aug. 2010
Playing the DNA game (2)
31-08-2010 22:25
Having analyzed so far
only ITS/28S data, I’m now trying to combine
different partitions from both nuclear and
mitochondrial DNA. The first step is to concatenate
ITS/28S and histone 3. So far, so good (but after
getting around some stumble blocks). Some useful
literature in this respect is Planet (2006). For
recent reviews of general methodologies, see Blair
& Murphy (2010) and Pausas & Verdú (2010).
References:
Blair, C. & Murphy, R.W., 2010. Recent trends in molecular phylogenetic analysis: where to next? - Journal of Heridity (in press; doi:10.1093/jhered/esq092).
Pausas, J.G. & Verdú, M., 2010. The jungle of methods for evaluating phenotypic and phylogenetic structure of communities. - BioScience 60: 614-625.
Planet, P.J., 2006. Tree disagreement: measuring and testing incongruence in phylogenies. - Journal of Biomedical Informatics 39: 86-102.
References:
Blair, C. & Murphy, R.W., 2010. Recent trends in molecular phylogenetic analysis: where to next? - Journal of Heridity (in press; doi:10.1093/jhered/esq092).
Pausas, J.G. & Verdú, M., 2010. The jungle of methods for evaluating phenotypic and phylogenetic structure of communities. - BioScience 60: 614-625.
Planet, P.J., 2006. Tree disagreement: measuring and testing incongruence in phylogenies. - Journal of Biomedical Informatics 39: 86-102.
Playing the DNA game
30-08-2010 21:02
This weekend I have
been busy playing the DNA game. Just imagine the good
old Tetris game, where coloured blocks have
to be sorted. Aligning DNA fragments looks very
much the same, only you have to move them
horizontally instead of vertically.
This screenshot is part of a file in which I manually tried to align three different parts of DNA (CO1, histone 3 and ITS2/28S). It serves the continuing phylogenetic research on the relationships of the Orthalicoidea.
This screenshot is part of a file in which I manually tried to align three different parts of DNA (CO1, histone 3 and ITS2/28S). It serves the continuing phylogenetic research on the relationships of the Orthalicoidea.
Biodiversity informatics
26-08-2010 10:23
Bioinformatics, or more
precise, biodiversity informatics, is an emerging
field in which much progress already has been made.
However, overarching scientific questions seem to be
absent and therefore major, guiding goals are
missing.
In a recent review, Townsend Peterson et al. (2010) have tried to bridge this gap by posing a number of Big Questions.
According to these authors, “biodiversity science in general can and should evolve from a purely descriptive cataloguing endeavour into a predictive, scientific exploration of space, time and form”. This seems only logical.
This figure presents a framework of biodiversity informatics data realms, showing potential cross-links between some of them that are currently unlinked.
Given this framework the following areas of analysis could become available.
1. Geography and ecology of past life.
This topic is part of global change biology and seems to be very important when we try to anticipate biotic responses to future environmental change and biodiversity loss. The interaction of intrinsic and extrinsic factors on species’ responses remains little known.
2. Biota-wide picture of diversification and interaction
Community ecology currently focuses on closely relatives or known mutualists. However, a broader perspective is needed, leading to a more integrative view of both biotic interactions and biological diversification. Phylogenetic frameworks, geographic distributions and species niche estimates are key elements. This could result in insights incorporating ecological dimensions and likely shifts in distribution during historic times.
3. Future (novel) communities
Palaeontological evidence shows that in the past communities existed differing from extant counterparts. The shifts in novel species assemblages due to changing climates and the introduction of alien species may need further developments in niche modelling, leading to environmental change scenarios and future distribution predictions.
4. Integrating phenotype and genotype
Linking rich biodiversity data sets on phenotypes and genotypes of individuals, populations and species could be integrated over space and visualized in various dimensions. This would provide a view on how phenotype and genotype interact with geography and ecology.
5. Synthetic conservation planning
Only recently, conservation planning involves prioritizing using multi-factor, multi-temporal scenarios, which have the potential of covering more of the true complexity. This could lead to a more synthetic and robust view of conservation and nature resources management.
Some the key next steps involve data integration across disparate databases, data quality assurance, detecting errors and avoiding pseudoreplication, and finally, dealing effectively with scale.
All this - and more details in the paper - provides a challenging outlook. Undoubtedly, biodiversity informatics will become Big in the (near) future. But for me the key question is: what is the taxon involved? Having seen various incidents where people loose sight of the organism at stake, and focus instead on methodological questions and techniques to be used. “It’s the taxon, stupid”; even if this involves a purely descriptive cataloguing endeavour...
Reference:
Townsend Peterson, A., Knapp, S., Guralnick, R., Soberon, J. & Holder, M.T., 2010. The big questions for biodiversity informatics. - Systematics and Biodiversity 8: 159-168.
In a recent review, Townsend Peterson et al. (2010) have tried to bridge this gap by posing a number of Big Questions.
According to these authors, “biodiversity science in general can and should evolve from a purely descriptive cataloguing endeavour into a predictive, scientific exploration of space, time and form”. This seems only logical.
This figure presents a framework of biodiversity informatics data realms, showing potential cross-links between some of them that are currently unlinked.
Given this framework the following areas of analysis could become available.
1. Geography and ecology of past life.
This topic is part of global change biology and seems to be very important when we try to anticipate biotic responses to future environmental change and biodiversity loss. The interaction of intrinsic and extrinsic factors on species’ responses remains little known.
2. Biota-wide picture of diversification and interaction
Community ecology currently focuses on closely relatives or known mutualists. However, a broader perspective is needed, leading to a more integrative view of both biotic interactions and biological diversification. Phylogenetic frameworks, geographic distributions and species niche estimates are key elements. This could result in insights incorporating ecological dimensions and likely shifts in distribution during historic times.
3. Future (novel) communities
Palaeontological evidence shows that in the past communities existed differing from extant counterparts. The shifts in novel species assemblages due to changing climates and the introduction of alien species may need further developments in niche modelling, leading to environmental change scenarios and future distribution predictions.
4. Integrating phenotype and genotype
Linking rich biodiversity data sets on phenotypes and genotypes of individuals, populations and species could be integrated over space and visualized in various dimensions. This would provide a view on how phenotype and genotype interact with geography and ecology.
5. Synthetic conservation planning
Only recently, conservation planning involves prioritizing using multi-factor, multi-temporal scenarios, which have the potential of covering more of the true complexity. This could lead to a more synthetic and robust view of conservation and nature resources management.
Some the key next steps involve data integration across disparate databases, data quality assurance, detecting errors and avoiding pseudoreplication, and finally, dealing effectively with scale.
All this - and more details in the paper - provides a challenging outlook. Undoubtedly, biodiversity informatics will become Big in the (near) future. But for me the key question is: what is the taxon involved? Having seen various incidents where people loose sight of the organism at stake, and focus instead on methodological questions and techniques to be used. “It’s the taxon, stupid”; even if this involves a purely descriptive cataloguing endeavour...
Reference:
Townsend Peterson, A., Knapp, S., Guralnick, R., Soberon, J. & Holder, M.T., 2010. The big questions for biodiversity informatics. - Systematics and Biodiversity 8: 159-168.
Photo of the day (107): Deroceras
24-08-2010 22:08
Some pictures of an as
yet unidentified slug, probably Deroceras
sp. According to my
colleague Ton de Winter, it is possibly only a form
of Deroceras
laeve (Müller, 1774). Only dissection and
comparison with well-identified material could reveal
their true identity.
The specimens were spotted in Ecuador, Prov. Pichincha, Bellavista. Photographs courtesy of Adrián González.
The specimens were spotted in Ecuador, Prov. Pichincha, Bellavista. Photographs courtesy of Adrián González.
Photo of the day (106): Plekocheilus
23-08-2010 09:11
Biodiversity sites are
popping up. And snails get interest too on these
sites, apart from the ‘usual suspects, like mammals,
birds, herps and plants.
This weekend I discovered the site of the Bigal River Conservation Project in northeastern Ecuador. This area (only 10 km2) is located near the vulcano Sumaco, on the border of Prov. Napo and Orellana.
The snail pictured here is not fully-grown, but undoubtedly a Plekocheilus.
This weekend I discovered the site of the Bigal River Conservation Project in northeastern Ecuador. This area (only 10 km2) is located near the vulcano Sumaco, on the border of Prov. Napo and Orellana.
The snail pictured here is not fully-grown, but undoubtedly a Plekocheilus.
Confusing types
19-08-2010 22:01
Messing up things can
happen to everyone. Even the Big Names in malacology
are not immune to this phenomenon. However, the
resulting confusion - especially when types are
involved - is what taxonomists don’t like at all.
Some historical malaco-trivia about messing up things with types... Our figureheads: Henry A. Pilsbry and William J. Clench.
In 1939, Pilsbry described several species from Ecuador and Colombia (Pilsbry, 1939). He based himself on material from R.W. Jackson, and Hno. Nicéforo Maria respectively. The taxa under dispute: Plekocheilus oligostylus, described from “Colombia”, and Plekocheilus nachiyacu, described from “Nachiyacu, Ecuador”.
P. oligostylus
Pilsbry, 1939
P. nachiyacu
Pilsbry, 1939
During a recent revision of Plekocheilus species from both countries, Francisco Borrero and I were pretty sure that we recognized both taxa. However, P. oligostylus was found among Ecuadorian material, while P. nachiyacu was identified with Colombian shells.
This seemed to be consistent with the data provided by Clench & Turner (1962):
When we asked the collections manager of the Philadelphia museum, Amanda Lawless, about details of P. nachiyacu, she provided proof of its label:
“Just to let you know that the label states that the lot is from Nachiyacu, Ecuador. I checked the original ledger as well and at the time this lot was donated by Pilsbry, he also donated two other lots from Ecuador and one from Colombia. The one from Colombia was a different species and had no other specific data, maybe Clench and Turner got confused by this one. With the lot, there is also an original handwritten slip of paper with specific locality info on it stating it is from Ecuador”.
This is the type of confusion I meant... Pilsbry right and Clench wrong, or vice versa? To be continued.
References:
Clench, W.J. & Turner, R.D., 1962. New names introduced by H.A. Pilsbry in the Mollusca and Crustacea. - Special Publications, Academy of Natural Sciences, Philadelphia, 4: 1-218.
Pilsbry, H.A., 1939. Sout American land mollusks, X. Species of Ecuador and Colombia. - Notulae Naturae 19: 1-6.
Some historical malaco-trivia about messing up things with types... Our figureheads: Henry A. Pilsbry and William J. Clench.
In 1939, Pilsbry described several species from Ecuador and Colombia (Pilsbry, 1939). He based himself on material from R.W. Jackson, and Hno. Nicéforo Maria respectively. The taxa under dispute: Plekocheilus oligostylus, described from “Colombia”, and Plekocheilus nachiyacu, described from “Nachiyacu, Ecuador”.
P. oligostylus
Pilsbry, 1939
P. nachiyacu
Pilsbry, 1939
During a recent revision of Plekocheilus species from both countries, Francisco Borrero and I were pretty sure that we recognized both taxa. However, P. oligostylus was found among Ecuadorian material, while P. nachiyacu was identified with Colombian shells.
This seemed to be consistent with the data provided by Clench & Turner (1962):
When we asked the collections manager of the Philadelphia museum, Amanda Lawless, about details of P. nachiyacu, she provided proof of its label:
“Just to let you know that the label states that the lot is from Nachiyacu, Ecuador. I checked the original ledger as well and at the time this lot was donated by Pilsbry, he also donated two other lots from Ecuador and one from Colombia. The one from Colombia was a different species and had no other specific data, maybe Clench and Turner got confused by this one. With the lot, there is also an original handwritten slip of paper with specific locality info on it stating it is from Ecuador”.
This is the type of confusion I meant... Pilsbry right and Clench wrong, or vice versa? To be continued.
References:
Clench, W.J. & Turner, R.D., 1962. New names introduced by H.A. Pilsbry in the Mollusca and Crustacea. - Special Publications, Academy of Natural Sciences, Philadelphia, 4: 1-218.
Pilsbry, H.A., 1939. Sout American land mollusks, X. Species of Ecuador and Colombia. - Notulae Naturae 19: 1-6.
Veronicellid phylogeny
17-08-2010 11:39
Veronicellidae are
large, tropical slugs, which are widespread in the
Neotropics. In South America 16 genera are known to
occur, and many species are recorded as agricultural
pests or intermediate hosts for nematodes, causing
public health risks.
In the southern part of the continent, six species of the genus Phyllocaulis occur. Recently, a phylogenetic study explored the relationships between these species (Gomes et al, 2010).
Most of the species have a sympatric occurrence in part of their distributional range.
The results showed that the different species of Phyllocaulis are in mutually exclusive and well-supported clades. Interestingly, a study of the divergent times showed that the vicariant species P. gayi (Chile) and P. soleiformis (Argentina) had their common ancestor during Pleistocene times (~ 0.6 Ma). Since this timing is after the final upheaval of the Andes, the distribution is explained by cross-Andean dispersal and subsequent speciation.
Reference:
Gomes, S.R., Britto da Silva, F., Mendes, I.L., Thomé, J.W., Bonatto, S.L., 2010. Molecular phylogeny of the South American land slug Phyllocaulis (Mollusca, Soleolifera, Veronicellidae). - Zoologica Scripta 39: 177-186.
In the southern part of the continent, six species of the genus Phyllocaulis occur. Recently, a phylogenetic study explored the relationships between these species (Gomes et al, 2010).
Most of the species have a sympatric occurrence in part of their distributional range.
The results showed that the different species of Phyllocaulis are in mutually exclusive and well-supported clades. Interestingly, a study of the divergent times showed that the vicariant species P. gayi (Chile) and P. soleiformis (Argentina) had their common ancestor during Pleistocene times (~ 0.6 Ma). Since this timing is after the final upheaval of the Andes, the distribution is explained by cross-Andean dispersal and subsequent speciation.
Reference:
Gomes, S.R., Britto da Silva, F., Mendes, I.L., Thomé, J.W., Bonatto, S.L., 2010. Molecular phylogeny of the South American land slug Phyllocaulis (Mollusca, Soleolifera, Veronicellidae). - Zoologica Scripta 39: 177-186.
Having one's own stamp
16-08-2010 10:48
Some postal companies
make it quite easy to have one’s own stamp. Just
upload a preferred picture to their site and they
will send your personalized stamps. Cuba, for sure,
is a country where this innovation has not been
introduced yet. Therefore it must have been a great
pleasure for Adrián González, to see one of his
photographs being used on a new stamp of the Cuban
postal service.
The original picture is shown in this blogpost.
The original picture is shown in this blogpost.
Preparing for dissection
10-08-2010 05:23
Yesterday, we spent a
large part of the day at the (Cincinnati) Museum to
sort out material that Francisco had brought during
his recent trip to Colombia. One of the things we
ended up doing, however, was to find a way to extract
the body from an Isomeria
species. These animals
are difficult to remove from their shells, not only
due to the constrictions in their aperture, but
mainly due to their body rapidly becoming very stiff;
even after preservation of only a few weeks in
ethanol.
From a literature search, it was not immediate evident where the retractor muscle was assumed to be attached in these specimens. Hence we decided to make a window in the last whorl.
As you don’t want to mess up a single specimen of a potentially new species, it was decided to first practice on a specimen with poor data. Tools to be used: a rotary-motortool with a diamond-tipped sewing disk, a dissecting needle, some pincers, and a laboratory spatule.
After some careful thought on where to begin and where to go, the lab was soon filled with noises that usually can be heard at the dentist. The smell of burned shell was also quite prominent.
After some time a window was opened, leaving the characteristics of the species (umbilical area, angled periphery) untouched. Time now to try to remove the body from the shell.
Due to the stiffness of the body, some poking on the foot was required to get the tissue throught the aperture. Then the body extraction could start.
In the end, the results were quite satisfying. An animal and a not too badly damaged shell.
From a literature search, it was not immediate evident where the retractor muscle was assumed to be attached in these specimens. Hence we decided to make a window in the last whorl.
As you don’t want to mess up a single specimen of a potentially new species, it was decided to first practice on a specimen with poor data. Tools to be used: a rotary-motortool with a diamond-tipped sewing disk, a dissecting needle, some pincers, and a laboratory spatule.
After some careful thought on where to begin and where to go, the lab was soon filled with noises that usually can be heard at the dentist. The smell of burned shell was also quite prominent.
After some time a window was opened, leaving the characteristics of the species (umbilical area, angled periphery) untouched. Time now to try to remove the body from the shell.
Due to the stiffness of the body, some poking on the foot was required to get the tissue throught the aperture. Then the body extraction could start.
In the end, the results were quite satisfying. An animal and a not too badly damaged shell.
Visit to the Field
07-08-2010 04:07
We finished our
manuscript on Dryptus and Plekocheilus, and decided
to deliver it in person to the editor of our chosen
journal (Zootaxa), Jochen Gerber. He is Collections
manager at the Field Museum in Chicago, which is not
horribly far from Cincinnati. Although, still a
5(+)-hours drive...
Making effective use of this visit, we studied Orthalicidae in the collection. The collection is very interesting and well-kept. Jochen just had received word of an awarded NSF-grant to enlarge the storage room. Needless to say that he was a happy man during that day.
The drive back to Cincinnati made it a very long and exhausting day, also because we hadn’t calculated the time difference between the two states (Chicago is one hour earlier than Cincinnati). All together it took 24 hours, but in the end we were happy with what we accomplished to do.
Making effective use of this visit, we studied Orthalicidae in the collection. The collection is very interesting and well-kept. Jochen just had received word of an awarded NSF-grant to enlarge the storage room. Needless to say that he was a happy man during that day.
The drive back to Cincinnati made it a very long and exhausting day, also because we hadn’t calculated the time difference between the two states (Chicago is one hour earlier than Cincinnati). All together it took 24 hours, but in the end we were happy with what we accomplished to do.
The coloratus saga
02-08-2010 19:01
One of the species in
our revision to be included is Plekocheilus (Eurytus)
coloratus (Nyst, 1845). Although there is no
type material known, it is as such fairly easily
identifiable but we found it in museum collections
quite mixed up with other taxa as well.
We’re not decided yet if we are going to solve this messy complex right now, but at least found five different morphotypes.
A preliminary elevational analysis shows the following ranges:
1 - 0-1800 m
2 - 0-1800 m
3 - 70-2300 m
4 - 1500-3600
5 - 325-1500 m
All this actually shows is that morphs 4 and 5 are at different elevations but all others overlap.
We may not be able to solve this puzzle at this very moment (and with shells only), but for now the coloratus saga continues...
We’re not decided yet if we are going to solve this messy complex right now, but at least found five different morphotypes.
A preliminary elevational analysis shows the following ranges:
1 - 0-1800 m
2 - 0-1800 m
3 - 70-2300 m
4 - 1500-3600
5 - 325-1500 m
All this actually shows is that morphs 4 and 5 are at different elevations but all others overlap.
We may not be able to solve this puzzle at this very moment (and with shells only), but for now the coloratus saga continues...