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Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
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Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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Dupuis JR, Judge KA, Brunet BMT, Ohlmann Chan S, Sperling FAH. Does hunger lead to hybridization in a genus of sexually cannibalistic insects (Orthoptera: Prophalangopsidae)? Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Allochronic isolation can be a strong mechanism for reproductive isolation and speciation. However, imperfect allochrony and the expression of phenological plasticity can erode temporal barriers to gene flow and result in hybridization between divergent lineages. Here, we combine behavioural ecology and genomics to investigate this scenario in two closely related species of grigs in the genus Cyphoderris. These species exhibit a unique mating system whereby females feed on the fleshy hind wings of the male during copulation, and copulation with conspecific males is more likely in food-restricted females than in well-fed females. In western Canada, Cyphoderris buckelli and Cyphoderris monstrosa are sympatric but largely allochronically separated, with C. buckelli breeding earlier. However, their breeding seasons can overlap, leading to potential for older C. buckelli females to mate with young C. monstrosa males to obtain resources via sexual cannibalism. We used behavioural assays to test whether female feeding status affects the propensity for interspecific mating between C. buckelli females and C. monstrosa males. We then tested for hybridization and gene exchange in wild populations of both species, using morphology, mitochondrial DNA and genome-wide nuclear markers. We found that interspecific courtship and mating can occur, but the relationship between food restriction and increased propensity for hybridization was not significant. Although we observed intraspecific population genetic structure in both species, we found no signatures of hybridization in the morphological or genetic datasets, which suggests that postmating reproductive barriers might be preventing successful hybridization in the wild.
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Affiliation(s)
- Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, KY, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin A Judge
- Department of Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Bryan M T Brunet
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Shawna Ohlmann Chan
- Department of Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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MacDonald ZG, Dupuis JR, Davis CS, Acorn JH, Nielsen SE, Sperling FAH. Gene flow and climate-associated genetic variation in a vagile habitat specialist. Mol Ecol 2020; 29:3889-3906. [PMID: 32810893 DOI: 10.1111/mec.15604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022]
Abstract
Previous work in landscape genetics suggests that geographic isolation is of greater importance to genetic divergence than variation in environmental conditions. This is intuitive when configurations of suitable habitat are a dominant factor limiting dispersal and gene flow, but has not been thoroughly examined for habitat specialists with strong dispersal capability. Here, we evaluate the effects of geographic and environmental isolation on genetic divergence for a vagile invertebrate with high habitat specificity and a discrete dispersal life stage: Dod's Old World swallowtail butterfly, Papilio machaon dodi. In Canada, P. m. dodi are generally restricted to eroding habitat along major river valleys where their larval host plant occurs. A series of causal and linear mixed effects models indicate that divergence of genome-wide single nucleotide polymorphisms is best explained by a combination of environmental isolation (variation in summer temperatures) and geographic isolation (Euclidean distance). Interestingly, least-cost path and circuit distances through a resistance surface parameterized as the inverse of habitat suitability were not supported. This suggests that, although habitat associations of many butterflies are specific due to reproductive requirements, habitat suitability and landscape permeability are not equivalent concepts due to considerable adult vagility. We infer that divergent selection related to variation in summer temperatures has produced two genetic clusters within P. m. dodi, differing in voltinism and diapause propensity. Within the next century, temperatures are predicted to rise by amounts greater than the present-day difference between regions of the genetic clusters, potentially affecting the persistence of the northern cluster under continued climate change.
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Affiliation(s)
- Zachary G MacDonald
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Corey S Davis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Scott E Nielsen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Dupuis JR, Sperling FAH. Phylogenomic test of mitochondrial clues to archaic ancestors in a group of hybridizing swallowtail butterflies. Mol Phylogenet Evol 2020; 152:106921. [PMID: 32758535 DOI: 10.1016/j.ympev.2020.106921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/05/2020] [Accepted: 07/28/2020] [Indexed: 11/20/2022]
Abstract
Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio machaon group of swallowtail butterflies. This species group contains three hybrid lineages (P. brevicauda, P. joanae, and P. m. kahli) that are geographically disjunct across North America and have complete fixation of a mitochondrial lineage that is otherwise primarily found in P. m. hudsonianus, a boreal subspecies of the Holarctic P. machaon. Genome-wide nuclear markers place the three hybrid lineages as a monophyletic group that is sister to P. polyxenes/P. zelicaon rather than P. machaon, although ancient hybridization between a subspecies of P. machaon and the ancestor of these three lineages is also shown by their greater nuclear affinity to P. m. hudsonianus than to other subspecies of P. machaon. Individuals from contemporary hybrid swarms in Alberta, where mitochondrial DNA fixation has not occurred, were more intermediate between their respective parent species, demonstrating diversity in mito-nuclear discordance following hybrid interactions. Our new phylogenetic findings for the P. machaon species group also include: subspecific paraphyly within P. machaon itself across its Holarctic distribution; paraphyly of P. zelicaon relative to P. polyxenes; and more divergent placement of a Mediterranean species, P. hospiton. These results provide the first comprehensive genomic evaluation of relationships within this species group and provide insight into the evolutionary dynamics of hybridization and mitochondrial introgression.
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Affiliation(s)
- Julian R Dupuis
- Department of Entomology, University of Kentucky, S-225 Ag Science Center North, 1100 South Limestone, Lexington, KY 40546, USA; Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, Alberta T6G 2R3, Canada.
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, Alberta T6G 2R3, Canada.
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Allio R, Scornavacca C, Nabholz B, Clamens AL, Sperling FAH, Condamine FL. Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution. Syst Biol 2019; 69:38-60. [DOI: 10.1093/sysbio/syz030] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/20/2023] Open
Abstract
Abstract
Evolutionary relationships have remained unresolved in many well-studied groups, even though advances in next-generation sequencing and analysis, using approaches such as transcriptomics, anchored hybrid enrichment, or ultraconserved elements, have brought systematics to the brink of whole genome phylogenomics. Recently, it has become possible to sequence the entire genomes of numerous nonbiological models in parallel at reasonable cost, particularly with shotgun sequencing. Here, we identify orthologous coding sequences from whole-genome shotgun sequences, which we then use to investigate the relevance and power of phylogenomic relationship inference and time-calibrated tree estimation. We study an iconic group of butterflies—swallowtails of the family Papilionidae—that has remained phylogenetically unresolved, with continued debate about the timing of their diversification. Low-coverage whole genomes were obtained using Illumina shotgun sequencing for all genera. Genome assembly coupled to BLAST-based orthology searches allowed extraction of 6621 orthologous protein-coding genes for 45 Papilionidae species and 16 outgroup species (with 32% missing data after cleaning phases). Supermatrix phylogenomic analyses were performed with both maximum-likelihood (IQ-TREE) and Bayesian mixture models (PhyloBayes) for amino acid sequences, which produced a fully resolved phylogeny providing new insights into controversial relationships. Species tree reconstruction from gene trees was performed with ASTRAL and SuperTriplets and recovered the same phylogeny. We estimated gene site concordant factors to complement traditional node-support measures, which strengthens the robustness of inferred phylogenies. Bayesian estimates of divergence times based on a reduced data set (760 orthologs and 12% missing data) indicate a mid-Cretaceous origin of Papilionoidea around 99.2 Ma (95% credibility interval: 68.6–142.7 Ma) and Papilionidae around 71.4 Ma (49.8–103.6 Ma), with subsequent diversification of modern lineages well after the Cretaceous-Paleogene event. These results show that shotgun sequencing of whole genomes, even when highly fragmented, represents a powerful approach to phylogenomics and molecular dating in a group that has previously been refractory to resolution.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut de Biologie Computationnelle (IBC), Montpellier, France
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Anne-Laure Clamens
- INRA, UMR 1062 Centre de Biologie pour la Gestion des Populations (INRA, IRD, CIRAD, Montpellier SupAgro), 755 Avenue du Campus Agropolis, 34988 Montferrier-sur-Lez, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Felix AH Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - Fabien L Condamine
- Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, AB, Canada
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Dupuis JR, Cullingham CI, Nielsen SE, Sperling FAH. Environmental effects on gene flow in a species complex of vagile, hilltopping butterflies. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Services, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Scott E Nielsen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Dupuis JR, Bremer FT, Jombart T, Sim SB, Geib SM. mvmapper: Interactive spatial mapping of genetic structures. Mol Ecol Resour 2017; 18:362-367. [PMID: 28987008 DOI: 10.1111/1755-0998.12724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 11/28/2022]
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 visualizing and exploring results of multivariate analyses in geographic space. This tool can be used to map results of virtually any multivariate analysis of georeferenced data, and routines for exporting results from a number of standard methods have been integrated in the R package adegenet, including principal components analysis (PCA), spatial PCA, discriminant analysis of principal components, principal coordinates analysis, nonmetric dimensional scaling and correspondence analysis. mvmapper's greatest strength is facilitating dynamic and interactive exploration of the statistical and geographic frameworks side by side, a task that is difficult and time-consuming with currently available tools. Source code and deployment instructions, as well as a link to a hosted instance of mvmapper, can be found at https://popphylotools.github.io/mvMapper/.
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Affiliation(s)
- Julian R Dupuis
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA.,Department of Plant and Environmental Protection Services, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Forest T Bremer
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA.,Department of Plant and Environmental Protection Services, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Thibaut Jombart
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College, London, UK
| | - Sheina B Sim
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA
| | - Scott M Geib
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Hilo, HI, USA
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