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Huang JP, Wu SP, Chen WY, Pham GJ, Kuan YH. Genomic data revealed inbreeding despite a geographically connected stable effective population size since the Holocene in the protected Formosan Long-Arm Scarab beetle, Cheirotonus formosanus. J Hered 2024; 115:292-301. [PMID: 38364316 DOI: 10.1093/jhered/esae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations from different mountain ranges of the Formosan Long-Arm Scarab beetle, a flagship species that receives strict protection, exhibited a single genetic cluster with no subdivision. Additionally, our result implied an association between the demographic history and historical fluctuations in climate and environmental conditions. Furthermore, we showed that, despite a stable and moderately sized effective population over recent history, all the individuals we studied exhibited signs of genetic inbreeding. We argued that the current practice of protecting the species as one evolutionarily significant unit remains the best conservation plan and that recent habitat change may have led to the pattern of significant inbreeding. We closed by emphasizing the importance of conservation genetic studies in guiding policy decisions and highlighting the potential of genomic data for identifying ideal empirical systems for genetic rescue, or assisted gene flow studies.
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Affiliation(s)
- Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Ping Wu
- Department of Earth and Life Science, University of Taipei, Taipei, Taiwan
| | - Wei-Yun Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Guan Jie Pham
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Liu Y, Olsson A, Larva T, Cantwell-Jones A, Gill RJ, Cederberg B, Webster MT. Genomic variation in montane bumblebees in Scandinavia: High levels of intraspecific diversity despite population vulnerability. Mol Ecol 2024; 33:e17251. [PMID: 38112228 DOI: 10.1111/mec.17251] [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: 10/04/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole-genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (NE ) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high NE and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in NE indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.
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Affiliation(s)
- Yuanzhen Liu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tuuli Larva
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Aoife Cantwell-Jones
- Department of Life Sciences, Georgina Mace Centre for The Living Planet, Imperial College London, Ascot, UK
| | - Richard J Gill
- Department of Life Sciences, Georgina Mace Centre for The Living Planet, Imperial College London, Ascot, UK
| | - Björn Cederberg
- Swedish University of Agricultural Sciences, Swedish Species Information Centre, Uppsala, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Fu X, Meyer-Rochow VB, Ballantyne L, Zhu X. An Improved Chromosome-Level Genome Assembly of the Firefly Pyrocoelia pectoralis. INSECTS 2024; 15:43. [PMID: 38249049 PMCID: PMC10816139 DOI: 10.3390/insects15010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
The endemic and endangered Chinese firefly Pyrocoelia pectoralis is a sexually dimorphic, nocturnal species. A previous attempt by this team to assemble a draft genome of P. pectoralis using PacBio and Illumina HiSeq X Ten platforms was limited in its usefulness by high redundancy and contamination. This prompted us to conduct an improved chromosome-level genome assembly of P. pectoralis. Ten chromosomes were further assembled based on Hi-C data to a 532.25 Mb final size with a 52.87 Mb scaffold N50. The total repeat lengths in the genome of P. pectoralis amount to 227.69 Mb; 42.78%. In total, 12,789 genes could be functionally annotated using at least one public database. Phylogenetic inference indicated that P. pectoralis and P. pyralis diverged ~51.41 million years ago. Gene family expansion and contraction analysis of 12 species were performed, and 546 expanded and 2660 contracted gene families were identified in P. pectoralis. We generated a high-quality draft of the P. pectoralis genome. This genome assembly should help promote research on the species' sexual dimorphism and its unique courtship behavior, which involves a combination of pheromonal and bioluminescent signals. It also can serve as a resource for accelerating genome-assisted improvements in the conservation of this species.
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Affiliation(s)
- Xinhua Fu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Firefly Conservation Research Centre, Wuhan 430070, China;
| | - Victor Benno Meyer-Rochow
- Department of Ecology and Genetics, Oulu University, SF-90140 Oulu, Finland;
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Republic of Korea
| | - Lesley Ballantyne
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, P.O. Box 588, Wagga Wagga 2678, Australia;
| | - Xinlei Zhu
- Firefly Conservation Research Centre, Wuhan 430070, China;
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Everitt T, Wallberg A, Christmas MJ, Olsson A, Hoffmann W, Neumann P, Webster MT. The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees. Genome Biol Evol 2023; 15:evad157. [PMID: 37625795 PMCID: PMC10484329 DOI: 10.1093/gbe/evad157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.
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Affiliation(s)
- Turid Everitt
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wolfgang Hoffmann
- Grupo de Biocalorimetría, Universidad de Pamplona, Pamplona, Colombia
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Matthew T Webster
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Koch JBU, Sim SB, Scheffler B, Geib SM, Smith TA. Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator. G3 (BETHESDA, MD.) 2023; 13:jkad119. [PMID: 37336593 PMCID: PMC10411558 DOI: 10.1093/g3journal/jkad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/08/2023] [Indexed: 06/21/2023]
Abstract
The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a federally listed endangered species. Due to habitat loss and large declines in population size, B. affinis is facing imminent extinction unless human intervention and recovery efforts are implemented. To better understand B. affinis biology and population genetic and genomic landscapes, we sequenced and assembled the B. affinis genome from a single haploid male. Whole genome HiFi sequencing on PacBio coupled with HiC sequencing resulted in a complete and highly contiguous contig assembly that was scaffolded into a chromosomal context, resolving 18 chromosomes distributed across the 365.1 Mb assembly. All material for both HiFi and HiC sequencing was derived from a single abdominal tissue segment from the single male. These assembly results, coupled with the minimal amount of tissue destructively sampled, demonstrate methods for generating contiguous and complete genomic resources for a rare and endangered species with limited material available and highlight the importance of sample preservation. Precise methods and applications of these methods are presented for potential applications in other species with similar limitations in specimen availability and curation considerations.
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Affiliation(s)
- Jonathan Berenguer Uhuad Koch
- Pollinating Insect Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Logan, UT 84341, USA
| | - Sheina B Sim
- Tropical Pest Genetics and Molecular Biology Research Unit, U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Hilo, HI 96720, USA
| | - Brian Scheffler
- Genomics and Bioinformatics Research Unit, Jamie Whitten Delta States Research Center, Agricultural Research Service, U.S. Department of Agriculture, Stoneville, MS 38776, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Hilo, HI 96720, USA
| | - Tamara A Smith
- Minnesota/Wisconsin Ecological Services Field Office, U.S. Fish and Wildlife Service, Bloomington, MN 55425, USA
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Perera OP, Saha S, Glover J, Parys KA, Allen KC, Grozeva S, Kurtz R, Reddy GVP, Johnston JS, Daly M, Swale T. A chromosome scale assembly of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), genome. BMC Res Notes 2023; 16:125. [PMID: 37370172 DOI: 10.1186/s13104-023-06408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVE The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America. Although partial transcriptome data are available for this pest, a genome assembly was not available for this species. This assembly of a high-quality chromosome-length genome of TPB is aimed to develop the genetic resources that can provide the foundation required for advancing research on this species. RESULTS The initial genome of TPB assembled with paired-end nucleotide sequences generated with Illumina technology was scaffolded with Illumina HiseqX reads generated from a proximity ligated (HiC) library to obtain a high-quality genome assembly. The final assembly contained 3963 scaffolds longer than 1 kbp to yield a genome of 599.96 Mbp. The N50 of the TPB genome assembly was 35.64 Mbp and 98.68% of the genome was assembled into 17 scaffolds larger than 1 Mbp. This megabase scaffold number is the same as the number of chromosomes observed in karyotyping of this insect. The TPB genome is known to have high repetitive DNA content, and the reduced assembled genome size compared to flowcytometric estimates of approximately 860 Mbp may be due to the collapsed assembly of highly similar regions.
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Affiliation(s)
- O P Perera
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA.
| | - Surya Saha
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY, 14853, USA
| | - James Glover
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Katherine A Parys
- Pollinator Health in Southern Crop Ecosystems Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - K Clint Allen
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Snejana Grozeva
- Institute of Zoology, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel, Sofia, 1000, Bulgaria
| | - Ryan Kurtz
- , Cotton, Incorporated, Cary, NC, 27513, USA
| | - Gadi V P Reddy
- Southern Insect Management Research Unit, USDA ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Mark Daly
- Dovetail Genomics, LLC, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA
| | - Thomas Swale
- Dovetail Genomics, LLC, 100 Enterprise Way, Suite A101, Scotts Valley, CA, 95066, USA
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