mei 2010
Online journals
12-05-2010 09:46
A website where (very
irregularly) two journals appear that might be
interesting for those interested in Neotropical
biology, is the website of the Caribbean Natural History
Group.
The first journal is Cocuyo. This journal started in 1994 and is presented as a Newsletter of the Invertebrate Zoologists of the Antilles. The content is mainly centered on Cuba. Several malacological papers have appear in the 17 issues to date. All issues can be downloaded as PDFs.
The other journal is Solenodon, Antillean journal of zoological taxonomy. In the eight issues that appeared since the start in 2001, no malacological papers have been published.
The first journal is Cocuyo. This journal started in 1994 and is presented as a Newsletter of the Invertebrate Zoologists of the Antilles. The content is mainly centered on Cuba. Several malacological papers have appear in the 17 issues to date. All issues can be downloaded as PDFs.
The other journal is Solenodon, Antillean journal of zoological taxonomy. In the eight issues that appeared since the start in 2001, no malacological papers have been published.
Pedro's presentation
11-05-2010 19:16
Pedro Romero,
guest at
Naturalis, gave today a brief
presentation to my colleagues. He told about his
previous research, viz. phylogenetics of land
snails populations in the coastal desert and
Amazonian forest of Peru.
Also he explained what he plans to do during his 3-month stay. More phylogenetical work.
To be continued...
Also he explained what he plans to do during his 3-month stay. More phylogenetical work.
To be continued...
Geo and GIS tools, again
10-05-2010 07:07
There are lots of handy
tools out there and when you trawl the internet long
enough you might find a good hit now and then. Some
people are sharing generously their tricks with
others and do this very focussed. Bob Mesibov, who has published
before on
the use of Google Maps, is one of them.
“I've previously posted here about the usefulness of Google Maps as a field tool and a kind of layman's GIS. There are a couple of new features and accessories worth noting. What follows is an edited version of a short contribution for Banksia (http://www.sasb.org.au/banksia.html), the newsletter of the Society of Australian Systematic Biologists.
(1) Plotting locality data
In the last Banksia I described how to plot a set of locations in Google Maps by home-crafting a KML file to sit on a Web server. There's an easier way to get the KML, although there could be a data security issue. A free Web service hosted by BatchGeo (http://www.batchgeo.com/) allows you to upload a whole spreadsheet full of locations and associated data. The locations are then plotted on Google Maps on BatchGeo's website. An option on the map is to save the data to a KML.
(2) Finding lat/longs
On Google Earth, you can get the lat/long of a point by hovering the cursor over it. The lat/long appears in the status bar at the bottom of the screen (or grid reference if UTM is selected in Google Earth Options).
Google Maps doesn't have this feature, but you can get nearly the same thing by first clicking on the tiny green lab flask at the top right of the Google Maps window, just to the left of the 'Help' and 'Sign In' links. A new window will appear, displaying the apps under development at Google Maps Labs. The two apps we're interested in are Lat/Lng Tool Tip and Lat/Lng Marker. If you enable the Tool Tip and save changes, Google Maps will now display the lat/long of the point under the cursor, in decimal degrees.
The Lat/Lng Marker works this way: hover the cursor over a spot, then right-click. At the bottom of the context menu is 'Drop Lat/Lng Marker'. Choose this, and a marker appears at the spot, again with lat/long in decimal degrees.
(3) Travel between localities
One of the most useful features of Google Maps is its ability to give you directions by road ('Get Directions'), with distances for each road segment travelled and an overall approximate travelling time. This feature can also be used with destinations specified by lat/long. Suppose you're in your office. Find the office on Google Maps and use the Lat/Lng Marker to get your lat/long. Enter the coordinates as starting place in the Get Directions box (A). Want to visit a locality for a museum specimen? Enter the locality as a lat/long in the destination box (B). Click the 'Get Directions' button and Google Maps plots a route for you from office to locality. You can add additional destinations and extend the route.
If you have a Google account, you can set up 'permanent' placemarks using My Maps, but the features described above can be used without a login.”.
Some people also have the need to show the errors in their data. If you dare to look at unexpected places, in this case spotters of military planes, you might find solutions you possibly hadn’t thought of. A KML generator Excel spreadsheet is at the bottom of this link. Although you may need to give it a thought first...
“It depends how you want to do it. You can either have points plotted as error circles, or points and their error circles as separate KML files.
The second is easier to do but less satisfying. Geo Utilities has an online tool for producing buffers around points; it's well-described at http://freegeographytools.com/2007/online-google-earth-utilities-for-buffering-and-area-calculations Note that the new KML file for the buffer circles has a fixed 'radius' (it's actually a bunch of points on the diameter). If you have a range of errors in your locality data set, that set has to be broken into its different error values. It should be possible to combine the KML files into a single 'MultiGeometry' file but I haven't tried it.
The first would be handy. You'd have a spreadsheet with separate fields for lat, long and error. You'd feed this to a KML generator, and it would produce placemarked circles with radius based on the value in the error field. I say 'would be handy' because I haven't seen this yet. Anyone?
There are of course GIS tools for doing this off the Web, e.g. http://www.spatialecology.com/htools/buffer.php For my own, humble GIS needs I run the venerable ArcView 3.2 (through Wine under Linux, works great). In AV3.2 I can show different size circles for different error values simply by displaying according to 'Unique Value' in the error field (e.g. 25, 50, 100, etc metres) in my attribute table, then adjusting the symbol size and colour to my liking.”
For the handling of errors in localities, see also the BioGeomanger workbench, which is highly interactive. You can change the radius of the error circle by dragging the yellow balloon.
Thanks Bob, for sharing the tools!
“I've previously posted here about the usefulness of Google Maps as a field tool and a kind of layman's GIS. There are a couple of new features and accessories worth noting. What follows is an edited version of a short contribution for Banksia (http://www.sasb.org.au/banksia.html), the newsletter of the Society of Australian Systematic Biologists.
(1) Plotting locality data
In the last Banksia I described how to plot a set of locations in Google Maps by home-crafting a KML file to sit on a Web server. There's an easier way to get the KML, although there could be a data security issue. A free Web service hosted by BatchGeo (http://www.batchgeo.com/) allows you to upload a whole spreadsheet full of locations and associated data. The locations are then plotted on Google Maps on BatchGeo's website. An option on the map is to save the data to a KML.
(2) Finding lat/longs
On Google Earth, you can get the lat/long of a point by hovering the cursor over it. The lat/long appears in the status bar at the bottom of the screen (or grid reference if UTM is selected in Google Earth Options).
Google Maps doesn't have this feature, but you can get nearly the same thing by first clicking on the tiny green lab flask at the top right of the Google Maps window, just to the left of the 'Help' and 'Sign In' links. A new window will appear, displaying the apps under development at Google Maps Labs. The two apps we're interested in are Lat/Lng Tool Tip and Lat/Lng Marker. If you enable the Tool Tip and save changes, Google Maps will now display the lat/long of the point under the cursor, in decimal degrees.
The Lat/Lng Marker works this way: hover the cursor over a spot, then right-click. At the bottom of the context menu is 'Drop Lat/Lng Marker'. Choose this, and a marker appears at the spot, again with lat/long in decimal degrees.
(3) Travel between localities
One of the most useful features of Google Maps is its ability to give you directions by road ('Get Directions'), with distances for each road segment travelled and an overall approximate travelling time. This feature can also be used with destinations specified by lat/long. Suppose you're in your office. Find the office on Google Maps and use the Lat/Lng Marker to get your lat/long. Enter the coordinates as starting place in the Get Directions box (A). Want to visit a locality for a museum specimen? Enter the locality as a lat/long in the destination box (B). Click the 'Get Directions' button and Google Maps plots a route for you from office to locality. You can add additional destinations and extend the route.
If you have a Google account, you can set up 'permanent' placemarks using My Maps, but the features described above can be used without a login.”.
Some people also have the need to show the errors in their data. If you dare to look at unexpected places, in this case spotters of military planes, you might find solutions you possibly hadn’t thought of. A KML generator Excel spreadsheet is at the bottom of this link. Although you may need to give it a thought first...
“It depends how you want to do it. You can either have points plotted as error circles, or points and their error circles as separate KML files.
The second is easier to do but less satisfying. Geo Utilities has an online tool for producing buffers around points; it's well-described at http://freegeographytools.com/2007/online-google-earth-utilities-for-buffering-and-area-calculations Note that the new KML file for the buffer circles has a fixed 'radius' (it's actually a bunch of points on the diameter). If you have a range of errors in your locality data set, that set has to be broken into its different error values. It should be possible to combine the KML files into a single 'MultiGeometry' file but I haven't tried it.
The first would be handy. You'd have a spreadsheet with separate fields for lat, long and error. You'd feed this to a KML generator, and it would produce placemarked circles with radius based on the value in the error field. I say 'would be handy' because I haven't seen this yet. Anyone?
There are of course GIS tools for doing this off the Web, e.g. http://www.spatialecology.com/htools/buffer.php For my own, humble GIS needs I run the venerable ArcView 3.2 (through Wine under Linux, works great). In AV3.2 I can show different size circles for different error values simply by displaying according to 'Unique Value' in the error field (e.g. 25, 50, 100, etc metres) in my attribute table, then adjusting the symbol size and colour to my liking.”
For the handling of errors in localities, see also the BioGeomanger workbench, which is highly interactive. You can change the radius of the error circle by dragging the yellow balloon.
Thanks Bob, for sharing the tools!
Photo of the day (96): Pseudogracilinenia
07-05-2010 09:00
In the same area as in the previous post, at Cuevas de las Lechuzas, Pseudogracilinenia huallagana (Pilsbry, 1949) was collected by Valentín Mogollón and Grace Montalván.
Bibliography of Cuban land snails
06-05-2010 19:12
Today the Bibliography of Cuban terrestrial Mollusca, including related and biohistorical papers on Cuban malacology appear as Technical Bulletin 12 at NCB Naturalis.
If interested you may order a copy for free. Within short it will available for download from the Naturalis Repository.
Abnormalities in Cuban snails
06-05-2010 09:21
Adrián González kindly
sent me some interesting pictures of abnormal Cuban
land snails. Some of you may call them weird and some
consider them as ‘freaks’ which are highly valued by
collectors.
The first pictures are of Zachrysia guanensis castanea Aguayo & Jaume, 1954, from the Cuajani valley in Viñales, Piñar del Río province. This is an animal with a split in the right ocular tentacle.
The second series considers Polymita muscorum from Holguín province. Here is P. m. splendida Torre, 1950 from municipality of Frank País, Corinthia:
Interestingly, this population shows very few or none of the spots that are normal in P. muscarum.
But Adrián also found an albino form that is very common in many populations; this one is also P. m. splendida from Cano Doce, Banes in Holguín province. Note the spots on the shell typically of P. muscarum and compare them with those on the last shell in this series, which is known as P. sulphurosa flammulata Torre, 1950.
The dots in this shell may indicate a hybridization process between P. sulphurosa and P. muscarum.
Finally, within the population of P. m. splendida at Cano Doce, there is a conical shaped form, described as variety subrocheri by Carlos de la Torre in 1950 (foreground left in the next picture). It is recommended that this population is studied before their habitat is converted into pasture land.
Within this population, some abnormal (‘teratological’) shaped specimens were observed.
Alejandro Fernández, Vicente Berovides and Bernardo Reyes-Tur have made important studies about Polymita (references in the bibliography on Cuban land snails). One of the papers is by Fernández & Berovides (1995), reporting on the different subspecies of P. muscarum in Holguín province. The distribution of these forms in this province would make a more detailed study, using DNA to clarify the phylogeography of the traits, very interesting.
Thanks Adrián, for sharing this information.
Reference:
Fernández, A. & Berovides, V., 1995. Las subespecies de Polymita muscarum en Holguín (Gastropoda: Helminthoglyptidae). - Cocuyo 4: 26-28.
The first pictures are of Zachrysia guanensis castanea Aguayo & Jaume, 1954, from the Cuajani valley in Viñales, Piñar del Río province. This is an animal with a split in the right ocular tentacle.
The second series considers Polymita muscorum from Holguín province. Here is P. m. splendida Torre, 1950 from municipality of Frank País, Corinthia:
Interestingly, this population shows very few or none of the spots that are normal in P. muscarum.
But Adrián also found an albino form that is very common in many populations; this one is also P. m. splendida from Cano Doce, Banes in Holguín province. Note the spots on the shell typically of P. muscarum and compare them with those on the last shell in this series, which is known as P. sulphurosa flammulata Torre, 1950.
The dots in this shell may indicate a hybridization process between P. sulphurosa and P. muscarum.
Finally, within the population of P. m. splendida at Cano Doce, there is a conical shaped form, described as variety subrocheri by Carlos de la Torre in 1950 (foreground left in the next picture). It is recommended that this population is studied before their habitat is converted into pasture land.
Within this population, some abnormal (‘teratological’) shaped specimens were observed.
Alejandro Fernández, Vicente Berovides and Bernardo Reyes-Tur have made important studies about Polymita (references in the bibliography on Cuban land snails). One of the papers is by Fernández & Berovides (1995), reporting on the different subspecies of P. muscarum in Holguín province. The distribution of these forms in this province would make a more detailed study, using DNA to clarify the phylogeography of the traits, very interesting.
Thanks Adrián, for sharing this information.
Reference:
Fernández, A. & Berovides, V., 1995. Las subespecies de Polymita muscarum en Holguín (Gastropoda: Helminthoglyptidae). - Cocuyo 4: 26-28.
Photo of the day (95): Peruinia
05-05-2010 08:52
This picture was made by Valentín Mogollón during his recent trip to Tingo María. It pictures Peruinia flachi tingomariae (Pilsbry, 1922), found at Microcuenca Las Pavas.
Fossil Cerions again
04-05-2010 19:52
As a sequel to
his previous
paper on
fossil Cerion
from the Bahamas,
Paul Hearty (2010) has published a new paper on
this topic.
His abstract is as follows:
Despite the nearly 600 named species of the land snail Cerion, studies of the geological and paleonto- logical framework of modern species are few. To address this deficiency, the biostratigraphic succession of Cerion was investigated at several areas on Long Island, Bahamas. A chronostratigraphic framework was developed through whole-rock and Cerion land snail aminostratigraphies. About 175 individual Cerion shells from last interglacial and Holocene deposits were age-ranked using stratigraphic position and amino acid racemization (AAR) geochronology. AAR ages were generated using an existing AAR-14C age model for Cerion from the central Bahamas. The age structure of Cerion fossils in sediments was determined with AAR ages, and the magnitude of ‘‘dead carbon’’ anomalies was evaluated using this chronological approach.
Temporal changes in gross shell morphology were examined from four study areas. The last inter-glacial, marine isotope stage/substage (MIS) 5e (Aminozone E) is characterized by generally large shells and in some cases, bimodal sets of very small (a shells) and very large forms (b shells) coexisting in the same stratigraphic levels (primarily soils), which may encompass the transition from between MIS 5e and 5d/c. Similar bimodality of nearly identical a and b shell forms and sizes is observed at other late MIS 5e sites from the furthest reaches of Great Bahama Bank (including Long, Exumas, Eleuthera, and New Providence Islands). The widespread distribution of a and b forms in soils capping MIS 5e marine and eolian deposits implies that there may have been a synchronous, regional morphological convergence on Great Bahama Bank. None of these forms are observed in Holocene deposits of Aminozone A.
The earliest MIS 1 Cerion appear in a oolite deposited 6500 a BP, and are of intermediate size compared to the Pleistocene a and b forms. As MIS 1 progressed, the diversity of shell sizes and shapes increased into modern times. The greater variety of shell forms over the past 1000–2000 a suggests that humans may have played a role in the introduction and redistribution of Cerion across the region. The potential for frequent and widespread human introductions, combined with the propensity of Cerion to hybridise freely may explain the farrago of shell sizes and shapes in the recent snail faunas of Long Island and other Bahama islands.
Reference:
Hearty, P.J., 2010. Chronostratigraphy and morphological changes in Cerion land snail shells over the past 130 ka on Long Island, Bahamas. - Quarternary Geochronology 5: 50-64.
His abstract is as follows:
Despite the nearly 600 named species of the land snail Cerion, studies of the geological and paleonto- logical framework of modern species are few. To address this deficiency, the biostratigraphic succession of Cerion was investigated at several areas on Long Island, Bahamas. A chronostratigraphic framework was developed through whole-rock and Cerion land snail aminostratigraphies. About 175 individual Cerion shells from last interglacial and Holocene deposits were age-ranked using stratigraphic position and amino acid racemization (AAR) geochronology. AAR ages were generated using an existing AAR-14C age model for Cerion from the central Bahamas. The age structure of Cerion fossils in sediments was determined with AAR ages, and the magnitude of ‘‘dead carbon’’ anomalies was evaluated using this chronological approach.
Temporal changes in gross shell morphology were examined from four study areas. The last inter-glacial, marine isotope stage/substage (MIS) 5e (Aminozone E) is characterized by generally large shells and in some cases, bimodal sets of very small (a shells) and very large forms (b shells) coexisting in the same stratigraphic levels (primarily soils), which may encompass the transition from between MIS 5e and 5d/c. Similar bimodality of nearly identical a and b shell forms and sizes is observed at other late MIS 5e sites from the furthest reaches of Great Bahama Bank (including Long, Exumas, Eleuthera, and New Providence Islands). The widespread distribution of a and b forms in soils capping MIS 5e marine and eolian deposits implies that there may have been a synchronous, regional morphological convergence on Great Bahama Bank. None of these forms are observed in Holocene deposits of Aminozone A.
The earliest MIS 1 Cerion appear in a oolite deposited 6500 a BP, and are of intermediate size compared to the Pleistocene a and b forms. As MIS 1 progressed, the diversity of shell sizes and shapes increased into modern times. The greater variety of shell forms over the past 1000–2000 a suggests that humans may have played a role in the introduction and redistribution of Cerion across the region. The potential for frequent and widespread human introductions, combined with the propensity of Cerion to hybridise freely may explain the farrago of shell sizes and shapes in the recent snail faunas of Long Island and other Bahama islands.
Reference:
Hearty, P.J., 2010. Chronostratigraphy and morphological changes in Cerion land snail shells over the past 130 ka on Long Island, Bahamas. - Quarternary Geochronology 5: 50-64.
A special guest
03-05-2010 20:35
Today, Pedro Romero
arrived at Amsterdam Schiphol Airport. He will stay
till end July as Martin fellow at NCB Naturalis.
Pedro is a recently graduated biologist (M.Sc., Universidad San Marcos, Lima, Peru) and will do phylogenetic work on Orthalicidae.
After previous email contact, I met him during my recent field trip in Peru. Here we are in a lomas near Ancón, where we collected snails and a flowering Tillandsia plant for Fernanda Salinas, a Chilean botanist who is studying DNA of populations in the Chilean and Peruvian coastal desert..
The next few months I hope to do much work in cooperation with Pedro. Welcome to Holland!
Pedro is a recently graduated biologist (M.Sc., Universidad San Marcos, Lima, Peru) and will do phylogenetic work on Orthalicidae.
After previous email contact, I met him during my recent field trip in Peru. Here we are in a lomas near Ancón, where we collected snails and a flowering Tillandsia plant for Fernanda Salinas, a Chilean botanist who is studying DNA of populations in the Chilean and Peruvian coastal desert..
The next few months I hope to do much work in cooperation with Pedro. Welcome to Holland!