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Evolution 2011

The 2011 Evolution meetings are in Norman. And I am maybe kinda blogging about it (trying to start blogging again, consolidate my disparate efforts at my own domain).


Eugenics, genetics and how they collided in the 20s and 30s

Roystonea, the royal palms, are the most striking palms in the Caribbean, and arguably, in the world (though, granted, a talipot palm in flower comes a close second). The name of the genus was coined by Orator F. Cook, an American botanist, in 1900, in honour of Roy Stone, an American general involved in the capture of Puerto Rico during the Spanish-American war.

I’ve wondered for years why Cook replaced what seemed to be a perfectly good generic name, Oreodoxa, with Roystonea…turns out that there were problems with Oreodoxa that were not easily addressed. Over the course of trying to figure that out, I started reading some of Cook’s writing. The article in which he first proposed the name1 gives fascinating insight into the state of botanical nomenclature a century ago (now there’s a subject I can imagine throngs of people being fascinated by), so I did a search on Web of Science to see what else of his I could easily find.


Evolution and conservation in Mexican dry forests

The characteristic peeling bark of <i>Bursera simaruba</i>.  Copyright Kurt Stueber, licensed under the GFDL

The characteristic peeling bark of Bursera simaruba. Copyright Kurt Stueber, licensed under the GFDL

Bursera simaruba has always been one of my favourite tree species. It’s a dry-season deciduous tree with compound leaves and a coppery peeling outer bark and a green (presumably photosynthetic) inner bark.  It’s a conspicuous element of tropical dry forests in Trinidad and Tobago, Puerto Rico and parts of southern Florida (where they call it the ‘gumbo limbo’ tree).  In all these places it’s the only representative of its genus.  In my experience, Bursera was Bursera simaruba, so I was surprised when I came across a Bursera that was grown from seed collected in Costa Rica that was obviously not B. simaruba.  Nonetheless, I still thought of Bursera as a relatively small genus.  Then I came across some information on the genus in Mexico which turned my picture of Bursera completely on its head.  There are 84 species of Bursera in Mexico – 80 of which are endemic – out of a total of approximately 100 species in the genus.  So why are 80% of the species of Bursera – a genus which ranges from Florida to Argentina – restricted to Mexico?

Species diversity patterns reflect several underlying processes – those that generate diversity, and those that maintain that diversity.  When species are grouped into a genus, the assumption is that they are more closely related to one-another than are they to any species in a different genus.  To get from that one ancestral species to its modern descendants, something must occur that allows the single ancestral lineage to split into several daughter lineages (a process known as speciation).  This figure from the Wikipedia article on speciation summarises the different modes of speciation.speciation_modes

In order to generate the type of pattern seen in Bursera, you need one of two evolutionary processes to be active.  Either Bursera originally diversified in Mexico, and a few species have spread beyond that ancestral range (giving rise to their own daughter species along the way) or something happened in Mexico that led to the diversification in a limited portion of the range of a widespread genus.  In the former case, Mexican diversity should be old, and the splits between the Mexican species should lie deep in the ancestry of the genus.  In the latter case, Mexican diversity is newer, and the splits between the Mexican species are likely to have been derived from more widespread species.

ResearchBlogging.orgIn a paper published in PLoS ONE in October, Judith Becerra and Lawrence Venable of the University of Arizona looked at the case of Bursera in Mexico.1 Bursera is an old genus – molecular phylogenies based on ribosomal DNA suggest that modern species share a common ancestor about 66-74 million years ago, and fossil evidence suggests that the genus was once ranged over a much wider portion of North America.2 It turns out that most of the Mexican species are more recent.  The number of lineages increased substantially within the last 30 million years3 and peaked between 10 and 17 million years ago (which coincides with the formation of the Western Sierra Madre and the Neovolcanic belt).1 Becerra suggested that the diversification of Bursera is likely to have coincided with the expansion of dry forests in central and southern Mexico.3 These dry forests were made possible by the uplift of the mountains which provided appropriate climatic conditions for the establishment of tropical dry forests by sheltering them from northern cold fronts.1

In previous work, Becerra has built a detailed phylogeny of the Mexican species of Bursera.  Using this phylogeny, she was able to show that the diversification of these species coincided with the formation of the Western Sierra Madre and the Neovolcanic belt.  In the PLoS ONE article she and Venable used this phylogeny and the distribution of existing Bursera species to predict where the various species are likely to have originated.  Despite the fact that it ranks third in Bursera species richness today, they found that the Southwest was actually the source of the largest number of species.  The Balsas River basin, on the other hand, has the most species (and the largest number of endemic species), but was the site fo relatively few diversifications.  Continued mountain-building led to an expansion of dry forest, into which new species wer able to spread.  Other new species were able to invade the Mexican highlands, the Sonoran Desert, upland oak forests or subhumid tropical forests.

Becerra and Venable termed the diversity-generators “source” areas and the non-dry forest habitats as “diversity sinks”.  Personally, this bothered me, as it felt like they were borrowing terminology from population ecology (where it applies to individuals within populations) and applying it to species in a way that is likely to bring unwanted baggage.  Sink populations recruit fewer individuals than are required to replace losses to the population, and as such will go extinct if they don’t continue to receive immigrants from the source population.  There’s nothing to indicate that Becerra and Venable are using ‘sinks’ to mean anything beyond the fact that these areas are occupied by species that evolved elsewhere.  Using this borrowed terminology is likely to mislead readers who are more familiar with the concept of source-sink dynamics in population ecology.

Since certain areas have been superior generators of diversity, Becerra and Venable suggest that prioritising them for conservation should yield superior long-term outcomes.  Protecting areas that can generate diversity should be more important than simply protecting areas that harbour greater diversity.  They write:

The differences between diversity and diversification mean that this may be transitory in the long run, analogous to protecting species in zoos. While it might sound unusual to try to conserve diversity based on events happened in the past, there may be cases in which the aerographic patterns of diversification have occurred repeatedly for a long time, giving us some kind of assurance that it will continue happening in the same way for at least the near future. In the case of Bursera, diversification seems to have been higher in one area for a long time, starting 15 million years ago or perhaps even longer. If not greatly perturbed, there is no reason not to believe that these same patterns of diversification will continue. This approach could be especially useful if there are no other stronger criteria to decide where conservation efforts should be directed. If we had to choose between conserving one of two areas and everything is equal except their history of being sinks or sources of diversification, there would be no harm and perhaps much gain in choosing the source. The long-term maintenance of biodiversity require us preserve its sources, to the extent that these can be accurately determined [8].

[Emphasis added]

I’m not sure if I agree, or disagree.  On one hand, there’s a lot of evidence that suggests that species assemblages are more transient than they were assumed to be in the past.  The simple fact that an area supports a large assemblage of species may reflect chance as much as some special property of the site.  So from that perspective, the areas that have generated diversity should be more important than the areas that harbour diversity.  On the other hand, why should we assume that an area that generated a lot of diversity in the past will continue to do so in the future?  The rate at which new species are being generated appears to have declined sharply in past 10 million years.3 If, as has been suggested, the generation of diversity was related to mountain-forming, is it reasonable to expect the process to continue?  It’s difficult to say what it is that generates a species flock in one area and not in another.

The other big question I found myself with was what is the purpose of conservation?  At what point will we be able to stop protecting species and environments?  When will the threats recede, or will they recede at all?  What will the world look like when the current human-driven extinction event has run its course?

This post is my contribution to PLoS ONE @ Two, a celebration of the second birthday of PLoS ONE.

  1. Judith X. Becerra, D. Lawrence Venable (2008). Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003436
  2. Judith X. Becerra (2003). Synchronous coadaptation in an ancient case of herbivory.  Proceedings of the National Academy of Sciences USA 100 (22): 12804-12807 DOI: 10.1073/pnas.2133013100
  3. Judith X. Becerra (2005). Timing the origin and expansion of the Mexican tropical dry forests.  Proceedings of the National Academy of Sciences USA 102 (31): 10919-10023 DOI: 10.1073/pnas.0409127102

Ideas in Ecology and Evolution

Ideas in Ecology and Evolution is a new open-access journal which “publishes only short forum-style articles that develop new ideas or that involve original commentaries on any topics within the broad domains of fundamental or applied ecology or evolution”.  They also have an interesting review process:

Referees for Ideas in Ecology and Evolution are not anonymous; they are paid – not just for their reviewing services, but importantly, they are paid to forfeit their anonymity.  In other words, in the event that the paper is published, payment of referees secures their consent to reveal their identities – directly within the published paper – as having refereed the paper.  Referee identity is also revealed to authors of rejected papers.  Referees must agree to these conditions in advance, before receiving the paper for review.  This is done on-line, and the referee is paid upon receipt of the review.

The author pays for the review process and publication.  It costs $400 to submit an article ($300 to pay two reviewers, $100 for the rest of the process) and an additional $300 upon acceptance. That’s the drawback of most open-access systems – that they require authors to incur substantial costs.  Not that ‘closed-access‘ journals publish your articles for free…but it can still be a barrier for some authors.  Granted, many of them are willing to waive their fees for authors who are unable to pay.  I haven’t seen anything of the sort here, but that isn’t surprising in a journal this new.

H/T Bora.

Speciose or species-rich?

As a graduate student I came across the word “speciose”.  It had an alluring sound to it that was lacking in its more pedestrian synonym “species-rich”.  Equally appealing, I suspect, was the fact that it supplied a formal-sounding alternative that was less accessible to the average person.  (If you’re lucky, you outgrow that affectation and learn that clear communication is what matters most.)

In the December issue of TREE, Michael Hart delves into the origin and use of the word speciose.  Although similar to “species”, speciose actually shares a root derives from “specious” in ‘beautiful’ or ‘lovely’.  Hart sees value in speciose – it’s no longer than “species-rich” and solves the hyphenation problem (i.e., the problem of not knowing when to join the words “species” and “rich” with a hyphen).  Both “species-rich” and “speciose” first show up in the Web of Knowledge database in 1957, and use of both terms has grown fairly consistently.  Although he cites Gill’s plea to cease ‘the misuse of ‘‘speciose’’ in the evolutionary biological literature,’ Hart sees value in this “lovely word” and urges “deliberate consideration” as to its future and fate.

I embraced “speciose” in my first or second year as a grad student.  I happily embraced it, using it both in writing and conversation.  And then, to my horror, I discovered Gill or some other pedant who insisted that “speciose” was being misused by ecologists.  With that discovery, I discontinued use of speciose immediately.  The only thing worse than using big words is misusing them.  Granted, it had been wearing thin already – my doctoral advisor, for example, had seen no inclination to adopt the word despite my repeated use of it.

And that’s where it’s stood ever since, for me, until now.  Granted, Al Gentry used to word, and being as amazing a biologist as he was, he had the right to use whatever word he wanted, however he wanted to…and be right.  After all, he was Al Gentry.  (And he had tragically passed away, doing a rapid assessment of biodiversity.)

Reading Hart made me re-think my opposition to “speciose”.  We have the right to re-define words from time to time.  This might be a good candidate.  I’m not sure if it’s for me, but I should be willing to accept that it is, after all, an acceptable term.

Hart, Michael W. 2008. Speciose versus species-rich. Trends in Ecology & Evolution, 23 (12):660-661 doi:10.1016/j.tree.2008.09.001

Exploring Life’s Origins

The Museum of Science in Boston has a great new website up called Exploring Life’s Origins.  The site, which is visually stunning, showcases the work of Janet Iwasa, a 2006-2008 NSF Discovery Corps Postdoctoral Fellow and Jack Szostak and his laboratory at Massachusetts General Hospital.

There are three main sections – A Timeline of Life’s Evolution, Understanding the RNA World and
Building a Protocell.  The Resources for Educators section allows you to download the movies (which are available under a Creative Commons (Non-Commercial, No Derivatives) license – basically they’re free to use for non-commercial purposes as long as you give proper attribution.

H/T Panda’s Thumb.

Evolution, creationism and the law

Titan at Promethus Retold has an interesting analysis of Jana McCreary published in the Southwestern University Law Review. McCreary makes the argument that evolution is a creation story for atheism (disputable, but beside the point), thus teaching evolution fails the Lemon Test – that the teaching of evolution advances on religion (atheism). According to Titan, McCreary then goes on to suggest that to counter this, government should mandate the teaching of creationism.

I’m no lawyer, but it seems to me that if something violates the law, the solution to the problem is not more violation of the law. As Titan puts it

If teaching evolution really violates the First Amendment, then we should stop teaching it.

That’s all. If you believe that teaching evolution violates the law by furthering one religion, the solution isn’t to argue for more law-breaking. That’s chaos, that’s vigilante justice. But that isn’t the way the law works. Even I know that much.

Titan goes on to argue that even if evolution supports one religious viewpoint over another, there’s no violation of the law because the primary purpose of teaching evolution is not to advance a religious viewpoint. Personally I find it more amusing to imagine what would happen if any law supportive of religion were found to violate the First Amendment. Murder is prohibited by most religions, as is incest. Most religions invoke a universal moral code which is present in our laws – which themselves derive, I suspect, from Roman and Germanic laws meant to further their religions.

It quickly becomes ridiculous. Which may, in fact, be the underlying point of the argument – if declaring laws which advance religion unconstitutional, the entire Lemon Test should be thrown out. And that, of course, might allow the teaching of creationism.

H/T Tim Sandefur at PT.