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Campbell P, Arévalo L, Martin H, Chen C, Sun S, Rowe AH, Webster MS, Searle JB, Pasch B. Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice ( Onychomys). Ecol Evol 2019; 9:12886-12896. [PMID: 31788222 PMCID: PMC6875671 DOI: 10.1002/ece3.5770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long-distance acoustic signals to attract and localize mates; Onychomys arenicola and Onychomys torridus are acoustically similar and morphologically cryptic whereas Onychomys leucogaster is larger and acoustically distinct. We used genotyping-by-sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, laboratory crosses between O. torridus and O. arenicola produced litters whereas O. leucogaster and O. arenicola crosses did not. Call fundamental frequency in O. torridus and O. arenicola was indistinguishable in allopatry but significantly differentiated in sympatry, a pattern consistent with reproductive character displacement. These results suggest that assortative mating based on a long-distance signal is an important isolating mechanism between O. torridus and O. arenicola and highlight the importance of behavioral barriers in determining the permeability of species boundaries.
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Affiliation(s)
- Polly Campbell
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California, RiversideRiversideCAUSA
| | - Lena Arévalo
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Developmental PathologyUniversity of BonnBonnGermany
| | - Heather Martin
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
| | - Charles Chen
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
| | - Shuzhen Sun
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Forest and Conservation SciencesForest Science CentreThe University of British ColumbiaVancouverBCCanada
| | - Ashlee H. Rowe
- Department of BiologyThe University of OklahomaNormanOKUSA
| | - Michael S. Webster
- Macaulay LibraryCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Department of Neurobiology and BehaviorCornell UniversityIthacaNYUSA
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Bret Pasch
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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Naidenov B, Lim A, Willyerd K, Torres NJ, Johnson WL, Hwang HJ, Hoyt P, Gustafson JE, Chen C. Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia. Front Microbiol 2019; 10:1446. [PMID: 31333599 PMCID: PMC6622151 DOI: 10.3389/fmicb.2019.01446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/07/2019] [Indexed: 01/21/2023] Open
Abstract
The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and E. meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations (MICs) for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies (ONT) and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning (ML) algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84, respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75, and 0.54, respectively. By producing two sets of quality biological predictors, pan-genome genes and core-genome SNPs, from long-read sequence data and applying an ensemble of ML techniques, our results demonstrated that accurate phenotypic inference, at multiple AMR resolutions, can be achieved.
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Affiliation(s)
- Bryan Naidenov
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Alexander Lim
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Karyn Willyerd
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Nathanial J. Torres
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - William L. Johnson
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Hong Jin Hwang
- 110F Henry Bellmon Research Center, Bioinformatics Graduate Certificate Program and Genomics Core Facility, Oklahoma State University, Stillwater, OK, United States
| | - Peter Hoyt
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
- 110F Henry Bellmon Research Center, Bioinformatics Graduate Certificate Program and Genomics Core Facility, Oklahoma State University, Stillwater, OK, United States
| | - John E. Gustafson
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
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