mei 2008
Flora of the Venezuelan Guayana
16-05-2008 21:01
Finally I received my copy of the introductory volume
of this milestone work, which was published already
in 1995. I decided to buy it, since I'm intrigued by
the 'Lost World' and it's one of my
research
topics.
Otto Huber, who is undoubtedly
the
expert on this region, wrote or contributed to all
chapters. Chapter 1 gives a description of the
geography and physical features, with details on the
different tepuis. The history of botanical
exploration is laid out in chapter 2, covering
well-known explorers from the past (Alexander von
Humboldt, Aimé Bonpland, Robert Schomburgk) as well
as more recent ones (William Phelps, Julian
Steyermark, Paul Berry). Chapter 3 gives an overview
of the vegetation, also documented on the
accompanying map. A floristic and phytogeographical
analysis is presented in the next chapter, while the
concluding one deals with conservation issues of the
region.
Further details on the remaining volumes can be found on the website of the project, where also a photo gallery presents a nice impression of the area.
I was very impressed by all the data and the nice photos in the book, which will serve as a very useful reference work during my research.
Further details on the remaining volumes can be found on the website of the project, where also a photo gallery presents a nice impression of the area.
I was very impressed by all the data and the nice photos in the book, which will serve as a very useful reference work during my research.
Mixing morphology, taxonomy and genetics
15-05-2008 20:49
Recently I came across the PhD-thesis of Kathleen
Beese* on the evolution of reproductive traits in
gastropods. In one of her papers she analyses the
complexity of the carrefour, based on a comparative
study in 47 snail species, two of which are
Orthalicids. The data used for this part of her study
were sequence data. These were taken from literature
(Wade et al., 2006), but I was surprised that the
source of these data seemed completely inadequately
quoted:
It not only seemed a simple misidentification, but also a faunal confusion. Bulimulus semicinctus [= B. lherminieri] occurs on Guadeloupe, West Indies; B. sporadicus is a species from southern Brazil, Uruguay, Paraguay, Bolivia and northern Argentina. The same with Drymaeus: D. papyraceus lives in eastern Brazil, D. discrepans in Central America. For a taxonomical thesis this would be a severe lapsus, but luckily the thesis is about morphology...
Now on this subject it is quite interesting as she distinguishes four types of carrefour qua complexity and links that to shell size, longevity, reproductive strategy and habitat preference. The Orthalicidae are among the groups that have the most complex type of carrefour, but the evolutionary analyses suggest that this evolved independently. Thus convergence.
Upon searching for the source of confusion, it appeared that the data on the anatomy of the carrefour (derived from Van Mol, 1971) have been mingled with data on sequences (as used by Wade et al., 2006). That is a nice combination of morphology and genetics, leaving the taxonomist sandwiched in between and puzzled.
References:
Beese, K. (2007). The evolution of male and female reproductive traits in simultaneously hermaphroditic terrestrial gastropods. Universität Basel, Basel.
Van Mol, J.J. (1971) Notes anatomiques sur les Bulimulidae (Mollusques, Gastropodes, Pulmones). Annales Soc. Royale Zoologique Belgique, 101, 183-226.
Wade, C. M., P.B. Mordan & F. Naggs. (2006). Evolutionary relationships among the Pulmonate land snails and slugs (Pulmonata, Stylommatophora). Biol. J. Linnean Soc, 87, 593-610.
It not only seemed a simple misidentification, but also a faunal confusion. Bulimulus semicinctus [= B. lherminieri] occurs on Guadeloupe, West Indies; B. sporadicus is a species from southern Brazil, Uruguay, Paraguay, Bolivia and northern Argentina. The same with Drymaeus: D. papyraceus lives in eastern Brazil, D. discrepans in Central America. For a taxonomical thesis this would be a severe lapsus, but luckily the thesis is about morphology...
Now on this subject it is quite interesting as she distinguishes four types of carrefour qua complexity and links that to shell size, longevity, reproductive strategy and habitat preference. The Orthalicidae are among the groups that have the most complex type of carrefour, but the evolutionary analyses suggest that this evolved independently. Thus convergence.
Upon searching for the source of confusion, it appeared that the data on the anatomy of the carrefour (derived from Van Mol, 1971) have been mingled with data on sequences (as used by Wade et al., 2006). That is a nice combination of morphology and genetics, leaving the taxonomist sandwiched in between and puzzled.
References:
Beese, K. (2007). The evolution of male and female reproductive traits in simultaneously hermaphroditic terrestrial gastropods. Universität Basel, Basel.
Van Mol, J.J. (1971) Notes anatomiques sur les Bulimulidae (Mollusques, Gastropodes, Pulmones). Annales Soc. Royale Zoologique Belgique, 101, 183-226.
Wade, C. M., P.B. Mordan & F. Naggs. (2006). Evolutionary relationships among the Pulmonate land snails and slugs (Pulmonata, Stylommatophora). Biol. J. Linnean Soc, 87, 593-610.
Photo of the day (11): Coloniconcha
15-05-2008 16:01
Jozef Grego sent me a photograph, which he had
received from
Pedro Genaro,
a naturalist from Dominican Republic and an
excellent photographer. As I don't want to
infringe on his copyrights, I have made a direct
link. And you absolutely should do, as it is
really a very artistic picture and a very
interesting blog!
In fact it is Coloniaconcha prima Pilsbry, 1932 and when I received the first picture made by Eladio Fernandez, another excellent photographer and naturalist from the same country, it looked so strikingly like a Gaeotis (occurring on Puerto Rico), that I'm still not decided yet on the basis of the pictures alone. This is a puzzle that remains to be solved...
In fact it is Coloniaconcha prima Pilsbry, 1932 and when I received the first picture made by Eladio Fernandez, another excellent photographer and naturalist from the same country, it looked so strikingly like a Gaeotis (occurring on Puerto Rico), that I'm still not decided yet on the basis of the pictures alone. This is a puzzle that remains to be solved...
Zootaxa paper
14-05-2008 11:53
Today my first paper after too many years of
scientific silence (or more precisely, malacological
silence) has been published. It is co-authored with
Francisco Borrero and appeared in
Zootaxa.
This journal calls itself "the most rapid journal
for systematic zoologists". Well, this paper took
at least 6 months from the time of submittance and
I know for sure that another journal will beat
this time with 2 months :-) Just wait and see
later this year...
Lagging behind
14-05-2008 09:49
The past few days I had no internet connection at
home, which was very uneasy right after the long
Pentacote weekend. I feel I'm lagging behind,
although I had quite some backlog with literature and
references that partly was done during these
days.
Biomapper
08-05-2008 21:14
Biomapper is another software program for species
distribution modeling. Personally I have run it only
once (on my old Windows machine, but I prefer
cross-platform solutions). Their discussion forum,
however, is very informative, issuing regularly an
update on recent literature dealing with ENFA or
Biomapper. I wished some other groups also delivered
this service... Below are the 6 most recent
publications, all available as PDFs on the
Biomapper
site.
References:
* Calenge, C., Darmon, G., Basille, M., Loison, A. & Jullien, J.M. (2008) The factorial decomposition of the Mahalanobis distances in habitat selection studies. Ecology, 89(2), 555-566.
* Strubbe, D. & Matthysen, E. (2008) Predicting the potential distribution of invasive ring-necked parakeets Psittacula krameri in northern Belgium using an ecological niche modelling approach. Biol Invasions, on-line.
* Allouche, O., Steinitz, O., Rotem, D., Rosenfeld, A. & Kadmon, R. (2008) Incorporating distance constraints into species distribution models. Journal of Applied Ecology, 45(2), 599-609.
* Long, P.R., Zefania, S., Ffrench-Constant, R.H. & Szekely, T. (2008) Estimating the population size of an endangered shorebird, the Madagascar plover, using a habitat suitability model. Animal Conservation, 11(2), 118-127.
* Praca, E. & Gannier, A. (2008) Ecological niches of three teuthophageous odontocetes in the northwestern Mediterranean Sea. Ocean Science, 4(1), 49-59.
* Skov, H., Humphreys, E., Garthe, S., Geitner, K., Gremillet, D., Hamer, K.C., Hennicke, J., Parner, H. & Wanless, S. (2008) Application
of habitat suitability modelling to tracking data of marine animals as a means of analyzing their feeding habitats. Ecological Modelling, 212(3-4), 504-512.
References:
* Calenge, C., Darmon, G., Basille, M., Loison, A. & Jullien, J.M. (2008) The factorial decomposition of the Mahalanobis distances in habitat selection studies. Ecology, 89(2), 555-566.
* Strubbe, D. & Matthysen, E. (2008) Predicting the potential distribution of invasive ring-necked parakeets Psittacula krameri in northern Belgium using an ecological niche modelling approach. Biol Invasions, on-line.
* Allouche, O., Steinitz, O., Rotem, D., Rosenfeld, A. & Kadmon, R. (2008) Incorporating distance constraints into species distribution models. Journal of Applied Ecology, 45(2), 599-609.
* Long, P.R., Zefania, S., Ffrench-Constant, R.H. & Szekely, T. (2008) Estimating the population size of an endangered shorebird, the Madagascar plover, using a habitat suitability model. Animal Conservation, 11(2), 118-127.
* Praca, E. & Gannier, A. (2008) Ecological niches of three teuthophageous odontocetes in the northwestern Mediterranean Sea. Ocean Science, 4(1), 49-59.
* Skov, H., Humphreys, E., Garthe, S., Geitner, K., Gremillet, D., Hamer, K.C., Hennicke, J., Parner, H. & Wanless, S. (2008) Application
of habitat suitability modelling to tracking data of marine animals as a means of analyzing their feeding habitats. Ecological Modelling, 212(3-4), 504-512.
The choice of a model
07-05-2008 17:01
It is not the most recent piece of literature, but I
came across a paper of Wintle et al. (2005)* that
neatly gives an overview of the choice of different
models in relation to the availability of data.
1) Little or no data: Habitat Suitability Indices
These are conceptual 'models' that were developed for impact assessments and conservation planning. They relate each measured variable of the environment to the suitability of a site for a particular species. Since they are wholly expert-driven, the lack of independent data weakens their credibility.
2) Presence-only data
a) Use of species data without reference to environmental data. Geographical envelopes that are primarily useful for range estimation are examples of these 'models'. The maps in my revision of the Buliminae in 1979 are a clear reference. These 'models' are sensitive for missing data and spatial errors.
b) Modeling species-environment relationship in reference to species presence data. BIOCLIM and DOMAIN models as implemented in DIVA-GIS are examples.
c) Modeling species-environment relationship by comparison to the 'background' environment across the region of interest. ENFA, GARP and Maxent are models of which is ample literature available. A comparative study is Elith et al. (2006)*.
Presence-only models are most commonly used, also because occurrence data are readily available from natural history museum collections and databases.
3) Presence-absence data, when localitions that are occupied or unoccupied by a given species are recorded, usually in a systematic way, involving some level of geographical and environmental stratification in the sampling design. There are a number of models available (see the paper for references), but comparative studies have found that logistic regression is relatively well performing.
Two other categories can be distinguished, viz. models usable for counts (when actual numbers of individuals are available) and ordinal categorical data (using coarse abundance categories). Literature on these models can be found in the paper of Wintle et al.
Reference:
Elith, J. e. a. (2006). Novel methods improve prediction of species' distributions from occurrence data. Ecography, 26, 129-151.
Wintle, B. A., J. Elith & J.M. Potts. (2005). Fauna habitat modelling and mapping: a review and case study in the Lower Hunter Central Coast region of NSW. Austral Ecology, 30, 719-738.
1) Little or no data: Habitat Suitability Indices
These are conceptual 'models' that were developed for impact assessments and conservation planning. They relate each measured variable of the environment to the suitability of a site for a particular species. Since they are wholly expert-driven, the lack of independent data weakens their credibility.
2) Presence-only data
a) Use of species data without reference to environmental data. Geographical envelopes that are primarily useful for range estimation are examples of these 'models'. The maps in my revision of the Buliminae in 1979 are a clear reference. These 'models' are sensitive for missing data and spatial errors.
b) Modeling species-environment relationship in reference to species presence data. BIOCLIM and DOMAIN models as implemented in DIVA-GIS are examples.
c) Modeling species-environment relationship by comparison to the 'background' environment across the region of interest. ENFA, GARP and Maxent are models of which is ample literature available. A comparative study is Elith et al. (2006)*.
Presence-only models are most commonly used, also because occurrence data are readily available from natural history museum collections and databases.
3) Presence-absence data, when localitions that are occupied or unoccupied by a given species are recorded, usually in a systematic way, involving some level of geographical and environmental stratification in the sampling design. There are a number of models available (see the paper for references), but comparative studies have found that logistic regression is relatively well performing.
Two other categories can be distinguished, viz. models usable for counts (when actual numbers of individuals are available) and ordinal categorical data (using coarse abundance categories). Literature on these models can be found in the paper of Wintle et al.
Reference:
Elith, J. e. a. (2006). Novel methods improve prediction of species' distributions from occurrence data. Ecography, 26, 129-151.
Wintle, B. A., J. Elith & J.M. Potts. (2005). Fauna habitat modelling and mapping: a review and case study in the Lower Hunter Central Coast region of NSW. Austral Ecology, 30, 719-738.
Euromalac2008
06-05-2008 21:44
Not a Neotropical subject per sé, but I do want to
draw your attention that the 5th Congress of the
European Malacological Societies will be held from
2-6 September in Ponta Delgada, San Miguel, Azores.
One of the keynote speakers is Robert Cameron on
'Time, space and very slow motion: patterns in the
diversity of snails'. An intriguing title that sounds
very promising...
As there is no travel budget at Naturalis for associate researchers I will not attend, but still it is interesting to know this upcoming gathering. Full details can be found on the congress website.
As there is no travel budget at Naturalis for associate researchers I will not attend, but still it is interesting to know this upcoming gathering. Full details can be found on the congress website.
Photo of the day (10): Corona
01-05-2008 11:54
Last year Gabriela Cuezzo was so kind to send me a
photograph that she took during a visit to Los
Amigos, near Maldonado, Peru. It is a specimens of
Corona regina (Ferussac, 1821).
