The state of debates at the 2018 Society for Systematic Biologists meeting

Posted on 27 Sep, 2017 by Rob Denton

This is a guest post from Ohio State PhD Candidate Megan Smith
On June 1-4, 2018, the Society for Systematic Biologists will host its third annual stand-alone meeting. The meeting will be held in Columbus, OH and will include workshops, lightning talks, and debates. The planning committee is hard at work on the schedule, and we’re interested in your input!

The aim of the debates is to discuss ideas and issues that are central to the field of systematic biology. In past meetings, debaters have presented a short introduction to the topic before engaging the audience and other discussants in the topic. If all goes well, audience members will talk as much as the debaters and moderators, and the discussion will push itself forward with little need for the pre-determined questions developed by the moderator. We hope that the debates will be engaging for graduate students, postdocs, and faculty alike, and a big part of designing discussions that will engage all levels of professionals is getting input from as many of you as possible about the topics that interest you.
These topics can be wide-ranging and could focus on both theoretical and empirical issues. For example, you might think about problems that you run into when using next-generation sequence data (or other data) to answer questions that interest you. Are you at a loss when you try to decide on a method to answer a particular question? In what ways are the methods falling short of the data, or vice-versa?
Last year’s four debates covered a wide-array of topics, varying in their focus on theoretical and practical issues. Scott Edwards and Gavin Naylor kicked off the debates by delving into the theory behind gene tree variation, and Mark Holder and Rachel Schwartz wrapped things up with a more applied question: how do I deal with my missing data? In between, Emily Jane McTavish and Matt Hahn argued about when we should use gene trees and when we should use species trees, and Frank Burbrink and Robb Brumfield discussed the ever-present question: what are we actually delimiting when we use ‘species delimitation’ methods?
This year, we hope to come up with just as wide an array of questions, and we hope that you’ll help us organize debates that will make you want to stand up, grab the mic, and get involved (which is highly encouraged)!
If you have ideas, please email them to one of the meeting organizers listed here or comment below. We can’t wait for another productive meeting!
 
Megan Smith (megansmth67@gmail.com)
Bryan Carstens (carstens.12@osu.edu)
Laura Kubatko (lkubatko@stat.osu.edu)
Marymegan Daly (daly.66@osu.edu)

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We have the technology. Is sequencing getting better, smaller, faster?

Posted on 21 Sep, 2017 by Kelle Freel

Okay, I know some version of the phrase “recent developments in rapid and affordable sequencing have made blah blah blah possible…” is something you’ve probably read 10,000 times. However, third-generation sequencing platforms have turned out to be pretty darn astounding. The leaders in this area include Pacific Biosciences (aka PacBio) as well as Oxford Nanopore Technologies (think MinION). Multiple studies have recently been making the most of the portable technology provided by Oxford Nanopore, and have used the MinION to analyze reptiles in the Ecuadorian Chocó rainforest, Arabidopsis species in the Croesor Valley in Wales, and microbes from the McMurdo Dry Valleys in Antarctica.
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Posted in bioinformatics, evolution, fieldwork, genomics, methods, next generation sequencing | Tagged , , , | 1 Comment

DNA sequence data shows that this "living fossil" isn't so fossilized after all

Posted on 19 Sep, 2017 by Jeremy Yoder

A nautilus, very much alive and not replaced by mineral accretions at all, thank you. (Flickr: muzina_shanghai)


Living fossils are a tricky concept for evolutionary biology. In principle it seems simple: living organisms that closely resemble creatures seen in the fossil record going back millions of years. Usually they’re a single representative of a fossil record containing a multitude of diverse close relatives — survivors from a lost clade — and rare, or living in habitats that humans can’t easily access. As a consequence, living fossils’ shared ancestry with other living species goes back deep into the history of life, and they’re often treated as examples of “primitive” forms. The term has been applied to species including the coelacanth, dawn redwoods, ginkgo trees, and hoatzin.
However, as molecular ecologists well know, two organisms may look identical in terms of morphology, especially features like shells and skeletons that fossilize reliably, and still be quite different in ways less obvious to the human eye. Color or pheromones or behavior may change without leaving any fossil traces; and every living thing is locked in an ongoing coevolutionary race against parasites and pathogens, which necessitates rapid evolution at the molecular level. We can’t find evidence of these changes in fossils (well, except for relatively very recent ones), but we can see it in DNA sequence data from putative living fossils.
That’s the premise of a paper out ahead of print in Molecular Ecology, which reports the first substantial, genome-wide population genetic dataset for nautiluses. Nautiluses are cephalopod mollusks, most closely related to octopuses, with beautiful spiral shells. Though there are five recognized species in two genera, they are collectively considered living fossils, as the fossil record includes species from at least five other genera, and all of them are different enough from other cephalopods to rate placement in a separate suborder, the Nautiloidea. David Combosh, Sarah Lemer, and colleagues at Harvard, the University of Guam, and the University of Washington collected genome-wide SNP data from 140 samples of all five species using the ddRADseq protocol, and used it to take the first good look at nautilus diversity.
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Habitat-matching dispersal facilitates local adaptation

Posted on 15 Sep, 2017 by Reid Brennan

Migration disrupts local adaptation. At least, this is the first reaction I have when I consider these two processes. In fact, my initial thought is almost always: how strong does selection have to be to overcome gene flow? Gene flow can work to diminish adaptation by swamping out locally adapted alleles and homogenizing populations. Depending on the level of gene flow, selection may have to be quite strong to prevent the swamping of adaptive alleles. This line of thinking is, of course, too simplistic (For a review of gene flow and local adaptation, see Tigano and Friesen 2016).
First, gene flow can provide a source of adaptive genetic variation, known as adaptive introgression; think Heliconius butterflies. Secondly, migration and gene flow aren’t necessarily random. That is, individuals may preferentially migrate to habitats where their fitness is maximized. This can lead to adaptation instead of inhibiting it. This latter point is one I think is commonly overlooked and goes by names including habitat-matching dispersal, phenotypic sorting, matching habitat choice, directed movement, phenotype-dependent dispersal, and others (See Edelaar et al., 2008 for a good overview of the topic.). Habitat-matching dispersal can work to facilitate rather than hinder adaptation and is has a very different effect on adaptation than random dispersal.
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Current geography has little to say about gene flow during divergence

Posted on 13 Sep, 2017 by Ethan Linck

The terms we use to describe the geography of speciation are deceptively simple. Mention allopatry, parapatry, or sympatry, and most biologists will have a clear picture of the underlying conceptual model of range limits (and probably some strong opinions about their relative frequency). Yet from a genetic perspective, these definitions can often obscure more than they clarify. For example, it’s hard to know what exactly allopatry means in highly vagile species like seabirds. Sure, coastal populations in western and eastern Pacific might appear discrete on a map, but if it’s a relatively easy trip between the two areas for volant migrants, are they actually diverging in isolation? A population genetic approach to the same terms therefore rely on relative rates of gene flow, from none (allopatry) to a lot (sympatry). But as speciation is an inherently geographic process, this is also an imperfect solution. Whether these alternate definitions can cross predict has largely remained unclear.
Penalba et al’s new preprint addresses this question by looking at whether the geographic arrangement of contemporary bird species ranges predicts relative gene flow between species pairs during divergence. Using “suture zones” where eight Melaphagoid species pairs meet at biogeographic barriers across Northern Australia and New Guinea, the study collected SNP data and sequenced the mitochondrial gene ND2 to assess population structure, relative divergence, probability of migration throughout the speciation process, and the fit of various models of parapatric speciation, e.g. whether measures of genetic distance shows a linear or nonlinear increase. The authors also modeled changing species distributions through time with maximum entropy and environmental layers from the present, mid-Holocene, and last glacial maximum.

Figure 1 from Penalba et al. (2017).


If you’re familiar with the comparative phylogeography literature, their basic results are unsurprising: taxa varied widely in their divergence history, and their contemporary distributions did little to predict rates of gene flow during divergence. Among the many possible explanations for this discordance, an important one is the inherent lability of species ranges through time, even though they can appear as fixed, static entities on human timescales. (Losos and Glor’s 2003 paper provides a nice discussion of range dynamism over geologic time in a phylogenetic context.) Penalba et al.’s species distribution modeling provides support for this hypothesis by identifying distance and total range connectivity throughout all time periods as a better predictor of gene flow during speciation than current geography alone.  
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Of Of Mice and Men: High school English class lives on in scientific paper titles

Posted on 11 Sep, 2017 by Jeremy Yoder

“The reviewers hated the title” (C.E. Brock illustration for Pride and Prejudice, 1895, via Pemberly.com)


Writing titles for scientific papers is hard. The title is the one element of the paper everyone reads if they so much as skim a journal’s table of contents e-mail. These days, you also want something that’ll fit in a tweet with room for the DOI link. So you want something informative, but also memorable — and ideally something that prompts people to click the link. That certain je ne sais quoi.
But also you don’t want to look unprofessional. You can’t go around calling your study organism cute even if this is quantifiably the case; you can’t reference risqué cocktail names or clichés about penises or especially trashy fantasy movies. What can you use to be more fun than just reporting your results, but, like, in the safest possible way?
One popular answer, based on a highly unsystematic survey of PubMed, is to use the title of a book that you probably read in high school English class. There are lots of excuses (no, really, as many as 1,061) to title a paper with Of Mice and Men in biomedical research. (And, um, in blogging about said research.) Following up on this Twitter exchange, I went to PubMed with some familiar old titles to see if any other members of the junior-year canon are more popular than John Steinbeck’s sad little tale.
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Friday action item: Figure out how to support a grad student without DACA

Posted on 8 Sep, 2017 by Jeremy Yoder

(Flickr: Ana Paula Hirma)


On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!
We haven’t done an Action Item in a while, but this week’s seen a decision from the Trump Administration that hits quite close to home, here in southern California: the announced end to DACA, the Obama administration policy that provides limited legal status for people who came to the U.S. as children without immigration documentation. Wednesday morning, my California State University colleague Terry McGlynn posed a question on Twitter that seemed, to me, pretty simple:

It turns out that this is not an easy question to answer. As CSU chancellor Timothy White explained in an interview with NPR the same day, California and the CSU system provide tuition support that doesn’t require legal status, and which will remain in place if DACA goes away six months from now, as it will if Congress doesn’t act. But going to graduate school isn’t, of course, only a question of tuition. In biology, we expect to be able to provide stipend support for grad students, usually through teaching and research assistantships as well as external fellowships. That makes graduate students employees, in a limited sense — and that may severely limit what biology departments and principal investigators can do to support students who lack documentation, even with the resources California provides.
Here at CSU Northridge, admission to the graduate program does not involve any inquiry into immigration status. But every employee provides evidence of eligibility to work in the U.S., whether as a citizen or as a documented immigrant with a work permit. According to a guide (PDF) available from the CSUN Dream Initiative website, it’s potentially possible to pay student researchers (including, I think, graduate RAs) with funding from some specific sources; but not with money from university funds, or from a governmental source like NSF. As the guide says under “Research”:

Sometimes undocumented AB 540 students [who have limited resident status in California without immigration documentation] are paid for this type of work in the form of a “stipend.” A stipend is a sum of money allotted on a regular basis, such as a salary for services rendered or an allowance. Undocumented AB 540 students may be eligible for stipends if the source of funding is tax-exempt. If the stipend comes directly from a public college or university’s funds, undocumented AB 540 students are not eligible. Remember, government funds are not available to undocumented AB 540 students.

CSUN’s FAQ on the DACA repeal explicitly calls out this issue — DACA recipients have had work permits that may or may not continue to be valid after the end of the program.
If you have current graduate students with DACA status, you’re probably already thinking about exactly these issues. If you don’t, now is as good a time as any to figure out what you’d do if you found out that a promising applicant to your lab might not have a work permit by the start of the next school year. Check to find out whether your campus has an equivalent to the Dream Initiative, or publications or resources provided in the wake of Tuesday’s announcement. If you can’t find those resources, maybe it’s time to get together with some colleagues to tell your administration that this is a priority. As for me, with CSUN’s and California’s resources in place — I’ll be thinking about who I can hire with any given funding source as I prioritize grant proposals for this semester.

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In the aftermath of fire, bluebird species boundaries may blur

Posted on 5 Sep, 2017 by Jeremy Yoder

Mountain bluebirds and western bluebirds, illustrated in Birds of the Pacific Coast (Flickr: Biodiversity Heritage Library)


One of the most clear-cut reasons that species evolve to fill different ecological niches is competition. Two otherwise similar species that use the same resources experience strong selection favoring the use of less-similar resources, if they have the option. The classic example is Darwin’s finches, which evolved different beaks to better use different seeds, and have radiated (or are radiating) into an array of different species as a result.
However, nothing is simple in evolutionary biology. Competition also brings closely related species into contact, as they jostle for access to the resources over which they’re competing. A new paper in the American Naturalist shows that, for two North American songbird species, this kind of interaction may provide an opportunity for interbreeding where none would otherwise exist — competition creating, in this case, a reduction in the genetic isolation between those two birds.
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GeOMe aims to organize the "what, where, and when" of molecular ecology

Posted on 31 Aug, 2017 by Jeremy Yoder

The GeOMe query form (Deck et al. 2017, Fig. ??)


This post is a guest contribution by Michelle R. Gaither, Eric Crandall, and Cynthia Riginos, collaborators on the GeOMe project.
Many molecular ecologists spend weeks or even months in the field each year collecting samples for molecular analysis. Even before each sample reaches a molecular lab, it is characterized by important information that describes the what, where and when for that sample, that is the collection metadata. While granting agencies and publishers enforce data accessibility and open access requirements for genetic data, and there are huge public repositories dedicated to archiving these data, these repositories do not require or provide an easy way to archive the vital metadata that accompanies each DNA sequence (or file of massively parallel sequences) or genotype. Basic information such as latitude and longitude, date of capture, and habitat are often lost or attached in an ad hoc manner, such as supplementary files held by the publisher or deposited in a repository such as Dryad.
GeOMe, the Genomic Observatories Metadatabase, fills this “metadata gap” and makes archiving sample metadata easy. GeOMe links collection metadata to publically available genetic data in the NCBI Sequence Read Archive (SRA), providing a user-friendly search portal of contextual information that until now has been missing from widely shared databases. We are not re-inventing the wheel with respect to storage of the genetic data and these data remain BLAST-able. The GeOMe database thus enables a “genomic observatory” model of data collection, wherein individual researchers and institutions can easily share and reuse data in a global pool.
With GeOMe, researchers are able to find and access genetic data collected at specific times and places anywhere in the world, enabling them to ask big questions about the structure and sustainability of life on the planet. Future researchers might investigate how the inhabitants of a specific altitude throughout the world have shifted as our planet’s climate has changed, for example, or assess the stability of microbial communities facing increasingly acidic marine environments. Publically archiving these metadata is essential to ensure scientific reproducibility and synthesis as well to maximize potential re-use of sequence data as new techniques develop. GeOMe is a bottom-up effort with buy-in from over 50 laboratories. The database is growing and adding new capacity while also setting the industry standard for metadata publication.
The accompanying videos give a brief overview to GeOMe’s functionality. A full description of GeOMe can be found in PLOS Biology.
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Missing symbionts: do some animals lack resident gut microbiomes?

Posted on 28 Aug, 2017 by Elin Videvall

It seems like the field of “gut microbiomics” is having major breakthroughs almost every month these days. It’s very exciting to follow what is being discovered and gut microbes have now been linked with an array of important host traits, such as health, disease resistance, digestion, behavior, and longevity. The more one reads about gut bacteria and other microbes, the more convinced one gets of their importance for animals as hosts.
However, evidence are starting to emerge as to question whether all animals truly harbor gut microbiomes. Tobin Hammer and colleagues recently published a paper in PNAS where they laid out the case for the missing gut microbiomes of caterpillars. Hammer et al. (2017) sequenced guts and feces from 124 leaf-eating caterpillar species of 15 families and found unusually low densities of bacteria and fungal microbes present in their guts. Most bacteria present were highly similar to the ones present on their food (plant leaves), and therefore only transient and not residing in the caterpillar gut.

Figure 1 from Hammer et al. Comparisons of bacterial density, relative abundance of plant DNA, and intraspecific variability between caterpillars and other animals expected to host functional microbiomes. Please see the paper for detailed description. 

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