No subject


Sun May 2 12:18:05 CEST 2010


Mark then Peter

The main potential problems that I see with the ways that phylobase is usin=
g NCL now are:
1. in NCLInterface.cpp there are lots of call to RemoveUnderscoresAndSpaces=
 to get rid of spaces and _ in names.  That makes names easier to deal with=
, but at some point will bite you (somebody will have dataset with a taxon =
labelled "AB" and another with "A B", after transformation there will be a =
name clash).

I agree that this is something to address.  Not only might there be clashes=
 but changing names, will be annoying to users.  Brian or Derrick could ans=
wer better, but I assume this is because some of the code used to parse the=
 tree string can't handle the underscores and spaces.

Has just bitten me! There is a deeper problem here in that readNexus uses t=
he NCLInterface code to get the data frame as parsable R code - with stripp=
ed spaces and underscores - but the tree block is passed over as a block of=
 raw text from the file. These names _aren't_ then stripped of underscores =
and spaces by read.nexustreestring() and so the name checking throws an err=
or.

Obviously there is an ongoing deeper discussion about how to handle passing=
 the tree from NCL and how to handle the dismayingly wide range of official=
 valid PAUP identifiers using regex but currently we've got a simpler probl=
em of different handling. Underscores in names are very commonly used to av=
oid the quoting problem with spaces so I think this current problem will co=
me up a lot.

Cheers,
David






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_______________________________________________
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<ATT00002..txt>

_______________________________________________
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Mark Holder

mtholder at ku.edu<mailto:mtholder at ku.edu>
http://phylo.bio.ku.edu/mark-holder

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Department of Ecology and Evolutionary Biology
University of Kansas
6031 Haworth Hall
1200 Sunnyside Avenue
Lawrence, Kansas 66045

lab phone:  785.864.5789

fax (shared): 785.864.5860
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D










--_000_26B0386422C04E31859C43A7B5D63919imperialacuk_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<html><head></head><body style=3D"word-wrap: break-word; -webkit-nbsp-mode:=
 space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>I'd=
 agree with this - we have to be able to cope with any taxon names and, ide=
ally,&nbsp;if we can avoid having to make the taxon names syntactically val=
id R, then we should change them as little as possible (apart from the obli=
gatory unquoted underscore to space translation) and keep them as character=
 strings.</div><div><br></div><div>What would NCL pass as a token given the=
se two?</div><div><br></div><div>'taxon\1'</div><div>'taxon"1'</div><div><b=
r></div><div>I think these are the problem cases - R needs to escape the ba=
ckslash and double quote, but handles the double quote better than the back=
slash:</div><div><br></div><div><div>&gt; x &lt;- c('taxon"1', 'taxon\1', '=
taxon\\1', 'taxon\one', 'taxon\\one')</div><div>Warning messages:</div><div=
>1: '\o' is an unrecognized escape in a character string&nbsp;</div><div>2:=
 unrecognized escape removed from "taxon\one"&nbsp;</div><div>&gt; x</div><=
div>[1] "taxon\"1" &nbsp; "taxon\001" &nbsp;"taxon\\1" &nbsp; "taxonone" &n=
bsp; "taxon\\one"</div><div><br></div><div>Cheers,</div><div>David</div><di=
v><br></div></div><div><br></div><div><br></div><div><br></div><div><br></d=
iv><div><br></div><div><div><div>On 29 Apr 2010, at 20:19, Mark Holder wrot=
e:</div><br class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><=
div style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-=
break: after-white-space; "><div><div>Hi,</div><div><span class=3D"Apple-ta=
b-span" style=3D"white-space:pre">	</span>I'll chime in despite being fairl=
y ignorant of a lot of the use cases for phylobase.</div><div><br></div><di=
v>My experience dealing with files from users is that you have to be prepar=
ed for anything occurring in a taxon name. &nbsp;So I'd say that you have t=
o have a system in which the name can be any character string, not a system=
 in which the taxon name can be a variable name in R. &nbsp;So I would reco=
mmend getting the charcter string from NCL, and then using whatever R-speci=
fic character escaping conventions are needed to generate the equivalent st=
ring literal in R (you'll have to use \ before any quote or \ characters).<=
/div><div><br></div><div><br></div><div><br></div><div>Phylobase *could* st=
rip problematic symbols out of the names easily enough but:</div><div><span=
 class=3D"Apple-tab-span" style=3D"white-space:pre">	</span>1. it is confus=
ing to user's because the name of the taxon changes (usually only slightly,=
 but it still changes), and</div><div><span class=3D"Apple-tab-span" style=
=3D"white-space:pre">	</span>2. then you have to deal with name clashes (if=
 a file has 'a b' and 'ab' as taxa names, then stripping spaces will cause =
a clash).</div><div><br></div><div>NEXUS has syntactic rules for tokenizing=
. &nbsp;They usually don't change the internal representation much, but NCL=
 uses the syntactic rules to build a character string in memory. &nbsp;In t=
he following table I'll use double-quotes to delimit the character string t=
hat NCL would store in memory (the quotes are not part of the name).</div><=
div><br></div><div>Syntax &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; =
&nbsp;Internal representation</div><div>t1 &nbsp; &nbsp; &nbsp; &nbsp; &nbs=
p; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;"t1"</div><div>'t 2' &nbsp; &nbsp; &nb=
sp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; "t 2"</div><div>t_2 &nbsp; &nbsp; &n=
bsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; "t 2"</div><div>t.3 &nbsp; &=
nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; "t.3"</div><div>'t.3=
' &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; "t.3"</div><div>t=
-4 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; not a val=
id name this is 3 tokens "t", "-" and "4"</div><div>'t-4' &nbsp; &nbsp; &nb=
sp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; "t-4"</div><div>'t''5 x' &nbsp; &nbs=
p; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;"t'5 x"</div><div>'t_6' &nbsp; &nbsp; =
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; "t_6"&nbsp;</div><div><br></div><=
div>Basically, the syntactic rules just let you group tokens with token-bre=
aking symbols (white space and punctuation). &nbsp;The exceptions are the c=
ase t_2 &nbsp;and 't''5 x' above. &nbsp;Both of those case involve substitu=
tion&nbsp;(in the second case the internal pair of single-quotes is collaps=
ed to single quote in the internal representation).</div><div><br></div><di=
v><br></div><div>What really confuses users is the fact that in some format=
s a_b might refer to the name "a_b", but in NEXUS it is "a b" So the same s=
yntax has different interpretation in different formatting rules. &nbsp;NCL=
 uses the NEXUS tokenizing for NEXUS files and newick tree files (NCL suppo=
rts fasta, phylip, and relaxed phylip formats, but does not impose NEXUS qu=
oting rules on those formats). So if you use NCL to read a FASTA and NEXUS =
file both of which use the name a_b (without any quotes) then in the taxa g=
leaned from the FASTA file, the internal name will be "a_b", but the same n=
ame will have the internal representation of "a b" when read from NEXUS. &n=
bsp;That invariably trips people up, but I don't think that there is anyway=
 to avoid it because that behavior is mandated by both standards.</div><div=
><br></div><div>I think that if phylobase just include a brief discussion o=
f this issue in a README or other documentation, then that is about as good=
 as you can do.</div></div><div><br></div><div><br></div><div>all the best,=
</div><div>Mark</div><div><br></div><div><div><div>On Apr 29, 2010, at 10:5=
1 AM, Orme, David wrote:</div><br class=3D"Apple-interchange-newline"><bloc=
kquote type=3D"cite"><div style=3D"word-wrap: break-word; -webkit-nbsp-mode=
: space; -webkit-line-break: after-white-space; ">Sorry - I take it back ab=
out the 'not problematic in a character string' - the quotes and the backsl=
ash are of course fairly problematic.<div><br></div><div>Cheers</div><div>D=
avid</div><div><br><div><div>On 29 Apr 2010, at 16:43, Orme, David wrote:</=
div><br class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-brea=
k: after-white-space; ">Hi,<div><br></div><div>I know this isn't the bible =
- but the PAUP manual specifies the following:</div><div><br></div><div><di=
v style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-l=
eft: 0px; font: normal normal normal 12px/normal Palatino; ">"Identifiers" =
are simply names given to taxa, characters, and other PAUP input elements s=
uch as character-sets, taxon-sets, and exclusion-sets. They may include any=
 combination of upper- and lower-case alphabetic characters, digits, and pu=
nctuation. If the identifier contains any of the following characters:</div=
><div style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; marg=
in-left: 0px; font: normal normal normal 12px/normal Palatino; ">( ) [ ] { =
} / \ , ; : =3D * ' "` + - &lt; &gt;</div><div style=3D"margin-top: 0px; ma=
rgin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal =
normal 12px/normal Palatino; ">or a blank, the entire identifier must be en=
closed in single quotes.</div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/=
normal Palatino; "><br></div><div style=3D"margin-top: 0px; margin-right: 0=
px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/n=
ormal Palatino; "><div>They're going to be rare but they will happen.&nbsp;=
Any of those are problematic in a valid R name - although not in a characte=
r string. The taxon identifiers could come into R as character vectors just=
 as they appear in the Nexus file (possibly stripping the enclosing single =
quotes). The next question is then whether we need them to be valid R names=
 rather than character strings - in which case make.names() could be invoke=
d.</div><div><br></div><div>Cheers,</div><div>David</div><div><br></div><di=
v><br></div></div><div><div>On 28 Apr 2010, at 22:30, Fran=E7ois Michonneau=
 wrote:</div><br class=3D"Apple-interchange-newline"><blockquote type=3D"ci=
te"><div><br>Hi all,<br><br> &nbsp;Sorry if this is a dumb question, but wh=
y do we need to remove spaces<br>and underscore from the species names when=
 building the data frame? The<br>only character that I can think of that co=
uld be an issue is ", and I<br>don't think that it's allowed by software us=
ing NEXUS/used.<br><br> &nbsp;In other words, do we really need to use Remo=
veUnderscoresAndSpaces in<br>NCLInterface.cpp?<br><br> &nbsp;Thanks,<br> &n=
bsp;-- Fran=E7ois <br><br>On Mon, 2010-04-26 at 12:11 +0100, Orme, David wr=
ote:<br><blockquote type=3D"cite">I'd guess we want the names to be syntact=
ically valid R names - and ideally that would be through running make.names=
() across them. The problem is then that the NCLInterface can easily pass t=
he raw PAUP identifiers for the data (which we can then make.names()) but t=
hat the tree input is currently via a text string. Again, probably easy eno=
ugh to have the raw PAUP names in the string but these would be horrible to=
 extract with regex. Is there any way that NCLInterface can pass the tree u=
sing numeric symbols and then pass a translate block as a vector? Then make=
.names() could be run easily on both the data names and the tree names...<b=
r></blockquote><blockquote type=3D"cite"><br></blockquote><blockquote type=
=3D"cite">Cheers,<br></blockquote><blockquote type=3D"cite">David<br></bloc=
kquote><blockquote type=3D"cite"><br></blockquote><blockquote type=3D"cite"=
><br></blockquote><blockquote type=3D"cite"><br></blockquote><blockquote ty=
pe=3D"cite">On 23 Apr 2010, at 14:30, Fran=E7ois Michonneau wrote:<br></blo=
ckquote><blockquote type=3D"cite"><br></blockquote><blockquote type=3D"cite=
"><blockquote type=3D"cite"><br></blockquote></blockquote><blockquote type=
=3D"cite"><blockquote type=3D"cite">Hi,<br></blockquote></blockquote><block=
quote type=3D"cite"><blockquote type=3D"cite"><br></blockquote></blockquote=
><blockquote type=3D"cite"><blockquote type=3D"cite"> Ouch! We need to fix =
this.<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote ty=
pe=3D"cite"><br></blockquote></blockquote><blockquote type=3D"cite"><blockq=
uote type=3D"cite"> There might be some hope if we use Rcpp to build the da=
ta frame<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote=
 type=3D"cite">instead of building and parsing a string.<br></blockquote></=
blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blockq=
uote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"> Let =
me talk to Dirk about it and see what we can do.<br></blockquote></blockquo=
te><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blockquote></b=
lockquote><blockquote type=3D"cite"><blockquote type=3D"cite"> Cheers,<br><=
/blockquote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite=
"> -- Fran=E7ois<br></blockquote></blockquote><blockquote type=3D"cite"><bl=
ockquote type=3D"cite"><br></blockquote></blockquote><blockquote type=3D"ci=
te"><blockquote type=3D"cite">On Fri, 2010-04-23 at 13:59 +0100, Orme, Davi=
d wrote:<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote=
 type=3D"cite"><blockquote type=3D"cite">Hi all,<br></blockquote></blockquo=
te></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><blockq=
uote type=3D"cite"><br></blockquote></blockquote></blockquote><blockquote t=
ype=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite">From an e-=
mail on 03/03/10:<br></blockquote></blockquote></blockquote><blockquote typ=
e=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blockq=
uote></blockquote></blockquote><blockquote type=3D"cite"><blockquote type=
=3D"cite"><blockquote type=3D"cite">Mark then Peter<br></blockquote></block=
quote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><blo=
ckquote type=3D"cite"><br></blockquote></blockquote></blockquote><blockquot=
e type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite"><blockq=
uote type=3D"cite"><blockquote type=3D"cite">The main potential problems th=
at I see with the ways that phylobase is using NCL now are:<br></blockquote=
></blockquote></blockquote></blockquote></blockquote><blockquote type=3D"ci=
te"><blockquote type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D=
"cite"><blockquote type=3D"cite"><span class=3D"Apple-tab-span" style=3D"wh=
ite-space:pre">	</span>1. in NCLInterface.cpp there are lots of call to Rem=
oveUnderscoresAndSpaces to get rid of spaces and _ in names. &nbsp;That mak=
es names easier to deal with, but at some point will bite you (somebody wil=
l have dataset with a taxon labelled "AB" and another with "A B", after tra=
nsformation there will be a name clash).<br></blockquote></blockquote></blo=
ckquote></blockquote></blockquote><blockquote type=3D"cite"><blockquote typ=
e=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blockq=
uote></blockquote></blockquote></blockquote><blockquote type=3D"cite"><bloc=
kquote type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite">I =
agree that this is something to address. &nbsp;Not only might there be clas=
hes but changing names, will be annoying to users. &nbsp;Brian or Derrick c=
ould answer better, but I assume this is because some of the code used to p=
arse the tree string can't handle the underscores and spaces.<br></blockquo=
te></blockquote></blockquote></blockquote><blockquote type=3D"cite"><blockq=
uote type=3D"cite"><blockquote type=3D"cite"><br></blockquote></blockquote>=
</blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><blockquot=
e type=3D"cite">Has just bitten me! There is a deeper problem here in that =
readNexus uses the NCLInterface code to get the data frame as parsable R co=
de - with stripped spaces and underscores - but the tree block is passed ov=
er as a block of raw text from the file. These names _aren't_ then stripped=
 of underscores and spaces by read.nexustreestring() and so the name checki=
ng throws an error. <br></blockquote></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blo=
ckquote></blockquote></blockquote><blockquote type=3D"cite"><blockquote typ=
e=3D"cite"><blockquote type=3D"cite">Obviously there is an ongoing deeper d=
iscussion about how to handle passing the tree from NCL and how to handle t=
he dismayingly wide range of official valid PAUP identifiers using regex bu=
t currently we've got a simpler problem of different handling. Underscores =
in names are very commonly used to avoid the quoting problem with spaces so=
 I think this current problem will come up a lot. <br></blockquote></blockq=
uote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><bloc=
kquote type=3D"cite"><br></blockquote></blockquote></blockquote><blockquote=
 type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite">Cheers,<=
br></blockquote></blockquote></blockquote><blockquote type=3D"cite"><blockq=
uote type=3D"cite"><blockquote type=3D"cite">David<br></blockquote></blockq=
uote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><bloc=
kquote type=3D"cite"><br></blockquote></blockquote></blockquote><blockquote=
 type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite"><br></bl=
ockquote></blockquote></blockquote><blockquote type=3D"cite"><blockquote ty=
pe=3D"cite"><blockquote type=3D"cite"><br></blockquote></blockquote></block=
quote><blockquote type=3D"cite"><blockquote type=3D"cite"><blockquote type=
=3D"cite"><br></blockquote></blockquote></blockquote><blockquote type=3D"ci=
te"><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blockquote></=
blockquote></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"=
><blockquote type=3D"cite"><br></blockquote></blockquote></blockquote><bloc=
kquote type=3D"cite"><blockquote type=3D"cite"><blockquote type=3D"cite">__=
_____________________________________________<br></blockquote></blockquote>=
</blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><blockquot=
e type=3D"cite">Phylobase-devl mailing list<br></blockquote></blockquote></=
blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><blockquote =
type=3D"cite"><a href=3D"mailto:Phylobase-devl at lists.r-forge.r-project.org"=
>Phylobase-devl at lists.r-forge.r-project.org</a><br></blockquote></blockquot=
e></blockquote><blockquote type=3D"cite"><blockquote type=3D"cite"><blockqu=
ote type=3D"cite"><a href=3D"https://lists.r-forge.r-project.org/cgi-bin/ma=
ilman/listinfo/phylobase-devl">https://lists.r-forge.r-project.org/cgi-bin/=
mailman/listinfo/phylobase-devl</a><br></blockquote></blockquote></blockquo=
te><blockquote type=3D"cite"><blockquote type=3D"cite"><br></blockquote></b=
lockquote><blockquote type=3D"cite"><br></blockquote><blockquote type=3D"ci=
te">_______________________________________________<br></blockquote><blockq=
uote type=3D"cite">Phylobase-devl mailing list<br></blockquote><blockquote =
type=3D"cite"><a href=3D"mailto:Phylobase-devl at lists.r-forge.r-project.org"=
>Phylobase-devl at lists.r-forge.r-project.org</a><br></blockquote><blockquote=
 type=3D"cite"><a href=3D"https://lists.r-forge.r-project.org/cgi-bin/mailm=
an/listinfo/phylobase-devl">https://lists.r-forge.r-project.org/cgi-bin/mai=
lman/listinfo/phylobase-devl</a><br></blockquote></div></blockquote></div><=
br></div></div><span>&lt;ATT00002..txt&gt;</span></blockquote></div><br></d=
iv></div>_______________________________________________<br>Phylobase-devl =
mailing list<br><a href=3D"mailto:Phylobase-devl at lists.r-forge.r-project.or=
g">Phylobase-devl at lists.r-forge.r-project.org</a><br><a href=3D"https://lis=
ts.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl">https://l=
ists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl</a><br><=
/blockquote></div><br><div>
<span class=3D"Apple-style-span" style=3D"border-collapse: separate; font-f=
amily: Monaco; font-size: medium; font-style: normal; font-variant: normal;=
 font-weight: normal; letter-spacing: normal; line-height: normal; orphans:=
 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2;=
 word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-=
vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-te=
xt-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class=3D"Appl=
e-style-span" style=3D"border-collapse: separate; font-family: Monaco; font=
-size: 12px; font-style: normal; font-variant: normal; font-weight: normal;=
 letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px;=
 text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -=
webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px=
; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto;=
 -webkit-text-stroke-width: 0px; "><div style=3D"word-wrap: break-word; -we=
bkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class=
=3D"Apple-style-span" style=3D"border-collapse: separate; font-family: Aria=
l; font-size: 14px; font-style: normal; font-variant: normal; font-weight: =
normal; letter-spacing: normal; line-height: normal; orphans: 2; text-inden=
t: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing:=
 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spaci=
ng: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust=
: auto; -webkit-text-stroke-width: 0px; "><div style=3D"word-wrap: break-wo=
rd; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><spa=
n class=3D"Apple-style-span" style=3D"border-collapse: separate; font-famil=
y: Arial; font-size: 14px; font-style: normal; font-variant: normal; font-w=
eight: normal; letter-spacing: normal; line-height: normal; orphans: 2; tex=
t-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-s=
pacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertica=
l-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size=
-adjust: auto; -webkit-text-stroke-width: 0px; "><span class=3D"Apple-style=
-span" style=3D"border-collapse: separate; font-family: Courier; font-size:=
 14px; font-style: normal; font-variant: normal; font-weight: normal; lette=
r-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-=
transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit=
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kit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webk=
it-text-stroke-width: 0px; "><span class=3D"Apple-style-span" style=3D"bord=
er-collapse: separate; font-family: Courier; font-size: 14px; font-style: n=
ormal; font-variant: normal; font-weight: normal; letter-spacing: normal; l=
ine-height: normal; orphans: 2; text-indent: 0px; text-transform: none; whi=
te-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-s=
pacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations=
-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width=
: 0px; "><span class=3D"Apple-style-span" style=3D"border-collapse: separat=
e; font-family: 'Andale Mono'; font-size: 14px; font-style: normal; font-va=
riant: normal; font-weight: normal; letter-spacing: normal; line-height: no=
rmal; orphans: 2; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -=
webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: no=
ne; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span=
 class=3D"Apple-style-span" style=3D"border-collapse: separate; font-family=
: 'Andale Mono'; font-size: 14px; font-style: normal; font-variant: normal;=
 font-weight: normal; letter-spacing: normal; line-height: normal; orphans:=
 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2;=
 word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-=
vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-te=
xt-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class=3D"Appl=
e-style-span" style=3D"border-collapse: separate; -webkit-border-horizontal=
-spacing: 0px; -webkit-border-vertical-spacing: 0px; font-family: 'Andale M=
ono'; font-size: 14px; font-style: normal; font-variant: normal; font-weigh=
t: normal; letter-spacing: normal; line-height: normal; -webkit-text-decora=
tions-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; te=
xt-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacin=
g: 0px; "><span class=3D"Apple-style-span" style=3D"border-collapse: separa=
te; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing=
: 0px; font-family: 'Andale Mono'; font-size: 14px; font-style: normal; fon=
t-variant: normal; font-weight: normal; letter-spacing: normal; line-height=
: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webk=
it-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: n=
ormal; widows: 2; word-spacing: 0px; "><span class=3D"Apple-style-span" sty=
le=3D"border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -w=
ebkit-border-vertical-spacing: 0px; font-family: 'Andale Mono'; font-size: =
14px; font-style: normal; font-variant: normal; font-weight: normal; letter=
-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: =
none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: non=
e; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span c=
lass=3D"Apple-style-span" style=3D"border-collapse: separate; -webkit-borde=
r-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; font-famil=
y: 'Andale Mono'; font-size: 14px; font-style: normal; font-variant: normal=
; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit=
-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adju=
st: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2;=
 word-spacing: 0px; "><div><div><span class=3D"Apple-style-span" style=3D"f=
ont-family: Arial; "><div class=3D"AppleMailSignature" id=3D"BD214290-7324-=
48EC-A16C-4BCD48002BDD"><span class=3D"Apple-style-span" style=3D"font-fami=
ly: Courier; "><span class=3D"Apple-style-span" style=3D"font-family: 'Anda=
le Mono'; "><div><div><span class=3D"Apple-style-span" style=3D"font-family=
: Courier; "><div class=3D"AppleMailSignature" id=3D"BD214290-7324-48EC-A16=
C-4BCD48002BDD"><span class=3D"Apple-style-span" style=3D"font-family: 'And=
ale Mono'; "><div><div><font class=3D"Apple-style-span" face=3D"Arial">Mark=
 Holder</font></div><div><font class=3D"Apple-style-span" face=3D"Arial"><b=
r class=3D"webkit-block-placeholder"></font></div><div><font class=3D"Apple=
-style-span" face=3D"Arial"><a href=3D"mailto:mtholder at ku.edu">mtholder at ku.=
edu</a></font></div><div style=3D"margin-top: 0px; margin-right: 0px; margi=
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"Arial"><div style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0p=
x; margin-left: 0px; "><font style=3D"font: normal normal normal 12px/norma=
l Helvetica; "><font class=3D"Apple-style-span" face=3D"Arial" size=3D"4"><=
span class=3D"Apple-style-span" style=3D"font-size: 14px; "><a href=3D"http=
://phylo.bio.ku.edu/mark-holder">http://phylo.bio.ku.edu/mark-holder</a></s=
pan></font></font></div></font></div><div style=3D"margin-top: 0px; margin-=
right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class=3D"Apple-st=
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v><div style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; mar=
gin-left: 0px; "><font class=3D"Apple-style-span" face=3D"Arial">=3D=3D=3D=
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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</font></div><div><fo=
nt class=3D"Apple-style-span" face=3D"Arial">Department of Ecology and Evol=
utionary Biology</font></div><div><font class=3D"Apple-style-span" face=3D"=
Arial">University of Kansas</font></div><div><font class=3D"Apple-style-spa=
n" face=3D"Arial">6031&nbsp;Haworth Hall</font></div><div><font class=3D"Ap=
ple-style-span" face=3D"Arial">1200 Sunnyside Avenue</font></div><div><font=
 class=3D"Apple-style-span" face=3D"Arial">Lawrence, Kansas 66045</font></d=
iv><div><font class=3D"Apple-style-span" face=3D"Arial"><br class=3D"khtml-=
block-placeholder"></font></div><div><font class=3D"Apple-style-span" face=
=3D"Arial">lab phone: &nbsp;785.864.5789</font></div><div><br></div><div><f=
ont class=3D"Apple-style-span" face=3D"Arial">fax (shared):&nbsp;785.864.58=
60</font></div><div style=3D"margin-top: 0px; margin-right: 0px; margin-bot=
tom: 0px; margin-left: 0px; "><font class=3D"Apple-style-span" face=3D"Aria=
l">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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div><div style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; m=
argin-left: 0px; "><font class=3D"Apple-style-span" face=3D"Arial"><br></fo=
nt></div><font class=3D"Apple-style-span" face=3D"Arial"><br></font></div><=
/span></div></span><font class=3D"Apple-style-span" face=3D"Arial"><br></fo=
nt></div></div></span></span></div><font class=3D"Apple-style-span" face=3D=
"Monaco"></font></span><br></div></div></span></span></span></span></span><=
/span></span></span></span><br class=3D"Apple-interchange-newline"></div></=
span></div></span><br class=3D"Apple-interchange-newline"></span><br class=
=3D"Apple-interchange-newline">
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