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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To present data is human, to communicate data is divine

Finding new and engaging ways to communicate science is of paramount importance. But, how many opportunities are there to practice the art of communication?

That’s how I began the lead-in piece for a series of student posts over a year ago (see piece here and the student posts can be found here).

Giving students the opportunity to hone their communication skills is a must. They need to be adept at engaging with all sorts of people who will cross their paths … from policy makers to scientists in the same field to an interested person when you’re in the field.

Clichés are normally clichés for a reason …. practice makes perfect (or at least a lot better). 

I’ve been lucky enough to expand my Science Communication course at the University of Alabama at Birmingham since I last taught it two years ago this fall (time does fly … more about that in a future post on the meetings I was supposed to cover <<insert chagrin here>>).

Students in the first round were able to write a blog post about a topic of their choice. Each student that submitted the blog post to Jeremy and myself got them published. Not only did they learn how to distill the primary literature, but they each got another line on their CV.

Over the last academic year, I have taught an Evolution course and the revamped Sci Comm, in which grad students in both courses had the opportunity to write a blog post again. I was impressed with the quality and excitement in the first round. I also wanted to try to provide other opportunities for students. As regular readers will know, I have found my time at TME to be incredibly rewarding.

Starting next Tuesday, each week a new blog post written by a student from my graduate Sci Comm course or from the graduate section of my Evolution course will go live.

There’ll be another series of student-written posts in the new year from my new Conservation Genetics course. I’m hoping this can be a series that will continue each time I teach a course with grad students at UAB.

The more I think about science communication … the more I wonder.

Illustration by Maki Naro

Is science communication a bit redundant? Should we not simply communicate? It’s probably a philosophical argument best saved for another day when a two-year review, a late piece for a society newsletter, and several manuscripts aren’t looming.

I hope you enjoy reading the posts over the next few weeks as much as I did working with the students to turn these into publishable pieces of science communication.

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Not my problem

Do American scientists know that doing research in America is a necessary step for many scientists from other parts of the world in order to get a permanent job in academia in their home country?

Once in the US, these researchers face many challenges outside of academia that can significantly affect their survival and well-being, and ultimately, their scientific output. These challenges include health care, visa issues, housing, taxes, the school system, and child care. In America, people can easily fall through the cracks. Many other countries have a safety net that protects you while working at an academic institution. In the US however, offices will not coordinate and fix problems without the affected individuals being involved.

Pssst! The following text is only for postdocs. (I also mean grad students and visiting scholars).

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Evolution 2018: assortative mating, combinatorial speciation and genome dynamics

The Evolution conference in Montpellier is over, and as the sun, wine and great science become a memory, here is my recap of some conference highlights following on from a great first day:

A sea of scientists waiting for a plenary lecture. Photo: Alex Twyford.

Sharon Strauss (University of California Davis) gave the ASN Presidential Address entitled “Diversity and coexistence in close relatives, and reflections on 150 years of the ASN”. In her talk, she discussed the coexistence of closely related plant species, and whether phylogenetic similarity predicts ecological similarity. Her work centres on herbaceous plant communities at the UC Bodega Marine Reserve in California and combines reciprocal transplant experiments with phylogenetic analysis. One of her main results was a curvilinear relationship in species performance and genetic divergence, i.e. that species perform best in sites of conspecific taxa that share similar ecological preferences, and in sites of distant relatives where there is less competition. She also showed rare species advantage, reproductive character displacement, and fine-scale exclusion within the plant community. The second part of her talk discussed the history of the American Society of Naturalist, a topic covered by the Molecular Ecologist earlier this year.

Tim Birkhead (University of Sheffield) gave the SSE Stephen Jay Gould Prize lecture, entitled “The most perfect thing: the inside (and outside) of a bird’s egg”. This was a fascinating general natural history talk full of wonderful facts about eggs. I had no idea that an hour before most birds lay an egg it rotates 180 degrees and is then laid point first, or that wrynecks are indeterminate egg layers and if you remove eggs as they are produced they will go on to lay 70 eggs. However, Tim’s talk did attract feedback on Twitter for using his lecture to vocally criticise other scientist’s research.

Luke Harmon (University of Idaho) gave the SSB Presidential Address on “Scaling the tree of life”. The talk addressed the broad biological issue of why some parts of the tree of life are so species rich. He also introduced the technical issue of why phylogenetic studies often find high speciation in young clades (Rosenblum et al. 2012). Luke suggested we are in the golden age of time-calibrated phylogenies, where we can now address these types of questions in replicate systems. I’ll save the details here as it’s hard to summarise briefly macroevolutionary pulses and hierarchical models, but it seems clear we need to take a critical view of how we measure speciation rates across trees.

Hopi Hoekstra (Harvard University) gave the SSE Presidential Address entitled “The genetic basis of Behavioural Ecology”. This brilliant talk described the genetic basis of parental behaviour in Peromyscus mice. She showed that differential expression of vasopressin underlies differences in nest-building behaviour (Bendesky et al. 2017), with genetic transformation of key genes changing this behaviour. This talk was one of the best examples of how merging ecological observations, population genomics, and functional genetics can improve our understanding of the evolution of key traits.

Highlights from presentations given in the parallel sessions include:

  • David Marques (University of Bern) used genomic sequencing to trace the origin of Lake Constance sticklebacks. He revealed this population has a complex mosaic genome, and proposed the new term combinatorial speciation to explain the growing number of cases where admixture is involved in the establishment of new taxa.
  • Axel Myer (Universität Konstanz) presented the genetic basis of large-lips in a lake radiation of cichlid fish. Large lips are advantageous as they aid crevice feeding. He showed that a single major QTL underlies this phenotype, and suggested experimental manipulation of lip size (using gelatine!) could be used to test the fitness benefit of this extraordinary phenotype.
  • Lesley Lancaster (University of Aberdeen) showed that the damselfly Ischnura elegans is expanding into colder climates beyond the range predicted by climate change.
  • David Baum (University of Wisconsin–Madison) described how species definitions are ‘artistic’ and there is no single correct species taxonomy. He also introduced exclusivity factors (which build on concordance factors) as a new approach to improve objective species delimitation.
  • Andrew Leitch (Queen Mary University of London) presented ecological evidence that nitrogen and phosphorus are limiting in the wild and that N + P rich environments have species with larger genomes (Guignard et al. 2016). He included a back-of-the-envelope calculation that polyploid genomes must lose around 367bp per generation to explain extant genome sizes, and asked what selective pressures explain this process of diploidization.
  • Greg Owens (The University of British Columbia) showed the importance of knowing the parents in studies of hybrid speciation. A long-term study of artificial hybrids intending to recreate the hybrid sunflower species Helianthus annuus subspecies texanus (with proposed parents H. annuus and H. debilis) revealed selection on particular haplotypes. But sequencing of natural populations revealed other species are more likely to be contributing to the hybrid species than H. debilis.

Common themes from the talks I saw were assortative mating, chromosomal structure and recombination, and balancing selection. I’m expecting these topics to continue to feature heavily as genomic data from more study systems become available.

The conference finished with a wonderful evening at Abbaye de Valmagne, a 13th century abbey surrounded by vineyards.

The stunning Abbaye de Valmagne, Montpellier. Photos: Alex Twyford.

Looking forward to the next Evolution meeting in Providence Rhode Island!

References

Bendesky A, Kwon Y-M, Lassance J-M, et al. (2017) The genetic basis of parental care evolution in monogamous mice. Nature 544, 434.

Guignard MS, Nichols RA, Knell RJ, et al. (2016) Genome size and ploidy influence angiosperm species’ biomass under nitrogen and phosphorus limitation. New phytologist 210, 1195-1206.

Rosenblum EB, Sarver BA, Brown JW, et al. (2012) Goldilocks meets Santa Rosalia: an ephemeral speciation model explains patterns of diversification across time scales. Evolutionary Biology 39, 255-261.

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ESA 2018 Recap

Something old, something new, something borrowed, something BLUE

…in which I shoe-horn a summary post of this giant meeting into a cutesy subtitle, but it mostly works.

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Evolution 2018 Day 1: From genomics in the wild, to new models of selection

It’s Evolution conference time! Evolution has long been my favourite fixture in the conference calendar, with its diverse mix of theoretical and empirical studies that span the full range of evolutionary biology. This year it’s the second Joint Congress on Evolutionary Biology, which brings together the European Society for Evolutionary Biology, the American Society of Naturalists, the Society for the Study of Evolution and the Society of Systematic Biologists all under one roof in the lovely city of Montpellier in the south of France.

The conference kicks off with the ESEB Presidents’ Award delivered by Loeske Kruuk (Australian National University), with a talk entitled ‘Evolutionary dynamics and fitness in wild populations’. Studying quantitative genetics in the wild is challenging because many classical theoretical predictions don’t apply, and because robust inferences require long-term studies that genotype complete populations. Loeske discusses how her work generating a completely pedigree, along with large-scale phenotypic data, for the superb fairy-wren (Malurus cyaneus), has given insights into quantitative genetics in the wild. Interestingly she shows temporal covariance between body size and fitness, but this is because body size is related to other traits, and therefore there is no expectation of body size showing an evolutionary response. She also shows date of moult is heritable, and suggests this means that ‘the early bird gets the girl’. She finishes up by saying that there are less than 10 estimates of fitness for wild populations, and that there are some consistent effects between species (like cohort effects) but lots of variation. I’m really looking forward to seeing the paper where these comparisons of fitness are presented.

The superb fairy wren. Image JJ Harrison/Wikipedia.

Next up is the session ‘Consequences of hybridization: from swamping to speciation’, one of 78 thematic symposia in 13 parallel sessions. The highlight talk for me is Molly Schumer (Harvard University) discussing hybridisation in swordtail fishes. These remarkable fish all demonstrate over 10% hybrid ancestry in their genomes, suggesting a pervasive role of hybridisation in adaptation and speciation. She goes on to discuss how low coverage sequencing and local ancestry analyses reveal the minor parent ancestry being purged over time, as well as assortative mating related to hybrid ancestry. It’s a great demonstration of how fine-scale genomic analyses of independent geographic populations can reveal the repeatability of evolution. Other interesting talks in the session include Mario Vallejo-Marin (University of Stirling) discussing rapid evolution of hybrid monkeyflowers, and Amy Goldberg (Duke University) discussing global ancestry proportions inferred by mechanistic models.

The readily hybridising fish genus Xiphophorus. Image: Wikipedia.

After a lunch, I hop over to the session ‘Towards an integrated understanding of genomic and phenotypic divergence’. Thom Nelson (University of Montana) tell us how comparative genomic analyses of the monkeyflowers Mimulus lewisii and M. cardinalis show substantial genomic rearrangements, but with low divergence (as measured by Fst) and without elevated divergence in translocations and inversion. Konrad Lohse (who has the office next to me at the University of Edinburgh) gives a critical appraisal of verbal models of island of divergence, and discusses recent work to produce better genome scans for divergence. This talk seems particularly relevant given the widespread use of genome scans and the use of arbitrary cut-offs for outliers (something many of us have been guilty of at some point). Finally, David Field (IST Austria) gives an exciting overview of a hybrid zone between snapdragon (Antirrhinum) subspecies with contrasting flower colours. This study is an exceptional case of generating a pedigree of a plant population that incorporates all the complexities that occur in the wild (e.g. most Antirrhinum plants are annuals but 20% are perennial, and seeds can persist in the seedbank). These data reveal strong home-site advantage for the two subspecies, with strong clines for loci underlying flower colour in the hybrid zone.

The first day really shows the breadth of evolutionary research. Evolutionary biologist no longer appear to be getting dazzled by new technology (only one photo of a sequencer today) and genomic sequencing is now just a routine tool for investigating evolutionary questions. It’s also been nice to see such a well-organised conference, with clear cut-offs for talks to prevent people overrunning (using an interesting choice of music!), facilities for childcare, and minimal use of disposable materials.

Please let me your favourite moments of Evolution 2018 via Twitter (@alex_twyford) and I’ll include a selection in a conference round-up post once the conference dinner hangover eases.

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