Speciation: What the and the why hows??

Speciation (process of species forming) seems simple enough on the surface.  Over time adaptation and evolution drive a divergence between two populations.  Let's take a population of birds.  The population splits as it colonizes around a large mountain range.  As each subset of the original population colonizes farther and farther around the mountain range, each subset is undergoing natural and sexual selection pressures.  Of course, these pressures are not the same on both sides of the mountain, you have different light, weather, environment, predators, nesting sites, etc. When the two subsets reach the other end of the mountain range and re-converge they no longer recognize each other as of the same species.  They choose different nest sites and even sing slightly different songs.  They are both different from each other and from the original source population.  This particular mechanism is referred to as "ring species."  The image below shows why.

As a side, when looking for an image to help show this I found a lot of creationism websites that use ring species and speciation as reason to show evolution does not exist.  They cite that such species are not stead fast and singular and thereby are not showing evolutionary process.  To this I say, by being fluctuating and changing they certainly aren't showing that they were put on this Earth in their perfect form then are they?  Ecology and evolution are messy, that's why they're so interesting.  If anyone actually knew the straight answer to everything, they'd get paid a lot more.

Now that aside, that issue of fluctuating species is the major point I actually want to talk about.  Apparently unbeknownst to our extreme creationist friends, it is not necessarily speciation that does the fluctuating, it is the way in which we define it.  Our example above shows speciation, up to three species total in the end.  The problem arises when we try to draw lines.  What about all of the colonies in the middle?  They're a little bit of everybody and would probably breed with more than one group.  What are they?  Hybrids may be the answer.  Mixes between two populations.  But that leads to all sorts of problems.  Let's take a step back first and look at why defining species is so hard in the first place.  Don't worry, we'll get back to this later.

Two guys named Coyne and Orr took time in their 2004 book on Speciation to figure out just how many different ways we had to identify species. Nine. Nine MAJOR ways with sub groups among them.  These range from change of habitat, to reproductive isolation, to genetic change, to biochemical effects and so on.  Now firstly I'd like to dispel the "genetics is the answer to all" idea.  I more than understand and respect using genetic code changes, especially since genetics of course is one of the necessary basic constructs for evolution to occur.  But bear with me and follow me through an example.

When I took my Phycology course (study of algae) I was confronted with a interesting and (at the time) frustrating situation.  We were in lab learning to identify different species of algae.  I was identifying one using the standard dichotomous key.  For those of you who are unfamiliar, a dichotomous key takes characteristics for a given specimen and splits them into 2 groups-Spines are present or absent.  You follow the pathway for your given sample and if you play your cards right you use these split characteristics to arrive at the proper identification.  See below for a very general example.


Now, when I had reached the end of the road I had two choices that led to two related but separate species.  The way to tell the difference was by color.  More specifically, I had to decide whether my specimen was "dark lime green" or "apple green".  Ooookay, so I was stumped, thinking what is the actual difference between these colors (since my 64 crayons box was at home) and was it distinct enough for the average person to get right, even with the correct illumination.  So I brought my professor, here on the Triggerfish, over and explained.  Hand on my heart, the conversation went thusly.  Triggerfish quickly told me the answer.  I was surprised and asked how it could tell.  Triggerfish responded that it just knew.  I asked if the coloration was useful, it replied no, there was almost no way to make a correct assessment based on that.  (Okay, so for you following along by in large these two species look the same).  When I asked how it knew, Triggerfish replied that it knew the genetic coding for the species in the area (Okay so the genes were different).  I then asked in the two species had any ecological differences, looking for habitat choice, temperature tolerance, nutrient requirements.  The answer? No. Bluntly.  (So functionally these species were identical).  Then angry Triggerfish walked away.  I promise you will hear about Triggerfish again, it was a particular thorn in my side and the side of my other grad student counterparts.  Facebook page dedication and all (of course not under Triggerfish, combined with a terminator spoof if I recall).  I'll discuss this in my teaching posts as well, "I just know" and "try harder" are things you never tell a student.



Anyway, I digress, my point is these two algae were separated into different species groups because they were genetically distinct somewhere in their lines of code.  This to this day seems completely pointless to me, different shades of green and a little obscene if you will.  Moreover it shows that what seems to be the most straightforward way of assigning species isn't any more irrefutable than some of the others.  There's always a dance of where to draw the line, and people will argue violently on where to draw the line.

Next time we'll hit on other popular ways to define species and where those have pitfalls as well.

Don't forget, questions or comments are welcome!


"In science the credit goes to the man who convinces the world, not the man to whom the idea first occurs."
Sir Francis Darwin

Ecology: complicated and delicious, just like your ex's facebook status

Ecology was truly love at first sight.  Now I'm not normally one for complicated relationships, but something about ecology has always made my toes tingle. Ecology is the study of the relationship of species and their environment. Like all relationships, this one is dirty, convoluted, and complicated.  Like a good relationship though, I can also be very rewarding and exciting.  Upfront the idea of ecology may seem very simple. You take a species and see how it responds or affects its habitat.  And it's insanely relevant, answers to those questions can help inform conservation, forestry, zoos, climate change, habitat management, zoning, invasion, biological control, and so on.  You also end up incredibly well rounded, using mathematics theory, statistics, experimentation, laboratory control, cross departmental collaboration, biology, physics, chemistry, aquatics, animal behavior, and evolution. Okay, so now you can see how this can get so complicated.

My bio stats professor once said that ecology will always be a strong career because there's never any way to answer everything about even one question. Realistically, the possibilities are endless.  You could have 9 hypotheses to test and none of them be the correct theory.  Moreover, ecology is almost never controlled by one variable. Let's look at the situation that originally got me interested in ecology my junior year in college as a simple starting point.

I still have the original article, I never got rid of it.  It's a 1997 article in Science (one of the top 2 science journals in the world, likely only second to it's London counterpart, Nature).  "Cichlid Fish Diversity Threatened by Eutrophication That Curbs Sexual Selection."  Okay, let's look at this concept bit by bit.

1. The species: Cichlid fish are found in many places in the world, although warm water.  They are well studied for their species divergence by population.  In other words, often when a population of cichlids becomes isolated in a lake or water way they specialized and diverge.  If they are reintroduced to the population they come from (the source) there will no longer be any breeding between the populations.  
2. Eutrophication: In aquatics, the water quality and clarity is often generalized into 3 majors groups
1. Oligotrophic: clear crystal water with little algal blooming or fertilizer
2. Mesotrophic: moderate clarity with some algal blooms likely giving the water a hue of blue or green for parts of the year
3. Eutrophic: murky, dark water with little clarity and high algal blooms giving the shoreline a very green color. SO when we say "eutrophication" we mean a lake that is moving (or being pushed) towards poor water clarity and quality.  In this case reducing vision within the water column. 
3. Sexual selection: Alright so this term should be more familiar since we talked about it in my evolution post.  Specifically here it is important to know that females choose their male mates based on color and color brightness.  So there is selection pressure on the males to be a certain color and to be a very bright variant of that color.  Think about how this would be different if there were a predator? 
4. So the kicker with this research is that over time, as the lake becomes more euthrophic and more murky, the females have less ability to visually choose their males and often do so indiscriminately.  They breed across the lines of sub species as well, no longer able to choose by color.  As a result, there is no benefit for the male to invest a lot of energy in being colorful so there is a reversal (another term you know!) to being dull fish.  The males and females were becoming dull grey in color and the populations were almost completely intermixed again as a result!!!

Alright, I will continue to talk about ecology next week and how it becomes more complicated.  If you have any questions so far, let me know!

"Science is one thing, wisdom is another. Science is an edged tool, with which men play like children, and cut their own fingers." Sir Arthur Eddington

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