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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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Each year, the American Birding Association (ABA) selects a particular species as its Bird of the Year.  The species is selected based on a combination of character of the bird itself, how it related to birders, and how it can serve as a symbol for the birding community.  This year, the ABA Bird of the Year is the Evening Grosbeaks, and as I have been studying Evening Grosbeaks for the past three years, I was especially excited by this choice.  I figured the added attention on this species might lead people be curious to know about them and their biology, and so here is a bit of information on them.

Evening Grosbeaks are a fascinating species for many reasons.  One of these reasons, and the one that first caught my attention, is that there have been so few studies done.  For being so common a visitor to backyard bird feeders, especially in winter, I was amazed at how little was known about these beautiful birds.  Do Evening Grosbeaks have a song?  What do the courtship rituals involve?  How many subspecies exist?  Where do birds go to throughout the year?  How do birds find food sources?  All of these are big unknowns for the Evening Grosbeak, and that intrigues me.

But before we get into more of the unknown, here is some of what is known about this bird.  It belongs to a group called the Cardueline Finches.  This group includes such species as House, Cassin’s and Purple Finches; Pine Grosbeak; the Goldfinches; the Crossbills; the Redpolls; and all the Siskins.  This group is found across North and South America and Eurasia.  Many of these species do not have regular migratory routes, but are referred to instead as nomads.  Unlike many birds, which have breeding grounds where they can be found in summer and non-breeding grounds where they can be found in winter, nomadic species move across the landscape to follow food resources wherever they happen to be.  This means that where groups of birds are to be found at any given time of year can be very unpredictable.  They seem to congregate where there are large concentrations of food, although how they find their food is a mystery.  For the Evening Grosbeak, these food resources are usually large insect outbreaks or areas where the coniferous trees have big crop of cones.  Other foods that Evening Grosbeaks seem to like are the Safflower and Black Oil Sunflower seeds they find at bird feeders.  One interesting dietary foible is that they seem to have a strong affinity for salt.  They have commonly been reported coming down to drink from mineral springs, and also have been shown to prefer soils that have had salt added over soils that have had nothing added.

Geographically, the Evening Grosbeak has been expanding its range into the eastern United States in the past hundred years or so.  The first recorded sighting of an Evening Grosbeak in New England came in the 1890s, and the first breeding record was in 1940.  One thought as to why this eastward has been taking place is the extinction of the Carolina Parakeet.  When the Carolina Parakeet, North America’s only native parrot, was alive their diet consisted predominantly of large seeds.  When they were driven to extinction, this food resource was left open, and the Evening Grosbeak had the equipment to break into such seeds as Bald Cypress cones which other birds were too small to tackle.

The number of subspecies of Evening Grosbeak has been a developing story since the late 1800s and has had its’ fair share of confusion.  In 1874 a natural historian, Ridgeway, found that birds in Mexico looked different from the birds he was used to seeing in the eastern United States. The yellow eye-stripe of the male Mexican birds was longer and wider than eastern birds and the bills were longer, wider, and less curved.  This led him to separate birds in the western half of the continent from the birds in the eastern half of the continent thereby creating two subspecies.  In 1917, Joseph Grinnell at the Museum of Vertebrate Zoology at the University of California, Berkeley, took a closer look.  He noticed that the birds that Ridgeway had found were representative of the birds in Mexico, but that they were subtly different from birds found in other parts of the western US.  Grinnell agreed that the eastern birds represented one subspecies, but he separated the birds in the western US into four subspecies based on differences in plumage color and brightness, and slight differences in bill shape and size.  The resulting five subspecies were the accepted taxonomy until 1957 when the American Ornithologists Union decided that the slight differences in bill shape and size that Grinnell had described were not enough to warrant subspecies status for some of these populations.  Instead, they settled on three subspecies.  The eastern birds represented one subspecies, as everyone agreed, the birds from Mexico represented a second, and birds from the rest of the western United States represented a third.  Since 1957, these subspecies have been the three to have accepted taxonomic status.

Regardless of how many subspecies exist, some people have taken notice of trends that stretch across the whole species.  One disturbing trend was found by scientists at the Cornell Lab of Ornithology who examined Christmas bird count and breeding bird survey data and found that numbers of Evening Grosbeaks have been declining across the country. Over the past two decades, Evening Grosbeaks have been seen at fewer and fewer sites.  Additionally, the sites that still have their Evening Grosbeaks have been observing smaller and smaller flocks.  Since these birds are so unpredictable in their movements, and they frequently live in the back country where Christmas bird counts are rare, it is possible that the birds are simply going to places where they are not being seen.  However, since the Cornell scientists only found declines all across the country, and found no population increases even at small local locations, the continent wide population decline seems like a real possibility.

In terms of vocalizations, Evening Grosbeaks present other interesting traits.  Evening Grosbeaks have a number of vocalizations.  One kind of vocalization is the flight call.  This is a short, single-note call that seems to function in flock movement coordination.  This call has been observed to vary from population to population in different parts of the country, and the different variations seem to be quite distinct.  Each variation was called a Type and given a different number.  So, now different birds have been identified as producing Type 1 flight calls or Type 2 flight calls all the way up to Type 5.  No bird has ever been found to make more than one Type of flight call, but birds that produce different flight call types do sometimes occur in the same place at the same time.  Interestingly, when the distributions of these different flight call Types are mapped across the continent, they match where Joseph Grinnell mapped out his five subspecies!

So what is going on here?  Can birds use flight calls to identify other individuals such as their mate?  Do they prefer to associate with other birds that make the same type of flight call?   Do the different flight call types play a role in choosing a mate?  Do birds that make different flight call types prefer different sized seeds?  Are the birds that make different flight call types genetically different as well?  How are the differences in flight call types able to persist when these birds move around and overlap with each other?  These, and other questions, are what I hope to find out.  So do you have Evening Grosbeaks, the ABA Bird of the Year, coming to your feeders?  Let me know, and I will report back on what I find!

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There is a post doc working for my adviser who is from Glasgow, Scotland, named Lindsay.  She and I have been comparing birds in North America to their counterparts in Europe.  One especially interesting example to me was the Northern Harrier of North America and the Hen Harrier of Europe.  These birds are considered different species by some and different subspecies of the same species by others.  The reasons for having some kind of distinction between the two populations usually rests on the fact that they are separated by an ocean and also on slight differences in size.  However, we being students of behavior, Lindsay and I were talking about behavioral differences between the two, and there was one that really jumped out at us.  She was surprised to see so many harriers in the agricultural land around the town of Davis.  In Scotland, the Hen Harrier generally keeps to more natural landscapes of moor and meadow.  Here in the U.S. The Northern Harrier is a common sight in human dominated landscapes such as empty lots and agricultural fields.  In fact, they even breed in these fields fairly frequently which was quite a surprise to my Scottish friend.  This demonstrates how important the study of behavior can be.  The outward, physical differences between birds from these two populations are slight, but they have these distinct behavioral differences in where they hunt and where they breed.  Surely this kind of information could , and should, be used when defining species!

I want to collect such differences in behavior between different populations, so do you know of any?  They can be from any continent or any combination of continents, and involve any species.

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Subspecies are a fundamentally important unit of taxonomy.  They represent the diversity of adaptations that various groups can acquire as they respond their local environment.  In circumstances where barriers are long-lasting, they can represent the first steps in speciation.  When barriers are less permanent, they can tell us about the dynamics of how major features of a landscape can change through time.  Subspecies can also offer information in areas of mate choice and sexual selection, breeding behaviors, dispersal and gene flow, colonization events, and phenotypic plasticity.  With so much to offer, subspecies warrant a great deal of attention from biologists from a wide range of disciplines.

From a conservation point of view, protecting subspecies ensures that a wide range of the genetic, morphological, and behavioral variation within a species is preserved.  This leads to the preservation of the greatest possible adaptive potential for the species as a whole.  From a policy perspective, subspecies that are declining are protected by law under the endangered species act of 1973.  Therefore, proper identification is needed for decisions on listing and delisting designations and for the assignment of money and labor that result from such decisions.  From an evolutionary biology standpoint, subspecies can represent the transitory step of one species becoming many.  The process of observing and mapping such speciation events is one of the primary goals of evolutionary and population biology.

However, despite the importance and need for accuracy in subspecies designations there is little agreement or consistency with regard to how it is done.  Some of these inconsistencies arise from problems of definition.  Defining a species is a tricky task with different situations lending themselves to different criteria.  The biological species concept, the morphological species concept, the phylogenetic species concept and the rest all have their supporters, and each species definition leads to a different subspecies definition.

The biological species concept states that a species is a group of individuals that can breed and produce viable offspring with other members of the group, but not with individuals from outside the group.   This is the most widely used and accepted species definition in raptor biology.  The major difficulty with applying this definition to subspecies (a subspecies is a group of individuals which can breed and produce viable offspring with any other member of the group, but not with individuals from outside the group, but who usually breed with only a subset of the group) is that it is not easy, and sometime impossible, to trace movement and breeding patterns among different populations.  The morphological species concept is the oldest form of classification.  It states that a species is a group of individuals that all share a suite of physical characteristics with each other, but not with individuals from outside the group.  This concept is not well supported in modern biology; however it is the most frequently used as the method for designating subspecies.  The phylogenetic species concept states that a species is comprised of all of the descendants of a single common ancestor.  This idea is gaining strength as genetic techniques to determine descent become easier, faster, and cheaper.  However, this species concept does not have specific levels of separation that mark species and subspecies, so any such designations become much more subjective.

These different definitions lead to many problems.  Each of these definitions has areas of grey where disagreements can, and do, arise.  How much interbreeding is enough to consider two groups part of the same subspecies?  Which morphological characteristics are included in the diagnostic suite, and how different do they have to be?  How much genetic divergence is enough to warrant species or subspecies designation?  These are the questions that need to be settled when designating and naming subspecies.

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