Posts Tagged ‘Systematics’

E.O. Wilson, 'Darwin's natural heir,' dies at age 92
E. O. Wilson examining a leaf. He advocated for a world where all species have the space and resources to survive. Photo courtesy of National Geographic.

E. O. Wilson died yesterday at the age of 92. The sciences of entomology, biodiversity, biology, ecology, and evolutionary biology have suffered a huge loss. Beyond those specific scientific disciplines, the world has lost an amazing science communicator and advocate of nature.

Edward Osborne Wilson was born in Birmingham Alabama, USA on June 10th, 1929. He grew up chasing snakes and birds and insects around Birmingham, Washington D.C., the various other towns he grew up in (his parents were divorced and each moved several times during his childhood) and also on the many hiking and camping trips he took into the surrounding areas. This early interest in the natural world solidified into an obsession with ants which he studied throughout his undergraduate and graduate work.

In his early career, E. O. Wilson worked with another scientist named Robert MacArthur to develop a way of explaining why species tend to be scattered across the planet in the patterns that we see. Originally, these two focused on explaining, with mathematical equations, why and to what extent big islands have more species than small islands, and islands close to continents have more species than remote islands. This set of concepts became known as Island Biogeography. It was quickly recognized as having much wider applications. Not only did it work for islands, but for other features as well. Lakes could be seen as ‘islands’ set in land masses. And even further, nature preserves could be seen as ‘islands’ set in inhospitable and highly modified landscapes. Island biography can be used to predict how large a nature preserve is needed to save a certain number of species. It can be used to determine how far apart nature preserve ‘islands’ can be and still maintain viable populations of animals, plants, and fungi.

On top of island biogeography, E. O. Wilson pioneered work in sociobiology by exploring how behaviors of insects and behaviors of humans and other vertebrates are similar in many ways. He popularized the term biodiversity and spent considerable effort in working toward the preservation and documentation of life on this planet.

E. O. Wilson was also a tremendous writer. His list of written works includes over 30 books and 430 scientific articles, and these span a range of scientific and popular science material. He made scientific topics accessible to a wide range of public readers and inspired countless people (including myself) to pursue these topics further. His book “Letters to a Young Scientist” is one of the best and most inspiring books I have ever read.

Without a doubt, Wilson was a giant in the field. He developed really impactful ideas. He mentored a huge number of other scientists. To popularized science to the wider world.

We have all lost a treasure.

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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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As my wife and I were driving out of Berkeley a few days ago, we saw a group of five Wild Turkeys walking down the side walk of one of the  major streets.  When we turned a corner at the next intersection we saw another group of five crossing the street in front of us.   Many people were stopping their cars or coming out onto their front porches to watch and photograph the birds as they sauntered by.  The turkeys were completely unfazed by the attention as they calmly walked through the neighborhood.  With the Thanksgiving holiday just past, and this encounter fresh in my mind, I thought it would be appropriate to post on the Wild Turkey population of California.

Wild Turkeys (Meleagris gallopavo) are native to North America, and there are six recognized subspecies.  In the late 1800s they were nearly driven to extinction by a combination of heavy hunting and habitat loss which reduced the continent wide population to around 30,000 individuals restricted to remote locations.  In the 1970s reintroduction programs began to successfully bring the Wild Turkey back to large portions of its historical range.  But, Wild Turkeys are not native to the west coast.  The first recorded introduction of Wild Turkeys to California was in 1877 on a ranch on Santa Cruz Island where they were released for the express purpose of hunting.  More introductions followed, especially from the 1950s to the 1970s, and now there is an estimated population of 240,000 birds in California alone and they are found across 54 of 58 counties.  The birds we have here are largely of the Rio Grande subspecies (M. g. intermedia).  This subspecies is particularly long legged, generally weighs between 20 and 25 pounds, have body feathers that have a coppery-green sheen, and tail feathers and upper tail coverts that are tipped with tan.

As the population of Wild Turkeys in California has grown, they have increasingly moved into suburban areas.  Like deer, turkeys can adapt to human dominated landscapes and learn to thrive there.  This has led to an increase in human-turkey interactions.  Some of these interactions come in the form of turkeys doing damage to gardens and landscaped areas.  Agriculturally, turkeys eat wine grapes and have become a nuisance in many vineyards. And while males can become aggressive during the breeding season, the vast majority of the interactions between Wild Turkeys and humans are completely benign; just don’t feed them.

As an interesting aside, the reason they are called Turkeys has always puzzled me since these birds are not found in the country of Turkey at all.  I recently learned that the when these birds were first being imported to Europe from the new world they all came through trade routes that stopped in Turkey before being distributed to the rest of the continent.  The name of the bird became entwined with the shipping location, and the name has stuck ever since.

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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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