A unifying perspective on pathogen specificity

Linking microevolutionary processes to macroevolutionary patterns

I have always been interested coevolutionary interactions, particularly host-parasite interactions. I have often wondered if the local patterns of interaction between host and parasite (e.g. local adaptation) can scale up and lead to patterns of host specificity. Having a thorough understanding of these selective forces may help us better understand the conditions for disease emergence and perhaps disease virulence evolution.

WORDLE_Antonovics_etal_2013

Population genetics is concerned with the processes that generate evolutionary change within species and populations. A major question in evolutionary biology is whether these same processes ultimately generate patterns of diversity at higher organizational levels. While interactions between species such as hosts and their parasites (or plants and pollinators, herbivores and plants) have long been implicated as a means of generating patterns of diversification (Ehrlich and Raven, 1964,Thompson, 1994, 2005), the process by which microevolutionary forces generate macroevolutionary patterns is not well understood for coevolutionary systems.

Highly specific interactions between pairs of species can result in population level patterns. Both theoretical and empirical studies show that genetic specificity combined with specific gene flow patterns lead to parasites tracking of local host populations (Dybdahl and Storfer, 2003,Gandon et al., 1996,Gandon and Michalakis, 2002,Kaltz and Shykoff, 1998). In a mutualism between plant and pollinator, the seeming match between the length of a flower corolla and bill may be the result of strong selective pressure. Although we have many good examples of the processes that work at the population level, we have little evidence as to how those processes generate patterns of diversity among interacting species (Thompson, 2005). At the macroevolutionary scale, the processes leading to the observed patterns of host specificity have remained unclear.

The authors of a recent perspective piece in Evolution have addressed this exact issue by asking:

“Can microevolutionary adaptive processes acting at the within-species level explain macroevolutionary patterns across host and pathogen taxa?” (Antonovics et al., 2013)

What processes can explain why most pathogens cannot infect all encountered hosts ?

Continue reading

Friday Coffee Break: snail coauthors, rejection letters, Swiss cheese plants, and more

coffee_at_origin_roasting_IMG_0172-784070Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

Which Coauthor are you? Sadly during the winter due to snowboarding constraints CJ thinks she is the snail.

Are you looking for an academic job like Jeremy (@JBYoder) and Devin (@devindrown)? Be sure to check out the rejection letters here when you are feeling glum.

More mammal news from Sarah (@sarahmhird) this week: The news on NIH research Chimps being retired and moved to sanctuaries made her pretty happy.

Via Amy: Cornell Launches Archive of 150,000 Bird Calls and Animal Sounds, with recordings going back to 1929.

The Swiss Cheese plant, one of CJ’s favorite tropical plants, is in the news. Can you have only one favorite tropical plant…laughable? Why not check what Christopher Muir has to say over at the American Naturalist or the BBC.

Mutts digest carbs?!?! Oh yeah, that makes perfect sense to Sarah (@sarahmhird). Why not check out what researchers propose as a pathway from wild wolf ancestors to domesticated dogs.

Did your office succumb to the seasonal flu this year? CDC reports had some scary outlooks this winter. Fear not, researchers have ended the moratorium on influenza H5N1 research have resumed work on these important strains.

Friend of the blog Chris Smith is recruiting “citizen scientists” for Joshua tree work. Hear what he has to say over at KNPR.

Of Salty Bahamian Ponds and Adaptive Radiation

A Mexican pupfish, Cyprinodon veronicae

One of the central hypotheses about how the diversity of life is generated is known as “adaptive radiation“. This term, popularized by G.G. Simpson in the mid 20th century, encapsulates an idea that is relatively easy to grasp: that the spectacular arrays of morphological and species diversity that we observe in the world are often the result of great bursts of speciation and morphological change. These bursts occur because a single species colonizes a new area, acquires a new adaptation, or suddenly escapes its competitors or natural enemies (possibly by their extinction). This opens up a new universe of possible lifestyles that evolution then drives that species to take up by rapid diversification. Think of the Hawaiian honeycreepers or Darwin’s finches.

The idea holds great sway because it is simple and powerful, but testing it empirically has proven very difficult. This is in part because the actual mechanisms underlying speciation and morphological diversification are exceedingly complex, and in part because many of the groups of organisms which we suspect have adaptively radiated did so long ago, leaving much of the evidence of those mechanisms buried under millions of years of subsequent evolutionary change. A recent experiment by Martin and Wainwright (2013) attacks these issues by manipulating a nascent adaptive radiation of Cyprinodon pupfishes on the island of San Salvador, Bahamas.

Cyprinodon are small fishes that have a habit of becoming isolated in unexpected places. In the United States they are best known for tentatively clinging to life in tiny springs in deserts of the southwest, where they’ve been embroiled in conflicts between conservation and urban and industrial interests over water rights. Almost all of them are dietary generalists that tend to eat a lot of algae. Martin and Wainwright’s study focused on three species that occur in another such unexpectedly isolated locale, a pair of hypersaline lakes on the island of San Salvador, Bahamas.

Continue reading

Friday Coffee Break, barnacle sex, crab lice, and chimps

credit ilovecoffeebook.com

credit ilovecoffeebook.com

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

Amy was learning about Synesthesia this week over at the Neurocritic Blog. Do you taste shapes or hear in colors?

Noah (@NM_Reid) must be getting tired of winter and read up on Brazilian bikini waxes making crab lice an endangered species. Tom Houslay (@tomhouslay) asks via Twitter if we need protected areas or migration corridors setup. The Bug Girl (@bug_girl) has a different point of view that you should check out.

CJ says, who doesn’t love barnacle sex? Check out the lasted news that shocked scientists, well not CJ, over at Science NOW.

Do you have a diet of milk, meat, blood? Jeremy (@JBYoder) suggests you take a look at the Empirical Zeal blog to learn how the Maasai of Kenya can consume over 200% of the daily cholesterol intake yet remain relatively healthy.

How did they get here? A new study in PNAS shows ‘gene flow’ from India to Australia 4000 years ago. See the digested report here.

Sarah (@sarahmhird) is about fairness and chimps this week. Chimps may have a sense of fairness similar to humans. If you’re curious for yourself, on the BBC lab site, you can find out how your sense of “fair” relates to others with a morality test. The Lab UK site also has other tests and your results are used for scientific research.

Late breaking addition from CJ: Being Married Helps [MALE] Professors Get seo companies Ahead.

Averting the Approaching Apocalypse

This post is a guest contribution by Dr. Levi Morran, NIH postdoctoral fellow at Indiana University. Levi studies the role that both coevolutionary relationships and mating systems play in shaping evolutionary trajectories. His research using experimental coevolution to test the Red Queen hypothesis recently appeared in Science and was featured on NPR and the BBC.

electron micrograph of the aerobic soil bacterium Pseudomonas fluorescens(photo credit http://bacmap.wishartlab.com/organisms/500)

Electron micrograph of the aerobic soil bacterium Pseudomonas fluorescens
(credit BacMap)

I’ll begin by acknowledging that the title of this entry is probably a bit more dramatic than it needs to be. Nonetheless it’s pretty catchy isn’t it?

Given that the human population seems to have survived that whole 2012 Mayan calendar thing without incident, I know several of my friends (I won’t name names, but you know I love you) that would immediately think about zombies upon reading this title.  However, I am not particularly concerned about the extinction of the human race at the hands of zombies. For one thing, I need more evidence (or in fact any evidence whatsoever) before I buy the whole “zombies will rise up and end us all” fear. Further, Max Brooks (son of Mel Brooks) has given us a hilarious and potentially mildly effective guide to surviving the zombie apocalypse. Ultimately I am far more concerned about bacteria. To avoid inducing mass panic, I’m not talking about a terrified level of concern here, but certainly concerned enough to give it some thought.

Why bacteria? Well, the human population is currently in an evolutionary arms race with many of the bacterial species that infect us.  We continue to hurl scores of antibiotics at bacterial infections, imposing very strong natural selection, with little regard for the evolution of antibiotic resistance in those bacterial populations. Using current strategies in medicine, we are forced to administer greater doses of drugs or develop novel antibiotics to combat infections as the bacteria evolve greater levels of resistance (Levy and Marshall 2004, Martinez et al. 2007). This is a vicious cycle. I believe it is time to develop new strategies of managing our pathogens and treating infections. Thankfully there are many people that agree and are conducting ground-breaking research in this area, like Andrew Read’s group at Penn State University.

A paper by Quan-Guo Zhang and Angus Buckling (2012) takes an experimental evolution approach to begin addressing this issue empirically. In search of a different strategy for curbing the evolution of antibiotic resistance in their experimental populations of the bacterial species Pseudomons flourences, Zhang and Buckling treated their bacterial populations with either antibiotics, a bacteriophage or “phage” (a virus that attacks bacteria), or a combination of the antibiotic and phage. Zhang and Buckling predicted that the combination treatment might be more effective than either antibiotics or phage alone because the combination treatments should better reduce bacterial population sizes and limit their response to selection (Alisky et al. 1998, Chanishvili 2001, Comeau 2007). Additionally, bacterial mutations that confer resistance to antibiotics generally do not also confer resistance to phage, so evolution of resistance to the combination treatments would likely require at least two mutations, and thus require more time to evolve resistance than the other treatments (Chanishvili 2001, Kutateladze 2010). Continue reading

Friday Coffee Break, more news than a Giant Squid

Asian Palm Civet  (Wikimedia Commons)

Asian Palm Civet (Wikimedia Commons)

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

Just about everyone here found the news from the Discovery Channel about the video footage of the giant squid facinating.  If you haven’t seen it yet, check out the clip at the bottom, it is just so bad ass looking. CJ recommends the blog Species New to Science for some additional background.

Following up on Sarah’s awesome post on Women in Science, why not check out how folks at the Eigenfactor Project compiled raw data on gender bias in publications and made a beautiful visualization. Devin (@devindrown) thinks it is particularly cool how the authors figured out how to sex the authors in the large corpus that is JSTOR. Be sure to read the methods for the details.

Sarah (@sarahmhird) points out this excellent blog post form Dr. Bik on the Postdoc life which follows up on the fallout from the Forbes story about Professors having least stressful job.

Via Jeremy (@JBYoder) see how conservationists are using the DNA inside fly guts to census biodiversity from Ed Yong (@edyong209) over at the Not Exactly Rocket Science section of Phenomena.

THE most unbelievable title and figure Sarah’s (@sarahmhird) ever seen. Check out this apt named publication in PLoS Neglected Tropical Diseases. Curse words are not just for when you experiment goes awry anymore.

Apparently nothing is absolute anymore. A study in published in Nature cooled quantum gas below absolute zero. Amy didn’t know that it was possible, did you?  Don’t lag behind the times. Check it out now. (You can get the story over at Scientific American as well.)

CJ is all about visual animals today and the Tardigrade is no exception. Check out this one because his face is so darn cute.

Via Amy: A study in Europe finds that choosing your child’s name poorly may make him/her dumber and lonelier.  If you’re thinking about procreating, this might be topically relevant for you.

When extreme violence can’t be explained, is genetic analysis warranted? You can read the Nature editorial here.

Amy highlights this exciting news: JSTOR begins offering free yet limited access to its online academic seo company library. Very helpful for when you are outside your institution, or lack access generally.

Did you know this existed, 2012 in Science? Now you do thanks to Sarah (@sarahmhird).

And now, what you’ve been waiting for, the Giant Squid!

Self-confidence of women in science and a camel

Science kind of has a lady problem. While nearly equal numbers of males and females begin the path to a career in Science/Academia, more females drop out as they progress on the trajectory than men. This has been called a “leaky pipeline” – at each progressive career stage, there are fewer women. There are many publications about this and the surrounding causes/effects (I’ve included a non-exhaustive list at the end of the post). One recent “Spotlight” in the journal Trends in Ecology and Evolution by Cameron et al. caught my eye. In it, they summarize much recent research on the topic – including that women:

– publish fewer papers.

– have lower grant success and receive lower grant amounts.

– get promoted more slowly.

– have lower retention rates.

The reason I’m bringing up this topic at this time is because Cameron et al. raised an issue that really rubbed me the wrong way. Cameron et al. construct a flow chart of interacting factors that contribute to women choosing to leave science. Central to their diagram is “Lower self-confidence in women”*. The authors say the way women “experience the scientific community” lowers women’s self-confidence which initiates a feedback loop through lower publication rate, lower grant success and lower professional success that inevitably spits a woman out at the bottom. In this framework, women are less competitive and therefore they don’t get hired or fail to get tenure. This may very well be true. But I don’t like it. I don’t like that the underlying reason women would leave science is low self-confidence.

Figure 1 from Cameron et al. (2013). Does lower self confidence cause attention to detail? Hmmmm....

Figure 1 from Cameron et al. (2013). Does lower self-confidence cause attention to detail? Hmmmm….

How important is self-confidence in Science? How important is the generally unbearable stress of it all?

Science is difficult. Despite the belief that professors have low-stress desk jobs, people in academia have to work almost all the time because we have no upper limit on our job – there’s literally always more to do and it’s always up to you to do it. Relatively few job openings and relatively many people with doctorates ups the stress and competition factors as well. You really have to want to stay on this career path. Like really, really. But there’s got to be a limit for how much any one person can take before the cons outweigh the pros and the reasonable thing to do is leave – the amount of straw that breaks the camels back, if you will. No matter how strong (i.e., self-confident) the camel is. Right? I wonder if it’s less about self-confidence and more about the sum of all the parts. I’ve reworked Cameron et al.’s flowchart into something I call: “Not a flowchart but instead a hand-drawn picture of a camel”:

CamelDuties

The cumulative load of obligations, stresses and environment may be the ultimate reason women leave science (in my opinion).

All the above facts/observations make it seem (to me) that women may just have more straws on their backs – i.e.,  more reasons to leave academia. Maybe I’m splitting hairs because I like the framing a little better. But all of the ways and reasons that there is a gender bias in science add up to a (however slightly and not in every case) less good environment that women may feel less loyal towards.

Cameron et al. conclude with “Enhancing self confidence and expectations may be the single most significant step in encouraging and retaining women in science.” I’m not sure how to do this – especially on an institutional scale. I think we should focus on lessening the number of straws for women, the biggest of which may be family oriented.  So maybe we should work on institutionalizing allowing time off the tenure clock for maternity and paternity leave and increasing affordable childcare on campuses. Maybe actively recruiting female mentors/mentees in STEM disciplines will help (programs like this!). Maybe the fact that I’ve never been told women aren’t good at math is a sign that we’re growing out of an outdated way of thinking. We all need to apply for things we think might be out of our league and we’re all susceptible to low self-confidence from time to time. A good social support system (of men and women and four-legged friends and beer) is invaluable to me personally when I begin to crack. For the record, I have no evidence – it’s just what I think.  My opinion is that this is important and to fix the leak, we need to keep talking about this subject.

One final point – they discuss these concepts under the title question: “Is publication rate an equal opportunity metric?” Apparently, the answer is “no”. Strictly looking at the number of someone’s publications doesn’t accurately summarize their publication history (or worth as a future colleague/grant recipient/whatever) and they argue this puts women at a disadvantage. Regardless of how realistic or useful a “quantity only” metric system is, this article has prompted me to action! How about including number of citations and/or journal impact factor on the publications section of a C.V.? Instead of a traditional citation, perhaps this?:

Hird SM and Sullivan JS. 2009. Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus). Molecular Ecology, 18: 3097-3109. Citations: 16. 2011 Journal Impact Factor: 5.522.

Including these metrics makes sense for anyone – it allows your publication record to be most fairly evaluated. Well, that’s enough from me but I’d love to hear from you. What do you think of Cameron et al.’s flowchart? How important is self-confidence in science? Should we put quality metrics on our C.V.s? Please leave comments below!

* There is no hard evidence that I could find that women in science have lower self-confidence than men, which is central to the Cameron et al. argument. If you know of any studies regarding this – please let me know!

References and further reading (additional suggestions welcome):

Barres BA (2006). Does gender matter? Nature 442: 133-136.

Bedi G, Van Dam NT, Munafo M (2012). Gender inequality in awarded research grants. The Lancet 380: 474.

Cameron EZ, Gray ME, White AM (2013). Is publication rate an equal opportunity metric? Trends in Ecology & Evolution 28: 7-8.

Damschen EI, Rosenfeld KM, Wyer M, Murphy-Medley D, Wentworth TR, Haddad NM (2005). Visibility matters: increasing knowledge of women’s contributions to ecology. Frontiers in Ecology and the Environment 3: 212-219.

Holmes M, O’Connell S (2007). Leaks in the pipeline. Nature 446: 346-347.

Hutson SR (2006). Self-citation in archaeology: Age, gender, prestige, and the self. Journal of Archaeological Method and Theory 13: 1-18.

Martin LJ (2012). Where are the women in ecology? Frontiers In Ecology and the Environment 10: 177-178.

McGuire KL, Primack RB, Losos EC (2012). Dramatic Improvements and Persistent Challenges for Women Ecologists. BioScience 62: 189-196.

Moss-Racusin CA, Dovidio JF, Brescoll VL, Graham MJ, Handelsman J (2012). Science faculty’s subtle gender biases favor male students. Proceedings of the National Academy of Sciences 109: 16474-16479.

O’Brien K, Hapgood K (2012). The academic jungle: ecosystem modelling reveals why women are driven out of research. Oikos 121: 999-1004.

Symonds MRE, Gemmell NJ, Braisher TL, Gorringe KL, Elgar MA (2006). Gender differences in publication output: towards an unbiased metric of research performance. PLoS ONE 1: e127.