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Australian Green Pythons - DNA Study Needed

richardwells Sep 14, 2003 08:12 AM

Hello Everyone,

Well, although I do agree that the Australian population of Chondropython is taxonomically distinct from viridis sensu stricto, this is based purely on features of external morphology, and differences in behaviour and reproductive biology that I have observed. Ray Hoser’s description of Chondropython viridis shireenae - from a purely descriptive point of view of course – obviously conforms to the requirements of the Code, but I am still trying to get an issue of the original publication of the Type Description which reportedly appeared in the Macarthur Herpetological Society Newsletter.
As for the description as it appears on Ray Hoser’s Web Site, well even for me it is a bit weak to take it on face value. I am sure that others would have really liked to see at least some testable meristics for this taxon’s main differences from other populations of viridis, but who am I to complain about brevity of Type Descriptions anyway! However, to compensate for the omission of hard morphological data, by the inclusion of his old DNA smoke screen again is not just unnecessary - it is really quite unacceptable in a formal taxonomic description. Generally speaking, I think it is wise to be sceptical of the value of blind acceptance of DNA power-arguments from non-geneticists. As usual, Ray provided no direct DNA evidence to support his assertions in his original description of Chondropython viridis shireenae. But I guess we just have to trust him, because all will be revealed if we somehow manage to get access to a copy of his book “Smuggled 2”. In a subsequent post to Kingsnake’s Taxonomy Forum, Ray guides us to this secret stash of DNA data – the Queensland Government! Now, thanks to Ray, one may have to resort to that new friend of the taxonomist the Queensland Supreme Court Record to identify an Australian snake. Hoser's type description has now made “Queen Vs Buckley and attached documents” essential reading for anyone interested in testing his hypothesis. This saga seems to get more bizarre by the minute. That Ray would so confidently use results from the uncited proceedings of a Court of Law to support a taxonomic hypothesis, merely casts a shadow over his description, because the paucity of hard data is underscored by this act. Legal records should not be relied upon as scientific records. They often contain information that may be highly subjective, and prone to manipulation because of the adversarial nature of our legal system. Putative conclusions or results of some legal prosecutions, even those purportedly based upon scientific evidence, may be open to differing interpretations, and as Ray himself has found on other occasions, they may not represent a true and accurate record or interpretation of a matter at hand.
Well, is there reliable DNA evidence in existence - published or otherwise - that could be used to support Hoser's erection of his new taxon? I don’t know of any such DNA data…other than what Ray has claimed, and we have to accept his assurance that this data is reliable. Well, I would be rather surprised if the DNA data that Ray infers he has used is of a standard that could unequivocally demonstrate population differences between the populations in question. I say this because this particular DNA investigation by the Queensland Government may have had a design and methodology that may have made a subsequent use of the data as a taxonomic tool an unwarranted extrapolation of the results. I can’t help saying that I would be rather surprised if there actually were any significant DNA differences between the Australian population and that from eastern PNG anyway. A comparison between Indonesian material and that from Australian might be more revealing though.
If we must go through this so-called evidence of DNA differences, I would be interested in knowing the precise details of this original DNA investigation, and this would of course necessitate inquiries to others well beyond the simple legal citation of “Queen vs Buckley”. Questions have to be now answered before we can rely on Hoser's use of this DNA "evidence". A few that spring to mind are: Who carried out the testing? Where was this investigation undertaken? When was this investigation undertaken? What techniques were used in this investigation? How were the samples collected? Were the specimens retained for re-testing or independent validation? And of course, perhaps the most relevant question of all - What control population was used as the comparison or baseline population to assess the significance (if any) of the Australian population? One would presume that any DNA investigation of the genetic variation in Chondropython viridis would of course utilize samples derived from all known populations of the species, including of course topotypic Chondropython viridis (from Indonesia) as the primary control. Anything less would be inadequate, inconclusive, and consequently invalid. I think I see a great PhD project for someone who doesn’t mind the usual reduced life span from parasitic infections that come with field work in tropical Australasia. Any takers?

Best Regards

Richard Wells

Replies (14)

rayhoser Sep 15, 2003 02:47 AM

Subject:
Re: [OzHerpLaw] Australian Green Pythons and the Rules of Evidence
Date:
Mon, 15 Sep 2003 11:10:17 -0700
From:
Raymond Hoser
To:
OzHerpLaw@yahoogroups.com
References:
1

1/ Thanks for your long post - below.
2/ Your comments about the courts of law in Australia would according
to a judgement of His Honour Geoffrey Eames would probably consititute a
gross contempt of court as he has ruled that it is illegal to infer
doubt on the ability of Australian courts to find truth. I have put
everything I own on the line and that decision is being appealed next
month (6 Oct). Unfortunately I have been advised that the result has
been predetermined in favor of Eames.
3/ The type locality of Green Pythons is Aru Islands, which while
forming part of Indonesia is in fact located between New Guinea and
northern Australia.
4/ While I've got your (Richard's) attention, perhaps I can make some
passing remarks in relation to some of your other posts.
- Your claim that I have failed to give unqualified support for your
papers is in fact partially correct. There are several reasons for
this, but most importantly in that most of the taxonomic moves made by
yourself in your two big papers have not been looked at closely by
myself and hence I cannot give unqualified support for what I have not
inspected, as would be expected to be the case (in terms of anyone
else's taxonomy, even if used by myhself at one time or other).
Notwithstanding that, history has shown that by and large I have given
your taxonomic positions MORE support than any other extant
herpetologists in Australia, including for example my rearguard action
to save your name Varanus keithhornei from the piracy of the latter
name V. teriae Sprackland. My submissions to the ICZN as published by
them were instrumental in that case being won and the name keithornei
being directed as the correct one.
I thought you'd be grateful for this time consuming action by myself,
which incidentally predated my papers on taxonomy, but that wasn't to be
so - instead I got barbs from you. That I suppose is your perogative.
Likewise after I gave your papers recognition in later publications and
including naming high-profile snake taxa after you and co-author Rross
Wellington (2 taxa).
Finally, no matter what barbs are thrown my way, I will accept without
reservation the reality that most of the taxonomic moves made in your
two major papers are eminently sensible and in many cases obvious (in
hindsight) and hence will tend to support your positions in that
direction, even if I think your choices of names like "hawkei" were not
sensible choices.
Doing so will put me offside in some quarters, but as you know, I
believe getting things right is more important that staying friends with
those who get it wrong.
I may not be perfect and hence may get things wrong, but as least I try
to be.
All the best in herp to you Richard and the others who read this.
ALL THE BEST
Richard W. Wells wrote:
>
> Hello Everyone,
>
> Well, although I do agree that the Australian population of
> Chondropython is taxonomically distinct from viridis sensu stricto,
> this is based purely on features of external morphology, and
> differences in behaviour and reproductive biology that I have
> observed. Ray Hoser's description of Chondropython viridis
> shireenae - from a purely descriptive point of view of course –
> obviously conforms to the requirements of the Code, but I am still
> trying to get an issue of the original publication of the Type
> Description which reportedly appeared in the Macarthur
> Herpetological Society Newsletter.
> As for the description as it appears on Ray Hoser's Web Site, well
> even for me it is a bit weak to take it on face value. I am sure
> that others would have really liked to see at least some testable
> meristics for this taxon's main differences from other populations
> of viridis, but who am I to complain about brevity of Type
> Descriptions anyway! However, to compensate for the omission of hard
> morphological data, by the inclusion of his old DNA smoke screen
> again is not just unnecessary - it is really quite unacceptable in a
> formal taxonomic description. Generally speaking, I think it is wise
> to be sceptical of the value of blind acceptance of DNA power-
> arguments from non-geneticists. As usual, Ray provided no direct DNA
> evidence to support his assertions in his original description of
> Chondropython viridis shireenae. But I guess we just have to trust
> him, because all will be revealed if we somehow manage to get access
> to a copy of his book "Smuggled 2". In a subsequent post to
> Kingsnake's Taxonomy Forum, Ray guides us to this secret stash of
> DNA data – the Queensland Government! Now, thanks to Ray, one may
> have to resort to that new friend of the taxonomist the Queensland
> Supreme Court Record to identify an Australian snake. Hoser's type
> description has now made "Queen Vs Buckley and attached documents"
> essential reading for anyone interested in testing his hypothesis.
> This saga seems to get more bizarre by the minute. That Ray would so
> confidently use results from the uncited proceedings of a Court of
> Law to support a taxonomic hypothesis, merely casts a shadow over
> his description, because the paucity of hard data is underscored by
> this act. Legal records should not be relied upon as scientific
> records. They often contain information that may be highly
> subjective, and prone to manipulation because of the adversarial
> nature of our legal system. Putative conclusions or results of some
> legal prosecutions, even those purportedly based upon scientific
> evidence, may be open to differing interpretations, and as Ray
> himself has found on other occasions, they may not represent a true
> and accurate record or interpretation of a matter at hand.
> Well, is there reliable DNA evidence in existence - published or
> otherwise - that could be used to support Hoser's erection of his
> new taxon? I don't know of any such DNA data…other than what Ray has
> claimed, and we have to accept his assurance that this data is
> reliable. Well, I would be rather surprised if the DNA data that Ray
> infers he has used is of a standard that could unequivocally
> demonstrate population differences between the populations in
> question. I say this because this particular DNA investigation by
> the Queensland Government may have had a design and methodology that
> may have made a subsequent use of the data as a taxonomic tool an
> unwarranted extrapolation of the results. I can't help saying that I
> would be rather surprised if there actually were any significant DNA
> differences between the Australian population and that from eastern
> PNG anyway. A comparison between Indonesian material and that from
> Australian might be more revealing though.
> If we must go through this so-called evidence of DNA differences, I
> would be interested in knowing the precise details of this original
> DNA investigation, and this would of course necessitate inquiries to
> others well beyond the simple legal citation of "Queen vs Buckley".
> Questions have to be now answered before we can rely on Hoser's use
> of this DNA "evidence". A few that spring to mind are: Who carried
> out the testing? Where was this investigation undertaken? When was
> this investigation undertaken? What techniques were used in this
> investigation? How were the samples collected? Were the specimens
> retained for re-testing or independent validation? And of course,
> perhaps the most relevant question of all - What control population
> was used as the comparison or baseline population to assess the
> significance (if any) of the Australian population? One would
> presume that any DNA investigation of the genetic variation in
> Chondropython viridis would of course utilize samples derived from
> all known populations of the species, including of course topotypic
> Chondropython viridis (from Indonesia) as the primary control.
> Anything less would be inadequate, inconclusive, and consequently
> invalid. I think I see a great PhD project for someone who doesn't
> mind the usual reduced life span from parasitic infections that come
> with field work in tropical Australasia. Any takers?
>
> Best Regards
>
> Richard Wells
>
> ------------------------ Yahoo! Groups Sponsor ---------------------~-->
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> http://us.click.yahoo.com/l.m7sD/LIdGAA/qnsNAA/APOolB/TM
> ---------------------------------------------------------------------~->
>
> To unsubscribe from this group, send an email to:
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>
>
>
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Tormato Sep 21, 2003 05:30 AM

Hey Hoser- why do you think "hawkei" is a bad name? Ive seen one of your scientific names stemming from your compassion towards your wife!!
No bad blood, just truly curious why "hawkei" is not so sensible? Im not pro hawkei or anti hawkei.
-----
"People change and your changing"
Seals and Crofts 1976

rayhoser Sep 21, 2003 06:41 PM

Dear person who posted previously.
If you are genuinely interested in the background to A. hawkei and why it is not a good choice of name (that we are stuck with), you should read a longer explanation in chapter 12 of the book
"Victoria Police Corruption"
all the best
Victoria Police Corruption
Victoria Police Corruption

WW Sep 28, 2003 11:12 AM

The irony is, of course, that the data on mtDNA variation in Morelia viridis HAS been published in the mainstream scientific literature, so no need to chase up the Qld. court system:

Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity
Rawlings LH, Donnellan SC
MOLECULAR PHYLOGENETICS AND EVOLUTION
27 (1): 36-44 APR 2003

Abstract:
Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes. (C) 2002 Elsevier Science (USA). All rights reserved.

Of course, Ray could not be expected to know this - after all, the paper appeared in the *scientific* literature, with which he clearly has considerably less interaction than with the Australian judiciary.

Note also that the major genetic subdivision is between populations from north and south of the Central Mtns of New Guinea, not between Australia and New Guinea. Certainly not particularly in favour of Ray's ideas.

Cheers,

Wolfgang
-----
WW

WW Home

rayhoser Sep 28, 2003 05:46 PM

Er, it wouldn't occur to a moron like WW that my python papers were written and submitted long before the paper cited by WW came out.
Pity WW doesn't have a life other than getting onto Kingsnake and attacking Hoser every time he publishes something.
WW, if you are reading this, let us all know how your pet Acanthophis crotalusei Hoser 1998 is going?
Cheers

WW Sep 28, 2003 11:33 PM

>>Er, it wouldn't occur to a moron like WW that my python papers were written and submitted long before the paper cited by WW came out.

Ray,

I was simply referring to your inability to cite the paper when asked for the DNA evidence by others - quite amusing, really, since this is the first time that DNA evidence actually exists relating to one of the taxa you describe. However, your comment on relative timing spurred me on to actually look at your paper, so here are a couple of interesting observations:

The Rawlings and Donnellan paper appeared in the April 2003 number of Molecular Phylogenetics and Evolution.

Your paper (.pdf version from your site, "exactly as it appeared in printed form in The Newsletter of the Macarthur Herpetological Society" quotes a post by Richard Wells on kingsnake.com, dated 1 August 2003. Unless you are gifted with clairvoyancy, that rather suggests that your paper was written AFTER said post by Richard Wells, i.e., ~4 months AFTER the Rawlings & Donnellan paper came out.

Thanks for an early morning chuckle that brightened up a dull and grey British autumn day.

Cheers,

Wolfgang
-----
WW

WW Home

rayhoser Sep 29, 2003 02:42 AM

Or did you kill it when you found it had one of my names?
Cheers!
PS Don't blow a fuse.

wulf Sep 28, 2003 11:39 PM

G'day Ray,

you shouldn't feel offended every time. Just relax and take it this way: As the source you refer to in your paper is hard to come by with, WW just gave us the oppertunity to get the paper from a "more available" source. As sundberg said, I don't want to buy books for just a reference mentioned in an article

Cheers,
Wulf

btw.: When ever you got something new, you do the same This must be real love...you can't live without (or at least it wouldn't be that much fun), right
-----
http://www.leiopython.de ,
http://www.herpers-digest.com

richardwells Oct 04, 2003 02:23 AM

Hi Wulf,

I was very pleased to hear about the DNA paper kindly quoted by Wolfgang. It more or less confirms what I already suspected in part in regards to the relationship between the Aussie population and that of southern New Guinea. I have previously had experience with the different forms and they are not really all that "cryptic" morphologically. As I mentioned earlier, I intend publishing a little note on the Chondro's and the DNA paper will of course be used as an important reference. However, in relation to Ray's paper that was supposedly published in the Newsletter of the Macarthur Herpetological Society, I have not yet been able to obtain an original of the issue, despite requests to both the publisher and of course Ray. The author has promised me so many times to send me a copy and yet delivered nothing, that I fear I may be off his reprint list! As for the publisher - the Macarthur Herpetological Society - they have been going through a period of committee reorganization of late, so I expect that would explain the delay. That I have been unable to obtain, or even sight an original of this work, even though I applied to the publisher within days of its stated date of publication by Hoser, does not look good for the Code's criteria of availability being met by Ray. Similarly requests to the National Library of Australia and the State Reference Library in NSW (the legal deposit libraries) have been unsuccessful, as neither library has actually received it either. Surely it HAS been published, but I am afraid until I see an original, I have my doubts on its legality as a new taxon. Has anyone to your knowledge actually obtained a copy as yet, and if so does it constitute a publication as legally defined in the Code?

With Best Regards

Richard Wells

rayhoser Oct 04, 2003 07:10 PM

Richard, please calm down.
I sent you a hard copy of the whole newsletter a while back as did Julia Carr, the old editor.
I think she said hers bounced which is no surprise as I had the same problem before when sending material to you.
I assume you've got the bloody huge parcel I sent you as it had about four mags in it - namely two Crocodlians and a Boydii and the newsletter - all with taxonomy stuff in them.
I can't send you more for obvious reasons - they keep dissapearing, - and/or you claim not to get them - however, rest assured that hard copies are all over the place and you can download the newsletter in pdf format or MS Word as originallyprinted from my website aT;
http://www.smuggled.com/PytRev11.htm
Scroll to the bottom of the page for the options.
I personally have distributed about 100 hard copies of the newsletter that I photocopied at my own cost, which I'd expect beats the print run of your 1987 weigeli paper, for which I never was able to track a single copy, instead relying on a photocopied then faxed version.
By the way, I've just spent the last hour or so explaining to someone why A. saxocola has precedence over stimsoni, which I assume pleases you.
ALL THE BEST
Pythons - incl. a new chondro

richardwells Oct 05, 2003 05:30 AM

Ray,
Thank you for supposedly sending me a bundle of journals and papers - which I HAVE NOT RECEIVED.
You can choose to believe me or not, but at this stage I choose not to believe you.
As for emails being sent to me bouncing, well I must admit that this does happen - mainly because I receive around 1000 a week, and if someone sends me something taking up hundreds of meg then my mailbox may reject it. Although I would appreciate an email of any article, you know as well as I do, that this is not what I require. I am after an original issue of your publication that describes the new Chondropython. I have already read the article - obtained as a copy from your webpage from one of my colleagues - because I was unable to access your "smuggled.com" site. From that copy I can see that it conforms to the Code in its structural content. However, it is becoming clear to me that this new name may not constitute an Available Name, as the work it appears in, may not constitute a publication in the sense of the Code of Zoological Nomenclature. Prove me wrong Ray by sending me an original. I don't care one iota about the anonymous one hundred others that have supposedly got one - I am just saying that I am still to see one.
As for the weigeli paper, it was formally published in the meaning of the Code - permanently printed (on gloss paper too), and copies sent to a number of libraries. You are quite correct though that it eventually became quite hard to get, because copies in most of the libraries were discarded or removed under advice from various persons. For instance the copy in the NSW NPWS library was removed, along with all the Australian Journal of Herpetology issues (a complete set) after the suppressionist John Barker told Gwen the librarian that the works had been suppressed and were not to be used. Similarly, copies at Macquarie University were removed as a result of a request from one of the lecturers in the School of Biological Science (name known), and the same for Sydney University. This later case was even more interesting. After I noticed that the works were no longer present in the Badham Library collection, I formally requested an explanation from the librarian. She told me that under instruction from a lecturer in the School of Zoology (Bill Dawbin was named as the one responsible) the works were to be removed from the collection. I complained to the head of the Student's Union about this Suppression, who then advised the library that unless the articles were restored, they would take the matter up with the Vice Chancellor's Office AND the media. The articles reappeared in the library, but were eventually removed again for extended periods, but the weigeli paper was removed permanently. There are only a handful of original copies of the weigeli paper left in libraries. Most copies in other hands as you say are photocopies - and these mostly originate with an original held in a major public library. I understand that a biologist in Germany has passed on one such photocopy to a forensic scientist in the German Police to ascertain whether it has been derived from such a permanently printed work. I am quite confident that it will pass such a test, but I am not so sure how your article will stack up to such examination should the same tactics be used against your work as they are doing to mine.
Other matters or implications of your post on OzHerp will be ignored at this time, because I have to go to the toilet.

Richard Wells

rayhoser Oct 05, 2003 06:55 AM

Richard I'll ignore the jibes at the start of your last post, but note that the rest was of interest and doesn't surprise me.
All the best

RSNewton Oct 05, 2003 12:51 AM

From what is written within the abstract, the Australian population appears to have originated in the southern part of New Guinea. This fact alone will not be able to tell us whether the Australian population is recognizable as a separate subspecies or even a separate species. One must look at such other things as mating behavior, karyotype, ecological differences and hemipenial structure, or perhaps even microdermatoglyphics to determine the taxonomic status of the Australian population.

RSNewton Oct 05, 2003 12:42 AM

I don't believe DNA study is going to tell us whether two populations are the same species or not. Two populations of the same species form a clade; two sibling species also form a clade. The DNA results for both situations are identical. In some cases DNA data may even mislead. Suppose for example that A is a paraphyletic ancestral species and B is the descendant species. The mtDNA of B may be closer to the population of A from which it evolved than this population is to other populations of A. In fact, B and its parental population in A may form a crown clade, with other populations of A as the basal outgroup! Yet all populations of A are able to interbreed with each other whereas B may not be able to interbreed with its own parental population in A. A naive molecular systematist may group B with one population of A as a single species!

To determine whether two isolated populations represent two populations of the same species or two species, one must scrutinize all aspects of their biology which may present potential obstacles to interbreeding, including for example karyotype, mating behavior, hemipenial morphology, and ecological niche. A population that is nocturnal and desert dwelling is probably not going to interbeed successfully with another population that is a diurnal woodland dweller. A hybrid between the two will most likely not be well adapted enough to suvrive in either type of environment. If Australian populations of Chondropython are only slightly different ecologically than other populations, then subspecies may be recognizable. If the ecological differences are as great as that between diurnal woodland and nocturnal desert dwelling, then perhaps speciation may have occurred.

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