Posts Tagged ‘taxonomy’

Identifications…

Tuesday, January 11th, 2011
Ah… well, yesterday I started to do some research on an article which may have the title of  ” The Vampires of the Sea.”  A twilight  article dealing with…

those bloodsuckers, bar none – Pyramidellid snails.   

Whether or not I develop this article fully depends on a lot of things, not the least of which the direction my muse (and I do have one – a characteristic I find “amusing”…  🙂 ), takes me.  And also, of course, whether or not, I can find an editor who will accept it.  Anyway I am still in the very early stages of this thing, and I am trying to find some more background information about Pyrams. 

Now, like Yogi, I figure I am a bit “better than the average bear” with my knowledge of the group, but I really need to know more before I do anything that can be considered to be a reasonable and – hopefully – entertaining article about them.

Basically, the Gastropod family Pyramidellidae is a very large group of small… white… snails without any really nice identifying characteristics.  There are, quite literally, thousands of names applied to these snails, and how those names relate to the actual species – if any – of those snails is really open to question.  As with many marine groups – probably as with MOST marine groups – of animals, they are a taxonomic mess.  There are three basic reasons for this, the primary one is that they are all – dare I say it, again – small,  white, and feature-less snails.  If you think about it, once you have the basic constraints of a small, helically-coiled, shell, there are NOT a lot of ways that those constraints can be varied.   In point of fact, back in the 1960s, a paleontologist named David Raup, wrote a series of nice papers noting that virtually all marine animals with a “shell” can be easily described mathematically (Raup, 1962; 1966; 1969). 

The term “shell” in this sense is restrictive and excludes arthropods – even though they are “shellfish” they don’t have a “shell” in the way that Raup meant: “a non-living external covering to the animal.”  What arthropods have is an “integument” – a covering that is made of an intricate and complex fusion of living and secreted elements that is an integral part of the animal’s body, interiorally and exteriorly.  If you try to remove a shrimp’s “shell,” you are left with a mass of dead flesh.  If you try to remove a snail’s or a clam’s shell, you will find that, in many cases, it is quite possible to do this and still have a living animal.  And that animal may remain alive – in the case of some snails – indefinitely.  Clams without a shell perish in short order, as they can’t feed.  But snails without a shell can generally do everything shelled animals can do.   Everything, that is, except withstand the bite of a predator’s jaws.  Virtually every biologist who studies large populations of marine snails occasionally finds a shell-less one; probably an animal whose shell was eroded away by a sponge, or whose shell was cracked by a crab and, by a miracle, the shell was removed.  As an example, over the course of three years, I encountered two almost-naked specimens in one species, Ophiodermella inermis, that I worked on many years ago.

Ophiodermella inermis, photographed in Dyes Inlet, Washington.

Anyway… Raup found that virtually all mollusk and brachiopod shells were basically helical in shape, and that all fundamental shell shapes could be described by only three parameters, 1) the shape of the shell’s aperture, 2) the rate at which the shell’s aperature coiled around the central axis, giving the width of the animal, and 3) the rate at which the coiling moved along the central axis which determines the animal’s length.  As all of the functions occur simultaneously, how each of the parameters varies in relationship to the others changes both the absolute and relative proportions of the shell’s shape.

This diagram below shows how the shell parameters determine the difference in shell shapes for some snails commonly found in marine reef aquariums. The top shows a Nerite; here the shell aperture just moves in a spiral around the axis of coiling and moves outward at a rate that is not very large.  This results in a spirally-coiled shell where the whorls appear to overlap.  The other shells are trochoideans.  And here the parameter of “aperture shape” is circular.  The aperture moves around the axis of coiling at various rates – giving a turbinate or trochoid shape.  Additionally, the aperture moves along the axis of coiling determining whether the shell is squat or elongate.  Although the flat Stomatella seems to be very different from a conical Trochus in structure, with a little thought, it is easily possible to see how those shell shapes are related.

.Shell parameters illustrated by various snail shells; all shells grow in three dimensions but the position of the aperture in each successive whorl may change due to only 3 parameters. A. Growth of a shell where the aperture shape moves in a spiral within one plane; the nerite shell is an example of this. B. Here the aperture moves along the axis of coiling but remains tangent to that axis; the illustrated turbinid is an example of that growth. C. Here the aperture moves along the axis of coiling, but also translates or moves outward from that central axis. An opening called an umbilicus in the center of the shell is the result. The illustrated trochid shows this growth form, with the earlier positions of the growth generating aperture shown in gray. The shell of Stomatella is auriform, an extreme example of the prominence of the whorl translation rate.

Given that all molluscan shells can be basically described in this manner, if shells lack much distinctive coloring, sculturing, or extra ornamentation, it should be apparent that there really are not a lot discrete characteristics that can be used to uniqually differentiate any given shell from all others that are basically similar in shape.

That lack of potential characters is the first factor that has caused taxonomic problems with pyramidellid shells.

The second and third problems were two malacologists, William Healey Dall and Paul Bartsch.  Dall was the first curator of mollusks at the United States National Museum (aka the Smithsonian Institution).  Bartsch was his “disciple” and successor.  As curators at the Smithsonian, a lot (really A LOT!!!) of specimens (= dead shells) were sent to them by various collectors.  As they tried to identify these shells, they often found that the shells were not “quite” like shells in the museum’s collection – or in other museums’ collections.  This meant that these shells were then new to science and needed to be taxonomically, or scientifically, described.  Virtually all animals that are described from United States regions or by American authors have representative or “type” specimens deposited in the Smithsonian’s collections, so they had a lot of comparative material.  Presently, that is a huge number of specimens, several millions.  Back in Dall’s time, the collections were a lot smaller… but still relatively very large…  So, they had a lot of material with which to compare any given specimen in their descriptions.  Thus, if they decided a given specimen was a “new” species the odds would seem to favor the fact that it was new. 

Maybe…

Typically what these two ol’ boys did, was to let specimens accumulate until they had enough to write a short (or sometimes very LONG paper describing them all).  At the time, the custom was to describe a molluscan species on the basis of one shell. 

ONE

THE

TYPE.

The type was supposedly an “average” or representative shell that “typified” the species.  By the way, Dall and Bartsch were by no means alone in the way in which they described “their” species.  It was the standard method of the era.  They were, however, especially prolific, and it seems, especially “gifted” with the inability to find unique precise and useful descriptive terms.  Simply put, many of their descriptions are “precisely ambiguous,” they are written in ways that seem to precisely describe the specimen, but which don’t allow a reader to determine if a given questionable shell that they are holding in their hand is from that unique species.  I think this was because they didn’t include much or any information addressing variations between specimens of the same species.

And what about those variations?  Well, Dall, at least paid lip service to the concept of variation, but he generally didn’t include any useful way to describe variations in the species he described.  Any good field biologist knows that variation is quite literally “the stuff of life.”  For example, for little white snails, such as pyrams, if one collects one hundred specimens from a known species, they will vary in length, width, the number of whorls, slight color variations occur, the proportion of length to width will vary a bit, the number of ribs on whorl may vary, and on and on and on…  One specimen really can’t do it.

Nonetheless, the conception of a species at the time, which was reinforced by rules of Linnaean taxonomy implied that there was no variation in a species.  This was a result of considering all species to be divinely created.  If a creator designed each species, he/she/it/they would obviously get it right the first time and there could be no variation.  That was all fine and dandy up until the publication of The Origin of Species in 1859.  Once the concept of evolution became established, the concept of a species HAD to include variation.  And so it did.

In concept.

But in practice…  Well, let’s just say the idea of variability in a species was not an easy one to get across.  Modern descriptive statistics is just that, modern, so at that time there was no formal way to estimate variability.  The concept of a standard deviation wasn’t there.  Even including a range of sizes in a species description was rarely done.

In essence, for any species – the idea of that species was “crystalized” within a single typical specimen, the type.

Over his lifetime, Dall described 5,302 species in every group of animals defined at the time, from mammals to mollusks.  Most, however, were snails.  Bartsch described an additional 905.  The heyday of these descriptions extended from the 1870s through about 1925 for Dall (several years after he died, actually, as Bartsch published some of Dall’s descriptions after his death).  Bartsch retired in 1945 and died in 1960, and I think his last taxonomic publications were in the 1950s.

Modern day molluscan taxonomists who work in the Pacific where these men had the largest taxonomic effect have a love-hate relationship with them.

Love…about 0.000001%,  Hate… well, do the subtraction.

Simply put, it is essentially impossible to differentiate most small snail species described by these men.  They gave lip service to the concept of species variability, but using the typological approach and their writing style such variability was impossible to descibe.  Interestingly enough, that is not the case with many other prolific describers of molluscan species that were writing at the same time.  Henry Pilsbry was another malacologist who described a lot of species; according to his article in Wikipedia, he wrote over 3,000 scientific papers and described over 5,000 species.  His descriptions have stood the test of time well, so the problems with Dall and Bartsch were due to Dall and Bartsch.

How bad is the situation, really? 

Pretty bad.   Really!

For example, if a large collection of pyramidellids or other small snails is taken from one bay or locality, their parameters will vary, of course.  If those specimens can be determined by other means (ecological parameters, for example) they are all found to by one species, it would be nice – satisfying even – to put one valid name on them.  And… by examining the works of Dall and Bartsch, one can often find numerous – perhaps several dozen – entirely satisfactory species names that will fit within that single collection of specimens from a single species from a single small bay.

Amongst the references I downloaded (thanks to Google’s digitizing, many books in the public domain are downloadable) was:

Dall, W. H. and P. Bartsch. 1909. A monograph of West American Pyramidellan Mollusks.  United States National Museum, Bulletin 68. 1-258 pp, 30 pl.

This monograph contains 258 pages of species descriptions…  And 30 plates of illustrations…. As an example , take a look at this one.

This is one of many plates of illustrations showing species of TurbonillaTurbonilla is one of the genera of pyrams that has species that will attack Tridacna.  Do you think you could use such images as these to differentiate between any two them reliably?

Could anybody?

When I discuss specific animal groups in my articles for the reef aquarium hobby, I like to give examples of those species…

CORRECTLY IDENTIFIED examples of those species.

And, please excuse me, so that I may now go and start beating my head against the wall.

Because it will feel soooo good when I quit. 

An aside… 

Oh… for those of you who might know mammals, the Dall sheep and the Dall porpoise were named after William Healey… AND here is something I will bet you probably didn’t know.  His name “Dall” was pronounced rhyme with “Gal,” NOT “Gall,” as it is most often used.   See… I even give you a piece of “party” trivia to amuse your friends with.  Of course, if you do so, you risk never being invited to such parties again.

References:
Raup, D. M. 1962. Computing as an aid in describing form in gastropod shells. Science. 138:150-152.

Raup, D. 1966. Geometric analysis of shell coiling: general problems. Journal of Paleontology. 40:1178-1190.

Raup, D. M. 1969. Modeling and simulation of morphology by computer. Proceedings of the North American Paleontological Convention. September 1969:71-83.

Until later,

Cheers,

Coral Problems

Friday, December 17th, 2010

Hi Folks,

A most interesting and interesting article discussing the problems with identifying stony corals, in particular, some species of Hawai’ian Montipora has recent been published.

The background for the article is that last year several parties petitioned to have 83 stony corals to be listed under the United States Endangered Species Act. The National Marine Fisheries Service (NMFS), a branch of the National Oceanic and Atmospheric Administration (NOAA) is charged with assessing the coral species in question to determine, among other things, if they actually are endangered.  If the corals are listed, the act is supposed to provide some more protection for the species, and probably most importantly, designate critical habitat for these corals.

Of course, the whole “assessment” process ultimately depends upon somebody’s ability to identify individual colonies of coral species in question and that, in turn, depends upon the validity scientific description of those species.  The basic fundamental issues are:

1) Is the given species well-enough described to be reliably identified?  Keep in mind, that by being listed on the petition, at least somebody thinks the indivual colonies in that species can be identified.

2) If the species is identifable, can it be assessed to determine if it is endangered?

The article discussed in the Coral feature was officially published on 2 December, 2010, in the electronic (online and free access) peer-reviewed journal, PLoS One:

 

Forsman ZH, Concepcion GT, Haverkort RD, Shaw RW, Maragos JE, et al. (2010) Ecomorph or Endangered Coral? DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli PLoS ONE 5(12): e15021. doi:10.1371/journal.pone.

I urge you all to read, at least, the Abstract (= the authors’ short summery) of the article, but I am also a realist and realize that while a few of you will look at the Abstract, and some of you may actually read or download and save the article, most people who scan this blog probably won’t.

So…

Here is a brief summary of the summary – if you will, an abstracted abstract.  And if this is creative document would it then be “abstract art?”    Yeah, I know, “Boo!… hiss!”

The researchers examined the genetic codes for a relatively large number of well-known and well-characterised proteins found in the corals’ cells, as well, they also looked at how the subcellular structures called mitochondria vary genetically between the samples.  They also microscopically compared, in fine detail, some of the visible physical structures of each specimen.  

When added together, these different examinations revealed four distinct groupings of specimens (called “clades”), and when each specimen was identified with traditional taxonomic methods, the four clades contained these species: I) M. patula/M. verrilli, II) M. cf. incrassata, III) M. capitata, IV) M. dilatata/M. flabellata/M. cf. turgescens.  So, sophisticated statistical analyses of skeletal microstructure and genetics separated specimens of 7 “species,” based on traditional taxonomy, into 4 groups that represent -probably- actual groups.  I think whether or not one wants to consider that each of these groups represents a species is probably dependent on how one feels about this type of analysis.  To me, yup, I’ll buy in to consideration of each group as representation of a species.  The microcharacters of the size and shape of verrucae or papillae were the only reliable physical characters that could be used in identifying the groups, while gross features such as any aspect of colony-level morphology was so highly variable as to be useless.

The authors noted that previous studies on how observable structures in corals vary from specimen to specimen have revealed that fragments taken from the same colony can exhibit strikingly different growth forms if grown in different environments.   Additionally, the extent of both genetic and morphological intraspecific variation in corals is poorly understood. This is clearly creates problems for assessment of species in the context of the Endangered Species Act as  structurally-based taxonomy – not molecular or genetic information – is the current basis for estimating species distributions, abundance, and extinction risk.

This study identified no fixed genetic or fine-scale morphological differences between M. flabellata, M. cf. turgescens, and M. dilatata, or between M. patula and M. verilli; in other words, these 5 named species appear to be only 2 natural species.  The authors noted that the geographic ranges of these groups are likely to extend beyond Hawai’i into the central Pacific and that individuals within “species” of these complexes are either actively interbreeding (which means they are not separate species), or they are from separate species that are very closely related (e.g., evolutionarily separated within the last one million years) and cannot be distinguished from one another.  Now that these complexes have been identified, work is needed to determine if the nominal species within each complex freely interbreed.

Finally, the authors note:

Unfortunately, this study provides little guidance for determining if these specific species are valid and should be listed under the ESA, but perhaps more importantly; it highlights major gaps in the present understanding of species as opposed to population-level variation in corals. This study is an example of how knowledge of species boundaries in corals is not only necessary for understanding patterns and processes of biodiversity and evolution, but is essential for conservation.

In short, the article is a “fun read.” 

One of the many take home messages is obviously that corals are exceptionally difficult critters to identify.  Generally, if we choose the proper characters, we can identify them to genus.  Beyond that… don’t even try.  As it stands now, we have so few data across the range of most tropical stony reef-forming (and presumably, non-reef forming as well) corals, that distinguishing any specific species is an impossible task. 

Enjoy the article!!

Cheers,