Genes suggest rhinos, tigers, humans and all other mammals had insect-eating ancestors

Paleontologists have long noted how mammal fossils seem to change dramatically in form from one era to the next. In fact, few things in the fossil record seem to contrast more than the mammals that lived alongside the dinosaurs and those that survived after most dinosaurs went extinct some 66 million years ago.

One of the most obvious changes is that the Mesozoic (dinosaur era) mammals were generally very small and had teeth with sharp, pointed ends, both of which are characteristic of modern insect-eating mammals. Post-Mesozoic mammals, however, attained much larger body sizes and had teeth that were clearly used for grinding up plant material or slicing meat.

Why did mammals change? The typical thought among scientists is that when dinosaurs were the dominant land animals, they occupied nearly all of the herbivore and carnivore niches, restricting mammals to insect-eating and therefore small body sizes. Then when these dinosaurs went extinct, mammals were able to evolve and adapt to occupy these newly vacant ‘jobs’ within their respective ecosystems.

The last dinosaur
The extinction of most dinosaurs is thought to have allowed mammals to adapt and diversify

Together, this implies that all modern herbivores and carnivores, ranging from rhinos and cows to tigers and dolphins, descended from tiny, insect-eating ancestors. At some point, these ancestors began foregoing their insect prey in favor of plants and/or meat, and their bodies changed in form and function along with these newfound diets. To help you imagine the scope of what this means, picture the small insectivorous Mesozoic mammal below (top left), being the greatest of grandmothers to the herbivorous mammals in the images alongside it.

My colleagues and I wondered if there might be any evidence of this pattern, implied by the fossil record, in the genomes of modern day mammals. We looked at a gene encoding an enzyme called acidic mammalian chitinase (CHIA), which is produced in the stomach and other digestive organs and can break down the chitin-rich exoskeletons of insects [1]. We reasoned that if modern day herbivores and carnivores evolved from insect-eating ancestors, then they might have remnants (pseudogenes) of this gene in their genome.

Interestingly enough, we found that there are actually five chitinase genes, not one, and our analyses suggest that all five are common to the largest group of mammals (i.e., placental mammals). This implies that there were five in the common ancestor of these mammals, which we think lived in the Mesozoic alongside dinosaurs. Interestingly, modern mammals that have all five chitinase genes are all strongly insectivorous, suggesting that this ancestor was primarily an insect-eater too, consistent with the fossil evidence.

Chitinase gene family
Phylogeny showing the similarity between the different chitinase genes (closed circles) and pseudogenes (open circles). Colors and silhouettes correspond to different groups of mammals.

Furthermore, we found that in modern-day meat-eaters and plant-eaters, every species we examined has pseudogene remnants of one or more chitinase genes. So herbivores, like sloths, elephants, manatees, fruit bats, horses, rhinos, camels and rabbits, and carnivores, such as tigers, polar bears, walruses and dolphins, have remnants of genes that were likely once used to digest the prey of their ancestors: insects!

Chitinase pseudogenes
Chitinase gene remnants in herbivores and carnivores. Arrows indicate disabling mutations shared by two or more species.

What’s more is that many of these mammals that are thought to be related, based on DNA and anatomical similarity, share the exact same mutations in some or all of the chitinase genes. For example, horses and rhinos look quite different from one another, yet have been considered by anatomists, paleontologists and geneticists to be related for over a century and a half. They are both herbivores, which implies their diet was inherited from a common ancestor, and indeed the earliest fossils that resemble them had teeth and jaws that appeared to be particularly good at eating plants. Such adaptations would have rendered insect-digesting genes relatively useless. Indeed, horses and rhinos have pseudogene remnants for four of the five chitinases, and they share at least one disabling mutation in each gene, suggesting they inherited defunct copies from a plant-eating ancestor.

Humans also possess three chitinase pseudogenes, alongside a single functional chitinase gene. Two of the pseudogenes share the same inactivating mutations with monkeys and apes, and a third shares a mutation only with apes. Interestingly, many of the earliest primate fossils appear to have been insect-eaters, but as monkeys and apes appeared, plants, as well as meats, became more important for their diets, so insect-digesting genes were likely less useful.

Together, these data suggest that in our very own genomes, we retain ‘molecular fossils’, that hearken back to a time when our distant ancestors were not the top of the food chain, but rather scurried along amidst dinosaurs, eating insects.

Questions for Creationists

Why would the Creator design humans, rhinos, tigers and other mammals that never or almost never eat insects with remnants of insect-digesting genes? Is it just a coincidence that the earliest mammal fossils, found alongside dinosaurs, appear to have been insect eaters, and modern herbivores and carnivores have remnants of insect-digesting genes? For those that believe that all animals were plant-eaters in the Garden of Eden, why do so many herbivores have remnants of insect-eating genes? If mammals were created in the last 10,000–6,000 years, how could they evolve from insect-eaters to herbivores and carnivores so quickly, modifying their teeth, jaws, intestinal tracts, etc. to be optimized for their new diets?

References

1. Emerling, C. A., Delsuc, F., & Nachman, M. W. (2018). Chitinase genes (CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals. Science advances, 4(5), eaar6478.

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Claw gene remnants point to legs in snake ancestors

Nonfunctional remnants of genes (pseudogenes) can often provide evidence of the evolutionary history of life. I once wondered if snakes have any pseudogenes that pointed to a time when they once had legs, a conclusion suggested by comparative genetics and the fossil record. but I had trouble imagining what kinds of genes would provide a record of this hypothetical history. After all, there aren’t ‘leg’ genes or ‘arm’ genes, as the genes involved in making limbs participate in the development of a number of body structures.

However, I was excited to learn that there are indeed some genes that appear to be specific to a portion of the limbs: the claws. These genes, known as keratins, seemed like good candidates for investigation, and led to me to study the evolutionary history of snakes. But first, let me share a few details about keratins to give you some context

Keratins are known as structural proteins, meaning they form physical structures that are often visible to the naked eye. Though proteins are involved a wide variety of functions, ranging from vision to carrying oxygen to tissues throughout your body, most do not clump together in large enough quantities to be visible to the naked eye. Keratins, on the other hand, are often quite visible, and include things as different as hair, nails, feathers, porcupine quills and rhino horns.

Claws are also made of keratin, just like your nails, and a pair of studies found that at least two of these keratins appear to be localized almost entirely in the claws of lizards [1,2].

In addition to showing that these keratin genes, HA1 and HA2, are turned on in the fingers and toes of lizards, and staining techniques demonstrated that HA1 is produced at the base of lizard claws, the researchers showed that the HA1 gene is present and intact in every lizard that they looked at, except for one. The exception? A legless, and therefore clawless, lizard, known as the slow worm [3]. They didn’t find the gene completely absent in this animal, however, but present in the genome with two mutations that lead to a nonfunctional keratin. This points to a time when legless lizards and limbs and claws, consistent with studies of DNA and developmental biology.

Furthermore, they tried to look for the gene in snakes, but to no avail. I, on the other hand, benefit from working in the world of genomics. Since this initial paper was published, multiple snake genomes have been sequenced and assembled, so I made an effort to look for both claw keratin genes, HA1 and HA2, in eight species of snakes.

Whereas I could not find HA2 in the snakes, no matter how hard I looked, I found a degraded portion of HA1 in the genomes of six of the snake species [4]. What was perhaps even more exciting, is that all of these species, which included species as different as a python, vipers, rattlesnakes, and a cobra, all shared the exact same disabling mutation: an eight letter (base pair) insertion in the first portion of the gene. This suggests that these snakes share a common ancestor that once possessed a functional claw keratin gene, along with claws, digits and limbs.

This provides another exciting example where DNA and fossils tell the same story: one where a group of lizards evolved into the legless snakes that we love (or loathe) today.

Question for Creationists

Why would the Creator create a broken claw keratin gene in legless snakes and a legless lizard? Wouldn’t it make more sense to simply create them without a broken gene? If these animals evolved from ancestors with claws and legs after the flood, why and how did they lose their legs so quickly? Why do they all share the same mutation, even though they are different ‘kinds’? Is it just a coincidence that snakes have remnants of a claw gene, show DNA evidence of descending from legged lizards and also have fossil evidence of formerly possessing legs?

References

1. Eckhart, L., Dalla Valle, L., Jaeger, K., Ballaun, C., Szabo, S., Nardi, A., … & Tschachler, E. (2008). Identification of reptilian genes encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair. Proceedings of the National Academy of Sciences, 105(47), 18419-18423.

2. Alibardi, L., Jaeger, K., Valle, L. D., & Eckhart, L. (2011). Ultrastructural localization of hair keratin homologs in the claw of the lizard Anolis carolinensis. Journal of morphology, 272(3), 363-370.

3. Dalla Valle, L., Benato, F., Rossi, C., Alibardi, L., Tschachler, E., & Eckhart, L. (2011). Deleterious mutations of a claw keratin in multiple taxa of reptiles. Journal of molecular evolution, 72(3), 265-273.

4. Emerling, C. A. (2017). Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes. Molecular phylogenetics and evolution, 115, 40-49.

Genetics of South American rodents points to evolution

Rodents are an extremely successful group of mammals. There are more species of rodents than any other type of mammal, and they inhabit nearly every stretch of land on earth.

Some rodents are geographically restricted, however, with a number of groups being located entirely in the Americas. Chinchillas and viscachas (Chinchillidae) are exclusively found in South America, as is the pacarana (Dinomyidae), chinchilla rats (Abrocomidae), degus and kin (Octodontidae), tuco-tucos (Ctenomyidae), the coypu (Myocastoridae), and cavies (Caviidae). Spiny rats (Echimyidae), agoutis (Dasyproctidae), capybaras (Hydrochoeriidae) and the paca (Cuniculidae) live in South America but have also ventured into Central America. American porcupines (Erethizontidae) occupy both North and South America, and the hutias (Capromyidae) only live on Caribbean islands.

According to genetics, however, these rodents aren’t simply friendly neighbors: they’re relatives! Molecular phylogenetics has routinely shown that these rodents are all more genetically similar to each other than they are to other rodents, implying that they descended from a common ancestor. This is despite these rodents encompassing species with very different adaptations, including runners (maras, agoutis), tree-dwellers (porcupines), burrowers (coruro, tuco-tucos), swimmers (coypu, capybaras), and some species have particularly spiny hairs (spiny rats, porcupines).

Below is a phylogeny [1] that compared 35,603 letters of DNA between 164 different species of mammals, showing this very result. Click and zoom in on the figure and you’ll see the rodents among the blue branches, more than half way down. Use the capybara painting to help orient yourself, and refer to the family names I introduced above (e.g., Chinchillidae, Caviidae) to help you find all of these rodents in this genetic family tree.

Mammal phylogeny
Mammal molecular phylogeny

So given that these rodents are more genetically similar to each other than to other rodents, and they predominantly live in South America, it suggests that an ancestral species came to South America and diversified into a wide array of forms.

But is it that simple? What does the fossil record say? As you can see below [2], with the exception of a few dubious 56–33.9 million year old spiny rat fossils in East Asia, each of these families of rodents is completely restricted to the Americas. The oldest fossils are found in South America (33.9–28.1 million years ago), before ultimately reaching the Caribbean (20.44–15.97 million years ago) and North America (1.8–0.78 million years ago). Click on the image below to get a closer look.

south american rodent fossil distribution
South American rodent fossil distribution

How those first rodents got to South America is another question, but perhaps they would be proud to know that their great-great-great-etc. grandchildren successfully conquered a continent in an array of different forms.

Questions for Creationists

Why are all of these American rodents more genetically similar to each other than to other rodents? Are they all part of the same ‘kind’ and just recently evolved into these various forms? If so, is this degree of evolution, leading to forms adapted to running, burrowing, having spiny quills, etc. consistent with Creationism? If they are different kinds, why did they all go to the Americas together? And if they did, is it just a coincidence that they are genetically similar to one another? If these ‘kinds’ were all on Noah’s ark, shouldn’t we find fossils of these animals elsewhere in the world? How did they cross the Atlantic Ocean? If humans brought them, why are they all genetically similar?

References

1. Meredith, R. W., Janečka, J. E., Gatesy, J., Ryder, O. A., Fisher, C. A., Teeling, E. C., … & Murphy, W. J. (2011). Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science, 334(6055), 521-524.

2. Paleobiology database

Where did the Mesozoic mammals go?

Based on the fossil record and geological dating methods, we think mammals have been around for a long time. So long, that they appear in the fossil record right around the same time as the dinosaurs, and indeed coexisted alongside them throughout the “Age of the Dinosaurs”, the Mesozoic era (252–66 million years ago). But before you start fantasizing about scenarios of Tyrannosaurus rex feasting on elephants or lions stalking a Triceratops, let me provide a picture of a typical Mesozoic mammal.

Juramaia sinensis
Juramaia sinensis

Not too thrilling, is it? This mouse-y, shrew-y looking mammal, Juramaia, was typical of Mesozoic mammals. Hailing from the Jurassic, some 160 million years ago, this is thought to be the earliest known relative of placental mammals, such as elephants, bats, armadillos and ourselves. All of the large and charismatic species we’ve grown accustomed to didn’t start to appear until after the dinosaurs were wiped out in mass extinction at the end of the Mesozoic era.

Though this animal doesn’t look too outlandish, and you may think you’ve seen something similar in a zoo, there is nothing like them today. There are a number of distinct anatomical features in Mesozoic mammals not present in modern species, which has led to the classification of quite a few different types of Mesozoic mammals, some of which are shown below.

You probably noticed these animals were relatively similar to one another, despite being found in rocks spanning about 100 million years. Indeed, evolutionary biologists tend to think that mammals were largely limited to being small, insectivorous and nocturnal during this period, possibly due to predation by and/or competition with other Mesozoic creatures, including the dinosaurs.

Not all Mesozoic mammals were so simple in their anatomy, however, with a number of recent discoveries finding species similar to mammals that exist today. Paleontologists have found gliders, much like flying squirrels, mole-like species, and even carnivorous mammals that fed on dinosaurs! But these are not flying squirrels, moles or modern carnivores. Their anatomy is very distinctly mammalian, but it is also very different from any modern species.

These mammals weren’t isolated to just a single part of the world either. Mesozoic mammals have so far been found on every single continent except Antarctica [1].

Distribution of Mesozoic mammal fossils
Distribution of Mesozoic mammal fossils: purple = Triassic, blue = Jurassic, green–yellow = Cretaceous

Mammals survived the extinction that wiped out the dinosaurs at the end of the Mesozoic, and began diversifying into a dizzying number of forms after this event. However, most types of Mesozoic mammals, including all of the species illustrated above,  disappeared from the fossil record. As much as I would be delighted to stumble across a Juramaia, Repenomamus, or Volaticotherium out in a rainforest, it appears that these mammals have gone the way of the dinosaurs.

Questions for Creationists

Where did the Mesozoic mammals go? Being small-sized, wouldn’t they have fit easily onto Noah’s Ark? If they dispersed from Mt. Ararat, how did they make it to most of the worlds continents? Why don’t we find archaeological evidence of them living alongside humans?

References

1. The Paleobiology Database

For further reading

Luo, Z. X. (2007). Transformation and diversification in early mammal evolution. Nature, 450(7172), 1011.

Turtles, birds and crocodylians have genetic remnants of a ‘third eye’

Many lizards have a so-called ‘third eye’, more formerly known as a parietal or pineal eye, which is located smack dab in the middle of their heads.

 

If you dissect a parietal eye, you’ll see that it very much resembles a normal eye, with structures similar to a cornea, lens and retina, as well as a nerve projecting from the light-sensitive retinal cells.

tuatara-parietal-eye-e1407353354308

Just like our normal (‘lateral’) eyes, these structures absorb light and translate it into electrical signals, which are then sent to the brain, communicating information about the abundance and composition of light in the environment. Though the function of the parietal eye is not fully agreed upon, it appears that it at least helps lizards to know how long they need to stay in the sun to warm up, since removing it or blocking it from sunlight leads to lizards staying out the sun longer than normal.

basking_lizard_by_raeyenirael_stock
Basking monitor lizard

While this third eye is only found in lizards and the closely-related tuatara, there is evidence in the fossil record that it was formerly much more widespread. If you look at the skulls of many types of fossil reptiles, you’ll find a little hole at the top of their skulls, just like in modern day lizards that have a parietal eye. What’s also interesting is that some fossil species that show similarities to birds, crocodylians and turtles also have this hole in their skulls, despite the fact that these modern birds, crocs and turtles do not have a parietal eye.

image_3197_2e-Eunotosaurus-africanus
Sequence of fossils from primitive reptiles to the earliest turtles

For example, the image above is a phylogenetic hypothesis showing a sequence of early reptiles that all have a hole at the top of their skulls (parietal foramen) until the appearance of some of the earliest turtles (Proganochelys).

Recent research has isolated a couple of proteins that are expressed in the parietal eyes of lizards. These proteins, parietopsin and parapinopsin, function as pigments that absorb light in the parietal eye [1].

Screen Shot 2017-06-16 at 3.47.37 PM
Iguana parietal eye with parapinopsin (magenta) and parietopsin (green) staining [1]
In a recent study [2], I found both the parapinopsin and parietopsin genes in birds, crocodylians and turtles, but they are full of mutations that prevent the formation of functional proteins. This is consistent with the idea that the ancestors of birds, crocodylians and turtles had parietal eyes with functional parietopsin and parapinopsin, but ultimately lost the need for them. The reasons for the loss of this organ are a bit mysterious, but the consistent story told by both genetics and the fossil record makes a convincing argument for these birds, crocs and turtles having evolved from animals with a third eye.

Questions for Creationists

Why did the Creator create birds, crocodylians, and turtles with remnants of genes that are found in the ‘third eyes’ of lizards? Is it just a coincidence that fossils of animals that look similar to these species had holes in their skulls that correspond with the parietal eye of lizards?

References

1. Wada, S., Kawano-Yamashita, E., Koyanagi, M., & Terakita, A. (2012). Expression of UV-sensitive parapinopsin in the iguana parietal eyes and its implication in UV-sensitivity in vertebrate pineal-related organs. PLoS One7(6), e39003.

2. Emerling, C. A. (2017). Archelosaurian Color Vision, Parietal Eye Loss, and the Crocodylian Nocturnal Bottleneck. Molecular biology and evolution34(3), 666-676.

Photo credit

Parietal eye 1, parietal eye 2, parietal eye 3, pre-turtle skullsbasking lizard

DNA points to reptilian ancestry of birds

As I discussed in the previous post, the fossil record tells a story that at first seems implausible: birds are descendants of dinosaurs. Part of what’s surprising about this idea is that dinosaurs typically appeared very reptilian, whereas birds do not.

Without providing a formal definition of “reptile”, you probably have a general image in your head. This is because reptiles possess a suite of characteristics that intuitively unite them into a group. For instance, reptiles are covered in scales, walk around on all fours, have tails, typically have simple conical teeth and warm up by basking in the sun.

Birds, by contrast, are covered in feathers, walk around on just their hind legs and/or fly, lack tails, have no teeth whatsoever, and are able to generate their own heat, similar to mammals.

Anybody that is at least vaguely aware of animal diversity probably would never mistake a bird for a reptile. So besides a pattern in the fossil record and remnants of tooth genes in their genomes, is there any other evidence that birds are descended from dinosaurs and, ultimately, other reptiles?

One line of evidence comes from comparisons of DNA. When researchers have compared the genes of birds, reptiles, and other animals, they find something that perfectly fits the conclusion of the fossil record: birds are genetically nested within reptiles. In fact, crocodilians are more genetically similar to birds than they are are to turtles or lizards. As just one example of a study that demonstrates this, Chiari et al. [1] compared 248 genes, with a total of 187,026 letters of DNA, among multiple species of reptiles, birds and other vertebrates and found this very pattern:

12915_2011_Article_592_Fig1_HTML

The green branches on this phylogenetic tree indicate lizards, red are turtles, blue are crocodilians and purple are birds.

The link between crocs and birds isn’t entirely surprising to anatomists, who have long remarked that modern and ancient crocodilians share a number of traits with dinosaurs, including teeth set in sockets (thecodonty), holes in the skull in front of the eyes and in the lower jaw (antorbital and mandibular fenestrae), and an extra ridge (trochanter) on the femur. However, birds no longer have most of these traits, and the one trait that they do have (antorbital fenestrae) is not found in modern crocodilians. As such, this conclusion was not always intuitively obvious.

Nonetheless, here we have an excellent example of where DNA and fossils tell the same story. Fossils appear to document a transition from large reptilian progenitors to modern birds and DNA suggests that birds are not only relatives of reptiles, but are descendants of reptilian ancestors shared with crocodilians, turtles and lizards..

Questions for Creationists

Why do birds have DNA more similar to crocodilians than crocodilians do to turtles and lizards? Is it just a coincidence that bird DNA and the fossil record seem to be telling the same story, that birds are descended from reptiles? What kinds of evidence might overturn this hypothesis?

References

1. Chiari, Y., Cahais, V., Galtier, N., & Delsuc, F. (2012). Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). Bmc Biology10(1), 65.

Photo credit

Alligator, caiman lizard, terrapin, tuatara, nightjar, cranes, sandgrouse, sunbird

Fossils document how dinosaurs gave rise to birds

Everyone knows that dinosaurs are extinct. As children, many of us gazed in awe at the fossils of these magnificent beasts. As adults, a lot of us still do!

Except that dinosaurs aren’t extinct, at least based on the most recent interpretations of the fossil record and analyses of DNA. The collective evidence points to a conclusion that once seemed improbable: birds are dinosaurs. I still recall the awe and wonder that beheld me when I learned this in college, and when I’ve taught it to children (all of whom are bonafide dinosaurs experts), I can see the same amazement on their faces.

So what evidence is there in the fossil record for this supposed ancestor – descendant relationship?

Prior to the Triassic, there were a lot of reptilian looking animals that no longer exist today. One such animal, Protorosaurus, has been found in rocks dating to about 260-251 million years ago (Ma). Typical of its contemporaries, it walked around on four limbs, each of which terminated in five fingers or five toes, possessed a long tail and teeth, and was almost certainly covered in scales. At this point in time, Protorosaurus and its fellow reptiles had seemingly little in common with today’s birds.

Not too much later, about 245 million years ago, animals like Asilisaurus appear in the fossil record. Though this species likely walked on all fours, it had shorter arms, suggestive of an increased ability to walk and/or stand on its hindlimbs.

asilisaurusx2
Asilisaurus

In another nine million years, we see animals like Marasuchus (236-234 Ma): clearly reptilian in form, very dinosaur like, and notably bipedal, just like birds.

Marasuchus_white_background
Marasuchus

Eodromaeus and its kin are among the earliest true dinosaurs, popping up a mere five million years after Marasuchus (231.4-229 Ma). One of its typical dinosaurian traits is a hip socket with a hole in it (perforate acetabulum). What’s additionally notable about this species and some of its contemporaries is how its fingers have changed. Modern birds do not have fingers, but their wing bones terminate in what appears to be the remnants of three fingers. Starting this trend toward digit reduction, Eodromaeus has five fingers, but the ring and pinky are very reduced in size.

Fast forward about 30 million years, and we have more modern-looking dinosaurs on the scene. Coelophysis (203-196 Ma) is typical of the early carnivorous dinosaurs (theropods), and continues the march towards birdiness. The pinky finger is practically non-existent at this point, and the toes have also reduced in number. Whereas earlier dinosaurs and other reptiles have five toes, Coelophysis has only four, with a tiny remnant of the fifth high up on the foot. Notably, birds have four toes, three in the front and one in the back, so this trait had already appeared at least 200 million years ago.

Whereas Coelophysis had four fingers on its hands, Sinosaurus (201-196 Ma), appearing two million years later, only has three fingers, having lost the ring finger altogether.

Sinosaurus_triassicus_white_background
Sinosaurus

While other bird-like traits accumulated over time, perhaps the most significant change is found in rocks that date to 50 million years after dinosaurs like Sinosaurus. Archaeopteryx (150.8-148.5 Ma), the first documented transitional fossil, has a striking mix of bird- and reptile-like traits. Perhaps most significantly is the appearance of feathers in this species.

NGS Picture ID:422890
Archaeopteryx

There is reason to think that feathers appeared prior to Archaeopteryx, however. Soft tissues like feathers don’t typically preserve well as fossils, but over the last 20+ years, a number of exceptionally preserved specimens have demonstrated that plenty of non-flying dinosaurs had feathers. This suggests that these structures didn’t appear for the purpose of flight, but rather for a simpler function, such as thermoregulation. Just like hair keeps us and other mammals warm, feathers provide a similar insulating layer for birds.

Archaeopteryx clearly had wings, though, suggesting some ability to glide or perform flapping flight. It had another bird-like feature, known as the furcula. Also known as the wishbone, the bone frequently broken apart as a Thanksgiving dinner ritual in the United States, this bone formed by the fusion of the two clavicle bones present in earlier species like Coelophysis. This fusion is thought to be important in withstanding the stressors caused by flight, but it is also present in many other carnivorous dinosaurs, suggesting it initially appeared for a different reason.

Furcula_evolution4

Despite these innovations, Archaeopteryx is still not as bird-like as you’d think. For one, it still very clearly had three fingers, along with claws, on its hand. It also had a long bony tail, a structure reduced to a nub (pygostyle) in modern birds. Last but not least, Archaeopteryx had teeth, whereas birds have lost their teeth entirely in favor of a beak made of a protein called keratin.

After another 15 million years, other dinosaurs, like Sinornis (135 Ma), were just a few steps away from modern birds. The tail bones had finally become shortened and fused into a pygostyle in Sinornis, providing a structure tail-feather attachment. The sternum also became keeled increasingly keeled, allowing for the attachment of more powerful flight muscles, suggesting that Sinornis was a better flyer than Archaeopteryx. Despite these innovations, Sinornis still retained teeth and three distinct clawed fingers, traits that are not present in modern birds.

sin-skeleton
Sinornis

40 million years later, when tyrannosaurs and pachycephalosaurs were still roaming the earth, some extremely bird-like animals appear in the fossil record. At first glance, Ichthyornis (93-83.5 Ma) may be difficult to discern from a modern seabird. Many of the limb bones, including the fingers have become fused in Ichthyornis, resulting in a skeleton that was probably well-adapted for powered flight. Nonetheless, as one of the final holdouts of its reptilian past, Ichthyornis still had teeth. Interestingly, however, its jaw tip appears to be covered by an incipient beak, suggesting the transformation is nearly complete.

Ichthyornis_Clean
Ichthyornis

After most dinosaurs disappeared from the fossil record, coinciding with geological evidence for a disastrous meteor impact and intense volcanism, birds persisted and began to really thrive. Among the earliest species is Waimanu (60 Ma), which appeared just five million years after this mass extinction event. Not only does Waimanu have the appearance of a modern bird, paleontologists think it was the earliest known penguin, suggesting the surviving bird species have already begun to resemble some of their modern forms.

i-f1cdf2d13781a91c89e9a9770eee8d25-waimanu
Waimanu

Over a period of about 200 million years, the fossil record appears to document the gradual appearance birds from reptilian forebears. With the advent of bipedalism, the reduction in fingers and toes, derivation of feathers and wings, reduction of the tail, and loss of teeth, fossils seem tell the story that birds are, in fact, dinosaurs. Do not hesitate to remember this the next time you feed a duck or eat a chicken wing!

Question for Creationists

Where did all of these fossil animals go? Could they not fit on Noah’s ark? Wouldn’t species with some capacity for flight, such as Sinornis, Archaeopteryx, and Yi qi, be able to avoid the Flood? Why does the fossil record appear to document a transition between reptilian animals and birds? If Noah’s Flood is responsible for the placement of these fossils, why did they appear in this particular sequence? Is it just a coincidence that the fossil record appears to document birds descending from ancestors with teeth and birds have remnants of tooth genes in their genomes?

Photo credit

Protorosaurus, chickenAsilisaurus, Marasuchus, Eodromaeus, Eodromaeus handCoelophysis, Coelophysis handSinosaurus, Archaeopteryx, Sinosauropteryx, Beipiaosaurus,  Sinornithosaurus, Microraptor, Psittacosaurus, Epidexipteryx, Similicaudipteryx, Anchiornis, Changyuraptor, Yi qi, furcula, Sinornis, Waimanu

Why cats, hyenas and seals don’t love sugar

The molecular basis for taste is relatively straightforward. On your tongue, you have numerous taste buds that harbor cells with little proteins hanging out on the top. These proteins have the capacity to bind a number molecules on your tongue, and thereby transmit information regarding nutritional content.

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Mammalian taste receptor proteins and molecules that activate them.

One of these proteins is TAS1R2, which, along with the protein TAS1R3, binds sweet tasting molecules. This sweet receptor is what allows you to savor the delicious sucrose (table sugar), fructose (fruit sugar) and even artificial sweeteners such as saccharin and aspartame. If you love cake, ice cream, and cookies, be grateful that you have a functional sweet receptor!

Not all animals are fortunate enough to enjoy these treats, however, and evolution is likely to be blamed. Many species are particularly adapted to eating foods that are nearly devoid of sugars, and therefore are not expected to benefit from maintenance of the gene encoding TAS1R2. Indeed, scientists [1] have found that a number of carnivorous mammals, including cats, hyenas, seals, the banded linsang, fossa and Asian small-clawed otter have a pseudogenized (nonfunctional) version of the TAS1R2 gene.

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Examples of TAS1R2 pseudogenes in various carnivores

This helps explain why cats behaviorally seem uninterested in sugar. The scientists also confirmed that the Asian small-clawed otter also is not drawn to sweets, consistent with its TAS1R2 pseudogene. By contrast, they found that the spectacled bear, which has an intact TAS1R2 gene and is a known devourer of sweet things like fruits and honey, prefers sugary solutions over water.

spectacled-bear

These data suggest that the ancestral carnivores did eat sweets on occasion, but certain species avoided sugary foods for so long that sweet receptors were no longer necessary. Eventually mutations rendered the TAS1R2 gene nonfunctional in different carnivore lineages, rendering these species impervious to the effects of sweets.

Questions for Creationists

Why did God create some carnivores with a nonfunctional version of the sweet taste receptor gene? Would it not have made more sense for Him to create them without the gene altogether? Is it just a coincidence that He also created other animals with specialized feeding strategies, such as giant pandas and whales, to lack certain taste receptors?

References

1. Jiang, P., Josue, J., Li, X., Glaser, D., Li, W., Brand, J. G., … & Beauchamp, G. K. (2012). Major taste loss in carnivorous mammals. Proceedings of the National Academy of Sciences109(13), 4956-4961.

Photo Credit

Taste receptors, hyena, harbor seal, banded linsang,  fossa, otter, pseudogene figure, spectacled bear

DNA of wingless insects points to evolution

Perhaps you haven’t thought of it much before, but relatively few species of insects completely lack wings. One kind of wingless insect is known as a silverfish, an animal that perhaps you have discovered crawling in your home or hanging out in your pantry.

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Typical of insects, they possess six legs, a chitinous exoskeleton, compound eyes and a pair of antennae. Unlike most other insects, they are wingless and have three filaments that jut out from the tail portion of their bodies. The latter traits are typical of multiple species of insects beyond silverfish, including the firebrat and bristletails, a group that I was taught was called Thysanura growing up.

Despite thysanurans seemingly being united by these distinctive characteristics, when scientists began comparing insect DNA, they found that thysanurans didn’t group together. Instead, the results from DNA suggest that they represent two distinct lineages of insects that just happen to look very similar. Below is a molecular phylogeny that included 1478 genes from 144 species of insects and insect-like animals (arthropods) [1]:

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You can see the thysanuran species at the top of the phylogeny. One lineage of thysanurans is now called Archaeognatha, which includes the animals below:

The next group is called Zygentoma, which includes the silverfish and others, such as some oddball species that are blind, lack color and live exclusively with ants and termites:

Despite their striking similarities to one another, zygentomans are actually more genetically similar to winged insects, with forms as diverse as praying mantises, butterflies and beetles. This might seem surprising, but it’s quite plausible if evolution is true.

One scenario in which this is possible is if Archaeognatha and Zygentoma independently evolved a very similar body form, known as convergent evolution. Evolutionary biologists typically expect this to occur when different organisms adapt to very similar lifestyles. However, since these lineages split off in relatively rapid succession, it’s more likely that the earliest insects looked like thysanurans, and archaeognathans and zygentomans retained this ancestral body type.

Questions for Creationists

If God created archaeognathans and zygentomans, as well as the DNA that determines how they look, why is it that their DNA is so different? Shouldn’t animals that look similar have more similar DNA?

References

1. Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., … & Niehuis, O. (2014). Phylogenomics resolves the timing and pattern of insect evolution. Science346(6210), 763-767.

Photo credit

Silverfish 1Archaeognatha 1Archaeognatha 2, Archaeognatha 3, Archaeognatha 4, Silverfish 2, Zygentoma 2Zygentoma 3

Fetal whales have hindlimb buds

DNA suggests that whales are descended from hoofed mammals, and the fossil record also appears to document a transition of four-limbed whales to modern species that only have forelimbs. Looking at the ontogeny, or development, of whales also provides evidence of a past when the ancestors of these aquatic creatures walked on land.

Below is a picture of an Atlantic spotted dolphin (Stenella frontalis), which very clearly has forelimbs (flippers) but no hindlimbs, typical of whales.

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But when this and related species are still embryos, you can see that tiny hindlimb buds form [1].

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If you look at a series of embryos through their development, the hindlimb buds form but then they disappear.

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Interestingly, dolphins seem to retain some of the genetic developmental machinery to make hindlimbs. Occasionally, people have found individual dolphins that have hind flippers, such as the one in the picture below.

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This is called an atavism, and is thought to arise from one or more mutations that somehow turn the development of the hindlimbs back on.

Together, this is a remarkable example where DNA, fossils and ontogeny all tell the same story, specifically that whales descended from ancestors that walked on four legs. These animals appear to have gradually lost their hindlimbs,  presumably as an adaptation to streamline their bodies for swimming, but their ontogeny seems to retain a record of their fully-limbed past.

Questions for Creationists

Is it just a coincidence that DNA, fossils and ontogeny all suggest that whales descended from four-limbed ancestors? Why would God create dolphins with hindlimb buds that simply disappear? Is it just a coincidence that we see the same pattern of limb buds forming and then disappearing in legless lizards?

References

1. Thewissen, J. G. M., Cohn, M. J., Stevens, L. S., Bajpai, S., Heyning, J., & Horton, W. E. (2006). Developmental basis for hind-limb loss in dolphins and origin of the cetacean bodyplan. Proceedings of the National Academy of Sciences103(22), 8414-8418.

 

Photo credit

Adult spotted dolphin, dolphin embryo, embryo series, dolphin atavism