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Archive for the ‘Evolution’ Category

A few years ago I wrote a post on niche partitioning amount herons and egrets. That post was inspired by watching several species of herons and egrets foraging for food along Putah Creek near Davis, CA, and the resource they were partitioning into niches was food.

Recently, as part of my work at the Sacramento-San Joaquin Delta Conservancy, I encountered another example of niche partitioning by herons and egrets. This time, the resource these birds are partitioning into niches is nesting trees.

One of the grants that I manage at the Delta Conservancy is at the Cosumnes River Preserve and it includes and grove of large Valley Oak Trees that many herons, egrets, and cormorants use as a rookery (a rookery is a colony of breeding animals, generally birds). One way that the various species have evolved to utilize the same trees, and yet avoid directly competing with each other, is for each species to utilize a different part of each tree to nest in.

Great Blue Herons typically nest on the very tops of the crowns of trees, Great Egrets typically nest only in the upper one-third of the canopy, Snowy Egrets typically nest in the middle one-third of the canopy, and Black-crowned Night-Herons prefer to nest in the lower one-third of the canopy (see the image below).

Niche partitioning of nesting locations within a tree by heron and egret species

I think this stratifying of nesting locations is amazing! Species have evolved to fill so many different niches, and so many niches can be divided into finer and finer gradations. I wonder if there is really any limit to how many species can evolve, and how complex an ecosystem can develop, in a give location.

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A news story has been circulating a fair bit in the past couple of weeks. This story has been picked up by numerous news and science outlets. How it is being reported and explained is just plain misleading and inaccurate.

Image result for aldabra rail

The Aldabra Rail is a subspecies of the White-throated Rail.

Here are a few titles that show how the subject is being covered.

Science Magazine – Evolution Brings Extinct Island Bird Back into Existence

Smithsonian Magazine – How Evolution Brought a Flightless Bird Back from Extinction

CBS News – An Extinct Bird Species Has Evolved Back into Existence, Study Says

From these titles, and from the bodies of the articles themselves, readers would think that the same species of bird existed at some point in the past, went extinct (as in died out completely), and then re-evolved!

That does not happen.

Here is what actually did occur.

The small atoll of Aldabra is a pretty spectacular spot. It is very remote. It is quite beautiful. It is home to a bunch of unique animals found no where else on earth. It has one of the longest fossil records on any island in the Indian Ocean.

That fossil record includes a lot of the animals that have called the atoll home over the past few million years. One of those animals was the Aldabra Rail. This rail was a small flightless bird that was probably found hunting through reed beds along the edges of water. The Aldabra Rail went extinct about 136,000 years ago at about the same time that global sea level was rising and submerging oceanic islands like Aldabra. After a few thousand years, sea level dropped and Aldabra became an exposed island once more. Not long after that fossils of a rail on Aldabra start showing up again.

There are a couple of possible explanations. One is that some remnant population of the Aldabra Rail hung on, some how, and did not die. These were flightless birds, so it is not clear how this might have happened, but perhaps a small population managed to survive on a floating raft of vegetation long enough to reach an exposed bit of land. This seems like a very long shot. It is much more likely that the Aldabra Rail simply died out completely. It went extinct.

The other possible explanation is much more likely and widely understood and accepted, and it is this: the Aldabra Rail went extinct when the atoll went under water. Then after it re-emerged, a group of birds likely from the same parent stock of the original Aldabra Rail re-colonized the atoll (quite probably from Madagascar). This new group of colonizers eventually became flightless and filled the same, or very similar, ecological niche as the original Aldabra Rail.

This is a process called iterative evolution and it is pretty rare. The definition of iterative evolution is: the evolution of similar or parallel structures in the development of the same main line.

But iterative evolution does not produce the same species twice. It may produce similar species, but to produce the same species twice would require starting with the same gene pool twice. The group of birds that first colonized Aldabra, and became the Aldabra Rail 1.0, had a unique combination of genes to work with. The group of birds that later colonized Aldabra, and became the Aldabra Rail 2.0, had a unique combination of genes to work with. Those two combinations of genes may have been similar, but they were not the same. Therefore the decedents of those two groups would not be the same.

I really think that the implications of how this story is being reported is really misleading and possible even damaging.

Misleading because they imply that a species can evolve twice. To go back to the definition of  iterative evolution, it the evolution of “similar or parallel structures…” Similar or parallel structures are not the same as identical species. Two rails that evolved at different times in the same place and that are both flightless, are not the same species.

Damaging because there is weight to the idea of extinction. Extinction is forever. It means that an entire evolutionary lineage has ended, and any potential future that that lineage may have had is gone. If the idea of extinction becomes an impermanent one, it looses its urgency and tragedy. People may well not worry about extinction as that species can just re-evolve. No harm, no foul.

Again, no species can ever occur twice. Once a species goes extinct, that is it for that evolutionary lineage. Even if some other lineage emerges that is close, it will not be the same and will not have the same evolutionary trajectory or potential.

When reporting on science, I feel strongly that the ideas behind the science should be accurately represented. I think it is especially distressing when the sources of the misrepresentations are otherwise reputable sources for science.

I hope the current Aldabra Rail has a long future filled with descendants, and I mourn the loss of the previous rail of Aldabra and the lineage it might have left behind, but never will.

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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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Single feather, and a mite, preserved in Late Cretaceous amber found in Canada.

Single feather, and a mite, preserved in Late Cretaceous amber found in Canada.

In the movie, Jurassic Park, humans are able to get dinosaur DNA from insects that were preserved in fossilized amber millions of years ago. Well, it has been very convincingly shown that any DNA that might get trapped in amber during the age of dinosaurs would degrade too badly over time to still be viable today. However, this does not mean that amber is useless in preserving amazing structures that we can find and learn from and marvel at.

A recent report that appeared in the journal Science is an excellent example of what I mean. Researchers examined a number of fossilized feathers that were preserved in amber during the Late Cretaceous. These feathers likely came from dinosaurs! And they are beautiful, having been spectacularly preserved in the amber that surrounds them. At this point, no one is exactly sure if these some of these feathers came from early members of what would become the bird lineage, or if they came from non-avian dinosaurs, but either way, the feathers are stunning. In fact, the feathers are in such high quality condition that even tiny features can be observed. Impressively, many of these tiny features on the dinosaur feathers look exactly like the tiny features one would see on the feathers of a modern bird. One example of this is the way that the barbs of some of the feathers twist like a corkscrew. This is a feature also found in modern water birds and may suggest that the dinosaur that those feathers came from lived in close association with water as well. The researchers can even take a stab at figuring out what color some the feathers were; colors that range from white to brown to black. This backs up a lot of other research that has suggested that dinosaur feathers probably had a wide range of colors and patterns, some of them quite bright and dramatic!

A feather found in Late Cretaceous Canadian amber. The dark masses all along the filaments are regions of pigment concentration. This feather was probably medium to dark brown.

A feather found in Late Cretaceous Canadian amber. The dark masses all along the filaments are regions of pigment concentration. This feather was probably medium to dark brown.

Another exciting outcome of all these fossils is that they represent a range of stages in feather evolution. Some of the fossils are little more than very thin filaments, sometimes referred to as protofeathers (or dino fuzz). These protofeathers are probably some of the earlier stages in the evolution of the structures that would eventually become the tail feather of a Peacock or the crest feather of a Royal Flycatcher. These filaments have been found preserved in the rock surrounding other non-avian dinosaur fossils, but they have never been seen in such detail as they can be in the amber. Others of these fossil feathers show much more elaborate feathers that have many of the same complex features of modern feathers.

Follow this link: http://io9.com/5840854/dinosaur-feathers-discovered-in-canadian-amber to see more photos of feathers fossilized in amber. And next time you see a member of the only living lineage of dinosaurs (a.k.a. a bird), take a moment to think about the feathers that cover its body and to realize that millions of years ago, there were animals sporting feathers that look just about the same. Pretty amazing!

A cluster of 16 feathers preserved in Canadian Late Cretaceous amber.

A cluster of 16 feathers preserved in Canadian Late Cretaceous amber.

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Powered flight, the ability to propel oneself through the air against the force of gravity, requires a great deal. From specialized bones to specialized skin, and everything in between, the demands of flight penetrate all aspects of an animals’ life. And yet, despite how mechanically difficult powered flight is to achieve, it has evolved three different times in vertebrate evolution, once in birds, once in bats, and once in the now extinct pterosaurs. One of the things that make the three different evolutions of flight especially interesting is that the three different groups accomplished the feat is such different ways.

A pterosaur wing has a large upper arm bone, two smaller forearm bones, a few wrist bones, and then four fingers. The first three are small fingers that have small claws at their tips and are free to move and grasp objects. The fourth finger is extremely long, extending all the way to the tip of the wing. The bones of this fourth finger are longer and thicker than the bones of the other fingers, and this is because this fourth finger supports the entire wing membrane. The wing membrane attaches all along the rear surface of the fourth finger, the rear surface of the arm, and then to the side of the trunk of the animal and even to the leading edge of the hind legs. That means that, when a pterosaur is in flight, the whole weight of the animal is being supported on once finger of each hand! Some pterosaurs got to an estimated 550 lbs (although most were about 25 lbs) with a 10 or 11 meter wingspan, so those are some strong fourth fingers!

A bat wing is the same upper arm bones of the pterosaur, but the hand is very different. Instead of supporting al the body weight of the animal on just one finger, all five of the fingers of a bat are elongated (the thumb is the only finger that is small and clawed and free to grasp). In between each of these fingers, and extending from the pinky finger to the body are membranes that the bat can stretch or fold as needed by moving the bones in its fingers, hands, and arm. Since all the fingers are sharing the load, each one is proportionately much finer and thinner than the fourth finger of a pterosaur. Additionally, bats have thin muscles that cover the surfaces of the membranes just beneath the skin. By tensing or relaxing these muscles, the bat has very fine control over the sharp and tension of the wing membranes, and this turns out to be very important in bat flight. It is not known if pterosaurs had similar muscles on the membranes of their wings, but it seems likely that they did.

A bird wing also has the same basic upper arm bones seen in the other groups, but instead of elongating bones and making them delicate and distinct, birds go the opposite direction. Most of the bones in the hand and fingers of a bird are fused together. This makes a structure that is short, thick, and strong. Out of this support structure extends feathers. Not a membrane made of skin like a pterosaur or a bat, but a completely different evolutionary innovation. Feathers, and flight feathers in particular, are strong and thin and light. Flexible enough to bend a bit to change shape, but rigid enough to support the weight of the bird and the forces of air-speed, drag, lift and gravity that all flying organisms have to contend with. In modern birds, muscles in the skin at the base of the feathers allow for independent control of each feather. This allows birds to have amazing control over the shape of their wing.

Flight is a fascinating example of how a complex structure or function can arise by natural selection. In these three cases, natural selection favored three very different, and ultimately successful, experiments in how to get an animal airborne. All three were very different solutions, which is worth remembering. Most of the problems out there, even really hard ones, probably have many different solutions, you just have to tinker and figure them out.

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Check out my post on The Ethogram (which is the Animal Behavior blog of U.C. Davis) on Hagfish at: http://theethogram.com/2015/01/26/creature-feature-hagfish/

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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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The Greater Sage Grouse is one of the iconic birds of the western U.S.  It is huge, dramatic, and has fascinating breeding behavior that has made it the focus of many, many studies.  It is also declining.  These birds need extensive expanses of sagebrush to survive, and such expanses are being reduced by everything from grazing to road building to invasive plant species to oil and gas drilling.  One particular population of the Greater Sage Grouse has just been listed as federally threatened under the Endangered Species Act.  It is a geographically isolated and genetically distinct population that lives on the boarder between central California and central Nevada, hence the name the Bi-State Sage Grouse.  Only six groups of this grouse still exist and four of them are in immediate danger of destruction.  Endangered Species Act listing will make it a federal crime to harm these animals or the habitat they rely on.  Specifically, the listing guidelines set aside 1.86 million acres along the California-Nevada board as Bi-State Sage Grouse habitat to be protected for their conservation.

This population is the most southwesterly population of the species.  As such it has the potential to be especially important to the species conservation in the face of climate change.  As temperatures warm, on a global scale, organisms that are adapted to colder climates will tend to move north, but they will have a harder and harder time finding suitable habitat.  The organisms that are adapted to warmer climates will also tend to move north, but they will have a higher likelihood of finding suitable habitat as they do so.  This means that the Bi-State Sage Grouse has a high potential of being able to move into the rest of the Sage Grouse range and prevent the species from going extinct.  This is one of many reasons why protecting subspecies and distinct population units is so important.  If this population is allowed to go extinct, it could greatly effect the overall extinction risk of the species in the future.

A decision on whether or not to list the Greater Sage Grouse as an endangered species throughout its range is expected in 2015.  It is considered likely that the whole species will be listed, so the rest of the species will also be protected at that point.

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