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The Hayflick Limit: why humans can't live forever1 month ago in Genomics, Medicine, and Pseudoscience
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Course Corrections4 months ago in Angry by Choice
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The Site is Dead, Long Live the Site2 years ago in Catalogue of Organisms
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The Site is Dead, Long Live the Site2 years ago in Variety of Life
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Does mathematics carry human biases?3 years ago in PLEKTIX
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A New Placodont from the Late Triassic of China5 years ago in Chinleana
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Posted: July 22, 2018 at 03:03PM6 years ago in Field Notes
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Bryophyte Herbarium Survey6 years ago in Moss Plants and More
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Harnessing innate immunity to cure HIV8 years ago in Rule of 6ix
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WE MOVED!8 years ago in Games with Words
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post doc job opportunity on ribosome biochemistry!9 years ago in Protein Evolution and Other Musings
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Growing the kidney: re-blogged from Science Bitez9 years ago in The View from a Microbiologist
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Blogging Microbes- Communicating Microbiology to Netizens10 years ago in Memoirs of a Defective Brain
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The Lure of the Obscure? Guest Post by Frank Stahl12 years ago in Sex, Genes & Evolution
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Lab Rat Moving House13 years ago in Life of a Lab Rat
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Goodbye FoS, thanks for all the laughs13 years ago in Disease Prone
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Slideshow of NASA's Stardust-NExT Mission Comet Tempel 1 Flyby13 years ago in The Large Picture Blog
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in The Biology Files
Name the Bug # 15
Perhaps a bit of a softball this time around but we shall see. How soon can someone identify what these are specimens of? Attribution, as always, to follow.
As the subject of this post is a mollusk, I'd like to take the opportunity to dedicate it to Aydin Örstan whose wife has recently had to take up hospice residency. Best wishes, Aydin, and I hope the care she receives allows both of you to make the best of your time together.
A Question of Availability
About a year ago, I wrote a post discussing the potential difficulty of establishing whether a taxonomic work of restricted availability has been validly 'published'. If you head over to Mickey Mortimer's Theropod Database Blog, you'll be presented with a perfect (and perfecty 'orrible) example of just this issue, concerning the dinosaurological publications of one Stephan Pickering. Mickey has regarded the works as not validly published; Pickering himself has posted a number of comments to argue otherwise.
The arguments that have been made there about copyright (a completely separate issue from ICZN availability), private publication and peer review (in which the ICZN effectively has no interest) are irrelevant to the question of whether the works count as published for ICZN purposes. The important details in that regard are:
As a reminder, the ICZN requirements for a work to count as 'published' are:
Do Pickering's works meet those requirements? 50 copies is low for a publication run but I don't think it can be argued to fail the requirements of 8.1.3. Publications existing in similar or lower numbers have been accepted as valid in the past. Similarly, the fact that Pickering distributed copies to various recipients suggests at least a nominal accordance with 8.1.2 (that most of these recipients, such as Michael Crichton and Stephen Spielberg, appear to have not been working palaeontologists is problematic but does not violate any explicit ICZN requirement). However, I think that a strong argument can be made that by refusing to place any copies in public depositories, Pickering has failed to meet the requirements of 8.1.1, a "public and permanent scientific record", whatever his original intentions may have been ("by their fruits you shall know them", to insert a touch of pretension). To provide a permanent scientific record, it is necessary that future researchers be able to evaluate the publication; if they are unable to gain access to a copy then they are unable to evaluate it. Unless any of the recipients of Pickering's publications take it upon themselves to secure the future availability of the works, they will end up being lost to history. As already noted by Mickey, the _Prehistoric Times_ insert, having had a much wider distribution, is a potential exception to this problem; my personal inclination would be to accept the names diagnosed therein as available though again the future availability of the work is a pending question.
Indeed, hovering over all of this is a much broader question about the publication requirements of the ICZN. Implicit in the current rules is the assumption that "once available, always available" but time, of course, is a great destroyer. In my earlier post, I discussed the rare Japanese journal Lansania, for some issues of which only a handful of (or even single) copies survive while others may have been lost entirely. There can be no doubt that the publisher of Lansania, Kyukichi Kishida, intended these issues to provide a "public and permanent scientific record"; they have evidently failed to meet that intention. What becomes of taxa whose original descriptions can no longer be evaluated?
The arguments that have been made there about copyright (a completely separate issue from ICZN availability), private publication and peer review (in which the ICZN effectively has no interest) are irrelevant to the question of whether the works count as published for ICZN purposes. The important details in that regard are:
- 1. Pickering had 50 copies of each of the works professionally printed in 1995 (at least one was printed later in 1999). I have not personally seen the works in question, but the indications are that the diagnoses presented therein would satisfy ICZN requirements.
- 2. No printed copies of the works were deposited in institution libraries (and Pickering has objected strenuously to suggestions that he should have done so); however, copies were distributed to various recipients. At least some copies were distributed shortly after printing.
- 3. An excerpt or reprint of one of the works was distributed as an insert in 1996 with an issue of the popular magazine _Prehistoric Times_.
As a reminder, the ICZN requirements for a work to count as 'published' are:
8.1. Criteria to be met. A work must satisfy the following criteria:8.1.1. it must be issued for the purpose of providing a public and permanent scientific record,
8.1.2. it must be obtainable, when first issued, free of charge or by purchase, and
8.1.3. it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies.
Do Pickering's works meet those requirements? 50 copies is low for a publication run but I don't think it can be argued to fail the requirements of 8.1.3. Publications existing in similar or lower numbers have been accepted as valid in the past. Similarly, the fact that Pickering distributed copies to various recipients suggests at least a nominal accordance with 8.1.2 (that most of these recipients, such as Michael Crichton and Stephen Spielberg, appear to have not been working palaeontologists is problematic but does not violate any explicit ICZN requirement). However, I think that a strong argument can be made that by refusing to place any copies in public depositories, Pickering has failed to meet the requirements of 8.1.1, a "public and permanent scientific record", whatever his original intentions may have been ("by their fruits you shall know them", to insert a touch of pretension). To provide a permanent scientific record, it is necessary that future researchers be able to evaluate the publication; if they are unable to gain access to a copy then they are unable to evaluate it. Unless any of the recipients of Pickering's publications take it upon themselves to secure the future availability of the works, they will end up being lost to history. As already noted by Mickey, the _Prehistoric Times_ insert, having had a much wider distribution, is a potential exception to this problem; my personal inclination would be to accept the names diagnosed therein as available though again the future availability of the work is a pending question.
Indeed, hovering over all of this is a much broader question about the publication requirements of the ICZN. Implicit in the current rules is the assumption that "once available, always available" but time, of course, is a great destroyer. In my earlier post, I discussed the rare Japanese journal Lansania, for some issues of which only a handful of (or even single) copies survive while others may have been lost entirely. There can be no doubt that the publisher of Lansania, Kyukichi Kishida, intended these issues to provide a "public and permanent scientific record"; they have evidently failed to meet that intention. What becomes of taxa whose original descriptions can no longer be evaluated?
Big Bad Wolfies (Taxon of the Week: Lycosidae)
The wolf spiders (I usually call them simply 'wolfies') of the family Lycosidae are one of the more easily recognisable groups of ground-dwelling spiders. Their eyes are placed in three rows clustered together at the front of the cephalothorax with the median posterior eyes large and sitting above a straight row of the small anterior eyes. Some wolf spiders reach relatively large sizes and large wolfies tend to usually be some variant of brown or grey with longitudinal stripes. Most members of the family, particularly the larger species, tend to be morphologically quite conservative and despite the recognition of well over 2000 species in the family (a number that is increasing with no sign of slowing down) distinguishing those species is not usually easy without close examination. Wolf spiders are not often inclined to bite humans and their bites are not usually regarded as dangerous (though a bite from a large species could be painful).
Wolf spiders get their name because most members of the family are active hunters rather than snare builders though a smaller number of genera build distinctive sheet webs with a silk retreat tunnel. Most authors have regarded the sheet web builders as retaining the ancestral behaviour for the family but phylogenetic analysis has not determined this conclusively (Murphy et al., 2006); if web building is ancestral then it has been convergently lost on numerous occasions. Those lycosids that do not build sheet webs may be permanently vagrant or they may dig themselves a home burrow into which they retreat when not hunting. All wolf spiders wrap their eggs in a silken egg-sac which the female carries on the underside of her spinnerets; after the eggs hatch she carries her young around clinging to her abdomen.
Recent studies have shown the need for a fair amount of revision of lycosid systematics; the main genus Lycosa in particular had been shown to be a polyphyletic assemblage of conservative large lycosids. Researchers are slowly chipping away at the necessary revisions; a great deal of progress has been made (see, for instance, Volker Framenau's webpage on Australian lycosids), but a great deal remains to be done. Matters have not been helped by the fact that wolf spiders were another group of arachnids to be subjected to the loving care and attention of Carl-Friedrich Roewer, demonstrating his usual talent for producing extensive revisions based on the most superficial and inconsequential of characters. Also, until recently there was debate over the identity of Lycosa's type species, the Mediterranean L. tarantula originally named by Linnaeus. This species, it should be noted, was the original tarantula; it was only later that the name became associated with South American mygalomorph spiders.
REFERENCES
Murphy, N. P., V. W. Framenau, S. C. Donnellan, M. S. Harvey, Y.-C. Park & A. D. Austin. 2006. Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior. Molecular Phylogenetics and Evolution 38 (3): 583-602.
How to Write a Key
My current job primarily involves insect identifications with any type of insect (or arachnid or terrestrial mollusc) potentially requiring an ID. Because I am not intimately familiar with every single insect species found in Australia (terribly remiss of me, I know), this means that I find myself using a lot of identification keys. The construction of an identification key can be a somewhat underrated part of the taxonomic process; a key often gets tacked on to a review without much apparent concern, but the key has the potential to be the most regularly used section of the review. Also, the skills involved in constructing a good key may not be the same as those in constructing a good taxonomy and an excellent taxonomist will not always be an excellent key-writer. As a result, the available keys out there can vary from the impressive to the appalling. So, with the typical hubris of any snotty customer, I offer a few guidelines for the construction of a successful key*. Some of these rules may clash on occasion and a little discretion may be required about whether you should follow them (except for Rule 1 which should never be broken).
*These guidelines apply primarily to the writing of a linear key where the user is guided through a series of alternatives in a predetermined order. These days, an increasing number of computer-based non-linear keys are available, such as those constructed using LUCID, where the user can choose in which order they want to look at characters. Both linear and non-linear keys have their advantages and disadvantages: a non-linear key is less likely to leave the user stranded at a single indeterminable couplet but a linear key can sometimes offer more guidance as to which characters the user needs to look at.
Rule 1: A key has one purpose, and one purpose only. That purpose, of course, being to provide an identification. A key is not a classification and the characters that are useful in determining taxonomy are not necessarily the characters that you should be emphasising in a key. For instance, your insect classification may be heavily influenced by characters of the genitalia but that doesn't mean that you should be requiring users to dissect out genitalia right from the first couplet (especially if said genitalia are only found in adult males). Conversely, a note to users: just because two species sit next to each other in a key doesn't necessarily mean that they're closely related.
Rule 2: Don't assume that your users know the organism being identified as well as you do. Indeed, the fact that they need to work through a key in the first place suggests that they probably don't. This is one of the trickiest rules to follow because you tend to forget that you didn't always know everything you know now; sometimes, it seems that the more qualified someone is to write a key, the worse is the key that they end up producing. Try to avoid jargon, and be especially careful if the group you're working on has any conventions in the use of terms that differ from their 'common-sense' meanings. For instance, one key I've used regularly distinguishes fulgoroids (a group of leafhoppers) from other Auchenorrhyncha (cicadas and leafhoppers) by whether the antennae are 'in front of' or 'below' the eyes; however, this refers to their position relative to the rest of the insect's face which is not straight up and down but may be angled backwards at up to 45°. So to anyone who doesn't know this convention (e.g. me, when I first started using the key), an antenna can easily appear 'below' the eye when it is really 'in front of' it.
Rule 3: First, eliminate the obvious... If only one of the species you're providing a key for has a bright blue head when the rest are unicolor, or only one species has a large horn when the others are unarmed, then split off that species first. Don't make the user work through twenty couplets of more difficult characters when they could have spotted the ID straight off bat.
Rule 4:...but make sure the 'obvious' is actually obvious. How a specimen has been collected and preserved may affect how it appears. Colours may be bleached, soft body parts may have their shapes distorted. So try to choose characters that are as resistent to distortion as possible.
Rule 5: Start on the outside and work your way in. Again, try to start with characters the user can find easily with a minimum of specimen manipulation. Don't make them cut anything open unless they really have to.
Rule 6: Start at the middle and work your way out. This mainly applies to arthropods, but I'm sure that other organisms have analogous situations. Insect and arachnid specimens regularly lose legs, antennae, etc. Using characters on the main body when possible reduces the risk that the user may not be able to identify the required character state.
Rule 7: Offer alternatives where possible. Another way to get around the above issue is to suggest informative characters elsewhere on the organism. 'Hind tibia spinose; antennae branched' means that if the specimen's tibiae are missing, the user may still be able to antennae.
Rule 8: Illustrations are good. The best way to explain to the user just what you mean by 'spinose' or 'well-developed' is to show them.
Rule 9: Define relative characters when possible. Remember Rule 2? If you want to separate taxa depending on whether a feature is 'small' or 'large', then say exactly what you'd regard as 'small'. Something that a mite worker regards as 'large' might not seem large to someone used to working on butterflies. On the other hand, rather than using direct measurements (which can be difficult to judge, especially with small organisms), try using comparative measures - 'wings shorter than legs', for instance.
Rule 10: Don't require multiple specimens. I've had a couple of occasions when a key asks me something like whether the male has larger eyes than the female. Not very useful when I don't have both. Especially when I don't know the animal in question well enough to tell which is the female and which is the male.
Rule 34: Individual breast larger than head... Lolo Ferrari.
Individual breast smaller than head... 2.
*These guidelines apply primarily to the writing of a linear key where the user is guided through a series of alternatives in a predetermined order. These days, an increasing number of computer-based non-linear keys are available, such as those constructed using LUCID, where the user can choose in which order they want to look at characters. Both linear and non-linear keys have their advantages and disadvantages: a non-linear key is less likely to leave the user stranded at a single indeterminable couplet but a linear key can sometimes offer more guidance as to which characters the user needs to look at.
Rule 1: A key has one purpose, and one purpose only. That purpose, of course, being to provide an identification. A key is not a classification and the characters that are useful in determining taxonomy are not necessarily the characters that you should be emphasising in a key. For instance, your insect classification may be heavily influenced by characters of the genitalia but that doesn't mean that you should be requiring users to dissect out genitalia right from the first couplet (especially if said genitalia are only found in adult males). Conversely, a note to users: just because two species sit next to each other in a key doesn't necessarily mean that they're closely related.
Rule 2: Don't assume that your users know the organism being identified as well as you do. Indeed, the fact that they need to work through a key in the first place suggests that they probably don't. This is one of the trickiest rules to follow because you tend to forget that you didn't always know everything you know now; sometimes, it seems that the more qualified someone is to write a key, the worse is the key that they end up producing. Try to avoid jargon, and be especially careful if the group you're working on has any conventions in the use of terms that differ from their 'common-sense' meanings. For instance, one key I've used regularly distinguishes fulgoroids (a group of leafhoppers) from other Auchenorrhyncha (cicadas and leafhoppers) by whether the antennae are 'in front of' or 'below' the eyes; however, this refers to their position relative to the rest of the insect's face which is not straight up and down but may be angled backwards at up to 45°. So to anyone who doesn't know this convention (e.g. me, when I first started using the key), an antenna can easily appear 'below' the eye when it is really 'in front of' it.
Rule 3: First, eliminate the obvious... If only one of the species you're providing a key for has a bright blue head when the rest are unicolor, or only one species has a large horn when the others are unarmed, then split off that species first. Don't make the user work through twenty couplets of more difficult characters when they could have spotted the ID straight off bat.
Rule 4:...but make sure the 'obvious' is actually obvious. How a specimen has been collected and preserved may affect how it appears. Colours may be bleached, soft body parts may have their shapes distorted. So try to choose characters that are as resistent to distortion as possible.
Rule 5: Start on the outside and work your way in. Again, try to start with characters the user can find easily with a minimum of specimen manipulation. Don't make them cut anything open unless they really have to.
Rule 6: Start at the middle and work your way out. This mainly applies to arthropods, but I'm sure that other organisms have analogous situations. Insect and arachnid specimens regularly lose legs, antennae, etc. Using characters on the main body when possible reduces the risk that the user may not be able to identify the required character state.
Rule 7: Offer alternatives where possible. Another way to get around the above issue is to suggest informative characters elsewhere on the organism. 'Hind tibia spinose; antennae branched' means that if the specimen's tibiae are missing, the user may still be able to antennae.
Rule 8: Illustrations are good. The best way to explain to the user just what you mean by 'spinose' or 'well-developed' is to show them.
Rule 9: Define relative characters when possible. Remember Rule 2? If you want to separate taxa depending on whether a feature is 'small' or 'large', then say exactly what you'd regard as 'small'. Something that a mite worker regards as 'large' might not seem large to someone used to working on butterflies. On the other hand, rather than using direct measurements (which can be difficult to judge, especially with small organisms), try using comparative measures - 'wings shorter than legs', for instance.
Rule 10: Don't require multiple specimens. I've had a couple of occasions when a key asks me something like whether the male has larger eyes than the female. Not very useful when I don't have both. Especially when I don't know the animal in question well enough to tell which is the female and which is the male.
Rule 34: Individual breast larger than head... Lolo Ferrari.
Individual breast smaller than head... 2.
Star Sands (Taxon of the Week: Calcarinidae)
About a month ago, I presented my first post on the marine shell-bearing protists known as foraminiferans. That post was on forams that constructed their shell by gluing together sand but I mentioned that there were other families that secreted their shells themselves. Some of these families can reach sizes large enough to be seen with the naked eye (over a millimetre and sometimes well over a centimetre in diameter); the Indo-Pacific calcareous Calcarinidae are one of these larger families. Such large forams live in association with endosymbiotic algae and have been given the evocative name of 'living sands' (Lee, 1995).
Among the living sands, the shape of Calcarinidae is distinctive. Their basic form is trochoid (i.e. shaped like a top shell, a Trochus) and similar to species of the related family Rotaliidae (Cushman, 1940) but extra shell material and chambers are laid down over and around the central trochoid structure. Large blunt external spines radiate from the sides of the foram, often giving the whole a star-like appearance when viewed from above. A system of canals runs between the chambers and along the spines allowing for the passage of cytoplasm between the chambers and the outside world. The chosen symbionts of calcarinids are diatoms which are held in special vacuoles inside the chambers. Symbiotic forams do still feed on other micro-organisms as well as deriving nutrients from their endosymbionts (Lee, 1995) but laboratory studies have shown that calcarinids are capable of living solely on nutrients derived from their diatoms in the absence of another food supply (Röttger & Krüger, 1990). If the algal symbionts are killed, the forams cannot live long without them though they may replace them if the opportunity arises in time (Lee, 1995).
Calcarinids can make up a significant part of coastal calcareous deposits in the Indo-Pacific region; one of the most fun expressions of this abundance was made by Lee (1995) who commented that calcarinid deposits in one part of Japan were "so abundant that they can be scraped together by hand to build sand castles". Because of their dependence on their diatom symbionts, calcarinids are only found in shallow waters, mostly preferring high energy environments (Lobegeier, 2002). Many calcarinids live as epiphytes on macroalgae and seagrasses where they attach themselves to their substrate by means of cytoplasm extended through the spine canals (Röttger & Krüger, 1990); among filamentous algae the spines themselves may form a mechanical anchor among tangled filaments (Lobegeier, 2002).
REFERENCES
Cushman, J. A. 1940. Foraminifera: their classification and economic use, 3rd ed. Harvard University Press: Cambridge (Massachusetts).
Lee, J. T. 1995. Living sands. BioScience 45 (4): 252-261.
Lobegeier, M. K. 2002. Benthic foraminifera of the family Calcarinidae from Green Island Reef, Great Barrier Reef province. Journal of Foraminiferal Research 32 (3): 201-216.
Röttger, R., & R. Krüger. 1990. Observations on the biology of Calcarinidae (Foraminiferida). Marine Biology 106 (3): 419-425.
Scattering the Sheaves (Taxon of the Week: Elymus)
Elymus is a cosmopolitan genus of perennial tufted and/or rhizomatous grasses that, depending on the taxonomic treatment used, may include from 20 to 200 species found mostly in cool temperate parts of the world (Quattrocchi, 2006). Bit of a difference between those extremes, you may be thinking? Elymus is part of the Triticeae, the grass tribe that includes wheat, rye and barley. Establishing relationships within the Triticeae has always been a difficult prospect; hybridisation and polyploidy have been major factors in the evolution of the tribe. Until the mid-1980s, most western authors continued to use a classification whose basic philosophy went right back to Linnaeus' Species Plantarum (Barkworth, 2000). This system, in which Elymus contained perennial grasses with 2 or more 2- to 6-flowered spikelets at each node of the rachis (the flower spike), was unashamedly pragmatist and concerned with facilitating species identification rather than describing relationships. A more modern classification had been proposed by a Russian author, Nevski, in the early 1930s but had not been widely accepted outside the communist countries. Among Nevski's most significant changes was the realisation that reduction in the number of flowers at each spikelet to one had occurred multiple times in various genera and his Elymus included species with from one to six flowers.
Starting in the 1940s, an increasing number of cytogenetic studies had established that many of the genera of Triticeae contained chromosomally disparate subgroups that could be identified by the chromosome pairing patterns in hybrids between taxa. A number of authors had integrated some cytogenetic data into revisions of Triticeae but two authors in 1984 independently suggested that Triticeae classification should be based entirely on cytogenetic data alone. Not surprisingly, this lead to a botanical rift - even if one was willing to credit that genetic characters might be a better indication of relationships than morphology (and not everyone was), they were of limited use for field identifications. Before gene sequencing became widely feasible, identifying the cytogenetic nature of a grass required observation of cells undergoing meiotic division. However, genomic data remains a significant factor in Triticeae classification (Barkworth, 2000).
Each of the genome groups that has been identified in Triticeae has been assigned a letter code: A, B, N, R, etc. Polyploid taxa of hybrid origin may carry chromosomes from more than one genome group; the genus Triticum (wheats), for instance, is characterised as AB (or some further complication thereof, such as AAB). The basic chromosome type of Elymus for North American representatives is StH, representing their descent from one or more hybridisation events between the genera Pseudoroegneria (St) and Hordeum (H; Hordeum includes the barleys) (Mason-Gamer, 2001). Taxa from other parts of the world currently assigned to Elymus all carry the St genome, but may have it combined with different genomes such as Y or W*. Future investigation is required to establish whether these taxa are appropriately placed in Elymus.
*As ploidy level increases, the genome codes for various taxa can get a little hideous. The North American octoploid genus Pascopyrum, for instance, has the genome code StStHHNsNsXX.
Economically speaking, a number of Elymus species are used as pasture grasses for feeding livestock. Quattrocchi (2006) indicates that Elymus grain is usable for food but I haven't found any references to specific species being regularly used as such (apart from indirectly with Elymus species being used in wheat outcrossing). Elymus repens, couch grass, is a particularly tough rhizomatous species that seems to be encouraged in some situations and regarded as a curse in others (many authors refer to couch grass as Elytrigia repens instead but it carries the genome StStH - Barkworth, 2000).
REFERENCES
Barkworth, M. E. 2000. Changing perceptions of the Triticeae. In Grasses: Systematics and Evolution (S. W. L. Jacobs & J. Everett, eds) pp. 110-120. CSIRO: Melbourne.
Mason-Gamer, R. J. 2001. Origin of North American Elymus (Poaceae: Triticeae) allotetraploids based on granule-bound starch synthase gene sequences. Systematic Botany 26 (4): 757-768.
Quattrocchi, U. 2007. CRC World Dictionary of Grasses: common names, scientific names, eponyms, synonyms, and etymology vol. 2. CRC Press.
In Which, Despite Not Being The Crowd Favourite, Drosophila funebris Holds D. melanogaster Down and Kicks It Repeatedly in the Teeth
It's been two years in the making, but the ICZN decision on Drosophila has finally been announced (ICZN, 2010). You may recall that an application had been submitted (Linde et al., 2008) to make Drosophila melanogaster, the subject of countless genetic studies, the type species of the genus instead of the current holder of that title, D. funebris. See previous posts here and here for background details.
And the verdict: by a surprisingly large margin (23 to 4, with one absence), the Commission has turned the proposal down. Drosophila funebris remains the valid type species of the genus; D. melanogaster retains the potential for reclassification. Those of you with a particular interest in the workings of nomenclature* would do well to get hold of a copy of the decision. In light of the higher than usual public interest in this case, the unusual step has been taken of publishing individual comments from each of the commissioners on the reasoning behind their decisions. As well as the insight provided into this particular case (and it's worth noting that some of the commissioners on both sides of the floor ended up voting against their own initial sympathies), some of the comments provide interesting talking points about the role of nomenclature in general.
*Yes, we do exist. I'm afraid the doctors say that there's nothing they can do.
Some of the reasons given for voting against the proposal were reasonable, others less so. A. small number of commissioners voiced the complaint that the proposal was asking the ICZN to endorse a particular taxonomic method; as I argued in one of the previous posts, it did no such thing and I am rather disappointed that this issue was raised. Some commissioners also turned down the proposal on the grounds that it was premature (Miguel Alonso-Zarazaga stated that he "felt that the authors of the case had not allowed the community to have a healthy discussion of their proposals, since the ‘detailed phylogenetic studies’ mentioned in the case were still largely unpublished, and were thus hypothetical"). However, while the proposal may have been precipitated by an as-yet unpublished study, the results of that study are hardly novel. As pointed out by László Papp in his comments on his supporting vote, the issue that any subdivision of Drosophila would require the removal from that genus of D. melanogaster has been under discussion for at least 35 years (a time when, I should note, purely phylogenetic considerations were often considered less significant).
Less trivial are the concerns that the proposal introduced a higher overall nomenclatural instability than the current status quo and that it may have set an uncomfortable precedent. The commission was being asked to choose between maintaining Drosophila for a smaller number (about 300) of species including some very well-known taxa, or a potentially much larger number (up to about 1100) of mostly less familiar species. Should "celebrity names" carry that much greater weight? Also, while the combination Sophophora melanogaster may be unfamiliar, there is no actual ambiguity about to what it refers.
Some commissioners, as well as many of the ICZN's press statements, raised the argument that "drosophila" could still be used as an informal name for Sophophora melanogaster. True, as far as it goes, and not unprecedented: names such as "azalea" and "cosmos" continue to be used despite the genera of those names being stricken from the technical literature long ago. Nevertheless, this is not anywhere near a satisfactory solution. As a corollary example, a number of recent authors have proposed restricting "Aves" to the crown group of birds on not unreasonable grounds. The supposed divide between technical and vernacular names has done nothing to dissuade people from objecting to the idea that creatures such as Archaeopteryx and Ichthyornis may no longer be "birds".
My thanks go to Kim van der Linde (first author of the proposal) and Elinor Michel (secretary of the ICZN) for sending me copies of the decision. Kim's own reaction to the ruling can be read here.
REFERENCES
Linde, K. van der, G. Bächli, M. J. Toda, W.-X. Zhang, Y.-G. Hu & G. S. Spicer. 2007. Case 3407: Drosophila Fallén, 1832 (Insecta, Diptera): proposed conservation of usage. Bulletin of Zoological Nomenclature 64 (4).
There He Goes! (Taxon of the Week: Indriidae)
The Indriidae (sometimes, just to be confusing, spelt as Indridae or Indrisidae) is a family of lemurs found in (of course) Madagascar. As generally recognised, the species of Indriidae are divided between three living genera, Indri (the indri), Avahi (the avahi[s]) and Propithecus (sifakas). Some authors (e.g. Marivaux et al., 2001) have included the bamboo lemurs of the genus Hapalemur in the Indriidae but most (e.g. Orlando et al., 2008) place Hapalemur in the Lemuridae. Also, two subfossil families of large lemurs, the Archaeolemuridae and Palaeopropithecidae, are closely related to the Indriidae and are included therein as subfamilies by some authors.
The three genera of indriids are united by a number of very distinct features. Perhaps the most obvious is that they all have the hind legs significantly longer than the fore legs, as demonstrated in countless nature documentary sequences featuring sifakas. Because of this disparity in limb length, the normally arboreal indriids cannot walk on all fours on the ground and, when forced to cross open spaces, hop upright on their hind legs only with the fore legs held upright. Indriids will also often sit upright with their arms held up in the same manner, leading to an old story that they are sun worshippers. Also noteworthy is the indriid dentition which has fewer teeth than many other primates*: two (pairs of) incisors, one canine, two premolars and three molars above and the same below except for the absence of the second incisors or the canines (depending who you ask) (Nowak, 1999). All indriids are strict vegetarians.
*When this post was originally put up I said that indriids had the lowest number of teeth for primates but a number of commenters below have pointed out my mistake.
The number of species in the family has been the subject of much recent activity. Nowak (1999) listed one species each of Indri and Avahi and three in Propithecus but recent publications and reviews have increased the number of species in Avahi and Propithecus to nine each (Mittermeier et al., 2008). In the case of Propithecus this increase has mostly been due to 'subspecies' being redefined as 'species' but most of the Avahi species have been named within the last ten years, mostly distinguished primarily or entirely by molecular evidence alone. The avahis are small, mostly brown and grey nocturnal lemurs that might be expected to be morphologically conservative but still, I can't say as I'm entirely happy with the situation.
The indri (Indri indri) is without a doubt the most remarkable of the indriids. The largest living lemur (up to 10 kg), the indri is immediately distinguished by its striking piebald coloration and vestigial tail. Indris live in small family groups. Groups communicate within themselves and with each other by means of loud calls that can be heard up to 2 km away:
However, there seems to be no basis for the oft-repeated claim that the "indri" is miscalled and that the name is actually Malagasy for "there it goes" or "look at that" or something similar. As explained by Hacking (1981), the mistake was attributed to the naturalist Pierre Sonnerat, one of the first Europeans to observe the indri. However, Sonnerat's experience with the indri was no brief encounter. Tame indri were often kept in the area in which he travelled (Markus Bühler, in a response to the "creepy Megaladapis" picture I posted here a while back, informed me of a probably-apocryphal claim that tame indris were used to hunt birds) and Sonnerat himself took one back to France with him. Hacking (1981) points out that it strains credulity that Sonnerat could have become so familiar with the animal yet never had anyone correct him on a basic point. It is more likely that, as with a similar story about the kangaroo, the legend has developed from a failure to consider that different groups of people may use different names for the same animal.
REFERENCES
Hacking, I. 1981. Was there ever a radical mistranslation? Analysis 41 (4): 171-175.
Lei, R., S. E. Engberg, R. Andriantompohavana, S. M. McGuire, R. A. Mittermeier, J. R. Zaonarivelo, R. A. Brenneman & E. E. Louis. 2008. Nocturnal lemur diversity at Masoala National Park. Special Publications, Museum of Texas Tech University 53: 1-41.
Marivaux, L., J.-L. Welcomme, P.-O. Antoine, G. Métais, I. M. Baloch, M. Benammi, Y. Chaimanee, S. Ducrocq & J.-J. Jaeger. 2001. A fossil lemur from the Oligocene of Pakistan. Science 294: 587-591.
Mittermeier, R. M., J. U. Ganzhorn et al.. 2008. Lemur diversity in Madagascar. International Journal of Primatology 29 (6): 1607-1656.
Nowak, R. M. 1999. Walker's Mammals of the World, 6th ed., vol. 1. JHU Press.
Orlando, L., S. Calvignac, C. Schnebelen, C. J. Douady, L. R. Godfrey & C. Hänni. 2008. DNA from extinct giant lemurs links archaeolemurids to extant indriids. BMC Evolutionary Biology 8: 121.
Dinosaurs All Over the Place
Though once considered a contentious subject, most recent authors have agreed that dinosaurs represent a monophyletic group. However, a paper just released today (Parera et al., 2010) analyses the most extensive selection of reptilian taxa to date and turns the current scenario on its head, not only finding strong support for dinosaur (and particularly theropod) polyphyly but calling for significant changes to our images of Mesozoic reptiles. The failure of earlier studies such as Mortimer (2004) to recognise theropod polyphyly seems due simply to their failure to include enough taxa.
Animals traditionally regarded as 'dinosaurs' are placed by Parera et al. in three separate places in the reptile family tree. Ornithischians, sauropodomorphs and most theropods are in their usual place as sister to the clade including modern crocodiles and Parera et al. restrict the name 'Dinosauria' to this clade. However, dromaeosaurids and oviraptorosaurs clade with birds separately from the main dinosaur clade. Instead, this new clade (which Parera et al. simply refer to as 'Aves') appears as sister to the Triassic rhynchosaurs. While, to the best of my knowledge, such an arrangement has not been suggested before, it does not seem entirely incredible - for a start, both birds and rhynchosaurs have well-developed beaks.
The most surprising result of all, perhaps, is that compsognathids and therizinosaurs are also not dinosaurs. Instead, they form part of a large clade also including ichthyosaurs, plesiosaurs, pterosaurs and lepidosaurs for which Parera et al. resurrect the long-disused name Gryphi. This further corroborates the recent demonstration by Lingham-Soliar et al. (2007) that the supposed 'protofeathers' found in the compsognathid Sinosauropteryx are in fact collagen fibres from a thick insulating dermal layer. The supposed 'melanosomes' described from Sinosauropteryx by Zhang et al. (2010), cited as further evidence for a 'protofeather' interpretation of the fibres, are shown by Parera et al. (2010) to instead represent the eggs of skin-burrowing parasites that afflicted this poor individual.
The additional presence of preserved dermal fibres in ichthyosaurs and pterosaurs suggests that such a dermal layer was an ancestral feature of the Gryphi. The clade appears to have been ancestrally aquatic - aquatic lifestyles have been proposed previously for compsognathids by Bidar et al. (1972) and for pterosaurs by Wagler (1830), and Parera et al. further demonstrate the accuracy of these interpretations. The ancestors of lepidosaurs, found by Parera et al. to be sister to pterosaurs, must have at some point left the aquatic habitat and consequently lost their insulating dermal layer. However, perhaps the aquatic iguana of the Galapagos Islands represents the sole remnant of the Gryphi's long marine history?
REFERENCES
Bidar, A., L. Demay & G. Thomel. 1972. Compsognathus corallestris, nouvelle espèce de dinosaurien theropode du Portlandien de Canjuers (Sud-est de la France). Annu. Mus. Hist. Nat., Nice 1: 1–34.
Lingham-Soliar, T., A. Feduccia & X. Wang. 2007. A new Chinese specimen indicates that ‘protofeathers’ in the Early Cretaceous theropod dinosaur Sinosauropteryx are degraded collagen fibres. Proceedings of the Royal Society of London Series B - Biological Sciences 274 (1620): 1823-1829.
Mortimer, M. D. 2004. The phylogeny of Neotetanurae (Theropoda, Dinosauria). Annals of the Museum of Natural History at the University of Ohio at
Springfield 2004: 1-369.
Parera, A. S., H. M. Whio & T. V. Pari. 2010. A comprehensive analysis of reptile phylogeny demonstrates theropod polyphyly, with notes on the life habits of compsognathids and pterosaurs. Transactions of the Royal Society of Hull 238 (1): 4-136.
Wagler, J. G. 1830. Natürliches System der Amphibien. München, Stuttgart, Tübingen.
Zhang, F., S. L. Kearns, P. J. Orr, M. J. Benton, Z. Zhou, D. Johnson, X. Xu & X. Wang. 2010. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 463: 1075-1078.
Animals traditionally regarded as 'dinosaurs' are placed by Parera et al. in three separate places in the reptile family tree. Ornithischians, sauropodomorphs and most theropods are in their usual place as sister to the clade including modern crocodiles and Parera et al. restrict the name 'Dinosauria' to this clade. However, dromaeosaurids and oviraptorosaurs clade with birds separately from the main dinosaur clade. Instead, this new clade (which Parera et al. simply refer to as 'Aves') appears as sister to the Triassic rhynchosaurs. While, to the best of my knowledge, such an arrangement has not been suggested before, it does not seem entirely incredible - for a start, both birds and rhynchosaurs have well-developed beaks.
The most surprising result of all, perhaps, is that compsognathids and therizinosaurs are also not dinosaurs. Instead, they form part of a large clade also including ichthyosaurs, plesiosaurs, pterosaurs and lepidosaurs for which Parera et al. resurrect the long-disused name Gryphi. This further corroborates the recent demonstration by Lingham-Soliar et al. (2007) that the supposed 'protofeathers' found in the compsognathid Sinosauropteryx are in fact collagen fibres from a thick insulating dermal layer. The supposed 'melanosomes' described from Sinosauropteryx by Zhang et al. (2010), cited as further evidence for a 'protofeather' interpretation of the fibres, are shown by Parera et al. (2010) to instead represent the eggs of skin-burrowing parasites that afflicted this poor individual.
The additional presence of preserved dermal fibres in ichthyosaurs and pterosaurs suggests that such a dermal layer was an ancestral feature of the Gryphi. The clade appears to have been ancestrally aquatic - aquatic lifestyles have been proposed previously for compsognathids by Bidar et al. (1972) and for pterosaurs by Wagler (1830), and Parera et al. further demonstrate the accuracy of these interpretations. The ancestors of lepidosaurs, found by Parera et al. to be sister to pterosaurs, must have at some point left the aquatic habitat and consequently lost their insulating dermal layer. However, perhaps the aquatic iguana of the Galapagos Islands represents the sole remnant of the Gryphi's long marine history?
REFERENCES
Bidar, A., L. Demay & G. Thomel. 1972. Compsognathus corallestris, nouvelle espèce de dinosaurien theropode du Portlandien de Canjuers (Sud-est de la France). Annu. Mus. Hist. Nat., Nice 1: 1–34.
Lingham-Soliar, T., A. Feduccia & X. Wang. 2007. A new Chinese specimen indicates that ‘protofeathers’ in the Early Cretaceous theropod dinosaur Sinosauropteryx are degraded collagen fibres. Proceedings of the Royal Society of London Series B - Biological Sciences 274 (1620): 1823-1829.
Mortimer, M. D. 2004. The phylogeny of Neotetanurae (Theropoda, Dinosauria). Annals of the Museum of Natural History at the University of Ohio at
Springfield 2004: 1-369.
Parera, A. S., H. M. Whio & T. V. Pari. 2010. A comprehensive analysis of reptile phylogeny demonstrates theropod polyphyly, with notes on the life habits of compsognathids and pterosaurs. Transactions of the Royal Society of Hull 238 (1): 4-136.
Wagler, J. G. 1830. Natürliches System der Amphibien. München, Stuttgart, Tübingen.
Zhang, F., S. L. Kearns, P. J. Orr, M. J. Benton, Z. Zhou, D. Johnson, X. Xu & X. Wang. 2010. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 463: 1075-1078.
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