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Benham PM, Cicero C, DeRaad DA, McCormack JE, Wayne RK, Escalona M, Beraut E, Marimuthu MPA, Nguyen O, Nachman MW, Bowie RCK. A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri). J Hered 2023; 114:549-560. [PMID: 37395718 PMCID: PMC10445514 DOI: 10.1093/jhered/esad042] [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: 04/14/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023] Open
Abstract
The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
| | - Devon A DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, CA, United States
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, United States
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Harvey DP, Black JM. Problem-solving performance in wild Steller’s jays using a string-pulling task. BEHAVIOUR 2021. [DOI: 10.1163/1568539x-bja10057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Animals that exploit resources from human-modified environments may encounter unique problems when searching for food. Pulling a string tied to a food reward (string-pulling task) is one of the most widespread methods of testing a species’ problem-solving performance in non-human animals. Performance in problem-solving tasks may be influenced by an individual’s characteristics and social interactions, especially in its natural habitat. We examined problem solving by free-ranging Steller’s jays (Cyanocitta stelleri) when extracting food from a string-pulling task presented in their natural habitat. During the study, seven of 50 jays successfully solved the task on their first to eighteenth experimental opportunity; solvers differed from nonsolvers by showing higher levels of persistence by pulling the string in more trials. Of the successful jays, five birds solved without observing others, while two birds were present during successful trials and subsequently completed the task. All seven jays demonstrated improvement in the task by using less string pulls over additional successful trials. Nineteen other jays in the population interacted with the apparatus and pulled the string, but not enough to acquire the food. These 19 jays were significantly bolder (shorter latencies to approach), more explorative (contacted more parts of the apparatus), and had observed solvers more than the 24 individuals that did not pull the string. These results indicate a broad spectrum of individual differences in propensity for solving novel tasks in our population of Steller’s jays.
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Affiliation(s)
- Derek P. Harvey
- Department of Wildlife, Humboldt State University, 1 Harpst Street, Arcata, CA 95521, USA
| | - Jeffrey M. Black
- Department of Wildlife, Humboldt State University, 1 Harpst Street, Arcata, CA 95521, USA
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Legg EW, Ostojić L, Clayton NS. Caching at a distance: a cache protection strategy in Eurasian jays. Anim Cogn 2016; 19:753-8. [PMID: 26984123 PMCID: PMC4891366 DOI: 10.1007/s10071-016-0972-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/08/2016] [Accepted: 03/02/2016] [Indexed: 02/06/2023]
Abstract
A fundamental question about the complexity of corvid social cognition is whether behaviours exhibited when caching in front of potential pilferers represent specific attempts to prevent cache loss (cache protection hypothesis) or whether they are by-products of other behaviours (by-product hypothesis). Here, we demonstrate that Eurasian jays preferentially cache at a distance when observed by conspecifics. This preference for a ‘far’ location could be either a by-product of a general preference for caching at that specific location regardless of the risk of cache loss or a by-product of a general preference to be far away from conspecifics due to low intra-species tolerance. Critically, we found that neither by-product account explains the jays’ behaviour: the preference for the ‘far’ location was not shown when caching in private or when eating in front of a conspecific. In line with the cache protection hypothesis we found that jays preferred the distant location only when caching in front of a conspecific. Thus, it seems likely that for Eurasian jays, caching at a distance from an observer is a specific cache protection strategy.
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Affiliation(s)
- Edward W Legg
- Department of Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB, UK.
| | - Ljerka Ostojić
- Department of Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB, UK
| | - Nicola S Clayton
- Department of Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB, UK
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Tornick JK, Rushia SN, Gibson BM. Clark’s nutcrackers (Nucifraga columbiana) are sensitive to distance, but not lighting when caching in the presence of a conspecific. Behav Processes 2016; 123:125-33. [DOI: 10.1016/j.beproc.2015.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/30/2015] [Accepted: 10/31/2015] [Indexed: 11/28/2022]
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