Thursday, October 16, 2014

Evolution of monarch butterflies

A quick note on a new paper in Nature on the evolution of monarch butterflies. 

The authors (Zhan et al.) examine genomes of 101 genomes from the Danaus genus. 

First, basic ignorance. I had no idea there were so many populations of monarchs around the world. That was nice to know.

Second, the ability of genomic research to identify the specific genes that were the basis of selection is really astounding. As someone who measures a lot of plant traits, to dive into the genomes of so many populations and species to identify traits that define species is pretty special. 

With the genomic work, they really are identifying traits that we didn't know exist at the organismal level. 

For example, the authors identify selection on a collagen gene that affects flight muscle function. 

That's not easy to identify empirically. 

In all, I'll admit I'm jealous of what the authors could put together on the monarchs and related species. Biogeography, evolution, and function all wrapped up into one paper redefining our understanding of monarch butterflies.

I'm royally jealous. 

Friday, October 10, 2014

How large a bison herd?

The idea of the buffalo commons provoked many people to think in the late 80's and early 90's. With the commons, a large herd of bison--maybe millions--would roam the open expanses of the West.

Today, bison reintroductions continue, but most of the herds are small. Maybe a few hundred. By comparison, the largest public herd--Yellowstone--is roughly at 4000 animals.

So, realistically, how much larger could we get? How big a herd is possible?

There are a few constraints on figuring out how large a bison herd is realistic.

If you don't cull the bison, then you have to rely on predation. Unfortunately, wolves just are not a significant check on bison population. Yellowstone National Park, which has the most active wolf packs interacting with bison, still relies on culling animals when they leave the park to hit their target population size, which is actually about 1000 animals less than what are out there. Wolves don't keep them in check.

If predation isn't a check, then the upper limit becomes food and/or disease. This is an effective regulator, but that means periodic mass starvation and/or disease epidemics. 

I'm not sure people in North America have the stomach for that yet. 

Even Oostvaardersplassen hasn't quite made it to that level of hands off.

In reality, periodic culling is going to be necessary to manage a large bison herd.

If so, how big a herd is realistic?

Assuming that land area is not a limitation, a couple key numbers here to work off of.

First, is the intrinsic growth rate of a bison herd. This is going to vary, but a 25% growth rate is reasonable for most herds.**

**This is going to vary with sex ratios and other factors, but it's a good start.

Second, is how many animals a work crew could process. Bison have to be rounded up, worked individually, and then sorted. Some of those animals go back to the herd. Some are sorted off to go to market.

In general, a single crew can work about a bison a minute. 400 bison in a day is a good estimate of how many bison can be worked in a day. That translates to 2000 bison in a week. If you dedicate a month to working animals, then that would be approximately 8000 bison.

With a growth rate of 25% and 8000 bison that you can work in a month, that means a winter herd size of 6400 and culling off of 1600 animals.

So, if you dedicate one work crew and corral system for one month to processing animals, then your maximum herd size is 8000.

8000 animals in a corral at one time, is not a small corral. And it would take a lot of hay to keep them fed while they are being processed.

What if we relax the assumption that some animals are returned?

What if just the first 8000 get shipped off?

This would mean calves, yearlings, males, females. Whoever is caught in the "net" goes.

If you remove the assumption that 75% of the animals are returned to the herd, then roughly that would let you have a herd size of about 32,000 animals. This would roughly be stable if every year 8000 animals are shipped off and growth rate is 25%.

Assume natural mortality regardless of how ugly: no limit on herd size.
Assume you don't have to round up animals, but could just shoot them in place: no limit as long as you feel comfortable shooting thousands of animals.
Assume have to round up with one crew for a month, but don't sort the animals: 32,000.
Assume have to round up with on crew for a month, but do sort the animals: 8,000.

Can you add corrals, or sort longer than one month? Yes, but there is no precedent for this.

What about field harvests? With field harvests, animals are often shot in the field and processed in trailers on-site. Yet, the typical rate for a crew is 8 animals per day. Over a 6 month period, that's still just a 1000 animals per day. Harvesting bison sustainably this way would never permit a herd size of more than a few thousand at best.

So what are the likely prospects for a bison megaherd?

Assuming you can get the land, it's going to be hard to have more than 8000 animals in a herd.

So, how big an area is that? Depending where you are in the world, it might be about 100,000 - 200,000 ha (40-80k ha). Put in perspective, that's a square about 10-20 miles on a side.

That's really nothing. Maybe $20-$100 million to buy the land for that (depending on a lot).

Wednesday, September 17, 2014

What does a grazed grassland look like?

Panorama of the trap pasture in Broken Kettle, IA

Over the past few days, I had a chance to visit some great prairies to do some work on bison.

The first was Broken Kettle in Iowa. Owned by The Nature Conservancy, it's the largest intact native tallgrass prairie in Iowa.

The second was Ordway Prairie in North Dakota. Also owned the The Nature Conservancy, it's unofficial claim to fame is having some of the largest bison in the US.

Each prairie is grazed, but they have different histories and current management.

While at each one, we talked about what grazed grasslands looked like and what to expect. For the managers, they need to try to fill conservation goals for bison, but also for birds that require habitats with different amounts of grass as well as promoting plant diversity.

A simple question of how many bison to stock becomes a complex analysis of examining the prairies.

So part of the what we talked about at each site was whether there was enough grazing, or too much.

One of the interesting features of the grazed areas at each site was how many forbs there were and at what density.

At Broken Kettle, a recently burned area looked like this:

When you look closely, the grasses are grazed down to golf course green height. Forbs are rare, but large. It reminded me of some grasslands in England and Scotland, except with Solidago instead of Cirsium.

The plant community at Broken Kettle in many spots is still recovering from aerial spraying of herbicides so one might not expect to have a broad distribution and diversity of forbs. 

In contrast, Ordway Prairie seems to be grazed less intensively (at least this year). It's hard to find places that were grazed hard. 

A lot of the grass seemed to be smooth brome (Bromus inermis). When you do find areas with forbs, it doesn't look the same as what was at Broken Kettle. The grasses aren't grazed down as hard and the forbs often seem crowded.

In all, there is still debate about what grazed grasslands look like. How much grass (and what species) should there be for sustainable grazing? How many forbs to expect?

It's a complex question, and I'm glossing over a lot.

Still, there's a lot of basic ecology left to work out about grasslands. A lot of people have different opinions, which are colored by their local site.

At the very least, I'd really like to see a coffee table book of just photos of grazed grasslands. Just seeing the diversity of grasslands out there would be an eye opener.**

Thursday, September 11, 2014

Short thought: funny line

"Amidst the whirlwind of molecular biological discovery it often seems overlooked that important metabolic processes are ultimately constrained not by biochemical pathways, but rather by the physics of plant structure."

Brodribb, T. J. 2009. Xylem hydraulic physiology: The functional backbone of terrestrial plant productivity. Plant Science 177:245-251.

Roots, water, and really tall grasses

Photobombing mom in front of some really tall grasses in Montpellier. 

Grasses are often synonymous with turf. Short plants that we can walk on.

But some grasses can grow to half the height of a redwood--50 m in height.

The physiological limits of tall height are often thought to reside in how a plant constructs its stems or leaves. Roots are important too, but mostly from an engineering perspective. They have to make sure the plant doesn't fall over. 

Turns out there is another role for roots that is unique to tall plants. They have push water up to the top.

Usually, when we think of roots and water, the soil-plant-water continuum concept of water movement has roots as semi-passive straws. Their job is to come in contact with water so it can be sucked up to leaves through the xylem.

But when water in the xylem is under tension it can embolize, producing an air gap in the rope of water that extends from the soil to the leaves. The consequence? Water ceases to flow.

Poke a hole in a straw and try to suck soda, if you want to test this out.

What's a plant to do once xylem embolizes? 

One approach is to grow new xylem and sacrifice the old. A lot of trees do this. 

Grasses can't do this, so they need to dissolve the embolism. Like squeezing a bottle of soda to get the bubbles to go back in, this takes pressure. 

How do some plants do this? Apparently, they close their stomata at night and let the roots start to pump up the pressure. 

Because of the gravitational forces at work, a short plant doesn't require much force to pressurize the entire shoot. A tall plant requires more.

Showing this had never been done before, but Cao et al (2012)** tested this with bamboos. 

**I'm apparently a few years slow in realizing how neat this paper is.

Turns out tall plants produced more root pressure at night than short plants. 

The work raises some interesting questions about the evolution of plants in general. 

Can short grasses produce as much pressure as tall plants, but just don't? It takes energy to produce pressure, but there might also be adaptations that coordinate root and shoot function. 

Also, for bamboos with stems, the point of growth is elevated off the ground. They don't grow from basal meristems. For cells to expand at the top of the plant, positive pressure is required. So, the root pressure should serve dual functions. 

Also, since we tend to think of xylem as under tension, we worry about air leaking into xylem. But, xylem can also be under positive pressure. Are there unique adaptations to making sure that water doesn't leak out of xylem at the wrong place? Hydraulic lift is thought to be passive based on the relative negative water potentials of plants and soils, but when roots are pressurizing the whole system, can't that force water out of some roots? 

None of this information is going to help create grasses that don't have to be mowed as often, but it sheds serious light into the evolution of height in plants (even grasses).

Cao, K. F., S. J. Yang, Y. J. Zhang, and T. J. Brodribb. 2012. The maximum height of grasses is determined by roots. Ecology Letters 15:666-672.

Wednesday, September 10, 2014

From The Haiku of Writing a Paper: Introduction

Some people have said that I can write papers quickly. I'm not sure if that's true or not, but I have learned to write them faster than before. And part of that is having a standard structure to guide the writing process.

A long time back, I tried to crystallize what I had learned about putting together scientific papers. Mostly from making a lot of mistakes. I did it mostly just to get all the different ideas organized for myself.

The general approach was to reduce the structure of the paper down to a skeleton outline. Not quite a haiku, but close.

Apparently, the full document has been passed around a bit--I'm always surprised when people tell me they were using it.

As an example, introductions can be tricky to write. In most of my papers I try to follow the 3+1 model. With this model, you funnel from big ideas to specific points to be tested.
First Paragraph: Big question. This is the general broad reference to your work. For example, it might be that atmospheric CO2 concentrations are rising, or nitrogen is an important driver of ecosystem dynamics. 

Second Paragraph: Proximal question. Within the broader framework, the proximal question should be stated that you are directly addressing. For example, although atmospheric CO2 concentrations are rising, the controls over soil C storage are poorly known. Or although nitrogen controls ecosystem dynamic, there are important questions regarding the role of denitrification in controlling N availability. Note that a proximal question can often be framed as the big question—it’s all a matter of perspective and how you want to tell the story.

Third Paragraph:  Scope of research with hypotheses. In order to better understand the role of soil C storage in responses of ecosystem to elevated CO2, we tested whether elevated CO2 increased the C stored in the soil within soil aggregates.

The "Plus One" Paragraph: Competing hypotheses. The best introductions and research designs test between competing hypotheses. Often when there is a single hypothesis that is rejected, the authors can derive alternative explanations that don’t require the theory to be rejected. Therefore, might as well start with competing hypotheses since there are always competing hypotheses. Framing the hypothesis in the null form is not necessary when using competing hypotheses. For example, in testing the role of N in decomposition, an experiment could test whether stoichiometry predicted responses of decomposition to greater N availability. Or we can test between stoichiometry or N mining in predicting the responses of decomposition to greater N availability. No on experiment is generally able to reject a theory, so you can test between two theories and whether data supports one theory or another.

Note, I call the last paragraph the +1 paragraph, because it isn't always there in a paper--it depends on design.

Still, using this model, you should be able to write your introduction in 3 or 4 sentences. Once you have that you can expand each sentence to a paragraph. These can be expanded out more to maybe 2 paragraphs, but if you deviate too far from this, the introduction is likely running long and will be confusing to readers.

There are tricks to writing other sections efficiently and a lot of details to look after as you get through the sections.Still, once you settle in on your framework for papers, it makes writing the paper a lot more fun, since you can concentrate on the message rather than the structure.

Tuesday, September 9, 2014

Modeling water flow in soils and plants

Reading more about modeling water uptake by plants.

Like this figure from Lobet et al. 2014, so I though' I'd add it here.