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Archive for the ‘Systematics’ Category

Information is important. With information each of us as individuals, and our society as a whole, can learn about the world. With information, we can all make decisions that make sense. With information, we can all discuss ideas.

Without information none of that is possible. Without information, we are, at best, at the mercy of our current, limited knowledge, and our base instincts. Without information we are, at worst, at the mercy of the limited knowledge and instincts of someone else.

This is why the gag order, and insistence that all reports and data be pre-screened before release to the public, issued by the President to the EPA are so concerning to me, and I think should be so concerning everyone else. This is exactly the kind of action that limits access to, and spread of, information. It will only hamper all of our abilities to operate as rational, critically thinking individuals. It is the kind of action that is put in place to control what we, as citizens, know and when we know it. This is censorship and it has no place in science or a free society.

#thisisnotnormal

pansy-white-blue

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The American Ornithologists Union (AOU) is, among other things, the arbiter of avian taxonomy in Middle and North America. They are the organization that rules on whether a species should be split in two, or if two species should be lumped together. They are the organization that rules that Loons are no longer the most basal group of North American birds, but that they group that contains ducks, geese and swans holds that honor. The AOU releases all these decisions in the form of annual Supplements to the official AOU Checklist (which is a complete list of all bird species and subspecies listed in taxonomic order).

A lot of science has to be done before the AOU makes any of these ruling, and these ruling are subject to change as more science is done, but at any given time, the current AOU Checklist represents the best available knowledge on how many species of birds there are and on how they are  all related to one another.

Well, the AOU just released their most recent Checklist Supplement and it has, among the many updates and changes, an interesting change for California. Since that is where I live, I am particularly interested in this one. It concerns a common member of the corvid family that anyone who has spent any time outside has seen. The Western Scrub-Jay (Aphelocoma californica).

This species has actually already had an interesting history in the taxonomy world. Before 1995, there was one species recognized as a Scrub Jay (Aphelocoma coerulescen). This species was found across the western USA and also in Florida. In 1995, the AOU split the Scrub Jay into three distinct species. They were the Florida Scrub-Jay, which retained the original scientific name (Aphelocoma coerulescens), recognizing the Florida population as genetically distinct; the Island Scrub-Jay (Aphelocoma insularis) recognizing the population found on the Channel Islands off the coast of southern California as genetically distinct; and the Western Scrub-Jay (Aphelocoma californica) which included all the remaining populations in the western continental USA.

California Scrub-Jay - Frank Lang

California Scrub-Jay (Photo credit: Frank Lang)

Now, in the most recent AOU Checklist Supplement, the Western Scrub-Jay has been split again. We now have the California Scrub-Jay (Aphelocoma californica) recognizing that the population along the Pacific Coast is actually genetically distinct from the Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) found in the inter-mountain west.

Woodhouse's Scrub-Jay - Robert Mortensen

Woodhouse’s Srcub-Jay (Photo credit: Robert Mortensen)

In addition to the genetic distinctions, these two new Jay species also have behavioral and morphological differences. The California Scrub-Jay is darker in color, generally lives in Oak woodlands, and eats a range of seeds including a lot of acorns and so has a heavier bill. In contrast, Woodhouse’s Scrub-Jay is lighter in color, generally lives in the Great Basin pinon-juniper scrublands, and correspondingly eat a great deal of pinon pine nuts and juniper berries and so have a slimmer bill.

So, update your life lists, start getting used to using the new four-letter codes of CSJA (now standing for California Scrub-Jay) and WSJA (Now standing for Woodhouse’s Scub-Jay, and not Western Scrub-Jay that it used to identify), and enjoy picking apart the finer levels of identification between these two newly recognized species!

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As a graduate student, teaching biology labs is a regular part of my week and the lab that I teach most quarters is on phylogenetics and biodiversity.  Recently I have been having discussions about phylogenetic terms with my students, fellow TAs, and the staff and professors who are in charge of the class.  Terminology often gets confusing in phylogenetics, and words are sometimes used to mean different things by different people.  One of the facets that makes these terms extra confusing is that they are not mutually exclusive and depend on the groups being discussed, so for example, a trait can be both a synapomorphy and an autapomorphy (see below) depending on the groups being examined.  So, in an attempt to clear things up in my own mind, and so hopefully be able to teach them more effectively, here are some commonly used terms in cladistics with accompanying definitions and explanations.

Apomprphy – A derived character state.  This is anything that is an innovation along an evolutionary linage.  So anything that is different from the ancestral character state.  For example, within the phylum Chordata, the evolution of a vertebral column, which is something lineages that branched off earlier in Chordate evolution do not have and so is new in the Class Vertebrata, would be an apomorphy.

Synapomorphy – A shared, derived character state.  This is an apomorphy that two taxa share and that is assumed to have been present in the common ancestor of those two taxa.  An example would be feathers in birds.  All birds have feathers, and it is assumed that they have feathers because the common ancestor to all birds had feathers and passed that characteristic down through the generations.

Plesiomorphy – An ancestral character state.  This is any trait that was inherited from the ancestor of a group.  For example, reptiles are exothermic, they do not maintain a constant internal body temperature.  They have this characteristic because the ancestor of all reptiles was exothermic.  This differs from a synapomorphy because some descendants of the first reptiles are not exothermic (birds are endothermic).  In other words, this trait is ancestral, but is shared by some, but not all, of that ancestors; descendants.

Symplesiomorphy – A shared, ancestral character state.  This is any trait that was inherited from the ancestor of a group and has been passed on into more than one descendant lineage.  To carry on with the example for a plesiomorphy, the fact that crocodiles and turtles are both exothermic, but

Autapomorphy – A derived trait that is unique to a particular taxa.  These are not useful in determining how groups are related since only one group will have the particular trait.  However, these are extremely useful in identifying taxa.  For example, feathers only occur in birds.  This makes the character “feathers” and autapomorphy for class Aves.  The character “feathers” is also a synapomorphy for taxa within class Aves.  Raptors and songbirds both have feathers and they inherited them from a common ancestor.

Phylogenetic Diagrams

Open circles = ancestral character state, filled circles = derived character state.

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To be completely honest, this post is a bit of a tirade on my part.  I have been hearing some views of evolution that have really been annoying me lately.  I am not talking about people who do not think evolution happens or anything like that (that would be a bigger tirade, trust me).  No, these views come from biologist who should know better.  But first, some background.

As a graduate student, I serve as a teaching assistant each quarter.  The most common position I have held is teaching labs for one of the big introductory biology classes that pretty much everyone has to take in college.  Specifically, the labs I teach are part of the class on phylogenetics and biodiversity (BIS 2C for any U.C. Davis people reading this).  While teaching these labs, I have the opportunity to interact with lots of other people who work a U.C. Davis including members of the faculty, administrators, and staff.  Since the class covers the diversity of all life on earth, these people all come from very different academic backgrounds from spider phylogenetics to fungal biology to microbial diversity to botany.  This week we are finishing up plants for the quarter and as part of the plant labs there are several botanists who help the students out.

And here is where my trouble lies.  Several of the botanists have asked students some variation on the following question: why do ferns have fewer herbivores than flowering plants?  This is a perfectly reasonable question.  My complaint comes with the answer that they give which is some variant of: ferns have been around longer and so have had more time to evolve defenses against herbivory than flowering plants. I have so many problems with this answer, I am not even sure where to start!

Now it is true that ferns, which are Monilophytes, diverged from the rest of plants earlier than flowering plants, which are Angiosperms.  As such Monilophytes display more ancestral traits than the more modernly diverged Angiosperms.  However, this does not mean that they have had more time to evolve!  All life on earth can trace its lineage back to a universal common ancestor.  All life.  Since we all started at the same point, every organism that is alive today has been evolving for the same amount of time!  We humans classify different organisms into different group and arrange the formation of these groups into chronological order, but that only indicates that the lineages that make up those groups have changed more or less over the course of the last 3.6 billion years, not that some of them are shorter or longer.

Another reason why this answer gets me hot-under-the-collar is that is reenforces the mindset that some organisms are older than others and therefore more primitive, or less evolved.  Natural selection has been operating on all lineages all the time which means that every organism that is alive today is just as evolved as every other organism that is alive today.  It may sound crazy to say that a single-celled bacteria is just as evolved as a human, but it is true.  The bacteria simply found a strategy for surviving very early on, and that strategy has kept on working really well.  Our ancestors, on the other hand, have had to keep altering their strategy over time to the point where they now look very different from how they did when they started.  Remember that the starting point for both groups was at the same point something like 3.6 billion years ago.  All of phyogenetics basically boils down to tracking which genetic lineages have accumulated what changes over their 3.6 billion year history.  We are all equally evolved!  Or as Neal Stephenson wrote, “Like every other creature on the face of the earth, Godfrey was, by birthright, a stupendous badass, albeit in the somewhat technical sense that he could trace his ancestry back up a long line of slightly less evolved stupendous badasses to the first self-replicating gizmo – which, given the number and variety of its descendants, might justifiably be described as the most stupendous badass of all time.”

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I saw two male Orange-crowned Warblers (Oreothlypis celata) chasing one another through the yard this morning.  This is somewhat unusual at this time of year since these birds are in all likelihood wintering birds, and as such they should not be that interested in defending territory and such.  That will all start in about a month (at the earliest) here in central California when the earliest males will arrive for breeding in mid February and the bulk of the rest will arrive by mid March. So these males may have just been doing some practice competing.  Some halfhearted pursuing just to make sure they have not lost the edge they will need again soon.

Of the four subspecies that are widely agreed upon in this species, the one we have here is O. c. lutescens.  It is a coastal subspecies that breeds from Alaska to southern California and winters from northern California to Baja California.  That places central California in the happy position of being in the overlap where we can see Orange-cornwed Warblers all year long.  I hope that is the case here in my specific neighborhood.

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My first memory of Rich Stallcup is actually not a bird memory at all, but rather a frog memory.  I was probably about ten years old when my mother, brother and I joined him on a bird walk.  But the very first thing he stopped to show the group were several Bullfrogs.  He got his scope on them and let us watch them breath.  He told us about how they were an invasive species and voracious predators that were eating the tadpoles and larva of other animals and so driving down their populations.  My second memory of Rich is a bird memory.  We went on a bird walk to Limantour Beach that Rich was leading that focused on gull identification.  I remember standing looking at a large flock of gulls and listening to him point out the subtle differences between different species, and the even more subtle differences between different aged birds of the same species.  I remember being amazed at the level of detail that he could notice and even more amazed by the concept that there was so much more detail out there to be noticed then I had ever realized before.

These memories, and so many more, point out what I feel were some of Rich’s greatest qualities.  He was a naturalist in the truest sense of the word.  He was the best birder I have ever known with an encyclopedic knowledge of birds, but he also knew tremendous amounts about mammals, reptiles, butterflies, and dragonflies.  He even kept a wildflower life list.  In an age of ever increasing specialization on smaller and smaller scales of knowledge, Rich went the other way and proved that a person does not have to choose between being a jack of all trades or a master of just one, but instead could master quite a few.  It is a lesson that I have tried to learn and an ideal that I continue to strive for.  And his attention to detail was incredible.  While standing watching a group of Bushtits work their way through a willow stand, he finally decided that he was not missing any other birds in the flock when he started recognizing individual Bushtits in the flock!

Of course, Rich’s professional accolades are many.  One of the prominent discoverers of the amazing natural history of Point Reyes and the fact that the outer point acts as a tremendous vagrant trap attracting unusual birds from across the continent when they are disoriented by a predator attack or a storm.  The outer point now also attracts birders from around the world.  Rich was also one of the founders of the Point Reyes Bird Observatory, an organization that is now one of the foremost international conservation NGOs.  He has written books, papers, and articles; and also led countless bird walks and pelagic birding trips, all with the aim of introducing people to nature.

I had the good fortune to be able to bird with Rich for many years.  When he and Ellen Blustein started the PRBO Youth Bird-a-thon Team in 1999, the four founding youth members were myself, my brother,and two of my best friends.  I have continued to participate in that event ever since.  Even after I got old enough that I could not count as a youth anymore, Rich seemed happy to have me stay on as a mentor to the incoming generations of youths.  When he learned that I was expecting my first child he told me that, as long as the kid was more than two days old, I should bring him or her on the Point Reyes Christmas Bird Count!  I was very happy that he was able to meet my wife a couple of times, and saddened that my child will never get the chance.

Rich Stallcup died on the 15th of December, 2012 of Leukemia.  His loved ones were at this side.  He was a naturalist who inspired me and many others with his knowledge, passion and generosity, and he will be greatly missed.

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In the western U.S., Spotted Owls (Strix occidentalis) are one of the banner species for the protection of old growth forests, and several subspecies are federally endangered.  A small owl, it has a huge impact on conservation in North America.  But now they face a threat that is harder to deal with even than human disturbance and habitat loss.  It is a fellow owl, the Barred Owl (Strix varia).  The two species are very closely related.  The Barred Owl is most commonly found in the eastern portion of the continent, but that is changing.

Due to an increase in the number of planted trees in the central parts of the continent, the breaking up of large tracts of continuous forests by timber harvesting, and probably other factors that we do not yet understand, the Barred Owl has been expanding its range westward.  There are now breeding populations of Barred Owls in Washington, Oregon, and California, and this posses a special problem for the Spotted Owl.  With their larger size and more aggressive behavior, Barred Owls can drive out Spotted Owls from nesting territories, sometimes eating the Spotted Owls!  However, even when the Spotted Owls stand their ground (and don’t end up being a meal) a problem still exists.  Since the two species are so closely related, they can interbreed.  The hybrid, or Sparred Owl, can then mate with other Sparred Owls or members of their parent species.  Since the total Spotted Owl population is small and the total Barred Owl population is large, and getting larger, the overall result is that the Spotted Owl is getting absorbed into the Barred Owl.

Now, we face a dilemma: what should we do to save the Spotted Owl?  For that matter, what can we do to save the Spotted Owl?  Ideas abound across a wide spectrum.  At one end are those that feel that the Spotted Owl must fend for itself.  This viewpoint is generally driven by the idea that a species its range is a natural process and should not be interfered with.  If one species out competes  another where they come in contact, that is just how the world works.  Many advocates of this viewpoint point out that if the two species are so closely related that they can interbreed, they probably should not have been categorized as two different species in the first place, but are rather two populations of the same species.

At the other end of the spectrum are those that feel that the Spotted Owl should be protected at almost any cost.  Proponents of this viewpoint feel that a large part of what brought these two species together were human induced changes to the land, and we are therefore responsible for the results.  Among the most drastic of the plans that have been suggested is to actually kill Barred Owls when they are found near known Spotted Owl nesting territories.

So, who is right?  The debate continues.  There may be nothing we can do to stop the Spotted Owl from disappearing.  But we can learn.  Ecosystems are incredibly complex, and we did change the landscape in such a way as to allow this situation to occur.  In the future, we need to consider carefully the possible consequences of our actions and perhaps apply the precautionary principle a bit more often.

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