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Miles LS, Waterman H, Ayoub NA, Garb JE, Haney RA, Rosenberg MS, Krabbenhoft TJ, Verrelli BC. Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. J Hered 2024; 115:241-252. [PMID: 38567866 DOI: 10.1093/jhered/esae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/19/2024] [Indexed: 05/12/2024] Open
Abstract
Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.
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Affiliation(s)
- Lindsay S Miles
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Hannah Waterman
- Department of Biological Sciences and Research and Education in Energy, Environment, and Water Institute, University at Buffalo, Buffalo, NY, United States
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA, United States
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Robert A Haney
- Department of Biology, Ball State University, Muncie, IN, United States
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Trevor J Krabbenhoft
- Department of Biological Sciences and Research and Education in Energy, Environment, and Water Institute, University at Buffalo, Buffalo, NY, United States
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, United States
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Verrelli BC, Alberti M, Des Roches S, Harris NC, Hendry AP, Johnson MTJ, Savage AM, Charmantier A, Gotanda KM, Govaert L, Miles LS, Rivkin LR, Winchell KM, Brans KI, Correa C, Diamond SE, Fitzhugh B, Grimm NB, Hughes S, Marzluff JM, Munshi-South J, Rojas C, Santangelo JS, Schell CJ, Schweitzer JA, Szulkin M, Urban MC, Zhou Y, Ziter C. A global horizon scan for urban evolutionary ecology. Trends Ecol Evol 2022; 37:1006-1019. [PMID: 35995606 DOI: 10.1016/j.tree.2022.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 10/31/2022]
Abstract
Research on the evolutionary ecology of urban areas reveals how human-induced evolutionary changes affect biodiversity and essential ecosystem services. In a rapidly urbanizing world imposing many selective pressures, a time-sensitive goal is to identify the emergent issues and research priorities that affect the ecology and evolution of species within cities. Here, we report the results of a horizon scan of research questions in urban evolutionary ecology submitted by 100 interdisciplinary scholars. We identified 30 top questions organized into six themes that highlight priorities for future research. These research questions will require methodological advances and interdisciplinary collaborations, with continued revision as the field of urban evolutionary ecology expands with the rapid growth of cities.
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Affiliation(s)
- Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Marina Alberti
- Department of Urban Design and Planning, University of Washington, Seattle, WA 98195, USA
| | - Simone Des Roches
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA
| | - Nyeema C Harris
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University, New Haven, CT 06511, USA
| | - Andrew P Hendry
- Department of Biology, Redpath Museum, McGill University, Montreal, QC H3A 0C4, Canada
| | - Marc T J Johnson
- Department of Biology, Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Amy M Savage
- Department of Biology and Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ 08103, USA
| | | | - Kiyoko M Gotanda
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada; Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Lynn Govaert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Lindsay S Miles
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - L Ruth Rivkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON L5L 1C6, Canada; Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kristin M Winchell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kristien I Brans
- Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cristian Correa
- Instituto de Conservación Biodiversidad y Territorio, Centro de Humedales Río Cruces, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Sarah E Diamond
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ben Fitzhugh
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Grimm
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sara Hughes
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI 48109, USA
| | - John M Marzluff
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jason Munshi-South
- Louis Calder Center & Department of Biological Sciences, Fordham University, Armonk, NY 10504, USA
| | - Carolina Rojas
- Instituto de Estudios Urbanos y Territoriales, Centro de Desarrollo Sustentable CEDEUS, Pontificia Universidad Católica de Chile, El Comendador 1916, Providencia, 7500000, Santiago, Chile
| | - James S Santangelo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON L5L 1C6, Canada
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Schweitzer
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37917, USA
| | - Marta Szulkin
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Mark C Urban
- Department of Ecology and Evolutionary Biology & Center of Biological Risk, University of Connecticut, Storrs, CT 06269, USA
| | - Yuyu Zhou
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, IA 50011, USA
| | - Carly Ziter
- Department of Biology, Concordia University, Montreal, QC H4B 1R6, Canada
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