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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed Aug 02, 2006 3:37 am 
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Ah, thanks for the heads up on this thread, Kari.

First, I do have access to Hedin & Bond (in press), as well as Bond & Hedin (in press); the papers are available at the Molecular Phylogenetics and Evolution website, but you have to have institutional access to receive them. To my knowledge, the authors have not received galley proofs for the paper, so the paper is still in manuscript form. If I have time, I will download them at school tomorrow and send them via email.

Morphology and molecules go hand-in-hand. Each dataset provides an independent test of the other, but I certainly don't feel morphology is better than the molecular data (or vice versa). A lot of old school systematists hate molecules, but that's only because they are not trained in molecular systematics (or they may not have access to the equipment/reagents).

Steve, you raised an interesting point about molecules uncovering many paraphyletic groupings. Does this mean that the molecules are poor markers? I don't think so. Does this mean the morphological characters were wrong? Maybe, maybe not. The problem with morphology in mygalomorphs is that the spiders are homogeneous, providing few solid synapomorphies that unequivocally support clades. This is undoubtedly shaped by natural selection on similar life history strategies (see Bond & Opell, 2002, Biol. J. Linn. Soc., available for download at core.ecu.edu/biol/bondja). Most morphological characters are homoplastic! I think that when multiple independent molecular markers uncover paraphyletic groupings, the groups were not natural to begin with! Incomplete lineage sorting is a real issue at the species/population interface, but much less of a problem at deeper levels... so I am inclined to believe the molecules.

In tarantulas, there are few morphological characters. The genus Aphonopelma is a mess because there is so much variation between and within species. Molecules may be the only answer!

But, I think that a robust phylogeny should include all available data (total-evidence approach)... let the characters fall as they may!

Keep this thread going guys!


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed Aug 02, 2006 4:40 am 
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Steve, have you read any of Ward C. Wheeler's work? Either alone or with others, such as with Lorenzo Prendini?

One of their ...hmm.. word.... ideas :rolleyes: is similar to your train of thought about homoplasies. But, the key is a character is a character, regardless if it's convergent or not, derived, etc.... So all must be taken as they are and at face value. We don't really know if this character is convergent or not, but a thorough analysis, i.e., not using Prendini's exemplar approach (i.e., one species of a species group or genus instead of testing as many as possible) will help weed out the convergences, symplesiomorphies and synapomorpies, etc., naturally, by self-weighting (the computer analysis, that is) the characters as they fall out and not applying (via operator, matrix designer) a weight to any character regardless if we "know" it's derived or plesiomorphic/primitive.

But, like I said before, I am not skilled at this as much as is Brent. But this is the way I understand things, particularly in the battle between Soleglad/Fet vs. Wheeler/Prendini. Which, by way of weighing characters and how (methods used to apply weightiness) they are weighted, then I am inclined to lean (redundant?) toward Wheeler/Prendini.

OK, good night....


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed Aug 02, 2006 4:20 pm 
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Kari McWest wrote:
Brent will be writing a grant proposal in the not-too-distant future. Our tax dollars hard at work! And for a GOOD cause!


We'll see what happens with this... I still need to find a good slant for the work. I don't know how focused I want to be (i.e., species level stuff or higher phylogeny). The thing is, we need preliminary data to submit a solid grant proposal, and that's where the members of the society can become intimately involved in this project. I am always in need of specimens. While I am most interested in North American species, donation of pet trade specimens is helpful, too (especially because we cannot just get up and travel to South America/Africa/Asia/Australia, etc. to collect).


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed Aug 02, 2006 4:31 pm 
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When it comes to weighting characters, I think equal weights IS the way to go... how can we place more weight on a particular character a priori? Why would one character be favored (i.e., given more weight) over another?

Kari, I know that David is not a fan of the exemplar approach, but it is a highly effective means for dealing with higher level phylogeny. By selecting two or three members from a group (that appear to be distantly related), you are rigorously testing the monophyly of those groups. Sure, more taxa is better, but as you add taxa, the number of possible trees increases exponentially and then some, and computers have problems evaluating the scores of trees with large numbers of taxa (but computers are far better than humans at evaluating these things -- trust me!). The key is to remember that classifications are simply hypotheses -- they can tested and retested at any time as new data become available.

And I cannot stand the word "cladist"... there are those who consider themselves cladisits, but I'd rather be called a phylogeneticist (I think the latter is more open minded)! :)


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Thu Aug 03, 2006 12:56 am 
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Brent, haven't you noticed that I did not use the word cladist in any of those replies!?

Exemplar approach: I don't know whether or not David "likes" the exemplar approach, but it's fine with me for higher-level analyses. But, as far as the work REVSYS is doing, then DNA sequencing and analyzing characters of as many individual species as possible must be the way to go, agreed? Like with theraphosids, we really don't have a knowledge of where the genera lie, or if there are "species groups", etc., so the best investigation would be one that looks at as many species as possible. Of course, I agree with you on the problems that can arise from such an undertaking, and I would suspect weighting of charaters would be inevitable due to synapomorphies that must be found to analyze or determine a group or complex of related species (good lord, I sound like Victor!).

Please enlighten me, Dr. Hendrixson, if I am off the tracks with this train.

Steve: yes, Victor Fet. And no, I haven't seen a lot from Vignoli lately. As you might know, Australian scorpiologist N. Adam Locket died last November.

Kids are here so my brain is fried, as you can tell by my thinking!


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Sat Sep 09, 2006 3:24 am 
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What kind of DNA data is being collected? RFLP, sequencing of specific genes or loci, microsattelite analysis? I work on cancer genetics, but I'm new in the tarantula hobby. It would be nice to use my expertise in molecular genetics within the hobby. Maybe I can convince the Baylor human genome sequencing center to sequence a few tarantula genomes. Ha.
Keith


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Thu Mar 22, 2007 7:29 pm 
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I am reposting two previous messages from a different thread because this particular thread is "sticky" and won't run the risk of disappearing into oblivion.

*********************************

As I have discussed in previous posts, tarantula enthusiasts and dealers can contribute SO much to the scientific community. I will likely make a plea for your help at this year's conference and encourage everyone to contribute to our collective quest for knowledge, especially in taxonomy, but I will make an initial stab at it here, too. I have had a long-standing interest in Aphonopelma systematics since I was an undergraduate student (shortly after Smith's revision was published), but I am also extremely interested in higher-level classification of the Theraphosidae (e.g., subfamilial composition and relationships). A few studies have used morphology to address some of these issues, but theraphosids - as you all know - are morphologically homogeneous, and there simply is not a lot of characters that can be used to resolve relationships.

Aside from a recent paper published by Petersen and colleagues (of which Rick West was a co-author), there has been no attempts to resolve relationships among theraphosids using molecular data (i.e., DNA sequences). Fortunately, I have the interest to do this work and access to a lot of these expensive tools; unfortunately, I do not have access to specimens. Live spiders are critical for good DNA yield, and what's nice about tarantulas is that non-invasive (or relatively non-invasive) techniques can be used to collect and extract DNA. The Petersen et al. paper discussed a way in which DNA can be obtained from exuviae; unfortunately, it is only useful for mitochondrial DNA (which is fine, but may not be informative for the deeper level relationships I want to obtain -- this requires nuclear DNA, thus REAL live tissue). Can this be done without harming or killing the spider? Certainly! One way is to simply autotomize a leg (I know, a seven-legged spider isn't necessarily attractive, but the leg can regenerate with minimal effects on the spider); or, I have read an unpublished Master's thesis by a young woman from Kansas State that suggests we can get quantifiable and high quality DNA from hemolymph obtained by a slight puncture in a leg joint (these generally clot and heal quickly). Even recently deceased spiders (within 24 hours) can be useful if they are immediately placed into a freezer (-20 C is fine and is generally the temperature of most household freezers); if left at room temperature for much longer than a day, DNA-ase enzymes begin to rapidly break down the DNA, severely hampering any ability to obtain high-yield/high-quality molecular data.

So, how can everyone here help out? I think you have already read between the lines. I need spiders! :D I am amazed at the number of enthusiasts that selflessly donate their animals to the ATS raffle (for the benefit of the society and its membership), but would the same individuals also be as interested in donating any of their spiders for the benefit of scientific research, and in particular, to a researcher that is part of the membership? If so, this is where real progress regarding certain aspects of theraphosid taxonomy can take place. Fortunately, pet trade specimens without locality data are fine (as long as they can be identified to genus).

I would obviously have to keep the spider (I cannot just obtain DNA and send it back because every DNA sequence needs to be, or at least should be, associated with an actual voucher specimen), but what's in it for you? Any publications resulting from donated specimens will have your name in the acknowledgments; you would be granted access to the publications (many scientific articles are difficult to come by if you do not have access to a university library, and even then, many universities do not maintain all journals); you may receive high-quality/high-resolution digital images of the spiders, possibly including scanning electron micrographs (SEM images); I will forever be in debt to you; and the general satisfaction of knowing that your donation made a significant contribution to science. :)

I hope you will mull this over and give strong consideration to this proposal; if there is decent interest, I can post my proposed generic taxonomic sampling for the classification project. As for Aphonopelma, this is an entirely different beast. I have to be more rigid on accurate locality information, but anybody who has access to these spiders in your area, please contact me regarding this because we can definitely start seeing real progress in the near future.

Cheers,

Brent


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Thu Mar 22, 2007 7:30 pm 
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Here is the second message:

**************************************

What I didn't mention above is that adults are preferable because they have the "diagnostic characters" for the genus (important for vouchering), although subadults and well-established immature spiders can be extremely useful, too, particularly if they are easily identifiable. Spiderlings are problematic because if there is a problem getting DNA and the spider dies, it poses issues for vouchering (and the voucher specimen is especially important).

Here is the proposed generic sampling for this project (but any genus would be happily accepted, especially non-theraphosine genera):

Avicularia, Ephebopus, Iridopelma, Psalmopoeus, Tapinauchenius

Citharischius, Eumenophorus, Hysterocrates, Phoneyusa

Acanthopelma, Catumiri, Chaetopelma, Holothele, Ischnocolus, Plesiophrictus, Sickius

Ceratogyrus, Eucratoscelus, Harpactira, Harpactirella, Pterinochilus

Cyriopagopus, Haplopelma, Ornithoctonus

Chilobrachys, Coremiocnemis, Lyrognathus, Poecilotheria, Selenocosmia, Yamia

Annandaliella, Euphrictus, Selenogyrus

Encyocratella, Heteroscodra, Stromatoplema

Acanthoscurria, Aphonopelma, Brachypelma, Cyriocosmus, Grammostola, Hemirrhagus, Lasiodora, Pamphobeteus, Phormictopus, Theraphosa

Haploclastus, Thrigmopoeus


If anybody is interested in this project, please PM me.

Thanks,

Brent


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed Apr 11, 2007 2:11 am 
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I've been able to acquire more Aphonopelma from California thanks to Alice; the tarantulas are starting to come out folks, so please, if you come across any, keep me in mind for some of the work I have planned. In the long haul, it benefits all of us!


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed May 30, 2007 2:15 am 
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Brent,

I strongly recommend you initially refine your request towards specimens from the type species of each genera you listed. Failing getting those, then widen your appeal to other congeners unless it is for smaller or genera supported by several morphological characters.

One of the greatest challenges for the near future of theraphosid systematics is to deal with the lack of cohesion (non-monophyly) of serveal poorly defined genera.

Let me know the genera you are having trouble getting, maybe like the austrailasian ones and i will see what i can do to help.

stuart.


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed May 30, 2007 12:59 pm 
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Stuart -

Thanks for the comments. I certainly agree that the type species for each genus is extremely important (and an absolute "must have" for genus-level revisions). Our first big project, however (if the grant is funded), is a higher-level phylogeny to resolve subfamilial relationships. While type species would still be ideal, they wouldn't be entirely necessary for this level of work (and again, we're just trying to accumulate as much as we can at this point). But I do plan (over much time) to gather the types of each genus for exactly the reasons you spoke of... I suspect paraphyletic/polyphyletic groups are rampant throughout the Theraphosidae.


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Fri Jun 08, 2007 4:06 am 
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What is your opinion on the identification of theraphosidae using mitochondrial DNA sequence from the cytochrome c oxidase subunit I gene derived from cast exuviae? Must a database from live specimens be made first, or would this method give you the information needed with such closely related species?
What about morphological data? Must you document the morphological characters, as i might assume in say the description of a new species?

I refer to:

Petersen, S.D. et. al., (2007) Species identification of tarantulas using exuviae for international wildlife law enforcement. Conserv. Genet 8:497-502 DOI 10.1007/s10592-006-9173-2



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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Fri Jun 08, 2007 1:11 pm 
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Zach -

A number of folks have asked me about this, and while it does have some utility, we need to gather data from all sources of information (genes, morphology, behavior, geography, etc.).

Petersen et al.'s approach is known as DNA barcoding (after Paul Hebert and colleagues), whereby we can presumably identify species based on a short piece of DNA from the mitochondrial genome (COX1). While it sounds promising, there is a ton of literature that discusses why this is not the "final" say on species delimitation/identification.

Being able to extract DNA from an exuvium is really exciting, but again, we're only able to get (if we're lucky) mitochondrial DNA. If we're interested in single-copy genes from the nucleus, good luck getting that from an exuvium!

I certainly acknowledge DNA barcoding (and it does work in many cases), but in my opinion, there is a lot of unnecessary hype surrounding this approach. Regardless, it has stirred up a lot of controversy in the systematics world -- and that is always a good thing!


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Sat Jun 09, 2007 1:51 am 
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thanks for the insight Brent.



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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Wed Mar 26, 2008 4:22 am 
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Mori Collins wrote:
There's research going on as far as Brachypelma and Brachypelmides spp DNA and their genetic relations here in Canada at a university near my house.


Recently There has also been research in london done on brachypelma, published in the Journal of Arachnology. They used induced autospasy to collect legs samples for DNA of natural populations. I posted a thread inquiring about autospasy.

U have to be an AAS member to read this artical right now, but in few months it will be open to the public on the american arachnological society web site.


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Thu Sep 25, 2008 7:03 am 
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Mori Collins wrote:
There's research going on as far as Brachypelma and Brachypelmides spp DNA and their genetic relations here in Canada at a university near my house.


Which University is this?


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 Post subject: Re: Theraphosid systematics: DNA Analysis
PostPosted: Sun Jun 14, 2009 4:01 am 
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Don't know if this would be of any help, but I'm pretty sure that some research was done at SpiderLab at Nottingham University (UK) where I work that found a way to get viable DNA samples from spider skins. Some of those used were about 15 years old.

They had all been stored in a carrier bags (hundreds of skins) and great success was achieved. The study was on the genetics of the fen raft spider Dolomedes plantarius (Clerk).

Surely instead people could send in moults of spiders?


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