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Center for Comparative Genomics 

July 25, 2012

CCG PhyloCluster updates

July 25, 2012

We have added some new apps to the PhyloCluster and upgraded others:

NEW:

BayesTraits - A program by Mark Pagel that enables the analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits.

Structure 2.3.4 - Structure by Pritchard, Stephens and Donnelly can be used for inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

UPDATED:

BEAST updated to 1.7.2 - We have also added the ability to select a random seed for each analysis. This will permit users to run multiple independent analyses of the same input file and combine them as a single large analysis with uniques starting seeds. This is useful if you are not getting acceptable “efeffective sample size” (ESS) values (typically below 100) with single runs and need to run many more generations. For e.g., if a 50 million generation run is not producing acceptable ESS values you could run 8 simultaneous 50 million generation analyses and combine them for a total of 400 million generations. Having a unique starting seed improves independence. We have kept BEAST 1.6.2 in case you still have xml files generated by BEAUTi 1.6.2.

MrBayes updates to 3.2.1 - For more info about the Mrbayes update, please visit the Mrbayes website.

RAxML updated to 7.2.6 - We have added the ability to use constraint and backbone trees in your Likelihood analyses. The trees must be in Newick (phylip) format. standard NEXUS trees can be converted in TreeView or Mesquite and the taxon names MUST be identical to those in you input file. Please visit the RAxML manual for details.




Filed under: CCG Laboratory — brian @ 1:37 pm

April 19, 2012

Good bye Príncipe hello again São Tomé

I have returned to São Tomé after three days in Príncipe. My colleagues Jim Shevock and Miko Nadel will stay on Príncipe for another two weeks collecting mosses and lichens. Jim and Miko will be joined by Bob Drewes (Be sure to read Bob’s extensive Gulf of Guinea blog) and Andrew Stanbridge in a few days. I leave São Tomé tomorrow morning at 5 AM without a single limpet.  A positive spin on the lack of limpets is the fact that there are no limpets on these islands. This raises the question of why. Is it the rock composition? Do African limpet species have poor dispersal capabilities? Are limpets competitively excluded from the islands? Are the algae that limpets typically feed on excluded? São Tomé and Príncipe are volcanic oceanic islands created by a fissure in the African plate. They belong to an archipelago that also includes Bioko, which is the closest island to the African continent and Annobon, which is the furthest from the continent. São Tomé is younger than Príncipe and dates back to approximately 13 million years while Príncipe is about 35 million years old. Because Príncipe is considerably older than São Tomé and closer to the mainland I thought there would have been more opportunities for limpets to colonize Príncipe. Bioko Island is actually located on the continental shelf and is therefore not an oceanic island and hosts many more continental flora and fauna than do the oceanic islands of this archipelago. Rayna Bell will be traveling to Bioko in August and has generously offered to look for limpets on Bioko.gulf_of_guinea

Although I did not find any limpets on Príncipe I saw many other interesting sites and animals:bb_sanantonioSanto Antóniobb_coral2bb_coralbb_banan_bchBanana Beachbb_eel2bb_eelbb_monkeyFirst time I have seen a wild monkeybb_fishesbb_miko_dive1bb_tun


Filed under: Expeditions — brian @ 9:23 am

April 15, 2012

Heaven & Hell

The morning of my flight to Príncipe was dark and wet. The rain was pouring hard and steady while thunder rolled in the distance. The Omali Resort Manager informed me that the 9 AM flight would likely be delayed and that he would call me when he had more information. About an hour later at 9AM the Manager called my room and said the flight was on. He gave me a lift to the airport and dropped me off in front of what appeared to be an abandoned airport. If you stumbled upon this edifice you would assume it was a 20th century ruin; rusty rebar poking through decayed concrete walls, the hint of a long faded emblem on  the side, a crumbled sidewalk that melted into the muddy dirt road, and nobody to be seen. The openings of where doors once swung led into various rooms with no signage. I wandered around moving from abandoned room to abandoned room until I stepped into a room with a woman sitting behind a table pecking away at her phone. She looked up at me pointed to where I had just come and barked something at me. I had a good idea that she wanted me to leave, so I did. I walked back out to the crumbled curb and noticed a few people walking towards the building. After about 15 minutes there were 6 other people with bags looking like they had travel plans.  Soon a flatbed truck showed up hauling a half dozen men who all jumped off the truck as it rolled by. The truck never actually stopped, once all of the men were off the truck it continued on down the muddy road and disappeared into the jungle. The men dispersed into various rooms and started various construction activities including jack hammering.  I stood there, the only white guy, feeling quite out of place. I had no idea what was going on, was there a flight leaving for Príncipe? Was I in line for a different flight? Was this a bus station? Totally clueless and I am sure it showed. All the other folks clutching bags seemed at ease chatting on their phones. Finally, the barking woman appeared and barked again and everybody and their bags followed her into one of the rooms. She had each of us put our bags and then ourselves onto a scale with a giant dial that spun around a couple times then slowly waddled back and forth until it settled on a number. While keeping her eyes on her phone, she pointed to a door and barked at me again. Behind this door was a rusty conveyor belt that carried my belongings into a big white box that resembled a fallen junkyard refrigerator. I was asked to walk through a metal detector and was handed my belongings as I exited. I glanced over to the dead refrigerator looking for some kind of monitor that might reveal a shoe bomb or underwear explosive, but saw nothing. The seven of us ended up in a fairly typical terminal, lines of bench chairs and even some VIP-looking sofas. There was a closed duty-free shop with heaps of booze and other rubbish commonly sold at modern airports. There was a flat screen TV above the entrance to the duty-free shop tuned to some French channel. I will attempt now to share with you the horror of this otherwise reasonable waiting room. As I entered the waiting room, I was greeted with what sounded like a bullhorn amplifying a news broadcast. I actually stopped in my tracks looking to escape this horrible ruckus. I quickly realized it was the TV and surmised that it most certainly was turned up to 11. It was deafening. I moved to a seat as far away from the noise as possible. Incredibly, the other passenger sat in a row only meters from this horrible wall of sound and immediately stared up at the TV, where they stayed like statues for the entire time we were trapped in this prison. Out of nowhere sprang a playful cat that began doing figure eights around my legs. As I reached down to scratch the cat I was startled out of my seat by the sudden pounding of a jackhammer, which must have been just on the other side of the wall from my seat. I looked around the room and the TV zombies did not flinch from their collective objective of becoming deaf. I certainly couldn’t sit here. I moved to another seat that was equally far from the TV and the jackhammer.  I looked up at the TV and realized that not only was the volume so distortedly high that no one could possibly understand it, but also that the satellite signal was so choppy that the dialogues was stuttered and totally undecipherable or watchable. WTF were they looking at?  I sat trying to find some way out of this room. I set my bags on a chair and wandered back to the door that lead me into this torture chamber.  I slowly pushed the door open and leaned into the adjoining room only to see the barking woman sitting next to the fallen refrigerator glaring at me. I tried to stare back at her, but she intensified her squint and leaned slightly towards me, I quickly retreated back into the chamber fearing another barking episode. I resigned back to my seat and absorbed the wall of sounds hoping it would end soon. Of course, there were no monitors with flight info or someone to ask what the hell was going on. I sat with my head in my hands for over an hour until finally the barking woman stepped in front of the screaming TV, put her hands on her ample hips and moved her mouth as if she were speaking, but I heard nothing over the TV. She scanned the room, caught my eye, she seemed to give me an extra stare and may have furrowed her brow at me, then strolled back through the door. Nobody moved or said a word.  I had no idea what was going on, how long I would have to endure this hell, or if I was even waiting for the right flight. I began to believe that I knew what the guy in the Turkish prison from “Midnight Express” felt like. I aimlessly strolled around the terminal trying to get my mind off of the noise.  I even ambled between the zombies and the stuttering bull horn to test their reaction, none. I peered into the duty-free shop to see if I could find the most expensive item.  The current exchange rate is about 17,000$ dobras per US dollar. I think I spotted a large bottle of  Cointreau for $1.2 million dobras, awesome! For whatever reason, the terminal cat had been following me around the terminal. BTW, this cat would occasionally join the zombies and watch the TV (see photo). Just as I was contemplating a confrontation with the barking lady to escape this nightmare, she emerged from the door strolled to the TV and turned it off and made an announcement that got the zombies to grab their bags and rise to their feet. The sudden silence revealed that the jack hammers had also been silenced, something one would expect to notice while watching TV at a sane volume.

t_cat1

São Tomé TV watching terminal catt_cat2

Phew, we were now boarding this twin prop plane with two rows of seats that seated about 14 people. I was seated, naturally, next to one of the propellers. The pilot fired up the engine and the propellers began to spin, under normal circumstances I might have described them as deafening, but I could barely hear them over the ringing in my ears.

bb_plane

The tiny aircraft sped down the runway and immediately lifted off the ground and glided up and away from the island. Although there was a storm, the sea had few white caps, just appealing textures of dark and light blue sea rolled by as the plane headed towards the small island of Príncipe.

bb_map

As the tiny island came into view I could see its spectacular mountains and rock spires reaching into the clouds. This must be the kind of island where they film movies like Jurrasic Park or King Kong, just beautiful to look upon.

bb_air

After a smooth landing a dirt road led my driver to a movie star resort called Bom Bom Island Resort. I am not worthy. A manicured tile path snaked between palm trees and beach front cottages with private decks and beaches, a swimming pool, an elevated wooden walkway that spanned a lagoon to a tiny island with an amazing 360° view restaurant. This is what I imagine when I think of Ingrid Bergman and Humphrey Bogart on vacation, not a field station. I could go on extolling the beauty of this resort, but that is for a different blog. I will say, though, if you want to surprise a loved one with a trip to paradise, I cannot imagine a more romantic place.

bb_resort2bb_resort1bb_beachbb_restaurant


Filed under: Expeditions — brian @ 7:26 am

April 13, 2012

SCUBA diving, mountain climbing and frogging

There is much good news to report for today’s post. Seahorses, hybridizing frogs, mosses, lichens and the arrival of Velma and Roberta to São Tomé.

On a recreational SCUBA trip to Lagoa Azul I saw many cool things including a couple of species of eels and a beautiful seahorse. We took a boat ride around the northern tip of the island in a large zodiac and saw at least four large rusty shipwrecks along the way. Once in the water, the visibility was very good and the water was teeming with a variety of fish and invertebrates including some beautiful corals, but no limpets :’(

stp_eel3A gorgeous eel

lazul_seahorseSeahorse

Jim Shevock, Miko Nadel and Andrew Stanbridge returned from a successful two day hike up to Pico de  São Tomé where they collected over 300 specimens. The hike to the peak was quite treacherous, steep, wet and slippery which caused many falls and tumbles and they had a face-to-face meeting with a black cobra. Nobody was injured, but they are walking around very slowly this morning.

pico_st_view2A view from the Pico de São Tomé climb. Photo: Andrew Stanbridge

cobraAn African forest cobra
Photo: Andrew Stanbridge

Rayna Bell has made two very successful night treks into the jungle collecting frogs. She is using molecular data to characterize hybridization between two known species found here on Sao Tome. Her collecting sites are along the putative hybrid zone. The first night collecting, she and Bob Drewes collected a dozen little frogs and the following night I joined her and we found 18 frogs, including a mating pair. Once back at the resort Rayna examined the frogs closely and realized that the coupled pair were two different species – Wow! physical behavioral evidence of hybridization! Needless to say Rayna is very pleased.

frog

Photo: Andrew Stanbridge

Tomio Iwamoto, Rayna Bell, Andrew Stanbridge and I went on a snorkeling trip to Lagoa Azul. It was a beautiful sunny day and the water was clear and refreshing. We saw many fish, corals, sea slugs and I found another seahorse, Hippocampus algiricus.

seahorse-seahellPhoto: Andrew Stanbridge

Velma and Roberta arrived today to begin the public education component of the expedition.

Tomorrow (Sat) I fly alone to the smaller Island of Príncipe for a three day hunt to find limpets. I will stay at the Bom Bom Island Resort on the northern side of the island and will be joined by Shevock and Nadel on Sunday.


Filed under: Expeditions — brian @ 11:12 am

April 11, 2012

Rolas Island

Yesterday, Bob Drewes, Rayna Bell and I embarked on a journey down to the southern end of the island to catch a ferry to Rolas island to look for Cobra bobo and limpets.

sao_tome_map_tracks2

Meanwhile, Jim Shevock, Miko Nadel, Andrew Stanbridge, and three porters made an early start for a three day hike up the pico São Tomé to collect mosses and lichens. The bryologist woke to heavy rains, but decided to attempt the climb anyway. Unfortunately, by the time they reached the trailhead torrents of water were streaming down the trails and they postponed the expedition. This morning was sunny and hot and as far as we know they are on their way up the mountain.

Rayna, Bob and I made good time down the west coast until we ran into a river crossing that was submerged by the storm runoff. After a quick assessment of the submerged bridge we decided we should wait for an hour or so and hope the waters would recede.

drewes_flood

After about 45 minutes the water level dropped quite a bit and we made a successful run at it.

car_flooddrewes_flood_madeit

We arrived at the ferry dock with time to spare. The ferry was a 35 foot canoe with a very loud motor.

ferry

The 30 minute crossing was fairly rough, but nothing to be concerned about.

brian_bell_rolas_ferrydrewes_bell_rolas_ferry

Once on the island, we were joined by a couple of locals who enthusiastically offered to help us find the Cobra bobo. We hiked away from the small port into the jungle flipping logs and rocks, but the jungle floor appeared to have already been turned over; it looked like someone had gone over the entire jungle with a rototiller. I asked one of the locals about this and he told us that the pigs were responsible for this and that the pigs eat everything including cobra bobo.

bob_bell_rolas

After about 2 hours, we went back to the port and ate our packed lunch. Bob and Rayna decided to climb the main peak in the hope that the cobra bobo might be found at a higher elevations. I spent that time in the tidepools and intertidal looking for limpets. Guess what, no bloody limpets. BAH.

Rayna and Bob returned from their hike and reported that no where on that island is safe from the pigs; we saw pigs everywhere and lots of them.

The regular ferry was not available to take us back to São Tomé island so they offered to take us back on the SS Denis Rodman.

drewes_bell_rolas_return

While the collecting was unsuccessful we had a good trip and enjoyed the scenery and the people.

dock_jump_rolascentipede pto_allegra


Filed under: Expeditions — brian @ 7:23 am

April 9, 2012

Snakes, caecilians, mosses, lichens, but no limpets

We have traveled to most of the accessible parts of the island and still no signs of limpets.

sao_tome_map_tracks

We have found a few reptiles and amphibians and many mosses, liverworts, hornworts and lichens. Jim Shevock has collected more than a hundred species of mosses and discovered two new families of mosses to sao tome. Miko Nadel has collected over a hundred lichens so far.

Jim Shevock

jim_tree

Miko Nadel

miko_river

I found a few more Cobra bobos (new photos below), but while hunting them, I had a frightening encounter with the tail of a black Cobra (a real cobra introduced to the island).  As one does when looking for reptiles and amphibians, I was flipping rotten logs lying on the jungle floor. One particular flip produced the flash of a big black shiny tail that slithered away into the brush. The tail was no more than a foot from my hand. On  São Tomé , a black shiny tail can only belong to the black Cobra.  Fortunately, the business end of the cobra was pointing in the opposite direction of my hands.

cobra_bobo22cobra_bobo3

Man selling black cobra skins

cobra_man

On Satuday, April 7, 2012 Bob Drewes, Tomio Iwamoto, Rayna Bell, Pedro Pio and I hiked up to the ridge overlooking Lagoa Amelia on a 3 hour reconassaince trek identifying the best spots to find tree frogs for a future night time collecting trips.

lag_amelia_trek2lagoa_amelia_trek

In between collecting sites we visit small villages and the ruins of coco and coffee plantations.  São Tomé and Principe were once known as the “Chocolate islands” (more on the history of  São Tomé and Principe on a later post). The people in the small villages seem not to mind our invasions and the children flock to us in excitement.

kids2

Once again, no limpets to be found :(
(photo: Andrew Stanbridge)

brian_intertidal


Filed under: Expeditions — brian @ 12:35 am

April 3, 2012

Northwest side of São Tomé

Today, we explored the north and northwest sides of the island and again there were no limpets to be found. In fact, the intertidal rocks host very few organisms. We have seen many nerites, a few tunicates under rocks, small anemones, heaps of crabs, encrusting bryozoans, and two or three other species of snails.  However, we did find the Cobra bobo, a beautiful yellow caecilian native to the island,  we met many wonderful people, and saw spectacular landscapes.

Cobra bobo

cobra_bobo2

Mountains

mountains1
frizzy_hair

School kids

school_kids1
rock_diving

trunk

Laundry

laundry

Drying corn

corn_drying


Filed under: Expeditions — brian @ 11:03 am

Beach combing for limpet shells

I spent yesterday combing the beaches for limpet shells. São Tomé was hit with a big storm last week and there were many shells washed ashore. If there are indeed limpets here, some shells should have been washed ashore by the storm. I enlisted the help of some locals and they found many limpet-like shells but alas, none are true limpets.

limpet hunterslimpet hunters2


Filed under: Expeditions — brian @ 10:02 am

April 1, 2012

São Tomé Reconnaissance

Today was primarily a reconnaissance tour of São Tomé with a little collecting here and there.  Sadly, still no limpets.

Sao Tome is biologically, geologically, and culturally stunning.

Parrot beak
(Heliconia rostrata)

fruit

Pico Cao Grande (664m tall)

Pico Cao Grande

Kids greeting us by the road

kids

Fisherman
fisherman


Filed under: Expeditions — brian @ 3:51 pm

March 31, 2012

The first São Tomé limpet?

Is this the first São Tomé Limpet?

barnacle zoomed out

Nope, just a small barnacle

micro barnacle


Filed under: Expeditions — brian @ 11:13 am
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