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How Dataset Creates the Mammal Tree of Life

Scientists are working with a large genetic dataset to establish a timeline for understanding the mammalian family evolutionary history. The DNA matrix represents 99 percent of the biologic families investigated in the five year project.

Phylogenomics by William J. Murphy, PhD at Department of Veterinary Integrative Biosciences, Texas A&M UniversityWilliam Murphy, PhD in the Department of Veterinary Integrative Biosciences at Texas A&M University said: "Our findings now clarify how mammals should be properly classified, and provides us with a better understanding of the environmental and ecological basis for why mammals diversify, and a proper comparative and temporal framework for understanding the genetic changes that have led to their remarkably diversity in size and form."

The research encompasses phylogeny, the history of the evolution of a species or group, especially as it relates to lines of descent and relationships. Murphy and Mark Springer, PhD professor of biology from the University of California Riverside, have a monumental task facing them. The fossil record goes back 220 million years. Many specimens for their study were provided by the Society of San Diego. The San Diego Zoo operates the Institute for Conservation Research which attempts to save endangered species. Extinction is one of the events considered pivotal in the diversification of species being analyzed by the team.

To realize the focus of the project requires an understanding of the underlying biological picture. The hierarchical classification in biology is: kingdom, phylum or division, class, order, family, genus, species. Let?s illustrate the most familiar species for our readers – ourselves, Homo Sapiens.

The hierarchy in our case is: Kingdom = Anamalia, Phylim = Chordata, Class = Mammalia, Order = Primates, Family = Mominidae, Genus = Homo, Species = Homo Sapien.

Modern mammals evolved over 165 million years
Modern mammals evolved over 165 million years

The major group of modern mammals and their relationship is shown in the image from the New York State Museum. The earliest mammal is said to have appeared 165 million years ago.

Each gradation has an identifying definition. For example, primates are characterized by prehensile five-digit hands and feet possessing flat nails instead of claws, and acute vision with depth perception due to forward-facing eyes. The term "Homo Sapien" comes from the Latin meaning human being-clever/knowledgeable.

The knowledgeable team from Texas A&M and UC Riverside worked with many institutions from around the world, including those in Ireland, South Africa, Australia, Brazil and Switzerland. They have devised a way to relate evolutionary changes to changes in the earth?s environment. The study concentrated on several lines stemming from the Class Mammalia.

Murphy explains their mode of operation: "To produce reliable estimates (of rates of DNA changes across the tree of mammals) requires that we have access to a large collection of well established fossil constraints to estimate rates of changes on different branches of the tree, and then we can convert the tree of relationships into a time tree, in which the branches are scaled in proportion to time. This time tree allows us to examine when different groups of mammals originated and diversified, and then associate factors which might have been responsible for these diversification events."

Mark Springer, PhDThe scientists are trying to relate diversification rate changes to important events in Earth’s history – such as those associated with climatic events. Diversification increased about 80-82 million years ago, at the end of the Cretaceous Terrestrial Revolution – when a lot of different orders were going their own way. "This is when flowering plants diversified, which provided opportunities for the diversification of small mammals," Springer said.

The scientists looked for blips in the chart as mammals diversified. One occurrence took place when sea levels changed and continental boundaries became reorganized. Another blip shows at the end of the Cretaceous period  – 65.5 million years ago, when not only dinosaurs, but other large terrestrial vertebrates, and many marine organisms became extinct. This left a void that other species rushed to fill.

Only a portion of the species that have roamed the earth were in the current study. Of the studied lineages, 142 were 142 single species. Also included were five non-mammalian groups such as the zebra fish, an African clawed frog, a chicken and a house finch.

The group is planning to build a supermatrix, also based on gene sequences, which will include most of the 5400 mammalian species that still inhabit Earth today. That?s a big goal, considering their current results were obtained from only 164 mammalian species.

Their results of their project are published in Science Express (PDF Download) with supporting materials also in PDF format if you are looking for specifics at the research level. Murphy’s and Springer’s labs were supported by grants from the National Science Foundation.