Difference between revisions of "Scott Edwards"

From MolEvol
(Lecture Material)
 
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=== Duration of Stay ===
 
=== Duration of Stay ===
  
Friday Jul 24 - Wed. Jul. 29
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Wednesday August 7 - Sunday August 11
  
 
=== Institutional Website ===
 
=== Institutional Website ===
[http://www.oeb.harvard.edu/faculty/edwards/ Edwards Lab Web Site]
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[http://edwards.oeb.harvard.edu/ Edwards Lab Web Site]
  
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=== Lecture Material ===
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2019:[https://molevol.mbl.edu/images/7/79/Edwards_MBL_2019_partI.pdf  Lecture part I]
  
=== Lecture Material ===
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2019:[https://molevol.mbl.edu/images/9/92/Edwards_MBL_2019_partII.pdf  Lecture part II]
  
2015:[https://www.dropbox.com/sh/2i04mwtrp50it55/AAC71aXUJAkHazWPhsFDGbyda?dl=0  Lecture parts I and II]
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=== Lab Material (not presented in class, but available for exploration) ===
  
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2019: [https://molevol.mbl.edu/images/1/12/Edwards_tutorial_slides_2016.pdf Tutorial slides]
  
=== Lab Material ===
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2019: [[:Media:Edwards_species_tree_lab.zip |Edwards Lab data files and documentation]]
2015: [https://molevol.mbl.edu/images/1/1f/Edwards_lab_2015.zip Edwards Lab Notes and files]
 
  
2015: [https://molevol.mbl.edu/images/a/a3/Rphast_conservation_vignette1.pdf Conservation analysis R script]
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2019: [[:Media:phybase1.5-manual.pdf |Phybase manual]]
  
2015: [https://molevol.mbl.edu/index.php/Edwards_lab_notes Some notes for the lab]
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2019: [https://molevol.mbl.edu/images/2/2e/Manual_mpest2.0.pdf MP-EST v.2.0 manual]]
  
2015: [https://molevol.mbl.edu/images/1/13/Manual_phybase.pdf Phybase manual]
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2019: [https://molevol.mbl.edu/images/a/a3/Rphast_conservation_vignette1.pdf Conservation analysis R script]
  
 
=== Key Papers ===
 
=== Key Papers ===
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Liu et al. (2009): [https://molevol.mbl.edu/index.php/File:MPE_Review_2009.pdf  A review of methods and issues surrounding "species tree" phylogenetic methods]
 
Liu et al. (2009): [https://molevol.mbl.edu/index.php/File:MPE_Review_2009.pdf  A review of methods and issues surrounding "species tree" phylogenetic methods]
  
Oliver (2013): [https://molevol.mbl.edu/index.php/File:Oliver_Evolution_2013_coalesent_deep.pdf An empirical demonstration of coalescent effects at deep phylogenetic nodes]
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Degnan & Rosenberg (2009): [https://molevol.mbl.edu/index.php/File:Degnan_and_Rosenberg_2009.pdf An excellent review of the multispecies coalescent, including discussion of the anomaly zone]
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Liu et al. (2010): [https://molevol.mbl.edu/index.php/File:MP-EST_2010_Liu_etal.pdf MP-EST: A maximum likelihood species tree method]
  
Song et al. (2013): [https://molevol.mbl.edu/index.php/File:Song_etal_2012_PNAS_mammals.pdf  Another example of coalescent effects at deep phylogenetic nodes]
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Cloutier et al. (2019): [https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz019/5477409] Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone. Syst. Biol.  https://doi.org/10.1093/sysbio/syz019
  
Degnan & Rosenberg (2009): [https://molevol.mbl.edu/index.php/File:Degnan_and_Rosenberg_2009.pdf An excellent review of the multispecies coalescent, including discussion of the anomaly zone]
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Sackton et al. (2019): [https://science.sciencemag.org/content/364/6435/74] Convergent regulatory evolution and loss of flight in palaeognathous birds. Science 364: 74-78.
  
Liu et al. (2010): [https://molevol.mbl.edu/index.php/File:MP-EST_2010_Liu_etal.pdf MP-EST: A maximum likelihood species tree method]
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Hu, et al. (2019): [https://academic.oup.com/mbe/article/36/5/1086/5372678] Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Mol. Biol. Evol. 36: 1086-1110.
  
 
Rheindt et al. (2014): [https://molevol.mbl.edu/index.php/File:Rheindt_Zimmerius_introgression_SystBiol_2014.pdf An empirical example of using SNPs for phylogenetics]
 
Rheindt et al. (2014): [https://molevol.mbl.edu/index.php/File:Rheindt_Zimmerius_introgression_SystBiol_2014.pdf An empirical example of using SNPs for phylogenetics]

Latest revision as of 11:44, 8 August 2019

Scott Galapagos cropped.jpg

Duration of Stay

Wednesday August 7 - Sunday August 11

Institutional Website

Edwards Lab Web Site

Lecture Material

2019:Lecture part I

2019:Lecture part II

Lab Material (not presented in class, but available for exploration)

2019: Tutorial slides

2019: Edwards Lab data files and documentation

2019: Phybase manual

2019: MP-EST v.2.0 manual]

2019: Conservation analysis R script

Key Papers

Edwards (2009): A perspective arguing for the utility of phylogenetic methods using the multispecies coalescent

Liu et al. (2009): A review of methods and issues surrounding "species tree" phylogenetic methods

Degnan & Rosenberg (2009): An excellent review of the multispecies coalescent, including discussion of the anomaly zone

Liu et al. (2010): MP-EST: A maximum likelihood species tree method

Cloutier et al. (2019): [1] Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone. Syst. Biol. https://doi.org/10.1093/sysbio/syz019

Sackton et al. (2019): [2] Convergent regulatory evolution and loss of flight in palaeognathous birds. Science 364: 74-78.

Hu, et al. (2019): [3] Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Mol. Biol. Evol. 36: 1086-1110.

Rheindt et al. (2014): An empirical example of using SNPs for phylogenetics