are snow algae? And, why did about 25 people congregate in Potsdam to talk about them?

Continue reading →
Posted in adaptation, bioinformatics, citizen science, community ecology, evolution, fieldwork, mating system, microbiology, natural history, phylogenetics, phylogeography, population genetics, selection, speciation, transcriptomics | Tagged , , , , , , , , , , , , | Leave a comment

How island foxes are living on the edge

Posted on 23 Nov, 2018 by Patrícia Chrzanová Pečnerová
Against all odds. Photo source: WikimediaCommons/Pacific Southwest Region USFWS from Sacramento, US

Back in 2016, Robinson et al. (2016) published a genomic analyses of the Channel Island foxes and they showed that despite extremely low genome-wide diversity, the island foxes do not seem to be suffering from inbreeding depression. Read the post ‘What does the island fox say?’ summarizing this paper.

Most notably, their results question the general validity of the small population paradigm. One of the principal hypotheses in conservation genetics predicts that small populations are more vulnerable to stochastic extinction factors including the genetic processes of inbreeding and genetic drift. As a result, small populations are expected to be more likely to end up in an ‘extinction vortex’ and suffer from mutational meltdown and loss of adaptive potential, which compromise their chances of long-term survival.

Source: WikimediaCommons/
National Oceanic and Atmospheric Administration

Although the island foxes do have drastically reduced genetic variation and increased genetic load, they seem to be surviving just fine. How is it possible? Does it mean that genomic erosion is not a direct path to extinction?

Continue reading →
Posted in conservation, evolution, genomics, population genetics | Tagged , , , | Leave a comment

Fantastic beasts…and Canada is where to find them

Posted on 19 Nov, 2018 by Kelle Freel

Understanding how organisms are related to each other in the grand scheme of things has been a main goal of taxonomists, ecologists, and evolutionary biologists for centuries. While traditionally, what things look like (morphological characters) and what they eat or produce (phenotypic characters) have been used for classification. However molecular tools have been a game changer in terms of figuring out who is related to who and where they fit on the tree of life.

Last Thursday, a new letter out in Nature led by Alastair G. B. Simpson’s group in collaboration with other labs at Dalhousie University presented evidence that a group of eukaryotic protists (the Hemimastigophora) is MUCH more distinct than anyone thought. Although protists are tiny, they are still eukaryotes, so they have relatively complicated cell organization and are actually more closely related to us than bacteria (prokaryotes). The word “protozoan” means “early animals” and was first used in 1820 (Scamardella 1999). According to Simpson (in this informative article), protists most simply are “…all the eukaryotic organisms that are not animals, plants or fungi”. So…a whole bunch of stuff.

Continue reading →
Posted in Uncategorized | Leave a comment

Racing Against the Climate

Posted on 9 Oct, 2018 by Stacy Krueger-Hadfield

Sarah Livett wrote this post as a final project for Stacy Krueger-Hadfield’s Introduction to Evolutionary Processes course at the University of Alabama at Birmingham. Sarah was a 5th year MS student at UAB in Dr. Thane Wibbel‘s lab. She worked on Kemp’s Ridley sea turtles and is pursuing a MS degree in conservation and sustainability.

Unlike genetic sex determination in mammals, turtle sex is determined by temperature. In sea turtles, for example, males develop at lower temperatures, whereas females develop at higher temperatures. These temperature ranges are very small. We’re talking less than 3⁰C (Woo 2014). This means that a rise in global temperatures of just 3°C could shift the sex ratios from all female (Wibbels 2003).

Not only do higher nest temperatures produce more females, they also increase mortality of turtle hatchlings (Laloë et al, 2017).

Could heat shock proteins combat temperature-linked hatchling mortality?

Continue reading →
Posted in adaptation, blogging, evolution, natural history, Science Communication, transcriptomics | Tagged , , , , , | Leave a comment

Deep Sea Biology Symposium 2018

Posted on 5 Oct, 2018 by Katharine Coykendall

The bloggers here at The Molecular Ecologist have been regaling you with recaps of various conferences from The Ecological Society of America to Evolution  to  the more intimate  Lake Arrowhead Microbial Genomics Conference.  Although it contemplated skipping my synopsis to prevent conference summation fatigue in you, dear reader, I feel it’s important to highlight this one because it only happens once every three years and it’s fabulous.  Near the beginning of September, I attended the 15th Deep Sea Biology Symposium in Monterey California hosted by the Monterey Bay Aquarium Research Institute (MBARI).  The talks featured topics like robots, bioluminescence, hydrothermal vents, Yeti crabs, and larvaceans.  Though it’s an international meeting, it still felt intimate.  This year there were 405 attendants and at most two concurrent sessions.  The last one was in Aveiro, Portugal in 2015.  The next one will be in 2021 in Japan.

I’ll suppress the desire to mention everything I saw and most of what I didn’t, but the urge is strong.  There were so many stellar talks.  The great thing about deep sea talks, is that they often showcase breathtaking images of animals in the water column and under the microscope, as well as innovative technology used to get the images and data. In fact, there was an entire session devoted to technology and observing systems. There are robots that grow increasingly complex with regard to sampling effort and capacity.  There are long term oceanic observation networks that synthesize and send out data gathered from moorings and landers planted across the earth’s oceans. A couple of the highlights include a long term observation system to look at sub-seafloor crustal microbial communities (Beth Orcutt, Bigelow Laboratory for Ocean Sciences) and DeepPIV, an instrumentation package that includes continuous lasers and optics and a dye/particle injector all attached to an ROV, which enables in situ feeding experiments, measurement of filtration rates and structure of larvacean mucus houses (Kakani Katija, MBARI).

Continue reading →
Posted in conferences | Leave a comment

In it to win it: Selective Advantage through Host-Selected Mutations

Posted on 2 Oct, 2018 by Stacy Krueger-Hadfield

Julian Jackson wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Julian is a MS student and investigates symbiotic relationships in microbial communities in Dr. Jeff Morris‘ lab. Outside of the lab, Julian is an advocate for creating, maintaining, and teaching youth about urban farming where the goal is to help eliminate food deserts within urban  communities. He also enjoys photography and is a member of the Ground Floor Contemporary Studio. You can find Julian on Instagram @jul_yeeen.

Continue reading →
Posted in adaptation, evolution, genomics, microbiology, Science Communication, selection | Tagged , , , | 1 Comment

Cricket Plays a Song of Systems Biology

Posted on 25 Sep, 2018 by Stacy Krueger-Hadfield

Mina Momeni wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Mina earned her MS degree and is now a research technician at UAB in Dr. Nicole Riddle‘s lab. Her research focuses on HP1-Histone interactions and chromatin structure in Drosophila melanogaster. When she is not exploring the effects of overexpression of HP1B, she enjoys hiking, reading, and watching Netflix with my cat.

To what degree can a novel variant persist?

Typically, when trying to answer this question, scientists take into account the extent to which a mutation enhances an organism’s ability to reproduce. With the ‘sequencing revolution,’ it has become easier than ever to address this question at the molecular level and start to link phenotypes to genotypes.

Continue reading →
Posted in adaptation, bioinformatics, blogging, evolution, genomics, mutation, natural history, Science Communication | Tagged , , , , | Leave a comment