jun. 2009
100 Qs to bridge the gap
30-06-2009 07:30
Conservation issues are gaining more and more
attention. But it always the question if the academia
are researching subjects that matter to practitioners
and policy-makers. Sutherland et al. (2009) have
addressed this gap and set up a process to identify
scientific questions that, if answered, would have
the greatest impact on conservation practice and
policy.
Through a Delphi-approach they boiled down the initial list of 2291 questions to 1655, which were prioritized at a 2-day workshop of the participants. The resulting 100 questions are divided into 12 sections: ecosystem functions and services, climate change, technological change, protected areas, ecosystem management, organizational systems and processes, societal context and change, and impacts of conservation interventions.
Looking at this list from the viewpoint of a natural history museum researcher (not pretending an university), the first theme appeals. “Key research areas include investigating which components of biological diversity are essential for providing ecosystem services, ...”. The first question certainly seems relevant to me: “Do critical tresholds exist at which the loss of species diversity, or the loss of particular species, disrupts ecosystems functions and services, and how can these tresholds be predicted?”.
The last part of the question reminds me of a recent book published by Marten Scheffer, Critical transitions in nature and society. If you have time to look at the video of his lecture at the Stockholm Resilience Center in 2007 (54’, also available as audio file), you certainly should do. Very interesting...
Another interesting questions is in the theme Climatic change: “Which elements of biodiversity in which locations are most vulnerable to climatic change, including extreme events?”. I think a interesting potential example is the topic that I posted yesterday.
If you would like to see the remaining 98 questions, you can consult the paper here. But be warned, it is at a relatively high abstraction level compared to the usual topic of this blog.
Reference:
Sutherland et al., 2009. One hundred questions of importance to the conservation of global biological diversity. - Conservation Biology 25: 557-567.
Through a Delphi-approach they boiled down the initial list of 2291 questions to 1655, which were prioritized at a 2-day workshop of the participants. The resulting 100 questions are divided into 12 sections: ecosystem functions and services, climate change, technological change, protected areas, ecosystem management, organizational systems and processes, societal context and change, and impacts of conservation interventions.
Looking at this list from the viewpoint of a natural history museum researcher (not pretending an university), the first theme appeals. “Key research areas include investigating which components of biological diversity are essential for providing ecosystem services, ...”. The first question certainly seems relevant to me: “Do critical tresholds exist at which the loss of species diversity, or the loss of particular species, disrupts ecosystems functions and services, and how can these tresholds be predicted?”.
The last part of the question reminds me of a recent book published by Marten Scheffer, Critical transitions in nature and society. If you have time to look at the video of his lecture at the Stockholm Resilience Center in 2007 (54’, also available as audio file), you certainly should do. Very interesting...
Another interesting questions is in the theme Climatic change: “Which elements of biodiversity in which locations are most vulnerable to climatic change, including extreme events?”. I think a interesting potential example is the topic that I posted yesterday.
If you would like to see the remaining 98 questions, you can consult the paper here. But be warned, it is at a relatively high abstraction level compared to the usual topic of this blog.
Reference:
Sutherland et al., 2009. One hundred questions of importance to the conservation of global biological diversity. - Conservation Biology 25: 557-567.
Climate change and tepuis
29-06-2009 20:57
Conservationists may be alarmed (again), although it
doesn’t concern a charismatic or a flagship species.
It’s about the ecosystem of the
tepuis.
And, although the threat is not immediate, it is a
serious one.
Valentí Rull has written, alone or together with members of his research group, many papers of interest about the Guayana Shield (Pantepui). Recently, one more appeared dealing with the potential effects of climate change on the tepui ecosystem. By modeling the shift of the biotas due to temperature rises of 2 and 4 degrees, they calculated the effects on the vascular plants. Evidence is provided that up to 45% of Pantepui species may be endangered with extinction due to habitat loss before the end of the century, if the temperature rises with 4 degrees.
The bromeliads in which snails have been found are on the list of species involved. The ecological ties between plants and snails may turn out unfavorable for the snails, given the fact that they are only occurring on the upper part of the tepuis and these communities are bound to be affected. Due to the flatness of these mountaintops there will be no escape...
Reference:
Nogué, S., Rull, V. & Vegas-Vilarrúbia, T., 2009. Modeling biodiversity loss by global warming on Pantepui, northern South America: projecting upward migration and potential habitat loss. - Climatic Change 94: 77-85.
Valentí Rull has written, alone or together with members of his research group, many papers of interest about the Guayana Shield (Pantepui). Recently, one more appeared dealing with the potential effects of climate change on the tepui ecosystem. By modeling the shift of the biotas due to temperature rises of 2 and 4 degrees, they calculated the effects on the vascular plants. Evidence is provided that up to 45% of Pantepui species may be endangered with extinction due to habitat loss before the end of the century, if the temperature rises with 4 degrees.
The bromeliads in which snails have been found are on the list of species involved. The ecological ties between plants and snails may turn out unfavorable for the snails, given the fact that they are only occurring on the upper part of the tepuis and these communities are bound to be affected. Due to the flatness of these mountaintops there will be no escape...
Reference:
Nogué, S., Rull, V. & Vegas-Vilarrúbia, T., 2009. Modeling biodiversity loss by global warming on Pantepui, northern South America: projecting upward migration and potential habitat loss. - Climatic Change 94: 77-85.
Open Taxonomy again
26-06-2009 20:12
Continuing my earlier post of
restructuring
taxonomy.
On the Google discussion group on Open Taxonomy Projects, Bob Mesidov posted today an outline of tasks suitable for involving non-experts. His draft is here; be sure to read also this.
Excellent draft indeed. We might have to realize, however, that these tasks are aimed (IMHO) at the high-end of the potential target group, i.e. those people who already have a keen interest in 'taxonomy' and biology (although they might not realize it or might call it differently).
In my view, there could be at least two other groups that have potential as targets, albeit they will have to be approached in a different way.
a. People with a special interests and skills in one of the tasks but without a keen or proven interest in biology. They need to be either stimulated to link their skills to biological specimens or the biology component need to be 'wrapped' in such way that recognize it as something reasonable to do.
An example: Someone who has as hobby Photoshopping pictures, could do polishing some biological pictures from time to time when presented in the right context.
b. Ordinary people without any interest in biology, but offered some special tasks in the context of e.g. a game; also the example of Captcha could be such a context.
Examples: proofreading using Captcha, landmarking images using a game.
If so have any feelings about this topic, let me know via the comments or by becoming a member of the Google group.
Update: an outline of the workflow can be found here.
On the Google discussion group on Open Taxonomy Projects, Bob Mesidov posted today an outline of tasks suitable for involving non-experts. His draft is here; be sure to read also this.
Excellent draft indeed. We might have to realize, however, that these tasks are aimed (IMHO) at the high-end of the potential target group, i.e. those people who already have a keen interest in 'taxonomy' and biology (although they might not realize it or might call it differently).
In my view, there could be at least two other groups that have potential as targets, albeit they will have to be approached in a different way.
a. People with a special interests and skills in one of the tasks but without a keen or proven interest in biology. They need to be either stimulated to link their skills to biological specimens or the biology component need to be 'wrapped' in such way that recognize it as something reasonable to do.
An example: Someone who has as hobby Photoshopping pictures, could do polishing some biological pictures from time to time when presented in the right context.
b. Ordinary people without any interest in biology, but offered some special tasks in the context of e.g. a game; also the example of Captcha could be such a context.
Examples: proofreading using Captcha, landmarking images using a game.
If so have any feelings about this topic, let me know via the comments or by becoming a member of the Google group.
Update: an outline of the workflow can be found here.
Florida Liguus
25-06-2009 22:04
Thomas Watters has published a very useful book on
Annulariidae a couple of years ago and when I looked
him up on the internet, I found out that the Ohio
State University Museum (OSUM) at Columbus has part
of their site dedicated to Florida
Liguus.
Liguus is a genus of arboreal snails that can be found in Florida on ‘hammocks’.
The word “hammock” was first used by early inhabitants to mean a cool and shady place. Later, settlers of Florida used the word “hummock” to indicate areas that were slightly higher in elevation from the rest of the land. Today, the term hammock is used in Florida to describe forest habitats that are typically higher in elevation than surrounding areas and that are characterized by hardwood forests of broad-leaved evergreens. Tropical hardwood hammocks occur in south Florida and along the Florida coastlines where danger from frost is rare and tropical trees and shrubs common to the Caribbean islands (West Indian origin) are able to survive. (source: Karim & Mean, 2004)
On the OSUM there is a brief introduction to the Floridan Liguus. The many ‘varieties’ or ‘forms’ described in literature are nicely plotted on maps. What makes the museum collection important, is the availability of material collected in the beginning of the previous century when human “development” hadn’t spread out as far as it is today.
When you look at the maps, you can clearly see that the eastern colonies have been eradicated. Sometimes, museums act as the physical proof of lost biodiversity. Unfortunately, too many times...
Liguus is a genus of arboreal snails that can be found in Florida on ‘hammocks’.
The word “hammock” was first used by early inhabitants to mean a cool and shady place. Later, settlers of Florida used the word “hummock” to indicate areas that were slightly higher in elevation from the rest of the land. Today, the term hammock is used in Florida to describe forest habitats that are typically higher in elevation than surrounding areas and that are characterized by hardwood forests of broad-leaved evergreens. Tropical hardwood hammocks occur in south Florida and along the Florida coastlines where danger from frost is rare and tropical trees and shrubs common to the Caribbean islands (West Indian origin) are able to survive. (source: Karim & Mean, 2004)
On the OSUM there is a brief introduction to the Floridan Liguus. The many ‘varieties’ or ‘forms’ described in literature are nicely plotted on maps. What makes the museum collection important, is the availability of material collected in the beginning of the previous century when human “development” hadn’t spread out as far as it is today.
When you look at the maps, you can clearly see that the eastern colonies have been eradicated. Sometimes, museums act as the physical proof of lost biodiversity. Unfortunately, too many times...
Snails and spiders (4)
24-06-2009 21:35
Sometimes snails and spiders are difficult to
disentangle. While some species mimic
spider
behaviour,
some fellows might find themselves trapped in a
web.
Here are some Blaesospira echinus infernalis unlucky to have this fate.
The picture is courtesy of Adrián González.
Here are some Blaesospira echinus infernalis unlucky to have this fate.
The picture is courtesy of Adrián González.
On taxonomy again
23-06-2009 20:10
Persoonia
is a journal on molecular phylogeny and evolution of
fungi. I must admit that I had never heard of it,
before Peter Hovekamp send around this
link
pointing to an interesting short note of Seifert,
Crous & Frisvad on impact factors of taxonomic
journals.
One of the factors influencing the decline of taxonomy is the low ranking in the statistics that are used for the SCI-ranking of journals and the H-ranking for authors. On both, taxonomical work and authors usually can be found at the tail end. Needless to say that this reinforces the negative imago of taxonomy (a so-called ‘perverse feed-back loop’).
The authors propose a quite elegant principle to be followed by all taxonomists and taxonomic journals, called Appropriate Citation of Taxonomy. “The principle is to ensure that common elements of taxonomic papers, generally considered de facto citations by taxonomists but not by ISI, are presented in a format that is considered a valid citation by ISI”. In short, if you can’t beat them, join them...
By citing the original works of species names or DNA sequences, taxonomists can ensure that taxonomical work will be given appropriate citation. Even if the list of references is curtailed by the editors, one should at least cite five taxonomic papers.
The only remaining condition is, that the taxonomist is able to publish in a SCI/ISI-covered journal... That is not so simple as it may seem, as the original ISI-coverage was rather arbitrary (including e.g. the Journal of Conchology), while leaving out similar journals (e.g. Basteria and Archiv für Molluskenkunde). And as a befriended editor recently told me, it may only be possible to be included in the ISI-list by paying a substantial fee... Who said that taxonomists are on the loosing end of the battle for money?
As the authors say: taxonomists and taxonomic journals: ACT!
Reference:
Seifert, K.A., Crous, P.W. & Frisvad, J.C., 2008. Correcting the impact factors of taxonomic journals by appropriate citation of taxonomy (ACT). - Persoonia 20: 105.
One of the factors influencing the decline of taxonomy is the low ranking in the statistics that are used for the SCI-ranking of journals and the H-ranking for authors. On both, taxonomical work and authors usually can be found at the tail end. Needless to say that this reinforces the negative imago of taxonomy (a so-called ‘perverse feed-back loop’).
The authors propose a quite elegant principle to be followed by all taxonomists and taxonomic journals, called Appropriate Citation of Taxonomy. “The principle is to ensure that common elements of taxonomic papers, generally considered de facto citations by taxonomists but not by ISI, are presented in a format that is considered a valid citation by ISI”. In short, if you can’t beat them, join them...
By citing the original works of species names or DNA sequences, taxonomists can ensure that taxonomical work will be given appropriate citation. Even if the list of references is curtailed by the editors, one should at least cite five taxonomic papers.
The only remaining condition is, that the taxonomist is able to publish in a SCI/ISI-covered journal... That is not so simple as it may seem, as the original ISI-coverage was rather arbitrary (including e.g. the Journal of Conchology), while leaving out similar journals (e.g. Basteria and Archiv für Molluskenkunde). And as a befriended editor recently told me, it may only be possible to be included in the ISI-list by paying a substantial fee... Who said that taxonomists are on the loosing end of the battle for money?
As the authors say: taxonomists and taxonomic journals: ACT!
Reference:
Seifert, K.A., Crous, P.W. & Frisvad, J.C., 2008. Correcting the impact factors of taxonomic journals by appropriate citation of taxonomy (ACT). - Persoonia 20: 105.
Photo of the day (55): Drymaeus
22-06-2009 09:10
The tale of Blue
Drymaeus
continues.
Richard Goldberg send me a picture of
Drymaeus
immaculatus
(C.B. Adams, 1850), that he made in 1988 when on a
trip to Jamaica, St. Ann Parish.
So far, photographs show that this blue trait is present in several taxa in West Indies, but also in at least one in South America. No doubt that the source of “blueness” is in the genes. I suspect that more species with blue-bodied animals turn up, sooner or later. The interesting question is then, how to explain this distribution of the blue trait within this genus?
Thanks Rich, for sending this interesting picture.
So far, photographs show that this blue trait is present in several taxa in West Indies, but also in at least one in South America. No doubt that the source of “blueness” is in the genes. I suspect that more species with blue-bodied animals turn up, sooner or later. The interesting question is then, how to explain this distribution of the blue trait within this genus?
Thanks Rich, for sending this interesting picture.
A putty eating snail
19-06-2009 22:09
In my ‘malaco-terrarium’ in the lab I have not
only
Plekocheilus,
but since last week also some specimens of
Cepaea
nemoralis
(L.). Quite unexpectingly, I observed a strange
phenomenon: these snails are wolverines!
I expected them to feed on algae and on the ‘malaco-mix’ described here. But earlier this week I catched one feeding on reusable putty (also known under the brand name ‘Blu-Tack’).
Needless to say that their excrements are also blue...
I expected them to feed on algae and on the ‘malaco-mix’ described here. But earlier this week I catched one feeding on reusable putty (also known under the brand name ‘Blu-Tack’).
Needless to say that their excrements are also blue...
LifeDesks
18-06-2009 10:09
Yesterday I created a new LifeDesk on Neotropical
snails.
The site provides tools for classification, taxon pages, bibliography and image galleries.
Potentially this is a great tool and I hope that, in the end, it may contain all information that gives a relevant and accurate picture of this group. At least, I will start to supply data for the Orthalicidae. With one taxon page and one bibliographic item put up, the start has been made. Until now, I was unable to upload an image that I wanted to complement the taxon page.
The first potential improvement I noticed is a link to other sites, like e.g. MorphBank, that gather partially the same information (images, bibliography). It is a nuisance to do double work and to go through different learning curves; each site has its own way of navigating and managing. Inevitable, but tedious. Integration by linking should be the direction to move forward.
This is part of the ongoing Encyclopedia of Life project, aiming at making taxonomy available to anyone at a click of your keybord. However, to make this authoritative one has to rely on the few experts that are available. But also non-experts may contribute, albeit the tools are not in place yet for making direct contributions.
If you feel you can make a useful contribution to document the biodiversity of Neotropical snails, please become a member of the team. You are more than welcome!
The site provides tools for classification, taxon pages, bibliography and image galleries.
Potentially this is a great tool and I hope that, in the end, it may contain all information that gives a relevant and accurate picture of this group. At least, I will start to supply data for the Orthalicidae. With one taxon page and one bibliographic item put up, the start has been made. Until now, I was unable to upload an image that I wanted to complement the taxon page.
The first potential improvement I noticed is a link to other sites, like e.g. MorphBank, that gather partially the same information (images, bibliography). It is a nuisance to do double work and to go through different learning curves; each site has its own way of navigating and managing. Inevitable, but tedious. Integration by linking should be the direction to move forward.
This is part of the ongoing Encyclopedia of Life project, aiming at making taxonomy available to anyone at a click of your keybord. However, to make this authoritative one has to rely on the few experts that are available. But also non-experts may contribute, albeit the tools are not in place yet for making direct contributions.
If you feel you can make a useful contribution to document the biodiversity of Neotropical snails, please become a member of the team. You are more than welcome!
Chimantá
17-06-2009 19:27
The geological expedition that went to the Chimantá
massif last month, made this brief video that will
give you an impression of their results and about the
habitat of snails.
Inside the caves also snails have been found, belonging to the hydrobiids and yet to be described.
Inside the caves also snails have been found, belonging to the hydrobiids and yet to be described.
Tepui snails again
16-06-2009 20:37
More on
snails and
bromeliads.
Today some pictures that I received from Charles
Brewer-Carias, here pictured amidst
Brocchinia
on Churí-tepui. BTW: stunning landscape...
He found snails inside the hollow axes of these bromeliads, where they shelter during the day.
As they feed on the dead leafs during the evening and at night (! again, see previous post), it was assumed at first sight that this pattern on those dead leafs were the gnawing marks of radulas from these snails.
However, I found it hard to imagine that the snails would move so ‘uncontrolled’ over these leafs to make such a pattern. And if you really look in detail on the green leaf at the right-hand corner, you will see a similar pattern shining through the leaf. My conclusion is thus that the snails may feed on e.g. algae but are not causing this pattern on the leafs.
Credits to Kiko Mayoral and Javier Mesa for the photographs and to Charles for sharing the pictures.
He found snails inside the hollow axes of these bromeliads, where they shelter during the day.
As they feed on the dead leafs during the evening and at night (! again, see previous post), it was assumed at first sight that this pattern on those dead leafs were the gnawing marks of radulas from these snails.
However, I found it hard to imagine that the snails would move so ‘uncontrolled’ over these leafs to make such a pattern. And if you really look in detail on the green leaf at the right-hand corner, you will see a similar pattern shining through the leaf. My conclusion is thus that the snails may feed on e.g. algae but are not causing this pattern on the leafs.
Credits to Kiko Mayoral and Javier Mesa for the photographs and to Charles for sharing the pictures.
A new blog
15-06-2009 20:13
Richard Goldberg sent out his Worldwide Shell Notes
#1, containing a link to his recently opened blog
which he called
Art and Science of
Nature.
When I looked it up, I was pleasantly surprised to
see that it very relevant to Neotropical snails.
It contains some nice posts on a recent trip to Jamaica, with some video shots made traveling to rainy Dolphin Head. His observations on annulariids are really nice, given the (wet) circumstances that they were made. My attention was, however, draw by a picture of a crawling orthalicid. It is Orthalicus undatus jamaicensis (Pilsbry, 1899), caught at night. If you hadn’t figured out yet, once more a proof that being a malacologist is a very tough business...
Looking around on his site, I also found a highly attractive picture of Gaeotis nigrolineatus. When I asked Richard about this picture, he said that it was made under controlled conditions. While shooting a series of shots, it deposited its eggs on the leaf.
Notice the blue appearance of the animal. It reminds me of certain blue Drymaeus...
Keep the good work up, Rich.
It contains some nice posts on a recent trip to Jamaica, with some video shots made traveling to rainy Dolphin Head. His observations on annulariids are really nice, given the (wet) circumstances that they were made. My attention was, however, draw by a picture of a crawling orthalicid. It is Orthalicus undatus jamaicensis (Pilsbry, 1899), caught at night. If you hadn’t figured out yet, once more a proof that being a malacologist is a very tough business...
Looking around on his site, I also found a highly attractive picture of Gaeotis nigrolineatus. When I asked Richard about this picture, he said that it was made under controlled conditions. While shooting a series of shots, it deposited its eggs on the leaf.
Notice the blue appearance of the animal. It reminds me of certain blue Drymaeus...
Keep the good work up, Rich.
Restructuring taxonomy
12-06-2009 20:47
Last weeks there has been a discussion on the
Taxocom-list which mainly houses professional
taxonomists. Bob Mesidov was one of the people who
stressed that taxonomists are on the loosing end of
the battle for money, attention and the influx of
young people. See also
this
in the recent issue of The Scientist. “The best we
can hope for is the replace of dead and dropped-out
experts”, Mesibov said. First there was the
biodiversity crisis, now the taxonomy crisis...
The search for solutions has started and the main direction is clear. Online, online, online whatever can be done that way. Are there any inspirational examples perhaps?
Yes, there is one in an unrelated field like astronomy, Clickworkers. Imagine you would have a similar tool for any taxonomic group, identifying patterns of characters in images stored at a database.
Or look at this amazing project, Recapcha, proving that you don’t have to rely on a single participant’s biases.
The closest example of a participation of non-experts in taxonomy is the Collembola site, where many of the images were provided by amateurs.
The ultimate example would be a ‘taxonomy game’ where the players from all over the world got playfully help to contribute to taxonomic work (and perhaps have some interesting time as well seeing the diversity of life). As far as we know, such game doesn’t exist yet.
The common denominator is Open Taxonomy Projects.
The aim is to restructure the work done by biological taxonomists so that anyone, anywhere can contribute to a taxonomic project via the Web.
From the FAQ of this group:
Isn't the job nearly finished? Aren't most species known and classified?
That might be true for birds and mammals and tall trees, and for certain animal and plant groups of economic or medical importance. The rest of the living world is still largely unknown. A recent estimate is 8-9 million species in total on Earth. Taxonomists have so far named and described fewer than 2 million. Most of the undescribed species are small, rare or both.
Why invite non-specialists to help do taxonomy?
Because there aren't enough professional taxonomists in the world, and their numbers are decreasing. Despite this decline, taxonomic knowledge is still fundamentally important in medicine, farming, forestry, fishing, land management and conservation. Taxonomic work is also urgently needed to learn about species headed for extinction in disappearing habitats.
Isn't taxonomy too hard for ordinary people? Don't you need a university degree and special training?
You need special training and experience to become a professional taxonomist. You don't need either to do many of the basic tasks in taxonomy, like documenting and comparing specimens. Open taxonomy projects will sharpen your skills with online games and training.
How are open taxonomy projects going to work? Isn't there a risk that the results won't be as good as taxonomy done by professionals?
Open taxonomy projects will be structured and managed by professional taxonomists in the same way that open-source software is developed. There will be sub-tasks, sub-task maintainers, milestones, version checking and strict adherence to all the rules of formal taxonomy and taxonomic publishing. The difference will be in the results. More specimens will be identified and more species described in less time with more people involved and with better quality control.
Isn't a lot happening these days with digital tools to make taxonomy more efficient? Can't you get increased taxonomic output that way?
There are a lot of new 'cybertaxonomy' tools. What they do is speed up some steps in the taxonomic process, like checking the scientific literature and generating identification keys. Other steps remain slow because they have to be done by humans, not computers. This slower work includes collecting and documenting specimens, comparing specimens, looking for specimen characters to assist identification and classification, testing the usefulness of those characters, etc. Overall, taxonomic output is limited by the slowest steps in the taxonomic workflow. Open taxonomic projects will speed up those slower steps by linking busy, isolated specialists with online volunteer communities that are active 24/7.
If you are interested in this topic, don’t hesitate and participate!
The search for solutions has started and the main direction is clear. Online, online, online whatever can be done that way. Are there any inspirational examples perhaps?
Yes, there is one in an unrelated field like astronomy, Clickworkers. Imagine you would have a similar tool for any taxonomic group, identifying patterns of characters in images stored at a database.
Or look at this amazing project, Recapcha, proving that you don’t have to rely on a single participant’s biases.
The closest example of a participation of non-experts in taxonomy is the Collembola site, where many of the images were provided by amateurs.
The ultimate example would be a ‘taxonomy game’ where the players from all over the world got playfully help to contribute to taxonomic work (and perhaps have some interesting time as well seeing the diversity of life). As far as we know, such game doesn’t exist yet.
The common denominator is Open Taxonomy Projects.
The aim is to restructure the work done by biological taxonomists so that anyone, anywhere can contribute to a taxonomic project via the Web.
From the FAQ of this group:
Isn't the job nearly finished? Aren't most species known and classified?
That might be true for birds and mammals and tall trees, and for certain animal and plant groups of economic or medical importance. The rest of the living world is still largely unknown. A recent estimate is 8-9 million species in total on Earth. Taxonomists have so far named and described fewer than 2 million. Most of the undescribed species are small, rare or both.
Why invite non-specialists to help do taxonomy?
Because there aren't enough professional taxonomists in the world, and their numbers are decreasing. Despite this decline, taxonomic knowledge is still fundamentally important in medicine, farming, forestry, fishing, land management and conservation. Taxonomic work is also urgently needed to learn about species headed for extinction in disappearing habitats.
Isn't taxonomy too hard for ordinary people? Don't you need a university degree and special training?
You need special training and experience to become a professional taxonomist. You don't need either to do many of the basic tasks in taxonomy, like documenting and comparing specimens. Open taxonomy projects will sharpen your skills with online games and training.
How are open taxonomy projects going to work? Isn't there a risk that the results won't be as good as taxonomy done by professionals?
Open taxonomy projects will be structured and managed by professional taxonomists in the same way that open-source software is developed. There will be sub-tasks, sub-task maintainers, milestones, version checking and strict adherence to all the rules of formal taxonomy and taxonomic publishing. The difference will be in the results. More specimens will be identified and more species described in less time with more people involved and with better quality control.
Isn't a lot happening these days with digital tools to make taxonomy more efficient? Can't you get increased taxonomic output that way?
There are a lot of new 'cybertaxonomy' tools. What they do is speed up some steps in the taxonomic process, like checking the scientific literature and generating identification keys. Other steps remain slow because they have to be done by humans, not computers. This slower work includes collecting and documenting specimens, comparing specimens, looking for specimen characters to assist identification and classification, testing the usefulness of those characters, etc. Overall, taxonomic output is limited by the slowest steps in the taxonomic workflow. Open taxonomic projects will speed up those slower steps by linking busy, isolated specialists with online volunteer communities that are active 24/7.
If you are interested in this topic, don’t hesitate and participate!
New bibliographic tool
11-06-2009 21:04
A colleague from our library sent notice about a new
bibliographic tool. It is called
Mendeley
and it allows you not only to organize your
literature, but also find new publications, share
them with others who have the same interest and see
trends based on statistics. Besides a desktop client,
it is also a tool that allows you to have your own
library anywhere on the world at the click of your
mouse. Provided that you are in a place with access
to the internet, of course.
The software is currently version 0.6.5.1 and is far from perfect. When I tried it, importing over 1600 PDFs, more than 25% had errors in the metadata. Therefore, it might be preferable to import via EndNote or BibTex, if you have one of these (I haven’t). It seems advisable to correct all the errors before one starts to share references with peers. Otherwise it will be a large hump of junk.
As with many new tools you have a considerable learning curve before it is really beneficial and enhances your productivity. However, it is an interesting tool and surely woth closely following its development.
The trend is clear....online, online, online whatever can be done that way. Some interesting news ahead...
The software is currently version 0.6.5.1 and is far from perfect. When I tried it, importing over 1600 PDFs, more than 25% had errors in the metadata. Therefore, it might be preferable to import via EndNote or BibTex, if you have one of these (I haven’t). It seems advisable to correct all the errors before one starts to share references with peers. Otherwise it will be a large hump of junk.
As with many new tools you have a considerable learning curve before it is really beneficial and enhances your productivity. However, it is an interesting tool and surely woth closely following its development.
The trend is clear....online, online, online whatever can be done that way. Some interesting news ahead...
Snails and bromeliads
10-06-2009 22:04
Charles Brewer-carias kindly sent me some
observations on a
Plekocheilus
species that he found in southern Venezuela. The
species was found inside the rosettes of
Brocchinia
leafs, where the snails hide during day-time. In the
evening they become active and start feeding on the
dead leaves of the plants.
The fact that the fresh leaves are not touched may be explained by the hard and waxed surface of these leaves. Probably the decaying leaves are soft enough to be eaten by the snails.
The fact that the fresh leaves are not touched may be explained by the hard and waxed surface of these leaves. Probably the decaying leaves are soft enough to be eaten by the snails.
Priotrochatella (2)
08-06-2009 14:51
As a continuation of the previous post, first of all
a picture of
Priotrochatella
torrei
Clapp, 1918. It is the same picture that was
published in the book
Cuba:
the landshells paradise
(Greta
Editores).
The three Cuban species all occur in the northern part of Isla de Pinos, on isolated calcareous hills. This is the map from Clench & Jacobson (1970; reference see previous post), and gives a more or less schematic impression of the situation in the early 1930s.
Distribution of
Priotroachatella species. Blue circle,
P. constellata; green star, P.
torrei; purple triangle, P.
stellata. Modified after Clench &
Jacobson, 1970.
This is how this area looks today, viewed through Google Earth. The city has considerably expanded and the roads have been altered in part, but the hills are still there. However, part of Sierra de Casas has disappeared. See the red box.
Here is a magnification of the boxed area, which shows that a quarry is eating away the hill.
And here is a side view at ground level.
As noted in my previous post, Priotroachatella species are known to dwell on calcareous rocks. Contrary to the reports from Jamaica, the Cuban species are cave dwellers. Both constellata and stellata are seriously threatened by the exploitation of marble quarries, driving these species into extinction.
It may be noted that these species are highly restricted in range and habitat and easily meet the criteria for Critically Endangered of the IUCN Red List. As I have repeatedly argued before, it is a serious omission that so few land snails are included on this List. Many need to be recognized according to the categories of this List and to be protected. Not only on Cuba, but other (Neotropical and other) snails as well.
S.O.S., Save Our Snails!!!
The three Cuban species all occur in the northern part of Isla de Pinos, on isolated calcareous hills. This is the map from Clench & Jacobson (1970; reference see previous post), and gives a more or less schematic impression of the situation in the early 1930s.
Distribution of
Priotroachatella species. Blue circle,
P. constellata; green star, P.
torrei; purple triangle, P.
stellata. Modified after Clench &
Jacobson, 1970.This is how this area looks today, viewed through Google Earth. The city has considerably expanded and the roads have been altered in part, but the hills are still there. However, part of Sierra de Casas has disappeared. See the red box.
Here is a magnification of the boxed area, which shows that a quarry is eating away the hill.
And here is a side view at ground level.
As noted in my previous post, Priotroachatella species are known to dwell on calcareous rocks. Contrary to the reports from Jamaica, the Cuban species are cave dwellers. Both constellata and stellata are seriously threatened by the exploitation of marble quarries, driving these species into extinction.
It may be noted that these species are highly restricted in range and habitat and easily meet the criteria for Critically Endangered of the IUCN Red List. As I have repeatedly argued before, it is a serious omission that so few land snails are included on this List. Many need to be recognized according to the categories of this List and to be protected. Not only on Cuba, but other (Neotropical and other) snails as well.
S.O.S., Save Our Snails!!!
Photo of the day (54): Priotrochatella
05-06-2009 19:12
If you liked my post of
yesterday,
you will even like this post better (I guess).
Today is about the helicinid genus Priotrochatella Fischer, 1893. These snails are very, very beautiful and, to say the least, they are very peculiar.
On Cuba three species have been reported, all from the Isle of Pine. The first one of which I’ve got a picture is P. costellata (Morelet, 1847).
The second species is P. stellata (Poey, 1851).
The third species is P. torrei Clapp, 1918. For a picture, see Clench & Jacobson, 1970.
More on the ecology and conservation of these species in a later post. Many thanks to Adrián González for his kind permission to show these artistic photographs here.
The genus is also known from Jamaica, where two species occur: P. josephinae (C.B. Adams, 1849) and P. pulchra (C.B. Adams, 1851). According to Ira Richling, the former species lives on moss covered calcareous rocks. On Gary Rosenberg’s site on Jamaican landsnails, I found a picture of P. pulchra and it also shows the shell amidst moss and lichens, perfectly camouflaging itself.
Reference:
Clench, W.J. & Jacobson, M.K., 1970. The genus Priotrochatella (Mollusca: Helicinidae) of the Isle of Pine and Jamaica, West Indies. - Occasional Papers On Mollusks 3 (39): 61-80.
Today is about the helicinid genus Priotrochatella Fischer, 1893. These snails are very, very beautiful and, to say the least, they are very peculiar.
On Cuba three species have been reported, all from the Isle of Pine. The first one of which I’ve got a picture is P. costellata (Morelet, 1847).
The second species is P. stellata (Poey, 1851).
The third species is P. torrei Clapp, 1918. For a picture, see Clench & Jacobson, 1970.
More on the ecology and conservation of these species in a later post. Many thanks to Adrián González for his kind permission to show these artistic photographs here.
The genus is also known from Jamaica, where two species occur: P. josephinae (C.B. Adams, 1849) and P. pulchra (C.B. Adams, 1851). According to Ira Richling, the former species lives on moss covered calcareous rocks. On Gary Rosenberg’s site on Jamaican landsnails, I found a picture of P. pulchra and it also shows the shell amidst moss and lichens, perfectly camouflaging itself.
Reference:
Clench, W.J. & Jacobson, M.K., 1970. The genus Priotrochatella (Mollusca: Helicinidae) of the Isle of Pine and Jamaica, West Indies. - Occasional Papers On Mollusks 3 (39): 61-80.
Photo of the day (53): Callonia
04-06-2009 20:15
Adrián González is doing his best to turn me from a
specialist in Orthalicidae into an ardent lover of
Cuban land shells...:-) Look at these pictures of
urocoptids.
Both are from Cuba, Prov. Pinar del Río, Sierra de Guane. The picture above is Callonia ellioti (Poey, 1857), characterized by the upward pointed axial ribs. The one below is C. lowei (de la Torre, 1927). According to Jaume & de la Torre (1976) this species is characterized within the genus by the last whorl not being solute and not having pointed axial ribs. Well, a double negation but still a stunningly beautiful animal.
Does it suffice to say that I like to have the best of both worlds? Just an ardent lover of Neotropical snails...
Reference:
Jaume, M.L. & de la Torre, A., 1976. Los Urocoptidae de Cuba (Mollusca-Pulmonata). Ciencias Biologicas (Habana) 53: 1-122.
Both are from Cuba, Prov. Pinar del Río, Sierra de Guane. The picture above is Callonia ellioti (Poey, 1857), characterized by the upward pointed axial ribs. The one below is C. lowei (de la Torre, 1927). According to Jaume & de la Torre (1976) this species is characterized within the genus by the last whorl not being solute and not having pointed axial ribs. Well, a double negation but still a stunningly beautiful animal.
Does it suffice to say that I like to have the best of both worlds? Just an ardent lover of Neotropical snails...
Reference:
Jaume, M.L. & de la Torre, A., 1976. Los Urocoptidae de Cuba (Mollusca-Pulmonata). Ciencias Biologicas (Habana) 53: 1-122.
Photo of the day (52): Liguus
03-06-2009 20:51
After my
post
on Cuban Rapid Assessments reports, Adrián González
kindly pointed out to me that the new record in one
of those reports for
Liguus
fasciatus
from the Cubitas area, wasn’t in fact any news but
had been mentioned before in literature [reference to
be added].
These pictures are Liguus fasciatus crenatus (Swainson, 1821) from this area. Besides being a devoted malacologist, Adrián is a very skillful photographer to whom I like to give full credits.
These pictures are Liguus fasciatus crenatus (Swainson, 1821) from this area. Besides being a devoted malacologist, Adrián is a very skillful photographer to whom I like to give full credits.
Book review: Correoso
02-06-2009 19:27
The first comprehensive scientific overview of the
non-marine molluscs of continental Ecuador was
published at the end of the 19th century (Cousin,
1887). More than a century later this introductory
book to land and freshwater snails from this country
appears. As the author writes, it is “an integral
study on the biodiversity ..., and includes a
characterization of the principal families and
genera”.
After the introduction there are eight chapters. The first chapter gives a historical overview on malacology in Ecuador. The description of the current situation reveals that there is hardly malacological work being done at the moment, and the collection in the natural history museum in Quito is under revision. The second chapter lists the families (32) of land and freshwater molluscs, including bivalves. A key to families is included. Chapter 3 provides a short introduction to terrestrial snails. The following chapter presents a more elaborate characterization of the families of land snails, their habitat, ecological importance, experiences with rearing under laboratory conditions, geographical distribution and occurrence in Ecuador. There are many pictures of shells and living animals. Chapter 5 and 6 repeats the same scheme for freshwater molluscs. The final two chapters give an analysis of the biogeography, dividing the country into seven regions. In the Annexes, several maps are added.
This book is clearly aimed at a rather broad public of people with an interest in molluscs. As stated before, no introductory text to this group was available for Ecuador and the book clearly serves this aim. From a scientific point of view, there are several points which could be improved; e.g. not all literature mentioned in the text is included in the list of references and there are several typos. Hopefully there will be enough demand to make a second, revised edition possible.
The author has spent many years to gather all the data and made field observations that are worth to be included in a book like the ones for Cuba or Brazil (see literature). Despite lack of funds and difficult conditions (the production of the book took several years!), it is thanks to the perseverance of the author that this book has finally resulted.
References:
Correoso Rodríguez, M., 2008 [2009]. Los moluscos terrestres y fluviales del Ecuador continental. La biodiversidad desconocida: 1-179. - SIMBIOE, Quito. ISBN 978-9978-9959-1-4.
Cousin, A., 1887. Faune malacologique de la république de l’Equateur. - Bulletin Société Zoologique de France 12: 187-287.
After the introduction there are eight chapters. The first chapter gives a historical overview on malacology in Ecuador. The description of the current situation reveals that there is hardly malacological work being done at the moment, and the collection in the natural history museum in Quito is under revision. The second chapter lists the families (32) of land and freshwater molluscs, including bivalves. A key to families is included. Chapter 3 provides a short introduction to terrestrial snails. The following chapter presents a more elaborate characterization of the families of land snails, their habitat, ecological importance, experiences with rearing under laboratory conditions, geographical distribution and occurrence in Ecuador. There are many pictures of shells and living animals. Chapter 5 and 6 repeats the same scheme for freshwater molluscs. The final two chapters give an analysis of the biogeography, dividing the country into seven regions. In the Annexes, several maps are added.
This book is clearly aimed at a rather broad public of people with an interest in molluscs. As stated before, no introductory text to this group was available for Ecuador and the book clearly serves this aim. From a scientific point of view, there are several points which could be improved; e.g. not all literature mentioned in the text is included in the list of references and there are several typos. Hopefully there will be enough demand to make a second, revised edition possible.
The author has spent many years to gather all the data and made field observations that are worth to be included in a book like the ones for Cuba or Brazil (see literature). Despite lack of funds and difficult conditions (the production of the book took several years!), it is thanks to the perseverance of the author that this book has finally resulted.
References:
Correoso Rodríguez, M., 2008 [2009]. Los moluscos terrestres y fluviales del Ecuador continental. La biodiversidad desconocida: 1-179. - SIMBIOE, Quito. ISBN 978-9978-9959-1-4.
Cousin, A., 1887. Faune malacologique de la république de l’Equateur. - Bulletin Société Zoologique de France 12: 187-287.
Online publication (2)
01-06-2009 10:00
Today a paper was published which may possibly be
seen as a milestone in online publishing of taxonomic
works (Miller et al., 2009a). It is not about
Neotropical snails; it is not even about snails. It
is about Chinese spiders. Why then bother in this
blog?
While the future of taxonomy seems with online publication, there is much debate about it and more and more taxonomists have a preference for journals that are freely accessible (Penev et al., 2008). Until now, however, an example was lacking following a clear framework and tackling some of the remaininbg stumble-blocks (e.g. the poor quality of GBIF data). Penev et al. (2009) now propose the following scheme, which is used in the open access journal of ZooKeys.
Jeremy Miller, first author of the underlying taxonomic work, showed me last week already the datasets (Miller et al., 2009b, c) and how they worked. Especially the link with Google Earth is very nice, with data on the species showing up when the locality pin is clicked upon. A link to MorphBank is included, in which pictures of the species are stored.
This model provides a good methodology for online publication, while assuring at the same time that the data are of high quality and freely accessible.
References:
Miller J.A., Griswold C.E., Yin C.M. 2009a. The symphytognathoid spiders of the Gaoligongshan, Yunnan,
China (Araneae, Araneoidea): Systematics and diversity of micro-orbweavers. - ZooKeys 11: 9-195. doi: 10.3897/zoo-
keys.11.160
Miller J.A., Griswold C.E., Yin C.M. 2009b. Appendix B. Locality data (XLS format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: Microsoft Excel (1997-2003). doi: 10.3897/
zookeys.11.160-app.B.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Miller J.A., Griswold C.E., Yin C.M., 2009c. Appendix C. Locality data (KML format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: KML (Keyhole Markup Language) version
2.1 for GoogleEarth. doi: 10.3897/zookeys.11.160-app.C.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Penev L., Erwin T., Thompson F.C., Sues H-D., Engel M.S., Agosti D., Pyle R., Ivie M., Assmann
T., Henry T., Miller J., Ananjeva N.B., Casale A., Lourenco W., Golovatch S., Fagerholm H-P.,
Taiti S., Alonso-Zarazaga M., 2008. ZooKeys, unlocking Earth’s incredible biodiversity and
building a sustainable bridge into the public domain: From “print-based” to “web-based”
taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper. - ZooKeys 1:
1-7. doi: 10.3897/zookeys.1.11
Penev L., Erwin T., Miller J., Chavan V., Moritz T., Griswold C., 2009. Publication and dissemination of data-
sets in taxonomy: ZooKeys working example. ZooKeys 11: 1-8. doi: 10.3897/zookeys.11.210
While the future of taxonomy seems with online publication, there is much debate about it and more and more taxonomists have a preference for journals that are freely accessible (Penev et al., 2008). Until now, however, an example was lacking following a clear framework and tackling some of the remaininbg stumble-blocks (e.g. the poor quality of GBIF data). Penev et al. (2009) now propose the following scheme, which is used in the open access journal of ZooKeys.
Jeremy Miller, first author of the underlying taxonomic work, showed me last week already the datasets (Miller et al., 2009b, c) and how they worked. Especially the link with Google Earth is very nice, with data on the species showing up when the locality pin is clicked upon. A link to MorphBank is included, in which pictures of the species are stored.
This model provides a good methodology for online publication, while assuring at the same time that the data are of high quality and freely accessible.
References:
Miller J.A., Griswold C.E., Yin C.M. 2009a. The symphytognathoid spiders of the Gaoligongshan, Yunnan,
China (Araneae, Araneoidea): Systematics and diversity of micro-orbweavers. - ZooKeys 11: 9-195. doi: 10.3897/zoo-
keys.11.160
Miller J.A., Griswold C.E., Yin C.M. 2009b. Appendix B. Locality data (XLS format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: Microsoft Excel (1997-2003). doi: 10.3897/
zookeys.11.160-app.B.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Miller J.A., Griswold C.E., Yin C.M., 2009c. Appendix C. Locality data (KML format) for all specimens of the
spider families Th eridiosomatidae, Mysmenidae, Anapidae, and Symphytognathidae collected during an inventory of
the Gaoligongshan, Yunnan, China, 1998-2007. DATASET. File format: KML (Keyhole Markup Language) version
2.1 for GoogleEarth. doi: 10.3897/zookeys.11.160-app.C.dt. - ZooKeys 11: 9-195. doi: 10.3897/zookeys.11.160
Penev L., Erwin T., Thompson F.C., Sues H-D., Engel M.S., Agosti D., Pyle R., Ivie M., Assmann
T., Henry T., Miller J., Ananjeva N.B., Casale A., Lourenco W., Golovatch S., Fagerholm H-P.,
Taiti S., Alonso-Zarazaga M., 2008. ZooKeys, unlocking Earth’s incredible biodiversity and
building a sustainable bridge into the public domain: From “print-based” to “web-based”
taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper. - ZooKeys 1:
1-7. doi: 10.3897/zookeys.1.11
Penev L., Erwin T., Miller J., Chavan V., Moritz T., Griswold C., 2009. Publication and dissemination of data-
sets in taxonomy: ZooKeys working example. ZooKeys 11: 1-8. doi: 10.3897/zookeys.11.210