Should journals solicit submissions from preprint archives?

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.

Share
Posted in community, Molecular Ecology, the journal, science publishing | Tagged | Leave a comment

Earth BioGenome: The launch of biology’s moonshot

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). 

After this inspiring introduction most the audience were invigorated. My initial doubts were quickly dealt with. I came in questioning whether this goal is really possible. But I hadn’t realised how much had already been achieved. As a plant biologist I’ve been following the progress of the 10,000 Plant Genome Project in detail (Twyford, 2018). But many other ‘big genome’ projects had largely passed me by. There’s the Vertebrate Genomes Project (aim: 66,000 error-free vertebrate genomes), Bat 1K (1,300 bat genomes), 1000 Fungal Genomes, The i5K Initiative (5,000 insects and other arthropods), 10,000 Bird Genomes (B10K), with the list going on and on. Seemingly biologists studying every major organismal lineage have initiated their own genome project. And what’s exciting is that these projects have made substantial progress with many genome sequences published or soon to be released. Earth BioGenome unites these ongoing projects and builds on this experience. By setting data standards, recommending pipelines, providing infrastructure, and offering re-usable templates and agreements for sample sharing, Earth BioGenome makes new genomic-scale science more attainable.

How will Earth BioGenome work? What became clear at the meeting was that Earth BioGenome will be an aggregate of smaller projects with their own governance. Each project will find their own funding and proceed separately, but Earth BioGenome will provide the template for how to proceed and may also provide some centralised funding for specific goals. In particular, centralised funding may help developing countries build their own sequencing infrastructure and biobanks to support genomic research. This will also help train hundreds of the next generation of scientists necessary to make this research happen.

A key message from the meeting was that if we are sequencing representative genomes from all of life we need to do it well. There is little point in assembling fragmented genome sequences from Illumina short-read data if they are to be replaced by contiguous genomes from long-read data in the near future. The route to good genomes will differ depending on the organism, but likely includes a combination of long-read (Pacific Biosciences and/or Oxford Nanopore Technologies) and short-read Illumina technologies, often paired with inexpensive synthetic read data (e.g. 10X Genomics) and scaffolded with Hi-C or BioNano Genomics (see summary here). There was a remarkable consensus that given major innovations in genomic technologies the sequencing is one of the easy parts of the project, and that the greater challenge is in sourcing material (particularly from the tropics), putting a name to each sample, and curating voucher specimens.

At the same meeting, Mike Stratton introduced a second major new sequencing initiative, the Darwin Tree of Life Project. This ‘place-based’ rather than ‘taxon-based’ project aims to sequence a representative from all 66,000 eukaryotic species present in the United Kingdom. Why the UK? Its small size and limited diversity, its existing detailed collections, the presence of related datasets, and the existence of immediate funding for sequencing, all make it a good first choice. This project gets me excited (disclaimer: I’m hoping to be involved with the project by sequencing British plants, along with colleagues at the University of Edinburgh, Royal Botanic Garden Edinburgh, and Royal Botanic Garden Kew) as I see this as a superb opportunity for comparative genomic analyses that incorporate the large existing data sets of ecological attributes and species’ traits.

Where next? I think one important goal is for researchers to launch new comparative genomic projects, and for scientists to lobby funding agencies and governments to support new genomic research. If many new and diverse sequencing projects are started this will build the momentum for broadening the sequencing effort to global diversity. One initial aim should be to produce genome sequences representative of each organismal family, before moving to genera-references and then species (the ‘phylogenetic wave’). Another aim should be to sequence diverse genomes from multiple areas to develop tools for place-based projects. Personally I can’t wait to see the next stage of the genomics revolution take place.

References

Lewin, H. A. et al. (2018) Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences 115, 4325-4333.

Twyford, A. D. (2018) The road to 10,000 plant genomes. Nature Plants4, 312-313, doi:10.1038/s41477-018-0165-2.

Share
Posted in conservation, evolution, genomics, natural history, next generation sequencing, phylogenetics | Tagged , , | Leave a comment

Conference catch-up: The many colors of snow

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

Share
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

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

Share
Posted in conservation, evolution, genomics, population genetics | Tagged , , , | Leave a comment

Fantastic beasts…and Canada is where to find them

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

Share
Posted in Uncategorized | Leave a comment

Racing Against the Climate

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

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

Deep Sea Biology Symposium 2018

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).

Though presentations in most of the sessions included some facet of molecular ecology, they were concentrated in “Deep Sea Omics”, Taxonomy and Phylogenetics”, and “Connectivity and Biodiversity”.  Michelle Gaither from UCF showed that there is polygenic adaptation to depth in the deep sea fish, Coryphaenoides rupestris involving nine non-synonymous changes in six genes. Fish from 1800 m were all fixed for the same alleles. The authors posit that fish with different genotypes segregate by depth as they mature and the significance of 1000m vs 1800m depths might be access to the deep scattering layer.

Darrin Schultz (MBARI, UCSC) is developing an assembler to successfully assemble the genome of four species of ctenophores.  The challenge has been due to heterogeneity of the genome.  There are many heterozygous states, inversions, and indels between the paternal and maternal haplotypes. Large effective population sizes and short generation times hinders getting good quality genomes.

Maeva Perez (University of Montreal) utilized CRISPR (the same biological system used for gene editing in model organisms)  sequences to track symbiont diversity in hydrothermal vent tubeworms. Each palindromic repeat in a CRISPR sequence is a historical record of the viral infections a bacterial lineage has been exposed to, so can be used to discriminate between strains of closely related bacteria.

Jiao Cheng (Institute of Oceanology, Chinese Academy of Sciences) presented compelling results combining population and functional genomics of a species of Yeti crab, Shinkaia crosnieri. These crabs are interesting because they occur in both hydrothermal vent and methane seep environments.  Mitochondrial DNA results showed that no alleles are shared between these two environments. SNPs from RAD-seq results showed similar differentiation.  FST-based outlier loci and identification of orthologous genes via comparisons of transcriptomes between the two environments uncovered signals of both positive and purifying selection in genes having to do with sulfur metabolism,  oxidative stress, and detoxification, to name a few.

We were rewarded with outstanding plenary speakers, including Julie Packard, who spoke of the role the David and Lucille Packard Foundation has had on ocean stewardship and the partnership with MBARI to merge ocean conservation, technology, and research.  Shana Goffredi (Occidental College) summarized the discovery, biogeography, phylogenetics, physiology, and reproductive biology of the bone eating worm genus, Osedax.  Janet Voight (Field Museum) delighted the audience with some natural history of Pacific octopuses. Steve Haddock (MBARI) shared gorgeous video of various bioluminescent organisms, covered in greater detail here, and Tracey Sutton (NOVA Southeastern University) emphasized the need for baseline, time series data so when disasters like the Deepwater Horizon oil spill happen, we have the information necessary to start the process of recovery.

An excellent schematic from Chong Chen’s plenary talk. Photo by DK Coykendall.

Excursion to the Monterey Bay Aquarium. Showing my squat lobster bias. Photo by DK Coykendall

Charismatic megafauna entertainment while lunching. Photo by DK Coykendall

One morning was devoted to lightening talks where scientists presenting posters were allowed 2 minutes to summarize their findings.  Personally, I’m a fan.  When you see how many talks are scheduled, it’s intimidating, but I thought it was efficient and effective.  This meeting was the perfect size to make this type of thing worthwhile.  It definitely drew my attention to a handful of posters that I made sure to seek out during the following poster session.  In light of our society’s evolution to bite sized Twitter communications, perhaps this is the wave of the future – lightening talks and poster sessions to hold our increasingly diminished attention spans.

I could go on and on, dear reader, but I’m on a 160 foot boat right now off the coast of South Carolina in 11 foot seas participating in some deep sea research myself, trying not to barf on my screen. If any of these topics piqued your interest, I urge you to search #DSBS2018 on Twitter, and/or go to the The Deep Sea Biology Society web page and peruse the abstracts yourself.

Signing off.

Share
Posted in conferences | Leave a comment

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

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

Share
Posted in adaptation, evolution, genomics, microbiology, Science Communication, selection | Tagged , , , | Leave a comment

Cricket Plays a Song of Systems Biology

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

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

Nick Fountain-Jones wins Harry Smith Prize for study of virus transmission among urban bobcats

A camera-trapped bobcat near Anaheim, California, where Fountain-Jones et al (2017) examined Feline Immunodeficiency Virus transmission.
A camera-trapped bobcat near Anaheim, California, where Fountain-Jones et al (2017) examined Feline Immunodeficiency Virus transmission. (Observation from iNaturalist)

The Harry Smith Prize is awarded for the best paper in Molecular Ecology in the previous year led by an early-career researcher. The 2018 Prize has been awarded to Dr. Nick Fountain-Jones for his paper ‘Urban landscapes can change virus gene flow and evolution in a fragmentation‐sensitive carnivore’ (2017). Fountain-Jones’s et al. addressed the impact of urbanisation on disease epidemiology in native carnivores. The study paired molecular epidemiology of feline immunodeficiency virus with genetic analysis of a native host, the bobcat (Lynx rufus). Despite working across systems and in organisms that are inherently difficult to sample, the study describes an innovative and rigorous application of molecular tools to extract valuable practical insights into disease dynamics in human-altered landscapes.

Share
Posted in community, Molecular Ecology, the journal, phylogenetics | Tagged , , | Leave a comment