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taxonomy

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

I just came across a very interesting opinion paper titled “No name, no game” published in the European Journal of Taxonomy.

The paper was written by Yves Samyn of the “Belgian National Focal Point to the Global Taxonomy Initiative” (I think we all agree they need an acronym) and Olivier De Clerck of Ghent University. I’ve known Yves since we were both on a field trip in KwaZulu-Natal (South Africa) many years ago, and Oli is a great colleague and friend who I’ve worked with very closely for over ten years.

They argue that, in contrast to what Joppa et al. (2011) claim, today’s taxonomic workforce is not sufficiently large to describe the remaining pool of missing species within a reasonable amount of time. This is in the first place because much larger numbers of species remain to be described for many understudied taxa than for the well-studied groups of organisms that Joppa et al. (2011) included in their analysis. In addition, the massive numbers of unnamed species in the Genbank and BoLD databases suggest that there is another layer of undiscovered diversity remaining to be characterized (coined “dark taxa” by Rod Page). This is certainly relevant for algae as these unnamed species (e.g. “Rhodymenia sp. 1SA“) are discovered en masse when DNA barcodes are generated and “dark algal species” are accumulating rapidly in Genbank (see figure below; >75% dark taxa in the three main algal groups in 2011). The great majority of these discovered species remain without a proper name because formally describing them is much more laborious than discovering them.

algal dark taxa

Yves and Oli argue that this widening gap between the number of discovered and described species is problematic, focusing their argument on the fact that these newly discovered species do not have names. They argue that scientific names matter for society, for example because legislation (e.g. CITES) uses species names as currency.

While I agree with most of the paper, in particular the part about promoting an increasing role for developing countries in characterizing their biodiversity, I think that Yves and Oli fail to make a convincing case for their “no name, no game” statement. In my opinion, traditional binomials are not needed for legislation to work or for scientists and non-specialists to communicate about species. When the bird flu hit, the specialist as well as the greater audience knew and understood what H5N1 was. Just like professional and amateur astronomers have no trouble communicating about “55 Cancri e”. What would make biologists different? All one needs to communicate about a species is some sort of identifier, not necessarily a formally described species binomial.

When it comes to legislation and conservation, I agree that it is important to be able to pinpoint exactly what is being conserved. But once again, does it need a binomial? Not having to go through the process of describing a newly discovered species would permit that species to be conserved more rapidly. Furthermore, for legislative purposes, diagnosability of the species should be more important than the name of the species. And at least for algae, where DNA data have become the gold standard for species delimitation, DNA sequences are rapidly becoming much more reliable for species identification than morphological keys to named species. While the DNA vs. morphology contraposition should not play a major role in this discussion, it is relevant because the great majority of dark taxa are discovered through DNA sequencing and can future collections can easily be identified as the dark taxon in question with a DNA barcode. In other words, DNA sequencing has changed the game, and because of that I think we should think more along the lines of “no name, new game” instead of “no name, no game”.

Once again, I agree with what Yves and Oli wrote about the taxonomic workforce not being large enough to describe the remaining pool of species in understudied groups within a reasonable timeframe using traditional procedures. As do I agree with most other points made in the paper. But do we really need formal species binomials for all newly discovered taxa? Are there arguments that support the “no name, no game” statement that I have overlooked here? Or arguments in favor of the “no name, new game” alternative that I have not mentioned? I welcome your ideas in the comments.