The final nail in the coffin of Patagonian megafaunal extinctions

Are our ancestors responsible for Late Pleistocene megafaunal extinctions? Were the Ice Age giants doomed to extinction because they couldn’t adapt or is it human fault that there is no woolly rhino, giant deer and cave bear today?

Cueva del Milodón (Mylodon Cave) in Patagonia. Source: WikimediaCommons

Cueva del Milodón (Mylodon Cave) in Patagonia. Source: WikimediaCommons

A new contribution to the neverending debate came from an international collaboration led by Alan Cooper. Results of the study were published in Scientific Advances with Jessica Metcalf as the first author.

Following the success of the previous study on Holarctic megafaunal extinctions, which was published in Science last year, Cooper continued with the approach of generating time series’ of radiocarbon dates to find patterns shared by multiple species, but this time focusing on Southern Hemisphere.

It’s about the synergy

Already in 2010, Anthony D. Barnosky and Emily Lindsey used a small set of radiocarbon dates to show that “a synergy of human impacts and rapid climate change” was probably the final nail in the coffin for the Neotropical Pleistocene megafauna.

However, analyzing 93 dates spread across 15 genera and different locations can’t possibly give enough resolution to resolve South American megafaunal extinctions. Therefore, Barnosky & Lindsey (2010) finished the abstract introducing the studies to come: “These results highlight the need for future intensive dating efforts on South American megafauna and archaeological remains.”

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Introducing “How Molecular Ecologists Work”


I’ve always been fascinated by how people get all their work done. Scientists in particular make for a great study of working habits for two main reasons: they typically juggle a variety of tasks and they largely determine their own work schedules. This results in a huge variety of work habits: night owls, early birds, multitaskers, focus-taskers, and on and on. This might be particularly true for a scientist who self-identifies as a “molecular ecologist”, someone who presumably combine aspects of fieldwork, the generation of molecular data, informatics/analysis, and communication.

North_Carolina_biologist_Gabrielle_Graeter_makes_field_notes_(8191316356)_2I’ve been a long-time reader of Lifehacker’s “How I Work” series, an interview format in which folks from various organizations detail the secrets behind their work habits, allowing the reader to get a peek into the habits of someone whose work they admire. As I’ve read more and more “How I Work” articles, I began to think that this format would work well for scientists. So, we are bringing you a series of interviews that showcase how scientists get stuff done. We’re calling it “How Molecular Ecologists Work”.

The first installment of this series contains interviews with eight diverse scientists: from postdocs to fresh assistant professors to established faculty. I’ll be rolling these interviews out once a week until throughout July and August, plus maybe some bonus interviews that will go un-announced (!).

Schedule for How Molecular Ecologists Work

7/13 – Brant Faircloth, Assistant Professor (Louisiana State University)

7/20 – J. Chris Pires, Associate Professor (University of Missouri)

7/27 – Tracy Heath, Assistant Professor (Iowa State University)

8/3 – Aaron Shafer, Assistant Professor (Trent University)

8/10 – David Toews, Banting Postdoctoral Fellow (Cornell University)

8/17 – Sarah Hird, Chancellor’s Postdoctoral Fellow (UC-Davis) & Assistant Professor (University of Connecticut)

8/24 – Katerina Guschanski, Assistant Professor (Uppsala University)

8/31 – John McCormack, Assistant Professor (Occidental College)

All of these talented people have been more than gracious in conducting these interviews and the entire Molecular Ecologist team extends a huge “thank you” their way. I think you’ll really enjoy what they have to say.

If there is someone in your field who you admire and are curious how they get their work done, send me your suggestions for the next installment!

I know there are some Dennis Nedrys out there.

I know there are some Dennis Nedrys out there.

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Making Maps in R, volume 2: ggplots


The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the results of all that analysis. As molecular ecologists, we’re also interested in placing our analyses of genetic data, trait measurements, and evolutionary history into geographic context. For that, R has packages to make maps and estimate models of species distributions.

The map-making capabilities of R extend beyond what’s covered in our last post on that subject — in particular, there’s a suite of functions that bring geographic illustrations into the powerful ggplot2 graphics package, and provide access to publicly available geographic data that can produce professional figures for your next paper or presentation. Here’s a look at a few of those functions.

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Highlights from the 2016 Mammal Meeting

The American Society of Mammalogists’ annual meeting just wrapped up in beautiful Minneapolis, Minnesota. There were so many great talks and poster presentations that unfortunately I’m not able to highlight them all, but here are a few of my favorites!

Empirical mammal studies:

Ugly bat.

Having lost the ability to detect pheromones, the bat must rely on his good looks to attract a mate.

Laurel R. Yohe and Liliana M. Dávalos (Stony Brook): “Is vomeronasal system evolution in bats a one-way street?”

Laurel was the winner of the Anna M. Jackson award, and gave one of the first talks during the Day 1 plenary session. Her work on pheromone detection in bats combined phylogenetics, gene function analyses, and CT scanning, and revealed that bats have experienced multiple independent losses of the Vomeronasal organ.

Jeremy C. Crawford (UC Berkeley): “Elucidating the evolutionary consequences of mammalian sociality”

Jeremy also presented during the Day 1 plenary session as winner of the Elmer C. Birney Award. His comparative work looked at three systems with social and solitary sister species, and found that social species have increased rates of evolution for several immune system genes. Pathogen exposure and disease susceptibility appear to be a cost of being social.

Donovan J. Jackson and Joseph A. Cook (University of New Mexico): “Phylogeographic analyses of the meadow vole (Microtus pennsylvanicus), a widespread North American mammal” Continue reading

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Who’s really riding the subway with you? Characterization of the microbial communities on Boston transport

(Figure modified from Hsu et al., 2016, Boston transport map and wikicommons image of Boston)

Understanding the microbes around us is an important challenge to take on. There have been articles covering changes in microbial communities among rural and more urbanized environments and there’s a whole blog dedicated to microbes and the built environment. An interesting model system for studying the relationship between microbes that inhabit the built environment and humans include transit systems, some of the largest of which shuttle around more than 1 million passengers daily. Clarifying microbial community dynamics in transportation systems has implications related to human health and disease.

Figure 1. Hsu et al., 2016.

Figure 1. Hsu et al., 2016.

Sometimes progress related to understanding microbes in the built environment is accompanied by two steps back. Last year, a study on New York subways (which are part of the largest public transport system in the US) stated that the NY subway system harbored the bugs responsible for the plague (Yersinia pestis) and anthrax (Bacillus anthracis) (Afshinekoo et al., 2015). However, not long after the publication of this study, other authors demonstrated that the data was not actually properly analyzed (Ackelsberg et al., 2015).

Figure 2. Hsu et al., 2016.

Figure 2. Hsu et al., 2016.

Considering how integral public transport is to everyday life for so many people, it’s a bit surprising that there are very few studies focused on understanding the microbes associated with these systems. Just this week, the first attempt at obtaining a comprehensive microbial metagenomic profile was published by Hsu and colleagues this week.

Figure 3. Hsu et al., 2016.

Figure 3. Hsu et al., 2016.

Researchers sampled everything from seats to hanging grips across three subway lines, as well as the touchscreens of the ticketing machines at five subway stations. They obtained a total of 73 samples and using a combination of 16S amplicon and metagenomic sequencing allowed for the characterization of microbial community composition. They found that the type of surface sampled was more influential on taxonomic composition, in comparison to the material itself, or differences in train line or geographic location. You can take a sigh of relief, not many antibiotic resistance genes or virulence factors were identified. The authors suggest that this study as well as future similar attempts might indeed improve future transit system design.

Figure 4. Hsu et al., 2016.

Figure 4. Hsu et al., 2016.

Touchscreen microbial communities were more similar to other touchscreen samples, and train line didn’t seem to really influence community structure. The authors reported that location of ticketing machines (either indoor / outdoor or underground) did have some influence on community diversity, and specifically, indoor or outdoor exposure markedly influences its composition. Essentially, microbial communities in subways originate from human skin and the bacterial side of things was mainly made up of members from the Firmicutes, Proteobacteria, and Actinobacteria while the yeast Malassezia globosa, as well as Propionibacteriam phages accounted for the majority of the nonbacterial representatives. Interestingly, this study demonstrated that with the use of the appropriate methods, no pathogens were detected.

Figure 5. Hsu et al., 2016.

Figure 5. Hsu et al., 2016.

With the mountains of sequence data available, it’s essential that methods developed for analysis are able to accurately identify the presence of pathogens. This is essential in not only places like hospitals, but also on fresh produce and in public transportation systems. Previous instances where data was incorrectly assessed highlight the danger of not appropriately utilizing available methods for data analysis.


Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. Tiffany Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M. Hartmann, Afrah Shafquat, CaseyDuLong, Catherine Baranowski, Dirk Gevers, Jessica L. Green, Xochitl C. Morgan, John D. Spengler, and Curtis Huttenhower. 

Avoiding Pandemic Fears in the Subway and Conquering the Platypus. A. Gonzalez, Y. Vázquez-Baeza, J. B. Pettengill, A. Ottesen, D. McDonald, and R. Knight. 

Lack of Evidence for Plague or Anthrax on the New York City Subway. Joel Ackelsberg, Jennifer Rakeman, Scott Hughes, Jeannine Petersen, Paul Mead, Martin Schriefer, Luke Kingry, Alex Hoffmaster, Jay E. Gee. DOI: 10.1016/j.cels.2015.07.008

Modern methods for delineating metagenomic complexity. Afshinnekoo, Ebrahim, et al. Cell systems 1.1 (2015): 6-7. DOI: 10.1016/j.cels.2015.07.007

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Live from #Evol2016 — Tuesday highlights

The Molecular Ecologist team was all over this year’s Evolution meeting in Austin, Texas.

During our coverage of the meeting, we’ve been previewing presentations we’re excited about and recapping the highlights of each day here on the blog. As the main conference concluded on Tuesday evening, this is our final post in that format. However, you can still find all of the TME contributors on Twitter using the sidebar on the right or compiled in a handy Twitter list here. Additional meeting news and older tweets continue to pile up under the hashtag #Evol2016.

We’ll see everyone next year in the Rose City!


Among the many perks of holding the Evolution Meetings in Austin, this TME contributor was particularly excited to make the pilgrimage to the Texas Chili Parlour bar for Mad Dog Margaritas.

Highlights from Tuesday, June 21


Filepe Barreto “Functional and genomic consequences of mitonuclear coevolution during population divergence in a marine copepod” rRNA and tRNAs interacting with the mitochondrial genome (which ~20% divergent between populations) is under positive selection.

Cathy Newman and Chris Austin “Using sequence capture of UCEs for intraspecific phylogenetics and species delimitation of a large-genome salamander, Plethodon serratus” UCE loci worked well for phylogeography and species delimitation in salamanders despite huge ~20Gb genome size. Data suggested seven isolated populations are each different species.

John McCormack, Eugenia Zarza, Brant Faircloth, Whitney Tsai, Robert Bryson, John Klicka “Testing for hidden histories of gene flow in highland birds using genomic markers” Speciation with gene flow may be the norm rather than the exception.


Brian Moore; Sebastian Hoehna; Michael May; Bruce Rannala; John Huelsenbeck (Tuesday 21 June MR3): Bayesian analysis of macroevolutionary mixtures (BAMM): A critical appraisal Brian Moore and colleagues offered a solid, simulation-based appraisal of Bayesian

Analysis of Macroevolutionary Mixtures (a program from the Rabosky lab). John McCormack; Eugenia Zarza; Brant Faircloth; Whitney Tsai; Robert Bryson; John Klicka (Tuesday 21 June MR5): Testing for hidden histories of gene flow in highland birds using genomic markers John talked about his ongoing work with Aphelocoma jays in Mexico, the prevalence and driveres of gene tree discordance in the system, which lays the basis for future comparative phylogeographic studies in this region.

Julia Clarke*; Chad Eliason; Leah Hudson; Hector Garza; Taylor Watts (Tuesday 21 June MR6) Exceptional preservation and the fossil record of tetrapod integument Julia talked about her lab’s nice work on evolution of integuments in tetrapods, differences in the preservation potential of hair vs. feathers in the fossil record, and how taphonomy may have influenced our views of hair and feather evolution.


Justin Havird: Expression, selection, and co-evolution in mitonuclear genes — A tide of research on mitonuclear interactions continues to swell, but that doesn’t mean there aren’t a lot of big mysteries left. This talk started to approach one of them: mitochondrial genes involved in mitonuclear interactions are expressed much higher than nuclear genes. This discrepancy might have something to do with differential rates of transcription and translation, meaning mitochondria have to be prepared with proteins since they operate at a slower pace.

Geoffrey Hill: Mitonuclear Ecology — Hill brought an end to the cytonuclear interactions symposium with a review of this hypotheses relating mitonuclear compatibility and sexual selection. Buoyed by the recent discovery of the genes that control red pigmentation in bird feathers, Hill explained that the pressures on females to insure their offsprings have optimally-matched mitotypes might play a big role in male phenotypes.


Brant Faircloth: “Able was I ere I saw assembly errors.” Faircloth’s talk focused on how the combined effects of sequencing and assembly errors influence downstream phylogenetic analysis. Using simulations, he showed sequencing error could lead to concerning numbers of incorrect bases in the final assemblies of three popular programs — trinity, abyss, and velvet. (If you’re looking to make a choice based on this metric, abyss arguably performed the best). However, even the assemblies with the highest levels of error still resulted in phylogenetic trees with identical topology and similar branch lengths as the “error-free” dataset he used as a comparison.  My take away: we should be worried enough to start considering sequencing and assembly error more seriously, but not that worried, as for whatever reason it doesn’t seem to influence the overall conclusions of phylogenomics studies.


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Live from #Evol2016 – highlights from Monday and what to see on Tuesday June 21st


The Molecular Ecologist team is all over this year’s Evolution meeting in Austin, Texas.

As part of our coverage of the meeting, we’ve been previewing presentations we’re excited about and recapping the highlights of each day here on the blog.

You can find all of the TME contributors on Twitter using the sidebar on the right or compiled in a handy Twitter list here. Follow along with all meeting news using the hashtag #Evol2016.

Highlights from Monday, June 2oth


Lauren Schiebelhut, Brian Gaylord, Rick Grosberg, Laura Jurgens, Michael Dawson “Genetic and ecological recovery from a massive invertebrate die-off along the central coast of California” — Invertebrate species with the longest larval dispersal period had the greatest recovery and the least genetic population subdivision.

Colin Olito “The evolution of spawning strategies in broadcast spawners” — High fertilization success results in low per gamete returns Large and small males are under different selection regimes.


Kara Jones: One is the loneliest number … hypothesis testing in salamanders. The talk was pretty cool, but the plots of individuals with admixture represented as little squares was so cool, I will shamelessly steal this idea.

Christopher Eckert: Why range limits? The best line of the day: There’s a PhD thesis every 10 cm in California. Oh, California! But, it appears that metapopulations are more important in range limits than niche models.

Rushworth: Maintenance of asexual reproduction in complex natural environments. Sexual, asexual and hybrid asexuals. Really cool system, but one of the most important lines uttered in a talk: we need to understand more about asexual reproduction in natural populations.


Joel McGlothlin: Physiological resistance of garter snakes to toxic prey involves six genes in the voltage-gated sodium channel family. Garter snakes tolerate toxins produced by the newts they prey on thanks, in part, to a gene variant that pre-dates the existence of snakes — great run-through of some very cool evolutionary biology, which is already published:

Steven Franks: Selection causes rapid genome-wide evolution in Brassica rapa following a climatic change — a genome-informed update of a paper I’ve cited easily a dozen times: pnas.0608379104


What our contributors are excited about for Tuesday, June 21st


Justin Havird and Daniel Sloan “Expression, selection, and co-evolution in mitonuclear genes” (Ballroom A, 9:45) Three topics near and dear to my heart.

Jordan Satler and Bryan Carstens “Testing for co-diversification in an ecological community: an example from the Sarracenia alata pitcher plant system” (MR4 10:00) I’m excited to see a friend and colleague talk about this charismatic carnivorous plant.

Katherine Liu “What can we learn from experimental evolution?” (MR9AB 11:30) Very cool things I’m sure! I’m hoping this talk will point to the strengths of experimental evolution and caveats to keep in mind.


Louis-Marie Bobay: The prokaryotic species problem. (10:15am, 8, Species delimitation) I’m interested to see their thoughts on this and how they plan to go about working with prokaryotes.

Matt Rutter: Lessons from 200,000 Arabidopsis phenotypes: the power of unPAK. (9:00am, 6B, Mutation)Interested to see the power of getting undergrads involved in research and collecting data.


Nancy Moran: Harmony vs. discord in relationships of heritable symbionts and their hosts (9:00, Ballroom A, SSE Symposium: Co-evolving genomes: Cooperation and conflict in cytonuclear interactions)

Arthur Weis: Evolutionary Rescue through Assisted Gene Flow: Phenology Makes it Complicated (10:45, MR8, Conservation Biology)

Joel Sachs: Metapopulation dominance and genomic-island acquisition of Bradyrhizobium with superior catabolic capabilities (11:45, Ballroom C, Coevolution 3)

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