Spring and Summer, 2024

​Overall

• In April, Austin, Ash and Gavin making a successful field trip down to Baja California Sur to collect leaves from the rare Q. brandgeii for genetic analyses of its populations!
• In July, Sean received a Walder Biota Award, which will fund three years of efforts towards local and global biodiversity conservation! Specifically it will fund a large-scale assessment of the genetic conservation status of 200 North American trees, as well as local efforts for assessing health and distribution of the threatened butternut tree (Juglans cinerea, IUCN Threatened), in the Midwest and especially Chicago region. Partners include the US Forest Service, US Fish and Wildlife Service, and several local county Forest Preserves.  This award was presented at an in-person celebration at Lincoln Park Zoo. A video about Sean’s work, and the other 2024 awardees, can be found here.

• In August, Emma and Sean completed a trip to Vermont to meet collaborators working on butternut conservation. Butternut is a threatened and rapidly declining hardwood, dying off due to a fungal pathogen (read more here). It was historically ecologically and culturally important. During a brief 3-day trip, they met indigenous partners, local landowners, state and federal forest managers, and research partners. They toured a large moderately healthy population of >100 adult butternuts (see photo below) with >100 seedlings (in which they helped find even more seedlings), and shared knowledge and vision about the future potential of this site (studying seed dispersal, hybridization, and disease resistance). They also visited two other populations as well as a grafted orchard, at which they discussed good and poor growing conditions. At the site they also happened to meet USFS personnel who were taking data on an American chestnut orchard (both fully American chestnut and hybrid chestnut), so were able to tour this unique and invaluable tree breeding resource!

Events and Presentations

• ​In March, Sean gave a presentation to the International Union for Conservation of Nature Species Survival Commission, regarding the Convention on Biological Diversity Kunming-Montreal Global Biodiversity Framework, and his engagement over the past three years with this important global conservation commitment. He also discussed some of his work analyzing how countries reported on biodiversity in the past, and how they could report better in the future. There were more than 200 online attendees.
• In March, Sean also gave a presentation to The Crop Trust GROW (Genebank Resources On the Web) seminar series, to which over 250 persons registered. The Crop Trust provides resources and guidance to hundreds of genebanks worldwide. The topic of this presentation was Sean’s work over the past 10 years in terms of developing quantitative advice to botanic gardens about seed sampling and managing their collections, including several novel methods Sean’s team developed. This work was placed in the context of the Convention on Biological Diversity commitments, and how genebanks and gardens can actively assess their conservation progress and work to improve it. Work from past lab members including Emily Schumacher, Emily Beckman, and Kaylee Rosenberger, as well as collaborator Colin Khoury, were featured. The recorded webinar is here.
• In June, lab members attended the North American Congress on Conservation Biology (NACCB) in beautiful Vancouver, British Columbia! Sean presented on both the need and the ways of integrating genetic diversity into national and global biodiversity planning and monitoring, as part of a symposium on the Convention on Biological Diversity. Austin presented on a fast, affordable, inclusive monitoring of genetic diversity, which uses non-DNA data and therefore leverages very diverse types of data, with an application to >150 US Endangered Species Act species. Emma presented on the context and outcomes of the prairie experiment, a phylogenetically informed experiment to understand how ecosystem functioning is impacted by trait and taxonomic diversity, as well as resistance to invasive species.

Publications

• Pearman, P.B., Broennimann, O., Aavik, T. et al. Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts. Nat Ecol Evol 8, 267–281 (2024). https://doi.org/10.1038/s41559-023-02260-0
• Hoban, S., da Silva, J.M., Hughes, A., Hunter, M.E., Kalamujić Stroil, B., Laikre, L., Mastretta-Yanes, A., Millette, K., Paz-Vinas, I., Bustos, L.R. and Shaw, R.E., 2024. Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity. BioScience, p.biae006. (open access).
  • This publication stems from Sean Hoban’s (Tree Conservation Biologist) policy work – providing scientific advice and expertise to the Convention on Biological Diversity (CBD). The paper discusses an approach that he and colleagues developed for estimating genetic diversity status of hundreds of species quickly, affordably, and inclusively. The paper presents the advantages, perceived disadvantages, and practical solutions for this approach, known as “genetic indicators.” The paper is timely and important because genetic indicators are formally part of the CBD Global Biodiversity Framework, and several policy meetings this year will deal with the practicalities of actually monitoring biodiversity at large scale. This paper will help non-experts better understand the approach and decide whether to use it in practice for reporting on and managing biodiversity at national scales.
• Koontz, A. C., Schumacher, E. K., Spence, E. S., & Hoban, S. M. (2024). Ex situ conservation of two rare oak species using microsatellite and SNP markers. Evolutionary Applications, 17(3), e13650.
  • Link: http://dx.doi.org/10.1111/eva.13650
  • Summary: This publication is the result of several years of work coming out of the Hoban Lab seeking to understand the number of individuals required for genetically representing wild populations of threatened oaks (Quercus acerifolia and Q. boyntonii) ex situ. Specifically, this paper examines whether and how that number of required individuals changes based on the type of genetic marker used. The lab found that using a newer marker type (SNPs) tends to lead to a larger number of individuals that need to be protected ex situ, compared to an older marker type (microsatellites)–but not in all cases! These results have implications for botanic gardens trying to bolster the genetic diversity of their collections based on guidelines derived using microsatellite data.
• Margaret Hunter, Jessica M. da Silva, Alicia Mastretta-Yanes, and Sean M. Hoban. A new era of genetic diversity conservation through novel tools and accessible data.  Frontiers in Ecology and the Environment.
  • Genetic diversity is necessary for species to adapt to ecological changes, such as impacts from disease, invasive species, and climate change. Genetic diversity also supports ecosystem resilience and societal innovations. This editorial article reviews the ways in which genetic diversity can contribute to biodiversity monitoring and conservation action.
• Deborah M. Leigh, Amy G. Vandergast, Margaret E. Hunter, Eric D. Crandall, W. Chris Funk, Colin J. Garroway, Sean Hoban, Sara J. Oyler-McCance, Christian Rellstab, Gernot Segelbacher, Chloé Schmidt, Ella Vázquez-Domínguez & Ivan Paz-Vinas. Best practices for genetic and genomic data archiving. Nature Ecology and Evolution.
  • This article reviews opportunities and challenges for making genetic data and their metadata more archivable and FAIR (findable, accessible, interoperable and reusable), for data re-use, integrity and reliability.  We also review those potential re-uses of genetic data, including for global and collaborative biodiversity conservation, lessons which apply to biodiversity more broadly.  We suggest several best practices for this active area of research.
• Wu, Y; Linan, A; Hoban, S; Hipp, A; Ricklefs, R. 2024. Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak). Journal of Heredity, esae033, https://doi.org/10.1093/jhered/esae033 Published: 17 June 2024
  • This study focuses on a rare tree, maple-leaf oak (Quercus acerifolia).  It is limited to four mountain tops in Arkansas. We investigated whether maple leaf oak is receiving gene flow/ introgression from other oaks, up to the point of genetic swamping, including Q. shumardii, Q. buckleyi, and Q. rubra. Although hybrids were identified, maple leaf oak mostly remains resistant to introgression, possibly due to adaptation to its environment.  Interestingly we found more hybrids in ex situ collections in botanic gardens.  Currently, although hybridization is a concern especially ex situ, it is not a major threat to maple leaf oak in situ.
• Integrating genomic data and simulations to evaluate alternative species distribution models and improve predictions of glacial refugia and future responses to climate change. Sarah R. Naughtin, Antonio R. Castilla, Adam B. Smith, Allan E. Strand, Andria Dawson, Sean Hoban, Everett Andrew Abhainn, Jeanne Romero-Severson, and John D. Robinson. Ecography. Free Open Access.
  • This paper builds on previous work of this six year collaboration on understanding how species geographic ranges respond to climate change.  The collaboration was initially sparked by a CTS Fellow grant to gather the collaborators together at The Morton Arboretum in 2017, and to support genotyping of green ash.  This is the fourth paper to come from this teamwork.  The paper highlights how different species distribution models (SDMs) can lead to different pictures of species range responses, and shows a novel approach to solving this problem – the use of simulations and the ABC approach to identify the SDM most closely matching empirical genomic data.  Forecast projections of the range of green ash (Fraxinus pennsylvanica), using the SDMs selected by the ABC method, suggest that the species will experience only minor geographic shifts in its suitable habitat.
• Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework. Alicia Mastretta-Yanes, Jessica M. da Silva, Catherine E. Grueber, Luis Castillo-Reina, Viktoria Köppä, Brenna R. Forester, W. Chris Funk, Myriam Heuertz, Fumiko Ishihama, Rebecca Jordan, Joachim Mergeay, Ivan Paz-Vinas, Victor Julio Rincon-Parra, Maria Alejandra Rodriguez-Morales, Libertad Arredondo-Amezcua, Gaëlle Brahy, Matt DeSaix, Lily Durkee, Ashley Hamilton, Margaret E. Hunter, Austin Koontz, Iris Lang, María Camila Latorre-Cárdenas, Tanya Latty, Alexander Llanes-Quevedo, Anna J. MacDonald, Meg Mahoney, Caitlin Miller, Juan Francisco Ornelas, Santiago Ramírez-Barahona, Erica Robertson, Isa-Rita M. Russo, Metztli Arcila Santiago, Robyn E. Shaw, Glenn M. Shea, Per Sjögren-Gulve, Emma Suzuki Spence, Taylor Stack, Sofía Suárez, Akio Takenaka, Henrik Thurfjell, Sheela Turbek, Marlien van der Merwe, Fleur Visser, Ana Wegier, Georgina Wood, Eugenia Zarza, Linda Laikre, Sean Hoban. Ecology Letters. Free Open Access.
  • This paper is the culmination of a three year effort by 49 authors to test whether it is feasible to assess and monitor genetic diversity at national and global levels.  The research, led by Alicia Mastretta-Yanes, Jessica da Silva, and Sean Hoban, involved researchers and practitioners from academia, government institutions, and non-governmental organizations. Nine countries were involved, varying in economic status and biodiversity richness: Australia, Belgium, Colombia, France, Japan, Mexico, South Africa, Sweden, and the United States. The authors analyzed genetic indicators for 919 species, representing more than 5000 populations. The study covered all taxonomic groups, and notably several keystone trees were included, such as Mexican mountain juniper.  The findings were revealing: while the majority of analyzed species maintain most of their populations, 58% of them have many populations that are too small to sustain genetic diversity. Furthermore, the results show that the IUCN Red List does not represent genetic status, highlighting the critical importance of monitoring genetic diversity with a methodology such as that presented here.