Project updates

MESS

Isaac updates us

  • re-write of gimmeSAD to MESS codebase
    • huge performance improvements
    • clean, modern CLI and API
    • multi-island
    • phylogeny, traits (aka “Chase knob”), crude speciation
    • need help on speciation from mathematicians
    • “Gillespie knob” determines how speciation depends on abundance
  • online doc (!)
  • analysis of data
    • spider data (from Brent Emerson) look cool!
    • using genetic data we identify near equilibrium, but with abundance only we miss that signal
    • we should look at covariance of posterior estimates says Luke Harmon
    • Mauritius vs. Reunion: higher entropy on older island
    • bacterioplankton through time look awesome!
      • colonization and extinction constant and stochastic through time
      • $\Lambda$ and Shannon linear increase through time
  • Work to be done
    • new equilibrium definition: we have one from Rosindell and Harmon that might focus on only shallow time processes (e.g. abundance)
    • better goodness of fit metrics
    • right now it’s ABC, but machine learning would be great
    • how we could work with replicated datasets (in space and time)

alpha/beta

Luke M. updates us

  • how does in situ speciation affect different components of richness? We know $\gamma$ diversity has an uptick for larger islands where in situ speciation occurs—where does that come from? Does evolution influence $\alpha$, $\beta$ or both?
  • variables of interest
    • predictors
      • island speciation fraction
      • island area—is there a speciation threshold?
      • island age
      • environmental covariates
    • responses
      • island richness
      • plot-level richness (central tendency across plots for an island of both $\alpha$ and $\beta$)
      • should we look at plot-level abundance?
  • progress
    • cleaning script (standard format, culling non-natives)
    • rarefaction
    • exploratory analysis:
      • Azores arthropods: no effect of area or age at plot level
      • Hawaii trees: area affects $\gamma$, ages affects $\alpha$
  • goals
    • more data: Galapagos snails, African cichlids, HI arthropods, more!
    • work on speciation
    • more on analytics
    • reconcile predictors
    • what to do with $\beta$ div when local sampling is different across studies?
    • what about cichlids says Luke H.? do they have a threshold? also Hawaii says Jon. He points out the main focus is how evolution at macroscale and ecology at the plot scale feedback on each other

alpha/beta theory

Ben updates us

  • simple infinite alleles type model
    • pure immigration:
      • small islands—gamma = alpha; big islands—alpha saturates, gamma continues to rise
    • add simple speciation, just shift patterns up (i.e. more diversity overall)
    • if speciation rate increases with area we get an uptick in both gamma and alpha
  • next steps
    • $F_{st}$ type statistic to compare gamma and alpha
    • add a metacommunity
    • this week
      • division of labor

island ontogeny

Rosie updates us by proxi for Jairo

  • Jairo has generated a bunch of phylogeny data!
    • Hawaii: 12 arthropod lineages
    • Hawaii tree data
    • Macaronesia: 14 arthropod and 22 angiosperm lineages
    • Galapagos: 2 angiosperm
      • outline paper
      • decide on simulation setting (e.g. spatially implicit or explicit)
      • finish theory
  • can these data be helpful for alpha/beta team in determining speciaton fraction?

How to get genomics in the mix

Angela updates us

  • SNP data to look at early stages of speciation shortly after colonization
  • how does allele frequency spectrum vary through time—awesome!!
    • compare old island and young islands—where do we see the rare variants?
    • colonization without a bottleneck vs. colonization with a bottleneck: standing variation vs. novel variation
    • data:
      • Reunion nematodes—full genome resequencing which is great
      • Hawaii arthropod RAD seq forthcoming

island/mainland diversification

James updates us

  • Is diversification different on islands vs. mainlands?
    • Is it that clades that make it to islands are special?
    • Or does any random clade, once it’s on an island, diversify differently?
    • Compare sister lineages on islands vs. mainlands and island clades vs. random clades drawn from the global phylogeny
    • Data:
      • mammal phylo (Luke H. just gave us this alternative tree and it’s cherry)
      • birds to come
      • Kreft “islandness” shapefiles
      • new data:
        • amphibians?
        • lizards?
        • angiosperms
    • Analysis:
      • is it sufficient to look at clade age and clade richness
      • Luke H thinks whole phylo approach could be easier (methods are more straightforward but not without their controversy)

An introduction from Brent

  • Community based sampling to
    • characterize ecological patterns
    • identify drivers of speciation
  • Using:
    • standard plots and standard taxonomy combined with individual-based seq
      • 25 plots in laurel forests and expanding into dry habitat
      • spiders and beetles
      • 4 individuals per species sequenced for mtDNA and RADseq
        • shows some cool patterns like east-west community-wide divergence based on moisture discontinuity
      • also using metabarcoding
        • soil arthropods
        • shows clear differentiation (cool!) of habitats in ordination space: is that from species turnover or genetic structure within a constant set of species?
      • taxon-focused sampling to connect population process to phylo pattern
        • e.g. weevil that diversified a lot but doesn’t show clear adaptive differences between spp—is it acute dispersal limitation?
  • A main conclusion: recent events (e.g. Pleistocene) seem to be very important for diversification