Saturday action item: March for science

While the current administration is in office we’re posting small, concrete things you can do to help make things better, every Friday. Got a suggestion for an Action Item? E-mail us!

Today was the inauguration. Tomorrow, millions of people around the U.S. and across the world will say what they think about that. The Women’s March started as a Facebook post proposing a post-inauguration protest in Washington, DC, and it’s now grown to hundreds of sister marches worldwide. As the name suggests, the March was particularly motivated by the new president’s unapologetic sexism and the new vice president’s astonishingly poor record on women’s rights — but the March’s vision brings together the myriad objections people of goodwill have to the new administration, and its many partners range from the Natural Resources Defense Council to GLAAD to the AFL-CIO to the ACLU.

So make a poster featuring your favorite science, pick out a geeky tee-shirt (may we suggest?) and find a sister march close to you to attend tomorrow. We’ll see you in the streets.

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Highlights from the Standalone Society of Systematic Biologists meeting – part 2

The 2017 standalone meeting of the Society of Systematic Biologists included expert-led debates on major issues in molecular systematics. Didn’t make it to Baton Rouge? Don’t worry – Melissa DeBiasse and I report on some of the main points (and our favorite lightening talks) from Day 2 of the meeting. Be sure to read our rundown of Day 1 of this great meeting as well. Continue reading

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Free to go but required to stay: contrasting views on mitochondrial relationships

Ever since a bacterium found itself mysteriously engulfed in our eukaryotic ancestor, things have been, uh, complicated regarding our two genomes. One is big, one is small. One is circular, one is linear. One is numerous in each cell, the other centralized and singular (usually!).

Just look how comfy all those proteins from mitochondrial (yellow) and nuclear (green) genomes cuddle up.

Despite their differences in structure and mode of inheritance, our mitochondrial and nuclear genomes have continued to work together in providing some of the most basic functions that keep eukaryotes ticking. However, depending on what scientific discipline influences you the most, you might recognize one of two seemingly contradictory viewpoints on common patterns of mitochondrial and nuclear variation. A tidy new review led by Dan Sloan describes the conflict between these views:

On one hand, mtDNA may be at the forefront of speciation events, with coevolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted.

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When microbes can move mountains, studying microbial communities on glaciers

Image of the Baltoro Glacier, courtesy of wikicommons.

Bacteria are amazing, and as a recent article by Ambrosini and colleagues reminds us, they are quite literally, just about everywhere. Before reading this article, I have to admit, I was a little rusty on my definition of cryoconite holes, so I did a little reading. Essentially they are small ponds that form on glacier surfaces. For the pond to form, first cryoconite accumulates on glaciers, which is a dust composed of small rock particles, bacteria, and soot.

The buildup of this fine dust on glaciers has been termed “biological darkening”, and as you might guess, changes how the ice surface absorbs heat. This black dust can induce melting of the ice surface, forming cryoconite holes, which are basically pools of water that can be tiny (few centimeters across) or quite large (a meter across), and have been found to host microbial communities.

“These environments are an underexploited reservoir of biological functions with high biotechnological potentials, and the study of biological processes acting in them gained interest in the recent years owing to increasing evidence that they can strongly affect the engergy flows of glaciers and, consequently the climate.”

Figure 1. Location of sampling sites. Ambrosini et al., (2016)

It is important to understand the dynamics involved in changes that affect glaciers and ice sheets as they are extremely sensitive to climate change and have a huge influence on the rest of the planet. Since cryoconite holes potentially play a part in altering glacier melting rates, understanding these relatively biologically active sites and how they influence the glacier is important.

While previous research has shown that the microbial communities on different glaciers and in diverse regions (low-latitude mountain vs polar glaciers) can vary, there is still very little known about the characteristics of these communities and the mechanisms driving their formation and furthermore, how they affect the glacier on a large scale. The authors set out to study 30 different cryoconite holes on the Baltoro Glacier, which is 63 km long and runs through the Karakoram mountain range in Pakistan.

Figure 2. Mean relative abundance of OTUs sampled. Ambrosini et al., (2016)

Ambrosini and colleagues extracted the DNA from the water samples from the cryoconite holes, which were located in one of four main areas defined by differential elevations, and then amplified the V5-V6 hypervariable regions of the 16S rRNA gene. Finally, they sequenced everything using Illumina MiSeq and clustered the sequences into OTUs using a 97% cut-off value. They found that the communities in the cryoconite holes were dominated by Betaproteobacteria. Specifically, the genera Polaromonas and Limnohabitans of the order Burkholderiales were particularly abundant.

Figure 4. Association network among different OTUs. Ambrosini et al., (2016)

Overall, the five most abundant bacterial orders plus the Cyanobacteria made up the vast majority of bacteria at each site (more than 70%). One of the main environmental drivers that seemed to change the community composition was pH, which significantly affected bacterial community structure in one of the main 4 areas sampled.

As the authors note, obtaining additional environmental measurements such as nutrient concentration and salinity might have allowed them to verify the influence of these other important parameters. The sampling sites were clearly difficult to access, and transportation of the samples, as well as sample preservation, are understandably challenging. Regardless, the authors summarized the pitfalls in the study as well as the diversity of bacterial communities sampled.

In conclusion, our results suggest that microbial communities of cryoconite holes on Boltoro Glacier were dominated by Betaproteobacteria probably due to their highly versatile metabolism.

I thought the article was interesting in part since, even as a microbial molecular ecologist, I don’t always think about the role that bacteria have in diverse environments that aren’t a part of my day to day work. Piecing together how microbial communities in extreme environments influence the planet is important, it’s impressive to think that microscopic cells literally affect some of the largest and most dramatic and beautiful landscapes on Earth.

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Diving into the inbreeding depression

This post is going to be a little melodramatic, but I hope that despite all the reading on inbreeding depression, you won’t get depressed.

As the media finally started feeding us all the catastrophic news about the impact of global warming on the environment – every month being reported as the warmest in history, videos of melting ice sheets, and crazy graphs showing climate predictions – scientists are trying to figure out ways to prevent the worst.

Conservation biologists are probably going to be pretty busy, all these populations disappearing and becoming isolated because of changing environment and habitat fragmentation. Isolated and fragmented populations will be affected by stochastic factors, including genetic drift and inbreeding. The problem is that some basic concepts of these processes are still not completely understood. At least not in natural populations. And with that I’ll leave the word to Fred Allendorf and his colleagues:

“Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild.” (Kardos et al. 2016)

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Highlights from SICB 2017

The 2017 Society of Integrative and Comparative Biology meeting was held in New Orleans* on January 4th – 8th. This was my first time at SICB and I was amazed at the diversity and number of talks- over 1900 presentations on topics including (but not limited to) larval ecology, thermal adaptation, elastic mechanics, species delimitation, cardiovascular physiology, parental behavior, and the hilariously named session “I Dig Your Tail!” With 146 sessions over four days, I could only see a small slice of the science. Below I summarize my favorite molecular ecology talks and a few talks that had nothing to do with molecular ecology, but whose titles drew me in. You can find tweets about the meeting with the hashtag #SICB2017.

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Highlights from the Standalone Society of Systematic Biologists meeting – part 1

The 2017 standalone meeting of the Society of Systematic Biologists included expert-led debates on major issues in molecular systematics. Didn’t make it to Baton Rouge? Don’t worry – Bryan McLean and I report on the main points below, and highlight some of our favorite lightening talks of the day. We will post part two of our SSB summary next week.

Debate 1: What do we really know about gene tree variation? Led by Scott Edwards and Gavin Naylor, moderated by Jeremy Brown

In the early years of molecular systematics, there was a lot of focus on how to estimate a gene tree accurately from one or a few loci. After Maddison 1997, we started to expect (and often found) significant variation among gene trees. Now, our focus has shifted to understanding the sources of this variation and accommodating gene tree independence in our phylogenetic reconstructions.

In the phylogenomic era, we may be tempted to think that because we can collect so many data, we can solve all difficult phylogenetic problems. However, it is crucial to keep working to improve theory and methods. For example, while ILS is often accommodated by current models, other sources of gene tree variation (selection, horizontal transfer) are still harder to distinguish. The phylogenetic scale of the question (shallow vs. deep) should also inform models, as the relative importance of each process is somewhat scale-dependent.

Methods that identify gene tree outliers can be help identify patterns that are not consistent with model expectations. Posterior predictive simulations can also identify model inadequacies. Both of these approaches can be used to help us understand underlying biological processes. Still, another major need is in understanding how filtering different classes of outlier gene trees from analyses could bias results.

Put simply, there is a real need in molecular phylogenetics for ongoing theoretical and simulation work, as well as new ways to conceptualize phylogeny. Can we really keep considering phylogenies as bifurcating trees given the complexities of gene flow, horizontal gene transfer, hybridization, etc?

Debate 2: Species delimitation. Or is it? Led by Frank Burbrink and Robb Brumfield, moderated by Bryan Carstens

Species delimitation is still a developing field in molecular systematics. (This assumes, of course, that “species” are real things). Broad goals of delimitation are to identify groups, find the relationships among them, and estimate gene flow, migration, and divergence times. On our species delimitation wish list- a method/program that incorporates this multi-step process into one.

Would we feel more confident about delimitation if we thought about it as population delimitation? By a show of hands, many people said no! Delimitation of groups at lower levels is also a challenge.

Delimitation based on genetic signatures alone can get murky. Want less subjectivity? More integrative methods of delimitation such as iBPP (see our thoughts here and here) are attractive because they can incorporate rely on information other than just genes. Just beware of circularity when including other traits (e.g., those that have been previously defined by experts as taxonomically important).

The importance of species delimitation reverberates to higher levels as well. For example, does inaccurate species delimitation affect our other questions of trait evolution, for example? Must we put taxa into “species” bins? Or is a “tip” a “tip”? Luke Harmon thinks that the impacts of these issues on comparative studies are largely unknown.

Regardless of your view on species delimitation, there is no doubt that accurate delimitation is fundamental for conservation. Species are the unit recognized under the Endangered Species Act. Does that mean we should err on the side of delimiting more species? Or would this dilute conservation efforts?

Lightening Talks

Gustavo Bravo: Higher plumage brightness is associated with exposed habitats in dry regions in antbirds.

Laurel Yohe: Molecular evolution of the Trpc2 gene can predict olfactory morphology in bats.

Paul Hime: A single species hypothesis is rejected for the Hellbender, whose spatial patterns of gene flow and genetic diversity are non-random.

Laura Lagomarsino: Neotropical bellflowers show repeated evolution of bat and hummingbird pollination, but floral traits show differences in evolutionary mode.

Clare Brown: Long-distance migration has evolved multiple times in swallows (Hirundinidae) from an intermediate migrating ancestor.

From the Twittersphere

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