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.

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

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.

Screen-Shot-2013-09-14-at-2.52.32-PM
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.

F1.large
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

Egg yolk gene remnants point to mammals’ egg-laying past

When children learn about different animals and how to classify them, they are often taught that three features unite mammals: hair, milk, and live birth. This last trait is likely taught to contrast mammals with the many other vertebrates that lay eggs.

But this last point is not correct. Nearly all mammals give birth to live young, but a handful do lay eggs. These are known as the monotremes, which encompass the platypus and several species of echidnas or spiny anteaters, all of which live in Australia, Tasmania and New Guinea.

The fact that a few mammals lay eggs, plus that most other land-dwelling vertebrates do as well, points to the idea that the rest of mammals descended from egg-layers. So how might one test this hypothesis? David Brawand and his colleagues [1] had the idea of looking at the genomes of mammals to see if they have any remnants of egg yolk genes.

Besides monotremes, the remaining mammals can be divided into two general groups: (1) marsupials, whose offspring are born early in development and then finish developing in a pouch (marsupium), and (2) placental mammals, which develop with the help of a placenta connecting the mother to the fetus. When Brawand and his colleagues looked at the genomes of three placental mammals (human, dog, armadillo), they found remnants of two egg-yolk genes (VIT1, VIT3), both of which possessed loss-of-function mutations. These mammals share some loss-of-function mutations in the genes, suggesting that the genes were inactivated in a common ancestor. Similarly, the researchers found remnants of three egg-yolk genes (VIT1, VIT2, VIT3) in the marsupials they studied (opossum, wallabies), with shared loss-of-function mutations in each (Figure 1), which, again, imply loss in a common ancestor.

journal-pbio-0060063-g005

Figure 1. DNA sequence alignment of egg-yolk genes [1]. Highlighted portions indicate loss-of-function mutations. Gallus gallus = chicken; Monodelphis domestica = opossum; Macropus eugenii and Wallabia bicolor = wallabies.

By contrast, at least one egg yolk gene is intact in the egg-laying platypus. Together, these data suggest that the inactivation of egg yolk genes in placental and marsupial mammals is connected with the loss of their egg-laying ability through evolutionary time.

Questions for Creationists

Why do mammals that do not lay eggs have non-functional egg yolk genes in their genomes? If these species do not lay eggs and didn’t evolve from ancestors that lay eggs, why would God have put these in their genomes? Why do some mammals share some identical loss-of-function mutations in their egg yolk genes genes?

References

1. Brawand, D., Wahli, W., & Kaessmann, H. (2008). Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol6(3), e63.

Photo credit

Platypus, platypus eggs, long-beaked echidna, echidna egg,

Why pandas can’t taste meat

Many animals are omnivorous, having a variegated diet ranging from vegetation to fruit, meat to insects, and a host of other items. Consequently, being able to taste and distinguish these foods likely aids in acquiring items that satisfy particular dietary needs.

Having a specialized diet, on the other hand, eliminates the need to taste everything. For example, if an animal is adapted to exclusively eating plant material, it probably would not need to be able to taste meat. But what happens when an herbivorous animal descends from ancestors that ate meat? Can we find evidence that it used to be able to taste meat, but subsequently lost it?

GiantPandaEatingBamboo

The giant panda (Ailuropoda melanoleuca) is an animal that eats bamboo almost exclusively, but this contrasts with other bears, which are generally omnivorous. It also contrasts with the evolutionary family that bears belong to, known as the carnivorans. Carnivorans, which encompass dogs, cats, weasels, mongooses, hyenas, and others, appear to have adapted to eating meat some 60+ million years ago. Consequently, giant pandas are oddballs in this group.

So how did this shift in dietary preference affect the giant panda’s ability to taste certain kinds of food? Taste in mammals depends on the function of taste receptor proteins encoded by different genes. There is a gene for sweet, two for sour, one for salty, many for bitter and one for savory/umami, the flavor you associate with eating meats and cheeses.

Predictably, carnivorans typically have a umami taste receptor gene, but the giant panda’s copy has become a nonfunctional pseudogene [1,2]. This was discovered by Li et al. [1], who reasonably infer that this is due to the history of giant pandas specializing on eating bamboo. As giant pandas transitioned from eating meat to plants, they probably no longer needed to retain the ability to taste meat. Natural selection wouldn’t have weeded out any mutations that would lead the loss of function in the savory taste gene, and that would subsequently become the norm for giant pandas.

Questions for Creationists

It’s understandable why God might have created giant pandas without the ability to taste meat, but why would He create them with a nonfunctional version of the savory taste gene? Would it not have made more sense to create them without the gene altogether? Why do we see a pattern of taste receptor loss in both the giant panda and whales? Why did God create just one bear that specializes on eating plants?

References

1. Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., … & Zhang, Z. (2010). The sequence and de novo assembly of the giant panda genome. Nature463(7279), 311-317.

2. Zhao, H., Yang, J. R., Xu, H., & Zhang, J. (2010). Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo. Molecular biology and evolution27(12), 2669-2673.

Photo credit

giant panda, clouded leopard, malagasy ring-tailed mongoose, raccoon dog, brown hyena

Sloth and armadillo vision pseudogenes suggest history of underground lifestyle

“The eyes [of the nine-banded armadillo] are rudimentary and practically useless. If disturbed an armadillo will charge off in a straight line and is as apt to run into a tree trunk as to avoid it.” [1]

“If an infant sloth is placed five feet away from its mother on a horizontal branch at the same level, at once the young sloth begins to cry, the mother shows that she heard it calling and turns her head in all directions. Many times she looks straight in the direction of her offspring but neither sight, hearing nor smell apparently avail anything.” [2]

“Infuriated male [sloths] try to hit each other when they are still distant by more than a metre and a half.” [2]

It doesn’t take an expert to read these quotes and recognize that sloths and armadillos have terrible vision! Taking advantage of this knowledge, I recently published a paper [3] where I examined the genes required for cone-based (i.e., bright light) vision in the nine-banded armadillo (Dasypus novemcinctus), Hoffmann’s two-toed sloth (Choloepus hoffmanni) and an extinct ground sloth (Mylodon darwinii).

What I discovered is that all three species have deleterious mutations in several cone-based genes, rendering them rod monochromats. Rod monochromats are predicted to have zero capacity for color vision and an inability to see in bright light conditions.

We had access to DNA for some more sloths and armadillos, so I sequenced fragments of a gene crucial for cone function (PDE6C). I confirmed that Linnaeus’ two-toed sloth (Choloepus didactylus), the pale-throated three-toed sloth (Bradypus tridactylus), big hairy armadillo (Chaetophractus villosus), six-banded armadillo (Euphrates sexcinctus), southern three-banded armadillo (Tolypeutes matacus), and giant armadillo (Priodontes maximus) are also rod monochromats.

 

Additionally, several armadillos and all four sloths share deleterious mutations, respectively, suggesting that this gene (PDE6C) was inactivated in common ancestors of these lineages.

F1.large

Examples of deleterious mutations in various cone genes.

Why would sloths and armadillos lose their cone-based vision? Rod monochromacy has been found in animals that dive or live deep in the ocean or underground. The prevailing hypothesis is that natural selection wouldn’t maintain the ability to perceive bright light in animals that have lived in dark conditions for millions of years. If you live in complete darkness, what good to you is color vision?

In my last post I described how armadillos, sloths and anteaters, collectively known as xenarthrans, are more genetically similar to each other than to other mammals. An anatomical feature that unites them are extra articulations in their spine (“xenarthrous articulations). This extra bracing of the spine is useful for digging. Additionally, xenarthrans have a pelvis fused to their spine

_original

long curved claws

xenarthran_claws

and a second spine (=ridge) on their shoulder blade which allows for extra muscle attachment for digging

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The retention of these traits in modern and extinct xenarthrans suggests that their last common ancestor was a digging animal. Further evidence of this is that the earliest known xenarthran had limb bones that were proportioned for digging.

Add all of this up: I proposed that the earliest xenarthrans were subterranean, and most remerged to the surface later and adapted to new environments. This would explain the absence of cone-based vision and is corroborated by shared anatomy and the fossil record.

Questions for Creationists

Why would God create sloths and armadillos with such terribly poor daytime vision, especially when so many of them are active during the day? Why would He create them with cone pseudogenes when it would have been simpler to create them with no cone genes at all? Why do two-toed, three-toed and extinct sloths share the same deleterious mutations in a cone gene (PDE6C)? Why would God create sloths with features related to digging when they live in trees?

References

1. Newman HH. 1913 The natural history of the nine banded armadillo of Texas. Am. Nat. 47, 513–539. 

2. Goffart M. 1971 Function and form in the sloth, vol. 34. Oxford, UK: Pergamon.

3. Emerling CA, & Springer MS. 2015 Genomic evidence for rod monochromacy in sloths and armadillos suggests early subterranean history for Xenarthra. Proc. R. Soc. B282(1800), 20142192.

National geographic reporting on my paper: http://phenomena.nationalgeographic.com/2014/12/24/sloths-and-armadillos-see-the-world-in-black-and-white/

Birds, turtles and other toothless vertebrates have remnants of tooth genes

As stated in a previous post, the toothless baleen whales and the enamelless pygmy sperm whales retain remnants of genes that encode proteins important for developing the enamel crowns of teeth. However, these have become inactivated through deleterious mutations. There are other vertebrate species that lack teeth or enamel, and theory suggests that they descended from ancestors with enamel-crowned teeth. This predicts that these species may also have enamel pseudogenes.

Some examples of toothless/enamelless species include the toothless anteaters, pangolins, turtles, and birds

and the enamelless armadillos, sloths and aardvarks.

Several studies have demonstrated that several enamel genes in these species have become pseudogenes. For example, Meredith et al. [1] showed that the enamelin (ENAM) gene was repeatedly deactivated in the mammalian species listed above:

frameshift

This figure shows comparisons of toothless/enamelless species with their toothed relatives. Colored regions indicated deleterious mutations. A shows the inactivation of ENAM in the aardvark (Orycteropus); B displays a shared mutation in pangolins (Manis); C in baleen whales and pygmy sperm whales; D indicates shared mutations in sloths (Bradypus, Choloepus) and anteaters (Myrmecophaga, Tamandua, Cyclopes), and separately in armadillos (Dasypus, Tolypeutes, Chaetophractus, Euphractus).

Springer’s lab later demonstrated that two enamel genes in addition to ENAM, ameloblastin (AMBN) and amelogenin (AMEL) were lost in several of these mammals, as well as two turtles and five birds. Of particular interest, all three genes have shared mutations in the birds, indicating enamel genes were lost in the last avian ancestor.

1471-2148-13-20-1

Phylogeny showing distribution of shared and unique mutations in enamel genes across various vertebrates. B = AMBN; E = ENAM; A = AMEL.

This work provides further evidence that all of these species descended from ancestors with enamel-capped teeth, which they subsequently lost during their evolution.

Questions for Creationists

Why would God create toothless and enamelless animals with nonfunctional remnants of enamel genes? Birds and turtles have beaks without teeth, so why would they have these nonfunctional pseudogenes? Why would God create anteaters, sloths, pangolins, armadillos and birds to have shared inactivating mutations, respectively, in these genes? Do you think it’s possible that these animals could have descended from toothed ancestors? What sort of evidence might you expect in support of this hypothesis?

References

1. Meredith, R. W., Gatesy, J., Murphy, W. J., Ryder, O. A., & Springer, M. S. (2009). Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS genetics5(9), e1000634.

2. Meredith, R. W., Gatesy, J., & Springer, M. S. (2013). Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes. BMC evolutionary biology13(1), 20.

Nearly blind mammals retain vision gene remnants

Animals that live underground inhabit a lightless environment. Some aspects of vision in this context might not be useful, particularly those that facilitate vision in bright light. If a species has lived underground for millions of years, we would expect that many genes tied to vision have become pseudogenes, just like in animals that live in the dim-light conditions of the deep ocean.

I conducted a study [1] in which I investigated 65 vision genes across three different species of subterranean mammals, including the Cape golden mole (Chrysochloris asiatica), a member of the African golden moles (Chrysochloridae)

Chrysochloris_asiatica

the naked mole-rat (Heterocephalus glaber), an African mole-rat (Bathyergidae)

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and the star-nosed mole (Condylura cristata), a true mole (Talpidae).

050202_mole

You’ll notice that the naked mole-rat has tiny eyes, and you’ll see the same thing if you examine other pictures of the star-nosed mole. The golden mole has no external eyes; they’re completely covered with skin and fur! You can imagine that vision is not terribly important for these three mammals, especially golden moles.

What I discovered is that the golden mole has 17 vision pseudogenes uniquely derived in its lineage, the naked mole-rat has 12 and the star-nosed mole has 6. Interestingly, this corresponds with the amount of light each species likely experiences. Star-nosed moles frequently foray above ground and often swim; naked mole-rats are entirely subterranean but have an exposed eye; and golden moles are entirely subterranean but have eyes underneath their skin. By contrast, in the above-ground mammals that I used for comparison (e.g., elephants, cows, mice), nearly all of the vision genes were functional.

I then used a method to estimate when these genes might have been inactivated, and compared that to estimations of when these species might have invaded a subterranean habitat. The fossil record and molecular phylogenetics suggests that subterranean mammals descended from above-ground species, suggesting that these vision genes might have become pseudogenes as a result of this transition underground.

As described in my first post, the earliest golden mole, a transitional fossil, dates to 33.9-28.4 million years ago. However, we only have jaw fragments of this species, so we are unable to discern if it was subterranean. The next oldest species, Prochrysochloris miocaenicus (23-16 million years ago), has modifications to its skull to suggest that it lived underground. Of the 16 genes I was able to date, I estimated 13 were inactivated after the earliest date for Prochrysochloris.

African mole-rats are all subterranean, so their last common ancestor is inferred to have lived underground as well. Molecular clock methods estimate that this ancestor dates to approximately 28 million years ago. The earliest fossils don’t appear until 23 million years ago. Regardless, all 10 of the genes I was able to estimate inactivation times for post-dated both of these dates.

True moles vary in their mode of locomotion. Some are diggers, some live above ground, some spend a lot of time in the water, and star-nosed moles both dig and swim. Nonetheless, the oldest fossils of true mole limb bones show modifications for digging, and these date to 33.9-28.4 million years ago. I estimated that 4 of the 5 pseudogenes I found were inactivated after these fossils appeared.

I also examined two published vision pseudogenes in the Mediterranean blind mole-rat

_75272161_blindmolerat

and a single vision pseudogene in the marsupial mole.

MarsupialMole

These represent two more subterranean lineages, and both happen to have eyes beneath their skin.

The earliest digging blind mole-rat fossils date to 11.6-5.3 million years ago, and I estimated that both gene inactivation events took place after blind mole-rats invaded the underground habitat.

Finally, the only marsupial mole fossil dates to 23-16 million years ago and shows modifications for living underground. The pseudogenization event post-dates the fossil.

Put together, I estimated that 30 of the 35 vision genes across these five underground mammal lineages became inactivated after they became subterranean.

1-s2.0-S105579031400181X-gr3

Questions for Creationists

Why would God create mammals with eyes covered by skin and fur? Why would He also give them nonfunctional vision genes? Is it a coincidence that these genes were estimated to have been inactivated after their fossils appear? Do you think these results are consistent with mammals evolving from above-ground ancestors to underground species?

References

1. Emerling, C. A., & Springer, M. S. (2014). Eyes underground: Regression of visual protein networks in subterranean mammals. Molecular phylogenetics and evolution.

Toothless, baleen whales have remnants of tooth genes

Blue, gray and humpback whales, are among the largest animals ever to have existed on earth. To reach and maintain such an immense size, they need to consume copious amounts of prey. Yet, unlike most vertebrates, they completely lack teeth. Instead they have a plates of protein known as baleen. Baleen acts as a sieve to filter out tiny crustaceans from the water column, allowing whales to gulp down thousands of prey in a single meal.

Baleen
Baleen

While this feeding apparatus is unique to these massive whales, there is evidence that the ancestors of baleen whales had teeth. For one, other whales, such as dolphins and sperm whales, have teeth, and the earliest whales in the fossil record all had teeth. Second, the earliest baleen whale fossils included species that appeared to have teeth and baleen side-by-side (e.g., Aetiocetus). Third, when baby baleen whales are in the womb, they form tooth buds, which are then reabsorbed as they develop. This evidence might seem pretty convincing by itself, but is there anything else to suggest that such toothless whales formerly had pearly whites?

Sure enough, when researchers have looked at the genomes of baleen whales, they have found remnants of tooth genes [1–4]. These genes, which are critical for the development of healthy teeth, are full of mutations that keep them from functioning properly.

Below you can see alignments of gene sequences for the ENAM gene, a gene involved in forming the hard outer cap of enamel in teeth, and the C4orf26 gene, a gene that appears critical for tooth development, in various baleen whale species (e.g., Eschrichtius, Eubalaena, Balaenoptera, Megaptera).

You can see highlighted examples of inactivating mutations in these two genes, with some examples of shared mutations, suggestive of gene function loss in a common ancestor. One particular gene involved in enamel maturation, MMP20, has the same knock-out mutation in all baleen whales [3], a rare SINE retrotransposon insertion, providing evidence of a loss of teeth after baleen whales split from toothed whales.

Together, DNA, the fossil record and development provide compelling evidence that the largest whales evolved from ancestors with teeth, before eventually replacing them with their unique baleen filtering apparatus.

Questions for Creationists

Why would the Creator create nonfunctional tooth genes in whales that completely lack teeth? Why would the Creator put the exact same inactivating mutations in multiple species? Is it just a coincidence that baby baleen whales have tooth buds that are reabsorbed, molecular phylogenetics suggests whales descended from tooth ancestors, and the fossil record appears to show a transition from toothed ancestors to baleen-only species? Is it a coincidence that other toothless vertebrates have dental pseudogenes?

References

1. Deméré, T. A., McGowen, M. R., Berta, A., & Gatesy, J. (2008). Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Systematic Biology57(1), 15-37.

2. Meredith, R. W., Gatesy, J., Murphy, W. J., Ryder, O. A., & Springer, M. S. (2009). Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS genetics5(9), e1000634.

3. Meredith, R. W., Gatesy, J., Cheng, J., & Springer, M. S. (2010). Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings of the Royal Society B: Biological Sciences, rspb20101280.

4. Springer, M. S., Starrett, J., Morin, P. A., Lanzetti, A., Hayashi, C., & Gatesy, J. (2016). Inactivation of C4orf26 in toothless placental mammals. Molecular phylogenetics and evolution, 95, 34-45.