Showing posts with label phylogeny. Show all posts
Showing posts with label phylogeny. Show all posts

Sunday, July 3, 2011

Grasses of the World IV--Taxonomic differences


Relationships between leaf width and physiological drought potential for six genera of grass.


No one know exactly what the ancestral grass looked like or the environments it inhabited. But one could imagine a bright, open wet environment with a narrow leaved bunch grass or weakly rhizomatous grass inhabiting it.  Some tens of millions of years later the BEP and PACMAD clades would have diverged and the major radiations of grasses still a long way off. 

But what were the forces that drove the radiations. Aridity is often cited as one. Fire another. Grazers still a third. But this might be somewhat of a skewed, biased perspective, since there has been little work to characterize the modern ecology of the whole of grasses.

When we look at the global traitscape of grasses, we saw clear patterns for leaf width and drought tolerance. One can imagine some selective force favoring wide-leaved grasses and drought narrow leaved grasses, until an ecological or physiological tradeoff was reached.

But what does the pattern of radiations for individual clades look like?

If I map the distribution of 6 genera in traitspace, clear unique patterns show up. The genus Panicum, for example, has species with wide and narrow leaves, but none that are very drought tolerant. In contrast, Festuca species all have leaves that are narrow, but span the full range of drought tolerance.

We still haven't mapped all this onto a phylogenetic tree. That's coming. But the value of screening programs like this are pretty clear for understanding the ecology and evolution of grasses. 

But why the separation among genera? Are individual genera constrained physiologically, or are they constrained evolutionarily by the presence of other species that lead to the apparent differentiations. 

Part of what we still need to do is understand the importance of traits such as leaf width and understand the benefits (and constraints) of narrow and wide leaves.

Saturday, June 19, 2010

How to taxonomically structure comparisons

For a recent grant, we proposed to measure aspects of the nitrogen and water economy of 30 species at Konza. The novelty of the proposed research was in measuring both water- and N-related traits for a wide variety of species, and then test how well they explain the abundance of the species in a native grassland.

One point that came up was how to frame the research. Part of our framing was that the results should help us understand the evolution of plant strategies and selection forces on species. Reviewers seemed to disagree.

One reviewer said, “The problem here is that because of the close evolutionary relationships of many of the selected plants, traits and responses will be co-correlated through evolutionary relationship and will therefore give an inflated estimate of independence.”

Another said, “It seems to me that the work in this project will yield much in the way of an understanding of the influence of resource availability in the evolution of land plants, since gaining such insights would really require a more extensive phylogenetic and perhaps phylobiogeographic sort of approach.”

This is something I still do not understand. How many species does one have to measure to be able to infer selection pressures and evolutionary tradeoffs? Ironically, we had initially proposed to measure 100 species, but were encouraged to measured fewer species. 30 is not enough? Shouldn’t 2 well-contrasted species be sufficient to provide some inference? Most of the initial work on C4 photosynthesis compared 4 species. Granted the work is still being refined, but isn’t 30 a good start? Also, why would 30 species be enough to test ecological processes, but not evolutionary?

I think the standards here have less to do with the science, than the scientist.

The current review is immaterial—the panel summarized that “The placement of this research in evolutionary context was undeveloped but will not affect the quality and novelty of the project outcome.” Yet, the gap in our scientific process is clear in the lack of anabolic comments being paired with the catabolic ones. Experimental designs to test for evolutionary patterns seem to require I-know-it-when-I-see-it tests. Constructively, we need some resolution on standardizing designs. I’ve pushed before for a standard species set, but we also need resolution on some key questions outside of any standardized set.

If there is one question I'd like to see answered, it's "how many species need to be measured and how should they be related?"

I don't expect one answer to this, but if we are serious about wanting to understand the evolution of ecological traits, we have to make the bar visible, rather than always place it just above our leaps.


Wednesday, March 24, 2010

C4 photosynthesis and nitrogen

Comparison of foliar N concentrations among clades.

Since the beginnings of our modern understanding of C4 photosynthesis, it has been set that C4's are more efficient with water and nitrogen. Yet, there have long been unexplained patterns for C4's that didn't match the assertion of greater nitrogen use efficiency. For example, C4 grasses in the field often have lower foliar N concentrations, but also lower root N concentrations. Why would this be? If the leaves need less, shouldn't the roots get more? Also, some C3 grasses like Chionochloa can have foliar N concentrations as low as 6 mg g-1. Most C4's have higher concentrations and only a few have been observed to be below that. Also, foliar N concentrations for any given species are highly plastic and dependent on the balance between C and N supplies and demand. If a given species can have N concentrations that range 30 mg g-1, just how important is the C4 photosynthetic pathway.


Turns out, probably not much. Taylor et al. (2010) used a phylogenetically structured screening experiment to measure a number of morphological and physiological traits of grasses. In doing so, they could compare C3 and C4 species controlling for phylogeny. The research upholds the notion that C4 photosynthesis confers greater water use efficiency to plants. Yet, after controlling for phylogenetic relationships, there were no differences between C3 and C4 species in their foliar nitrogen concentrations. 


By no means the last word on the topic. For example, they only measured ~30 species. Yet, the authors have provided the best experiment to date to address the question and evidence to the contrary will have to be weighed against some strong evidence regarding the ecological consequences of the evolution of C4 photosynthesis.


Taylor, S. H., S. P. Hulme, M. Rees, B. S. Ripley, F. I. Woodward, and C. P. Osborne. Ecophysiological traits in C-3 and C-4 grasses: a phylogenetically controlled screening experiment. New Phytologist 185:780-791.

Saturday, February 27, 2010

Do I have to phylogenetically correct my grocery list?

The figure of Westoby et al. (1995) that summarizes their view of the tension between phylogeny and ecology in understanding trait relationships.

For some, a simple grocery list can pose a dilemma. Just yesterday, I went to the store with 21 items to buy. Others would look at my list and suggest I only bought 11 items. Fresh peas and frozen peas shouldn't really be counted as different items--they were both peas. Cauliflower, broccoli, and collard greens are the same species. Mustard part of the same genus as the previous three. Hot dogs and pork chops both from pigs (I hope). So although 21 items went into the cart, one could phylogenetically correct my list and arrive at the conclusion that I only bought 11 unique items.

It might seem silly to phylogenetically correct one's grocery list, but how to consider both phylogenetic and ecological data when examining species relationships lays bare the same fundamental tension as describing my last trip to the grocer.

In 1995, Westoby, Leishman, and Lord published a forum piece, “On misinterpreting the 'phylogenetic correction'”. The genesis for the forum piece came during the review process of a paper on seed mass in plants. Most likely, during the review of that paper, differences in opinions between reviewers and authors were laid bare. In the original paper, the authors showed that tall plants had large seeds. The reviewers likely insisted that the relationships between plant height and seed size could be due to phylogenetic relationship. The authors disagreed. Differences in opinions became forums, which by ecology standards unleashed a bit of a storm.

The questions associated with the topic of how to match ecological and phylogenetic data are ripe, but “phylogenetic correction” essentially adjusts relationships by weighting closely related species less than distantly related species. The fundamental differences of opinion pin whether closely related species hold similar traits because of phylogenetic constraint or ecological constraint. Closely related species might have similar traits because there has been little time for radiation, or because they are under similar ecological selection pressure. Distantly related species might have different traits because initial trait differences have long been conserved due to fundamental difficulties associated with character displacement or because they have been under the same ecological pressures for a long time.

The issues of how to identify adaptations or evolutionarily beneficial relationships cannot be covered here, but these fundamental issues have never been resolved, near as I can tell. The current détente that seems to exist is to examine ahistorical and “phylogenetically corrected” relationships among traits and hope that the patterns are the same. When setting to test relationships among species, choose congeneric species pairs from distantly related genera and hope the patterns work out consistently.

It’s currently an uneasy impasse. Both sides recognize that correlation does not necessarily imply causation. But outside of hoping that the evolutionary and ecological patterns parallel, there is still no resolution to the question of how to compare the traits of species.

I do know that if I want to shrink my grocery list, I'll start by not buying both cauliflower and broccoli rather than phylogenetically downweighting closely related taxa on my list.

Saturday, February 13, 2010

Phylogenetic correctness

It is axiomatic to state that grasslands are dominated by grasses. It is also axiomatic to state that the trait that allows grasses to dominate grasslands is an adaptation to the grassland environment. The identities of the traits are currently unclear. For example, meristem position used to be the oft-cited reason for grass dominance, despite the clear evidence of many less abundant eudicots with similar meristem position. Yet, whenever we discover what the trait is that separates grasses from other species and allows them to dominate grasslands, we will never be able to declare that trait an adaptation. Such is that state of phylogenetic correctness.

There are many important traits that arose only once. True wood, angiosperm xylem vessels, and Rubisco likely only evolved once and cannot be separated from phylogenetic origins. The conditions and the complexity of the trait did not lead to multiple origins, but instead served as the basis of radiations. Any trait that sits at the base of a tree cannot officially be considered an adaptation. Even if a trait had arisen twice, there would be no statistical basis for calling something an adaptation since it cannot be separated from phylogeny.

What are we left with then? We can apply phylogenetic corrections to account for relatedness when examining trait relationships, and it provides useful knowledge. But to what ultimate point if phylogenetic corrections will not ultimately rule out or in something as an adaptation.

It's currently a silent sticky point in our considerations of the evolution and ecology of plants. One to which I don't have a complete answer, but one of which would be helpful to have clearer consideration. In the end, we will likely determine how grasses differ from other species and why they come to dominate what we call grasslands. And when we do, it'd be nice to be able to recognize the adaptations of grasses for what they are.