DNA: Our ancient ancestors had lots more

The DNA of our human ancestors looked very different almost 2 million years ago, before they migrated out of Africa. That’s the conclusion of a new study. It mapped a range of differences, or diversity, in the human genome. This genome is the complete DNA instruction book present in nearly every human cell.

DNA is a long ladder-like molecule. Each of its rungs consists of two chemicals called nucleotides. Biologists refer to each step, or rung, as a base pair. Long sequences of base pairs make up chromosomes. These gene-carrying structures form the basis of the traits that each person inherits from his or her parents. Those traits can range from height and skin color to disease resistance.

The new study of human diversity shows that our ancestors carried 40.7 million more DNA base pairs than people do today. The researchers reported the results online August 6 in Science.

That extra DNA is enough to build a small chromosome, says Evan Eichler. One of the study’s authors, he works at the University of Washington in Seattle. He studies evolutionary genetics, or how genes change over time as a result of evolution.

Before spreading out around the globe, our human ancestors in Africa lost 15.8 million of those DNA base pairs, the researchers found. As people migrated to other continents, more chunks of DNA disappeared. Eichler and colleagues have followed these genetic bread crumbs. This trail has helped them to map global links between 125 human groups over time.

The range of changes

People didn’t just lose DNA. They also gained some. Compared to chimpanzees and orangutans, people have 728 extra pieces of DNA. This extra DNA was created as humans evolved. Throughout our lives, cells copy their genetic instruction book. Sometimes, errors may occur during the copying so that big pieces of the ladder are copied more than once.

Earlier maps of human gene diversity usually have not marked the large gaps left when bits of DNA get deleted. They usually also have not plotted out the new territory created by the insertion of extra copies of some stretches of DNA. Most diversity maps have focused on changes in single DNA base pairs. But these make up only 1.1 percent of the humans genome. Duplications and deletions, in contrast, have shaped more than 7 percent of that genome.

Duplications and deletions also involve larger chunks of DNA than changes in single base pairs do. That means their effect on human evolution also may be bigger. Both duplications and deletions have played a role in shaping human traits, such as bigger brains.

But researchers don’t yet know “whether what makes us human is in what was lost or what was duplicated,” says David Liberles. Working at Temple University in Philadelphia, Pa., he studies how genomes evolve.

To Eichler, “Duplications rock.” For instance, “they affect more base pairs in the human genome than any other type of [change].” Duplications make up 4.4 percent of the genome. Deletions make up only 2.77 percent. And duplications tend to involve genes — stretches of DNA that carry instructions for making proteins. In contrast, deletions often fall in spaces between genes, the team found.

The range of changes

Some of the newfound duplications might be important in medicine. For instance, some groups of people have up to six copies of genes known as CLPS. These genes instruct the pancreas to make enzymes that may help reduce blood sugar. That genetic trait could help prevent or control diabetes. Some African groups carry duplications of genes that may protect people against sleeping sickness, which is caused by parasites.

Another key finding is a very large duplication of about 225,000 base pairs in people living just north of Australia in Papua New Guinea (PAP-ooh-ah Nu GIH-nee). This nation of Pacific Ocean islands includes the eastern half of the island of New Guinea.

Papua New Guineans inherited the huge duplication from Denisovans (Deh-NEE-so-vuns). These extinct folk were relatives of Neandertals. Eichler’s team calculates that the original Denisovan duplication happened about 440,000 years ago. It was passed to Papuans and others in the region about 40,000 years ago. That occurred when their ancestors mixed with Denisovans. Today, about 80 percent of Papuans carry the duplication. Eichler thinks the duplication may have given Papuan ancestors some advantage for survival. But what that advantage might be is unknown.

Edward Hollox is a geneticist at the University of Leicester in England. He says researchers have made a strong case that duplications and deletions may play an important role in human evolution. However, he adds, the new study provides little evidence that such genetic changes really caused differences between groups. He does suspect, though, that the new gene map will point other researchers to parts of the genome where evolution may have left its mark.

Power Words

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archaic     An adjective meaning ancient. Something from a far earlier period in time, often thousands, if not millions, of years ago.

base pairs  (in genetics) Sets of nucleotides that match up with each other on DNA or RNA. For DNA, adenine (A) matches up with thymine (T), and cytosine (C) matches up with guanine (G).

blood sugar  The body circulates glucose, a type of simple sugar, in blood to tissues of the body where it is used as a fuel. The body extracts this simple sugar from breakdown of sugars and starches. However, some diseases, most notably diabestes, can allow an unhealthy concentration of this sugar to build up in blood.

chromosome  A single threadlike piece of coiled DNA found in a cell’s nucleus. A chromosome is generally X-shaped in animals and plants. Some segments of DNA in a chromosome are genes. Other segments of DNA in a chromosome are landing pads for proteins. The function of other segments of DNA in chromosomes is still not fully understood by scientists.

Denisovans  An ancient humanlike population whose existence is known only because of a few fossils discovered in a cave in Siberia.  

diabetes A disease where the body either makes too little of the hormone insulin (known as type 1 disease) or ignores the presence of too much insulin when it is present (known as type 2 diabetes).

diversity  (in biology) A range of different life forms.

DNA (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

deletion   (v. to delete) The process of removing some specific part or detail; or a reference to the things that has been removed.

duplication  The process of copying something.

enzymes Molecules made by living things to speed up chemical reactions.

evolution A process by which species undergo changes over time, usually through genetic variation and natural selection. These changes usually result in a new type of organism better suited for its environment than the earlier type. The newer type is not necessarily more “advanced,” just better adapted to the conditions in which it developed.

evolutionary genetics  A field of biology that focuses on how genes — and the traits they lead to — change over long periods of time (potentially over millennia or more). People who work in this field are known as evolutionary geneticists.

evolve  To change gradually over generations, or a long period of time. In living organisms, the evolution usually involves random changes to genes that will then be passed along to an individual’s offspring. These can lead to new traits, such as altered coloration, new susceptibility to disease or protection from it, or different shaped features (such as legs, antennae, toes or internal organs). Nonliving things may also be described as evolving if they change over time. For instance, the miniaturization of computers is sometimes described as these devices evolving to smaller, more complex devices.

extinct   An adjective that describes a species for which there are no living members.

gene   (adj. genetic) A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

genetic  Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.

genome  The complete set of genes or genetic material in a cell or an organism. The study of this genetic inheritance housed within cells is known as genomics.

heredity  The biological process through which genetic information is passed from parent to offspring.

Neandertal A species (Homo neanderthalensis) that lived in Europe and parts of Asia from about 200,000 years ago to roughly 28,000 years ago.

nucleotides  The four chemicals that link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA.

Oceania    Australia and a group of Pacific island nations to the north and to the east of Australia. Nations in the group include Papua New Guinea, New Zealand, Samoa and Fiji. Hawaii and Guam are also among the manyislands that fall within this broad swath of the populated Pacific.

parasite  An organism that gets benefits from another species, called a host, but doesn’t provide it any benefits. Classic examples of parasites include ticks, fleas and tapeworms.

proteins  Compounds made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells.