Friday, September 30, 2016

How We're Related to Other Four Legged Vertebrates

I'm doing battle with common misconceptions in biology, a lot of which we were all taught in school and people still being taught in school.  I'm not exactly sure the level of importance of this one but I think I can handle it fairly quickly.  As always, please correct any misconceptions or feel free to argue with me in the comments.

There is a common misconception, or rather a set of misconceptions, around the relationship of the groups in Tetropoda.  Tetropoda, or the tetropods, are amphibians, mammals, reptiles (really non-avian reptiles) and birds (which are reptiles, technically).  These are the major groups that are still around today.  When you look at a lot of cladograms for these groups they look something like this:
image by me, click to embiggen
What the cladogram actually looks like is something more like this:
image by me, click to embiggen
This is a minor difference, but it's an important one and there are several misconceptions that are portrayed by the first one.  First, and I've glibly added an explosion to humans at the crown in the first one to reinforce this, it portrays evolutionary time as always going from "less advanced" to "more advanced" with us humans at the very peak of...advanced-ness.  Evolution is not a movement towards more advanced.  Natural selection doesn't have any conceptions about what is more or less advanced, only what organisms are best at getting their genes to keep going.  Just check out the bacteria.  They're the polar opposite of what most would probably call "advanced" but they're darn good at making their genes survive for billions of years (and yes, a Domain is very different from these much smaller clades).  

Second, and I may be projecting here, but I think this also portrays the misconception that amphibians "evolved into" reptiles and then reptiles "evolved into" mammals.  But if that were true, wouldn't there only be mammals?  If reptiles evolved into mammals, why are there still reptiles?  

Partly because mammals did not evolve from reptiles, rather the two groups share a common ancestor.  Millions of years ago there was a population of animals that weren't mammals or reptiles.  As this population evolved it diverged into (at least) two distinct groups.  One is what we today call mammals and the other is what we call reptiles and birds.  You'll sometimes hear people use the term "mammal-like reptiles."  There's no such thing.  There are animals that came before the common ancestor of reptiles and mammals which are neither and there are animals after that common ancestor which are one or the other (sort of, this is a bit of a simplification).  There's a group of animals called Synapsids, which mammals are a part of, and early Synapsids didn't really look or behave much like modern mammals and maybe they were kind of reptile-ish (in that they were tetropods that weren't amphibians) so we've gotten stuck in the habit of calling those animals "mammal-like reptiles" even though they're really a lot more mammal than reptile.  

Third, this also may portray the misconception that reptiles have been around longer than mammals.  So again, it gets a bit complicated, but the two lineages that have led to what we currently call "mammals" and "reptiles" have actually existed for exactly the same amount of time.  That's because they share a common ancestor, they diverged from the same population of animals millions of years ago.  So what we might recognize as a "modern mammal" didn't appear until much later, these two clades have existed alongside one another since they both evolved from a common population.  

Let me know what I got wrong, what's confusing and what you're disagree with.  This was actually a bit harder to write than I thought and I hope that my simplifications make this understandable and fairly accurate.   

Friday, September 23, 2016


I recently finished the book Unseen City by Nathanael Johnson and rather than write a formal review (the upshot is that if you're knowledgeable about natural history, especially urban natural history you likely won't learn a ton but it's a good read, I would recommend it) I wanted to address a specific few sentences in the book about invasive species.  Johnson writes: "Immigrant species often do reduce native populations, sometimes significantly.  But the ecologist Mark Davis has pointed out that they rarely cause extinctions, and when they do it's of populations in isolated habitats like lakes or islands.  All this mixing may yield more biodiversity by producing more combinations, hybridization, and new species."  And in the book's conclusion: "These invasive species are not nature's destroyers, but rather its creators.  They begin setting up food webs, they evolve and diverge into new species."

While it's true that you can find examples, as Johnson sites, of stories where invasions are followed by an increased biodiversity I found it odd that he brings up this incredibly complex issue but only writes a little more than two sentences about it.  One of the big issues here is that we don't all agree on what an invasive species actually is.  I'll illustrate with three marine invertebrates that have been introduced to New England through human activity.  

One: Hemigrapsus sanguineus, the asian shore crab.  Introduced in 1988, this crab is considered a significant concern to local ecosystems primarily due to its voracious feeding.  This has two major impacts, one, it can easily out-compete local species like Cancer irroratus and borealis, two, it specifically has been correlated with a decline in juvenile lobsters (presumably it eats the post-larvals).

Two:  Carcinus maenas, the green crab.  Introduced in the early 1800s this larger crab species purportedly has an "insatiable" appetite and, unfortunately for us, seems to like many of the same animals we like such as clams and mussels.  It's also theorized that it may be contributing to salt marsh decline.  Which, I will point out right now, we think is bad.  I could ramble all day about salt marshes but the two highlights are that they are more productive than rain forests and sequester more CO2 than rain forests (which is why we should have been learning about them growing up in the 80s).

Three: Littorina littorea, the common periwinkle.  We have no idea when the common peri got to New England, and it could have been as long ago as circa 1000 AD when Vikings first came to North America.

Here's the rub: almost no one considers L. littorea an invasive.  Indeed, a NY Times article describing the research of Prof. Mark Bertness who has done some of the most robust work on the impact of periwinkles on New England coasts as far as I can tell, describes them as a keystone species.  You might call that the opposite of invasive.

And yet, when you put the present day ecological data on how periwinkles feed together with historic maps that show where there used to be salt marsh it seems very likely that periwinkles ate through a huge amount of algae and reduced much of that historic marsh to rocky shore.  And remember, we agreed above that salt marshes are good.

What's the difference between these three species?  Time.  There are a couple ways an invasive can be defined as such.  It's always non-native but to be invasive it's generally agreed that it has to have some negative impact on ecosystems and/or the economy.  For H. sanguineus and C. maenas it's easy to check those boxes but as soon as you look at the whole story for L. littorea you are forced to check the same boxes.  Struggling to define invasive (vs non-native, and why we don't call periwinkles invasive) I've often said "well, no one is suggesting any kind of management for periwinkles."  But no one is suggesting that for the others either.  At least when it comes to marine inverts, the plan is monitoring, education and the hopeful prevention of new invasives but there is no plan to manage the established invaders.  And while there are management plans in place for invasive terrestrial plants they will likely need to continue indefinitely.  So as far as I can tell, really the only difference is that periwinkles have been around for about a thousand years and no one remembers a New England ecology without them.  Heck, they might even be a keystone species!

So the weird thing is that when it comes down to it I do agree with Johnson that we shouldn't be losing our hair over invasives.  They are, in a lot of ways, just another example of the biological world moving and evolving and changing.  However, I'm hesitant to say, with such simplicity, that invasives (writ large) generate biodiversity.  Sure, you can find examples of that happening, but you can also find examples of invasives out-competing local species, close to extinction or completely altering huge swaths of ecosystems (and again, I'm going to make a value claim that salt marsh is more important than rocky shore, we can debate that in the comments if you like).

Through writing this I've been thinking about another book: Out of Eden by Alan Burdick.  In this book he doesn't so much argue that invasives are a good thing but that, well, there's not a heck of a lot we can do about them so...why freak out?  Again, I think that's where I land.  That's also a whole book, not a few sentences in a book that's not really about this complex and often really interesting issue.  They might be a problem but our relationship with invasive species is a huge part of the story of how we humans are forever changing the biosphere.  Maybe it's not great, I'm still not sure how to make a value claim about such a big, complex issue, but there's some really neat science going on there.

Also, kudzu stinks.


Johnson, Nathanael. (2016). Unseen City. New York, NY: Rodale Inc.

Meleagris gallopavo [Turkeys] at Mt. Auburn Cemetery

Thursday, September 8, 2016

No Such Thing as a Protist

So I care about cladistics, which is a way of classifying living things based on traits that are inherited from a common ancestor.  I might care about cladistics too much.  I've been trying for a while to understand why I care so much.  I think that it's because without an understanding of evolution and cladistics you're not really understanding the biological world.  I think the fact that birds are theropod dinosaurs just makes them a whole lot cooler and the fact that octopuses' closest relatives outside the other cephalopods are clams and snails is simply amazing.

I've also been after a life goal of not being such a pedant.  Sometimes my desire to revel in the true nature of a living thing comes into conflict with this.  (Like when I refer birds as "reptiles" without missing a beat and not really explaining myself.)  But I think that's where I've actually found the most fascinating discoveries.  There are moments when our words for the natural world start to break down because...well hundreds of years ago some people who really didn't understand evolution or cladistics came up with them and they don't actually work all that well a lot of the time.

So while I really am trying to be less of a pedant:  I have a real problem with Kingdoms.  Specifically Protista.  I'll show you why...protists don't exist.  Here's how you probably learned about the tree of life:

Here's a (probably fairly up to date) image of the actual tree of life, simplified to mainly show the eukaryotes which are living things that are like us...that is their cells are quite a bit bigger than a bacteria or archaea and their cells have a nucleus:

Vojtech.dostal CC BY.0-SA 3 click to embiggen
See the kingdoms?  Yeah you've got Bacteria and Archaea down at the bottom.  Fungi's right there just above bacteria inside opisthokonta.  Metazoa, that's animals, inside the same group as fungi.  Plants are also pretty obvious, inside archaeplastida next to green algae.  So...the $64K question: where is protista?
click to embiggen modification of the above illustration CC BY 4.0

OK I'm calm...I've been trying to reflect and figure out exactly why this bothers me so much.  I think I've got a decent analogy.  It has to do with monophyly which is when you group organisms into what are called clades (clades, cladistics same root word) which contain a set of living things and all common ancestors.  This is basically the idea that "kinds" of living things are ones that evolved from one another, you don't combine things that don't have a direct evolutionary relationship, you only combine things that are descendants.  So if you go back and look at the tree above it seems very obvious to me that there are six groups of eukaryotes plus bacteria and archaea.  You can call fungi a "kingdom" if you want but that means you also have to call malawimonas a kingdom...and well all of these things.  

So here's my analogy using a subset of the so called "protists" for my comparison.  Here are algae:
click to embiggen modification of the above illustration CC BY 4.0
(well actually there's things we call algae in several other groups in Eukaryota and also we sometimes call cyanobacteria [which if you couldn't tell from the a type of bacteria] algae but whatever, I'm just going with full clades of things we call algae for now).  We call these things algae, from what I understand (and full disclosure here, I am not a taxonomist, I am a science educator and I could have this wrong) because they are photosynthetic and they are not plants.  And also from my understanding, and I believe this is the rub here, photosynthesis appearing in at least many of these different groups is due to convergence, that is it has evolved multiple times.  So the different groups having photosynthesis is not because they are the "same thing" but because photosynthesis is useful and has evolved several times.

Here's my analogy: this is a (very, very) simplified cladogram of things with powered flight:
by me CC BY 4.0
As we all know, bats, insects and birds all have powered flight.  So, we could call all of them the same thing.  We could have a word like "flappydoo" to describe all of these things.  

Flappydoo are algae.  Algae are called that simply because they are tiny things most humans don't really understand that can photosynthesize.  Flappydoo are slightly bigger things that most humans reasonably understand that have powered flight.  I'm just lumping things in a pretty big clade (animalia) together due to a trait they evolved because its useful.  But that trait is convergent.  

I was talking about a similar thing just today and I think I reached another level of understanding of when I'm supposed to be pedantic and when it doesn't matter.  In my work I spend some amount of cognitive energy telling people that horseshoe crabs aren't crabs (they're related to spiders) and that starfish aren't fish (right, they're inverts in echinodermata) but *technically* hermit crabs are not "true crabs," that is they are in a different clade in a very closely related group.  But I don't think that matters.  Not one bit.  I also don't think it matters if someone calls a lobster a crab.  Why?  Convergence.  Most of decopoda, the group that contains lobsters, crabs, squat lobsters, shrimp, mantis shrimp, etc. probably had ten legs and probably some of those legs had claws.  That describes a crab and a lobster and a hermit crab.  They're the same thing.  Probably none of those traits evolved convergently.

I brought up falcons during my discussion today because they are not hawks and again convergence was the important thing.  It was agreed that it's important to distinguish hawks and falcons because they're convergent and ultimately, that's cool.  That's interesting.  The fact that hermit crabs and "true" crabs are not *technically* the same clade isn't interesting.[actually it is but I think for most people this is a level of detail that's over the line of pedantic].  They didn't really (probably) evolve anything really interesting through convergence. 

I think there's a lot of grey area here, clearly.  But my main goals are two: I hope that you care a little less about what things are called and spend more energy thinking about what is interesting about a particular group of living things.  Two?  I do hope you stop using the term "protist" and you stop using kingdoms and start only using domains if you haven't yet.  I think it's really silly that students in most schools are still learning about kingdoms.  

Then again I learned about the Bohr model of the atom in school.  Waste of time...