PBG298/2007: Readings

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(April 17)
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(June 6)
 
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=April 17=
=April 17=
More population genetics of polyploidy!
More population genetics of polyploidy!
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I did a literature search today and found several interesting papers.  I picked two for next week, but in the interest of time, I think we should focus on the first one (Walsh paper).  The Comai paper can be background reading for people who want to do a little polyploidy catch-up (like me).  Both Genetica and Nature Reviews Genetics are available online through the library.   
I did a literature search today and found several interesting papers.  I picked two for next week, but in the interest of time, I think we should focus on the first one (Walsh paper).  The Comai paper can be background reading for people who want to do a little polyploidy catch-up (like me).  Both Genetica and Nature Reviews Genetics are available online through the library.   
 +
<biblio>Walsh2003 pmid=12868616</biblio>  I read the beginning of this paper and scanned the rest.  It addresses some of the ideas we touched on at the end of the April 10th class.  It gets real mathy at the end, but it seems like a well-written paper (aka focus on the text and slide over the math parts).
<biblio>Walsh2003 pmid=12868616</biblio>  I read the beginning of this paper and scanned the rest.  It addresses some of the ideas we touched on at the end of the April 10th class.  It gets real mathy at the end, but it seems like a well-written paper (aka focus on the text and slide over the math parts).
 +
<biblio>Comai2005NRG pmid=16304599 </biblio> Nice review, lots of pretty pictures of difficult to visualize inheritance mechanisms.  Introduces some molecular genetic concepts not covered in other two papers.
<biblio>Comai2005NRG pmid=16304599 </biblio> Nice review, lots of pretty pictures of difficult to visualize inheritance mechanisms.  Introduces some molecular genetic concepts not covered in other two papers.
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=April 24=
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Ploidy shifts with Pat and Brian.
 +
 +
The yeast haploid superiority article (Zeyl, 2003, Science below) dovetails nicely with the Walsh reading from April 17 and the Otto review from April 10.
 +
 +
A recent paper on gene duplicate evolution in Teleost fish should further expand on experimental observations related to evolution specific to polyploid contexts.
 +
 +
 +
<biblio>Zeyl2003 pmid=12543972</biblio>
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<biblio> Brunet2006 pmid=16809621 </biblio>
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=May 1=
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Speciation with Dena
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[http://www.blackwell-synergy.com/doi/abs/10.1111/j.1095-8312.2004.00335.x Great paper] from the Solti, Pires, and Leitch groups from a meeting proceedings at Kew Gardens. Demonstrates that in this case the species barrier was not overcome just once in a freak accident.
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[http://www.journals.uchicago.edu/cgi-bin/resolve?id=doi:10.1086/501079&erFrom=-9161881067141926907Guest Polyploid tree frogs unite] to form a complex interspecies swarm. Demonstrates recurrent polyploid formation can play a role in animal polyploid speciation too. Go frogs.
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=May 8=
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Contemporary polyploidy hybrids with Debra Ayers
 +
 +
Abbott and Lowe paper on Senecios (HTML):
 +
http://www.blackwell-synergy.com/doi/full/10.1111/j.1095-8312.2004.00333.x
 +
 +
Urbanska paper on Cardamine:
 +
http://springerlink.metapress.com/content/g6977375111059p4/fulltext.pdf
 +
 +
Plus unpublished nuggets on local spartina and tumbleweeds!
 +
 +
=May 15=
 +
The triploid bridge with Brian
 +
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With so much new stuff to be discovered ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15266374&query_hl=8&itool=pubmed_docsum mathematical models] of polyploid establishment under mixed asexual/sexual breeding schemes) I decided to settle on some steady material.
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#For a review on the origins of polyploids I offer up the first (of two) reviews by Justin Ramsey and Doug Schemske ([http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.29.1.467 1998], or [http://links.jstor.org/sici?sici=0066-4162(1998)29%3C467%3APMAROP%3E2.0.CO%3B2-R here]). The sections about triploids and the triploid bridge are all I think we should focus on. There is a lot of meat in this review.
 +
#The second is [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1095-8312.2004.00339.x a paper by Brian Husband] that looks at the effect of triploid fitness on the evolution of polyploidy in populations.
 +
#Last is [http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030070 a paper from the Comai group] looking at the existence of variability in both triploid and aneuploid fitness. There is a methods paper in the plant journal (Henry 2006) and a previous paper in Genetics (Henry et al., 2005) that mirrors some of the figures presented in Ramsey and Schemske for maize (or Satina and Blakeslee 1936/37 for Datura).
 +
 +
The triploid bridge is not just for evolution. It gets used by breeders ocassionally, and talked about often. I have linked [http://www.springerlink.com/content/bfu4m241knur2u9u/ a paper by Carputo et al.] on the uses and usefulness of the "EBN", one of which is to make odd-ploidy hybrids as a bridge to allow gene flow between isolated species. I don't think there will be time to discuss it.
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=June 6=
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Polyploidy in Animals
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The time has to come to put on our zoology glasses and examine polyploidy in animal species.  I've picked two papers, one of which was on the initial "suggested readings list" passed out at the beginning of class.
 +
 +
Mable, B. K.  2004.  'Why polyploidy is rare in animals than in plants': myths and mechanisms.  Biological Journal of the Linnean Society 82:453-466 (http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1095-8312.2004.00332.x).  If people are interested, they can read the original paper "Why polyploidy is rarer in animals than in plants revisited" (Orr 1990; although if it is being revisited, there must be an older paper with a similar title). 
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Le Comber, S. C. and C. Smith.  2004.  Polyploidy in fishes: patterns and processes.  Biological Journal of the Linnean Society 82:431-422 (http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1095-8312.2004.00330.x.)

Current revision

UC Davis PBG298: Polyploid Genetics and Evolution Seminar

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Contents

April 10

Background with Pat!

  1. Otto SP and Whitton J. . pmid:11092833. PubMed HubMed [OW2000]

April 17

More population genetics of polyploidy!


I did a literature search today and found several interesting papers. I picked two for next week, but in the interest of time, I think we should focus on the first one (Walsh paper). The Comai paper can be background reading for people who want to do a little polyploidy catch-up (like me). Both Genetica and Nature Reviews Genetics are available online through the library.


  1. Walsh B. . pmid:12868616. PubMed HubMed [Walsh2003]
I read the beginning of this paper and scanned the rest. It addresses some of the ideas we touched on at the end of the April 10th class. It gets real mathy at the end, but it seems like a well-written paper (aka focus on the text and slide over the math parts).


  1. Comai L. . pmid:16304599. PubMed HubMed [Comai2005NRG]
Nice review, lots of pretty pictures of difficult to visualize inheritance mechanisms. Introduces some molecular genetic concepts not covered in other two papers.


April 24

Ploidy shifts with Pat and Brian.

The yeast haploid superiority article (Zeyl, 2003, Science below) dovetails nicely with the Walsh reading from April 17 and the Otto review from April 10.

A recent paper on gene duplicate evolution in Teleost fish should further expand on experimental observations related to evolution specific to polyploid contexts.


  1. Zeyl C, Vanderford T, and Carter M. . pmid:12543972. PubMed HubMed [Zeyl2003]
  1. Brunet FG, Roest Crollius H, Paris M, Aury JM, Gibert P, Jaillon O, Laudet V, and Robinson-Rechavi M. . pmid:16809621. PubMed HubMed [Brunet2006]

May 1

Speciation with Dena

Great paper from the Solti, Pires, and Leitch groups from a meeting proceedings at Kew Gardens. Demonstrates that in this case the species barrier was not overcome just once in a freak accident.

Polyploid tree frogs unite to form a complex interspecies swarm. Demonstrates recurrent polyploid formation can play a role in animal polyploid speciation too. Go frogs.

May 8

Contemporary polyploidy hybrids with Debra Ayers

Abbott and Lowe paper on Senecios (HTML): http://www.blackwell-synergy.com/doi/full/10.1111/j.1095-8312.2004.00333.x

Urbanska paper on Cardamine: http://springerlink.metapress.com/content/g6977375111059p4/fulltext.pdf

Plus unpublished nuggets on local spartina and tumbleweeds!

May 15

The triploid bridge with Brian

With so much new stuff to be discovered (mathematical models of polyploid establishment under mixed asexual/sexual breeding schemes) I decided to settle on some steady material.

  1. For a review on the origins of polyploids I offer up the first (of two) reviews by Justin Ramsey and Doug Schemske (1998, or here). The sections about triploids and the triploid bridge are all I think we should focus on. There is a lot of meat in this review.
  2. The second is a paper by Brian Husband that looks at the effect of triploid fitness on the evolution of polyploidy in populations.
  3. Last is a paper from the Comai group looking at the existence of variability in both triploid and aneuploid fitness. There is a methods paper in the plant journal (Henry 2006) and a previous paper in Genetics (Henry et al., 2005) that mirrors some of the figures presented in Ramsey and Schemske for maize (or Satina and Blakeslee 1936/37 for Datura).

The triploid bridge is not just for evolution. It gets used by breeders ocassionally, and talked about often. I have linked a paper by Carputo et al. on the uses and usefulness of the "EBN", one of which is to make odd-ploidy hybrids as a bridge to allow gene flow between isolated species. I don't think there will be time to discuss it.

June 6

Polyploidy in Animals

The time has to come to put on our zoology glasses and examine polyploidy in animal species. I've picked two papers, one of which was on the initial "suggested readings list" passed out at the beginning of class.

Mable, B. K. 2004. 'Why polyploidy is rare in animals than in plants': myths and mechanisms. Biological Journal of the Linnean Society 82:453-466 (http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1095-8312.2004.00332.x). If people are interested, they can read the original paper "Why polyploidy is rarer in animals than in plants revisited" (Orr 1990; although if it is being revisited, there must be an older paper with a similar title).

Le Comber, S. C. and C. Smith. 2004. Polyploidy in fishes: patterns and processes. Biological Journal of the Linnean Society 82:431-422 (http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1095-8312.2004.00330.x.)

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