Most Comprehensive Tree of Life Shows Placental Mammal Diversity Exploded After Age of Dinosaurs

Feb. 7, 2013 — An international team of scientists including University of Florida researchers has generated the most comprehensive tree of life to date on placental mammals, which are those bearing live young, including bats, rodents, whales and humans.


 

Appearing  February 7 in the journalScience, the study details how researchers used both genetic and physical traits to reconstruct the common ancestor of placental mammals, the creature that gave rise to many mammals alive today. The data show that contrary to a commonly held theory, the group diversified after the extinction of dinosaurs 65 million years ago. The research may help scientists better understand how mammals survived past climate change and how they may be impacted by future environmental conditions.

UF researchers led the team that analyzed the anatomy of living and fossil primates, including lemurs, monkeys and humans, as well as their closest living relatives, flying lemurs and tree shrews. The multi-year collaborative project was funded by the National Science Foundation Assembling the Tree of Life Program.

“With regards to evolution, it’s critical to understand the relationships of living and fossil mammals before asking questions about ‘how’ and ‘why,’ ” said co-author Jonathan Bloch, associate curator of vertebrate paleontology at the Florida Museum of Natural History on the UF campus. “This gives us a new perspective of how major change can influence the history of life, like the extinction of the dinosaurs — this was a major event in Earth’s history that potentially then results in setting the framework for the entire ordinal diversification of mammals, including our own very distant ancestors.”

Visual reconstruction of the placental ancestor — a small, insect-eating animal — was made possible with the help of a powerful cloud-based and publicly accessible database called MorphoBank. Unlike other reconstructions, the new study creates a clearer picture of the tree of life by combining two data types: Phenomic data includes observational traits such as anatomy and behavior, while genomic data is encoded by DNA.

“Discovering the tree of life is like piecing together a crime scene — it is a story that happened in the past that you can’t repeat,” said lead author Maureen O’Leary, an associate professor in the department of anatomical sciences in the School of Medicine at Stony Brook University and research associate at the American Museum of Natural History. “Just like with a crime scene, the new tools of DNA add important information, but so do other physical clues like a body or, in the scientific realm, fossils and anatomy. Combining all the evidence produces the most informed reconstruction of a past event.”

Researchers recorded observational traits for 86 placental mammal species, including 40 fossil species. The resulting database contains more than 12,000 images that correspond to more than 4,500 traits detailing characteristics like the presence or absence of wings, teeth and certain bones, type of hair cover and brain structures. The dataset is about 10 times larger than information used in previous studies of mammal relationships.

“It was a great way to learn anatomy, in a nutshell,” said co-author Zachary Randall, a UF biology graduate student and research associate at the Florida Museum. “While coding for humans, I could clearly see which anatomical features are unique, shared or not shared with other groups of mammals. This study is a great backbone for future work.”

Bloch and Randall collaborated with study co-authors Mary Silcox of the University of Toronto Scarborough and Eric Sargis of Yale University to characterize humans, plus seven other living and one fossil species from the clade Euarchonta, which includes primates, tree shrews and flying lemurs.

“I think this database is amazing because it’s being presented in such a way that it will be reproducible for the future generations,” Bloch said. “It illustrates exactly what we did and leaves nothing to the imagination — you can actually go to the pictures and see it.”

The evolutionary history of placental mammals has been interpreted in very different ways depending on the data analyzed. One leading analysis based on genomic data alone predicted that a number of placental mammal lineages existed in the Late Cretaceous and survived the Cretaceous-Paleogene extinction.

“It has been suggested that primates diverged from other mammals well before the extinction of the dinosaurs, but our work using direct evidence from the fossil record tells a different story,” Bloch said.

The team reconstructed the anatomy of the placental common ancestor by mapping traits most strongly supported by the data to determine it had a two-horned uterus, a brain with a convoluted cerebral cortex, and a placenta in which maternal blood came in close contact with membranes surrounding the fetus, as in humans.


Story Source:

The above story is reprinted from materials provided byUniversity of Florida.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. M. A. O’Leary, J. I. Bloch, J. J. Flynn, T. J. Gaudin, A. Giallombardo, N. P. Giannini, S. L. Goldberg, B. P. Kraatz, Z.-X. Luo, J. Meng, X. Ni, M. J. Novacek, F. A. Perini, Z. S. Randall, G. W. Rougier, E. J. Sargis, M. T. Silcox, N. B. Simmons, M. Spaulding, P. M. Velazco, M. Weksler, J. R. Wible, A. L. Cirranello. The Placental Mammal Ancestor and the Post-K-Pg Radiation of PlacentalsScience, 2013; 339 (6120): 662 DOI: 10.1126/science.1229237
University of Florida (2013, February 7). Most comprehensive tree of life shows placental mammal diversity exploded after age of dinosaurs. ScienceDaily. Retrieved February 10, 2013, from http://www.sciencedaily.com/releases/2013/02/130207141458.htm
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Actinobacteria as the Base of the Evolutionary Tree

ScienceDaily (July 26, 2012) — Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree.


 

They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 — Aug. 1 in Boston, Mass.

“Today the gene banks are enormous. They contain more than 600,000 genes from the genomes of more than 6,000 species,” says William Duax, a physical chemist and lead researcher on the team. However, many of the gene sequences, and the proteins they encode, are not systematically identified. Proteins that are structurally similar and perform the same function could be labeled with different numbers that obscure the fact that they belong to the same protein family. “Our first challenge is to make sure that we are comparing apples to apples and oranges to oranges,” says Duax.

Duax and his team have developed efficient ways to search through the gene banks looking for all copies of the same family of protein. They concentrated their efforts on proteins that are found on the surface of cell components called ribosomes. The ribosomal proteins are among the most accurately identified proteins, and because they are not transferred between individuals independent of reproduction, are good candidates for tracing the evolution of all species.

Ribosomal proteins in the same family twist into the same shape. The sequence of amino acids in a protein determines what 3D structure it folds into and Duax and his colleagues identified patterns that marked specific types of turns. They used these marker sequences to identify and almost perfectly align the proteins, similar to the way you could use five points to identify the shape of a star and align its orientation to match other star shapes.

Structurally aligning the proteins allowed the researchers to easily spot small differences that indicate organisms belong on different branches of the evolutionary tree. For example, a single amino acid difference in one ribosomal protein separates bacteria with one cell membrane from those with two.

At the ACA meeting, the researchers will present the results from the analysis of two different ribosomal protein families, called S19 and S13. Duax will present the analysis of protein S19, while high school student Alexander Merriman will present analysis of protein S13. Merriman joined Duax’s lab through a scientific mentorship program designed to give teenagers hands-on experience with cutting-edge research. “They are enthusiastic researchers and do great work,” Duax says of the students he welcomes into his lab each Friday.

Both analyses point to Actinobacteria as the last universal common ancestor. This agrees with previous work done by the group on proteins named S9 and S12. The researchers will continue to search for more evidence to add to their developing picture of the evolutionary tree. The group plans to analyze additional proteins, as well as DNA and RNA. “We are applying a systematic approach to make sense of a sometimes messy gene bank,” says Duax.