Monday, December 22, 2014

Conference: Speciation 2015! Register soon!

Hi all.  A quick announcement regarding an upcoming conference:

Who: You – or your grad students!
What: Speciation 2015
When: March 15–20, 2015
Where: Ventura, CA
Why: Modes of Diversification, Ecological Mechanisms, and Genomic Signatures
How: Register at http://www.grc.org/programs.aspx?id=16902

  There’s lots of additional information at the link above.  This is the world’s largest conference on speciation research, and they have put together a truly stellar list of invited speakers.  I wish I could go; so you should go, so that I can live vicariously through you.

  The conference is close to full, so get your registration in soon!

Friday, December 19, 2014

Best evolution/nature books

This is the time of year for lists: the best this, the most important that, and so on. Just such a list was circulating today on twitter about the best science books of the year, presumably also books you should be buying for Christmas presents. This discussion got me to thinking – what would be the best evolution books for Christmas? I don’t just mean published this year, I mean published in any year but still available. I also don’t mean technical books but rather popular books that you might give your friends or spouse or yourself. The kind of book you will read in bed at night rather than in your office in the morning. Books that are easy to read and a great advertisement for how cool evolution is and can be – either remotely or on the front lines of research. Meshing nicely with this idea was the realization that I have, over the years, benefited greatly from Christmas books about evolution – mainly from my Mom but also from students, friends, colleagues and other family members. With all of this in mind, here is my subjective and incomplete listing of the best evolution books for Christmas, or any time. (This post and list is updated nearly every year.)

1. Neanderthal Man by Svante Pääbo

I have only ever read two popular science/nature books twice - and this is one of them. Probably the best book ever by a scientist about his/her science and life. (Other good ones are Naturalist by E.O. Wilson and Privileged Hands by Geerat Vermeij). It combines fundamental insights into our evolutionary origins (interbreeding with Neaderthals and other archaic humans), a compelling narrative of a career (development of methods for studying "ancient DNA"), interactions with technological developments (e.g., Sanger, 454, and Illumina sequencing), personal life (Pääbo is the son of the secret second family of a Nobel Prize winner, whose discovery would later save Pääbo's life), and scientific administration (founding of a new Max Plank Institute). Written in an extremely frank and down-to-earth way, it makes the reader feel a part of - or at least an intimate observer - of the discoveries and controversies. I look forward to reading it again.


2. The Beak of the Finch by Jonathan Weiner.

This book, a Christmas present from my Mom in 1995, quite literally changed my life. It is a wonderfully written and engaging account of the importance of rapid evolution told mainly through the research on Darwin’s finches conducted by Peter and Rosemary Grant. Reading this book that fateful Christmas, I had an epiphany “you can actually watch evolution happen in real time” that almost instantly changed my career goals from wanting to study salmon to wanting to study evolution. To this day, my research focuses squarely on “rapid evolution” – I now even work on Darwin’s finches in Galapagos, as well as on other systems – most notably Trinidadian guppies – described in the book. This book is, for me, the best example of how important and dynamic evolution is and how exciting it can be to study. And it isn’t just me – the book won a Pulitzer Prize, as well as many other accolades. If you read only one book about evolution, if you give only one book about evolution, this should be it.


3. Nature’s Nether Regions by Menno Schilthuizen

This book was also a gift from my Mom, although not for Christmas. She had read it and found it so much fun that she had to buy it for me – in hard cover no less (I always wait for paperback and, even then, for books to go on sale). The book describes, in extremely entertaining prose, the evolution of gentalia in animals, including humans. It is jam-packed with fascinating and extremely well researched examples of how evolution is shaped by penis-driven internal courtship, as well as other titillating (but not superficially) topics. It is the sort of book that you can’t help but read out quotes to your spouse or students or at parties. The sort of book where you can’t help but laugh or exclaim out loud, or think “Wow, I had no idea the clitoris was that big” or that “As familiar as the old in and out is, there is nothing about the biology of reproduction that requires rhythmic penis movements.” (This last is an attempt to paraphrase from memory the infinitely more clever original sentence.) The book also proves that the best writers in English don’t have to be native English speakers.


4. The Voyage of the Beagle by Charles Darwin

Perhaps you weren’t expecting this one as it was published 175 years ago – yet it remains a compelling read. It has all of the innocence and excited of a pre-worried Darwin as he voyages around the world discovering new things. His excitement is contagious and much of the book reads as might a contemporary account of discovery, albeit set in an endearing (to the outside reader) context of the mid-1800s. I have given this book to a number of non-scientists and they have found it enjoyable. It is also worth saying that it is one of the best of the accounts of discovery from the golden age of natural history, among other great accounts I have read by Wallace and Bates and others. And, of course, one can’t help be chuffed by catching the early hints of Darwin’s emerging idea of evolution by natural selection.


5. The Song of the Dodo by David Quammen

Here is another book that, like the Beak of the Finch, has been around for quite a while (although not as long as the preceding book) and is critically acclaimed. It is a deft mash-up of island biogeography, conservation, invasion biology, and evolution. It describes in great detail and with personal stories and anecdotes from actual researchers on the ground how the geographic distribution of the world has shaped the distribution and evolution of animals and how this context has then shaped extinction risk through direct or indirect (e.g., invasive species) human influences. My only complaint is that the text is a bit bloated and, thus, sometimes tedious. I can’t help but think that cutting 20% of the book would have made it much more engaging.


6. Improbable Destinies by Jonathan Losos 

It is sometimes hard to read a book about a topic you work on that features many of the people you know. It is difficult to look beyond the sweeping statements you know to be too simplified and the sanitized versions of personalities. Indeed, this difficulty is why I never re-read The Beak of the Finch - I don't want my original naive enjoyment to be tempered by intimate experience with reality. Improbable Destinies is about the extent to which evolution repeats itself when different organisms encounter similar conditions - so-called "convergent" or "parallel" evolution. Set up as an exploration of Gould's famous "replay the tape of life" thought experiment, this book describes a diversity of research where those thought experiments become reality - in both the lab and the wild. In the end, I found this book to be an exceptional (if imperfect) digestible representation of these topics and controversies, as well as well being written and engaging. I have even recommended it to my own students working on this topic. I asked one of them recently: "So, are you finding it useful?" - to which she replied "Yes, but it is also really well written!" I agree - although I would replace "but" with "and".





7. Dark Banquet by Bill Schutt

Another Christmas present from my Mom, this relatively recent book describes the curious lives of blood feeders: ticks, chiggers, vampire bats, leeches, mosquitoes, and so on. This is another book that generates tons of anecdotes and comments that you just can’t help but share with others (George Washington’s death might well have been accelerated by doctors leeching too much blood). I even use it for teaching – my favorite way to discuss the kidney now is to talk about the difficult challenges and ingenious evolutionary solutions that vampire bats use to deal with their massive blood meals. On the negative side, it makes you itchy at night when reading about bed bugs. A great read though.


8. Dr. Tatiana’s Sex Advice to All Creation by Olivia Judson

This book is like Nature’s Nether Regions in that it takes on the titillating subject of sex and sexual selection. However, the main appeal is its clever gimmick. It is written as though the author is a sex advice columnist to various organisms who write in to describe their problems – sort of a Dr. Ruth or Dan Savage to the animal world. A fun read and it has been adapted into a TV show.


9. The Curse of the Labrador Duck by Glen Chilton

This book is a strange and whimsical choice but it is really fun to read. It describes the quest of the author – charged with writing a species account of the extinct Labrador Duck – to see, measure, and consider every Labrador Duck specimen in the world, something around 55 or so. He traipses around the world finding and measuring each specimen (often with considerable difficulty) and injects his own fun observations and perspectives on the places and people he visits. The numerous cute phrases are a bit much sometimes (and it isn’t really a book about evolution) but it is hard to find a book that feels more like spontaneous fun with natural history.  By coincidence, the duck on the cover is right outside my office door – but this has nothing to do with my affection for the book.



10. How to Tame a Fox by Lee Dugatkin and Lyudmila Trut

This is the second popular science book that I have read twice. The reason this time, however, was partly because I was confused about the way in the science was described. On the first reading, it had been so frustrating that I wasn't sure I liked the book. On the second reading, the description of the science was still a bit confusing but I was able to isolate those parts and instead enjoy the tale of intrigue, persecution, mystery, conflict, perseverance, excitement and success surrounding the nearly half-century long (and still running) Soviet/Russian experiment on domestication. Most importantly, this book gives a first hand (Lyudmila Trut ran the experiment nearly the whole time) look at extremely original and forward-thinking science behind the Iron Curtain.


11. Various books about strange critters

I often read species-centric books, such as Moa, Platypus, Tasmanian Tiger, and A Fish Caught in Time. These books have a singular focus on a particular taxon that allows the author to create a much more coherent narrative than more general books about general phenomena, such as sexual selection or blood feeding (although the above books do a great job regardless). Among these books, I recall with particular affection the Platypus book, by Ann Moyal, which is a fun account of how western science was long befuddled with the evolutionary position and significance of the playtypus. It describes the various well-known (Richard Owen) and obscure personalities who weighed in on the topic and how the discoveries changed our view of the evolution of vertebrates. A Fish Caught in Time, by Samantha Weinberg, is also outstanding.



Many other great books are out there but I don’t have time to describe them all – my apologies to many other great authors, with particular recognition of Carl Zimmer (Parasite Rex) and Rebecca Stott (Darwin and the Barnacle). I welcome further book suggestions by way of comments on this post. I would also like to apologize for any mistakes or bad grammar in the preceding. I only had the idea for this post an hour ago and it seemed appropriate to do NOW (enough time to buy those books) and I want to go play with my kids. So, until next time, clever spending and good reading. Happy holidays. 


Thursday, December 11, 2014

Retracing the legacy of guppy introductions past: local differentiation maintained despite high and rapid gene flow

[ This post is by Sarah W. Fitzpatrick; I am just putting it up.  –B. ]

When populations adapted to different environments come into contact through range expansions, invasions, or by human-assisted migration, the outcome is often unknown. How will immigrant individuals fare in the new environment and will they hybridize with native populations? If so, what impact does gene flow with non-native individuals have on the local populations? The question of whether gene flow between adaptively divergent populations promotes or constrains local adaptation is a long-standing puzzle in evolutionary biology and is increasingly relevant for designing effective conservation strategies.

In our recent study (Fitzpatrick et al., 2015) published in Ecology Letters, we turned to Trinidadian guppies, a model system for studying evolution in the wild, to ask questions about how gene flow affects fitness and local adaptation. The guppy system has proved powerful for understanding a diverse set of questions in ecology and evolution, but these rapidly evolving freshwater fish are perhaps most famous for the series of transplant experiments conducted in the streams of Trinidad. Caryl Haskins initiated the first introduction experiment in 1957, moving guppies from an environment where they experienced high mortality from predation to a site in a separate drainage where waterfall barriers limited the upstream colonization of most fish, including predators and native guppies. The introduction site thus represents a release from predation. John Endler and David Reznick and his colleagues have since repeated this transplant scenario in multiple independent drainages, and their studies of rapid adaptation and eco-evo feedbacks focusing on the introduced populations are iconic in evolutionary ecology.


In each of these introduction streams, native guppies existed downstream from introduction sites, and although the introduced populations were initially maladapted to their new environment, gene flow is expected because adaptive divergence has not led to reproductive isolation in guppies (Crispo et al., 2006). In fact, we expected much higher levels of downstream gene flow from introduction sites than what is observed in natural streams due to the fast life history of the introduced fish and female preference for novel males (Fig. 1; click to see at larger size).


Figure 1. Conceptual diagram illustrating the expected differences in amount of gene flow between natural streams and streams with introduced populations. In both hypothetical streams, predation level is colour-coded based on the species listed in the bottom key, and increases in the downstream direction. Black rectangles indicate waterfall barriers that limit upstream fish dispersal. The colour of fish indicates traits matched to a certain level of predation (e.g., the blue fish has traits that are adaptive in a low-predation environment). In the hypothetical natural stream, fish are perfectly matched to their level of predation and gene flow among populations is low, based on biological factors listed in the grey box. In the hypothetical introduction stream, guppies from high-predation (HP) environments were translocated upstream of naturally occurring low-predation (LP) populations. Gene flow is expected to increase relative to natural levels for the reasons listed in the grey box, and the effect of elevated gene flow on locally adapted traits remains unknown (indicated by grey fish and question marks).

Our team, from Colorado State University, asked what the effects of elevated levels of gene flow from an initially phenotypically divergent population would be on locally adapted phenotypes in downstream populations. Following the footsteps of Haskins, Endler, and Reznick, we sampled guppies from six historic introduction sites, from each of their source populations, and from multiple sites downstream from each introduction. We genotyped all individuals at ten microsatellite loci and quantified a suite of known fitness-related traits, such as male color, body shape, and some female life-history traits that tend to differ based on the level of predation experienced. We also included individuals from two native populations prior to the onset of gene flow, providing a powerful opportunity to compare pre- versus post-gene flow phenotypes and allele frequencies. At each site we classified the predator community as either low, medium, or high based on the complexity of the fish community observed.


Clockwise from back left: Jed Smith (undergrad researcher, CSU); Chris Funk (asst. prof, CSU); Sarah Fitzpatrick (PhD student, CSU); Lisa Angeloni (asst. prof, CSU).

We found that the genetic signature of introduced guppies swept throughout all downstream distances, indicating high levels of gene flow downstream from all introduction sites on a rapid timescale (Fig. 3a; click to see at larger size). However, despite genetic uniformity caused by introductions, guppies sampled from different predation communities along the streams maintained phenotypic traits that best allowed them to survive and reproduce, given the local predator community. In other words, genetic homogenization did not cause the loss of locally adapted phenotypes.


Figure 3. (a) Comparison of genetic differentiation (pairwise-FST) among all sites in natural streams vs. among all sites in streams after introductions took place. (b) Within-stream STRUCTURE plots and average pairwise-FST values for all six streams that experienced an upstream introduction. Each line in the plots corresponds to an individual with colours representing the proportion of an individual’s genotype assigned to a given genetic cluster. Old introductions show fine-scale genetic structure despite low genetic divergence (low FST). All sites from the three recent introductions conducted in the Guanapo drainage were included in the same analysis because they share the 5000 m and source sites. These recent introductions are more genetically homogeneous, with the exception of pre-introduction 0 m sites in Taylor and Caigual (shaded in blue) that are very distinct and genetically divergent (high FST) from the rest of the sites. Colored circles on the x axes indicate the predation level at each site: blue = low, green = mid, red = high, as defined in Fig. 1. All plots represent the (k) number of genetic clusters with the highest support (see Appendix S1).

We used the exchangeability analysis described in Hendry et al. 2013 to compare neutral genetic and phenotypic exchangeability among the common source site and two native low-predation sites that were sampled before and approximately 12 generations after gene flow. A major take-home message from our study can be gained from the results of this analysis. Namely, we found phenotypic divergence associated with the local predation regime despite neutral genetic homogeneity with the source of the introductions (Fig. 5; click to see at larger size).


Figure 5. Ordination plots and group classification based on discriminant analysis of principal components (DAPC) for neutral genetic loci (a) and phenotypic traits (b). Colours correspond to a priori groups based on population origin: native low-predation in purple, the same sites post-introduction in blue, and introduction source in red. Bar graphs below the dashed line show the mean (and 95% CIs) proportion of individuals from each population classified into each population. Each bar represents the classification of the population on the x axis, as labelled for one set of bars in (b). The bottom-left insets show eigenvalues of the four principal components in relative magnitude.

Phenotypes were measured from wild fish, so we are unable to separate the relative roles that phenotypic plasticity and adaptive evolution play in causing the observed phenotypic divergence, but we argue that both processes are likely involved. Ongoing work that includes common garden assays conducted before and several generations after the onset of gene flow, and wild pedigree reconstruction throughout the initial pulse and longer-term wave of gene flow, will add to our understanding of the mechanisms by which gene flow impacts adaptive evolution and population growth.

Although we expected to find high gene flow from the introduced populations, we were surprised by the near-extinction of native alleles, especially downstream from the set of recent introductions. However, differential rates of introgression across the genome may result in homogenizing effects of gene flow at neutral loci, while locally adapted native loci or genomic regions are maintained by selection.

Whether the loss of native genetic signatures at neutral loci represents a true detriment is an intriguing philosophical debate. The costs of gene flow between populations of the same species may be outweighed by the benefits in cases where selection for a local ecotype is strong, or where recipient populations are inbred. This study reveals how model systems that can be manipulated in the wild have the potential to inform smart management decisions for threatened populations.

Indeed, we have pioneers of model systems like Haskins, Endler, and Reznick to thank for building foundations that continue to generate creative questions and provide a deeper understanding of nature.

References

Crispo, E., Bentzen, P., Reznick, D.N., Kinnison, M.T., and Hendry, A.P. (2006). The relative influence of natural selection and geography on gene flow in guppies. Mol. Ecol. 15, 49–62.

Fitzpatrick, S.W., Gerberich, J.C., Kronenberger, J.A., Angeloni, L.M., and Funk, W.C. (2015). Locally adapted traits maintained in the face of high gene flow. Ecol. Lett.

Hendry, A.P., Kaeuffer, R., Crispo, E., Peichel, C.L., and Bolnick, D.I. (2013). Evolutionary inferences from the analysis of exchangeability. Evolution 67, 3429–3441.

Figures are cited based on the numbering in the manuscript.

Wednesday, December 3, 2014

Where to submit your paper – response to reviews.

My blog posted in open access Where to submit your paper. Or “If at first you don’t succeed, fail fail again … then try open access” has been viewed 2771 times in 5 days and has now been subject to some post-publication reviews. It seems appropriate to do a quick follow up in which I respond to those comments.

The original post made several points:
  1. If you have some great work, submitting to high-impact journals like Science/Nature is fine – even though the chances of acceptance are low. The whole process usually makes for a better paper.
  2. Traditional society-based journals are great outlets: they are well respected in the community and are frequently scanned for papers by many scientists. If you publish there, folks know you have received a rigorous and critical evaluation of your science from the perspective of its rigor AND importance.
  3. Rejection is an ever-constant companion for ALL scientists trying the above routes and it is good idea to find a coping mechanism that works for you.
  4. Open access journals are not good options (except as a last restort) because they don’t have the above properties.
Of the numerous comments on twitter and in personal emails, only item 4 seems to have - perhaps predictably - raised hackles, specifically in relation to citation rates. So let’s look at some of those comments and see what new insights they can bring.  
This statement is totally correct. Most of us think of PLoS ONE as the archetypal open access journal, which is why I didn't think to initially draw the distinction with "better" open access journals. I therefore added the follow comment after the post.

To make sure my opinion is clear, I am FOR open access PAPERS (in whatever journal) and even for open access journals as long as they are selective (e.g., PLoS Biology, Evolutionary Applications). What I am not for is for-profit open access journals where you pay your way to publish pretty much whatever you want. Those are merely profit making machines for publishing houses - they only make money when they publish your paper. PLoS ONE is non-profit but the problem there is that it is (rightly) viewed as a dumping ground for papers that people couldn't get published elsewhere. Thus, it is not good for exposure of your paper, for the influence of your paper (citations), or for your career. It should be a last resort when you are in a hurry or you (or your student) are sick of trying other places. Indeed, that is how many people already view it and you should too or people will think that was the case for your paper even if you submitted there first.

By far the best option as far as everyone (except for many publishers) is concerned is to publish in a respected traditional (often society based) journal and pay for the paper to be open access. Everyone wins. 


A number of other comments were along the lines that I had N = 2 for my PLoS ONE papers, which thus doesn't say much beyond my own limited personal experience. This is also entirely true given that the post was from my personal perspective and speaks only to my own experience.
But, wait, it turns out I have more experience than I thought (it seems I even ignore my own PLoS ONE papers). While reviewing another manuscript today, I remembered that I had another PLoS ONE paper - this one published in 2010. Yeeha: N = 3. I figured I better update my stats accordingly. I was a bit worried this time as I quite like the paper and know it has been cited at least a few times, so I was thinking that my new data point would mess up my story. Nope. Same thing - the worst cited of all my papers in that year.
Updated stats (adding 2010) for citations (Web of Science) to my PLoS ONE papers in comparison to citations to all my other papers in those years.
So, at this point, I can say with confidence that PLoS ONE is not working for me. In fact, it seems that I wasted three awesome papers by publishing them in an outlet where no one sees them or wants to cite them. I did receive a lot of comments from other people about their PLoS ONE papers also being very poorly cited (although at least one person said they had not noticed a difference). Then I was pointed (by a PLoS ONE senior editor) to something more quantitative.
The paper referred to here collected data on citations to 30 empirical ecological papers (selected in a "stratified" manner) published in 2009 in PLoS ONE, in some traditional ecology journals (Ecology, Oikos, Functional Ecology), in Ecology Letters, and in the big boys (Nature, Science). The results were that citations to ecology papers in PLoS ONE were roughly equivalent to those in Ecology and Functional Ecology and higher than those in Oikos. However, the citation rates in PLoS ONE were much lower than in Ecology Letters and the big boys.

From Wardle (2012 - Ideas In Ecology and Evolution)
These results run counter to my own experience and seem to suggest that PLoS ONE is a good target journal. The results were so different from my own that I decided to take a quick closer look at the question. For each of the three years in which I published a PLoS ONE paper, I used Web Of Science to search for all papers in PLoS ONE and Ecology (the sort of target journal I suggest shooting for) that had the word "ecology" as a topic (an objective way of comparing ecology papers from the two journals). I then used "citation report" to calculate all citations to those papers and, from that, calculated the mean citation rate (total citations divided by total papers).

Citations to "ecology" papers in PLoS ONE and in Ecology in each of three years.
 Of course, this analysis is still crude: I didn't actually read the papers, I didn't examine other journals, and I didn't examine more years. Nevertheless, these larger sample sizes than in Wardle (2012) seem more in line with my argument that citations are lower in PLoS ONE than in the canonical society-based journal. My papers, which are more evolution than ecology, are cited below these PLoS ONE rates. I wanted to do a similar analysis for PLoS ONE versus my own target journal Evolution but the "topic" "evolution" pops up too many other things in PLoS ONE that are not organismal evolution and I was too lazy to sort through them all. My suspicion (and that is all it is) is that the difference will be more severe in evolution than in ecology, where PLoS ONE is perhaps more accepted as a reasonable outlet. It would be awesome if someone did a proper analysis - but not my students - they need to be working on papers and not blogging.

Of course, none of this stuff is definitive in any way but these post publication reviews of the original blog have lead to revisions that bolster my original findings and thus strengthen my general conclusions. I hope that my blog is now acceptable for publication in your journal, whether open access or otherwise.

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More just for fun:


Monday, December 1, 2014

Carnival of Evolution #77: The Carnival is Dead, Long Live the Carnival

Carnival of Evolution #77 is now up at… the Carnival of Evolution blog.

Apparently, Eco-Evo-Evo-Eco had the unanticipated honor of hosting the very last independently hosted CoE, Carnival of Evolution #76, on 2 October 2014.  I guess Felipe P. J. did such an amazing job hosting that nobody wanted to try to follow his act; Bjørn was unable to find a host for November.  So Bjørn will now be hosting the CoE locally, on the CoE blog itself; he has apparently gotten tired of pleading for hosts.  It’s a bit sad, but not really unexpected; blog carnivals used to be more of a thing, but apparently kids nowadays have moved on to Twitter and such.  Case in point: you can follow Andrew at @EcoEvoEvoEco (but he has not yet announced his Snapchat handle).  CoE actually lasted much longer than most blog carnivals did.

But since Bjørn has apparently decided to keep it limping along on his own, it’s not actually dead yet (just pining for the fjords), and we’ll keep participating in it for as long as Bjørn keeps running it.  In #77, we have three posts; I’m not sure how that happened, since I always nominate just one, but there they are.  :->  First off is Andrew writing about how to choose a study system; second is Erik Svensson responding to the kerfuffle about the proposed Extended Evolutionary Synthesis; and third is Yoel Stuart writing about his fascinating work on character displacement in Anolis. I’m glad all three ended up in the Carnival; they’re all great posts!  Check out Carnival of Evolution #77 for lots more cool stuff.

Bjørn is referring to the new, local-hosted carnival as the “Phoenix Edition”, so in honor of his ongoing commitment to the Carnival of Evolution, here is a phoenix.  Thanks Bjørn.

Art credit: Enigma.

Check your (taxonomic) biases at the door

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