Read D. Spalink Caricae paper(s)

[rvanmazijk]

From the last couple of years.

Muthama mentioned that they use some interesting analyses.

[tle003]

Spalink et al. - 2018 - The spatial structure of phylogenetic and function.pdf Spalink et al. - 2016 - Biogeography of the cosmopolitan sedges (Cyperacea.pdf Spalink et al. - 2016 - Evolution of geographical place and niche space P.pdf

I found three papers from Daniel Spalink that Muthama might have been referring to. I took a brief look at them this evening and will look at them tomorrow. There are a couple of analyses that could be adapted for our work, but I think that we would have to use more current methods and approaches (especially with regards to the 2016 papers).

[tle003]

Spalink et al. 2016 - Evolution of geographical place and niche space (Carex)

Some ideas: we could do a similar visualization showing Schoenus richness per grid cell

• we have the data for the Southern African Schoenus
• I recommend searching out a better method to create the visualization
• speciation through time is possible with our data set (I think). We could look at this with different characters and do the BAMM analyses, such as in this paper, but I don't know if we would find anything interesting

I did not find the PGLS nor species tree/geography tree visualizations very informative. I think that if we want to compare the ranges for different Schoenus species in an evolutionary context, a different method would probably be more suitable for our data and questions.

[tle003]

Spalink et al. 2018 - The spatial structure of phylogenetic and functional diversity in the United States and Canada: An example using the sedge family (Cyperaceae))

Some ideas: there are some more analyses/visualizations that we can consider:

• create visualizations by major clade (each clade has its own colour); plot to QDGC
• in addition to species richness, we could also plot Faith's phylogenetic diversity (FPD), mean phylogenetic distance (MPD) and functional diversity. If we can include the Australian taxa, they would have a higher Faith's and MPD
• significant departure from expectations can also be calculated from the above
• can look at correlates of alpha diversity (modified t-test); are the species richness variables correlated within themselves? Are they correlated with functional diversity variables?
• we have the characters to calculate functional diversity (at least for the Southern African Schoenus)
• spatial patterns of functional traits
  • I think that this would be interesting
  • we could look into this using a different set of analyses

Predictions:

• Given that most sedge species occur in wetlands and that Arctic habitats are generally species depauperate, species richness should increase with both temperature and precipitation;
• Phylogenetic diversity should peak in the subtropical USA, where the merger of temperate and tropical lineages is likely to be most concentrated;
• Phylogenetic turnover should increase more strongly with distance along latitudinal than longitudinal gradients, but floristic turnover should increase approximately equally along both gradients

[tle003]

Spalink et al. 2016 - Biogeography of the cosmopolitan sedges (Cyperaceae) and the area‐richness correlation in plants

Some key points about the analyses:

• they used a BAMM analysis for the diversification rates
• BioGeoBEARS was used for the ancestoral area reconstruction.
• I liked the figure for the ancestoral area reconstruction more than Viljoen et al. 2013
  • Spalink et al. had separate columns for each major geographical area so it looks neater
• used PGLS with clade richness, clade range and diversification rates as response variables. Different Predictors included diversification rate, clade richness, average species range, etc.

Hypotheses:

• Clades occurring over large geographical and ecological extents are more diverse than spatially and ecologically restricted clades
• clade richness and diversification rate increase with the ratio of the average species range within a clade to the clade's overall range

[rvanmazijk]

Spalink et al. 2016 - Evolution of geographical place and niche space (Carex)

Some ideas: we could do a similar visualization showing Schoenus richness per grid cell

• we have the data for the Southern African Schoenus
• I recommend searching out a better method to create the visualization
• speciation through time is possible with our data set (I think). We could look at this with different characters and do the BAMM analyses, such as in this paper, but I don't know if we would find anything interesting

I did not find the PGLS nor species tree/geography tree visualizations very informative. I think that if we want to compare the ranges for different Schoenus species in an evolutionary context, a different method would probably be more suitable for our data and questions.

We discussed this paper in a recent journal club. I (and the rest of the journal club, likely) agree that the PGLS things they did was not particularly insightful. Their range/habitat data, also, makes sense for wider-ranging North American species, but not necessarily for ours.