From Alpacas to Yaks, Mammal DNA Yields Its Secrets

A large international team spent years searching for some of the most bizarre creatures on Earth to learn more about humanity. Scientists camped on an Arctic ice float to collect DNA from a narwhal with a single tooth, caught a tiny bumblebee in Southeast Asia's cave region, and went behind the scenes of a Caribbean Zoo to draw blood from a slender-snouted, solenodon.

Researchers compared genomes from these mammals to those of other mammals, such as an aardvark (a small mammal), a meerkat (a large mammal), a star-nosed mole, and humans. They were able, by doing this, to identify DNA stretches that had barely changed in the eons since mammal evolution began and which are likely to be crucial to human health and function.

They assembled a genetic database that contains the genomes of more than 240 species. This includes humans and over 80 percent of all mammalian groups on the planet. This could answer many questions about animals such as how and when they evolved, and what is the biological basis of some of their unique abilities.

Elinor Karsson, geneticist and co-leader of the Zoonomia Project at UMass Chan Medical School & Broad Institute said: "What amazing things can these species do that we can't?" We like to think that humans are the most unique species. It turns out we're actually quite boring in many aspects.

Zoonomia has some limitations. The Zoonomia data set has limitations. It only contains one genome per species, except for the domestic dog (which was sequenced twice) and it is missing thousands of mammals.

In a series of papers published on Thursday in Science, the Zoonomia group demonstrated the power of such multispecies data. It's only the beginning.

Michael G. Campana said, "Sequencing many genomes is no trivial task," a scientist in computational genomics at Smithsonian National Zoo and Conservation Biology Institute who was not involved with the project. What's important is to actually use these data.

Zoonomia is already being used by scientists for a variety of things.

Scientists searched for genetic sequences which had developed unusually fast in species who shared a trait such as the ability of hibernating.

Researchers focused their analysis on deep-hibernators such as the fattailed dwarf lemur or the greater mouse-eared frog, which are able to maintain low temperatures for several days. Researchers found "accelerated evolution" evidence in several genes. One gene is known to protect cells against temperature-related stress, and another inhibits a cell pathway associated with aging.

Dr. Karlsson stated that many species hibernating also live a long life, which led her to ask: Does the gene change contribute to this?

Researchers also studied the sense of smell in mammals. Animals possess a wide variety of olfactory molecules that can bind to specific odor molecules. Species with more genes for olfactory retinal receptors generally have better senses of scent.

The African savanna elephan took the top spot with 4,199 genes. The next two species were the Hoffmann's 2-toed Sloth and the nine-banded Armadillo. The Central American Agouti was fourth.

Dr. Karlsson stated that the agouti has "one of the most impressive olfactory libraries of any mammal for completely unknown reasons." It's a great reminder of the diversity that exists in the world, and we know nothing about it.

Cetaceans, a group which includes dolphins, whales, and other aquatic animals, have a smaller number of olfactory genes. This makes sense, given their aquatic habitats. Kerstin Lindsay-Toh is a geneticist from the Broad Institute at Uppsala University, and the other leader in the Zoonomia Project.

The species with the most olfactory receptors also tend to have more olfactory Turbinals in their nasal cavity, which aid olfaction. Dr. Lindblad Toh stated that the results show "that if certain traits are essential, they can evolve in different ways."

She said, "I believe that one of the most important things about our data set is the fact that it generates genome sequencing for many different species so that people can begin looking at their favourite characteristics."

Portraits of the population

In February 1925, during a diphtheria epidemic, a relay sled dog team delivered an antitoxin emergency to Nome in Alaska, which was isolated by snow. Balto, a dog that ran the last leg of the relay became famous. When he died a few years later, the Cleveland Museum of Natural History displayed his taxidermied corpse.

Zoonomia researchers have used a tiny piece of the taxidermied tissue in order to discover more about this celebrity sleddog and his canine counterparts. Kathleen Morrill is the author of the Balto article, and she performed the research while a graduate student in the UMass Chan Medical School. She is now a senior researcher at Colossal Biosciences. Here is this famous individual. We don't have much information about his biology. What can we tell about his genome?"

Balto was found to be genetically "healthier", with greater genetic variation inherited and fewer mutations that could cause harm. This is likely due to the fact that most sled dogs have been bred to perform and are a mix of breeds.

Researchers found that Balto had a variety of genetic variants not present in wolves, and which were either rare or absent in purebred modern dogs. The researchers found that many of the variants in these genes were involved in tissue formation and could have affected traits such as skin thickness or joint formation. Balto had two copies, one from each parent. This means that they were at least somewhat common among other Alaskan Sled Dogs at the time.

Katie Moon, postdoctoral research at the University of California Santa Cruz and author of the article, said, "We now have a much clearer image of his likeness and the population he would have come from." "And this picture is of working sled dog breeds that are really well adapted."

Scientists have debated for years how and when the diverse array of mammals today came to be. Did the mammalian tree only branch out after the dinosaurs died out 66 million year ago? Did the process begin before the disaster?

New analysis of the Zoonomia genes suggests the answer to both questions. Around 102 million ago, Earth's continents began fragmenting and the sea level began to rise. William Murphy, evolutionary geneticist and author of the study at Texas A&M University, said that the isolation of predecessors to the modern lineages across different landmasses was the result.

Researchers found that mammals experienced a second burst in diversification after the dinosaur extinction. This was due to the new land created by the new species and the absence of the dominant reptiles.

Scott Edwards is an evolutionary biologist from Harvard who wasn't involved in the study. It's the biggest of its kind when it comes to putting mammals on a timeline.

He called the Zoonomia package "a massive set of work." It's going set the standard in our understanding of mammal evolutionary biology going forward.

Mammals inherit most genetic sequences in two copies, one each from their parents. The size of previous animal populations can be determined by determining how closely these DNA sequences match. For example, long stretches of identical DNA can indicate inbreeding.

Aryn W. Wilder, conservation geneticist with the San Diego Zoo Wildlife Alliance, said that the genome of an animal shows "how closely related it was to its parents, grandparents, and so on."

Dr. Wilder's colleagues and she used the Zoonomia Genomes to estimate population sizes for different species over time. Comparing species with large populations, those with smaller past populations had a higher number of genetic mutations that could be harmful and were more likely classified as threatened by International Union for Conservation of Nature.

Researchers also examined the genomes for three species that were deemed to be at risk of extinction by the I.U.C.N. A lack of information made it difficult to determine the status of three species: the killer whale (which is exactly what you would expect), the Upper Galilee Mountains Blind Mole Rat, and the Java Mouse-Deer. The results indicated that the killer whale may be most at risk.

Beth Shapiro is a paleogeneticist and author of the study. She said that the approach could be a simple way to prioritise species for resource-intensive, more thorough risk assessments. She said that it could be an easy way to prioritize species for more thorough, resource-intensive risk assessments.