Monday, August 31, 2009

Eight Years, Eight Stings, and One Tiny Gecko

You're going to have a hard time finding someone who loves geckos more than Daniel Scantlebury. Dan's been keeping and breeding geckos since he was a teenager and now, at age 24, he continues to maintain a colony of hundreds of species sampled from across the gecko phylogeny. Eight years ago, one of Dan's aunts forwarded him a news article announcing the discovery of one of the world's smallest amniotes - a tiny gecko named Sphaerodactylus ariasae endemic to the southern tip of Hispaniola's Barahona Peninsula and the nearby satellite island of Beata (Hedges and Thomas 2001). Fast forward to today: Dan is PhD student in my lab working on the (much overlooked) adaptive radiation of West Indian Sphaerodactylus with a chance to finally realize his eight year old dream of finding what may be the world's smallest amniote.

For the past week, we've been in the town of Pedernales along the Dominican/Haitian border helping Dan gather ecological data and specimens for his thesis. Over that time we've found all of this region's endemic gecko species, with the exception of S. ariasae. We've been trying to get it for three days now. The first day, our efforts were thwarted by a roadblock along the road to Las Cuevas (a small community near the Bahia de las Aguilas that is the jumping off point for any trip into the range of S. ariasae). The roadblock was organized by locals protesting a Colombian cement companies lease on a waterfront property that they would like to see developed for ecotourism (photo 1 [sorry pics are so small, I need to figure out how to do this as slideshow...]).

The second day, we tried to avoid a costly and time-consuming marine expedition to known S. ariasae localities by making one of the forays that I've come to know as a "Google Earth Goose-chase" or "Google Earth Gambit" starting at the Bahia de las Aguilas. These jaunts involve heading toward promising localities that Dan has identified with the aid of the high resolution satellite images available in Google Earth. In Jaragua National Park and surrounding regions on the Barahona Peninsula, these gambits tend to involve a bit of hardship. Everything on the southern tip of the Barahona Peninsula is hard, sharp, and hot (see photo 2). The terrain is primarily jagged limestone outcroppings, the plants are comprised almost exclusively of spiny acacias and cacti, and the shade is difficult to come by (it's no surprise that this remains one of the most pristine natural areas in all of the Caribbean!). This region is also home to more than its fair share of wasps and bees. Our group has endured more than 20 stings so far, no one more than Dan, who sits atop the leader board with 8 stings (his hand remains swollen today after a three sting outing to a beach locality near Pedernales three days ago). Unfortunately, our attempt to bushwack to new Google Earth-identified localities resulted in hours of hiking, lots of scratches, considerable degradation of my leather boots, and only two geckos (both S. plummeri [see photo 3], a species we'd already sampled for more easily accessible localities). We also saw S. thompsoni, a rock-dwelling species endemic to this region (see photo 4)

Yesterday, with only one day left in Pedernales, Dan decided to stop messing around by heading straight for the type locality of S. ariasae. Because the only way to reach this locality is by boat, we arranged to depart at 6AM to avoid choppy seas along the 2+ hour trip from Las Cuevas to Cabo Beata and Isla Beata. Unfortunately, we didn't get far before our motor failed just off the coast (photo 5). After an hour at sea spent attempting to repair a bum carborator, we limped back to the docks. Given it was our last day in the region, our hopes of finding S. ariasae were in jeopardy. With a bit of quick thinking and luck though, we were able to find a local fisherman who agreed to take us to Isla Beata. We downgraded our motor from a 75 to a 40, but were assured that we could still get to the S. ariasae localities in less than 3 hours.

Once we'd transfered to the new boat, we took a route that hugged the coast in an effort to avoid the worst of the whitecaps. Nevertheless, we still endured a bone-jarring ride that I'm sure we'll be feeling for days. We stopped briefly at a mainland locality for S. ariasae (Cabo Beata, a.k.a. Piticabo), but had a hard time finding habitat that seemed appropriate. We quickly decided our time would be best spent on Isla Beata itself and made our way across the shallow channel to the Dominican navy outpost on the island's north side (photo 6). Knowing our time was short (we didn't get to the island until 2PM and knew that we would need to begin our return to the mainland by 4:30PM to avoid boating in the dark), we headed immediately to the type locality. Once there, Dan and Miguel (a Dominican naturalist and photographer who is the fourth member of our group) quickly descended into the limestone sinkhole described by Hedges and Thomas (photo 7), while Julienne and I began sifting through the leaflitter along the rim. After just a few minutes I heard Dan shout "I got one!" At virtually the same moment, I saw another directly in front of me, but, in the words of Albert Schwartz, I "failed to secure the specimen." The last photo is an adult male S. ariasae on my thumbnail.

In another two hours of searching I heard four more shouts of joy from Dan and Julienne as they observed one S. ariasae after another (inevitably, of course, these proclaimations were scattered around at least one shout of pain and suffering as Miguel was stung mid-back by the cliff nesting bee). Another cost of our quest for S. ariasae would be evident later when we broke out in nasty rashes on our arms and ankles from having spent time on our hands and knees searching in the litter beneath poisonwood trees).

At then end of the day, we made a triumphant return to Pedernales. Although I can't claim that finding S. ariasae was the culmination of an eight year dream, it was a joy to share even a small part of the satisfaction the day had brought to the lab's gecko enthusiast.

Role Reversal

Frequently on Dechronization, we are writing about scientific publications, hoping to point out new and interesting papers to the readers and inviting discussion. A new paper entitled, "Blogging Evolution", just published in Evolution: Education and Outreach (a relatively new journal founded by fellow AMNH'er Niles Eldredge and his son Gregory), though is a journal article about evolutionary blogs, including this one. Adam Goldstein, (the philosophy professor at Iona College, not the DJ who just died) gives a very thorough and very detailed summary of what blogs are and how they work (it was at some points like reading a users manual for blogging - and I mean that in a complimentary way). He divides up blogs into professional (by science writers, like Olivia Judson's), amateur (like ours -- not that we're not professional scientists, we just have day jobs), organization and project-based blogs, apostolic (his example is Pharyngula), imaginative (Carl Zimmer's The Loom, is one example), and networks of blogs. So, in the hope that this doesn't become too horribly circular, here's a posting about an article about our blog...

Thursday, August 27, 2009

A Day of Highs and Lows in Haiti

Field biology is full of highs and lows. A day spent looking for two anoles endemic to the western portion of Haiti's Massif de la Hotte resulted in highs and lows that were both metaphorical and literal.

We began the day with a visit to the type locality of the first endemic - the cliff dwelling Anolis rupinae. Like numerous Haitian anole species, A. rupinae is known from only a small area, in this case the cliffs along a small river valley adjacent to the remote mountain town of Castillon. After driving all day long on really bad roads to reach this locality, we were braced for the possibility that the only known locality had been wiped out by habitat destruction. Fortunately, this turned out not to be the case: although we did find the habitat in this region was severly degraded, some forest in the river valley was intact (mostly due to the fact that it exists on sheer cliff faces). After a short hike from of Castillon, we succeeded in finding a few A. rupinae skittering along an impressive rock face (one of the high points of our trip). The males - with their blue and red dewlaps - were particularly impressive to behold (top photo). We took ecological data on the animals we found, and even filmed a pair mating!

After checking A. rupinae off our list, our next goal was to find what we knew would be our most challenging Haitian endemic - Anolis darlingtoni. This highly unusual twig anole is legendary among anole biologists. Discovered as a single individual by the famed coleopterist and biogeographer P. J. Darlington in 1934, it went unseen for 50 years until Richard Thomas and Blair Hedges found a handful of additional specimens in 1984. By the time we arrived, another 25 years interval had passed without a reported sighting of A. darlingtoni. Thomas and Hedges noted that the locality they visited in 1984 was in the latter stages of deforestation,and we were certain it would be in no better condition when we arrived. Nevertheless, our local guide - Willie - ensured us that he knew the location of an intact forest patch that would be appropriate for a twig dwelling anole. Better still, the patch was only a few kilometers from the small shack we were staying in.

We arranged to walk to the forest patch the afternoon after finding A. rupinae. The plan was to hike to the locality with daylight, find the appropriate habitat before sunset, and to lay out a transect ahead of time for our night searching. The real search for A. darlingtoni would begin once the sun had set, as twig anoles are virtually impossible to find during the day (they're much easier to nab while sleeping on twigs at night). We set off with Willie at around 3PM, after being repeatedly ensured that this would give us plenty of time to reach the forest patch with a couple hours of daylight to get the lay of the land. We were dubious from the start, and we hiked HARD. After hiking up and down a slippery mountain trail for over an hour without seeing a single patch of accessible forest, we unexpectedly arrived at the home of Willie's family! With images of THE FOREST transfixed in our minds’ eyes, we were reluctant to stop, but we allowed a dose of genuinely warm hospitality to temporarily melt our callous resolve (second photo from top). At this family homestead, we were treated to some locally grown and roasted coffee, spiced with local herbs (delicious!), and we swapped snake stories (a timeless exchange).

After coffee and a quick greeting, we rapidly resumed our hike, tearing up and down slope and ravine, gaining and losing altitude in chunks greater than 150m numerous times along the way. After another hour we could see forest on the horizon, but it remained miles away (third photo from top). Willie reassured us that we'd make it but our doubts were growing as the sun set.We eventually reached the forest patch, but well after dark and after hours of brutal hiking. We can’t say a lot about where this forest lies, how extensive it is (we did come to several edges, but it’s hard to be conclusive from our night search), or what the surrounding area is like, as we never saw it in daylight. But we can say that the forest was magical after spending the entire day trekking through completely deforested land. Almost everything was growing directly on cavernous, toothy limestone, which is forbidding to work on, and probably largely responsible for the persistence of the remainging patch. The trees were larger than almost anything we had seen in Haiti, and they were luxuriously covered in moss and epiphytes. The patch was incredibly rich in land snails and Eleutherodactylus frogs, which formed a diverse and nearly deafening chorus. And yes, there were anoles! We found common species along the edges, and the beautiful Anolis monticola nearby. One real treat was a brilliant green Anolis ricordi – Haiti’s representative Crown-Giant anole - that we found sleeping on a large branch. Sadly, despite spending as much time as our lights would allow searching the patch, we did not find Anolis darlingtoni.

It was incredibly difficult to turn our backs on the forest without finding this enigma to face the daunting trail back to the vehicle, this time in the middle of the night. Just as we began our hike home, however, we recieved a bittersweet surprise. Luke noticed on the GPS that seemed very close to our truck and that we were taking a different route back. Willie then casually explained that our truck was just over the ridge, only a few kilometers away. What?!? We knew from the GPS that the truck was not, as the crow flies, far away, but we had been told on the way out that a direct path was impossible because of the mountainous terrain. As you can see on the map of our entire journey, this was not the case (bottom photo). We had hiked up and down the mountains for more than 7km to reach a locality that was only 2km from our truck! Yes, it certainly would have required a rather steep ascent, but one that was certainly doable.After plotting the location of Willie's home, the reason for the extended voyage became clear: Willie had brought us to his house for a bit of extracurricular show and tell! Although we were happy to skip the brunt of the return journey, we would have gladly searched longer if we had known the truck was in close range. Due to other circumstances, this ended up being our last shot at the forest patch on this expedition.

We were delighted to have found a seemingly decent patch of forest so close to Castillon, but somewhat less than happy that Willie's antics provided us with only a few nighttime hours to search this habitat. An exhaustive search for Anolis darlingtoni will have to wait for the next expedition (which, of course, is already being planned)!

[post coauthored by D. Luke Mahler]

Wednesday, August 26, 2009

Women in Science

As the sole woman member of this blog team, I think the duty of posting about this new publication falls upon me. The L'Oreal Foundation, along with Science, has just published a booklet called "Young Women in Science", which very attractively features a photo of a woman happily displaying an Anolis carolinensis on her face. Featured are 17 women in various scientific careers including herpetologist Devi Stuart-Fox, whose dissertation work was on dwarf chameleons.

Sunday, August 23, 2009

Make Killer Figures with R

The blog Learning R is featuring a series of posts about making awesome figures with the R libraries lattice and ggplot2. The examples don't directly involve phylogenetic trees or comparative methods, but the lessons are easily applied to data in our field. Check it out!

[Thanks to Jeet Sukumaran and Rafe Brown at KU for bringing this blog to our attention!]

Saturday, August 22, 2009

Amazing Anoles of the Tiburon Peninsula

I just arrived in the Dominican Republic after 2+ weeks of highly successful anole hunting in Haiti. Luke Mahler and I managed to snag all the Haitian endemics, with the notable exception of Anolis darlingtoni, an enigmatic twig anole that has only been collected twice previously. I hope to dwell on this failure a bit more in a subsequent post, but I'll focus on the positives here.

The photos to the right feature some highlights from our time on the Tiburon Peninsula. I'll work through them from top to bottom. (1) One major highlight for me was seeing A. distichus vinosus, a subspecies of a widespread and highly polymorphic trunk anole species that has a particularly spectacular red and white dewlap. My student Julienne Ng is actively studying speciation in A. distichus and the samples we collected on the Tiburon will be important contributions to her work. (2) The über long-snouted A. dolichocephalus was another of the Tiburon beauties. The males are virtually dewlap-less, but have some striking head coloration that may act to compensate for this deficiency. (3) Anolis coelestinus is a bright green trunk-crown anole found across southern Hispaniola. In this photo you can see a male displaying on an agave with a female out of focus in the background. Males from the western Tiburon have gray dewlaps that differ rather dramatically from the yellow dewlaps that predominant to the east. (4) The fourth photo is of A. monticola, a really attractive species with scapular spots that was recently featured on the cover of Losos's new book on anoles (photo by Luke Mahler). (5) The final photo is of a female A. koopmani, a grass anole that we found hanging out in an abandoned fort (photo by Luke Mahler). It was pretty cool to be searching for herps among abandoned 18th century canons!

Tomorrow I join my students on a search for dwarf geckos (Sphaerodactylus) near the remote Dominican fishing village of Pedernales - wish us luck!

Tuesday, August 18, 2009

Boas and bats in western Puerto Rico

Puerto Rico has a number of threatened, endangered, or extinct reptiles and amphibians. Among the most famous is the Golden Coquí (Eleutherodactylus jasperi; an ovoviviparous eleutherodactyline frog last seen in 1981) and the critically endangered Puerto Rican Crested Toad (Bufo lemur; a victim of fierce competition and predation from the ubiquitous invasive cane toad, Bufo marinus).

Also on the IUCN red list is the near threatened Puerto Rican Boa (Epicrates inornatus). Prior to my latest trip to Puerto Rico (with Luke Mahler in May), the only state in which I’d ever seen a Puerto Rican Boa was dead at the side of the road (as during this 2006 field trip with Butch Brodie).

However, in the karst region of northwest Puerto Rico it is still possible to see boas, sometimes several at a time, waiting patiently around cave mouths for the nightly emergence of tens of thousands of bats (and, hopefully, a warm meal).

These two great photos were taken by Luke at Mata de Plátano Reserve near Arecibo. The picture above is of two boas lying in wait, and the picture below captures the bat emergence in full glory (at least one snake is also visible in this latter photo, although it is more difficult to spot). Click on the image, above, to enlarge.

Monday, August 17, 2009

Microsoft Patents Phylogenetic Comparative Methods. . . Say What?

I read my first (and hopefully last) patent application today, entitled Clustering Phylogenetic Variation Patterns. Although the title of the application sounds more like a late 1950s era manuscript on numerical taxonomy than it does a modern (Jan. 29, 2009) patent filing; it is nonetheless invoking considerable concern in the systematics community, as well it should.

According to this interesting article on the filing by Elizabeth Pennisi (published in last week’s Science), David Hillis first response to the news that Microsoft had filed a patent pertaining to evolutionary inference from phylogenetic trees was that it must be a joke akin to “The Onion article about Microsoft attempting to patent 1’s and 0’s.

The patent filing, by Stuart Ozer, claims invention of a variety of techniques already in wide use by systematists and evolutionary biologists – and (so far as I could tell) none of these inventions are original in quality. The whole patent filing can be read (at ones own risk) in its entirety here, however I have also chosen a few select passages for reproduction, below.

Among the claims of invention in this patent filing, the author purports to originate:

“a method of generating biomolecular clustering patterns”

“mapping at least a portion of the plurality of sequences to an evolutionary tree, the evolutionary tree including a plurality of nodes corresponding to the sequences in a hierarchical arrangement”

“counting evolutionary events in each of the identified plurality of positions at each identified node in the evolutionary tree”

“pruning the evolutionary tree”

“identifying the identified node as a leaf node based on the species count of the corresponding child nodes” for example if “the species count for each of the corresponding child nodes is less than a predetermined number”

“mapping evolutionary events”

“counting evolutionary events further includes: generating an event rate . . . wherein identifying related positions includes identifying related positions based on the event rate”

Without knowing the details of these “new” methods, the claims of invention are hard to evaluate. However, the language of the patent is so broad that it seems possible that if this ridiculous patent is ever approved, we might find that in doing what systematists have done for years, we will be infringing on a patent held by Microsoft Corporation!

Perhaps most nefarious about the filing is the following claim (pointed out by Roberto Keller commenting on the Myrmecos blog):

“Efficient and accurate identification of related groups of monomers of biomolecular sequences is important in achieving biotechnological advances in research and development. However, there is currently no efficient method for determining groupings of monomers in a biomolecular sequence, or among related interacting sequences.”

The author of the patent filing is apparently unaware of the last 50 or so years of research in this area (and should perhaps familiarize himself with a wonderfully interesting chapter on the subject in Felsenstein’s book).

For more on this story, see the following links:

Elizabeth Pennisi's article (link also above)
Systematic Biology
John Hawks weblog
Myrmecos blog
Kevin Zelnio's blog

Monday, August 10, 2009

Haiti: Not a Tourist Destination

Here is a snapshot of the parking lot of our hotel in Motrois, Haiti. Our truck is the silver Mitsubishi sandwiched between the UN security and red cross vehicles. Suffice to say that we haven't come across many tourists during our field work in Haiti. We just arrived back in Port-au-Prince after our trip north. Along the way, we resampled a transect that was part of one of the first molecular genetic studies of cryptic species (see Webster and Burns 1973 Evolution paper on variation in A. brevirostris).

Sunday, August 9, 2009

The Haitian Cascade Anole - It Lives!

One of the most remarkable lizards in the world was discovered three decades ago on and around waterfalls in northern Haiti. With it's remarkably long, spider-like limbs and tendency to scramble over slick rocks and underwater when sighted the Haitian Cascade Anole (Anolis eugenegrahami) is unlike other lizards in the world. It's been reported only once since the 1980s (by a Dominican naturalist who visited Haiti around four years ago). The man who made the most recent observations reported that the species' only known habitat was heavily degraded, with extensive human activity and none of the impressive native trees that were reportedly present when the species was first discovered. A week ago, I came to Haiti on a trip led by my colleague Luke Mahler from the Museum of Comparative Zoology with the goal of reporting on the natural history and conservation status of this species, as well as obtaining fresh tissue samples for phylogenetic and population genetic analyses.

After two days of searching, we located a few streams near the type locality that seemed appropriate (albeit only marginally given the lack of large trees and rapidly flowing water). Then, while wandering up a small trickle that was being actively used by dozens of locals for bathing and the washing of clothes we spotted a striking black lizard on a rock face. Success! It was an adult male cascade anole! We quickly found a few more animals in the same vicinity. While capturing the first specimen, a gaggle of more than 30 local Haitians accumulated. By the time I caught it, there was literally a man playing a guitar immediately behind me, making the scene a bit surreal (see photo). Although we were initially overjoyed, the discovery was bittersweet. We couldn't find any more animals in the region, or even any more habitat that seemed remotely suitable. The exposed rock of the other streams in the region was 43C in the sun, hardly suitable for a black lizard whose only known locality was heavily shaded. Fearing we might cause the extinction of this remarkable animal, we released the only animals we caught.

The next day, we decided we needed to seek out more habitat and followed a tip from a local that we could find a series of waterfalls not far from the city of Plaisance if we walked a 6km trail. What we found after an hour and half of hiking was the most remarkable scene I've ever encountered during my career as a field biologist. As soon as we spotted the waterfalls I rose my binoculars to my eyes and began scanning the rock faces. Within seconds I'd spotted a large adult male cascade anole immediately adjacent to whitewater rushing over rocks. Moving further, we found that the rocks in this area were crawling with cascade anoles. We saw more than a dozen in less than an hour. After obtaining ecological data, video and tissue samples, we made our most remarkable observations when we watched the animals behavior underwater (more on that later!). Lizard lovers rejoice - the Haitian cascade anole lives on! Now the work must begin to preserve the scant habitat that remains.

Image legend: (1) an adult male cascade anole displaying! (photo by Mahler), (2) close-up of cascade anole, (3) cascad anole paradise, (4) attempting to noose a specimen from the waterfall locality (photo by Mahler), (5) first locality at which we found the cascade anole (note the people bathing and washing clothes and the pig in the foreground), (6) the scene behind me after catching the first animal.

Tuesday, August 4, 2009

Source of a Scourge

We now know that humans are the hosts of five different species of malaria parasites. The most virulent of these is Plasmodium falciparum, which is thought to be responsible for close to two million deaths a year. Early molecular phylogenetic studies proposed that humans acquired this parasite from chickens, but subsequent studies showed that that result was an artifact of taxon sampling and paralogous genes and that the closest relative of P. falciparum is a chimpanzee parasite, named Plasmodium reichenowi, which was discovered in the 1920's. For decades, though, only a single strain of P. reichenowi existed in the lab or in any form from which DNA could be extracted and sequenced. Recently, eight new isolates of P. reichenowi were obtained from wild and wild-born chimps and the phylogenetic history of these lineages was studied and published online yesterday in PNAS by Steve Rich of U Mass Amherst and colleagues. These new results now show very nicely that P. falciparum represents a recent host shift from chimps into humans, which may have occurred as recently as 10,000 years ago. It has long been known that these two parasites cannot be reciprocally cross-reared, i.e., chimps cannot be infected with P. falciparum and humans cannot be infected with P. reichenowi (the discoverers of this species tried to give it to themselves!). Rich et al. cite another recent study that demonstrated a different preference for erythrocyte receptors in the two parasites. Perhaps our human ancestors acquired these mutations for receptors and enjoyed a period of being malaria-free, only to have a new - and deadlier - parasite evolve that preferred the human receptor form. Unfortunately, blood smears were not made from these new chimpanzee samples, so it's not yet possible to confirm that these samples share the same distinctive morphology of P. falciparum, but Rich has assured me that they're working on this. It would also be interesting to add the second "ape" parasite, Plasmodium schwetzi, from gorillas, a species that no one has samples of for DNA analysis. What I liked the best about this new study, though, is that these results mean that P. falciparum as a species should be sunk. Think the medical community could handle that?

Monday, August 3, 2009

A Haitian Ghost

In honor of Rich's collecting trip to Haiti, which begins this week, I thought I'd do a little post on a creature that's even more elusive than Anolis dolichocephalus and which graced the pages of last week's Science: the solenodon. Solenodons are very unusual mammals - they are venomous, injecting it with their teeth, like snakes. They are also likely to be critically endangered - but it's hard to say since hardly anyone has ever seen one. In 2007, biologist Samuel Turvey went looking for them on Hispaniola for 11 days and found remains of just 3 dead ones (one of which had apparently been gnawed on by a hungry Haitian). A new survey to be conducted this October will try to get a better handle on the distribution of and threats to the solenodon as well as to do molecular phylogenetic work to help to unravel its taxonomy and population structure.