Leveraging museum specimens to ask ecological questions in the era of genomics

The ability to whole-genome sequence from a dried museum specimen (such as using a single leg from a 30 year old pinned butterfly) fundamentally changes the way we view the value of collections. Whole-genome sequencing will only continue to become faster and cheaper, and our ability to extract intact DNA from older material is also expected to greatly improve. Already, whole-genome sequencing has been a powerful tool in phylogenetics and systematics, uncovering both cryptic species, and showing unexpected relatedness between rather different-looking taxa , as well as extreme phenotypic convergence of long-diverged taxa (e.g., Nick Grishin’s work based on whole-genome [exomic] sequencing of all 800 North American butterfly species). What is less appreciated is that such sequence data can also be used to ask ecological questions, such as searching for signatures of selection (recent and/or ancient), either on specific traits or a random scan of the genome for genes underlying adaption.

In this seminar, I’ll review the basic logic of these genomic-based approaches, as well as discuss tests from paleontology based solely on changes in phenotypes over time. I’ll then mention both what sort of data are needed for tests of recent/ongoing selection versus long phylogenetic trends, and how large collections might move forward to start accumulating such samples.

This seminar also serves as an overview of topics that will be more fully developed in the Detecting Selection workshop on 8 November at ANU.

Target audience:  Evolutionary biologists, ecologists, paleontologists, geneticists, statisticians, museum curatorial staff, as well as the general public with an interest in natural history and evolution. 

About Bruce

Bruce Walsh received a BS in Mathematical Population Biology from UC Davis, a PhD in Genetics from the University of Washington (under Joe Felsenstein), and did a post-doc at the University of Chicago before moving to the University of Arizona, where he is currently Professor of Ecology and Evolutionary Biology. Dr. Walsh is also a Professor in the College of Public Heath, and Adjunct Professor in the Departments of Plant Sciences, Animal Sciences, and Molecular and Cellular Biology, as well as a member of the Graduate Interdisciplinary Programs in Applied Mathematics, Genetics, Statistics, and Insect Sciences. He is co-author of the two leading graduate textbooks in Quantitative Genetics (Genetics and Analysis of Quantitative Traits; Evolution and Selection of Quantitative Traits) and was presented with a lifetime achievement award in 2020 at the 6th International Congress of Quantitative Genetics in Brisbane. Dr. Walsh is especially active in teaching and training, having given more than 100 short courses on various topics at the interface of genetics, statistics, breeding, and evolution in 25 countries spanning six continents (still waiting on Antarctica).  Dr. Walsh is a founding instructor for both the African Plant Breeding Academy and the Tucson Plant Breeding Institute, and is presently on the scientific advisory board of the ARC Center of Excellence in Plant Success (out of UQ). Finally, Dr. Walsh also has a deep interest in Lepidoptera, having described a dozen new species of Arizona moths, and  collected the types for two dozen other new species, resulting in three patronyms  (Drasteria walshi Metlevski and Zolnerowich 2009; Apamea walshi Lafontaine 2010; Afilia walshi Miller 2021).  He is the founder of the Lep Course, taught yearly at the SW research station in Portal (Arizona), which has attracted students (ranging from serious amateurs to curators for National museums) from 20 countries (including several Australians).

Selected references:

  • Lynch, M and B. Walsh. 1998.  Genetics and Analysis of Quantitative Traits.  Sinauer Associations, 990 pp.
  • B. Walsh and M. Blows. 2009. Abundant genetic variation + strong selection = multivariate genetic constraints: A geometric view of adaptation.  Annual Reviews of Ecology and Systematics 40: 41--59.
  • Walsh, B. 2009. Lithophane leeae (Lepidoptera, Noctuidae, Xyleninaa), a striking new species from southeastern Arizona. Zookeys 10: 11-16.
  • J. D. Lafontaine, C. D. Ferris, and J. B. Walsh. 2010. A revision of the genus Hypotrix Guenée in North America with descriptions of four new species and a new genus (Lepidoptera: Noctuidae: Noctuinae: Hadenini). Zookeys 39: 225--253
  • Lafontaine, J. Donald, J. B. Walsh, and Clifford D. Ferris. 2014.  A revision of the genus Protorthodes McDunnough with descriptions of a new genus and four new species (Lepidoptera, Noctuidae, Noctuinae, Eriopygini).  ZooKeys 421: 139--155.
  • Walsh, B., and M. Lynch.  2018.  Evolution and Selection of Quantitative Traits.  1496 pages, Oxford.
  • B. Walsh, and M. Morrisey.  2019.   Evolutionary Quantitative Genetics.   In D. J. Balding, M. Bishop and C. Cannings (Eds), Handbook of Statistical Genetics, 4th Edition, pp.  421—457.
  • B. Walsh.  2022.  How full is the evolutionary fuel tank?  Science 376: 920—921.

Bruce's visit is co-funded by the Centre for Biodiversity Analysis, hosted by Hermes Escalona (CSIRO). Please get in touch if you would like to meet with Bruce during his time in Canberra (Nov 2023). Bruce is looking forward to meeting with CBA members, especially students and post-docs, during his stay both hear about their work and also to potentially provide feedback and/or advice.