Genetics of South American rodents points to evolution

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

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

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

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

Mammal phylogeny
Mammal molecular phylogeny

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

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

south american rodent fossil distribution
South American rodent fossil distribution

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

Questions for Creationists

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


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

2. Paleobiology database


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

Why do the biggest birds all live in the southern hemisphere?

As described in my previous post, DNA and anatomy suggests that large flightless birds, such as ostriches, emus and cassowaries, evolved from a common ancestor shared with tinamous, a group of quail-like birds. These birds, known as palaeognaths, all share a relatively reptilian-like jaw, unlike most other modern birds. Other large-bodied palaeognaths are known from the fossil record, some of which have gone extinct very recently.

One such lineage included the New Zealand moa (Dinornithoformes), a group of nine described species that reached up to 12 ft in height. The moa are the only birds known to have completely lost their wings, presumably as a result of remaining flightless throughout much of their evolutionary history. Though a few reports suggest they may have survived until the 1800’s, they effectively went extinct around 1440. This occurred less than 200 years after the Maori people arrived in New Zealand, suggesting overpredation led to their demise.


A female (larger) and male (smaller) South Island giant moa (Dinornis robustus), with a  pigeon for comparison.

Another major lineage of recently extinct palaeognaths is the elephant birds (Aepyornithoformes). These were similarly enormous birds, weighing up to half a ton, that lived on Madagascar and became extinct in the 1600’s or 1700’s.


Aepyornis maximus

Elephant birds maintain the world record for the largest known bird eggs: up to 3.3 ft in circumference, 13 inches long, 22 lbs, and a volume of approximately 160 times that of a chicken egg.

Christie's specialist James Hyslop holds a chicken egg next to a pre-17th century, sub-fossilised Elephant Bird egg in London

In addition to the New Zealand Moa and Malagasy elephant birds, all of today’s living palaeognaths live on southern continents: Africa (ostriches), South America (rheas, tinamous), and Australia, New Guinea and New Zealand (cassowaries, emu, kiwis). This is significant because all of these species are more genetically similar to each other than they are to any other birds.

One evolutionary model posits that a flighted palaeognath ancestor lived in the southern hemisphere, its descendant lineages dispersed to various southern continents, and many of these species became flightless over time. A flighted ancestry would explain why large-bodied palaeognaths possess tiny wings, even though they are incapable of flight. Alternatively, a creationist model suggests that all palaeognaths coincidentally headed south from Noah’s Ark, and flightless species somehow crossed oceans to arrive in Madagascar, New Guinea, Australia, New Zealand and South America.

Questions for Creationists

Why do all of the palaeognath birds live on southern continents? How did the flightless species cross oceans to get where they are today? Is it a coincidence that they are both more genetically similar to each other than to other birds and they all live on southern continents? Why would God create birds with wings that don’t allow them to fly?

Photo credit

Moa, elephant bird, elephant bird egg


Did 189 gecko species migrate to Australia together?

Lizards have a widespread distribution, having conquered much of the earth, but certain groups of lizards are localized to a single continent. Here I illustrate an example from geckos.

Carphodactylidae includes 28 species of geckos, all of which inhabit Australia. Species include the long-necked Northern leaf-tailed gecko (Orraya occultus)


and the smooth knob-tailed gecko (Nephrurus laevissimus).


Then there is Diplodactylidae, a family of 126 species of geckos that live in Australia, New Zealand and New Caledonia, an island east of Australia. This group includes the crested gecko (Correlophus ciliatus)


and the Northern spiny-tailed gecko (Strophurus ciliaris).


Finally, a group known as Pygopodidae, the 35 species of legless geckos, is found in Australia and New Guinea. Below is the hooded scaly-foot (Pygopus nigriceps).


These anatomically disparate gecko species have something in common besides all living in or very near Australia: they are all more genetically similar to each other than they are to other lizards or even to other geckos. Below is a molecular phylogeny by Pyron et al. [1] containing 4161 species of lizards and using up to 12896 letters of DNA for comparison. What you should notice is that the Australian geckos, Carphodactylidae, Diplodactylidae and Pygopodidae, are all clustered together at the top of the phylogeny to the exclusion of all other geckos (Eublepharidae, Sphaerodactylidae, Phyllodactylidae, Gekkonidae).


In the context of evolutionary theory, this has a very simple explanation: an ancestral gecko species invaded Australia and diversified into the many Australian geckos that survive today. An alternative creationist hypothesis posits that 189 species of gecko (along with any extinct forms) all walked/slithered across Asia and crossed some portion of the Indian ocean together. This hypothesis suggests that it is simply a coincidence that they are all genetically more similar to each other than they are to other geckos.

Questions for Creationists

If these geckos were on Noah’s ark, how would they know to head to Australia together? Did they swim across the ocean together? Why did they not head elsewhere in the world? Why are they more genetically similar to each other than to other geckos?


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

Orraya occultus, Nephrurus laevissimus, Correlophus ciliatus, Strophurus ciliaris

Sloths, armadillos and anteaters have been stuck in the New World for their entire existence

Sloths, armadillos and anteaters (xenarthrans), as different as they look, are genetically more similar to each other than they are to any other mammals. This suggests that these three very different groups of animals descended from a common ancestor. If this common ancestor lived on an isolated island, we would expect that all of its descendants might live on that same island.

Interestingly, all modern and extinct xenarthrans indeed live(d) on a very large island: the Americas. Based on fossil evidence, we think that the earliest xenarthrans lived in South America and some of them later dispersed North, particularly the extinct ground sloths, glyptodonts and pampatheres.


The only living xenarthran that naturally occurs on the northern continent is the nine-banded armadillo (Dasypus novemcinctus).


This makes sense as an evolutionary biogeographic scenario: xenarthrans originated in South America, diversified into many species, and dispersed to North America. They probably didn’t travel farther than this simply because the Americas are separated from other continents by oceans.

Questions for Creationists

Is it simply a coincidence that sloths, armadillos and anteaters are genetically similar and they all live in the Americas? If all xenarthrans lived on Noah’s Ark and left from it after the floodwaters receded, how did they get over to North and South America? Why did they go to North and South America at all? How did the slow-moving tree sloths make their way across such a vast distance? Given their poor vision, how did the xenarthrans effectively navigate such a tremendous journey?

Whales walked in India and Pakistan before swimming around the world

The fossil record, DNA and developmental biology all suggest that aquatic whales descended from ancestors that walked on land. The geographical distribution of some putative proto-whale fossils also seems to hint at this significant transition.

The proto-whale fossils that were almost completely land-dwelling, but likely spent at least some time in the water, include Indohyus and Pakicetus. When these animals first appear in the fossil record about 56–47.8 million years ago, they are found exclusively near the border of India and Pakistan [1].

Distribution of Ypresian cetaceans
The first appearances of proto-whales

In the next geological sequence, rocks dating to 47.8–40.3 million years ago, the proto-whale fossils show evidence of a stronger commitment to an aquatic lifestyle. For example, Ambulocetus and Remingtonocetus have anatomy that suggests they were similar to seals and sea lions, coming onto land occasionally but being particularly well-suited to life in the water. Rodhocetus, Artiocetus, and Protocetus take the aquatic commitment further with the presence of incipient blowholes and tail flukes. Georgiacetus was probably the closest to modern whales, having hindlimbs that were completely detached from the spine and therefore highly unlikely to support walking on land.

Some of these proto-whales and other are still found in the Indo-Pakistani region, much as you might expect if their ancestors arose from there.

Lutetian cetaceans in Indo-Pakistani region
The next generation of proto-whales in the Indo-Pakistani region

However, given their further commitment to an aquatic lifestyle, they had the capacity to disperse to new parts of the world. Whereas Indohyus and Pakicetus likely would have had an extremely difficult time trying to cross the Atlantic and Southern Oceans, these animals almost certainly could have swam across, even if at the more narrow points. Indeed, the next generation of proto-whales include fossils found in Africa, Europe, Asia and even Antarctica.

Global distribution of Lutetian proto-whales
Global distribution of the second generation proto-whales

Although the fine details are difficult to parse out given the relative coarseness of the geological record, the global distribution of proto-whale fossils seems to suggest that these animals originated in India and Pakistan, and, once they committed to the water they then spread across the globe.

Questions for Creationists

Why do we see this geographical pattern in putative proto-whale fossils? Why don’t we find the land-dwelling Indohyus and Pakicetus in places all around the world like we do for the aquatic photo-whales? Why would Indohyus, Pakicetus and some of the more aquatic proto-whales all migrate together to India and Pakistan after Noah’s Flood?


1. Fossil distributions from the Paleobiology database

Biogeography: Understanding where things live and why

It may not seem intuitive, but biogeography, the study of where organisms live and why they live there, is very consistent with the theory of evolution. However, there is an abundance of uncertainty in understanding how life has spread across the globe, and it may surprise those who accept evolution to learn that in some ways, evolution fares no better than creationism.

Let me start off by describing the two general ideas evolutionary biologists invoke to explain how life has moved around the planet. The first is by dispersal, a rather simple concept in which life moved from point A to point B by, well, dispersing! Some things are really good at dispersing, like birds and bats, so imagining them flying across continents and even oceans should not be difficult to fathom. Similarly, oceanic creatures would not be too hampered from dispersal as they can swim or float to a new coast or sea.

Hypothesis of cichlid dispersal

But what about land-dwelling organisms? How does a lizard from Asia get to a tiny island in the middle of the Pacific? It certainly didn’t fly and it’s very unlikely that it swam. This is where the more sketchy, yet technically plausible, hypothesizing comes in. Now and then, chunks of land can detach and float across great bodies of water. Perhaps, the idea goes, with the right currents, enough such events over time, and the lizard happens to be a female with babies on the way, then our seafaring voyager could land on a different island or continent and start a whole new life.

Though researchers are hard at work understanding what kinds of organisms can survive such transoceanic journeys and estimating the directions of currents in ancient seaways, one has to admit that these ideas are rather difficult to test. Importantly, I do not think such scenarios have a major impact in assessing the validity of evolution, but rather they can be used to understand how life dispersed assuming evolution is true.

The other major mechanism thought to influence the geography of life is a concept called vicariance, whereby a population of organisms is split into two or more populations by the formation of geological features. This idea generally rests on plate tectonic theory, which suggests that the earth is composed of plates that have moved, collided, separated, lifted, and destroyed one another over time. The consequence of this shuffling of plates is thought to have created all sorts of barriers between different forms of life. We think plate tectonics led to the formation of mountains as well as merged and separated continents, and life has cruised along for the ride. Plates do indeed move, a demonstrable fact, especially if you live in an earthquake prone zone, but how well does plate tectonic theory explain the distribution of life on earth?

Plate boundaries

Well, it depends. I give some examples in this blog that are very consistent with plate tectonic theory. However, in many cases, estimates of when species split from each other very frequently post-date the formation of such geological formations. For example, we might estimate continent A split from continent B 90 million years ago, but species X living on continent A split from species Y on continent B 70 million years ago. This leads us to the conclusion that, by default, dispersal must be responsible for where species X and Y live today. Again, this returns us to the problem of trying to figure out how the heck the organisms got to where they now live.

Where does Creationism fit into all of this? Of course dispersal is not an issue for Creationists: organisms move across the earth, and this is clearly demonstrable. For some Creationists, plate tectonic theory is even acceptable [1].

I think the major differences come down to three specific points. First, Creationists believe that all land-dwelling animals started from the same point: Mount Ararat in Turkey. After Noah’s flood, the story goes, animals dispersed from out of the ark and made their way across the world [1,2]. Second, though the dispersal of terrestrial life is in part thought to be natural, Creationists emphasize the importance of humans as agents of dispersal, carrying seeds and moving livestock for purposes such as food [1,2].

Noah's ark

By contrast, evolutionary biologists think that life started in a single unknown, and likely unknowable, location, but as new species were formed over time, they have been dispersing and drifting along with the plates. Furthermore, while humans have undoubtedly aided the dispersal of some organisms, evolutionary biologists believe this has been limited to the very latest part of earth’s history.

The third critical difference is that Creationists believe that all dispersals and/or plate tectonic events happened in just a few thousand years, whereas evolutionary biologists think they’ve occurred over billions of years. I will let the geologists tackle the notion of continents forming in thousands of years or less, but this time difference is key for comparing Creationism to evolution. For example, evolutionary biologists do not think that marsupials had to arrive in Australia 65 million years ago anymore than they could have showed up 25 million years ago. In theory, it could have at whatever point in time after marsupials originated, and it happened when it did because the right situation allowed for it to. Creationists, by contrast, are constrained in that marsupials must have arrived in Australia in just the past few thousand years.

I think you will find in my posts about biogeography that a universal origin of terrestrial life from Mt. Ararat, an extremely short time scale, and the agency of humans in dispersal turn out to be the most difficult details for Creationism to reconcile with the data collected by scientists. This turns out to be especially true when it comes to comparing the fossil record and DNA evidence with biogeography. Where Creationism fails in this respect, I believe you will begin to see that evolution triumphs.