This is my last posting this year. Like last year, I have scanned my photo galleries to see which picture captures some of my research interests and looks good at the same time. This is what I found:



The picture was taken at Churí-tepui in southern Venezuela by Charles Brewer-Carias, whom I like to thank for his kind permission to share it here.

Tags: varia, tepui

Today the ICZN published a new installment in the discussion on amending the rules on nomenclature to allow e-publications.

Internet usage is rapidly growing. According to usage statistics, Latin America has a fast growing number of users. More and more journals are being electronically published, especially in the ‘developing world’. Paper publishing really has had its hey days. A strong impetus exists for e-publications of new taxa.

One of the remarks being made in this installment, is that publishing as PDF is less future-proof than usually thought. XML is presumably a better format, while others prefer RTF as standard. This is, however, no a solution for graphic formats, such as graphs or tree files usually published as supplementary materials.

Another issue is publishing of new taxa electronically in obscure journals. “To avoid confusion as grey literature becomes more readily available online, I recommend wider use of disclaimers. With theses and dissertations increasingly being made freely available online, as well as abstracts and conference proceedings, authors should be directed to clearly disclaim first-time use of names in all non-peer reviewed, manuscript-like, grey literature-type online publications.”. Now electronic ‘self-publishing’ becomes relatively easy and cheap, this may become a major issue.

It is clear that different views are being held in the taxonomic society, with a majority leaning to endorse the possibility of e-publications. In the end, whatever the Commission decides, some people will be unhappy. But anyone has had the option to give his/her opinion.

Tags: publication, varia

The Biodiversity Heritage Library is constantly improving. Not only the amount of works increases (now 838 titles tagged with “Mollusks”) and important recent works have been added (e.g., Bouchet & Rocroi’s publication), also their services have substantially improved.
A few weeks ago I discovered that they offered the service of downloading selected pages from a work as PDF. Until then, the only way was to consult the work either online or download it as a whole. Especially when you have low bandwidth, this can be a very time-consuming action, as most titles comprise many Megabytes. Therefore this service seemed very useful. When I first tested it, however, no results could be obtained. It appeared that the service was still under development and somehow I had entered their beta-website.

When I retried yesterday, the service worked flawlessly despite being announced as BETA.


When you know the pages on which the paper of your choice appeared, you can directly go to the dropdown menu and ‘Select pages to download’. An overview of the content appears, in which you can tick the pages you want.
Click on next and you will be prompted to enter the email address(es) where you want the PDF delivered.


Then you may lean back and wait. First a confirmation will arrive in your mailbox. After a short while (yesterday on average 10-15 minutes later) a message with the link to the PDF will follow.


Great service!

Tags: literature

One of the persons I met last week in Portugal was Dora Lange Canhos, director of the Centro de Referência em Informação Ambiental, CRIA (Reference Center on Environmental Information). It is a Brazilian not-for-profit NGO aimed at a more sustainable use of biodiversity through the dissemination of high quality information.

One of the CRIA projects is SpeciesLink, a distributed database that integrates information from biological collections. I mentioned it before. Currently restricted to Brazilian collections, it plans to widen its scope and hope to encompass all collections related to the Amazon Basin. Maybe, also the Suriname collection in Naturalis will be integrated in this system; this collection is currently being digitized.
When I did the ‘Bulimulidae check’ I found 225 records listed.


There is a possibility to plot the data on Google Maps.



CRIA also publishes two journals. Biota Neotropica is an open access, tri-lingual journal on conservation and sustainable use of biodiversity. It is published online.
Checklist is a quarterly journal that publishes occurrence lists, geographic distribution maps and notes on the geographic distribution of taxa. It is also published online and open access.
So far, each of both journals has published only two molluscan papers (both on non-terrestrial snails). And although the relevance for Neotropical malacology of these journals is limited, I hope that in the future also papers on land snails will be published.

Tags: bioinformatics, publishing, varia

A quick wrap up of some points that filtered down these last days.

Collaboration between different institutions, in this case at the European level, is not as easy as it may seem. Between researchers no problem, but at an institutional level collaboration is not a piece-of-cake. With one more year to go, we’ll have to see where EDIT will end up and what will follow.

Anyhow, I was impressed by the viability of the Scratchpad tool. There is a wealth of options, most of which you can ignore to get the basics of the site. And one you have these basics, the ease with which different sources of information may be tapped and seamlessly integrate is quite fascinating. A major leap forward compared to what could be done, say, 30 years ago when I stopped my research.

When in the field, biologists (taxonomists) need to act as ‘walking dataloggers’, capturing data to be transferred to databases with as much ease as possible. Be upfront on the technology waves.
The important thing is to have the data platform independent and freely exchangeable, avoiding laborious reworking of data afterwards. A ‘flat’ spreadsheet file looks like a good starting-point here.

Finally, there is the paradox between the number of taxonomists and the number of job openings. Relatively few taxonomists are left, their ranks being diminished by retirement and then replacement by more ‘en vogue’ disciplines. It seems as if catastrophes are the only events which open positions in this field. To the frustration of many young people who are interested but simply don’t get a chance.
We should take more efforts to make good use of the interest of “pro-amateurs”, people who are often spending considerable time effort to what they see as a ‘hobby’. With some guidance their efforts could become more effective.

Tags: congress, varia

Taxonomy is a science with an enormous task and limited capacity. Estimates are 4-6000 taxonomists worldwide, 30-40000 amateurs that are involved in a professional way, plus an unknown number of citizens that are interested in natural history. Moreover there is a mismatch between the potential for web-based taxonomy and the technological and management resources available. Here comes in Scratchpads...

Scratchpads specifically enable community efforts and allow data to be uploaded and tagged in an intuitive way. The published data can be easily reviewed and maintained by the community, e.g. a group of collaborators.
This potential for sharing and building data made me decide to start using a Scratchpad. Hopefully, some of you will join me in this new way to participate in science.
See here, for more details on Scratchpads and what they are all about.

Functionality that I personally like are modules for bibliography, image galleries, phylogenetic trees, character matrices (under development), distribution maps. Also functionality is available for web fora and newsletters (both with email integration) and user blogs.

After an intensive day of training I have updated the Orthalicoidea site at several points. Have a look yourself!




Needless to say that this will always be a work in progress, evolving slowly, but hopefully steadily...

Reference:
Sarkar, I.N., 2009. Biodiversity Informatics: the emergence of a field. BMC Bioinformatics 10 (Suppl. 14): S1

Tags: publishing, blogging, bioinformatics

No pictures, just words...sharing some of the topics from today’s meeting in Portugal, Carvoeiro. Just brief summaries. Presentations may be found here.

Simon Tiller opened the meeting with putting some perspective. EDIT will run for one more year and it hasn’t been decided about any follow-up.
Its aim is about integration, so rather than funding research it is about the intergration of reseach. And more and more about how at the European level integration at the institutional may take shape. The EDIT Platform for Cybertaxonomy is one of the important products that comes out of EDIT.

Tony Rees gave an overview of the biodiversity informatics landscape.

Christine Hine presented a sociological view on user engagement and innovation in cybertaxonomy. Science comprise of different subcultures, which lead to ’trading zones’ when it comes to interdisciplinarity and collaboration (co-operative or coerced / homogeneous or different groups). This should be kept in mind when designing web-based tools. The user is known (e.g. through site statistics), but usually is isn’t known how the information is used.
Daphne Duin presented the results of a survey on users of Scratchpads. Why do people engage? User needs are best discovered when actually using the product (i.e. Scratchpad), customizing the product to make it perfect for themselves. This user-centered innovation processes are to be preferred, where users = innovators: they want to make something they can use (opposed to manufacture-centered processed systems designed to sell).

Christophe Haüser stressed the role of field work, gathering data in such a way that they are captured in a digital way, stored according to protocols and shared with the community, thereby eliminating the need to gather the same data again and again. He also stressed the importance of geographically focussed species reference lists / authority files used by systems and databases.

The next three presentations were all dealing with the EDIT Platform for Cybertaxonomy. Centered around the Common Data Model (CDM), the taxonomic editor and geographical tools were elucidated. Also crossmedia publishing based on CDM, using stylesheets, will be a deliverable of EDIT. So let’s see what comes out of it one year from now when the EDIT programme comes to an end.

The slides of the presentations may be put up a site later. I’ll keep you posted.

Tags: congress

My last two papers that appeared in Zoologische Verhandelingen and had not yet been included in the Naturalis Repository, were added today.
These are my 1978 paper with notes and descriptions (ZV 164) and my 1979 thesis with a revision of the Bulimulinae (ZV 168).

Tags: publishing

This week, EDIT will have its General Meeting from 15-17 December in Portugal, Carvoeiro. Representatives of the 28 member institutions will gather for several topics. The first day is devoted to presentations by young taxonomists. After the General Meeting a one-day Training Course on Scratchpads will be given.

As one of the representatives of Naturalis I will travel today to Portugal and join the General Meeting tomorrow. Hope to learn the basics of Drupal mastering during the Training Course on Thursday.
When the internet connections allow, I will post some impressions during these days. Otherwise you will see some scribbles here after my return.

Tags: varia

In reaction to this post, Gabriela Cuezzo sent me another picture of a Cyclodontina that she recently took in Argentina, Missiones, just across the border of Brazil.




According to her this is C. guarani (d’Orbigny, 1835), described from Prov. Corrientes. This species strongly resembles C. fusiformis (Menke, 1828), which is only known from Brazil and was recognized by Ignacio Agudo on the photograph (re-figured below).



Although the pictures are made at a different angle, the similarities are striking (e.g., the darker blotches on the upper whorls). Gabriela’s picture clearly shows the sculpture of strong axial striae; the lower-hand figure is too unclear to be decisive about this feature.

Of course, it could be a striking case of vicariance that one species (fusiformis) lives only on one side of the river and another (guarani) on the other side. At the same time, the possibility that this is a case of ‘administrative classification’ cannot be excluded, nor even a possibility synonymy.
Perhaps a good occasion for a joint excursion of some Argentinian-Brazilian malacologists to find out the true status?

Tags: Cyclodontina, Argentina

Bulimulus is one of the most inconspicuous genus groups in the Orthalicidae. Always corneous, always more or less the same size and shell shape.



Here is a picture of a living B. inconspicuus Haas, 1949, taken by Grace Montalván at Peru, Dept. Loreto, near Iquitos. A well-chosen name for this species. However, it clearly may be identified by the white line bordering the suture.



Thanks Grace!

Tags: Bulimulus, Peru

Continued from last month, today the radula of Plectostylus coquimbensis (Broderip, 1832) from Chile, Coquimbo. Radula formula: C/1 + L16/1 + M56/3.






From top to bottom, left to right: overview, showing half row; C+L1; teeth 18 (M2); teeth 56-57 (M40-41); teeth 30-31 (M14-15); teeth 44-53 (M28-37); teeth 27-34 (M11-18).

Tags: Plectostylus, Chile, radula

Another picture from the Panoramio site, this time from the Argentinan side of the river. The snail is Drymaeus interpunctus (Martens, 1887).



The classification of this species is slightly uncertain, usually placed in Drymaeus (Mesembrinus), but some give this subgenus generic status. The ID was made by Ignacio Agudo.

Tags: Drymaeus, Argentina

Another species from the same area as the previous post, is Leiostracus perlucidus (Spix, 1827).



The ID is by Ignacio Agudo.

Tags: Leiostracus, Brazil

A while ago, some snail photographs were posted by Andrew Vik on Panoramio, the site that links to places in Google Earth. Here is one of them, Cyclodontina fusiformis (Menke, 1828) from Foz do Iguaçu in southern Brazil, also occurring across the border in Argentina and Paraguay.



The ID was made by Ignacio Agudo and posted on the Conch-List, kindly brought to my attention by Gijs Kronenberg.

Tags: Cyclodontina, Brazil

Sometimes I’m wondering about the great variation in shell shapes and colour patterns observed within my group. They range from turrited to discoidal and everything in between. Many are unicoloured, but some are outrageous in their patterns.



Recently, a group of biophysics and mathematicians has published a paper about shell structure and patterns. Although it is focussed on aquatic snails, I think it is equally relevant for those interested in land molluscs.



Can you see which of the two is the real shell and which the simulated one?

With only a few parameters defining the morphospace, the authors were able to simulate a wide variety of shell shapes and colour patterns.

In this work, we have shown that a single neurosecretory model can replicate both the growth of mollusk shells and the enormous diversity of pigment patterns they exhibit. The model is built around the general property of local excitation coupled with lateral inhi- bition common to most neural networks. A noteworthy feature in this model is that the same network architecture operates in both the spatial and time directions because the pigment patterns develop sequentially as the mantle lays down periodic increments of shell and pigment. Thus, the shell pattern records the complete time history of its neurosecretory activity. One might think of the pattern as an electroencephalogram, or the history of the thoughts of a mollusk! In general, waves propagating through a 3-dimensional neural network (e.g., a cortical column) have this same property: Local excitation/lateral inhibition extends laterally, as well as back- wards in space from where the excitation came, which is essentially backwards in time.

We now start to understand how mollusks may arrive at the bewildering variety of shapes and how variation within a taxon may occur. It opens up exciting new venues for further, evolutionary research.

Thanks to Nicole Webster, who mentioned this work during her talk at our internal Molecular Meeting and sent me the paper.

Reference:
Boettiger, A., Ermentrout, B. & Oster, G., 2009. The neural origins of shell structure and pattern in aquatic mollusks. - Proceedings of the National Academy of Sciences 106: 6837-6842.

Tags: literature, varia

Tree snails in the Florida Keys have been studied for about a century now. They are a good subject to follow the fate of the different populations on different ‘hammocks’. Exactly what Fadely (2009) has done.

The study examined the past and present spatial distribution of the Florida tree snail, L. fasciatus solidus, in the Long Pine Key area of the Everglades National Park. Remote sensing and mobile GIS were used to create a GIS database of the field research results. Collection and survey-based data were used to create a current spatial distribution map of L. fasciatus solidus throughout the Long Pine Key area. The data collected during the 2006 survey were compared to a 1931 survey of the same study area conducted by Dr. William Clench of the Museum of Comparative Zoology (MCZ) of Harvard University. The data was used to determine the success of L. fasciatus solidus from 1931 to 2006, to evaluate a correlation between hammock size and the number of color forms, and to detect migration patterns of L. fasciatus solidus within the Long Pine Key area of Everglades National Park. Based on the average success rate for the seven color forms and the hammocks, the L. fasciatus solidus population in the Long Pine Key area
exemplifies one of a stable community. Each color form used for the analysis had a success rate between 67% and 100%. These percentages can only be the worst case scenario based on the fact that many Liguus were not observed, and any others that would have been observed, would only increase the success rate.



An interesting hypothesis is about the relation between the number of colour forms and the size of the hammock. The author supposed that there would be a linear relationship. However, as the figures show, this is clearly not the case. It is not evident from the data presented in his report to what extent re-introductions, migration and differences in data collection between the 1931 and 2006 surveys affect these results.

Reference:
Fadely, J.R., 2009. Population distribution of Liguus fasciatus solidus in Long Pine Key of Everglades National Park: i-xvi, 1-62. Thesis (M.Sc.), Florida Atlantic University, Boca Raton, Florida.

Tags: USA, Liguus, literature

The family Acavidae is a rare find in the Neotropics. This family may be found in the ‘Old World’ in Australia, Seychelles, Sri Lanka and Madagascar. And in Chile, where the genus Macrocyclis occurs with its sole species M. peruvianus (Lamarck, 1822).

This large species is up to 60 mm diameter. Although it is commonly known as the largest snail in the Chilean land snail fauna, its anatomy was hitherto unknown. Recently, da Silva & Thomé (2009) unveiled more details on the ecology and anatomy.


It was founds after a hard day of searching, under fallen logs near the vicinity of Lago Azul.



This is another case of Gondwanan distribution at the family level. It would be interesting to see if the affinities are confirmed by molecular evidence.

Reference:
da Silva, L.F. & Thomé, J.W., 2009. Macrocyclis peruvianus (Gastropoda, Acavidae), an endemic land snail from Chile. - Iheringa, Zoologia 99(2): 125-128.

Tags: Acavidae, Chile, Gondwana, literature

Richard Palmer today did a colloquium at Naturalis on Development and evolution of morphological asymmetries - A role for natural history.



Evolution by natural selection requires three steps.  New forms of organisms must arise, have an impact on fitness (survival or fecundity), and (ultimately) be heritable.  The first step - how new forms arise - remains controversial.  Traditionally, new phenotypes are ascribed to novel genotypes (mutants or recombinants).  But developmental plasticity - the same genotype yields different forms in different environments - may be a much more important source of new forms than generally recognized.
The absence of heritable variation for direction of asymmetry in species that show a random mixture of asymmetric forms (i.e., equal numbers of right- and left-handed forms), identifies a unique phenotype - "direction of asymmetry" - for which there is no genotype.  A wide-ranging survey of asymmetry variation within and among species of animals and plants offers some of the strongest evidence to date for a 'phenotype-precedes-genotype' mode of evolution.  But this survey remains woefully incomplete.  Museums, systematists and natural historians have much to offer.

Tags: varia