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Researchers Greatly Improve Evolutionary Tree of Life for Mammals

Posted September 22, 2011

Researchers Greatly Improve Evolutionary Tree of Life for Mammals

International team, led by Texas A&M and UC Riverside, provides robust molecular phylogeny for mammalian families.

COLLEGE STATION, TEXAS -An international research team led by researchers at the Texas A&M University College of Veterinary Medicine & Biomedical Sciences (CVM) and University of California, Riverside (UCR) has released for the first time a large and robust DNA matrix that has representation for 99 percent of mammalian families, and covers the deepest divergences among all living mammals.

"Our study, a collaboration led by researchers at Texas A&M University and the University of California, Riverside together with members of several international institutions, represents the culmination of a five year project aimed at using large genetic datasets to better understand the evolutionary history of mammalian families and genera," said William Murphy, associate professor in the Department of Veterinary Integrative Biosciences at the CVM, who co-led the research project with Mark Springer, professor of Biology at UCR. "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.

Phylogeny is the history of organismal lineages as they change through time.  A vast evolutionary tree, called the Tree of Life, represents the phylogeny of organisms, the genealogical relationships of all living things.

As most introductory biology textbooks will show, organisms are biologically classified according to a hierarchical system characterized by seven main taxonomic ranks: kingdom, phylum or division, class, order, family, genus, species.  For example, humans are known taxonomically as Homo sapiens.  Their genus is Homo, the family is Hominidae, the order is Primates and the class is Mammalia.

"To estimate when different mammal groups split we used a 'relaxed clock' approach which allows rates of DNA to change across the tree of mammals," said Murphy. "To produce reliable estimates 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."

Study results appear in the September 22 issue of Science Express.

"Our phylogeny, underpinned by a large number of genes, sets the stage for us to understand how the different mammalian species are related to each other," Springer said.  "That will help us understand when these species diverged from each other.  It will allow us to look for taxonomic rates of increase or decrease over time in different groups in various parts of the world so that we can understand these diversification rate changes in relationship to important events in Earth's history - such as the diversification of flowering plants and changes associated with climatic events. Researchers routinely make use of phylogenies in diverse fields such as ecology, physiology, and biogeography, and the new phylogeny for mammalian families provides a more accurate framework for these studies.

"When you understand how taxa are related to each other," Springer added, "you can start to understand which changes at the genome level underpin key morphological changes associated with, say, flight and echolocation in bats or loss of teeth in toothless mammals.  In other words, you can pinpoint key molecular changes that are associated with key morphological changes.  This would be extremely difficult, if not altogether impossible, without the kind of robust molecular phylogeny we have developed."

The research team looked for spikes in the diversification history of mammals and used an algorithm to determine whether the rate of diversification was constant over time or whether there were distinct pulses of rate increases or decreases.

"For example, we observed a distinct pulse of diversification when most of the mammalian orders began splitting from one another, near the end of the Cretaceous Terrestrial Revolutions when flowering plants and insects diversified, and also at a time when sea levels changed and continental boundaries became reorganized," said Murphy.

Murphy and colleagues also detected a second spike in the diversification history of mammals at the end of the Cretaceous - 65.5 million years ago, when dinosaurs, other large terrestrial vertebrates, and many marine organisms went extinct, opening up a vast ecological space.

"We also found evidence that the Cretaceous-Tertiary Mass extinction, which occurred 65.5 million years ago (Mya) and was responsible for the demise of the dinosaurs, other large terrestrial vertebrates and many marine organisms, also promoted diversification of mammals into their larger and more specialized modern forms by filling the ecological void left by the organisms that went extinct," Murphy highlighted.

The research team also reports that their results contradict the "delayed rise of present-day mammals" hypothesis. According to this hypothesis, introduced by a team of scientists in a 2007 research paper, the ancestors of living mammals underwent a pulse of diversification around 50 million years ago, possibly in response to the extinction of archaic mammals that went extinct at the end of the Paleocene (around 56 million years ago). The earlier extinction event around 65.5 million years ago, which resulted in the demise of the dinosaurs, had no effect on the diversification of the ancestors of extant mammals, according to the 2007 research paper.

"Our results contradict findings of an earlier study published in 2007 which claimed the rise of modern mammals was somehow delayed until around 50 Maya, presumably in response to the extinction of a group of archaic mammals. Our study finds no evidence for such a delay, and validates a role for the Cretaceous-Tertiary Mass extinction in the diversification of modern orders of mammals," Murphy said.

The researchers stress that their time tree is a work in progress.  In the next two years, they expect to construct a supermatrix, also based on gene sequences, and include the majority of living mammalian species.  The current work incorporates 164 mammalian species.

"This study is the beginning of a larger plan to use large molecular data sets and sophisticated techniques for dating and estimating rates of diversification to resolve much larger portions of the mammalian tree, ultimately including all described species, as well as those that have gone recently extinct or for which only museum material may be available," said Murphy. "Only then can we really begin to understand the role of the environment and events in earth history in promoting the generation of living biodiversity. This phylogeny also serves as a framework to understand the history of the unique changes in the genome that underlie the vast morphological diversity observed in the more than 5400 living species of mammals."

Murphy and Springer were joined in the study by researchers at UCR; the San Diego Zoo's Institute for Conservation Research, Calif.; University College Dublin, Ireland; PUCRS, Brazil; Eidgenössiche Technische Hochschule Zurich, Switzerland; UC Berkeley; Pepperdine University, Calif.; American Museum of Natural History, NY; University of Stellenbosch, South Africa; Chaffey College, Calif.; LaTrobe University, Australia; and Washington and Lee University, Virginia.

Jan E. Janecka, research assistant professor in genomics, and Colleen Fisher, Texas A&M graduate student, in Murphy's research group performed the bulk of the lab work at Texas A&M. The UCR researchers include John Gatesy, an associate professor of biology; Robert Meredith, a postdoctoral researcher and the first author of the research paper; Angela Burk-Herrick, a former postdoctoral researcher; and Nadia A. Ayoub, a former postdoctoral researcher.

Murphy's and Springer's labs were supported by grants from the National Science Foundation.

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