[ The video contains English subtitles :-) ]
[ The video contains English subtitles :-) ]
Submitting whole chloroplast genome sequences could be a complicated task because of all the files and their formats required by GenBank. I have documented all the steps necessary to complete this task in a bitbucket repository:
Please consider citing the paper: doi:10.1002/aps3.1151
Good luck with your submissions!
Con inmenso dolor les comunico que Santiago Diaz-Piedrahita ha muerto. Mis pensamientos están con su familia y amigos mas cercanos. Santiago murió ayer, 4 de marzo de 2014, luego de haber pasado varios días en cuidados intensivos debido a un derrame ocurrido el pasado 28 de febrero.
Santiago fue un incansable botánico e historiador. Su abundante producción académica se refleja en los numerosos artículos y libros que publicó. De su obra se destaca su aporte al conocimiento de la familia de las Compuestas y a la historia de la botánica en Colombia (ver lista de publicaciones).
Santiago ademas de ser docente y ejemplo a multiples generaciones de biólogos, era
excelente mentor, colega y amigo. No cabe duda que el Doctor Diaz nos va a hacer mucha falta.
I regret to inform you all that Santiago Diaz-Piedrahita has passed way. Mi thoughts are with his family and friends. Santiago died yesterday, March 4 2014, after being in intensive care after a stroke on February 28.
Santiago was an indefatigable botanist and historian. His abundant academic production is reflected in the numerous species, papers, and books he published. His contribution to the knowledge of the Compositae family of plants and the history of botany in Colombia is of remarkable importance (see entire list of publications).
In addition to being a docent and a role model for multiple generations of biologists, Santiago was a excellent mentor, a supportive colleague, and a loyal friend. There is no doubt we are going to miss him.
A new paper recently published my colleague Santiago Madriñán propose that páramos evolved faster than any other biodiversity hotspots. Here the text from from the NY times
A new species of lichen, discovered close to Bogota, Colombia was found on Diplostephium revolutum. See complete note here:
During the last week I had the fortune of visiting the Paramo of Frontino, one of the most important paramos of the Western Cordillera in Colombia and the largest of the Antioquia department. My aim was to identify and collect the species of Diplostephium living up there. Thanks to the collaboration of professor Fernando Alzate of "Universidad de Antioquia" I was able to join his team who is working in the flora of Antioquia's paramos, Alzate's team has been visiting the paramos of Antioquia cataloging their flora. Since the main objective of Alzate's students was to collect and photograph every single plant in flower or fruit and cover all the area, the visit lasted five days. Since my task was little in comparison with theirs, I served as a photographer for such a project.
To reach the Paramo of Frontino we traveled the whole day, first we had to travel to vereda of Chuscales close to the town of Urrao from Medellín. Then, we hiked from a farm in Chuscales at about 2400 m (7900 ft) to 3600 m (11800 ft) in about four and half hours. We rented horses that carried our backpacks, food, and equipment. We reached the location for camping at about 4 pm. On the second day, we started our botanical task collecting and photographing the flora surrounding our camp. There were so many plants that we had to press at night time suffering from cold. On the third day we decided to reach the highest point of the paramo, the "Alto Campanas" at about 4000 m (13100 ft). We hiked about 2 and half hours to reach Campanas, the hiked was mainly on the crest of a the mountain that reaches summit, since the crest is the highest at that point of the cordillera the wind was strong and imposing (watch video here). Once in Campanas we walked to the beautiful the lagoon next to it. In order to cover as much area as possible, on the fourth day of the expedition the team divided in two, while Santiago and Herber visited an area called llano grande, Astrid and me visited the swampy and the forest areas. The last day we returned to Medellin. In total we collected close to a hundred specimens and took more than five hundred photographs, which means we cataloged almost a hundred species including four species of Diplostephium.
We were lucky since it only rain a couple of times mostly at night time, and we had one night with no clouds when we were able to appreciate the beauty of this landscape at night. After such an beautiful visit there is no doubt that the paramo is the place where the earth and the sky get together.
Please click in the image to swap the photos or use your arrows
The lack of representation of some species in natural history collections may be due to some causes including: lack of a precise description of the location where type specimen was collected, change of name of locations, natural rarity of the species on the wild, lack of biological knowledge about the species, and habitat loss. These causes can hinder the collection of such species for research purposes.
Over the last week I embarked in the search of three species of Diplostephium that have poor representations in the herbaria I have consulted, D. huertasii, D. jaramilloi and D. jenesanum. Following the records I wanted to collect those species in order to include them in my phylogeny for my dissertation.
The fist species I was looking for was D. jenesanum, a species described in 2002 from a specimen collected on road towards a small town named Jenesano, Boyáca, Colombia. I was able to find a couple of other records from Ventaquemada and Villapinzón without specific localities. Thanks to google earth I was able to find a couple of roads crossing a small mountain between Villapinzon and Úmbita. It turns out that one of these roads drives up to the head of the Bogotá river to the "Páramo of Guacheneque" where a healthy and protected population of D. jenesanum was found along with D. rosmarinifolium, D. juajibioyi subsp. leucopappum, D. floribundum, and D. phylicoides. North of this location I searched for D. jenesanum at its typical locality, unfortunately I was not able to find it, it was clear that the lost of habitat has almost clear out this species from the type location.
The second species I devoted my search was Diplostephium huertasii; a species described originally from "The Paramo of Chingaza" and reported scarcerly with no more than two reports per department from Boyacá, Meta, and Cauca. As far as I know, the last time this species was collected was in 1981. Taking into account that I have look for this species several times at Chingaza, I decided to look for it in Boyacá. One of the two locations where the species has been found in Boyacá is a road that connects Sogamoso in the highlands with Yopal in the lowlands. The locations described a place named Vadohondo, both collections are kind of contradictory since they differ considerably in elevation. The first, made by Cuatrecasas, was close to the road at 2600 m while the second, made by Cleef, was on the mountain at 3600 with no specific reference of how to reach the exact collection spot. I started looking first for the location on the road asking locals for the name Vadohondo. Once I found the place, I walked around looking for the plant with no luck. After two hours of search, I decided to take a secondary road looking for places with less disturbance and more elevation trying to reach Cleef's collection site. On the secondary road I was able to spot a tertiary road that was abandoned but seemed promissory. I hicked the road upslope as fast as posible since it was already late. After one hour of hiking I was able to find one individual growing on the side of the path at 3300 m, the individual looked young and was not flowered. I decided to hike a little more to see if I was able to find more individuals and spot the habitat of the species. After a while, I ran into an abandoned house and a lagoon at about 3400 m, at that point I decided to go back to the car because I need it at least one hour of light to reach the car. I was satisfied with the collection, but I had the uneasy feeling of not finding the actual populations of D. huertasii. After returning to Bogotá, while checking the old records, I realized that the specimen collected by Cleef at 3600 m said the plant was common and use to grow on rocky places. It seems that D. huertasii like rocky places of high elevations something I was not able to confirm this time, but I hope to do it next time hiking even higher on that tertiary abandoned road. I know now that Cuatrecasas collection at 2600 m was atypical and does not represent the actual habitat of D. huertasii.
The last species I was looking for was D. jaramilloi , a very similar species to D. huertasii. The only two records available from 1972 and 1973 cited a location between Arcabuco and La Palma in Boyacá Colombia between 2600 and 2900 m. The location was easy to find but not the plant. The road crosses and azonal paramo located at 2600 where I looked intensively for the plant without luck. Taking into account my last experience, I tried to look for roads or paths to reach higher altitudes. I had no luck, mostly all the land at this location is private owned and some has mining activity. Again, it seems to me that those collections represents individuals that were growing sporadically in these locations while the actual habitat could be higher on rocky climbs. At least now I have a better understanding of the distribution of the species and hopefully in the future I will be able to find out where the populations are growing.
During my recent field trip to the "Nevados National Park" of Colombia, on June 6th and 7th 2013, I had the chance of meet all the species of Diplostephium reported for this area. Here I present their photographs in the order they observed while driving up the mountain. "Paramo rosemary" is the vernacular name of some species in Colombia.
Durante mi reciente visita al Parque Nacional los Nevados, en los dias 6 y 7 de Junio de 2013, tuve la oportunidad de conocer todas las especies de Diplostephium reportadas para esta area. Aquí presento sus fotografias en el orden en el que fueron observadas a medida que se sube la montaña. "Romero de páramo" es el nombre vernáculo con el se conocen algunas especies en Colombia.
Diplostephium floribundum was found at the upper limit of the tree line making part of the preparamo at 3600 m / fue encontrada en límite superior del bosque haciendo parte del preparamo a 3600 m
Diplostephium schultzii was found at 3700 m living on the paramo and the preparamo, this species is very common and it is known to make "romerales" where in conjuntion with other high altitude species form some kind of dwarf forest / fue encontrada a los 3700 m en el páramo y prepáramo, esta especie que es muy común forma romerales que en conjunto con otras especies de altitud ensamblan bosques enanos.
Diplostephium violaceum was found at 3700-3800 m, this species not that common seems to like growing close to creeks / esta fue encontrada a los 3700-3800 m, esta especie no es muy común en el area y parece crecer bien en las riveras de las quebradas.
Diplostephium rupestre was found at 4000 m making part of the paramo, very common species / fue encontrada a 4000 m en la vegetación típica de paramo, especie común a esta altura
Diplostephium eriophorum was the last species found at 4200–4300 m before the vegetation disappeared in the altitudinal gradient at the superpáramo / fue la última especie encontrada a los 4200–4300 m antes de que la vegetación desaparezca en el gradiente altitundinal.
To celebrate earth day I am sharing this illustration of Diplostephium phylicoides. The plate was made under the Royal Botanical Expedition to New Granada headed by the Spanish botanist Jose Celestino Mutis between 1783 and 1816 in Colombia. All the original plates are available on line at the Royal Botanical Garden of Spain at http://www.rjb.csic.es/icones/mutis/paginas/index.php
The illustrated species is very common in the páramos of Cundinamarca and Boyaca departments in Colombia. Here some photos.
The GPS tells that the team moved a total of 2390 km with a maximum speed of 110 km/h and average speed of 25.5 km/h (remeber this number includes the hiking). Here the map of the tracks and our vehicle: "the mountain tapir".
The team spend the last day of the expedition doing some shopping and trying exotic food before driving to Quito. The market at Otavalo (see photos) is famous for their souvenirs and handcrafts on Saturdays. The food was Yaguarlocro, a potato base soup with corn, peanuts, lamb stomach, and lamb blood. It was pretty good.
Day 9: the end of the road. After more than 2200 km and 9 different hostels we reached to the end of the collection trip. Today we collected at least 3 species at the paramo de la Virgen, on the road from Quito to the Amazon. After that, the team headed to Cayambe, the main aim of the visit there was to find Diplostephium cayambensis, unfortunately the roads to access the area were that species is found were closed. Tomorrow the team plan to drive back to Quito. Oven/herbarium/databasing/teaching work is waiting in Quito for the head of the project.
Cotopaxi was the volcano of the day 8. Roads to the volcano are west to it, not leaving the team to visit the eastern part of the volcano which is apparently more humid and more biodiverse, the team was able to collect D. ericoides. Landscape was surreal. After the visit the team headed to Papallacta a little town pass el páramo de la virgen on the road to the Amazon. The team enjoyed the iconic hot springs of the town as a preparation for the last two days of collecting.
Day 7 was about Chimborazo, an amazing volcano. The landscape was amazing, interestingly drier than the mountains at the east of the country (kind of similar to the Puna of Perú). Only two species of Diplostephium were found: D. ericoides and D. hartwegii (the most common species in Ecuador). Since the tour around the volcano ended around noon, the team decided to visit the next collection spot: a chain of mountains east of "El Chimborazo" named "El Altar". With no roads reported in the GPS neither google earth the expectations of getting to the paramo were low. In fact the roads do not cross the mountains and the team barely got to the base of the paramo with no luck finding Diplostephium. Enjoy the vicuña pictures.
The team visited a collection site between the towns of Gualaceo and Limon. It turns out to be one of the most diverse places in terms of Diplostephium. Five species were collected ! After the collection, the team traveled to Riobamba, a small city close to the next collection spot: Chimborazo.
Day five was a Cajas day. The team visited Cajas National Park (east to Cuenca) and collected two species of Diplostephium. Cajas is a beautiful place and it is a big big park. Although it seems clear that Diplostephium likes the east mountains better since more species are found there. I am tired, so please anjoy all the photos.
Day 4 was was quiet. We returned to Cuenca from Podocarpus National Park. We only sampled one locality in the paramo Del Carboncillo. We collected one species of Diplostephium (already collected before in a different location) and one species of Llerasia, the latter had beautiful yellow heads with a honey smell. I also bought a new hat in Cuenca. Tomorrow Cajas National Park is waiting for us.
One of the most amazing things of the hiking was the páramo, it was a very different páramo from the one of Colombia, in the peaks were the wind is really strong the vegetation was dominated by some dwarf Bambusoideae grass. In between this grass Diplostephium empretifolium was found, a compact subsrhub apparently adapted to the strong wind.
By the way, in one the pass up there the wind took my hat way, it blow 20 m high and then fell in the cliff, it was a funny/sad lost. That hat traveled with me for more than three years from 2009 to uncountable places, I hope I can find another one here.
Day 2 has been the most productive day for the team. Looking for paramos from Cuenca to Loja, the team was able to collect FIVE species of Diplostephium. Tomorrow a hiking day at the Podocarpus National Park is waiting for us.