Molecular and genetic evidence for evolution

Evidence for evolution

Molecular and Genetic Evidence for Evolution

One of the most unexpected discoveries in molecular biology came at the beginning of the 20th century. Scientists learned that animal proteins could evolve just as anatomical structures do. For example, since chimpanzees and humans have a more recent common ancestor than chimpanzees and kangaroos, chimpanzee hemoglobin will resemble that of humans more than that of kangaroos. This phenomenon can be found across all species and with all proteins, including albumins, gamma globulins, insulin, keratin, rhodopsin, etc.

Studies done in 1962 showed that proteinencoding genes mutate over time at a constant rate. When the DNA sequences of genes for the same protein in two species are compared, the number of differences between them is proportional to the time elapsed since the two species diverged from their most recent common ancestor. The methodology works like a molecular clock, making it possible to estimate when two species diverged. Thus, after analyzing countless proteins, scientists determined that chimpanzees and humans separated into two evolutionary branches between 5-8 million years ago, not between 14-16 million years as previously believed.

Imagine the surprise when molecular biologists discovered through the analysis of proteins that the basic chemistry of fungi was more like that of animals than plants.

Additionally, by the end of the 20th century, entire genomes had been sequenced. The hypothesis was confirmed: genomes, molecules, and organs all told the same story. The more recently two species diverged, the more similar their DNA. Let us look at some genetic studies that provide insight into how closely species or populations are related.

Our Closest Unicellular Relatives

Six hundred million years ago, multicellular creatures began populating the seas. Starting as simple colonies of cells, these creatures eventually gave rise to the complex organisms that exist today. The emergence of multicellular life was a biological revolution, an amazing innovation that allowed for animal movement and the growth and development of organs. Creatures could now eat, digest food, and detect the world around them.

The cells of a multicellular organism are specialized to perform different functions. Some cells line the outside of the organism maintaining its appropriate internal temperature and water content. Other cells go on to form organs. Amazingly, they can work together and communicate, both keys to building the vast diversity of animal bodies we see around us today.

It was initially believed that the machinery needed to develop animal bodies evolved at the same time multicellular life evolved. In other words, the genes and molecules that allowed cells to adhere and interact with each other did not exist before the emergence of multicellular life.

Eventually, scientists discovered that the genes needed to build animal bodies existed in single-celled eukaryotes called choanoflagellates, our closest unicellular relative. Choanoflagellates are models for reconstructing the last unicellular ancestor of multicellular life.

The fact that previously existing genes were used to create multicellular bodies is a beautiful example of how evolution does not reinvent; it simply retools. It uses what is useful and within its reach, adapting it to new situations.

Choanoflagellates

Sickle Cell Anemia

Sickle cell anemia is a human disease caused by a mutated gene that produces abnormal hemoglobin. The disease manifests itself when an individual is homozygous recessive; they inherit two defective sickle cell genes, one from each parent. An individual is heterozygous if the defective sickle cell gene is inherited from only one parent. They are carriers of sickle cell anemia but do not have the disease. In Africa, sickle cell anemia is much more common in tribes living in warm, humid areas, near lakes or coasts, than in tribes living at higher altitudes.

This is surprising. Why does the climate make a difference? The answer involves another fatal disease, malaria. Being a carrier of sickle cell anemia makes an individual more resistant to malaria and other parasites. This otherwise lethal gene has persisted in certain populations because it offers a reproductive advantage in environments where malaria is prevalent. As a result, there are more carriers of sickle cell anemia in the warmer, humid areas of Africa. This is known as heterozygote advantage. Carriers, heterozygous individuals, have adapted to an environment where tropical diseases prevail.

Lactose Tolerance

Lactose is a simple sugar in milk, which requires an enzyme called lactase for proper digestion. Nursing human babies can digest breast milk because they produce lactase. When a baby is weaned, the gene responsible for producing lactase is switched off, or repressed, which is why many adults are lactose intolerant. Incidentally, this happens in all young mammals. Ingesting lactose as an adult can cause flatulence, stomach cramps, diarrhea, and vomiting. However, some humans can tolerate lactose and consume dairy products without any issues.

Why is this the case? Adults who can consume dairy products descend from tribes that all have something in common. They descend from pastoralist societies, shepherds who raised domesticated animals that produce milk. These tribes include the Tutsi of Rwanda, the Fulani and Tuareg of West Africa, the Sindhi of North India, the Beja of Northeast Africa, and some European tribes. Scientists believe that thousands of years ago, their ancestors were forced to consume milk in times of famine. The individuals who were able to digest lactose were more likely to survive. They could readily digest lactose because of a mutation that caused the lactase-producing gene to remain active in adulthood.

Lactose tolerance gave them a reproductive advantage over the rest of the tribe. The mutated gene was beneficial and spread throughout the population. The nationalities today with a higher incidence of lactose intolerance come from traditionally non-pastoralist societies. They include people from Japan and China, the Inuit peoples of Alaska, Canada, and Greenland, Australian aborigines, and most Native Americans.

Vision in Mammals and Birds

The visual system in mammals is very different from that of birds. The main difference is the number of light-sensitive proteins called opsins found in each species. These proteins are found in the cells in the back of the eye, or retina. They are responsible for the absorption of certain wavelengths of light.

Mammals who rely on smell more than sight have two opsin genes and see the world in only two primary colors, yellow and blue. Humans and apes are among the few mammals that see the world in three primary colors, red, green, and blue. Trichromatic vision appeared when the first primates evolved from their mammalian ancestors. An opsin gene was duplicated, an adaptation that allowed individuals to discriminate between leaves and fruits of different colors.

Birds have excellent eyesight. Their visual systems are much more sophisticated than ours since they need to see while flying at high speeds. They inherited their vision from their reptilian ancestors when the lineage that gave rise to modern birds split from the dinosaurs. They have four types of opsin genes and see the world in four primary colors. Their range of color vision goes beyond what any human can experience or imagine. How did the differences evolve?

Both mammals and birds evolved from reptiles around 190 million and 40 million years ago, respectively. Therefore, all four opsin genes should have been inherited by all mammalian and avian species. The reason why most mammalian species only have two opsin genes can be explained by events that took place in the Jurassic Period, 150 million years ago. Our mammalian ancestors were nocturnal creatures, similar to modern-day shrews. The four opsin genes they inherited from their reptilian ancestors were a luxury these proto-mammals did not need. As we have learned, genes can have mutations that cause them to stop working properly. This can adversely affect an organism’s chances of survival and reproduction. However, when two of the four opsin genes mutated and stopped producing opsin proteins in these nocturnal creatures, it did not affect their survival or reproductive success. They were not using them anyway. Hence, most modern-day mammals have dichromatic vision.

Molecules Necessary for Vision

The molecules required for vision, such as rhodopsin and lens proteins, evolved in single-celled organisms. Rhodopsin can be found in all visual systems, from the simplest to the most complex. It even appears in prokaryotes, bacteria and archaea, the most basic life forms on Earth. (Archaea are unicellular organisms similar to bacteria but with different metabolic characteristics). In prokaryotes, rhodopsin is involved in the conversion of sunlight to other kinds of energy. This suggests that given enough time and the adaptive advantages of being able to discern light, the evolution of sight in multicellular animals was inevitable.

Night Vision

Some mammals are nocturnal or live most of their lives underground, such as night monkeys, galagoes, slow lorises, and mole rats or ratopines. Because they live in the dark, they do not depend on color vision. Like all mammals, they descended from diurnal creatures who could see in color. However, they now have repressed, or switched-off, opsin genes. Their opsin genes underwent mutations that made them useless. As they adapted to a nocturnal lifestyle, these genes became irrelevant, and their mutations did not affect the species’ chances of survival.

Mole rat

Mitochondrial DNA in Animals

Mitochondria are organelles that appear in all animal cells and play a vital role in the energy production of living organisms. Without them, there would be no cellular activity. Mitochondrial DNA has a unique characteristic: since cells make exact copies of themselves during cell division, an organism’s mitochondrial DNA is identical in every cell. In addition, living things inherit mitochondria from their mothers only. The mitochondria in sperm disintegrate during fertilization. Therefore, mitochondrial DNA is not affected by the genetic reshuffling that occurs when maternal and paternal chromosomes pair up. The mutations in mitochondrial DNA pass intact from generation to generation. In other words, our mitochondrial DNA is identical to our mother’s, maternal grandmother’s, maternal great-grandmother’s, etc... except for any mutations that may have occurred along the way.

Mitochondria perform a basic function in living cells and possess an incredibly stable structure. Therefore, mitochondrial DNA is uniform across the entire animal kingdom. The same 37 genes code for the same group of proteins in all animals. They are also organized along the mitochondrial DNA strand in a consistent manner.

Because mitochondrial DNA mutates at a steady rate with minor variations between and within species, scientists can use it to estimate the age of shared common ancestry and the evolutionary distance between populations. This technique has produced surprising results in our species: African populations are the oldest. Homo sapiens appeared in Africa, the birthplace of all modern humans, between 140,000 and 290,000 years ago. Human beings populated Australia and Papua New Guinea 50,000 years ago, and the Americas were colonized 15,000 years ago. Every human alive today carries the mitochondrial DNA of a common grandmother living in Africa 10,000 generations ago. Any person can now have their mitochondrial DNA analyzed to discover the genetic origins of their maternal lineage.

Mitochondria

Olfactory Genes

The winners of the 2004 Nobel Prize in Physiology and Medicine, Richard Axel and Linda B. Buck, discovered the olfactory genes in humans. These genes constitute more than 3% of our genome. They are only active in the nasal area and allow us to perceive between 5,000 and 10,000 different odors. Axel and Buck also discovered that several genes must work together to detect certain odors.

Their findings led researchers to study other species, with fascinating results:

• There are different genes for detecting odors in water and air.

• Primitive fish, such as lampreys, have few genes for smell and cannot distinguish between odors in water and air. These fish evolved before the olfactory genes split into two different types.

• More complex fish have more genes for smell, but they are only used to detect odors in water.

• Amphibians have both kinds of genes for detecting odors in water and air.

• Mammals and reptiles only have genes to detect odors in the air.

• Our genes for smell did not appear overnight. Many of our ancestors perceived fewer odors than we do, but their genes mutated and were duplicated during sex cell formation. Over time, these duplicated genes became specialized to detect new odors.

• Mammals with color vision, like us, have many disabled scent genes. One-third of human scent genes are disabled. We have prioritized vision genes over scent genes because we depend much more on our vision than our sense of smell.

Our ancestral history and our relationship with other species are written in the olfactory genes. Our genes are almost identical to those of other mammals who depend primarily on sight and have trichromatic vision, such as chimpanzees and gorillas. They are less like those of mammals with dichromatic vision, which only see two colors. These mammals rely more on their sense of smell. A dog’s olfactory system is a thousand times more sensitive than ours. Our genes resemble those of other animals less and less as we move further away from our branch of the evolutionary tree, from reptiles to amphibians, and finally, fish.

Primate Genomes and their Similarities

The human genome contains about three billion base pairs of nucleotides: adenine, thymine, guanine, and cytosine. 98.8% of this sequence is identical to a chimpanzee; only 1.2% of our genome is different, around 36 million base pairs.

Chimpanzees and humans parted company in evolution about six million years ago. From that point on, we can assume that half of those differences, eighteen million, occurred in our genome and the other half in the chimpanzee’s genome. The genomes of two individual humans differ by about three million base pairs.

The immediate question is: Do the fifteen million base pairs that differentiate humans from chimpanzees play a role in human evolution?

The order of genes along the chromosomes, or the sequence of genes, in the genomes of humans and mice is 96% identical. The common ancestor of humans and rodents lived around 75 million years ago. Therefore, the changes in their DNA sequences appear to be minimal. What makes the human species unique cannot be attributed to the relatively small differences found in our DNA. Scientists have learned that changes in gene control and expression, not the genes themselves, are responsible for human evolution.

In genetics, the term “junk DNA” refers to regions of DNA that are noncoding. (The sections of coding DNA provide instructions to create proteins in the cell). Geneticists now understand that these sections of “junk DNA” are not junk at all; they are made up of regulatory genes. Regulatory genes control when other genes are turned on or off. In conclusion, the difference between a chimpanzee and a human is not in their genes but in how they are expressed.

Female chimp with juvenile

Human Chromosome 2

Human chromosome 2 was formed by the fusion of two ancestral chromosomes that remained separate in other primates. This mutation occurred after the hominin ancestor branched off from the ancestor of the other apes.

Chimpanzees, gorillas, and orangutans have 24 pairs of chromosomes, while humans have only 23. Chimpanzees, our closest relatives, have the same gene sequence we have on chromosome 2 on chromosomes 12 and 13. The same is true for gorillas and orangutans, but these chromosomes have a greater number of differences.

Variation in Human Skin Color

Skin color is an obvious characteristic used to identify people from different regions of the world. It differs depending on the amount of melanin the individual’s cells produce. Did natural selection give rise to the rainbow of sepia tones that constitute human skin color?

In general, the driving force of natural selection comes from the environment. Considerable evidence establishes that nature selected for dark skin in early Homo species. Dark pigmentation was necessary for hairless individuals who lived near the equator and roamed the savannah. There are few bushes and trees in the African grasslands where humans evolved. Dark skin contains more melanin, which is essential protection against ultraviolet radiation. Until recently, biologists believed that darker skin protected our Homo ancestors from skin cancers caused by high UV radiation. However, skin cancer affects older individuals, usually after they have already successfully reproduced.

Nina Jablonski, an anthropologist at Penn State University, published a paper in 2000 proposing another hypothesis. She found research linking exposure to strong sunlight with low blood levels of a B vitamin called folate. She also learned that high UV exposure could cause low folate levels in pregnant women leading to various congenital disabilities in their babies. It also affects sperm production in men. Melanin essentially acts as a barrier, protecting the amount of folate underneath the skin. As a result, the individuals in early human populations with higher melanin content in their skin were more likely to reproduce successfully.

This is only one piece of the puzzle. How and why did lighter skin tones evolve?

Individuals who migrated north to places with lower levels of UV radiation no longer experienced the selective pressure to have darker skin to maintain appropriate blood folate levels. A new selective pressure emerged. Now, they needed to maintain adequate levels of vitamin D. Vitamin D is manufactured in our bodies with the help of UV radiation. It promotes calcium absorption and prevents a disease known as rickets.

Rickets causes bone deformations in children. It can have severe consequences for childbirth and early childhood development. Hence, at higher latitudes, humans with lighter skin now had a reproductive advantage over those with darker skin; the number of lighter-skinned individuals increased in these human populations.

This phenomenon has been confirmed by genetic analysis. The SLC24A5 gene is responsible for the production of melanin, the pigment in our skin and hair. In African populations, the SLC24A5 gene is functional. However, almost all Europeans have a mutation in the SLC24A5, which disables it. Asians have a functional SLC24A5 but have acquired other mutations favoring light skin and black hair. Therefore, we can conclude that the variations in human skin color in different regions of the planet are the result of natural selection.

The Water Snakes of the Sea of Cortes

The water snake, Thamnophis Validus, inhabits the waters of the Pacific coast of Mexico from the state of Sonora to the state of Guerrero. They live in rivers, irrigation canals, and swamps. Baja California is on the other side of the Sea of Cortes. It is possible to find these same snakes at its southern end in the Sierra de la Laguna. The question is: Why do the snakes of southern Baja California have their closest relatives on the other side of the sea and not on the same peninsula?

For decades, researchers assumed that since Baja California had been part of the mainland for millions of years, the peninsula’s snakes became trapped in the territory when the Sea of Cortes formed. They became geographically isolated from their relatives on the mainland, much like what happened with the species of Madagascar when the island separated from the African continent.

With the invention of genetic analysis, researchers decided to confirm this hypothesis. They were surprised to find minimal differences in snakes’ mitochondrial DNA from the east and west coasts of the Sea of Cortes. A new hypothesis had to be proposed because the Sea of Cortes is millions of years old; such a long period of time would have resulted in more differences in the DNA.

Based on genetic evidence, the populations were only separated a few hundred thousand years ago.

The only viable explanation is that the snakes arrived from the mainland to Baja California on rafts of branches and plants propelled by the wind and ocean currents. The environment was favorable, and the snakes reproduced.

Water snake

Similarities in Phylogenetic Trees

Phylogenetic trees are charts used to show the evolutionary relationships of species. Experts can represent the order in which evolution happened, depicting an ancestral species and its descendant species. Darwin drew the first-ever phylogenetic tree in the margins of his notes, famously adding the words, “I think,” next to it. He imagined that this was how a species gave rise to two or more new species.

For example, gophers, Geomyidae, always carry parasitic lice in their fur, Phthiraptera. When experts reconstructed the evolutionary trees of gophers and lice using their genomes, the trees were identical.

As the ancestral pocket gophers became geographically isolated, they became a distinct species. The lice living on them also speciated. Comparative genetic analysis can provide information often difficult to obtain with other tools.