Molecular Phylogenetics: 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:

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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

Molecular Phylogenetics: 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

Molecular phylogenetics: Genetics suggests birds of prey aren’t related

For eons, predatory birds have inspired people across numerous cultures. Religious texts have drawn upon them in metaphors, they have aided hunters in catching game fowl for millennia, America’s founding fathers adopted one as a national symbol, one bird of prey in action adorns the Mexican flag, and various sports teams have chosen them as mascots. While few people may pull over on the side of the road to snap a photo of a chickadee, a bald eagle or California condor would surely elicit excitement and cause people to jump out of their cars to witness their majesty.

Birds of prey, as their colloquial name suggests, appear designed for capturing and disemboweling animals. They tend to have large, and often forward-facing, eyes, which are useful for spotting prey, and their legs are strong and capable of grasping an unwitting animal. Finally, their curved, sharp beaks are excellent for tearing the flesh of their victims. Despite this, not all birds of prey are genetically similar to one another, as you can see in the phylogeny below.

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If you scour the figure, you’ll find one genetically distinct group of predatory birds known as Falconiformes, which includes Micrastur, Falco, Ibycter, and Caracara (~2/3 from the bottom of the phylogeny; marked with a small falcon with light blue and red feathers). These include the falcons, falconets, kestrels, and caracaras.

The phylogeny I’m referencing was derived from analyses utilizing 198 bird species with >390,000 letters of DNA [1]. That’s a lot of DNA and a very good sampling of species, so it’s safe to say that most of their results are statistically reliable. What is important to note for my point, however, is that that Falconiformes are genetically similar to things like parrots and perching birds, such as sparrows, crows and finches (all of the species below the falcon-like birds in the figure). Not very predatory species, are they?

Now compare where Falconiformes are in the phylogeny relative to the remaining birds of prey, known as Accipitriformes. You’ll find them at the top of the phylogeny in a separate dark-green box. This group includes eagles, hawks, osprey, kites, and vultures.

So despite their extremely similar anatomy, these groups are not genetically similar to one another. How can this be? One possibility is that their respective lineages independently adapted to a carnivorous diet, thereby adopting very similar features to capture and dismember prey. Another hypothesis, suggested by the scientists who generated the phylogeny above [1], is that many birds descended from a predatory ancestor and Falconiformes and Accipitriformes simply retained these ancestral features.

Regardless of how it happened, the point remains: their genetic similarity does not correspond with their anatomical similarity, a result that is seemingly counterintuitive, yet consistent with evolutionary theory.

Questions for Creationists

Why aren’t all birds of prey most genetically similar to one another? If God created their bodies and the DNA that provides the ‘blueprint’ for their anatomy, shouldn’t their DNA be very similar? Why are falcons more genetically similar to crows, parrots and chickadees?

References

1. Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature.

Photo credit

Phylogeny, crested caracara, Milvago, peregrine falcon, Phillipine eagle, Pacific baza, bearded vulture

Molecular phylogenetics: Not all “moles” are moles

Most people could probably identify the animals below:

Short stubby bodies, long powerful claws, regressed eyes, living underground: these are all moles. Aren’t they?

Counterintuitively, their DNA tells a different story. The mole at the top left is a true mole (Talpidae), a group of moles found in Eurasia and North America. Their DNA is not particularly similar to the other two moles. In fact, their DNA is much more similar to mammals like bats, whales and pandas.

The mole at the top right is a golden mole (Chrysochloridae), a group of mole-like mammals found exclusively in southern Africa. These “moles” are genetically more similar to a variety of mammals that hail from Africa, like tenrecs, aardvarks and elephants.

The “mole” at the bottom, munching on a centipede, is an Australian marsupial mole (Notoryctidae). Both species, like other marsupials, have a pouch in which they raise their young. You can probably tell where I’m going with this: they are more genetically similar to other marsupials than they are to the other “moles”.

So why is it that animals with striking physical similarities have such incredibly dissimilar DNA? Evolutionary theory predicts that unrelated species can appear very similar to one another if they adapt to very similar ways of life, a phenomenon called convergent evolution. If an animal becomes adapted for living underground, you can imagine that their eyes are likely to regress and their arms will become very good at digging. So even though their anatomy looks very mole-like, their DNA appears to tell the story of their ancestry.

Questions for Creationists

If God created all of these different types of moles, why is it that their DNA is so dissimilar? If DNA is the ‘blueprint’ to form an animal, and God created these ‘blueprints’ in all of these moles, shouldn’t their DNA be more similar to each other than to wildly different things like bats, elephants, and kangaroos?

References

1. Stanhope, M. J., Waddell, V. G., Madsen, O., De Jong, W., Hedges, S. B., Cleven, G. C., … & Springer, M. S. (1998). Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proceedings of the National Academy of Sciences95(17), 9967-9972.

Photo credit

true molegolden mole, marsupial mole, bat, whale, panda, tenrec, aardvark, elephant, dunnart, koala, wallaby

Molecular phylogenetics: Big birds don’t always flock together

If you had to think of the biggest bird you know, you’d probably conjure up an image of an ostrich (Struthio camelus).

Ostrich

If you have some familiarity with Australian fauna, the emu (Dromaius novaehollandiae) might also come to mind.

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If you’re a bird watching champion back home, you might even know about the cassowaries (Casuarius spp.) and the rheas (Rhea spp.).

Casuarius_casuarius_-Emmagen_Creek,_Queensland,_Australia_-adult_and_chick-8Rhea,_Greater_male_ClaudioTimm

Looking at these birds, it’s probably not difficult to see some similarities. I’ve heard children at zoos call rheas “ostriches” due to their obvious similarities (I’ve probably heard adults say the same thing). These birds are all large, have massive, powerful legs and are flightless, perhaps necessarily, with reduced or even completely absent wings. Besides these and other traits, these giant birds share what is called a palaeognathous jaw, which is more reptilian than most other birds. This gives them their scientific name: the “palaeognaths” (palaeo = “old”, gnathous = “jaw”).

The only other living palaeognaths are the much smaller kiwis (Apteryx spp.) and tinamous.

kiwibirdgenotinamou

Kiwis are similar to other palaeognaths in that they cannot fly, but tinamous do, although they have a tendency not to. Think of tinamous as the palaeognath equivalent of a quail.

As one might expect, the DNA of the large-bodied palaeognath species is more similar to each other than to, say, ducks or finches. However, despite being very quail-like, tinamous group with the ostrich-like birds. This shouldn’t be terribly surprising from an evolutionary perspective given that they share some anatomical characters, such as the palaeognathous jaw. However, what is strange is that tinamous are genetically nested (no pun intended!) deep within the palaeognaths.

Palaeognaths-page-001

Above is a part of molecular phylogeny from Prum et al. [1], in which the authors estimated relationships of these (and many other) bird species using over 390,000 letters of DNA. Branches representing tinamous are in gray, with other palaeognaths in black. Even though tinamous look more like quails than emus, they’re much more genetically similar to the latter. In fact, emus, cassowaries, and the rhea are all more genetically similar to tinamous than they are to the ostrich. This suggests that tinamous evolved from a large-bodied ancestor, or various palaeognaths repeatedly evolved large body sizes and flightlessness.

Questions for Creationists

Why would such tiny, quail-like birds be so genetically similar to large birds like ostriches and emus rather than quails or chickens? If God created birds’ DNA, and their DNA determines what they look like, why do birds that look so radically different have similar DNA? If these species all evolved from a  common ancestor rather than being directly created, what else might you expect them to have in common?

References

1. Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature.

Photo credit

OstrichEmuCassowaryRheaKiwiTinamou

Molecular phylogenetics: Legless reptiles are genetically nested within lizards

Typically when you one thinks of legless reptiles, snakes come to mind. Their long slithering bodies and forked tongues are unmistakable, and for many people, snakes conjure up their worst fears. If given the choice of holding a lizard or a snake, many people would not hesitate to choose the former.

Despite the superficial dissimilarities between snakes and other reptiles, snakes are genetically nested within lizards (group H in the figure below) suggesting that they are actually legless lizards. Specifically, scientists [1] think they descended from an ancestor shared with iguanas and monitor lizards (group E).

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This phylogeny from Pyron et al. [1] was estimated with 12896 letters of DNA. Click  to see more detail.

Not only are snakes more genetically related to things like iguanas than other lizards are, but various species of legless reptiles have DNA that is more like other lizards than it is to snakes.

One example is the dibamids: legless, burrowing lizards, with eyes hidden beneath scales. These species are found at the very base of the lizard portion of the tree (top of phylogeny), suggesting that they are a very early lizard offshoot.

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Then there are the pygopodids, which are genetically nested within geckos (section A of figure). Just like geckos, these species have the ability to make high-pitched squeaks. Snakes, by contrast, cannot vocalize. Additionally, pygopodids do not possess the forked tongue found in snakes.

Donated to Wikipedia

Section B of the phylogeny represents the scincoids. Unlike Gekkota, there are various examples of legless reptiles scattered throughout. For example, the seps (Tetradactylus) are found within the plated lizards (Gerrhosauridae). Seps have variable levels of leg reduction, with some completely legless and some with very tiny legs.

The seps (left) with a plated lizard (Gerrhosaurus; right) for comparison.

Above, Chamaesaura (left), which has highly reduced legs, is found within the girdled lizards (Cordylidae). To the right, an armadillo girdled lizard (Ouroborus cataphractus).

There are many examples of legless reptiles nested within the skink family (Scincidae), including Typhlosaurus (right above), and Neoseps, which has very small leg remnants (right below). To the left is a shingleback skink (Tiliqua rugosa), more typical of the skink family in having legs.

Section D of the phylogeny represents the lacertoids, which contains two prominent examples of legless reptiles. The first example is Bachia, which includes species without legs and species with diminutive legs.

Bachia_bicolor

The second is the amphisbaenians, also known as worm lizards. Some species are completely legless, such as the Iberian worm lizard (Blanus cinereus), while others have two front legs but no hind limbs, such as the aptly names Bipes.

Blanus cinereus (left) and Bipes (right)

Worm lizards have right lungs that are reduced in size whereas snakes have much smaller left lungs. Additionally, they are more genetically similar to the wall lizards (Lacertidae), such as the green lizard (Lacerta viridis) below, than they are to snakes.

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The final portion of the phylogeny with legless lizards is Anguimorpha (F in the figure). Some legless anguimorphs have eye lids and ear openings, both of which are absent in snakes. Examples include the anniellids (e.g., Anniella campi) and some anguids (e.g. Ophisaurus).

Both of these groups are more genetically similar to alligator lizards (below; Anguidae) than they are to snakes.

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In short, there are many examples of legless or nearly legless reptiles, including snakes, genetically nested within lizards. Evolutionary biologists believe that this is evidence that leglessness in lizards has evolved repeatedly, often in the context of living underground or in other habitats in which legs may hamper the locomotion of the animal.

Questions for Creationists

If God created DNA, and DNA encodes the anatomy of an animal, why is it that He created so many species of legless reptiles that are genetically similar to legged lizards? Shouldn’t all legless reptiles, including snakes, be most genetically similar to each other, to the exclusion of legged lizards? Why would God create lizards with diminutive, nearly useless limbs, like those of Seps, Chamaesaura, and Bipes? Would it not have made more sense to create legless and legged species, as opposed to species seemingly in between?

References

1. Pyron, R. A., Burbrink, F. T., & Wiens, J. J. (2013). A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC evolutionary biology13(1), 93.

Photo Credit

Dibamid, pygopodid, Tetradactylus, Gerrhosaurus, ChamaesauraOuroborus, Typhlosaurus, Neoseps, Tiliqua, Bachia, Blanus, Bipes, Lacerta, Anniella, Ophisaurus, alligator lizard

Molecular phylogenetics: Echolocating bats are not all genetically similar

In addition to being able to fly, bats are relatively unique in having the capability to echolocate. Echolocation in bats, just like in a submarine, involves directing sounds out into the environment and detecting the reflecting sound waves. By comparing where the reflecting sounds come from, bats flying in the dark can estimate their distance from prey items and obstacles.

echolocation

Most bats are relatively small, have tiny eyes and can echolocate by producing clicks from their larynx (voice box). The Old World fruit bats (Pteropodidae) tend to be large, have much bigger eyes and cannot echolocate, with the exception of the rousette fruit bats (genus Rousettus) which can produce tongue clicks.

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Rousettus aegyptiacus – Egyptian fruit bat

For many years, evolutionary biologists noted that the echolocating bats were anatomically very similar to each other, to the exclusion of the Old World fruit bats. The former were referred to as microbats, being typically smaller, and the latter were known as megabats. However, once scientists began examining their DNA, they found out that some of the echolocating “microbats”, including the minuscule bumblebee bat

bumblee-bat

are actually more genetically similar to the large-bodied, non-echolocating megabats

Giant golden-crowned flying fox

than to other echolocating species.

Myotis daubentoni

Though this was first discovered in 2000 by Emma Teeling and colleagues [1] using six genes with >6,000 letters of DNA, more recent studies using almost 2.4 million letters of DNA have confirmed these earlier results [2].

FIGURE 1

Why the discrepancy between anatomy and DNA? An evolutionary explanation is that the Old World fruit bats are adapted to a new lifestyle that no longer requires echolocation. Many fruit bats rely on their large eyes for navigation during flight, and since they are typically fruit or nectar eaters they presumably do not need to echolocate to detect their immobile ‘prey’!

Questions for Creationists

If God created bats and their DNA, why is it that some small, tiny-eyed, echolocating bats are much more genetically similar to large, non-echolocating bats with big eyes than other small bats? If God created the same animals with the same building blocks, wouldn’t all echolocating bats be more genetically similar to each other?

References

1. Teeling, E. C., Scally, M., Kao, D. J., Romagnoli, M. L., Springer, M. S., & Stanhope, M. J. (2000). Molecular evidence regarding the origin of echolocation and flight in bats. Nature403(6766), 188-192.

2. Tsagkogeorga, G., Parker, J., Stupka, E., Cotton, J. A., & Rossiter, S. J. (2013). Phylogenomic analyses elucidate the evolutionary relationships of bats. Current Biology23(22), 2262-2267.

Molecular phylogenetics: Sloths, armadillos and anteaters are each other’s closest relatives

When one thinks of sloths

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anteaters

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and armadillos

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it’s difficult to imagine mammals that are more different from each other.

Sloths look a bit like lorises and pottos: arboreal, tailless mammals that move quite slowly.

Armadillos look somewhat like pangolins, with their scaly armor.

Pangolin4

Technically, pangolins, also known as scaly anteaters, probably have more in common with anteaters. They have strong arms and curved claws for digging up termites and ants, long tongues for eating these prey, and completely lack teeth.

pangolin-tongue

Despite their overall anatomical differences, sloths, armadillos and anteaters are more genetically similar to each other than they are to any other mammals.

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Here’s a phylogeny [1] that utilized 35,603 letters of DNA and compared 164 different species of mammals. It shows that sloths (Bradypodidae, Megalonychidae), armadillos (Dasypodidae) and anteaters (Myrmecophagidae, Cyclopedidae) come out together (yellowish-orange part of tree at the bottom) to the exclusion of other mammals. Lorises and pottos (Lorisidae) come out with primates (blue) and pangolins (Manidae) come out with carnivores (green) on completely different parts of the tree.

Not only do sloths, armadillos and anteaters have more similar DNA, but they also have a few anatomical characteristics that unite them. An important and unique one is that they possess extra articulations between their vertebrae, which has given them their official scientific group name, Xenarthra (“strange joints”).

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The evolutionary explanation for why these three very different groups of animals could be genetically similar to each other is that they share a common ancestor that lived about 65 million years ago and have since evolved very different anatomical features and lifestyles. They retain signatures of their shared evolutionary history through the retention of genetic similarity and anatomical features, such as the xenarthrous vertebrae.

Questions for Creationists

If God created all animals, including their DNA, why are animals as different as sloths, armadillos and anteaters more genetically similar to each other than they are to animals that look more physically similar to them, like lorises and pangolins? Shouldn’t DNA similarity correlate with anatomical similarity?

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. Science334(6055), 521-524.

Molecular phylogenetics: Whales are hoofed mammals

If you were asked what kinds of animals a whale most resembles, what would you say? Fishes? Sharks? Manatees? Perhaps even seals and sea lions? Certainly they look more like those than a dog…or a bat…or a cow. So if God created all animals as they appear today, presumably the DNA of whales, the underlying ‘blueprint’ or code determining how they look, should be more similar to other swimming animals.

In fact, what we find is that whales are far more similar genetically to hoofed mammals, such as cows, pigs, giraffes, gazelles and camels, than they are to any other animals.

Humpback_stellwagen_edit

So this humpback whale…

klip

…is more similar genetically to this tiny antelope called a klipspringer…

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…than it is to this aquatic manatee…

Whale_shark_Georgia_aquarium

…or this whale shark.

An example of why we know this is from a study by my PhD advisor and his colleagues [1] in which they compared 164 different species of mammals using 35,603 letters of DNA. The results of their analyses showed that whales came out with hippos, nested smack dab within other hoofed mammals. In fact, whales are more genetically similar to giraffes, cows, goats and gazelles (among others) than camels or pigs are. Beyond that, whales are more similar to bats, or even giant pandas, than they are to the aquatic manatees.

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It might be difficult to see, but in the bottom of the green branches you’ll notice a humpback whale (the blue one) and a sperm whale (the gray one) are in the same group as the hoofed mammals (shown are a deer and an okapi).

This ties nicely into the fossil evidence that suggests that whales descended from terrestrial mammals.

Questions for Creationists

Why would God create whales to be more similar genetically to a giraffe or a cow than other large aquatic animals such as sharks, especially when whales do not even remotely resemble such hoofed mammals?

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. Science334(6055), 521-524.

Why molecular phylogenetics matters

Before I discuss another piece of evidence for macroevolutionary patterns in whales, I’m going to discuss a new concept: molecular phylogenetics.

Phylogenetics is the study, primarily the inference, of the evolutionary relationships between different species and/or populations. If you have ever seen something described as an “evolutionary tree”, this is the layman’s term for a “phylogeny”.

phylogeny_tree_med

Above is an example of a phylogeny which includes six species of vertebrates. What you’ll notice is that it takes on the structure of a bifurcating tree, i.e., a branch will occasionally split into two branches. What each branch represents is a hypothetical species, assumed to have existed prior to the present, which may or may not terminate into an actual known species, such as the chimpanzee or bear illustrated above.

Since each branch represents a hypothetical species, then the bifurcations represent a single species splitting into two. The point where they split can be thought of as a hypothetical common ancestor.

So looking at the phylogeny above, the bear and the chimpanzee share a more recent common ancestor than the other species. This means that these two are more closely related to each other than they are to all other species in the phylogeny. Chimp+Bear are then more closely related to the lizard than they are to all other species in the phylogeny. Chimp+Bear+Lizard are most closely related to newt, and so on.

So how do scientists make these phylogenies? Rather than simply being constructed based on a priori assumptions, they are constructed using algorithms and/or statistical methods applied data. In other words, a phylogenetic estimation is something the data tells scientists rather than something that scientists invent for the sake of telling a story.

Historically, this was done using morphology, or physical features of the anatomy. What scientists would do first is pick a feature in the species being examined. Let’s say, for example, hair. If you looked at all of the animals in the above phylogeny, you’d notice that two have hair and four don’t. Another feature could be ossified (bony) vertebrae: five animals above have this, and one doesn’t. You can keep doing this for as many features as possible and compare the distributions of character states (e.g., present vs. absent) and you’d discover overall patterns of similarity. What the methods would do then is assume evolution and a bifurcating phylogeny, and you’d get a phylogeny such as that above.

SalticidCharacterMatrix

An example of a character matrix used in morphology based phylogenetics.

A revolution in many fields took place when scientists began sequencing DNA, but for our purposes, it impacted phylogenetics in a big way. Rather than having to rely on morphological characteristics, which are painstaking to gather and are extremely limited in the number of characters you can compare, scientists began comparing DNA among different species. The amount of characters that can be compared is now in the thousands to millions and beyond rather than the hundreds typical of anatomical data. This, coupled with more rigorous statistical methods that compare different phylogenies and incorporate models of molecular evolution (e.g., how easily do the different letters in DNA mutate from one to another?), has resulted in far more robust phylogenies that present extremely consistent and easily reproducible results.

Alignment

An example of a DNA alignment used in molecular phylogenetics.

So back to what this title proposed to address: why does molecular phylogenetics matter? I’ll start explaining why by re-hashing a point in a discussion that I once had with a creationist. The creationist pointed out that it didn’t matter that the DNA between, say, a chimpanzee and a gorilla were similar. If God created them to look similarly, why shouldn’t their underlying DNA, the blueprint for their bodies, also be similar? This point would certainly be an apt one, except for a very important problem: quite often, species that are similar in form (morphology) are not necessarily similar at the DNA levelThis is to be entirely expected in evolutionary biology, since we believe that two different lineages of organisms can adapt to have very similar anatomical features (convergent evolution), but their underlying DNA should reflect their divergent past. By comparison, this seems to be much more difficult to explain from a creationist perspective.

Questions for creationists

What would you expect to happen to genes if species evolved through time? Is this consistent with what we find in nature? If God created life in its present form, how similar would you predict genes to be in different species? Would you expect similar looking plants and animals to have all of their genes more similar to each other or only those genes that are associated with similar characteristics?