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?

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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.

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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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