Monthly Archives: October 2010

Morphometrics and anatomy unravel cryptic speciation

Plagiodontes dealdaleus (Deshayes, 1851) is a variable species occurring in Argentina. Up till now, several subspecies have been recognized. A new study by Piz?? and Cazzaniga (2010) now shows that the nominate subspecies and P. d. strobeli (D??ring, 1877) are in fact two allopatric species.

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Like in a previous study [see Snailblog 24-08-2009], the authors have made detailed anatomical research and morphometric studies to investigate the differences found in western and eastern populations of Plagiodontes dealdaleus along the Pampean Sierras in Provs. C??rdoba and San Luis. Their study shows that the distinction between the two taxa mainly lies in subtle differences in shell morphology (but surely recognizable for the trained eye), and a different shape of penis and vagine (with their internal structures).

It would be interesting to see how the morphological differences between the nine species now recognized in Plagiodontes are reflected in molecular studies.

Afbeelding_1_09-12-18

Reference:
Piz??, J. & Cazzaniga, N.J., 2010. Allopatry and anatomical distinctiveness of two puzzling land snails in genus Plagiodontes, from Argentina (Gastropoda, Orthalicidae). – Malacologia 53: 1-24.

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Nomenclatorial forensics and Byzantinism in taxonomy

Harry Lee has just released two contributions on the excellent website of Bill Frank and himself (www.jaxshells.org) about the correct attribution of taxonomic names. What seems like a dispute about futilities is actually a good piece of detective work.

It all started in July 2010 in the Dominican Republic, Barahona Prov., Virgen de San Rafael area, where Alan Gettleman collected a Chondropomium and a Plagioptycha species. Harry identified these species as C. nobile and P. strumosa. However, he took the effort to carefully read the original description and discovered that it wasn’t as simply as thought on first sight.

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 Photo: Harry Lee

The story on C. nobile can be found here (www.jaxshells.org/10088.htm). It involved quite some bibliographic researching and interpretation of the ICZN rules to reach the correct taxonomic name.

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 Photo: Harry Lee

The authorship of Plagioptycha strumosa also involved forensic bibliographic research and can be found here www.jaxshells.org/0050a.htm. Harry’s assumption may be right that Reeve heard the reading of Pfeiffer’s paper at the meeting of the Zoological Society in London. However, I doubt he was able to immediately catch a vivid image of the shell in his mind by hearing its description being read. I have found, during my recent visit to the NHM collection, multiple instances where material described by Pfeiffer was returned to London accompanied by his handwritten taxon labels and later also used by Reeve. At the same time I have found material that was described by Reeve or Sowerby and that also bears labels in Pfeiffer’s handwriting. 

Although we cannot reconstruct the past as accurately as we would like, it may be a safe bet that during the 19th century there was more contact between malacologists than sometimes assumed, including swaps of material. Would there really have been that much byzantine machinations that we could say: “This clearly explains why Reeve was beaten senseless shortly after exiting a pub in the winter of 1855…..” (Kurt Auffenbach, in litt.)?

New taxa (26): Orthalicidae

In a paper published last week, four new taxa were described from Peru belonging to the Orthalicidae (Breure & Mogollón, 2010).


Sipas

Bostryx chusgonensis sipas n.subsp., described from Dept. Amazonas, Shipasbamba. Holotype RMNH 114059.

Fragilis

Bostryx fragilis n.sp., from Dept. Tumbes, Quebrada Santa Maria. Holotype RMNH 114063.

Altoensis

Scutalus (S.) phaeocheilus altoensis n.subsp. Type locality Dept. Piura, El Alto; holotype RMNH 114045.

Mariopenai

Scutalus (S.) mariopenai n.sp., described from Dept. Ancash. Catzcal. Holotype RMNH 114055.

See for New taxa (25) and earlier: www.ashbreure.nl > Snailblog > 8 October 2010. 
A link to a PDF of the paper can be found at the same website under Publications.

Reference:
Breure, A.S.H. & V. Mogollón, 2010. Well-known and little-known: miscellaneous notes on Peruvian Orthalicidae (Gastropoda, Stylommatophora). – Zoologische Mededelingen Leiden 84: 15-34.

What is simpler than a name?

The iPhylo blog had a few days ago a post about the relevance of taxonomic names (http://iphylo.blogspot.com/2010/10/are-names-really-key-to-big-new-biology.html). Do we need names? According to this blogpost, “formal taxonomic names don’t seem terribly necessary in order to do a lot of science“. This opinion was underpinned by referring to surrogate names (like ‘SAR-11’), which are commonly used in experimental studies. In many cases this may be appropriate, but if you have read my blogpost of yesterday, I would like to say: “think it over, it’s not that simple”.

This blogpost by Roderic Page continues by stating that names could be managed very simply if we had a complete bibliography of of group in a database, the combination of name and document would be enough to create a timeline of usage. Note the word ‘if’… A big proviso.
In his example the name / document pairs have the attractiveness of being digitally stored and are thus apt for computational operations. Here comes the taxonomic part. I quote:
Taxonomy

There are a few wrinkles to deal with. Firstly, names may have synonyms, lexical variants, etc. (….). Leaving aside lexical variants, what we want is a “view” of the [name,document] pairs that says this subset refer to the same thing (the “taxon concept”).

Concept

We can obsess with details in individual cases, but at web-scale there are only two ones that spring to mind. The first is the Catalogue of Life, the second is NCBI. The Catalogue of Life lists sets of names and reference that it regards as being the same thing, although it does unspeakable things to many of the references. In the case of NCBI the “concepts” would be the sets of DNA sequences and associated publications linked to the same taxonomy id. Whatever you think of the NCBI taxonomy, it is at least computable, in the sense that you could take a taxon and generate a list of publications ‘about” that taxon. 

So, we have names[name,document] pairs, and sets of [name,document] pairs. Simples.“. Unquote.
If life was so simple as pushing a few buttons… But the quintessence is of course the correct usage of a name. And that is not always so simple…

Morphology in ultrastructure

Sometimes Neotropical land snails are used for fundamental research. Moraes et al. (2010) investigated the ultrastructure of snail brains in Megalobulimus abbreviatus (Bequaert, 1948), viz. the dorsal body; this is an endocrine gland located above the cerebral ganglia in all pulmonate molluscs.

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The abstract of this paper shows that this species was strictly used in an endocrinological context. 

The ultrastructure of the reproductive gland, dorsal body (DB), of Megalobulimus abbreviatus was analysed. Electron microscope immunohistochemistry was used to detect FMRFamide-like peptides in the nerve endings within this gland. Nerve backfilling was used in an attempt to identify the neurons involved in this innervation. In M. abbreviatus, the DB has a uniform appearance throughout their supraesophageal and subesophageal portions. Dorsal body cells have several features in common with steroid-secreting gland cells, such as the presence of many lipid droplets, nu- merous mitochondria with tubular cristae and a developed smooth endoplasmic reticulum cisternae. Throughout the DB in M. abbreviatus numerous axonal endings were seen to be in contact with the DB cells exhibiting a synaptic- like structure. The axon terminals contained numerous electron-dense and scanty electron-lucid vesicles. In addition, the DB nerve endings exhibited FMRFamide immunoreactive vesicles. Injection of neural tracer into the DB yielded retrograde labelling of neurons in the metacerebrum lobe of the cerebral ganglia and in the parietal ganglia of the subesophageal ganglia complex. The possibility that some of these retrograde-labelled neurons might be FMRFamide- like neurons that may represent a neural control to the DB in M. abbreviatus is discussed.

However, what is interesting to note, is that this species was “previously cited incorrectly as Megalobulimus oblongus or Strophocheilus oblongus” (Moraes et al, 2010: 342). Quite confusing… Especially when such studies are used for comparative morphology (perhaps at a later stage). It may thus be important that biologists from a distinct discipline have a taxonomist involved, to check the correct taxonomic status of their object of study. It is to be regretted that the authors didn’t state to which studies they are referring to clear the potential confusion when this paper is later used in e.g. a review.

Reference:
Moraes, G.D., Achaval, M., Dal Piva, M.M., Faccioni-Heuser, M.C., Wassermann, G.F. & Zancan, D.M., 2010. Ultrastructural analysis of the dorsal body gland of the terrestrial snail Megalobulimus abbreviatus (Bequaert, 1948) – Brazilian Journal of Biology 70: 341-350.

Secondary RNA structures

Doing quite some DNA analyses lately, I become aware that modern biologists may get drowned by the superfluous amount of tools available. Unless they stick to protocols by peers or literature. And those who are bit on the conservative side, still stick with PAUP of course.

Sometimes the availability of newly developed tools may come in handy though. Francisco Cadiz, a Chilean student working in Brazil, kindly suggested me some literature. One of the papers is a ‘How-to manual’ for the analysis of secondary RNA structures (Schultz & Wolf, 2009) See also http://en.wikipedia.org/wiki/Biomolecular_structure.  

Schulzwolf2009

Keller et al. (2010) suggest that including these structures into the analyses, the accuracy and robustness is improved in reconstructing phylogenetic trees. Therefore, during the past weekend, I decided to test this myself. It proved not too hard to get this suite of software working. All based on Java and thus problem-free cross-platform. Chapeau developers! The documentation is somewhat crude, but by trial and error I made my own protocol. And the end result was pretty much confirming the results already obtained by other methods.

The danger is of course the dumb application of tools, without understanding of the biological meaning and taxonomical context. That’s always a challenge, especially for modern biologists.

References:
Keller, A., Förster, F., Müller, T., Dandekar, T. Schulz, J. & Wolf, M., 2010. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. – Biology Direct 5: 4 Link:http://www.biology-direct.com/contents/5/1/4 [open access].
Schulz, J. & Wolf, M., 2009. ITS sequence-structure analysis in phylogenetics: A how-to manual for molecular systematics. – Molecular Phylogenetics and Evolution 52: 520-523.