mklau / dissertation

Evolution of Ecological Networks. This is Matt Lau's dissertation projects folder. For more info, please contact him.

UPDATING

NEW SITE

1. FORK
2. CLONE
3. SETUP public submodule
4. Edit content, config.toml, theme (see minimo demo)
5. CHANGE deploy.sh CNAME url
6. BUILD (use blogdown)
7. sh deploy.sh
8. SETUP DNS for custom site domain
9. COMMIT main repo changes

For more info: http://blog.teamtreehouse.com/using-github-pages-to-host-your-website

dissertation's Issues

email art

Additional Analyses (from meeting with Tom)

1. check ses calculations, starting with ses = 10
2. how does an ses of 10 compare to other communities?
3. do tree level network modeling and compare that average to the stand level network structure
4. correlate ses and richness
5. correlate with xgal
6. look at age

Agent Based Modeling

simecol

http://cran.r-project.org/web/packages/simecol/vignettes/b-simecol-howtos.pdf

RNetLogo

http://onlinelibrary.wiley.com/store/10.1111/j.2041-210X.2011.00180.x/asset/j.2041-210X.2011.00180.x.pdf?v=1&t=hmujw3ks&s=e9d6a4c1bb41a35e1e9e08bd92274f23a334f8ba

Finish ComGenR.R

Results: Prelim Sunset lichen bipartite network

Read Ellis and Ellis 2012 = Signatures of autogenic epiphyte succession for an aspen chronosequence

See email from Lamit.

Grad College Deadlines

SPRING 2014
Jan 7
Graduate Assistant Appointment Start Date
Jan 14
Classes Begin
Jan 18
Open House for New Graduate Students and Graduate Assistants
Jan 21
Martin Luther King Holiday
Jan 25
Deadline to Submit AZ Residency Petition for Spring 2013
_Feb 8_
Applications for Doctoral Candidacy Due for May Graduation
_Feb 8_
Applications for May Graduation Due in Graduate College
Feb 22
Deadline to File Residency Reclassification Appeal for Spring 2013
Mar 18-22
Spring Break
_Apr 12_
Last Date to Submit Dissertation Defense Scheduling Form for May Graduation
_Apr 19_
Last Day to Submit Electronic Theses and Dissertations for Format Check: Email attachment only.
Apr 29
Graduate Student Awards Reception
_Apr 26_
Last Day to Hold Dissertation Defense for Spring Semester
May 3
Classes End
May 6-9
Finals
_May 8_
Final Approved Electronic Thesis and Dissertation (ETD) Submission Due
May 10
Graduate Assistant Appointment End Date
May 10-11
Commencement

Fall 2013
Oct 4
Deadline to File Residency Reclassification Appeal
Nov 11
Veteran’s Day Holiday
Nov 20
Last Date to Submit Dissertation Defense Scheduling Form for December Graduation
Nov 20
Last Day to Submit Electronic Theses and Dissertations for Format Check: Email attachment only.
Nov 28-29
Thanksgiving Holiday
Dec 4
Last Day to Hold Dissertation Defense for Fall Semester
Dec 11
Classes End
Dec 13, 16-18
Finals
Dec 17
Final Approved Electronic Copies of Theses and Dissertations Due
Dec 18
Fall-only Graduate Assistant Appointment End Date
Dec 19
Commencement

Gina's Data shows significant network structure resulting from genetic variation

Advising from afar (read this)

http://smallpondscience.com/2013/07/22/supervising-students-from-afar/

Lichen traits for interactions

Can you use traits to predict interaction network structure?

Art's unipartite networks are very sparse

Lichen interaction ecology

Vascular plant and epiphytic lichen communities in Canadian aspen parkland.

Factors Influencing Epiphytic Lichen Communities in Aspen-Associated Forests of the Bear River Range, Idaho and Utah

http://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=1458&context=govdocs

REVIEW: notes from last meeting with Tom

bernardson paper
grady city of flag grant bringing back the rio de flag

urban = instant climate change

• ling range climate impacts of cities
• cities as a selective agent
• abondined lots can be used for genetics in urban systems (cheatgrass, chenopodium)

Re-do all analyses

• account for height (can you combine both quadrats so that each tree has 100 cells?)
• do abundance, richness, community responses to roughness
• do stand level integrated and tree level co-occurrence (Gotelli and Araujo styles)
• do tree level co-occurrence analyses (Gotelli style)
• do tree level co-occurrence network analyses (Araujo style)
• look at response of co-occurrence patterns to A/cover, R, roughness
• conduct in the wild
• conduct in the onc
• conduct in pit
• other variables to explain variation?

Fix x_i notation

P(x_i) is repeated unparsimoniously.

Use?

P(x_i) = x_i * P(o_i) + (1-x_i) * P(a_i)

Genetics of leaf abscission

meeting with Tom (Jun2013)
%%%%% Genetics of Leaf Absiscion %%%%%
-- Known leaf abscision influenced by P. betae
-- Kown genetic basis to sink-source
-- Known differences in susceptibility
--- zero sum game for the aphid in terms of photosynthate
--- absciscic acid? unpublished paper that Tom reviewed

• Question: What is the genetic component to absiscion?
  Results
  -- Fig 1 Tom's poisson = don't share leaves
  -- Stats only. Genetope -> susceptibility
  -- Fig 2 Genetics -> leaf absiscion (control for density)
• Is there a relationship between leaf size and susceptibility?
• 1986 ecology evolution of teritoriality
• Compson sink source paper
• williams and whitham
• martinson paper
• Co-authors
  -- Zink
  -- Art
  -- Tom
  -- Joe?
  -- Todd?

email lluvia

car

final data collection

Get modifier counts from dead and senescing leaves

tangled nature model

http://www.maths.bris.ac.uk/~madjl/Laird_Lawson_JensenPREPRINT-TangledNature.pdf

Outline - Genetic Variation Contributes to Interaction Network Structure (Chp 3)

• Ecological interactions are local and both direct and diffuse
• Genetic variation in foundation species influences spatial distributions of species
• Here we explore how genetically based variation can contribute to the structure of ecological interaction networks by modularing the frequency of encounters between individuals
• To do this, we:
• simulate how genetically based variation leads to spatial patterns of species distributions
• model interaction networks from both a uni- and bi-partite network perspective
• analyze the structure of these networks

We argue that foundation species genetic variation leads to changes in species interaction network structure, and that these effects can then propogate through networks of associated species

Email Rikke and Cameron about lichen interactions

Email Cam and Rikke and get some lit from them.

Also email Lamit.

Look into analogous communities

E.g., biofilms and coral

ECD - read this paper on Evolutionary Conservation of Species Roles

http://www.bascompte.net/content/publications/Science-12.pdf

• How does this relate to effective community diversity?

Go over notes from lab meeting

Read Corroborative Network Analysis

Ulanowicz 1997 p132

Chapter Outlines

Plan for Writing

• Finish analyses
• Summarize results
• Outline main results
• Get feedback from Tom
• Write abstract
• Write methods
• Write introduction
• Write discussion
• Get feedback from group

The differences among genotypes (i.e. the community level effect of genetic variance) is unlikely to be constant over time, but to rise and fall like a tide depending on abiotic flux and the dynamics of the associated community.

Analyze ACN data from live leaves

Why intraspecific trait variation matters in community ecology

http://people.oregonstate.edu/~novakm/wp-content/uploads/2011/12/Bolnick_2011.pdf

IDEA: Put into real units

Find a study or theory estimating the amount of selection needed for evolution and look at the lower threshold given the structure of the interaction network of the community.

Analyze green leaf dataset

Data Imputation in R

Package VIM updated to version 4.0.0 with previous version 3.0.3.1 dated 2013-04-11
http://dirk.eddelbuettel.com/cranberries/2013/10/10#VIM_4.0.0

Outline - network question

• Ecology and evolution can function on similar time scales
• Genetic variation in plant species has been shown to influence community dynamics, however few studies have resolved the impact this has on the complex web of interactions among species
• In this study, using a foundation species model system, we address the question: how does genetic variation in a foundation species influence networks of interacting species?
• To do this we:
• model the structure of interaction networks at the scale of both the stand and the tree
• examine the topology of these networks at the level of individual species
• test for effect of genetics on network structure using null model based co-occurence and bipartite network analyses

We hypothesize that network structure will be directly influenced by genetically based variation in tree traitsand that the topological importance of species in the network will be positivley related to the numerical dominance of species.

Prep for meeting with Tom

• finish lco analyses
• finish acn analyses
• look at website

Apply for MCED

http://www.mced-ecology.org/?page_id=197

Use information theory to investigate the structure of these networks

Read scientific writing book

Publish land facet package with Brian

EMAIL: note from Tom

OK, Good, glad you will be joining us. I also agree with your comments on foundation species as stated below. Also, in the same conversation with Steve Shuster in which he related the issues about Kim, he said that he was anxious to get Eric back on track with the ECD. I told him of your interest in finishing it off. Before you do too much more, it would be good if you contacted Steve and/or Eric. Steve totally agrees that the ms is too important to let it languish more, so he is supportive in doing whatever it takes to get it out. Regarding genetic covariances between species, the aphid/cottonwood and the mite/cottonwood examples are best. Although I haven’t seen Kim’s latest, Luke’s published work is best. I wish we had a lot more, but unfortunately, we don’t. The cut-off of a species being a foundation species may best be defined by the interaction network. If you took all the species in one of your analyses, what would the shape of your distribution be? Bridgeland et al. (2010) had 700 species but only a handful were strong interactors as he defined them. I would like to see several metrics involved such as your network analysis, removal experiments as we have done several times, biomass, addition experiments. I think that generally, these several metrics would agree, but I’ve never seen anyone do it. See you in a few.

Enter LCO data

email committee

parallel computing

snowfall

http://cran.r-project.org/web/packages/snowfall/index.html

Opportunity for selection

http://www4.nau.edu/isopod/Pubs/Krakauer%20et%20al.%202011.pdf

Consider publishing methods

MEE
Journal of Artificial Societies and Social Simulation
Others?

Lichen and Arthropod Data?

• can you use ECD to compare models?
• how does ECD relate to other network metrics?

cgSim: whenever y==1 r2>0.48

Check equation values you have when y == 1.

YY variation scenarios of other ecological interactions

What is scenario YY == 1

Look into corrplot package

http://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html

ONC analysis

• find missing roughness values
• deal with cross year data

Coevolutionary games-A mini review

Coevolutionary games-A mini review

Look into OData

http://www.odata.org/introduction/

Things to think about... (from meeting with Tom)

• co-occurrence predictions from resource-interaction theory
• plant traits and community evolution
• think broad, how does this relate to other systems
• effective community diversity?
• think about information: a = -sum ti log tij/ti ?