Paleoecology: A long-term complicated relationship. I can't break-up, my CD's are in his truck

Sorry about the delay, I was on a bit of vacation. Not thinking about school or work in real life and the internet universe as well. I'll make it up to you though!

Now, continuing on my previous train of though.  There are many ways in which ecology gets complicated and tends not to look as pretty as the previous post shows.

Let's look at some of my MS (Master's of Science) work as a starting point.

I worked in a field called paleoecology in order to tie in aquatic species with water quality to look at pollution affects on a lake over time.  Diatoms (see Fig. 1) are a form of algae that is made up primarily of silica, and therefore fossilizes in the sediment of the lake they live in when they die. What we can do then is take a core of the lake bed. Each year a new layer of sediment is added to the bottom of a lake. We can take a core of a lake, date it using chemistry (such as Lead 210 dating) and compare what things are in each layer of the core with the associated date.  This allows us to track ecological community changes (the relative number of each species or population of diatoms in a year) through time.  NOW in addition to all that knowledge you can also run chemistry on the surface of the lake bottom (before the chemicals mix or breakdown).  You can compare the water chemistry (things like nitrogen, phosphorus, oxygen, pH, or temperature) with the species found and their relative numbers. This can tell you the preference and tolerance of these species to a given water chemistry factor. So species that have a lot of individuals fossilized at the same level as the water chemistry you tested do very well in those conditions (say high nitrogen, which remember is basically a fertilizer).  Species that are low in numbers (or not in the sample) do poorly under those conditions.  With me so far?
Fig. 1: Diatoms
Fig. 2: A core from the bottom of a lake (depth of mud at bottom)

Okay then so here's the kicker, with the relationship of species to water chemistry, you can look back at older layers of the lake sediment and count the number of species and individuals that are fossilized.  Once you know the community structure, you can use that information to estimate what the water chemistry was likely like!  You can start to understand how a lake has change over hundreds or even thousands of years!!

Now of course, is where is starts to get dirty.  Remember this is still ecology.  So what happened with me is, after 2 years (normal length of a MS program), it didn't work.  But in a way that's what made the project really interesting (and of course at the time very frustrating).  When I ran my estimates and compared them to known emission rates of nitrogen from the area they were exactly inverted! My model checked out well against expected ecological relationships (we call it r squared, or how tightly the relationship of your data is). For something more linear like chemistry or physics you would never accept and r squared value below 0.8 or so (on a scale of 0-1).  In ecology? Remember 0.4 is fantastic and numbers like 0.1 are not even unusual.  The reason is that there are many factors that effect an organism and its habitat and the variable you are testing is likely only one piece of a much larger puzzle.  That doesn't mean it's not important, it just means it's complicated and intertwined.

In my case what we think may be happening is one particular species tends to completely dominate the older sediments, and the problem it this species is a known generalist (often can do well in many different conditions and it quite good at competing with other species for a limited resource).  I proposed that the model needed to be able to ignore such species.  More in depth later.  As a result I have a very controversial paper in lieu since the model has been used for 30 years.  So it's been hard to publish.  See previous Science post for likely reasons why...



"Science is facts; just as houses are made of stones, so is science made of facts; but a pile of stones is not a house and a collection of facts is not necessarily science."  Henri Poincare

Ecology-drama and "it's complicated" written all over it

There are so many ways in which ecology becomes complicated.  The last example is a beautiful one-well studied, fairly well understood, and fairly simple.  The cichlid fish example works so beautifully because there happens to be only 2 major selection pressures driving coloration-sexual selection and water clarity.  But what if there was more to it?  What if suddenly a visual predator was introduced to both clear and murky systems?  Or what if there was increased fishing pressure?  More or less plant material?  Stark changes in diet?  Variables can add up very quickly and have enormous effects.

For example, salmon change to a beautiful bright red during breeding season in order to attract mates.  The bright the red, the more likely you are to pair up because you are PERCEIVED to be more fit.  Now a certain type of salmon called Kokanee got landlocked and now live in a lake system.  Most salmon derive their beautiful red color from their food, which contains a carotene for red coloration.  To adapt to their new environment, the Kokanee salmon improved their ability to obtain (sequester) red coloration from their food, which has much less carotene than the ocean available food of their counterparts.  Both Kokanee and "regular" salmon turn red during breeding season but if the regular salmon get into the lake system they are unable to turn red, because they cannot sequester such small amounts of carotene, and therefore are not chosen to breed, regardless of their actual fitness level.  A simple change in diet shifted mate choice based on coloration to a completely different and isolated level!  And of course, we have speciation as well much like the cichlids, which I do want to say is not necessary when these things occur.



Nothing gets this complicated variable idea across more than thinking about how to design an experiment.  For example, a study that aimed at looking at predation on small rodents by their larger, wolf and fox, predators took the home site of the rodents and fenced it off, denying access to the predatory mammals.  It is a tried and true method, good for animals or to protect plants or even insects from their known predators.  It didn't work here though, because the posts along the fence line attracted hawks and small falcons that wanted a perch, thereby increasing predation on the rodents via a predator that usually accounts for a very small amount of predation (if you're going to stop and rest why not grab a snack while you're at it?).  Oops.  So here even though we've removed the predator that based on observation and testing is the primary influence on the rodent life cycle, you see how moving one thing out of a niche (space/resource/habitat used by an animal in relations to others it shares said space with) how easy it is for something else to move into the open slot.



It is because species and their environments are so intermixed that these things happen.  There is no such thing as a food chain, only food webs.  One creature eating only one other species is the exception, not the rule.  Specializing can be good-if the source is available you become very efficient at handling and deriving nutrients from one thing.  However, the environment is shifty and even poor panda probably regrets it's monogamous relationship status with bamboo.  Moreover more than one thing will determine a species or individuals fitness-habitat, shade, food, water, nutrients, substrate, predation, etc.  Then, each of those factors is controlled by any number of additional factors, habitat for example-competition for space, degree of visibility required, predation, hunting, community of plants, nutrients, flooding, fires, access to mates, etc.  You can see how one thing rarely dictates the response of a given species.

To sum this up let's think about how this looks graphically.  You have your species and the response of said species (i.e. weight, survival, food choice, etc).  On the graph you get a huge cloud of points through which you draw a line, which represents your variable.  The line will likely trend the points with an r squared of maybe 0.1 or 0.2.  In other words, your variable can explain the response of the species about 10-20% of the time.  Seems low considering in chemistry you need above 80%.  But makes sense right?  It has to be one serious pressure to make up 80% of the life response of an individual!  Think about what controls your day to day activities?  Some things are certainly more important than others, but no one thing controls you.  Ecology sets out to find the more important things, from which we can glean the most information about that species in that environment.  Hence why the possibilities are endless!!

Stay tuned! Next week I'll talk about what I did my master's work in and how it puts a whole new twist on this complicated relationship!!



"When one admits that nothing is certain one must, I think, also admit that some things are much more nearly certain than others." Bertrand Russell

Evolution: let's get this straight people!

Being in the science field I've seen some pretty interesting misunderstandings about the theory of evolution.  Some funny and some scrape your eyes out painful.  Although the first painful argument I often hear is about evolution being a "theory", that merely stems from people not understanding scientific processes and scientific theories as they differ from your drunk roommate insisting the entire human race is partially controlled by lizard space beings called the Annunaki (this is a real CONSPIRACY theory, check it out).  However, I will delve into that in a later post.

For now I think I will take you through the basics of evolution, in a way I teach all my little youngens in my vertebrate evolution course.  As with class, feel free to ask questions, I will post answers.

Natural Selection: fundamental mechanism (process) by which evolution occurs.  It is based on the struggle for existence and organisms' competition for space and resources.  This includes migration, mutation, genetic disease, and death.  Natural selection requires 3 basic constructs to occur:

1. Variation: individuals within a population differ from each other in their traits (also referred to as phenotype or characteristics)
2. Inheritance: aforementioned traits need to have a genetic basis.  AKA I can pass my awesomeness down on to my children.  (Please note, traits for this CANNOT be acquired-e.g. picked up by the parent through the course of life-it needs to be in the DNA code.  Therefore if you adhere a horn to a horse and have that horse breed, its foals will not be born or develop horns [again, real study way back in the day, check it out])
3. Fitness: given competition and limited resources, not all individuals will have the maximum capacity to reproduce. The struggle for space, food, and survival will cause a gradient in success for mating and offspring.  Therefore, this inequality means individuals will contribute differently to the next generation (high fitness=higher contribution).

Sexual Selection: secondary mechanism that is based not on actual survival but on a potential mate's perception of your fitness.  E.g. red coloring in bird.  Being red does not make you a faster runner but indicates since you are very brightly colored and alive you're probably good at escaping predators.  This includes mate choice, coloration, size, combat, display, plumage, etc.  In some cases, sexual selection can actually work in the opposite direction of natural selection.  Certainly male peacock tail feathers do not benefit them for survival but the ladies think it's awfully sexy!


Constraint: evolutionary limits.  Evolution IS NOT progress towards a perfect organism.  Evolution is more like an engineer piecing together the best option out of some mismatched hunks.  Bear in mind that evolution (generally) occurs over a very long time, and many of the traits you see weren't developed to survive in THIS moment, they were developed THEN.  As their landscape, competition, and resources change they are constantly changing too.  But you don't get to wipe your slate clean every time, you have to use what you've got.  Pigs don't have wings, not because wings wouldn't be beneficial to a pig but because the pig's body design would certainly not support flight.

Teleology: explanations of a trait based on its PERCEIVED purpose rather than natural (mechanistic) origins.  Many non evolutionists fall into this trap, as have some scientists (everybody makes mistakes, it's what you do with them that matters, see later Science post for more on this).

Contingency: chance historic events.  These are things like catastrophes (lightning, eruptions, etc) or continental drift that may strongly impact the evolutionary path but is not based on fitness.  Sort of being in the wrong place at the wrong time kind of idea.



NOW, given the information above the way origins are traced and mapped is called PHYLOGENY.  Historically (aka before we started DNA sequencing everything) this was based on trait relationships, which in some cases were perceived since whether or not traits are similar because of function, common ancestry or common pressures is hard to tell.  You end up with two groups, or two and a half?

1. Homology: traits are similar because they are of common origin
2. Homoplasy: traits LOOK similar because two separate groups underwent similar natural selection pressures (like hopping mice in the African and American deserts-they're not related but they're traits are almost identical since there are only so many ways to deal with movement across sand!).
3. Reversals: this isn't so much a third group as much as a related issue.  Sometimes traits REVERSE or switch back to a previous evolutionary state due to a shift in selection pressures.  As you can imagine, this can really mess up how we try to order things. 

Many of these issues are starting to get worked out with DNA sequencing, where you can see and follow exact mutations and deletions in the code and follow them through time.  

Misunderstood information:

1. Missing link: there is no such thing and it wouldn't be necessary for there to be one.  Changes through evolutionary time are GRADUAL, you can tell because even today with our existing species there is an incredible amount of debate on what is a species and what is a subpopulation.  Certainly it is not any easier when you don't have the ancestor population with you as you make the comparison.  Not only is this process gradual, with small changes occurring and building up over time, but when it doesn't work the individual doesn't reproduce or they die quickly, such individuals are in low enough proportion that they don't contribute to the gene pool or the fossil record.
2. Species that are ill adapted to their system: sure, again GRADUAL.  Evolution takes time so often there is a little bit of a time lag between successful evolutionary adaptation and the landscape they are adapting too.

  

Remember, the idea is that through shifting adaptive landscapes (changes in their resources, climate, habitat, competitors, etc) exert pressure on a species.  The most successful (fit) individuals pass on their genes to the next generation (passing on awesomeness) while the less fit individuals do not (kill off lameness).  Therefore the next generation is proportionally more fit than the previous one and the pathway continues.  Sometimes there is more than one "equally" fit answer to a given problem or part of the population migrates and is presented with a new set of pressures.  This is (in part) how speciation occurs.  The success of some species over others within the same line and against sister lines is how evolution occurs.

There, now you all survived half of day 1 in my class.

"The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...' " Isaac Asimov