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Faculty/Staff Focus
Researchers greatly improve evolutionary tree of life for mammals
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) released for the first time a
large, robust DNA matrix that represents
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 [this research] 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 remarkable diversity
in size and form.”
Phylogeny is the history of organismal
lineages as they change through
Dr. William Murphy
52 • CVM Today • Winter 2012
time. A vast evolutionary tree, called
the Tree of Life, represents the phylogeny
of organisms, the genealogical
relationships of all living things.
Organisms are biologically classified
according to a hierarchical system with
seven main taxonomic ranks: kingdom,
phylum or division, class, order, family,
genus, and 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,” Murphy said. “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.”
The study results appeared in the
Sept. 22, 2011, 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,” Murphy said, “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.”
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
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 said.
The research team also reported 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
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