sep 2009
Photo of the day (64): Anostoma
30-09-2009 08:12
This is a picture of a shell that was presented as a
gift to Alexander von Bülding. It originates from
Brazil, State of Paraiba. The shell is badly worn,
its original colour totally disappeared. It is
an
Anostoma,
probably
rossi
Weber, 1925. But it always difficult to base your
judgement on a picture, especially if the angle of
viewing is different from what you need.
Thanks for sharing, Alexander!
Thanks for sharing, Alexander!
DNA: from field to lab
29-09-2009 07:16
Getting good DNA isn’t as easy as often thought. The
wet collections of museums are often not suitable,
either because samples have been fixed in formalin or
because they may have stayed in alcohol 70% for too
long. But many times, it remains unclear why one
sample doesn’t yield any DNA while seemingly similar
ones give fair to good results.
The assumption is that preservation in the field might play a crucial role.
To test this assumption we have started at Naturalis an experiment with 32 combinations of killing and conservation methods. Most of the combinations are based on practices in the field, not only from malacologists but also entomologists. We are using two species of common snails, collected in Dutch gardens.
Hopefully, this experiment will make clear which combination results in the best DNA yield, given the limitations when in the field.
The assumption is that preservation in the field might play a crucial role.
To test this assumption we have started at Naturalis an experiment with 32 combinations of killing and conservation methods. Most of the combinations are based on practices in the field, not only from malacologists but also entomologists. We are using two species of common snails, collected in Dutch gardens.
Hopefully, this experiment will make clear which combination results in the best DNA yield, given the limitations when in the field.
ACvB80: again
28-09-2009 21:19
On Saturday, the Dutch Malacological Society held a
special meeting to celebrate the 80th birthday of Dr.
Dolf van Bruggen. It was the final step in the
ACvB80-project.
A number of presentation were given, of which I like to mention especially Edi Gittenberger’s one on left- and right handedness in snails. Landsnails of the Venezuelan tepuis was the topic of my presentation.
Since the celebrator of the jubilee had received his Festschrift already on his birthday, it was necessary to have another gift for him. In the end, we decided to make a bibliophile edition of the Festschrift.
We also gave him the unique copy of the final proof of the volume.
Needless to say that Dolf van Bruggen appreciated both gifts.
A number of presentation were given, of which I like to mention especially Edi Gittenberger’s one on left- and right handedness in snails. Landsnails of the Venezuelan tepuis was the topic of my presentation.
Since the celebrator of the jubilee had received his Festschrift already on his birthday, it was necessary to have another gift for him. In the end, we decided to make a bibliophile edition of the Festschrift.
We also gave him the unique copy of the final proof of the volume.
Needless to say that Dolf van Bruggen appreciated both gifts.
DNA barcoding
25-09-2009 17:10
DNA barcoding
is thought to be a method to ease species
identification. Some even think that this method may
make conventional taxonomy obsolete once techniques
like
Lab-on-a-chip
are commonly used. Funding of barcoding projects is
usually aimed at building a reference library. Any
taxonomic problem-solving is seen as a useful
by-product at most (Rougerie,
Taxacom Discussion
List).
With the above in mind, it was interesting to see a recent publication by Davison et al. (2009) on DNA barcoding in land snails. In this paper they report on a study to test the accuracy of barcoding on stylommatophoran species. As basis of the study the CO1 sequences deposited in GenBank were used; this test set represented 129 species, including a number of Neotropical species (Orthalicidae, Polygyridae). Stylommatophorans frequently show extreme divergence of mitonchondrial DNA.
The following results are noteworthy:
- barcoding correctly identified species in 92% of cases.
- optimum threshold value is 4%, but with an error rate of more than 30%; it is therefore recommended that barcoding is backed-up by phylogenetic methods and conventional taxonomy.
- intra-specific variation in stylommatophorans is genrally much higher than in other organisms.
- relatively many (> 25) samples of each species are needed if barcoding is to be effective, due to the rather extreme divergence of CO1 in land snails.
The results point to the conclusion that plenty specimens should be sampled to study the occurrence of different haplotypes in a species. When the species occurs in a broad geographical area, care should be taken to cover this area as much as possible. This may be an important point to have in the back of your mind when doing fieldwork. At the same time it may prove to be difficult to realize when sampling range-restricted or rare species. In those cases one is often glad enough to find just one or a few specimens. Any resulting barcoding should thus carefully evaluated.
Another important conclusion of this study is the recommendation that barcoding should be part of a suit of methods, including traditional morphological taxonomy, to study the intra- and interspecific variation in land snail species.
Reference:
Davison, A., Blackie, R.L.E. & Scothern, G.P., 2009. DNA barcoding of stylommatophoran land snails: a test of existing sequences. - Molecular Ecology Resources 9: 1092-1101.
With the above in mind, it was interesting to see a recent publication by Davison et al. (2009) on DNA barcoding in land snails. In this paper they report on a study to test the accuracy of barcoding on stylommatophoran species. As basis of the study the CO1 sequences deposited in GenBank were used; this test set represented 129 species, including a number of Neotropical species (Orthalicidae, Polygyridae). Stylommatophorans frequently show extreme divergence of mitonchondrial DNA.
The following results are noteworthy:
- barcoding correctly identified species in 92% of cases.
- optimum threshold value is 4%, but with an error rate of more than 30%; it is therefore recommended that barcoding is backed-up by phylogenetic methods and conventional taxonomy.
- intra-specific variation in stylommatophorans is genrally much higher than in other organisms.
- relatively many (> 25) samples of each species are needed if barcoding is to be effective, due to the rather extreme divergence of CO1 in land snails.
The results point to the conclusion that plenty specimens should be sampled to study the occurrence of different haplotypes in a species. When the species occurs in a broad geographical area, care should be taken to cover this area as much as possible. This may be an important point to have in the back of your mind when doing fieldwork. At the same time it may prove to be difficult to realize when sampling range-restricted or rare species. In those cases one is often glad enough to find just one or a few specimens. Any resulting barcoding should thus carefully evaluated.
Another important conclusion of this study is the recommendation that barcoding should be part of a suit of methods, including traditional morphological taxonomy, to study the intra- and interspecific variation in land snail species.
Reference:
Davison, A., Blackie, R.L.E. & Scothern, G.P., 2009. DNA barcoding of stylommatophoran land snails: a test of existing sequences. - Molecular Ecology Resources 9: 1092-1101.
Photo of the day (63): Huttonella
23-09-2009 07:32
Bill Frank sent in some excellent pictures that he
took of
Huttonella
bicolor
(Hutton, 1834). He found these specimens when
re-visiting the site where he had collected the
(hitherto)
mysterious
Bulimulus
species.
Since this is a tiny species, he considered himself lucky to see it amongst the debris. “If it wasn’t red, I would never have noticed it”, Bill said.
H. bicolor was already known from Florida, but it is hitherto unknown how far north the species already has spread up the East Coast of the USA.
Since this is a tiny species, he considered himself lucky to see it amongst the debris. “If it wasn’t red, I would never have noticed it”, Bill said.
H. bicolor was already known from Florida, but it is hitherto unknown how far north the species already has spread up the East Coast of the USA.
Photo of the day (62): Megalobulimus
21-09-2009 18:35
Two pictures of
Megalobulimus
species were sent to me by Valentín Mogollón. Both
species were found in the area near Tingo Maria,
Dept. Huánuco, Peru.
M. capillaceus (Pfeiffer, 1855)
M. maximus (Sowerby, 1825)
These are really king-size snails...
M. capillaceus (Pfeiffer, 1855)
M. maximus (Sowerby, 1825)
These are really king-size snails...
On the move
18-09-2009 19:44
A few more videos of the
Thaumastus
species recently reported on. They show not only some
details of the animal, but also the behaviour of
tilting the head.
30 Million
17-09-2009 19:02
30 Million euro. That is the amount of money
allocated to the new
Netherlands Centre for
Biodiversity
(NLCB), which will be formalized at the beginning of
2010. The announcement was made by the Dutch
government when the official Budget 2010 was
presented on Tuesday (“Prinsjesdag”).
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The money is part of the budget of the Ministry for Education, Culture and Science and will be spread over the next five years. It was made after a proposal by Naturalis successfully made it through various rounds of competition.
On Wednesday the news was made public in the museum. As proposed 20 million will be spent on the collection, viz. digitalization and merging of collections. The remaining 10 million will be spent on research, investing in new laboratories and equipment.
There was coffee and cake to celebrate this, but hey! we might wait till the budget has been sanctioned by the Parliament...
The allocation of the money is a major step towards an integrated institute for biodiversity research. However, there are several more steps to make before the museum as a new, enlarged organisation can open up its doors of the new building, probably in 2015. Although it may be wise to have a ‘plan B’ given the financial situation of the government in the coming years, it surely is a hopeful sign of the current priority for taxonomy and biodiversity in the Netherlands.
The money is part of the budget of the Ministry for Education, Culture and Science and will be spread over the next five years. It was made after a proposal by Naturalis successfully made it through various rounds of competition.
On Wednesday the news was made public in the museum. As proposed 20 million will be spent on the collection, viz. digitalization and merging of collections. The remaining 10 million will be spent on research, investing in new laboratories and equipment.
There was coffee and cake to celebrate this, but hey! we might wait till the budget has been sanctioned by the Parliament...
The allocation of the money is a major step towards an integrated institute for biodiversity research. However, there are several more steps to make before the museum as a new, enlarged organisation can open up its doors of the new building, probably in 2015. Although it may be wise to have a ‘plan B’ given the financial situation of the government in the coming years, it surely is a hopeful sign of the current priority for taxonomy and biodiversity in the Netherlands.
Photo of the day (61): Orthalicus
15-09-2009 20:35
A
second
species
of
Orthalicus
was found by Alexander von Bülding in the same area.
With the same stipulations as made yesterday, my opinion is that this picture shows O. prototypus (Pilsbry, 1899).
With the same stipulations as made yesterday, my opinion is that this picture shows O. prototypus (Pilsbry, 1899).
Photo of the day (60): Orthalicus
14-09-2009 20:39
Alexander von Bülding asked me to identify these
photographs of an
Orthalicus
species. This is what I wrote to him:
“It is not an easy question that you poses, to identify some pictures of Orthalicus. Pisbry, one of the giants in malacology, writes on this group: "The group is undoubtedly difficult on account of the general similarity and the frequent occurrence of parallel or convergent variations in stocks of different areas". (Pilsbry, 1930: 360).
Therefore, I should be modest in my opinions, as this group - nearly 80 years later - still needs a revision. Good data on locations, ranges and biology are still scanty available (old collections largely use imprecise, e.g. "Brazil", or incorrect locations) and variation is hardly studied and understood. Given the variation in shell morphology (especially colouration), many names have been introduced which taxonomic status is uncertain.
That having said, I'm inclined to call this specimen O. capax (Pilsbry, 1930). Again, judging by these pictures only and unable to see the shell shape and certain details”.
The pictures were taken in Brazil, Paraiba State, near Araruna.
Many thanks Alexander, for giving me permission to show these pictures here.
Reference:
Pilsbry, H.A., 1930. South American land and freshwater mollusks: notes and descriptions, VII. - Proceedings of the Academy of Natural Sciences of Philadelphia 82: 355-365.
“It is not an easy question that you poses, to identify some pictures of Orthalicus. Pisbry, one of the giants in malacology, writes on this group: "The group is undoubtedly difficult on account of the general similarity and the frequent occurrence of parallel or convergent variations in stocks of different areas". (Pilsbry, 1930: 360).
Therefore, I should be modest in my opinions, as this group - nearly 80 years later - still needs a revision. Good data on locations, ranges and biology are still scanty available (old collections largely use imprecise, e.g. "Brazil", or incorrect locations) and variation is hardly studied and understood. Given the variation in shell morphology (especially colouration), many names have been introduced which taxonomic status is uncertain.
That having said, I'm inclined to call this specimen O. capax (Pilsbry, 1930). Again, judging by these pictures only and unable to see the shell shape and certain details”.
The pictures were taken in Brazil, Paraiba State, near Araruna.
Many thanks Alexander, for giving me permission to show these pictures here.
Reference:
Pilsbry, H.A., 1930. South American land and freshwater mollusks: notes and descriptions, VII. - Proceedings of the Academy of Natural Sciences of Philadelphia 82: 355-365.
Photo of the day (59): Thaumastus
09-09-2009 20:26
Giovanni Cuno Tisalema found this nice specimen
of
Thaumastus
thompsonii
(Pfeiffer, 1845) near Gualaceo, Prov. Azuay, Ecuador.
The pictures and the video show nicely the colours of the animal (yellowish with darker lines dorsally, and a blackish mantle).
The video may be found on YouTube, if you follow the link.
The pictures and the video show nicely the colours of the animal (yellowish with darker lines dorsally, and a blackish mantle).
The video may be found on YouTube, if you follow the link.
New phylogenetic data
07-09-2009 20:06
While there is an ongoing debate the role of
bioinformatics and the species concept (see
here
and below), the number of sequences of Neotropical
land snails in GenBank grows slowly. E.g. available
for Orthalicoidea are 159 nucleotide sequences of 48
species and 105 protein sequences of 38 species.
There remains some work to be done!
Recently, a paper was published by a Peruvian group (Ramirez et al., 2009). It describes an analysis of three species of the Orthalicidae, Bostryx scalariformis, B. sordidus and Scutalus versicolor, based on the 16S rRNA mitochondrial marker. Currently, only similar data are available on Placostylus bivaricosus. So, this paper is very useful in adding species of two more genera.
Both the tree in Neighbour-Joining (left) as Maximum Parsimony (right), and the analyses using Maximum Likelihood and Bayesian Inference (not shown here), show the orthalicoid genera as a closely related group.
Most data in GenBank are on other regions of the gene, notably CO1. Barcoding “species” becomes ‘en vogue’, but on the Taxacom list the following remark by Bob Mesibov was noted:
“I urge Taxacomers to read Roger Hyam's blog
(http://www.hyam.net/blog/archives/598) in full, but here's an
interesting chunk:
"Up to now the assumption has been that we are discovering taxa in
nature and then attempting to describe them. It is undoubtedly true that
taxa do exist in nature. However, in order to construct a usable map of
biodiversity, we need to turn this on its head. It is the act of minting
an identifier and linking it to a circumscription that creates the
taxon. We then discover which specimens in the wild fit into this taxon.
Philosophically this his how we act anyway (see Identifiers, Identity
and Me). Taxa are currently hypotheses (things we invent) that may break
down as our knowledge grows."
Much of the Taxacom discussion so far has been about species
identification, because species identification is what barcoding
promises. But Hyam says 'taxon'. Re-read the paragraph above
substituting 'genus' or 'family' for 'taxon'. Still OK? (That is, if you
thought the paragraph was OK when 'taxon' meant 'species'.) Note also
that barcodes could also theoretically be used to predefine taxa higher
than species, by relaxing the sequence requirements in ways indicated by
species sampling within the higher taxon.
Now, what strikes me as strange and wonderful is that OTTH I'm perfectly
happy with Hyam's approach when thinking about genera and families,
which are constructs with a lower-grade 'existence in nature' than
species. In fact, this is how I think genera and families get built into
classifications, traditionally. It's certainly how I go about erecting
new genera for my beloved millipedes
But OTOH, Hyam's approach just doesn't click with me when I think about
circumscribing new species. Not already recognised species, of the kind
we identify a la the Taxacom discussion, but previously unrecognised
species. Like, most of the world's species?
If I read Hyam correctly, his circumscription of new species, just like
that of old species, is by means of a barcode. Quick, simple and
unambiguous (caveats, caveats), this approach *replaces* morphospecies
with barcodes. The option of linking Hyam's Barcode Taxa to
morphospecies data (with keys, diagnoses, images, etc) is just that, an
option - to create 'secondary taxonomic products' (Hyam's phrase) or
not.
So you could produce a 'map of biodiversity' by barcoding madly on a
field trip and recognising - excuse me, defining - heaps of new species.
Think of that as step 1. Steps 2, 3, etc would be learning the answers
to questions like 'How big is it?', 'What life stage?', 'Male or
female?', 'Associated with what [plant/animal]?'. Lotta work there, but
that would certainly make the 'map of biodiversity' more usable. Take
biological control, for example. Don't know how far I could get with
'GenBank RQ561336 a possible parasite of GenBank AE699133', but it would
be a real comfort to know that these entities had been rigorously
circumscribed right from the beginning.”
Personally, I prefer a sound morphological hypothesis to start with. Any barcoding may then falsify or corroborating the hypothesis. Not vice-versa.
Reference:
Ramirez, J., Ramirez, R., Romero, P., Chumbe, A. & Ramirez, P., 2009. Posición evolutiva de caracoles terrestres peruanos (Orthalicidae) entre los Stylommatophora (Mollusca: Gastropoda). - Revista Peruana de Biologia 16: 51-56.
Recently, a paper was published by a Peruvian group (Ramirez et al., 2009). It describes an analysis of three species of the Orthalicidae, Bostryx scalariformis, B. sordidus and Scutalus versicolor, based on the 16S rRNA mitochondrial marker. Currently, only similar data are available on Placostylus bivaricosus. So, this paper is very useful in adding species of two more genera.
Both the tree in Neighbour-Joining (left) as Maximum Parsimony (right), and the analyses using Maximum Likelihood and Bayesian Inference (not shown here), show the orthalicoid genera as a closely related group.
Most data in GenBank are on other regions of the gene, notably CO1. Barcoding “species” becomes ‘en vogue’, but on the Taxacom list the following remark by Bob Mesibov was noted:
“I urge Taxacomers to read Roger Hyam's blog
(http://www.hyam.net/blog/archives/598) in full, but here's an
interesting chunk:
"Up to now the assumption has been that we are discovering taxa in
nature and then attempting to describe them. It is undoubtedly true that
taxa do exist in nature. However, in order to construct a usable map of
biodiversity, we need to turn this on its head. It is the act of minting
an identifier and linking it to a circumscription that creates the
taxon. We then discover which specimens in the wild fit into this taxon.
Philosophically this his how we act anyway (see Identifiers, Identity
and Me). Taxa are currently hypotheses (things we invent) that may break
down as our knowledge grows."
Much of the Taxacom discussion so far has been about species
identification, because species identification is what barcoding
promises. But Hyam says 'taxon'. Re-read the paragraph above
substituting 'genus' or 'family' for 'taxon'. Still OK? (That is, if you
thought the paragraph was OK when 'taxon' meant 'species'.) Note also
that barcodes could also theoretically be used to predefine taxa higher
than species, by relaxing the sequence requirements in ways indicated by
species sampling within the higher taxon.
Now, what strikes me as strange and wonderful is that OTTH I'm perfectly
happy with Hyam's approach when thinking about genera and families,
which are constructs with a lower-grade 'existence in nature' than
species. In fact, this is how I think genera and families get built into
classifications, traditionally. It's certainly how I go about erecting
new genera for my beloved millipedes
But OTOH, Hyam's approach just doesn't click with me when I think about
circumscribing new species. Not already recognised species, of the kind
we identify a la the Taxacom discussion, but previously unrecognised
species. Like, most of the world's species?
If I read Hyam correctly, his circumscription of new species, just like
that of old species, is by means of a barcode. Quick, simple and
unambiguous (caveats, caveats), this approach *replaces* morphospecies
with barcodes. The option of linking Hyam's Barcode Taxa to
morphospecies data (with keys, diagnoses, images, etc) is just that, an
option - to create 'secondary taxonomic products' (Hyam's phrase) or
not.
So you could produce a 'map of biodiversity' by barcoding madly on a
field trip and recognising - excuse me, defining - heaps of new species.
Think of that as step 1. Steps 2, 3, etc would be learning the answers
to questions like 'How big is it?', 'What life stage?', 'Male or
female?', 'Associated with what [plant/animal]?'. Lotta work there, but
that would certainly make the 'map of biodiversity' more usable. Take
biological control, for example. Don't know how far I could get with
'GenBank RQ561336 a possible parasite of GenBank AE699133', but it would
be a real comfort to know that these entities had been rigorously
circumscribed right from the beginning.”
Personally, I prefer a sound morphological hypothesis to start with. Any barcoding may then falsify or corroborating the hypothesis. Not vice-versa.
Reference:
Ramirez, J., Ramirez, R., Romero, P., Chumbe, A. & Ramirez, P., 2009. Posición evolutiva de caracoles terrestres peruanos (Orthalicidae) entre los Stylommatophora (Mollusca: Gastropoda). - Revista Peruana de Biologia 16: 51-56.
The death of a snail
05-09-2009 21:43
The second of my living
Plekocheilus
snails became totally inactive and didn’t react any
more to gentle probing. Before the decay really
started, I decided to kill the animal off. Ah, life
can be very cruel... Who wants to end up in a science
laboratory?
The interesting thing is to see how the animal discoloured after I put it in alcohol 70%. Its beige coloured body when alive, turned grayish while the alcohol showed a yellowish hue. Apparently the body colour dissolved, but I can’t remember to have seen that before when preserving snails; a quick search in Scholar didn’t return any useful hits. Something to sort out later.
As a consequence this is also the end of the living type specimen story. R.I.P. Hugo and Marisabel.
The interesting thing is to see how the animal discoloured after I put it in alcohol 70%. Its beige coloured body when alive, turned grayish while the alcohol showed a yellowish hue. Apparently the body colour dissolved, but I can’t remember to have seen that before when preserving snails; a quick search in Scholar didn’t return any useful hits. Something to sort out later.
As a consequence this is also the end of the living type specimen story. R.I.P. Hugo and Marisabel.