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1. Genomics confirms surprising ecological divergence and isolation in an endangered butterfly

Author:
Scott M. Geib,   et al.   ; Julian R. Dupuis; Kendall H. Osborne; Daniel Rubinoff;     Show all 4 Authors
Source:
Biodiversity and conservation 2020 v.29 no.6 pp. 1897-1921
ISSN:
0960-3115
Subject:
Euphilotes battoides allyni; biodiversity; butterflies; genomics; habitats; phylogeography; California
Abstract:
... Phylogeographic patterns in phytophagous organisms are often contextualized in light of geographic isolation and ecological (host, habitat) specialization. However, assessing the relative impact of these phenomena is not straightforward, even in areas where phylogeography is well-studied, such as the California Floristic Province. Here, we use genome-wide markers to elucidate population genomic an ...
DOI:
10.1007/s10531-020-01950-6

2. Implementing Low-Cost, High Accuracy DNA Barcoding From Single Molecule Sequencing to Screen Larval Tephritid Fruit Flies Intercepted at Ports of Entry

Author:
Scott M. Geib,   et al.   ; Ivonne J. Garzón-Orduña; Lisa Ledezma; Forest T. Bremer; Norman B. Barr;     Show all 5 Authors
Source:
Annals of the Entomological Society of America 2020 v.113 no.4 pp. 288-297
ISSN:
0013-8746
Subject:
DNA; DNA barcoding; Tephritidae; air transportation; fruit flies; fruits; introduced plants; California; Florida
Abstract:
... Exotic fruit flies in the family Tephritidae pose a threat to U.S. agriculture and natural resources. As part of ongoing fruit fly detection and exclusion programs, invasive fruit fly adults are periodically trapped in and introduced populations are eradicated from two major fruit producing states: California and Florida. Although the pathways used by flies to enter these states are not clear, one ...
DOI:
10.1093/aesa/saz071

3. The Genetic Diversity of Bactrocera dorsalis (Diptera: Tephritidae) in China and Neighboring Countries: A Review From Published Studies

Author:
Scott M. Geib,   et al.   ; Ivonne J. Garzón-Orduña; Norman B. Barr;     Show all 3 Authors
Source:
Journal of economic entomology 2019 v.112 no.4 pp. 2001-2006
ISSN:
0022-0493
Subject:
Bactrocera dorsalis; entomology; genetic variation; haplotypes; mitochondria; mitochondrial DNA; population genetics; China
Abstract:
... For more than a decade, various research groups have tracked the population genetics of the oriental fruit fly, Bactrocera dorsalis (Hendel) in China and neighboring countries using mitochondrial cytochrome c oxidase subunit I (COI) DNA. Although most research has reported high levels of mtDNA variation, to date no efforts have been made to integrate and compare the results from these studies simu ...
DOI:
10.1093/jee/toz073

4. Genomic‐wide sequencing reveals remarkable connection between widely disjunct populations of the internationally threatened bog buck moth

Author:
Scott M. Geib,   et al.   ; Julian R. Dupuis; Christian Schmidt; Daniel Rubinoff;     Show all 4 Authors
Source:
Insect conservation and diversity 2020 v.13 no.5 pp. 495-500
ISSN:
1752-458X
Subject:
Hemileuca maia; bogs; data collection; genomics; habitat conservation; habitat fragmentation; inbreeding depression; monophyly; population structure; threatened species; Great Lakes region; New York; Ontario
Abstract:
... Rare, threatened species often suffer from habitat fragmentation, which leads to smaller populations vulnerable to negative impacts including inbreeding depression and collapse of metapopulation dynamics. Therefore, understanding the population structure and relationships of each population of a threatened species is critical for prioritising habitat conservation and reintroduction efforts. The bo ...
DOI:
10.1111/icad.12432

5. Comparative proteomic profiling within each developmental stage of the solanum fruit fly, Bactrocera latifrons Hendel

Author:
Scott M. Geib,   et al.   ; Chiou Ling Chang;     Show all 2 Author
Source:
Journal of Asia-Pacific entomology 2018 v.21 no.4 pp. 1186-1197
ISSN:
1226-8615
Subject:
Bactrocera latifrons; Solanum; databases; developmental stages; environmental factors; epigenetics; fruit flies; gels; gene deletion; gene editing; mass spectrometry; protein synthesis; proteins; proteome; proteomics; transcriptome; two-dimensional gel electrophoresis
Abstract:
... Fruit fly development has been widely studied in details, understanding of “what”, “when”, “where”, “why”, and “how” many hundred thousand proteins exist in an insect cell interact and express during development at molecular level largely remained to be clarified. We conducted proteome mapping in all developmental stages of the solanum fruit fly, Bactrocera latifrons (Hendel), by comparing all age ...
DOI:
10.1016/j.aspen.2018.08.014

6. Population genomic and phenotype diversity of invasive Drosophila suzukii in Hawai‘i

Author:
Scott M. Geib,   et al.   ; Jonathan B. Koch; Julian R. Dupuis; Marcel-Kate Jardeleza; Nadiatou Ouedraogo; Peter A. Follett; Donald K. Price;     Show all 7 Authors
Source:
Biological invasions 2020 v.22 no.5 pp. 1753-1770
ISSN:
1387-3547
Subject:
Drosophila suzukii; altitude; amino acids; cytidine; deamination; genetic variation; genome; genomics; introduced species; phenotype; sodium; statistical analysis
Abstract:
... In the context of evolutionary theory, invasion biology provides a fantastic enigma: how does a species with limited standing genetic variation survive and adapt to a novel environment? Reduced genetic diversity is typically associated with low fitness and evolutionary potential, yet some introduced species have proven to be successful invaders despite undergoing a genetic bottleneck during the ea ...
DOI:
10.1007/s10530-020-02217-5

7. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Author:
Scott M. Geib,   et al.   ; Anna K. Childers; Sheina B. Sim; Monica F. Poelchau; Brad S. Coates; Tyler J. Simmonds; Erin D. Scully; Timothy P. L. Smith; Christopher P. Childers; Renee L. Corpuz; Kevin Hackett; Brian Scheffler;     Show all 12 Authors
Source:
Insects 2021 v.12 no.7 pp. -
ISSN:
2075-4450
Subject:
Agricultural Research Service; Arthropoda; arthropods; bioinformatics; crop production; ecological balance; food security; genome; genome assembly; pests; soil quality
Abstract:
... The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and globa ...
DOI:
10.3390/insects12070626

8. Proteomic interactions between the parasitoid Diachasmimorpha longicaudata and the oriental fruit fly, Bactrocera dorsalis during host parasitism

Author:
Scott M. Geib,   et al.   ; Chiou Ling Chang; Guang Hong Liang;     Show all 3 Authors
Source:
Journal of Asia-Pacific entomology 2018 v.21 no.1 pp. 335-344
ISSN:
1226-8615
Subject:
Bactrocera dorsalis; Diachasmimorpha longicaudata; biological control; early development; fruit flies; gene expression regulation; immunity; larvae; mass spectrometry; metabolism; muscles; parasitism; parasitoids; phosphopyruvate hydratase; proteomics; regulatory proteins; transferrin; two-dimensional gel electrophoresis
Abstract:
... The oriental fruit fly, Bactrocera dorsalis, is an important agricultural pest and biological control is one of the most effective control methodologies. We conducted an investigation on the molecular response of the fruit fly to parasitism by the larval parasitoid, Diachasmimorpha longicaudata using two-dimensional gel electrophoresis and mass spectroscopy. We identified 285 differentially expres ...
DOI:
10.1016/j.aspen.2017.12.002

9. Phylogenomics reveals conservation challenges and opportunities for cryptic endangered species in a rapidly disappearing desert ecosystem

Author:
Scott M. Geib,   et al.   ; Daniel Rubinoff; J. Bradley Reil; Kendall H. Osborne; Christopher J. Gregory; Julian R. Dupuis;     Show all 6 Authors
Source:
Biodiversity and conservation 2020 v.29 no.7 pp. 2185-2200
ISSN:
0960-3115
Subject:
Coleoptera; at-risk population; cryptic species; ecosystems; endangered species; genetic recombination; genome; habitat destruction; habitat fragmentation; habitats; humans; mitochondrial DNA; species diversity; California
Abstract:
... There is growing evidence for the decline of cryptic species across the planet as a result of human activities. Accurate data regarding patterns of poorly known or hard-to-find species diversity is essential for the recognition and conservation of threatened species and ecosystems. Casey’s June beetle Dinacoma caseyi is a federally listed endangered species restricted to the Coachella Valley in so ...
DOI:
10.1007/s10531-020-01968-w

10. Divergent Switchgrass Cultivars Modify Cereal Aphid Transcriptomes

Author:
Scott M. Geib,   et al.   ; Kyle G. Koch; Erin D. Scully; Nathan A. Palmer; Gautam Sarath; Tiffany Heng-Moss; Jeffrey D. Bradshaw;     Show all 7 Authors
Source:
Journal of economic entomology 2020 v.112 no.4 pp. 1887-1901
ISSN:
0022-0493
Subject:
Panicum virgatum; Schizaphis graminum; Sipha flava; bioenergy; cultivars; entomology; growth and development; starvation; transcription (genetics); transcriptome; unigenes
Abstract:
... Schizaphis graminum Rondani (Hemiptera: Aphididae) and Sipha flava Forbes (Hemiptera: Aphididae) are two common pests of bioenergy grasses. Despite the fact that they are both considered generalists, they differ in their ability to colonize Panicum virgatum cultivars. For example, S. flava colonizes both P. virgatum cv. Summer and P. virgatum cv. Kanlow whereas S. graminum can only colonize Summer ...
DOI:
10.1093/jee/toz053

11. Comparative rearing parameters for bisexual and genetic sexing strains of Zeugodacus cucurbitae and Bactrocera dorsalis (Diptera: Tephritidae) on an artificial diet

Author:
Scott M. Geib,   et al.   ; Thomas J. Fezza; Todd E. Shelly;     Show all 3 Authors
Source:
Journal of Asia-Pacific entomology 2018 v.21 no.1 pp. 283-287
ISSN:
1226-8615
Subject:
Bactrocera dorsalis; adults; artificial diets; color; eclosion; egg production; eggs; females; flight; genetic engineering; larvae; male sterility; males; pests; pupae; rearing; sex determination analysis; sterile insect technique
Abstract:
... The Sterile Insect Technique (SIT) is an important component of area wide programs to control invading or established populations of pestiferous tephritids. The SIT involves the production, sterilization, and release of large numbers of the target species, with the goal of obtaining sterile male x wild female matings, which yield infertile eggs. A major advance in SIT involved sex-linked, genetic ...
DOI:
10.1016/j.aspen.2018.01.007

12. mvmapper: Interactive spatial mapping of genetic structures

Author:
Scott M. Geib,   et al.   ; Julian R. Dupuis; Forest T. Bremer; Thibaut Jombart; Sheina B. Sim;     Show all 5 Authors
Source:
Molecular ecology resources 2018 v.18 no.2 pp. 362-367
ISSN:
1755-098X
Subject:
correspondence analysis; discriminant analysis; genetic variation; georeferencing; multidimensional scaling; multivariate analysis; population genetics; principal component analysis; spatial data
Abstract:
... Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata are not always easily integrated into these methods in a user‐friendly fashion. Here, we present a deployable Python‐based web‐tool, mvmapper, for vi ...
DOI:
10.1111/1755-0998.12724

13. Targeted amplicon sequencing of 40 nuclear genes supports a single introduction and rapid radiation of Hawaiian Metrosideros (Myrtaceae)

Author:
Scott M. Geib,   et al.   ; Julian R. Dupuis; Yohan Pillon; Tomoko Sakishima; Chrissen E. C. Gemmill; Srikar Chamala; W. Brad Barbazuk; Elizabeth A. Stacy;     Show all 8 Authors
Source:
Plant systematics and evolution 2019 v.305 no.10 pp. 961-974
ISSN:
0378-2697
Subject:
Metrosideros; biogeography; chloroplasts; data collection; genes; genetic variation; geographical distribution; molecular systematics; monophyly; morphs; plant taxonomy
Abstract:
... Compared to traditionally used plastid or ribosomal markers, nuclear gene markers provide many advantages for molecular systematics of plants, and high-throughput sequencing technologies are making large nuclear datasets available at an unprecedented rate. We used targeted amplicon sequencing of 44 nuclear genes to construct a time-calibrated phylogeny of genus Metrosideros (Myrtaceae), evaluate r ...
DOI:
10.1007/s00606-019-01615-0

14. Phylogenomics supports incongruence between ecological specialization and taxonomy in a charismatic clade of buck moths

Author:
Scott M. Geib,   et al.   ; Julian R. Dupuis; Richard S. Peigler; Daniel Rubinoff;     Show all 4 Authors
Source:
Molecular ecology 2018 v.27 no.22 pp. 4417-4429
ISSN:
0962-1083
Subject:
Hemileuca maia; biogeography; gene flow; genetic variation; genomics; geographical distribution; habitats; herbivores; host plants; models; moths; population structure; single nucleotide polymorphism; taxon descriptions; North America
Abstract:
... Local adaptation can be a fundamental component of speciation, but its dynamics in relation to gene flow are not necessarily straightforward. Herbivorous taxa with localized host plant or habitat specialization across their geographic range are ideal models for investigating the patterns and constraints of local adaptation and its impact on diversification. The charismatic, day‐flying moths of the ...
DOI:
10.1111/mec.14883
CHORUS:
10.1111/mec.14883

15. Contrasting diets reveal the metabolic plasticity of the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)

Author:
Scott M. Geib,   et al.   ; Charles J. Mason; Erin D. Scully; Kelli Hoover;     Show all 4 Authors
Source:
Scientific Reports 2016 v.6 no. pp. 1-13
Subject:
Acer saccharum subsp. saccharum; Anoplophora glabripennis; aerobiosis; artificial diets; biogeochemical cycles; cytochrome-c oxidase; gene expression; gene expression regulation; genes; hardwood; host plants; insect larvae; insect pests; midgut; mitochondria; plant-insect relations; protein degradation; proteins; symbionts; trees
Abstract:
... Wood-feeding insects encounter challenging diets containing low protein quantities, recalcitrant carbohydrate sources, and plant defensive compounds. The Asian longhorned beetle (Anoplophora glabripennis) is a wood-feeding insect that attacks and kills a diversity of hardwood tree species. We compared gene expression of midguts collected from larvae feeding in a preferred tree, sugar maple, to tho ...
Handle:
10113/63266
DOI:
10.1038/srep33813
PubMed:
27654346
PubMed Central:
PMC5031968

16. Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: Resistance to biological control catalyses resurgence of an old pest

Author:
Scott M. Geib,   et al.   ; Jonathan Bradley Reil; Camiel Doorenweerd; Michael San Jose; Sheina B. Sim; Daniel Rubinoff;     Show all 6 Authors
Source:
Molecular ecology 2018 v.27 no.22 pp. 4459-4474
ISSN:
0962-1083
Subject:
Oryctes rhinoceros; biological control; biological control agents; biotypes; catalytic activity; chemical control; computer software; data collection; ecosystems; environmental impact; indigenous species; invasive species; loci; metagenomics; phylogeny; pipelines; quarantine; Pacific Ocean Islands
Abstract:
... Biological control agents have several advantages over chemical control for pest management, including the capability to restore ecosystem balance with minimal non‐target effects and a lower propensity for targets to develop resistance. These factors are particularly important for invasive species control. The coconut rhinoceros beetle (Oryctes rhinoceros Linnaeus) is a major palm pest that invade ...
DOI:
10.1111/mec.14879
CHORUS:
10.1111/mec.14879

17. Identification of a carboxylesterase associated with resistance to naled in Bactrocera dorsalis (Hendel)

Author:
Scott M. Geib,   et al.   ; Po-Kai Hsu; Li-Hsin Huang; Ju-Chun Hsu;     Show all 4 Authors
Source:
Pesticide biochemistry and physiology 2016 v.131 pp. 24-31
ISSN:
0048-3575
Subject:
Bactrocera dorsalis; Drosophila melanogaster; amino acids; carboxylesterase; complementary DNA; databases; genes; naled; open reading frames; phylogeny; polyacrylamide gel electrophoresis; quantitative polymerase chain reaction; rapid amplification of cDNA ends; staining
Abstract:
... Compared to other organophosphate-resistant and -susceptible (S) lines of Bactrocera dorsalis, the carboxylesterase (CBE) BdE5 in the naled-resistant (nal-r) line has been found to possess remarkable quantitative elevation. Our study attempts to identify the role of BdE5 in naled resistance, and we discovered several points of interest. Firstly, activity staining on native PAGE revealed that the p ...
DOI:
10.1016/j.pestbp.2016.02.001

18. A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

Author:
Scott M. Geib,   et al.   ; Sarah B. Kingan; Julie Urban; Christine C. Lambert; Primo Baybayan; Anna K. Childers; Brad Coates; Brian Scheffler; Kevin Hackett; Jonas Korlach;     Show all 10 Authors
Source:
GigaScience 2019 v.8 no.10 pp. 1-10
ISSN:
2047-217X
Subject:
DNA; DNA fragmentation; Lycorma delicatula; adults; diploidy; endangered species; females; genes; genome assembly; haplotypes; invasive species; symbionts
Abstract:
... A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on ma ...
DOI:
10.1093/gigascience/giz122
CHORUS:
10.1093/gigascience/giz122

19. Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)

Author:
Scott M. Geib,   et al.   ; Erin D. Scully; Charles J. Mason; John E. Carlson; Ming Tien; Han-Yi Chen; Scott Harding; Chung-Jui Tsai; Kelli Hoover;     Show all 9 Authors
Source:
Scientific reports 2018 v.8 no.9620 pp. 1-16
ISSN:
2045-2322
Subject:
Acer; Anoplophora glabripennis; Populus nigra; Populus tomentosa; bacterial communities; beta-glucosidase; broadleaved trees; community structure; digestion; gene expression; gene expression regulation; genome; host plants; insect cuticle; intestinal microorganisms; metabolic detoxification; midgut; plant-insect relations; species richness; symbionts; transcriptome; tremulacin
Abstract:
... Polyphagous insect herbivores have multiple mechanisms in place to overcome the dietary challenges of feeding in multiple plant species including, but not limited to, transcriptional plasticity and associations with obligate or facultative symbionts. The Asian longhorned beetle (Anoplophora glabripennis) is a polyphagous wood-feeder capable of developing on over 100 broadleaf tree species and, lik ...
Handle:
10113/6743194
DOI:
10.1038/s41598-018-27476-0
PubMed:
29942001
PubMed Central:
PMC6018227

20. HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

Author:
Scott M. Geib,   et al.   ; Julian R. Dupuis; Forest T. Bremer; Angela Kauwe; Michael San Jose; Luc Leblanc; Daniel Rubinoff;     Show all 7 Authors
Source:
Molecular ecology resources 2018 v.18 no.5 pp. 1000-1019
ISSN:
1755-098X
Subject:
Dacus; bioinformatics; data collection; fruit flies; genomics; high-throughput nucleotide sequencing; insect pests; loci; phylogeny; transcriptomics
Abstract:
... High‐throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50‐ to 100‐fold more loci than those generated using traditional Sanger sequencing‐based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single‐tube, highly multiplexed amplicon sequencing, which we name HiMAP ...
DOI:
10.1111/1755-0998.12783
CHORUS:
10.1111/1755-0998.12783
Chorus Open Access:
10.1111/1755-0998.12783