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?

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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.

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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.

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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.

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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.

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Microbiomes of a small conference

The conference season is almost over. There are still a few gems out there worth attending before school starts.

I just came back from the Lake Arrowhead Microbial Genomics Conference which took place at a UCLA resort in the mountains. This conference is rather small and intimate. It lasts for five days and is structured into early breakfast – morning talks – bountiful lunch – two hours afternoon break – poster session – dinner – late evening talks – partying and/or sleeping. There are no concurrent sessions. Everybody (~156 people) has the same schedule. Speakers are all invited and represent people from the whole range of different universities and colleges, genomics products vendors, and industry owners or workers. Everyone can sign up to present a poster. There is free alcohol ad libitum. Why is California still drinking alcohol? I guess it gives us confidence to break the ice. People were very enthusiastic. Everybody said they looooved it and would come back. What is it that makes a conference that good?

I liked the venue, the intimacy, great conversations, helpful comments on my research/poster, good food, sharing my room with a role model, good weather, and the outdoors. Also, the majority of invited speakers was female.

There were 36 talks and more than 50 posters. Let me summarize a few presentations that make a good fit for The Molecular Ecologist.

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A Master Manipulator: How a bacterium tells a plant what to do

Katrina Sahawneh wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Katrina is working on her MS in Biology and her MA in Education. She currently is studying ER stress and pathogen immunity in Arabidopsis thaliana in Dr. Karolina Mukhtar’s lab. In her spare time, she enjoys drawing and painting. 

Have you ever been in the middle of two people giving you the opposite advice on what to do?

Well, it turns out, plants have this problem, too.

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Robin Waples receives 2018 Molecular Ecology Prize

Robin Waples, the 2018 winner of the Molecular Ecology Prize, received a plate commemorating the award in a ceremony Sunday at the Conservation Genetics 2018 conference. The prize recognized Waples’s extensive contributions in the use of molecular genetic data to estimate effective population size, gene flow, and population subdivision in natural populations and complex life-history scenarios.

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Are we restoring coral reefs for today or for tomorrow?

Elise Keister wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Elise studies the impact of climate change on coral 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 and Atmospheric Science (RSMAS) and then was involved in a myriad of research projects ranging from damage assessment for the Deepwater Horizon Oil Spill to the impact of thermal stress on Floridian coral species. Elise is passionate about working with these susceptible invertebrates that play such a foundational role in coral reef ecosystems. She hopes to determine some mechanisms coral utilize to promote resiliency to high temperatures, as this will only become more common in the decades to come. Elise tweets at @elise_keister.

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Big Data and Pretty Graphics Illustrate Surprising Global Trend in Marine Fish

Looking around for a topic to write about, I found a recent paper in Nature that struck me for four reasons.  The first is how it ties into my previous post about repeated patterns in evolution of sticklebacks in higher latitudes.  This new paper uncovers a surprising pattern in marine fish biodiversity – the fastest rates of speciation occur in polar regions of the globe – not tropical waters.  These results are paradoxical because polar regions also have the lowest species richness of fishes. The prevailing dogma is that lower latitudes harbor higher levels of biodiversity on land and in the sea and higher rates of marine species formation in the tropics have been inferred in fossil molluscs, plankton, and coral. However, the authors found the fastest overall rate of speciation occurs in the south polar seas within icefishes and their relatives.  The mean speciation rate is over two times greater in the Southern Ocean around Antarctica than in the Coral Triangle in the Indo-Pacific, the marine region exhibiting the highest species richness. Though there is little overlap in species that occur in the southern and northern polar regions, the northern seas exhibit high speciation rates as well. Moreover, there is a high correlation between endemism and speciation rate. A notable exception is the Mediterranean Sea, which shows high endemism, but a low speciation rate. Clearly, there’s something about the high latitudes that’s conducive to high rates of evolution in marine fishes.  How can it be that the tropical latitudes harbor the most number of species if the rate of species generation is so much higher in the polar regions? One obvious hypothesis is that the extinction rate is much higher at the poles as well.  The authors were unable to examine extinction rates in this study, but mention elsewhere that their current work is exploring this avenue.

The second reason this paper grabbed me is the sheer amount of data and analysis effort that went into this study.  First of all, the authors constructed a time calibrated phylogeny of all ray-finned fishes, including 31,526 tips, 11,638 with genetic data. The time calibration was achieved by surveying the palaeontological literature and museum collections to gather a 139-taxa fossil calibration set.  They generated or downloaded from Genbank sequence data for those 11638 taxa for 27 genes. They distilled geographic distribution information for all marine fish species with data available, using AquaMaps, but incorporated expert opinions and museum records to refine distributions to estimate geographic ranges to 150 x 150 km grid cell resolution for 12,050 marine species. They also calculated mean speciation rates for 232 marine biogeographic ecoregions.  All of this biogeographic data came from four major biodiversity occurrence aggregators (Global Biodiversity Information Facility, Ocean Biogeographic Information System, Fishnet2, and VertNet), which amounted to 13,322,575 marine fish occurrences. In addition, 132 institutions world-wide significantly contributed occurrence records to this study.

The authors estimated speciation rates in several ways, employing the diversification rate statistic, λDR, for each tip in the 31,526 taxon phylogenies, then averaged across the set of 100 trees generated with stochastic polytomy resolution and two Bayesian Analysis of Macroevolutionary Mixtures with and without time-varying rate regimes (λBAMM and λBAMM-TC). Finally, a simple node density estimate for a sequence of intervals between 0.25 and 50 Mya. Mean speciation rate was estimated by grid cell, by geographic region, and by latitudinal mid-point. There are nine extended data figures included with the otherwise brief paper that delve into how cell rates may change the results, taking into account depth of occurrence (in case the speciation rates are more of a deep sea phenomenon as opposed to a higher latitude one. It’s not.), endemism, and the temporal dimension of the rate heterogeneity, among others.  Clearly, the museum, digital archivist, ecological, evolutionary, palaeontological, taxonomic, and bioinformatic expertise needed for this work is staggering.

The third reason I wanted to draw attention to this paper was its uncovering of errors in Genbank. When exploring the files deposited in Dryad, I came across a table called “sequence_blacklist” that lists all the sequences that were excluded from the analyses and why.  Of the 577 records, 185 were excluded because they blasted to a different organism than what they were identified as, including two that blasted to Homo sapiens.  I mention this because databases are only as good as their entries.  It is up to us to provide Genbank with high quality submissions and to CORRECT ERRORS when they are uncovered.  If you, dear reader, have deposited any sequences into Genbank from any fish species, I implore you to check the table mentioned above.  It’s your open source scientific duty.

The final reason I wanted to highlight this paper is the glorious figure below. I confess that I often suffer from figure envy when I read papers. Constructing an elegant, visually captivating figure is a skill I do not have and would desperately like to cultivate. When I come across one like the one below, I immediately think of how I would go about making it on my own and I invariably come up short. I have so many questions for the authors. How long did this take? Was it originally more than one? How many different programs did you need to get the final version? Did anyone try to talk you out of a figure so complex? Were the fish drawn by hand, then scanned, or rendered in a graphics program? There is so much information packed into this figure, but it comes across clearly and completely considering the scads of data and analyses behind it. Truly a masterpiece.

References

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll, Michael E. Alfaro. An inverse latitudinal gradient in speciation rate for marine fishesNature, 2018; DOI: 10.1038/s41586-018-0273-1

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