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.


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]:


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?


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

Ontogeny recapitulates phylogeny: 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.


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


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


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.


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?


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

Biogeography: Why are there so many marsupials in Australia?

Marsupials are a group of mammals generally characterized by having their young develop in a pouch, known as a marsupium. Besides this trait, there isn’t anything obvious about them that screams out that they are more closely related to each other than they are to other mammals. When you place a kangaroo, Tasmanian devil, koala, marsupial mole, antechinus, bilby and cuscus side-by-side, they probably don’t strike you as cousins.

And yet, when we look at their DNA, we find that they are more genetically similar to each other than they are to other mammals. Below is a phylogeny [1] estimated from thousands of letters of DNA, and you can see that the marsupials (at the top in purple) cluster together to the exclusion of all other mammals.


What’s particularly interesting about their genetic similarity, is that where they live also seems to point to a common ancestry. Some marsupials, namely shrew opossums, opossums, and the monito del monte, live in South America and, in the case of the Virginia opossum, North America as well. The rest of the marsupials all live in Australia and the surrounding islands. Below is a world map showing the distribution of modern day marsupials.


What adds to this interesting pattern is that when you look at the marsupial phylogeny above, the American marsupial lineages (Caenolestidae, Didelphidae+Caluromyidae, Microbiotheriidae) split off one by one. All of the remaining marsupials, which are clustered together, hail from Australasia. To state this in no uncertain terms: Australasian marsupials are more genetically similar to each other than they are to American marsupials.

So here we have an example where both biogeography and DNA tell the same story: a single marsupial ancestor colonized Australasia and then split into many different species with a multitude of distinct body forms, ranging from kangaroos to marsupial moles and koalas to cuscuses.

Questions for Creationists

Why do marsupials, despite looking so different from each other, have such similar DNA? If God created the DNA ‘blueprint’ for all life, and DNA makes bodies look the way they do, shouldn’t marsupial moles have DNA more like other moles, and Tasmanian devils have DNA more like other carnivorous mammals? Why do most marsupials live in and around Australia? Is it just a coincidence that all Australasian marsupials are more genetically similar to one another than they are to American marsupials? If they didn’t evolve from a common ancestor, did they all walk together from Noah’s ark to Australia? If people brought them to Australia, why did they mostly only bring marsupials?


1. Meredith, R. W., Janečka, J. E., Gatesy, J., Ryder, O. A., Fisher, C. A., Teeling, E. C., … & Rabosky, D. L. (2011). Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science334(6055), 521-524.

Photo credit

Kangaroo, Tasmanian devil, koala, antechinus, bilby, cuscus

Where did the thalattosuchians go?

Crocodilians, which include crocodiles, gharials, caimans and alligators, are represented by relatively few species today. Not only are these animals not particularly speciose, they are also quite similar in appearance and habit. Looking at them, they are unmistakably crocodile-esque, with their toothy smiles and elongate bodies embedded with rows of bony scales. Crocodilians are generally ambush predators that hunt in the water or at the water’s edge. While some species mostly hunt fishes, the stereotypical image of crocodilians lying in wait for an unwitting animal to take a drink is not uncommon. Though they seem quite comfortable in water, crocodilians have a sprawling, somewhat awkward posture on land. Nonetheless, they will frequently leave the water to rest and bask in the sun.

Once upon a time, there was quite an impressive diversity in the forms of crocodilian-like animals, many of which appear to have had very different lifestyles from modern species. One group of these animals was the thalattosuchians, which were particularly specialized for living in the ocean. Some thalattosuchians superficially looked quite similar to modern crocodilians, particularly teleosaurids, which includes Platysuchus and Steneosaurus.

Others were more obviously adapted for an oceanic lifestyle, and would have looked quite different from your typical crocodile or alligator. These species include GeosaurusRhacheosaurus and Dakosaurus, known collectively as metriorhynchids. If you look closely at Geosaurus, you can see that the limbs were more fin-like in shape, and both Geosaurus and Rhacheosaurus preserve outlines of a tail fin, demonstrating evidence of their strong swimming abilities.

Thalattosuchians appear in rocks estimated to be 199.3 million  years old, and then seemingly disappeared 93.9 million years old [1]. Despite this long and successful history, for better or worse, they can no longer be found in our seas.


Questions for Creationists

Where did the thalattosuchians go? Why would God create them only to have them completely disappear? Since they lived in oceans, shouldn’t they have survived Noah’s flood? Why do modern crocodilians have very similar lifestyles whereas the other crocodilians seemed to have lived very differently?


1. Paleobiology database

Photo credit

Slender-snouted crocodile, gharial, black caiman, chinese alligator, Platysuchus, Steneosaurus, Dakosaurus, Geosaurus, Rhacheosaurus, metriorhynchid reconstructions

Transitional fossils: Manatees that walked on land

Manatees and the dugong, known collectively as sirenians, are herbivorous, aquatic mammals that are generally restricted to shallow, tropical waters. Like whales, sirenians have reduced the amount of hair on their bodies, have forelimbs shaped into flippers, lack external hindlimbs and have a paddle-like tail.

Despite their overall similarities, the DNA of sirenians is much more similar to that of elephants and the DNA of whales is much more similar to hoofed mammals like cows and giraffes. This suggests that both sirenians and whales independently adapted to living in an aquatic medium. In fact, the fossil record of whales suggests a transition from a land-based habitat to a completely aquatic way of life. Do sirenians show the same pattern?


Indeed they do! One of the earliest sirenian species appearing in the fossil record is Pezosiren, a mammal with an unmistakably sirenian-like skull, but the rest of its skeleton clearly suggests that it had the ability to walk on land. Unlike modern sirenians, this animal had forelimbs that are not shaped like flippers but instead were used to support their weight on land, as well as hindlimbs and a distinct hip bone (pelvis). Pezosiren has been found in rocks estimated to be ~47.8 million years in age, similar to the age that walking ‘whales’ were also found roaming the earth.


More recent sirenian fossils show evidence of fully committing to an aquatic lifestyle, including Halitherium, which is found in rocks estimated to be ~38 million years old. This species and similarly dated fossils had modified their forelimbs into flippers, possessed thick and dense ribs to provide ballast, and reduced their hindlimbs, presumably to minimize drag. Though it looked very much like modern manatees (see below) and dugongs, it had a better-developed, albeit very reduced, pelvis+hindlimb complex.


In addition to their better-developed limbs, early species of sirenians had a number of other traits that manatees and the dugong have lost. Pezosiren and others had multiple vertebrae in the hip region (sacral), much like their land-dwelling elephant relatives, whereas most fossil and all modern sirenians have fused these into a single bone. Modern sirenians also have reduced their teeth to a great extent compared to their fossil forebears. Earlier species had permanent premolars, canines and incisors, whereas modern species lack these teeth (dugongs have only one incisor). See below for a diagram of a fossil sirenian (Protosiren, ~47.8 million years old) showing the positions of the premolars (P), canine (C) and incisors (I).


Questions for Creationists

Where did the dozens of other sirenian species go? Given their aquatic adaptations, wouldn’t they have survived Noah’s flood? Is it just a coincidence that molecular phylogenetics shows sirenians as being genetically similar to land mammals like elephants and there are sirenian fossils that appear to document a transition from land to water? Is it coincidence that we see parallel evidence of a land to water transition in whales?


1. Springer, M. S., Signore, A. V., Paijmans, J. L., Vélez-Juarbe, J., Domning, D. P., Bauer, C. E., … & Meredith, R. W. (2015). Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Molecular phylogenetics and evolution91, 178-193.

Photo credit

Manatees, dugong, Pezosiren, Halitherium, manatee skeleton, Protosiren

Pseudogenes: 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.


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?


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,

Where did the gorgonopsians go?


The animal above might strike most people as something akin to a dinosaur. Paleontologists, however, think that it was most likely related to mammals.

This particular animal, known as Gorgonops, belonged to a group of similar extinct creatures known as gorgonopsians. Gorgonopsians have been found in African and Asian rocks estimated to be 272 to 252 million years old [1].

Though the reconstruction above suggests that these animals had fur, there is currently no evidence that they really did. However, they have several mammal-like features in their skulls, including teeth that differ in shape and structure (heterodonty). If you look at a typical lizard or crocodile, you’ll notice that their teeth look almost identical. Gorgonopsians and mammals, by contrast, have distinctly different teeth, including incisors, canines, premolars and molars.


These creatures ranged in size from a dog to a bear, and their skull anatomy suggests that they were carnivorous. Below is one of the largest species, known as Inostrancevia.


Gorgonopsians disappeared at the end of the Permian period some 252 million years, in what paleontologists interpret as a mass extinction. They vanished at the same time as organisms as diverse as hyoliths, glossopterids, captorhinids and sea scorpions, likely due to massive climate change.

Questions for Creationists

Where did the gorgonopsians go? If they lived across Asia and Africa, why have we never encountered one in the wild? Did Noah not have any room for them on his ark? Is it just a coincidence that they disappear in the same rocks as hyoliths, glossopterids, captorhinids and sea scorpions?



Photo credit

Gorgonops, gorgonopsian skullInostrancevia

Transitional fossils: The earliest platypuses


Platypuses are strange creatures, even to evolutionary biologists. They have hair, webbed feet, a beaver-like tail, and duck-like bills with which they can sense electrical currents, they lay eggs, and the males possess venom glands on their hind limbs. When a drawing and a pelt of the animal were first sent to British scientists at the end of the 18th century, the incredulous naturalists assumed it was a hoax. In college, I had a t-shirt that made light of their bizarre features:


Given the idiosyncrasies of this animal, you might imagine that they’re a bit of an enigma to evolutionary biologists. In fact, I recall a creationist acquaintance of mine once declaring that they must be an “evolutionist’s worst nightmare”. To be sure, there are a lot of gaps in our knowledge regarding how they might have evolved. What the evidence points to pretty clearly is this: 1) they’re mammals, as they have hair, produce milk for their young, and their DNA is much more similar to other mammals than it is to, say, birds or lizards, and 2) they split from other mammals a long, long time ago, somewhere on the order of 220 million years. The fossil record of their relatives, known as monotremes, is extremely spotty, with the earliest dating to over one hundred million years ago. Unfortunately, the specimens are extremely fragmentary, frequently consisting of only part of a jaw or arm, preventing researchers from making many firm conclusions about their evolution.

However, at least one fossil animal gives some insights into their ancestry. Obdurodon includes several species of platypus-like monotremes that are estimated to have lived ~28.1 to 5.3 million years ago. Below you can see a comparison between Obdurodon dicksoni (left; 23-11.6 million years ago) and the modern platypus (right).


You’ll notice differences between the two, but overall they look extremely similar. Clearly the duck-like bill has been around for a while! However, at least one feature  points to Obdurodon being a transitional fossil, namely the fact that it has teeth. Modern platypuses have teeth when they are very young, but shed these by adulthood and replace them with horny pads (see below).


Considering these horny pads are a very uncommon feature in mammals, and vertebrates as a whole, biologists interpret it as an evolutionary novelty. With Obdurodon, we have support for this hypothesis, with evidence that a toothed ancestor preceded the modern platypus dental condition.

Questions for creationists

Where did the other platypus species (i.e., Obdurodon) go? Could Noah not fit them or their eggs on his ark? Is it a coincidence that there are fossil platypuses that had teeth as adults, much like typical mammals, but modern platypuses replace them during development with horny pads?


1. Musser, A. M., & Archer, M. (1998). New information about the skull and dentary of the Miocene platypus Obdurodon dicksoni, and a discussion of ornithorhynchid relationships. Philosophical Transactions of the Royal Society of London B: Biological Sciences353(1372), 1063-1079.

Photo credit

platypus, t-shirt image, platypus Obdurodon comparison, horny pads

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.


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?


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

Ontogeny recapitulates phylogeny: Fetal sloth teeth point to evolutionary history


Sloths are strange creatures in many ways. In addition to their slow movements and suspensory way of life, they have a chambered stomach like a cow, algae species that are found on their hair and nowhere else in the world, moths whose life cycles are entirely tied to sloths (“sloth moths”), surprisingly degenerate vision, and strange teeth.

Their teeth are bizarre in a number of ways: they lack enamel, they don’t have baby teeth (i.e., they are born with the only set of teeth they will ever have), and their teeth are notoriously difficult to categorize. By this I mean that scientists aren’t really sure if sloths have canine teeth or premolars. What does seem clear is that they do not have incisors, the front teeth typically present in mammals.

Based on evolutionary theory, scientists think that sloths descended from mammals that had all of the typical mammalian tooth traits, leading to the prediction that they may retain some features suggestive of this earlier dental history. For example, despite lacking enamel, sloths retain defunct remnants of enamel genes in their genomes. The ontogeny, or development, of sloths might give more hints of their toothier past.

Lionel Hautier and his colleagues [1] set out to examine sloth fetuses using CT scans to test this idea. After examining 25 sloth specimens, they found that sloths had very tiny teeth that are not present in adults. At least one set of teeth in the two-toed sloths (Choloepus) are replaced, suggesting they do indeed have baby teeth, but they do not remain once the sloths are born.


dCf stands for deciduous, or baby, teeth. Note that the two-toed sloth fetuses (A, B) have baby teeth (dCf) right next to the adult teeth (Cf) before the former disappear entirely when they’re born. C is a three-toed sloth for comparison.

Additionally, the researchers discovered that some of the tiny teeth in the three-toed sloths are incisors, which characteristically develop on the premaxilla of the upper jaw (red coloring in the images above and below). However, these appear to be resorbed by the time of birth. Interestingly, not all of the sloths develop with these tiny incisors, suggesting that they may currently be evolving such that they will eventually be completely lost.


Three-toed sloth fetuses, some of which (C,D) have incisors (dVpmx) that are not retained in the adults, as well as other teeth that disappear before birth (dv).

Questions for Creationists

Why do sloths have teeth that begin to develop and then disappear altogether? Would it not have been simpler for God to create sloths with only one set of teeth and not teeth that no longer function? Is it just a coincidence that sloth fetuses replace their baby teeth with adult teeth and have incisors, just like early fossil mammals and most mammals today? Why do we also see a similar pattern in baleen whales, which lack teeth entirely as adults?


1. Hautier, L., Rodrigues, H. G., Billet, G., & Asher, R. J. (2016). The hidden teeth of sloths: evolutionary vestiges and the development of a simplified dentition. Scientific reports6.

Photo credit

Three-toed sloth, deciduous teeth, incisors