molecular evolution from a paleo perspective
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Reconstructing Pleistocene Beringia and the Transition into the Holocene

This heading includes several more specific ancient DNA research projects currently underway in the Shapiro lab. We are interested in how Arctic species and populations responded to environmental and habitat change throughout the Pleistocene, and what role ecology, natural history, climate and community-level dynamics played in the megafaunal mass extinctions ca. 10-15,000 years ago. Key collaborators: Duane Froese, Grant Zazula, Daniel Mann.

Environmental DNA as a tool for paleogenomics and conservation

The genetic legacy left by organisms that lived or passed through an environment has the potential to provide new and important insights into how and why communities changes over timeā€¦ if it can be recovered and studied. To this end, we are developing new tools and approaches to recover and analyze DNA preserved in environmental samples, and using these to study how ecosystems vary over geography and time and what biotic and abiotic factors might be driving this variation. Key collaborators: Bob Wayne, Rachel Meyer, Harris Lewin, Hendrik Poinar, Laura Epp, Mike Garvin, Bruce Finney, and many others!

For more information on some of the environmental DNA projects in which we are collaborating, check out CALeDNA, the Earth Biogenome Project, and our HHMI-funded undergraduate research and education program, eSIE.

The evolution of humans and archaic hominins

Working with genomic data from modern human populations and archaic hominins, we are interested to learn more about what makes our lineage distinct from other hominins, about the demography of admixture between our species and other, closely realted lineages, and about the timing of human movement into and throughout the American continents. Key collaborators: Alysson Muotri, Cleber Trujillo, Lars Fehren-Schmitz, Paul Fine, Diane Gifford-Gonzalez, Kent Lightfoot, Bob Ballard, Jack Ives.

from wikiedia commons

The rise and fall of the passenger pigeon

The passenger pigeon was an iconic North American bird whose population decllned from billions of individuals to extinction within less than a century. While we're pretty sure it was our (humans) fault, we still don't know how quickly that extinction happened,what exactly our role was, or wither it was at all avoidable. We are taking a geoimc approach to this question, and even thinking of ways to bring this bird back to life. Maybe. (Check out Beth's talks about #deExtinction from TEDxDeEXTINCTION and the Royal Institution, and some great information from Revive & Restore).


The alligator genome and evolution of temperature-dependent sex determination

Like many reptiles, American alligators become eithe rmale or female depending on the temperature at which their developing embryos are incubated. Using a combination of genomic and transcriptomic data, we are investigating the mechanistic basis of this form of sex determination. Key collaborators: Ed Braun, Satomi Kohno, Lou Guillette.


The evolution of horses

Are feral horses that roam the North American west today genetically different from the wild horses that went extinct in North America at the Pleistocene/Holocene transition? We are using a range of genomic and population genetic techniques to address this question, and to learn about the origin and diversification of modern equids. Key collaborators: Ludovic Orlando, Ross MacPhee, Eric Scott, Grant Zazula.


The evolutionary consequences of interspecies admixture

As we progress further into the age of comparative genomics, it is increasingly apparent that admixture between closely related species is a common occurrence. Working with several admixing species pairs (e.g. brown bears and polar bears, bison and cattle, humans and Neandertals, and wolves and coyotes), we aim to understand how admixture influences the evolutionary trajectories of species and, perhaps, to better understand the process of speciation itself. Key Collaborators: Ian Stirling, Alexander Malev, Bob Wayne, Mike Heaton, Tim Smith


More data! Better data!

Paleogenomic and forensic research is limited by the quantity and quality of data that can be recovered from what are often small and degraded organic remains. A major area of research in the Paleogenomics Lab is therefore to improve the recovery (experimentally and computationally) of authentic ancient DNA. Our progress in this realm has led to several exciting advances (and more than one start-up company!), and we are particularly interested in recruiting graduate students and postdocs with backgrounds in biochemistry, molecular biology, and/or computational genomics to join us in this work.


There's so much more! Check out our latest publications to learn more about our current projects.









Extracting and characterizings DNA from fossil remains.

Understanding the evolutionary constraints underpinning diversity and evolution in pathogens

Investigating patterns and processes in genome evolution.