Chris Smith

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Anonymous — Thu, 12 Sep 2019 00:00:00 +0000

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation Anonymous (not verified) Wed, 09/11/2019 - 18:00

Chris Smith , Sam Flaxman

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian Computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo observed datasets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (1) more data, (2) haplotype‐based summary statistics, and (3) locus length. Compared with a hypothetical RADseq dataset with 2.5Mbp of data, using a 1Gbp dataset consisting of 100Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (i) locus‐specific recombination rates, and (ii) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.

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Chris Smith: Evolution Meeting

Anonymous — Wed, 26 Jun 2019 00:00:00 +0000

Chris Smith: Evolution Meeting Anonymous (not verified) Tue, 06/25/2019 - 18:00

Chris Smith

I just got back from the Evolution Meeting in Providence and I’m full of information and ideas for research. I had the opportunity to reconnect with past colleagues and meet some new people. Other CU ��«��Ƶ folks attended, including the labs of Dan Doak, Nancy Emery, Nolan Kane, Stacy Smith, and Scott Taylor (sorry if I missed any others).

Although most of the research represented at Evolution is empirical research on understanding and preserving biodiversity, many attendees were excited to discuss methods. In particular, producing large amounts of DNA sequencing data - both empirically, and using computer simulations - is no longer limiting in many cases. Therefore, the challenge of developing theory and methods for analyzing these data has received more attention in recent years.

Highlighting a couple of talks I thought were memorable: Paul Hohenlohe (U. Idaho) described the array of reduced representation sequencing approaches that are available and important trade-offs among them. Adam Jones (also U. Idaho) used simulations to see if and how pleiotropy and epistasis affect scans for loci involved in adaptation; he reported that pleiotropic effects don’t really affect outlier scans and that some important loci are still detected in the presence of genetic interactions. Zach Gompert (Utah State) presented a cool approach for quantifying fluctuating selection.

My presentation was part of the session on Population Genetics Theory, which is too broad of a name for the session because the talks were each focused specifically on inferring historical population sizes and admixture. Multiple speakers used ancient DNA to infer population history and used computer simulations to validate their approach. Other speakers, including myself, were trying to “break” commonly used tools that infer population history, to understand which parameters and data work best, or worst.

On a fun note, we got to see the “WaterFire” event in downtown Providence next to the convention center. This event is a big deal. There were thousands of attendees packed onto bridges and standing in the park along the river. Leading up to, and during the event, large amplifiers played music covering a range of- and alternating dissonantly between- intense classical music, tribal music, country music, and horns. At dusk, they lit small bonfires floating on the river. That’s it.

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Barn swallows may indeed have evolved alongside barns, humans

Anonymous — Tue, 30 Oct 2018 00:00:00 +0000

Barn swallows may indeed have evolved alongside barns, humans Anonymous (not verified) Mon, 10/29/2018 - 18:00

Cay Leytham-Powell

As humans evolved and expanded, so too did barn swallows, new research from CU ��«��Ƶ suggests

The evolution of barn swallows, a bird ubiquitous to bridges and sheds around the world, might be even more closely tied to humans than previously thought, according to new study from the ��«��Ƶ.

Chris Smith (left) and Rebecca Safran (right) re-examined the evolution of barn swallows and found that they may indeed have evolved alongside barns. Photographs courtesy of Rebecca Safran and Patrick Campbell/��«��Ƶ.

The research, published this week in Molecular Ecology, offers preliminary insight suggesting that the barn swallow and its subspecies evolved alongside—but independently from—humans. These new results make it one of the only known species, in addition to microscopic organisms like bacteria or viruses, to have developed in such a way, upending previous assumptions that barn swallows evolved prior to human settlement.

“Humans could be a really big part of the story,” said Rebecca Safran, a co-author of the study and an ecology and evolutionary biology (EBIO) associate professor at CU ��«��Ƶ. “There’s very few studies that can point to the exact influence of humans, and so here, this coincidence of human expansion and permanent settlement and the expansion of a group that relies really, really heavily on humans is compelling.”

Barn swallows are found across the northern hemisphere and are characterized by their mud-cup nests that are built nearly exclusively on human-made structures. Despite their prevalence, however, not much is known about their evolutionary history, the timing of their expansion from northern Africa (where they originated) or how the six subspecies evolved so physically and behaviorally different yet remain almost genetically identical.

Previous studies published in the Proceedings of the Royal Society of London and Molecular Phylogenetics and Evolution looked into these questions and found that the different subspecies split early, well before human settlement.

This new study, however, gave the topic a fresh look by examining the whole genome of 168 barn swallows from the two sub-species farthest apart on an evolutionary scale: H. r. savignii in Egypt (a non-migratory species that lives along the Nile) and H. r. erythrogaster in North America (a species found throughout North America that migrates seasonally to South America).

Barn swallow subspecies are found throughout the northern hemisphere. Barn Swallow illustrations courtesy of Hilary Burn, and map courtesy of the Safran lab.

These data—which are on the order of 100,000 times bigger than the previous dataset used—were then analyzed with more sophisticated computational resources and methods than previously available. This allowed researchers to get a more complete picture that places the timing of barn swallow differentiation or speciation (i.e., when the barn swallow subspecies separated) closer to that of when humans began to build structures and settlements.

“The previous studies were playing with the idea of potential impact on population sizes due to humans,” said Chris Smith, a graduate student in EBIO and the Interdisciplinary Quantitative Biology program, and the study’s lead author. “Our results suggest a much more substantial link with humans.”

These new preliminary findings also suggest that this evolutionary link may have been forged through a “founder event,” which is when a small number of individuals in a species take over a new environment and are able to expand their new population there thanks to an availability of resources and an absence of competitors. For barn swallows, this event may have occurred rapidly when they moved into a new, relatively empty environment: alongside humans.

“Everyone is always wondering how do you study speciation? It’s been viewed as this long-term, million-year (process), but in barn swallows, we are not talking about differentiation within several thousands of years,” said Safran. “Things are really unfolding rather rapidly.”

Smith concurred: “It’s interesting to study speciation in the beginning steps.”

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IQ Biology student wins 2015 GRFP fellowship from NSF

Anonymous — Thu, 28 May 2015 00:00:00 +0000

IQ Biology student wins 2015 GRFP fellowship from NSF Anonymous (not verified) Wed, 05/27/2015 - 18:00

BioFrontiers

The National Science Foundation recently announced the recipients of the coveted 2015 Graduate Research Fellowship (GRFP) awards. These prestigious awards have been given since 1952 to graduate students who show a demonstrated potential for significant achievements in science and engineering.

Chris Smith, a first-year student from the BioFrontiers Institute’s Interdisciplinary Quantitative Biology PhD Program, received a 2015 fellowship. Second-year IQ Biology student, John Nardini, was given an honorable mention.

Smith is rostered in the Department of Ecology and Evolutionary Biology. His interests are focused on evolutionary genomics and how they are affected by local adaptations and speciation. He plans to use his fellowship funding to support him in the development of computational methods for biologists to use when researching genomics.

The NSF fellowships provide three years of financial support over a five-year period. This is split into a $34,000 annual stipend and a $12,000 cost-of-education allowance to the graduate institution. The fellowships also provide opportunities to participate in international research collaborations and access to NSF-supported research infrastructure. From over 16,500 applicants, a total of 2,000 Graduate Fellows were awarded in 2015, 23 of which went to CU-��«��Ƶ students. Over the past five years, 30 percent of students in the IQ Biology program at BioFrontiers have either received a GRFP award or been given an honorable mention.

The University of Colorado, ��«��Ƶ students won 30 NSF fellowships, and CU-��«��Ƶ was among the top 20 universities with NSF fellows last year. BioFrontiers and the IQ Biology program are honored to have students involved in the NSF Graduate Research Fellowship Program, which is one of the most prestigious awards available for student researchers.

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Chris Smith

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

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Chris Smith: Evolution Meeting

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Barn swallows may indeed have evolved alongside barns, humans

As humans evolved and expanded, so too did barn swallows, new research from CU ��«����Ƶ suggests

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IQ Biology student wins 2015 GRFP fellowship from NSF

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As humans evolved and expanded, so too did barn swallows, new research from CU ��«��Ƶ suggests