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Monthly Archives: October 2012

These are the notes for a presentation I just uploaded to SlideShare. I gave this as a seminar at the University of Melbourne last Tuesday and at LaTrobe University two days later.

 

Slide 1

  • introduce

Slide 2

  • outline of the talk

Slide 3

  • student Dioli Payo
  • genus Portieria
  • pretty thallus shape – well-described with fractals
  • only two species known worldwide
  • her goal was to look at population structure of the species

Slide 4

  • her sampling localities in the Philippines

Slide 5

  • sequenced rapidly evolving marker from mt genome
  • we applied GMYC to the data
  • this is a quick ‘n dirty method to detect species boundaries
  • she found 21 species instead of 1
  • these are distinct species that have been separated for millions of years
  • species are cryptic => impossible to distinguish morphologically
  • they have limited distribution ranges, often a single island or bay

Slide 6

  • what does this mean globally?
  • our global sampling is not nearly as good
  • we’re at 50 species and counting
  • difficult to extrapolate but it could be well over 100 spp

Slide 7

  • we have a situation where much of what we think we know about species diversity is wrong
  • not only the case for Portieria, we know this is true for many algae, although perhaps not as spectacularly high diversities
  • what does this mean…
  • as a taxonomist to describe => they all look identical
  • every conservation decision that has ever been made that involves seaweeds needs to be revisited
  • more work for me at all levels: (1) difficult to study biodiversity patterns in meaningful way, (2) cannot trust a single species record from the literature or from online databases, (3) much denser sampling is needed in the field and DNA sequencing for every single specimen

Slide 8

  • move on to biodiversity
  • focus on understanding processes => diversification
  • geographic and ecological dimensions

Slide 9

  • our approach consists of this

Slide 10

  • our approach for the more visually inclined
  • start with phylogeny calibrated in geological time

Slide 11

  • add information about contemporary species
  • in this case macroecological: sea surface temperature

Slide 12

  • inference about past using models of evolutionary change
  • this way we can study how evolution of thermal affinities relate to figure below
  • since the phylogeny includes speciation events (bifurcations) we can relate niche evolution to diversification

Slide 13

  • these are the three model systems we’ve developed
  • very dense global sampling
  • starting to get to grips with what the species are and where they occur

Slide 14

  • start with geographic patterns of diversification

Slide 15

  • we aimed for general patterns, not individual case studies
  • hence focus on entire order of brown algae, the Dictyotales
  • you see some of the genera illustrated here

Slide 16

  • they are Olivier’s pet group so we know a lot about them
  • distributed worldwide across tropics and temperate water
  • we have > 2000 barcoded or accurately identified specimens belonging to 236 species
  • gives us pretty good idea of the distributions of the species

Slide 17

  • we want to know…
  • we have …
  • so we need a window into the past to see what happened

Slide 18

  • as explained before, models of evolutionary change offer a solution
  • relevant evolutionary events are parameters in the model, which is then optimized
  • with optimized model, we can infer things about the evolutionary events and estimate the ancestral situation
  • for biogeography => relevant parameters relate to how species move around
  • simple form with areas A/B
  • explain parameters for dispersal-extinction-cladogenesis
  • generalize to more areas
  • what it can do => phylogeny + current distribution => biogeographic history

Slide 19

  • we did this for Dictyotales
  • simple subdivision of world in three biogeographic regions: northern temperate, tropical, southern temperate
  • remember colors

Slide 20

  • change to Preview (cf. next page)

Slide 21

  • zoom in on terminal species, legend corresponds to colors in slide 19
  • reconstructed ancestral states are also there
  • show example of speciation associated with S to N shift
  • show example of speciation within region
  • base of Dictyoteae: temperate southern hemisphere
  • some lineages stay there (e.g. Dilophus)
  • at base of Dictyota more generalist
  • gives rise to a mixture of tropical and temperate lineages
  • top lineage: origin is tropical, moves into N temp on several occasions
  • next lineage down: all temperate, with S origin, dispersing into N
  • lineage all the way at bottom: starts in tropics, moves into S, later moves from S into N

Slide 22

  • tree is great to look at specific cases but doesn’t global picture
  • these are summary graphs
  • dispersal rate through time => 3 types are substantially higher than others
  • movement out of tropics
  • movement from S to N

Slide 23

  • put this in perspective
  • slide shows decreasing SST through Cenozoic
  • narrowing tropical belt
  • more temperate habitat opening up in S and N
  • movement from tropics to temperate
  • north is major sink because there was almost no temperate habitat => tropics and S feed into N

Slide 24

  • move on to macroecological correlates of diversification

Slide 25

  • case study Halimeda
  • diversity map => high diversity in tropics, with a few species in temperate habitat
  • so where is the origin? tropics or temperate
  • how often to niche shifts between temperate and tropical occur?

Slide 26

  • we have lots of DNA barcodes
  • we get SST for localities using satellite imagery
  • we get an idea of SST affinities of species
  • how do affinities evolve?

Slide 27

  • similar methods as before => model optimized
  • every tip is species
  • color gradient shows SST affinities
  • tropical origin
  • marker conservatism for tropical SST in clades 2-5
  • conservatism lostin clade 1 => 4 transitions into temperate
  • in perspective: show time frame and correspondence to narrowing tropics

Slide 28

  • do these modes of speciation and the shifting niches have implications for the distribution of biodiversity on the planet?

Slide 29

  • typical diversity patterns: well-characterized => bell-shaped around tropics
  • many possible explanations
  • my goal is to provide macroevolutionary perspective
  • higher species turnover in tropics => higher rate of diversification

Slide 30

  • seaweeds don’t follow general rules => bimodal diversity pattern
  • do same evolutionary processes hold or is diversification faster in temperate habitats?

Slide 31

  • Codium is suitable case study with similar diversity map

Slide 32

  • evolution of SST affinities traced along phylogeny
  • clade 3: almost half of all species in young clade, only 25 Ma
  • seems to be associated with move from temperate into tropics

Slide 33

  • logical question: is diversification faster in tropics

Slide 34

  • model of diversification dynamics in which diversification is function of SST

Slide 35

  • optimum value of beta => positive association between SST and diversification
  • higher rates in tropics
  • so process seems similar to other organisms and reasons for bimodal diversity pattern has to be sought elsewhere

Slide 36

  • so why is Codium richer in colder water?
  • probably due to historical causes
  • origin is in temperate waters and a lot of the branches remain in those temperate waters
  • it appears that the genus has only invaded the tropics recently and that, because of that, the majority of species is still in temperate water

Slide 37

  • no such thing for Dictyota => constant diversification explains it better

Slide 38

  • previous test only checked for very simple relationship between SST and diversification
  • many other types of relationships you could imagine
  • for example one could expect that clades whose niches are more evolvable manage to diversify more rapidly
  • we do seem to find that in Dictyota
  • split phylogeny up in major clades
  • positive relationship between rate of SST evolution and diversification
  • slope very deviant from that simulated under null model

Slide 39

  • lineages with many allopatric sister species along latitudinal thermal gradient diversify more rapidly
  • we seem to have a situation where clades that some clades manage to speciate more often along the latitudinal thermal gradient than others
  • clades that do, diversify more rapidly, probably because their presence in both temperate and more tropical habitats permits further radiation in those habitats

Slide 40

  • so, we saw that evolvability of the macroecological niche leads to more rapid diversification
  • where does that evolvability come from?

Slide 41

  • student Vanessa Marcelino was studying the evolution of microhabitat traits and macroecological traits in Halimeda
  • she decided to investigate in more detail whether there could be an interaction going on between micro and macro
  • Halimeda is mostly tropical and of tropical origin
  • found in different habitats on coral reef
  • exposed wave-swept and more sheltered e.g. reef slope but also lagoon
  • one could expect that SST evolution is faster for species in exposed microhabitats because they experience more extreme environments (low tide, wave action, etc)

Slide 42

  • compare model in which rate of SST evolution is constant with one in which it depends on whether or not species lives in exposed habitat

Slide 43

  • 2-rate model performs considerably better
  • difference in AIC 7.6 => integrated across uncertainty in exact pattern of evolution of microhabitat preference
  • lineages from exposed habitat 4.3x faster
  • so, it appears that microhabitat specializations can be exaptations for macroecological shifts

Slide 44

  • wrap up
  • for speciation, no “one rule fits all” => examples of everything you can imagine (allopatric vs. within region, associated with niche shift vs. conservatism)
  • for distributions, some patterns did come out => tropics act as source, with confirmation of “out of the tropics” hypothesis for Dictyotales; north is major sink because so recent
  • for diversification, all kinds of things going on: (1) simple relation with historical effect in Codium, (2) role of evolvability in Halimeda and Dictyota, (3) I think the evolvability aspect may emerge as a general pattern as more taxa are studied
  • reach out => (1) better models can be designed, (2) evolutionary dimension is applicable to any problem that any biologist is working on

Slide 45

  • these folks did the hard work

Slide 46

  • funding agencies
  • collaborators and collectors => due to the dense sampling that we need, lots of samples are required, and we could not do what we do if it wasn’t for all these people volunteering their time
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I’ve just posted a presentation I gave at the Evolutionary Potential in Marine Populations at the AWI station in Sylt to SlideShare. The notes that go with the slides follow below.

 

Slide 1

  • different talk than most in this workshop
  • deeper back in time, coarser picture
  • many species and overall patterns

Slide 2

  • these folks did the hard work

Slide 3

  • title says adaptation to environmental change => focus is on temperature
  • this is how sea surface temperature evolved during the Cenozoic

Slide 4

  • instead of using fossils, our goal was to see if similar conclusions could be achieved using phylogenies
  • starting from phylogeny and values for sea surface temperature affinities at tips

Slide 5

  • inference about past using models of evolutionary change
  • this way we can study how evolution of thermal affinities relate to figure below
  • since the phylogeny includes speciation events (bifurcations) we can relate niche evolution to diversification

Slide 6

  • main goal is exploration of techniques
  • these are the specific questions we set out to answer

Slide 7

  • our two model systems

Slide 8

  • first question

Slide 9

  • evolutionary change in continuous character usually modeled using simple diffusion model
  • graph => several simulations under same rate
  • parameter => rate of change => sigma^2

Slide 10

  • bigger sigma^2
  • optimize the model => rate of change is quantified (estimated)

Slide 11

  • to answer question whether niches evolve faster when climate is changing
  • we subdivided the tree into upward, downward and stable trends in SST
  • optimize diffusion model with 3 different rates
  • how does sigma^2 compare between conditions

Slide 12

  • big difference between sigma^2 of stable vs the other two
  • more evolution in warming and cooling periods => looks promising
  • model is a substantially better fit than the null model with only one identical rate for the regimes
  • how accurate are these estimates => don’t know => simulations being done to find out

Slide 13

  • Codium is very different story
  • likelihood surface as flat as a pancake
  • not enough information to solve the parameter optimization problem

Slide 14

  • next question => adaptation

Slide 15

  • model derived from diffusion model
  • selection in addition to diffusion
  • rate of diffusion sigma^2
  • selective force (measured by alpha) towards an optimum value (in our case temperature optimum)

Slide 16

  • we’re going to try and find out whether optimum theta differs between warming, stable and cooling
  • sigma squared and alpha are kept constant at their ML estimates

Slide 17

  • model with selection does a better job at explaining evolution of SST preferences in both cases
  • Dictyota => very strange result => higher optimum for cooling periods than for warming periods
  • potential reasons: (1) flat likelihood surface with slightly better fit for this, (2) shaky molecular clock
  • Codium did optimize nicely this time
  • somewhat more reasonable order of values although 120º for stable condition is problematic

Slide 18

  • does the profile predict the adaptation optimum at a fine scale?
  • does this predict the pattern of SST evolution better than models in which there is no such association?

Slide 19

  • new procedure that permits testing these sorts of questions
  • skip the details (1) it is based on the same type of model as before, (2) not all parameters were automatically optimized, (3) SST optimum was varied through time following profile
  • I’ve been having some unanticipated problems with the matrix calculations involved in the optimization => work in progress

Slide 20

  • last question => are speciation-extinction dynamics influenced by niche evolution

Slide 21

  • work stems from my interest in diversity patterns
  • typical diversity patterns: well-characterized LDG
  • many possible explanations => focus here is on species turnover and how rates of diversification relate to the niche

Slide 22

  • seaweeds don’t follow general rules => bimodal diversity pattern
  • do same evolutionary processes hold or is diversification faster in temperate habitats?

Slide 23

  • Codium is suitable case study with similar diversity map

Slide 24

  • evolution of SST affinities traced along phylogeny
  • clade 3: almost half of all species in young clade, only 25 Ma
  • seems to be associated with move from temperate into tropics
  • logical question: is diversification faster in tropics

Slide 25

  • model of diversification dynamics in which diversification is function of SST

Slide 26

  • optimum value of beta => positive association between SST and diversification
  • higher rates in tropics
  • so process seems similar to other organisms and reasons for bimodal diversity pattern has to be sought elsewhere

Slide 27

  • that’s what we found for Codium

Slide 28

  • no such thing for Dictyota => constant diversification explains it better

Slide 29

  • previous test only checked for very simple relationship between SST and diversification
  • many other types of relationships you could imagine
  • for example one could expect that clades whose niches are more evolvable manage to diversify more rapidly
  • we do seem to find that in Dictyota
  • split phylogeny up in major clades
  • positive relationship between rate of SST evolution and diversification

Slide 30

  • slope very deviant from that simulated under null model

Slide 31

  • lineages with many allopatric sister species along latitudinal thermal gradient diversify more rapidly
  • we seem to have a situation where clades that some clades manage to speciate more often along the latitudinal thermal gradient than others
  • clades that do, diversify more rapidly, probably because their presence in both temperate and more tropical habitats permits further radiation in those habitats

Slide 32

  • there are definitely caveats to the approach proposed here

Slide 33

  • overview of some caveats

Slide 34

  • for me, three conclusions emerge from these experiments
  • results are very taxon specific => very little generality in what we find
  • lots of uncertainties and sometimes simply not enough data to even get the models to optimize => these techniques can be a piece of the puzzle but with them alone we’re never going to get a fly-on-the-wall perspective of what happened during evolutionary history
  • it’s going to take a lot of intimate face-to-face time with my computer to get a better understanding of how far we can take these methods

I’ve just uploaded new versions of Maxent Model Surveyor and MatrixGradients to my website.

Two minor changes have been introduced in version 1.07 of Maxent Model Surveyor. First, users can now specify the amount of memory that Maxent can use with the -jm flag. Second, I’ve updated the parser of the Maxent options file, in which Maxent flags can be specified. The parser now prints out a warning if the user tries to change options for which MMS doesn’t allow user control. In addition, it will terminate the program if the user attempts to manually toggle a predictor or a species. More information is provided on the website about what to do if you want to exclude predictors a priori and how to specify flags in the Maxent options file (I’ve included an example file). Thanks to Mark Andersen for bringing these issues to my attention.

MatrixGradients is a perl script that draws colored matrices in which the colors correspond to the values in the matrix. It is now in version 1.02, which includes the option to transform values in the matrix to be plotted. This is useful if many values in the matrix are close to the maximum or minimum value and you want to exaggerate the color differences in that part of the values range. This is illustrated below for a matrix in which many values are close to zero, but with a few values that are considerably higher (up to 22.4). If plotted without transformation (left panel), the entire matrix is green, with just one red value, i.e. not very informative. If a log10 transformation is applied to the same matrix, a much clearer picture of what happens in the near-zero values emerges (right panel) simply because the color gradient is compressed near zero. The new version can also print the values in the matrix as shown in the figure.

MatrixGradients transformation