1. Embryology as Evidence for Evolution

We learned previously that one way that we know that two structures are homologous is because they originate in a similar patch of embryonic tissue. In the diagram to the left, the same patch of tissue develops into the wing of a bird and the arm of a human being. As the animal develops into its adult form, the structure becomes modified to serve a different function.

The study of embryos reveals additional evidence for evolution. To see how, let’s return to an image from Unit 6 about how developmental genes are expressed in a hierarchical sequence.

As we saw in Unit 6, the images below show embryos from different types of vertebrates — animals with backbones — at equivalent phases of development. The top row consists of photographs with some modifications (a yolk sac removed in the salamander). The bottom row shows drawings by Ernst Haeckel, a famous 19th-century biologist.

The similarity in embryonic form provides a few additional pieces of evidence for evolution. First, the similarity of form is a homologous trait. The common pattern of development in all vertebrates is a feature that was inherited from a common ancestor.

Second, examining embryos reveals two vestigial traits that disappear later in development.

• Pharyngeal slits (also called “gill slits”) appear in humans, rabbits, and chickens. These slits are openings from the neck into the back of the mouth. Fish never lose these slits: they use them to pass water over their gills so that they can absorb oxygen from water. In all the tetrapod vertebrates (the four-limbed amphibians, reptiles, birds, and mammals), these slits disappear later in development.
• Tails appear in humans and chickens and then disappear later in development.

Why do humans, rabbits, and chickens expend the energy to create embryonic gill slits, only to break them down and absorb them later? It’s because having gill slits is part of a developmental pattern inherited from a vertebrate ancestor. In early embryos, the genes for this plan are still expressed.

The same is true of the tail. All vertebrate embryos have a pronounced tail. That includes animals like humans and birds, which as adults don’t have tails. Why do these embryos have tails? Because having a tail is a vestigial trait. It’s a vestige of a developmental pattern inherited from a common ancestor.

What’s the takeaway? Embryological development allows us to more clearly see the homologies that come about through adaptive radiation.

• All vertebrates descend from a common ancestor.
• As vertebrates develop, their body plan unfolds in a way common to all vertebrates. That embryonic pattern is itself a homology.
• As development continues, the form of each lineage diverges. The same patch of tissue will develop into a wing of a bird or the forelimb of a lizard, rabbit, or frog.
• The homologous structure of the forelimb in the adult form of each animal reflects adaptive radiation from a common ancestor.

Finally, note that this same pattern of embryonic similarity followed by development into diverse forms can be found in any other group of organisms descended from a common ancestor. You can learn about the differentiation of insect mouthparts in this article on Wikipedia.

2. Flashcards: Embryological Evidence for Evolution

3. Molecular Homologies Part 1: Proteins.

Above and in previous tutorials, we’ve discussed how homologous structures serve as evidence for evolution. Molecules can be homologous too, establishing another line of evidence for evolution.

The table below shows two proteins that are widely shared among many species.

Cytochrome c is a protein that’s used in cellular respiration.	Hemoglobin is a protein used to carry oxygen in red blood cells.

Cytochrome c and hemoglobin are found in many species with either an identical or highly similar sequence of amino acids and a correspondingly similar three-dimensional shape. Why do so many different species share these molecules? Because they inherited the genes for making these molecules from a common ancestor.

To learn more, complete the following interactive reading.

What’s the takeaway?  The sharing of common proteins like cytochrome c and hemoglobin among animals isn’t unusual. Most of the proteins found in human beings are also found in other animals. The sharing of these proteins is a homology, indicating descent from a common ancestor.

4. Molecular Homologies Part 2: Homologous DNA Sequences and Genes

What’s true of proteins is also true of DNA. The image below shows a stretch of DNA from seven animals. Why is there so much overlap between the sequences? Because all of these animals share a common ancestor. The more recent the common ancestor, the more overlap between the sequences. This similarity in the sequence is called sequence homology, and it’s become the best evidence for drawing evolutionary trees (a topic we’ll take on later in this unit).

Protein-coding genes can also be homologous. Based on how the term “gene” is defined, humans have between 20,000 and 25,000 genes. Almost all of these genes are also found in other animals. We share these genes with other animals because we inherited them from a common ancestor.

Here are two examples:

1. Genes coding for eye development

A gene called eyeless codes for eye formation in fruit flies (and other insects). In the image on the right, you can see what the eyeless phenotype looks like.

The eyeless gene is homologous to a gene called small eye in mice (and other mammals).

How do we know that the genes are homologous?  First, because of the shared sequence of nucleotide bases in each gene. Second, because of a series of experiments in which these genes were transferred from fruit flies to mice, and vice versa.  The eyeless gene has been experimentally inserted into mutant mice embryos that are from a strain of mice that don’t develop eyes. The result? The functional eyeless gene from fruit flies induced eye development in mice (a mammal) The reverse is also true. Inserting the mouse gene into embryos of mutant fruit flies that don’t develop eyes, and eyes will develop.

2. Genes coding for body segments: Almost all animals are built using a similar developmental plan. The plan involves the development of a head, a middle region, and a hind region. In many animals, these regions can be subdivided into segments.

The genes that control how each segment develops are called Hox genes, and they’re shared between insects and mammals. How do we know they’re homologous? Because of sequence homologies, and because of gene transfer experiments. In other words, the same gene that directs the formation of structures on the head in an insect also directs the formation of a head in mammals (including you). These genes are shown in red in the diagram to the right. The same is true of the structures on the rest of the body, from head to tail (even if your tail is just a vestige).

What do these genetic homologies tell us? That mice and fruit flies share a common ancestor from which they both inherited the same genes for eye development and body segment identity. That common ancestor existed 500 million years ago when the line leading to vertebrates split apart from the line leading to arthropods (insects, crabs, spiders, etc.) And just to make this personal, that means that insects are our very ancient cousins. Think of that the next time you swat a fly.

5. Genes can be vestigial, too: pseudogenes

If we think about vestigial structures like the hind limbs of whales, it’s clear that evolution doesn’t necessarily delete the genes for traits that are no longer needed. Rather, the evolutionary process involves diminishing the size of structures (such as the hind limbs of whales) or allowing mutations to accumulate in these structures (such as the vestigial eyes of blind cavefish) so that they’re no longer functional. As Jerry Coyne argues in his book Why Evolution is True, this allows us to make a prediction. In the genomes of many species, we should be able to find “silenced or dead genes: genes that once were useful but are no longer intact or expressed.”

The non-functional remnant of a formerly functional gene is called a pseudogene. Pseudogenes can be silenced for a variety of reasons. The image below shows all of these compressed into one (but note that any one of the causes shown could be sufficient for preventing gene expression).

In some cases, pseudogenes result from gene duplication, followed by a mutation in the duplicated gene. In that case, there’s no loss of function, because the original gene is still expressed.

But in other cases, a functional gene becomes silent. An example is the ψGLO pseudogene (the symbol ψ designates a gene as a pseudogene). The functional GLO gene, in other species, codes for L-Gulonolactone Oxidase, an enzyme that’s part of a pathway that converts glucose (C₆H₁₂O₆) into vitamin C (C₆H₈O₆). L-Gulonolactone Oxidase is found in a functional form in almost all mammals, except for bats, guinea pigs, and primates (the order of mammals that includes monkeys, apes, and humans). The groups that don’t make vitamin C have lost the ability to do so because they live in environments where they could obtain vitamin C from fruit in their environment. Consequently, any mutation that silenced the gene for producing L-Gulonolactone Oxidase would have no negative effect on fitness.

What happens without vitamin C? It took an unintended experiment — sailors undertaking long sea voyages without any available fruit — to see that vitamin C deficiency causes scurvy, the symptoms of which include anemia, weakness, spontaneous bleeding (especially in the gums), loss of teeth, pain in the limbs, and swelling. Prolonged vitamin C deficiency can be fatal. In 1757, a Scottish physician named James Lind persuaded the British Navy to start issuing lime juice to sailors. That ended scurvy in the British Navy, and is why British sailors (and even British people) are sometimes called “Limeys.”

About 40 million years ago, an ancient early primate developed a mutation that deactivated the GLO gene. This created the ψGLO pseudogene, which was passed on to all of his or her descendants, which now includes almost all the primates, except for lemurs and Galagos.

In a few other mammal lineages — guinea pigs and bats — the GLO gene was also silenced, and these lineages have their own version of the ψGLO pseudogene. But because this silencing happened independently from the silencing that happened in primates, the bat and guinea pig pseudogenes are significantly different from the one shared by primates (source: Coyne, 2009). In other words, the existence of the ψGLO pseudogene in primates, bats, and guinea pigs is another example of parallel evolution.

As with shared genes and amino acid sequences for cytochrome c and hemoglobin, the ψGLO pseudogene is not in any way remarkable or unusual. Pseudogenes are common in the human genome. We might have as many pseudogenes as we have genes. In the two decades since the human genome was first sequenced, the number of pseudogenes that have been identified has come to number in the thousands (compared to the 20,000 or so protein-coding genes in the human genome).

6. Flashcards: Molecular Evidence for Evolution

7. Checking Understanding Quiz: Embryonic and Molecular Evidence for Evolution

8. The Deepest Homologies

8a. Homologous features found in all eukaryotes

Our domain, the eukaryotes, arose about 1.5 billion years ago. Despite their incredible diversity, eukaryotes share a single common ancestor. How do we know? Because of the homologous features possessed by all eukaryotes.

Here’s a short list of the homologous features that all eukaryotes share.

1. Mitochondria
2. Complex cells with internal compartments such as the rough and smooth endoplasmic reticulum, the Golgi apparatus, and lysosomes.
3. A membrane-bound nucleus encloses the cell’s chromosomes, separating the chromosomes from the cytoplasm.
4. Linear chromosomes (as opposed to the circular chromosomes in bacteria and archaea).

Note that multicellularity is not a shared eukaryotic feature (because many eukaryotes are unicellular).

8b. Homologous features found in all living things

We can go one level deeper, from traits that unify eukaryotes to traits found in all living things.

All living things possess molecular and genetic homologies that point to one of the most profound insights from the study of biology: that all living things are related. We’re all cousins. “We,” in this context, doesn’t just mean all human beings (though that’s true). We’re also cousins to sparrows, leaf-cutter ants, oyster mushrooms, rhododendrons, kelp, Archaeans that live in hot springs, the photosynthetic bacteria that live in the oceans, and the E. coli bacteria that live by the billions in our guts.

To see what these homologies are, and to distinguish the conserved features of all life from the conserved features that bind together the eukaryotes, complete the quiz below.

9. Flashcards: The Deepest Homologies

10. What’s next?

To finish Topics 7.6 – 7.8, Evidence for Evolution,  click the following link for Evidence for Evolution cumulative flashcards and a multiple-choice quiz.