University Place

Evolution of the Chicken

– Welcome everyone to Wednesday Nite at the Lab. I’m Tom Zinnen, I work here at the UW-Madison Biotechnology Center. I also work for UW-Extension Cooperative Extension and on behalf of those folks, and our other cool organizers, Wisconsin Public Television, Wisconsin Public Radio, the Wisconsin Alumni Association, and the UW-Madison Science Alliance, thanks again for coming to Wednesday Nite at the Lab. We do this every Wednesday night, 50 times a year. And tonight is the start of our 13th year so pretty happy about that. Tonight, it’s my pleasure to introduce to you Mark Berres. He works here at the Biotechnology Center. He’s gonna be talking about the evolution of the chicken. He was born in Centralia, Illinois, which is in the central part of Illinois. [laughter] But somewhere in his family, somebody was smart enough that by the time he was in high school, they moved up to Eau Claire, Wisconsin, which is where he graduated from Regis High School, and then he went over to the dark side of the St. Croix to go to the University of Minnesota at St. Paul to get an undergraduate degree in genetics and cellular biology. Then he saw the light and came back to UW-Madison to get his PhD in zoology, a department which no longer exists, he just told me. Is that correct?
– It’s now the department of integrated biology.
– Well, that’s even better. Okay, he’s been on this campus since 1995. You remember that. And he’s been with the biotechnology center since 2016. This is something we’ve all been looking forward to. This is Mark’s second Wednesday Nite at the Lab. Please join me in welcoming Mark Berres back to Wednesday Nite at the Lab. [applause]

– [Mark] Thanks for stopping by tonight. As Tom indicated, we’re going to talk about the evolution of chickens. This is really at least a similar foggy, in terms of our understanding of the origins of these wonderful birds. We’re gonna discuss it at some detail tonight. It’s a story that really spans more than 300 million years. And we’re gonna cover it from the basic kind of origins of birds themselves, then we’ll jump into a discussion of chickens as a very small group of birds. There’s really only four species collectively termed jungle fowl, that are extant species. I want to talk a little bit about how they’re integrated into an understanding of how our own human culture has originated, and in particular, dispersed across the globe. In fact, the evolution of chickens, is extraordinarily important for monitoring human dispersal. So a lot of anthropologists make use of domestic animals, not just the chicken, but the chicken is one of the more interesting examples of how humans actually bring their domesticated animals with them when they disperse to new areas. And lastly, I want to kind of talk about some of the unknown trajectories, in terms of evolution, that the chicken may actually be taking. It’s a very big challenge, and we still don’t know, precisely, the complete story of the evolution of the chicken. It’s unlikely that we ever will.

Unfortunately, it’s difficult to predict where it’s going as well, and I’d like to give you some perspective on that as well. So let’s start about the first aspect of birds, for birds’ sake. The evolutionary origins of birds, actually remain, to this day, very obscure and controversial. And part of the complexity arises from the fact that we need to account for not only birds themselves, but also features that they possess, features such as feathers, the ability to fly, and even physiology and behavior. So most of us are probably familiar with archaeopteryx one of the oldest known birds. It’s about 145 to 150 million years ago. It actually has features so similar to modern birds that they’re actually nearly indistinguishable. Both Charles Darwin on the left and his ardent supporter, Thomas Huxley on the right argued that archaeopteryx was a sideline of the avian evolution and really not a direct lineage leading to any modern-day birds. And indeed, the consensus is, that’s probably true.

Archaeopteryx is already a bird in the modern sense, at least 145 million years ago, equipped with flight adaptations, including his wonderful coat of feathers. Unfortunately as such, it can tell us very little about the ancestry of birds overall, particularly for the early stages in the evolution of feathers, birds, and flight. Since the discovery in geologic dating of Archaeopteryx, many other avian lineages, as you can see here, in fact, have been discovered but all but one are in fact extinct. Nevertheless, archaeopteryx is very important for exploring the relationships between modern birds and reptiles, especially with respect to skeletal structures and most importantly, the flight adaptations that accrued over the evolution of the bird and also the timing of events in the geological record. And so the fossil record is a great piece of evidence that allows us to place organisms and their lineages on a geological time scale and in fact, it permits us to see changes in diversity in morphological change over time. The importance of the availability that fossil evidence simply cannot be overly stressed. It provides a morphological, feature-based timeline of evolutionary change. But there’s an insidious problem with the fossil record. Any sequence of events derived from that fossil record, is merely one hypothesis.

And the reason for that is that the fossil record is incomplete and moreover, it’s imperfect, but nevertheless, it’s all that we have and as scientists we must use that in order to answer evolutionary questions. Most of the major groups of Mesozoic reptiles, things like lizards, pterosaurs, crocodiles, and dinosaurs themselves, have at one time or another been considered the ancestors of birds. And after more than a century, still to this date, the ancestry of birds still remains highly controversial. Recent evidence which I am going to present today, actually seems to favor a synthesis, actually previously disparate hypotheses rather than any one single hypothesis. So recall that the amniotes are a group of tetrapod vertebrates with terrestrial adapted eggs. Anatomically, amniotes are characterized by features called fenestra which essentially are holes in the skeletal structure of any bone. The diapsid reptiles have in each side of their skull two temporal fenestra behind their eye orbits, right here. And so except for turtles and tortoises, living diapsids are in fact, extraordinarily diverse and include all extant crocodiles, lizards and snakes. And there’s one more major lineage that we’re gonna get to in a few minutes.

While temporal fenestration has long been used to classify all of these amniotes using the fossil record, the function of these fenestra have long been debated and no consensus has been reached. Many believe that they actually allowed muscles to expand and lengthen resulting in a jaw musculature to enable better predation. Others believe that they actually house the pneumatic sinus, which is in fact, very important in the evolution of warm-blooded animals because it’s connected to water vapor retention. Despite those questions, two lineages of diapsid reptiles actually remain. One group is the Lepidosauromorpha which include modern snakes and lizards. The other group is the Archosauromorpha which actually gave rise to a group of reptiles called the basal archosaurs or just more commonly, the thecodonts, and thecodont is the term that I’ll use for the remainder of our discussion today. The name, thecondont, itself refers to the presence of teeth that are set in well-defined sockets. Moreover, thecodonts are specifically identified by a fenestra in front of their eye socket called antorbital fenestra. So geologically using the fossil record, we can clearly identify, in most cases, these types and characteristics which enable us to group these animals in specific classifications.

The descendants of these so-called basal archosaurs, or thecodonts, include crocodiles, pterosaurs, and dinosaurs and certainly our mystery group, as we’ll discuss, birds themselves. Now on the geologic time scale, this area right here, corresponds to about 300 million years ago, towards the later portion of the Carboniferous Period. That’s when all the tree ferns and all the explosions of the ferns had occurred. The diagram shown here, kinda shows the general descent of the thecodonts and in fact, most scientists accept the relationships that are depicted here regardless of their specific views on the origin of birds. But two facets of this figure actually create substantial confusion that I think it would be helpful to our discussion. Firstly, while pterosaurs were indeed flying reptiles, they are not at all related to birds, in fact, the wing structure is a great example that you’ll find in every basic biological textbook of convergence. Second are the terms that are used to group the two major lineages of dinosaurs. The term bird-hipped or ornithischian refers to the backward-facing pubis or opisthopubic formation. It’s a characteristic of many herbivorous dinosaurs such as stegosaurus.

This term was used in the older literature because modern birds also have a backward-facing pubis. In this case, the confusion arises as a terminological rather than a taxonomical relationship. In contrast, the reptile-hipped or saurischian dinosaurs have a forward-facing pubis. These include the herbivorous sauropods and carnivorous bipedal theropods all of which are classified as dinosaurs. In general two theories of the avian evolution exist. First there’s a pseudosuchian thecondont, or just plainly thecodont theory. This was postulated by Robert Broom in 1913 and later championed by Gerhard Heilmann, very smart guy. Secondly there is just a theropod, or a dinosaur origin of birds. This was actually postulated by Thomas Huxley, the contemporary of Darwin back in 1868.

We’ll talk a little bit more about that. But really, the primary proponent, after the acceptance of the thecondont theory was John Ostrom. Unfortunately a full discussion’s gonna take so much time, so that we’re gonna only focus on Heilmann and Ostrum because they’re key players, they weren’t the originator of the ultimate hypothesis, Broom and Huxley were and potentially others, that’s debatable, before them. But throughout our discussion, remember that we actually need to consider simultaneously, not only the origin of birds, but feathers and flight too. Normally in a course I used to teach, it took about four weeks to do that, so we’re gonna burn through this, but I think you’re gonna be able to accept what we have to say. The primary difference between the two theories, really are the specific line of decent, in other words, who begat who, and the actual timing of divergence. Heilmann down here believed that birds evolved directly from a thecodont or archosaurian ancestor early in the Triassic Period. Quite a different theory was postulated and championed by Ostrum, he believed that birds evolved from theropod dinosaurs, which actually didn’t appear in the fossil record until late in the Triassic. Among Heilmann’s many accomplishments, he also advanced an arboreal model of feather evolution.

Feathers were adaptations to improve aerial gliding capability, ultimately leading to flapping flight. And so for this theory actually to work, an avian ancestor must have been able to climb trees, such as depicted in this cartoon here, and we’ll come back to this, so that it could actually use gravity to accomplish flight. On this basis alone, Heilmann considered a dinosaur, a thecodont, I’m sorry, wait, that was a big faux pas, that is a thecodont, not a theropod, a key to bird ancestry. The quadrupedal motion used by euparkeria enabled it to climb trees where he believed that flight could have evolved under this so-called arboreal model. It had other anatomical features consistent, skeletal features, that are found in modern birds as well. And so, when he first postulated this synthesis, this idea of an arboreal avian ancestor sat really well with most researchers. After all, so the argument went, it makes aerodynamic sense for key flight adaptations to evolve arboreal, where gravity is your friend. So then Heilmann really argued that birds evolve directly from an ancestor of those thecodonts early in the Triassic euparkeria, not that birds descended from dinosaurs or theropods, which occurred at time much later in the Triassic. Well from the time that he postulated that, his theory actually remained strong and relatively unchallenged until 1973 when John Ostrum, based on newly-acquired fossil evidence, revived Thomas Huxley’s original theropod, or dinosaur origin of birds.

Ostrum refined Huxley’s theory and suggested that a specific subset of theropods, these so-called Dromaeosaurs, like deinonychus and velociraptors, were the ancestors of birds. Now I have to digress for a moment. You’re all familiar, likely, with the movie, Jurassic World, Jurassic Park, et cetera, et cetera. You all remember the velociraptors. Does that look like the velociraptor that you actually saw in the movie? No, in fact, they call that velociraptor. In fact velociraptors were probably about the size of a small turkey or so and deinonychus, kind of the quintessential dromaeosaur that Ostrum used to forward his theories, was in fact, what’s represented in that movie, although I think deinonychus is not as cool sounding as velociraptor. Nevertheless, it really broke my heart when I saw that because now I can’t believe everything that I see on television and in movies. [audience laughs] In any case, in contrast to Heilmann, feathers were essentially co-opted for flight, having in Ostrum’s mind originally serving an insulative mechanism. And so Heilmann believed that feathers actually evolved in terms of the acquisition of flight, through his arboreal model.

In contrast, Ostrum believed that feathers had nothing to do with flight at all and only later in the evolution of feathers themselves, were they co-opted to actually serve a flight function. So you should be able to see now, you gotta worry about not only birds themselves, but how feathers came onto the scene, how flight evolved, et cetera. But one major objection to Ostrum’s theory was the obligate bipedal nature of theropods. Essentially, people asked how do you get a bipedal theropod up a tree? It’s not easy. [audience chuckles] A key piece of evidence supporting this objection was the fact that theropods actually have a forward-facing pubis which would definitely interfere in their ability to climb trees. That is in addition to actually trying to just use two feet or maybe using your forelimbs as well to do it. Perhaps most damningly, the acquisition of flight from ballistic jumping, or so-called ground up, or cursorial mode of evolution in the acquisition of flight, that was just equivalent to aerodynamic heresy at the time. That’s a big story, it is still continuing to this day. But most importantly, there was always a big problem at the time Ostrum was promoting his hypothesis.

The oldest bird, archaeopteryx, was older than any of the feathered theropod dinosaurs that were previously found typically in the range of around 25 to 30 million years, therefore, the critics of Ostrum claimed that feathered dinosaurs could not have been ancestral to birds because all feathered dinosaurs thus far discovered were younger than archaeopteryx. Well, really Ostrum’s theropod dinosaur theory has always been troubled by the absence of those feathers on dinosaurs older than archaeopteryx, but what did I say earlier about the fossil record? It’s imperfect and incomplete. All you have to do, pun intended, is wait a little while and you’re gonna have a discovery. And in fact, in 2009 an incredible find in China provided the critical last bit of evidence that really tended to suggest that Ostrum was, in fact, correct. Anchiornis huxleyi, a completely feathered theropod was found and dated to about a geological time of 164 million years, which is much older than archaeopteryx itself. Archionics, I’m sorry, anchiornis is a troodontid. You can see it’s just a tiny, little ankle-biter here. It’s a small, very small sized theropod. It had unusually long legs compared to other theropods, consider birds of modern day and with a large curved claw on retractable second toe, right here.

This is very similar to the sickle claw of the dramaeosaurs, like deinonychus that we saw earlier. Troodontids also have some other features that correlate with modern day birds. They had unusually large brains among the dinosaurs. Their eyes were also unusually large and pointed forward, indicating that they probably had some good binocular vision, just like birds today. The ears of troodontids were also different from other theropods having extremely enlarged middle ear cavities, indicating possibly a very acute hearing ability. Now, in the past 20 years, hardly a week goes by without reports of newly discovered fossil birds adorned with all types of feathers and they are, in general, many of them are in fact, much older than archaeopteryx and all of them are classified as theropods. This one was just recently published earlier this year, last month, in February. This is a fossil image of a bird called caihong juji, which I believe means rainbow crest. It actually was demonstrated to have iridescent plumage, in other words, highly organized substructures of melanochromes which give, hummingbirds is gonna be the best example here in Wisconsin, that beautiful iridescence on their gorget.

This continues to happen, primarily out of Mongolia and that is the happening place for this type of work. But Ostrum still faced the problem of how to get an obligately bipedal theropod up a tree. And so if he could only assert that a small size bipedal theropod could actually somehow gain access to the trees, the arboreal model, that at the time everybody preferred, that model ensues automatically. And evidence suggests that these theropods were probably coelurosaurs which included the dromaeosaurs. Compsognathus was a coelurosaur and was probably at least facultatively arboreal. Now I know if you saw Jurassic Park 2, you all saw what a little compsognathus looked like that was on the beach that attacked that little girl on that island and essentially compsognathus was actually the dinosaur, the coelurosaur that Thomas Huxley used and actually compared it to the modern-day chicken that allowed him to formulate his theories, to actually consider that in fact, there was a dinosaur origin to birds. So by allowing that bipedal theropod to climb a tree, we can actually eliminate a very complicated cursorial or ground up model for the evolution of flight ensuing an arboreal model. Well a new, relatively new, about 20 years ago or so, theory to explain how a bird’s flight apparatus first evolved is that it’s forelimbs may have added traction to run up inclined slopes like trees. And so no one is actually postulating that a bipedal organism just uses its feet to run up the tree, forelimbs were actually involved.

And in fact, the forelimb, the apparatus in birds, has been extensively remodeled in order to accommodate flight. A researcher named Ken Dial in Montana observed the behavior of chukar partridges, chicks essentially, as they ran, and adults too, and worked out why they actually flap their wings during climbing events. He found that birds employed something called wing-assisted incline running. Here the flapping motion of the bird’s forelimbs did not lift the birds as if it were to fly, but rather quite the opposite. The flapping action actually resulted in the physical force that pressed them downward for better traction, much like spoilers work on high-performance race cars. He found that even day-old hatchlings can easily traverse inclines of up to 45 degrees without flapping. They just kind of move their unfeathered, well at least downy-feathered forelimbs, but if they flapped they could actually scale greater slopes so hatchlings could climb a 50 degree incline. Four-day old chicks could climb a 60-degree slope. Twenty-day old chicks could actually climb a 95-degree slope, an almost vertical surface.

Adults can get up to 105-degree overhang and it’s just by flapping and they’re not using their wings to actually gain flight. This is to gain traction. I gotta throw this in here because this is so cool. I just put it in just a few minutes before I came in here. In 1985 Walter Bock elaborated upon a hypothesis published originally in 1880 that suggested flying originated in small arboreal quadrupeds similar to euparkeria, that may have jumped tree-to-tree or tree-to-ground, for any variety of reasons, feeding, predator avoidance, mobility, et cetera. This later became the arboreal model of flight evolution that was championed by Gerhard Heilmann. After all, there were all kinds of non-flighted animals that do just this. You can actually go outside, lemurs, flying squirrels, even reptiles like snakes, okay, contributed to his understanding of a sequence of evolutionary form change that would enable possibly birds to acquire flight. Walter Bock elaborated Marsh’s theory, which was originally, he was the credited originally to the arboreal flight model back in 1880, to depict an evolutionary pathway following a simple and direct route without these so-called hopeful monsters or those organisms without elaborate intermediate evolutionary steps.

These steps included climbing the tree, jumping off a limb, parachuting, gliding, eventually acquiring powered flight. He explained the adaptive value of arboreal life in this, it’s really cool, it’s called the invasion of trees model and it’s really regaining a lot of traction. In 2003 the best evidence of a tree climbing, feathered, facultative biped, bird-like theropod was in fact, named microraptor gui. Take particular note of its shape. Does this remind you of Bock’s gliding animal? I mean look at this. This was done in 1985 before any such fossil evidence of an animal similar or near the anatomical structure of microraptor had ever been known. I mean this is a classic prediction followed by observation. This is what science is supposed to be, that’s why I had to throw that in there, a plug for science. Despite the way Heilmann and Ostrum are used in a mutually exclusive manner, it now actually seems that they were both right and both wrong.

I wouldn’t really fault them too much because they really had to work with extraordinarily complicated composite hypotheses requiring them to simultaneously account for the origin of feathers, birds themselves, and flight. That’s a lot to deal with and at the time, the information that we have available was not available. Nevertheless the most recent evidence that we’ve acquired just in the past 30 years or so, supports a more unified theory and I’ve got that depicted over here. After more than a century, recent evidence supports a more unified composite theory. Birds, chickens as we’ll see in the next few slides, are derived from theropods, which themselves are egg-laying reptiles that originated around some 216 million years ago. The first unequivocal bird archaeopteryx, which appeared on the scene around 145, 150 million years ago, yep, bird, but in fact, did not give rise to modern birds per se. And the modern birds actually evolved from a group of carnivorous dinosaurs called the dramaeosaurs which were around around 120 million years ago. These are some examples that we’ve discussed, to include velociraptor, deinonychus, anchiornis, and the like. So the diversification of these proto-avian forms actually occurred vary rapidly until the onset of the Cretaceous extinctions here at around 65 million years ago when nearly all dinosaurs went extinct.

So these are all kind of the bird-like organisms in this area here. A small group of dinosaurs, of theropod dinosaurs, the so-called transitional shore birds did survive and then quickly diversified into the 10,000 or so modern bird species that we actually see today. And so indeed, now you know, really, take my word for it. Birds are truly the only remaining lineage of dinosaurs that in fact, survived the Cretaceous experience. The dinosaurs never went extinct, they changed. They evolved into birds themselves. But all of the incredible bird diversity that we have today, only four species, collectively called jungle fowl, are considered ancestors of the modern chicken. Jungle fowl belong to the order galliformes, which includes all of the pheasants and quail. It’s a small, it’s not the biggest order, around 214 species or so, but the special feature which distinguishes jungle fowl from all other birds, is the presence of both the presence of a distinct, enlarged cone and accompanying waddles and there are a tremendous variety of these in existence.

The jungle fowl, as a whole, are widely distributed across Central and Southeast Asia, but each species tends to have a specific habitat preference. The red jungle fowl has the largest range of the forest species and in contrast to the others, red jungle fowl exhibit marked geographic variation, especially in male plumage. Females do not exhibit that much variation in their plumage characteristics. All of these jungle fowl are omnivorous and they all exhibit behaviors that are essentially like those that we see in modern domestic fowl. One key difference, however though, is their vocalizations, particularly males differ considerably. Jungle fowl typically breed once per year, laying only clutches of around four to eight eggs. Curiously, red jungle fowl also have white skin, while most domestic chickens have yellow skin, including the gray jungle fowl and that’s going to be really important in just a few minutes. So, unlike the sequence of mammalian domestications which are fairly well known, the origin of the domestic chicken, just like the origin of birds themselves, is very controversial and has been debated forever. So not only has the site and timing of the first domestication event remained contentious, but because multiple species of jungle fowl exist in close proximity, the possibility that domesticated chickens originated from multiple wild ancestors also remain unresolved.

And so there are three major questions, there’s hundreds of questions, but three major questions that have perplexed researchers and people are actively investigating this, are domestic chickens derived exclusively from one of these extant breeds of chicken? And we’ll see that most people believe that red jungle fowl was the ancestor. Alternatively, did others, did any of the other species, any of the other three, or were there any other closely related species that actually made a contribution? And where did people first domesticate chickens? And when did this occur? These questions and the answers, more importantly, to these questions have much more meaning than just evolutionary importance. They can provide insight into our own history and I’m gonna show you a number of examples of that. And each has implications in both the use of chickens as model for biomedical research and also revealing a genetic basis for rapid evolutionary adaptations, essentially the foundations of our modern animal and plant agriculture. For example, nearly all modern chicken production depends on two breeds of chicken, the white Cornish and the single comb white leghorn. Incredibly only after about sixty years of intensive agricultural selection, efforts have yielded these powerhouse birds. We’ll talk more about that. I want to talk a little bit about the basis of how Darwin believed that through character differences in the fossil record and also cross-breeding experiments, Darwin concluded that the domestic chickens were derived solely from red jungle fowl. And he did this in “The Variations of Animals and Plants under Domestication,” which was published in 1868.

In that argument, he also based some of his evidence on translations of Chinese documents published in 1609, which indicated to him that chickens were first domesticated in China at around 1400 years B.C. These actually, these beliefs again were relatively unchallenged when early in the 1940’s, they began to receive some criticism by a number of researchers who believed that perhaps two, three, or all four of the varieties of different jungle fowl may have contributed to chicken domestication. Moreover, these same authors that were challenging Darwin, also believed that chickens were first domesticated much further to the west, here in the Indus Valley, in near modern-day Pakistan, around 2,000 B.C. And this is a belief that prevailed throughout the latter half of the 20th century and still is fairly commonly cited to this day. The answer to the species contribution question may have actually been answered. The majority of chickens used for commercial egg and meat production have yellow skin. The occurrence of the yellow skin, and also in the legs, is influenced by the amount of carotenoids, which is a type of a xanthophyll, in the feet. More carotenoids produce more intense yellow color, a condition that’s favored by many consumers. And in fact, in the modern chicken industry, marigold petals continue to be used in certain areas, to control the color of egg yolks because people have a preference for the intensity of the yellow pigmentation, which are carotenoids, in egg yolks.

Nevertheless, researchers evaluating the origin of yellow skin in modern day chickens, they discovered that in fact, is was caused by a recessive regulatory mutation in the gene called BCDO2, which is beta-carotene dioxygenase 2, in skin. Essentially, that gene cleaves yellow carotenoid pigments into colorless byproducts, thus a reduction in the expression of that particular gene, BCDO2, produces yellow skin because there’s nothing to cleave the carotenoid and result in that yellow color. Essentially this is a recessive loss of function and mutation. Now researchers concluded that yellow skin must be a hybrid trait resulting from a cross between gray jungle fowl and red jungle fowl. There remain some questions to this research including the extant crosses of red jungle fowl to gray jungle fowl tend not to produce fertile hybrids. There’s a lot of contention and there are some issues regarding the source of the red jungle fowl and the gray jungle fowl actually having been contaminated by the introgression of modern day genetic elements into their genome. There’s also an issue where hybrids in which the BCDO2 allele exists, we don’t know whether the yellow skin or the white skin allele of that particular enzyme is ancestral or derived. So their evidence is pretty good to suggest that there’s a hybrid origin of our modern chickens, but it’s by no means a closed case. Up until 1988, most people believed that the domestication site, as I said, occurred in Central Asia in the Indus Valley, but new archeologically-driven evidence provides a new interpretation of both when and where chickens were first domesticated.

The anthropologists actually use carbon-14 data from bones found essentially in trash piles, again because of the unique internal structure of avian bones, they can discriminate bones that were derived from birds and presumably chickens, from mammalian bones. And what these researchers found was that over 16 archeological sites in China, here, actually predate the Indus Valley carbon-14 date of birds by about 4,000 years. Moreover, at least 13 sites have been identified much further to the west in Europe and Western Asia, all of which also are older than those bones that were in fact, found in the Indus Valley. And so the reason for that are two trade routes, a northern route and a Mediterranean route, are thought to have supplied the western cultures with domesticated chickens. And by 100 B.C. essentially chickens were everywhere across western Europe, but strangely, despite the two trade routes, maybe you can see, India actually was bypassed completely and did not acquire any domesticated chickens until much later in human evolution. One curious aspect is that the site of Chinese domestication did not overlap the extant range of red jungle fowl and this has important implications. It means that either the present range of red jungle fowl has contracted somewhat, alternatively, red jungle fowl were obtained elsewhere, so perhaps more southerly area and moved northward into China and which has a corollary in that red jungle fowl actually domesticated by cultures elsewhere and then subsequently transported to the Chinese. Let’s move to our side of the world. Analysis of the cultural diffusion of domestic chickens has intriguing relevance to our side of the globe too.

The presence of chickens in the American continents, both North and South America, traditionally has been attributed to Spanish introductions of European chickens after their arrival in the mid-portion of the 15th century. However, there is very heated debate about whether Amerindians in South America possessed chickens before the arrival of the Spanish, particularly in relation to several unusual Chilean breeds that lay blue-shelled eggs and possess distinctive plumage patterns, namely ear tufts and the lack of a rump. The possibility of chickens being present in the Americas, pre-Columbian, continues to gain traction having been popularized by a number of books by Gavin Menzies. He actually believes that pre-Columbian contact with the Chinese in the early 15th century provided chickens to the region. Other researchers actually link linguistics, cultural artifacts, cultural use, primarily religious ceremonial use, and names for chickens. They actually suggest contact with Asia much, much earlier than even Gavin believes had occurred. Based on mitochondrial DNA sequences, and again carbon-14 dating of chicken bones that were discovered in middens, a New Zealand group claimed firm evidence for a pre-Columbian introduction of chickens to the Americas. In one particular bone obtained in Chili, here a mutation was discovered that also occurred much further west in the Pacific along and among the islands of Tonga, American Samoa, which are actually dated to times much earlier. And so the idea was that the well known seafaring activities of the Polynesians kinda fit well with this genetic mitochondrial DNA evidence.

Anthropologically, this evidence was really intriguing because of speculation of ancient Polynesian contact, which itself was popularized by the voyage of Kon-tiki. Some of you probably remember that. I think it was a Norwegian guy. He was going in the opposite direction, I believe. He was going from South America to Polynesia, but nevertheless, it’s a sensible connection. In particular, Easter Island, Rapa Nui, is very important because it may have facilitated the contact, essentially, kind of the trans-shipping point of people between Polynesian and South American cultures. As such, the New Zealand researchers went on to conclude that the South American chicken had been introduced by Polynesian voyagers way before our first European contact, probably around in 1300’s or so. Well, later that year, a challenge was posited by a completely different group, an Australian group. Those guys conducted a much more elaborate study and concluded very vociferously that there was absolutely no support for Polynesian-South American contact as indirectly derived from analysis of DNA sequences and carbon-14 data.

Their primary evidence was that a Pacific and Chilean pre-Columbian chicken sequences fall into a particular haplogroup, which just means a variant or an allele of the mitochondrial DNA sequence, which actually consists primarily of widespread Indian, European, and sub-continental Chinese haplogroups. And so importantly, haplotype E would have been introduced by the Spanish in the 15th century as well as with many European breeds being transported subsequently to the Americas through the colonial era trade. But in agreement with the New Zealand group, the Easter Island specimens were classified as pre-European, but none of those Easter Island haplotypes have been detected in either ancient or modern South American chicken breeds. And even if they did, their study concluded that there is no evidence at least supporting that they persisted, so they may have made it there, but we don’t know because none exist today. There was also the matter of the, an issue with the carbon-14 data being affected by seawater isotopes. This group claimed in fact, that their carbon-14 dating information was biased to be much older than it actually was. We don’t have time to talk about that. It’s reasonable, but it’s still acrimonious at best. We’re finding further ancient DNA techniques.

The Australian group further expanded the study and showed that the individual bone used previously by the New Zealand group, to link Easter Island and South America was in fact, contaminated by exogenous DNA. Unfortunately this is monumental problem with ancient DNA studies, but fortunately standardized protocols have since been developed which minimize, but they do not eliminate these types of problems. So, in fact, we do this type of work here in the Bio-Tech Center. We need suits and everything. It’s quite an involved procedure. Additional analyses performed by the Australian group reaffirmed connections between chickens off of the mainland and throughout Micronesia, but in fact, no evidence of any chicken haplotypes ever went further east. For now, they stopped at Easter Island. Let’s switch gears a little bit and talk more about kind of more of a modern age of chickens. And so when most domesticated animal species were used from the beginning as a food source, some, like dogs, cattle, and horses, primarily served as work animals, but the situation with chickens is actually considerably different.

Archeological and historical records indicate that the first use of domesticated chickens was actually cultural, particularly in religious and superstition ceremonies, decorative arts, and in fact, at least what they call, entertainment, namely cock fighting. Only much later were chickens utilized as source of human food. The oldest form of entertainment was undoubtedly cock fighting. Male jungle fowl naturally fight and it was this innate tendency that actually, probably, somewhat possibly, who knows, contributed to the first domestication efforts. Breeds like the Assil here and the Shamo are testaments to the efficacy of selection efforts put forth by their human breeders. Some of you, any presidential historians here? You probably all heard the story about Honest Abe Lincoln, that one in fact, there is some evidence to suggest that that’s a sanitized interpretation because he had returned some money from an individual who had overpaid at a shop, in fact, I’m trying to confirm this, I don’t know if it’s true. I’d love to get an email or a phone call from someone who is an expert in this area. But in fact, the moniker of Honest Abe actually came from Abraham Lincoln’s ability to fairly judge cock fights in early American history. Not sure, I’d love to find out for sure.

Manipulated for thousands of years, there are now hundreds, if not thousands, of chicken breeds in existence throughout the world. They’re roughly divided by primary use, whether for eggs or meat or ornamental purposes and with some of the being considered dual purpose breeds, like for both eggs and meat. Commercial chicken breeders have an impressive record at improving the efficiency of egg and meat in poultry production, which has actually helped to make poultry products affordable and available for, excuse me, consumers worldwide. Incredibly concerted efforts to improve significantly the chicken for use in US agriculture only had taken place very recently, starting after just World War I, but primarily in the years following World War II. Along with their important use for food, chickens also play a critical role in improving human health. Right here on campus, they’re are many researchers advancing our understanding of biochemical and disease processes using chickens as biomedical models. Moreover, just in time for the later portion of the influenza season, thank a chicken for the vaccine. Even though it may not have been perfectly effective, it was still made from hen’s eggs in its entirety. Over the last 50 years, since World War II or so, genetic selection in poultry has been proven to be extraordinarily successful resulting in specialized egg laying breeds and fast-growing meat breeds that far exceed the production of their wild ancestors.

Approximately 60 breeds or so of chicken that have been raised in the United States post-World War II, actually were abandoned by commercial enterprise in favor of just a handful of very high performers. Today five industrial breeds of chicken supply almost all of the chicken meat and brown eggs and white eggs sold as food across the world. Layer strains are obviously– are mainly selected for high egg output and efficient feed conversion. White eggs, now, come almost exclusively from a single breed of white leghorn and brown leghorns are derived from breeds related to Rhode Island reds. Today hens from modern layers can produce on the average of nearly 300 eggs per year which is a far cry from a single clutch of four to eight of the wild red jungle fowl. Under a commercial perspective, the general breeding goal for chickens or any farm species for that matter, is balanced performance profile suitable for efficient production of meat or eggs under the prevailing or expected future conditions. Poultry breeding is no different. It’s part of the food chain and goals have to be defined according to the expected demands of consumers and those who produce and market the animal products. Increasing the tension to agricultural sustainability in farm animal breeding includes the objective to produce animals under conditions which meet ethical standards of society.

And one key aspect of this in fact, is disease management. In an era with increasing environmental change, particularly the emergence of exotic infectious agents, we should really be on high alert about the immunocompetence of our agricultural animals. Intensive selection has reduced genetic variability, the raw material for evolutionary adaptation which has profound impacts, not only for the well-being of our ag animals, but also for our human society. One example that if you were here in 2015 in the Midwest, was the widespread occurrence of a high path H5N2 avian influenza epidemic. At least 60 million birds, chickens, and turkeys, and probably much more than that, were actually destroyed and in doing so, incurred more than a $3 billion economic loss, just within this country. But with regard to immunocompetence, genes, for example, in the major histocompatibility locus play an important role in not only immune responses of animals but us as well. It is responsible for the resistance of many sources of disease including viruses, bacteria, and even internal and external parasites. To answer the question if selective breeding has reduced the level of MHC variation, which in and of itself is a good thing, we assayed more than 1,300 commercial broilers and layers that were derived from multiple commercial and research lines and we found actually 78 unique haplotypes, or different forms of the MHC locus that were actually assigned to 22 families. Analysis of that data showed that our approach was sufficient to identify all previously identified haplotypes, which was done serologically by a scientist named Briles down at UI-UC.

But we were also able to differentiate many new haplotypes. At this time the work was completed, we actually concluded that lots of MHC diversity exists in domestic chicken lines and the connection to the health and MHC of an organism is really in terms of disease resistance. A lot of variation in the MHC loci are gonna provide more opportunities to combat diseases whether they’re bacterial, parasitic, or viral in origin. Together with a former student of mine, Hoa Nguyen, we actually designed a project to assess MHC variability in the ancestors of the domestic chicken. The reason that we did that is because the evaluation of the MHC haplotype variation in commercial, highly-derived lines was essentially an N of 1, we just saw what was in fact, in these commercial lines. We had no idea what was available in terms of allelic variation in other chickens. We actually focused our efforts in the Annamite Range. This is a plateau in south central Vietnam. It’s extraordinarily topographically diverse and it supports an amazing diversity of life and particularly phasianinates, or chickens and pheasants and quails, extraordinarily diverse here and very abundant.

I suspect that this is probably a species diversification center where in fact, the chicken may have indeed been first domesticated. Nevertheless, within the Annamite Range and surrounding areas, we captured hundreds of red jungle fowl from four different ecotypes. There’s Hon Ba here which is kind of a deciduous forest in the foothills of the Annamite Range, similar to types of forests that we have here, but much more diverse floristically. Yok Don is further inland adjacent to the Cambodia, it’s very dry, seasonally dry, deciduous forest, seasonal fires, red jungle fowl are everywhere in that particular area. This is almost totally devoid of human habitation as well. Lowland areas in Cat Tien, this area produces the best protected habitats of typical lowland rainforests in the Southeast areas, bamboo forests predominate, again, abundant with red jungle fowl, they love bamboo. And then Lo Go Sa Mat, this is also an area that borders Cambodia. Now this one’s moderately disturbed as human activity is common in the area, but nevertheless, there seems to be relatively undisturbed population of red jungle fowl. There’s one, this guy right here, this is Cambodia here, this is Vietnam here.

That guy would cross without any impunity going back and forth. He’d go over here for the day and then at night he’d come back and nobody cared. [audience laughs] Anyway, importantly, these areas were protected and with the exception of Lo Go Sa Mat, they were very remote as to avoid any genetic introgression from domestic stocks, that plagues studies that compare so-called jungle fowl. Many of these species, specifically the birds that they use in these studies, have been introgressed with domestic species. Great time, really hard work, we received a lot of assistance from a lot of the locals no matter where we went. This is Mr. Ha, he could draw blood like nobody’s business out of a bird, never used a syringe. He had the steadiest hands I’ve ever seen. Mr. Ton, again, he was the one who kind of told us that our trapping techniques were moronic, I think was the translation. [All laugh] And he was absolutely correct because we thought, oh, yeah, we’re gonna use what we use to like, collect sage grouse or greater prairie chickens, these little cloverleaf traps.

They work really well here in America. You bring those over to Vietnam, the chickens they look at ’em, pfft, no. They’re way smarter than any thing that we have over here. Mr. Ton really taught us how to actually capture these birds. We even had a lot of the forest service people in some of these areas help us out too. These guys are practicing on a domestic species of bird. It was really a great collaboration between Hoa and myself. Hoa is native Vietnamese National and it was the funnest time, I think, of my life in that area doing that fieldwork. In any case, interrogating that MHC locus in the same manner as before, the results of the red jungle fowl analysis were really quite striking.

Without any doubt, even though we did discover some MHC variations in domestic lines, it was a far cry of what we uncovered in red jungle fowl across those four areas. This information really prompted a reconsideration of what MHC diversity actually really means. We expanded the study to domestic heritage breeds. So these heritage breeds are those modern domesticated chickens but tend to be not selected intensively like our commercial breeds. Heritage breeds are diminishing but still are present worldwide, they’re everywhere. In particular the Finnish Landrace breed that we investigated actually traces its origins almost a thousand years ago with multiple lineages maintain of small populations in isolated villages typically by very wealthy people. In Finland only the wealthy could actually keep chickens historically, but certainly that has all gone away. The breed is extraordinarily well-adapted to cold, Finnish climates. They’re very broody hens and very infrequent egg layers, but they can forage like nobody could ever believe.

Conservation efforts to protect this endangered species actually initiated by a hobbyist breeder in the ’60’s. A national conservation program was established near 2000, I think it was 1998 or something like that, and now consists of at least 12, there’s many more actually now, different populations that are currently maintained by a network of amateur hobbyist breeders. In the 12 Finnish samples, I’m sorry, in the 12 Finnish Landrace populations we sampled, we found 36 haplotypes. 16 were known previously from the domestic commercial and research lines. There were none in common, in fact, we have not found any MHC haplotypes in common with the red jungle fowl that we kept from Vietnam. The 16 that were actually previously reported, had been seen in New Hampshire, Rhode Island, reds and white leghorn breeds, suggesting that there was actually introgression with the existing domestic stocks that were imported into Finland post-World War II. We moved over to Germany. We sampled approximately 1,500 individuals from German heritage breeds. There we discovered 104 haplotypes and in this sample, only 20 were known previously, which leaves us with an abundant 84 novel haplotypes.

We’re currently assessing haplotypes from chickens in other parts of the world, namely, Africa, Asia, and also the Caribbean. So earlier I mentioned that most of the MHC haplotypes, even those that have been known for decades, were not associated with any particular disease resistance. We know that MHC confers resistance to diseases, but we don’t have a lot of evidence of specific haplotypes conferring resistance. There’s one exception, it’s the B21 haplotype which confers resistance to Marek’s disease, a really nasty disease that affects chickens. Those of you that keep chickens as backyard here, when you order your chicks, you always say, do you want a Marek’s vaccination, check “yes,” definitely. But clearly whatever immunity the Midwestern chickens had during that H5N2 outbreak in 2015 was not sufficient to protect them. But we have seen tremendous MHC diversity exist not only in the progenitors of domestic chickens, the red jungle fowl, but also the heritage breeds living throughout the world and also living in many different and disparate environments. And so combined with genetic information, I really believe that kind of a phenotype, genotype connection will be more emergent and accessible than ever before. This is important because the loss of genetic diversity will not only decrease the ability of chickens, and really all life, to evolutionarily respond to environmental change, but will also likely sacrifice useful biological information, such a stock genetic diversity and a suite of potentially important novel and as of yet, untapped genetic resources.

But we have to take the appropriate steps to protect these valuable genetic resources. We need to preserve and study what we have remaining. For example, who knows what the MHC in that guy looks like? [audience laughs] This is a breed, it’s called the dong tao. It’s a heritage breed in Vietnam. These birds are typically purchased around holidays, namely Tets, Christmas time here. Birds like this guy, this guy was selling in Ho Chi Minh City, Saigon, $3,000 US. That’s a cheap one. [laughs] Very expensive, so this is a culturally driven breed. You might think, oh my god, that bird has the worst mite infection I’ve ever seen.

No, it’s not, in fact, those are not mites, that emargination of the scales is genetic and so these are not pretty chickens. Beauty is in the eye of the beholder. Nevertheless, my point here is to understand that it is for you to understand and appreciate that while we have all these great animal, agricultural enterprises are that we have to be cautious about what we’re doing to them. Until 2015, the prevailing attitude about high path avian influenza affecting the chicken and the turkey products on the commercial level, no, it’s not gonna happen. Well it did, and gangbusters and unfortunately despite all the implementation of biosecurity protocols, I hate to say it, but it probably will happen again, albeit, I hope not. It’s not good for anybody, including the animals involved. And so those of you who do keep chickens or who are involved in educating yourself about the usefulness of genetic diversity, I certainly hope that you can see that chickens are much more than maybe, Sunday dinner, or a source of eggs. The evolutionary importance in terms of research, birds are models for a lot of human diseases like fetal alcohol syndrome, speech impediment learning, vocal communication, things like that, bone morphogenesis, chickens are one of the greatest models. We also have a connection to human culture as well and so chickens are important facets.

We have no time, I’m over time, my apologies. But there’s just so much cool stuff, particularly in the cultural aspects, namely the religious importance of chickens. In Vietnam, often on Catholic churches, you’ll actually see a weather vane of a rooster and I’ve noticed that some older North American towns, you can see that on many churches as well. There’s none around here, but I know over in Michigan, I’ve seen a number of them, one near Hope College, in fact. But the point here is, we have the tools available to conserve our genetic resources, to conserve our agricultural animals and also the natural biodiversity. We can’t sit aside and let it go by. It’s just too valuable and too important for the evolution of our own future. So, thanks so much for attending. [audience applauding]