# Ideas for discussion



## Rick (Apr 19, 2008)

1) Maybe all new names for species and varieties should include the GPS coordinate in the name or as the name? You don't get to name it without verifiable collection data.


2) Anyone familiar with Cox et al 1997. A phylogentic tree of Paphs was developed based on rDNA ITS sequences. A summary figure is in Cribb's book.

It shows a mix of what we would suspect and some pretty surprising relationships. Like tigrinum is most related to druryii, and sukhakulii is much more related to venustum than wardii. Pretty crazy.

I don't know anything about ITS sequences, so all I can do is shrug my shoulders and say Huh!


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## practicallyostensible (Apr 19, 2008)

Really interesting!


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## PaphMadMan (Apr 19, 2008)

Rick said:


> 1) Maybe all new names for species and varieties should include the GPS coordinate in the name or as the name? You don't get to name it without verifiable collection data.
> 
> 
> 2) Anyone familiar with Cox et al 1997. A phylogentic tree of Paphs was developed based on rDNA ITS sequences. A summary figure is in Cribb's book.
> ...



I believe this phylogenetic tree can be found at http://www.slipperorchids.info/taxonomy

Ribosomal DNA sequences used for this type of comparison are chosen because they are not functional genes, so not subject to selective pressures of evolution. Changes are presumably random and relatively constant over time, so similarities or differences in DNA sequence between species are roughly proportional to how recently they had a common ancestor in the mother line, since ribosomal DNA is inherited only from the pod parent. Within its limitiations it is a non-subjective assessment of relatedness.


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## kentuckiense (Apr 20, 2008)

PaphMadMan said:


> I believe this phylogenetic tree can be found at http://http://www.slipperorchids.info/taxonomy/index.html
> 
> Ribosomal DNA sequences used for this type of comparison are chosen because they are not functional genes, so not subject to selective pressures of evolution. Changes are presumably random and relatively constant over time, so similarities or differences in DNA sequence between species are roughly proportional to how recently they had a common ancestor in the mother line, since ribosomal DNA is inherited only from the pod parent. Within its limitiations it is a non-subjective assessment of relatedness.



Correct me if I'm wrong here, but ribosomal DNA sequences are most certainly functional genes. The reason they are used for phylogenetics is that ribosomes are so essential to life and thus more slowly accumulate mutations. The end result of this is that if a polymorphism in rDNA sequence is found in two species, then you can be reasonably sure that polymorphism is due to homology and not homoplasy. Thus, rDNA is great for investigating deeper homology, but has its downsides when working with terminal extant clades.

I think what you're thinking of are the "molecular clock" genes that are not under selection (neutral theory, etc.) and thus accumulate random mutations at a relatively consistant rate.


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## ohio-guy (Apr 20, 2008)

*link*

The link to the website about genetic relatedness did not seem to work. Is it still there? 

As far as the GPS idea, the flaw in it is the problem of poaching when a new variety is discovered. Plus some are discovered in cultivation, as was Phap spiceranium I think, and more recently, Phrag fischeri.

As far as the discussion of the genetics, it is very interesting, but Zach, I think I am having a hard time following all of your scientific jargon. And I have a science background<G>.

Also, wasn't there a recent news item (some months back) about gene sequencing on orchids that was being used to differentiate closely related species? 
I don't recall if I saw it here or somewhere else.


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## cdub (Apr 20, 2008)

PaphMan has the general idea (with some inaccuracies) and Kentuckiense is partially right. 

Ribosomal sequences are targeted because they are conserved across large groups of organisms, which is why these sequences are valuable for resolving evolutionary relationships between distantly related organisms such as vertebrates, or families of plants. Ribosmoal ITS DNA are the "InTernal Spacer" sequences of the ribosomal DNA. These sequences, as the name implies, occur in between the coding regions for the separate subunits of the ribosomal RNA (because ribosomes are made of 2 or more subunits). These sequences by virtue of their proximity to the coding sequences are easily targeted with molecular techniques, because primers are readily available for the flanking coding regions. Also, the ITS sequences accumulate DNA changes at a higher rate than the coding regions and can be used to evaluate evolutionary relationships between more closely related organisms, such as plants within the same genus (Paphiopedilum). This is what Kentuckiense means by "neutral" (or nearly neutral) sequences. 

I wrote a paper in school on this using data from the Cox et al. paper and data from Cribb's book.


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## PaphMadMan (Apr 20, 2008)

kentuckiense said:


> Correct me if I'm wrong here, but ribosomal DNA sequences are most certainly functional genes. The reason they are used for phylogenetics is that ribosomes are so essential to life and thus more slowly accumulate mutations. The end result of this is that if a polymorphism in rDNA sequence is found in two species, then you can be reasonably sure that polymorphism is due to homology and not homoplasy. Thus, rDNA is great for investigating deeper homology, but has its downsides when working with terminal extant clades.
> 
> I think what you're thinking of are the "molecular clock" genes that are not under selection (neutral theory, etc.) and thus accumulate random mutations at a relatively consistant rate.



rDNA ITS (internal transcribed spacer) is used like a nonfunctional section of DNA in this instance. It is assumed to be under little functional constraint.


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## PaphMadMan (Apr 20, 2008)

ohio-guy said:


> The link to the website about genetic relatedness did not seem to work. Is it still there?




I have attempted to fix the link. It was my first try at inserting a link here.


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## kentuckiense (Apr 20, 2008)

cdub said:


> PaphMan has the general idea (with some inaccuracies) and Kentuckiense is partially right.
> 
> Ribosomal sequences are targeted because they are conserved across large groups of organisms, which is why these sequences are valuable for resolving evolutionary relationships between distantly related organisms such as vertebrates, or families of plants. Ribosmoal ITS DNA are the "InTernal Spacer" sequences of the ribosomal DNA. These sequences, as the name implies, occur in between the coding regions for the separate subunits of the ribosomal RNA (because ribosomes are made of 2 or more subunits). These sequences by virtue of their proximity to the coding sequences are easily targeted with molecular techniques, because primers are readily available for the flanking coding regions. Also, the ITS sequences accumulate DNA changes at a higher rate than the coding regions and can be used to evaluate evolutionary relationships between more closely related organisms, such as plants within the same genus (Paphiopedilum). This is what Kentuckiense means by "neutral" (or nearly neutral) sequences.
> 
> I wrote a paper in school on this using data from the Cox et al. paper and data from Cribb's book.



Ah, thanks for clearing that up.


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## Rick (Apr 20, 2008)

ohio-guy said:


> As far as the GPS idea, the flaw in it is the problem of poaching when a new variety is discovered. Plus some are discovered in cultivation, as was Phap spiceranium I think, and more recently, Phrag fischeri.



No names for poached plants, or plants collected by locals and sold to collectors sitting in the market should be considered an anonymous plant of the pot plant trade if the location of the population the plant was extracted from cannot be verified from a reputable source (with GPS in hand). I realize there are still ways to fake this but it could lead to another level of taxonomic scrutiny. The race for names and hiding the secret honey hole is half the problem why names are as screwed up as they are.


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