1
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Kagawa O, Hirota SK, Saito T, Uchida S, Watanabe H, Miyazoe R, Yamaguchi T, Matsuno T, Araki K, Wakasugi H, Suzuki S, Kobayashi G, Miyazaki H, Suyama Y, Hanyuda T, Chiba S. Host-Shift Speciation Proceeded with Gene Flow in Algae Covering Shells. Am Nat 2023; 202:721-732. [PMID: 37963116 DOI: 10.1086/726221] [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] [Indexed: 11/16/2023]
Abstract
AbstractHost shifts represent the advancement of a novel niche and often lead to speciation in symbionts. However, its mechanisms are not well understood. Here, we focused on the alga Pseudocladophora conchopheria growing on the shells of intertidal snails. Previous surveys have shown that the alga has host specificity-only attaching to the shell of Lunella correensis-but we discovered that the alga attaches to the shells of multiple sympatric snails. A genome-wide single-nucleotide polymorphism analysis (MIG-seq) was performed to determine whether host-associated speciation occurred in the algae. As a result, there was no gene flow or limited gene flow among the algae from different hosts, and some algae were genetically differentiated among hosts. In addition, the demographic estimate revealed that speciation with gene flow occurred between the algae from different hosts. Therefore, these results support the idea that host-shift speciation gradually proceeded with gene flow in the algae, providing insight into the early evolution of host shifts.
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2
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Lackey ACR, Murray AC, Mirza NA, Powell THQ. The role of sexual isolation during rapid ecological divergence: Evidence for a new dimension of isolation in Rhagoletis pomonella. J Evol Biol 2023. [PMID: 37173822 DOI: 10.1111/jeb.14179] [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: 05/03/2022] [Revised: 03/05/2023] [Accepted: 03/23/2023] [Indexed: 05/15/2023]
Abstract
The pace of divergence and likelihood of speciation often depends on how and when different types of reproductive barriers evolve. Questions remain about how reproductive isolation evolves after initial divergence. We tested for the presence of sexual isolation (reduced mating between populations due to divergent mating preferences and traits) in Rhagoletis pomonella flies, a model system for incipient ecological speciation. We measured the strength of sexual isolation between two very recently diverged (~170 generations) sympatric populations, adapted to different host fruits (hawthorn and apple). We found that flies from both populations were more likely to mate within than between populations. Thus, sexual isolation may play an important role in reducing gene flow allowed by early-acting ecological barriers. We also tested how warmer temperatures predicted under climate change could alter sexual isolation and found that sexual isolation was markedly asymmetric under warmer temperatures - apple males and hawthorn females mated randomly while apple females and hawthorn males mated more within populations than between. Our findings provide a window into the early speciation process and the role of sexual isolation after initial ecological divergence, in addition to examining how environmental conditions could shape the likelihood of further divergence.
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Affiliation(s)
- Alycia C R Lackey
- University of Louisville, Louisville, Kentucky, USA
- Binghamton University, Binghamton, New York, USA
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3
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Briševac D, Peralta CM, Kaiser TS. An oligogenic architecture underlying ecological and reproductive divergence in sympatric populations. eLife 2023; 12:82825. [PMID: 36852479 PMCID: PMC9977317 DOI: 10.7554/elife.82825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The evolutionary trajectories and genetic architectures underlying ecological divergence with gene flow are poorly understood. Sympatric timing types of the intertidal insect Clunio marinus (Diptera) from Roscoff (France) differ in lunar reproductive timing. One type reproduces at full moon, the other at new moon, controlled by a circalunar clock of yet unknown molecular nature. Lunar reproductive timing is a magic trait for a sympatric speciation process, as it is both ecologically relevant and entails assortative mating. Here, we show that the difference in reproductive timing is controlled by at least four quantitative trait loci (QTL) on three different chromosomes. They are partly associated with complex inversions, but differentiation of the inversion haplotypes cannot explain the different phenotypes. The most differentiated locus in the entire genome, with QTL support, is the period locus, implying that this gene could not only be involved in circadian timing but also in lunar timing. Our data indicate that magic traits can be based on an oligogenic architecture and can be maintained by selection on several unlinked loci.
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Affiliation(s)
- Dušica Briševac
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary BiologyPloenGermany
| | - Carolina M Peralta
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary BiologyPloenGermany
| | - Tobias S Kaiser
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary BiologyPloenGermany
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4
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Zhang J, Chai X, Zhao F, Hou G, Meng Q. Food Applications and Potential Health Benefits of Hawthorn. Foods 2022; 11:foods11182861. [PMID: 36140986 PMCID: PMC9498108 DOI: 10.3390/foods11182861] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Hawthorn (Crataegus) is a plant of the Rosaceae family and is widely grown throughout the world as one of the medicinal and edible plants, known as the “nutritious fruit” due to its richness in bioactive substances. Preparations derived from it are used in the formulation of dietary supplements, functional foods, and pharmaceutical products. Rich in amino acids, minerals, pectin, vitamin C, chlorogenic acid, epicatechol, and choline, hawthorn has a high therapeutic and health value. Many studies have shown that hawthorn has antioxidant, anti-inflammatory, anticancer, anti-cardiovascular disease, and digestive enhancing properties. This is related to its bioactive components such as polyphenols (chlorogenic acid, proanthocyanidin B2, epicatechin), flavonoids (proanthocyanidins, mucoxanthin, quercetin, rutin), and pentacyclic triterpenoids (ursolic acid, hawthornic acid, oleanolic acid), which are also its main chemical constituents. This paper briefly reviews the chemical composition, nutritional value, food applications, and the important biological and pharmacological activities of hawthorn. This will contribute to the development of functional foods or nutraceuticals from hawthorn.
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Affiliation(s)
- Juan Zhang
- Department of Key Laboratory of Molecular Pharmacology and Drug Evaluation, School of Pharmacy, Yantai University, Yantai 264005, China
| | - Xiaoyun Chai
- Department of Organic Chemistry, School of Pharmacy, Naval Medical University, Shanghai 200433, China
- Correspondence: (X.C.); (Q.M.)
| | - Fenglan Zhao
- Department of Key Laboratory of Molecular Pharmacology and Drug Evaluation, School of Pharmacy, Yantai University, Yantai 264005, China
| | - Guige Hou
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Qingguo Meng
- Department of Key Laboratory of Molecular Pharmacology and Drug Evaluation, School of Pharmacy, Yantai University, Yantai 264005, China
- Correspondence: (X.C.); (Q.M.)
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5
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Kunerth HD, Bogdanowicz SM, Searle JB, Harrison RG, Coates BS, Kozak GM, Dopman EB. Consequences of coupled barriers to gene flow for the build-up of genomic differentiation. Evolution 2022; 76:985-1002. [PMID: 35304922 DOI: 10.1111/evo.14466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023]
Abstract
Theory predicts that when different barriers to gene flow become coincident, their joint effects enhance reproductive isolation and genomic divergence beyond their individual effects, but empirical tests of this "coupling" hypothesis are rare. Here, we analyze patterns of gene exchange among populations of European corn borer moths that vary in the number of acting barriers, allowing for comparisons of genomic variation when barrier traits or loci are in coincident or independent states. We find that divergence is mainly restricted to barrier loci when populations differ by a single barrier, whereas the coincidence of temporal and behavioral barriers is associated with divergence of two chromosomes harboring barrier loci. Furthermore, differentiation at temporal barrier loci increases in the presence of behavioral divergence and differentiation at behavioral barrier loci increases in the presence of temporal divergence. Our results demonstrate how the joint action of coincident barrier effects leads to levels of genomic differentiation that far exceed those of single barriers acting alone, consistent with theory arguing that coupling allows indirect selection to combine with direct selection and thereby lead to a stronger overall barrier to gene flow. Thus, the state of barriers-independent or coupled-strongly influences the accumulation of genomic differentiation.
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Affiliation(s)
- Henry D Kunerth
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Brad S Coates
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, Iowa, 50011
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, 02747, USA.,Department of Biology, Tufts University, Medford, Massachusetts, 02155
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
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6
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Yee WL, Goughnour RB, Forbes AA, Milnes JM, Feder JL. Sensitivities to Chill Durations and No-Chill Temperatures Regulating Eclosion Responses Differ Between Rhagoletis zephyria (Diptera: Tephritidae) and its Braconid Parasitoids (Hymenoptera: Braconidae). ENVIRONMENTAL ENTOMOLOGY 2022; 51:440-450. [PMID: 35137031 DOI: 10.1093/ee/nvac009] [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: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Seasonal temperatures select for eclosion timing of temperate insects and their parasitoids. In western North America, the fruit fly Rhagoletis zephyria Snow (Diptera: Tephritidae) is parasitized by the hymenopterous wasps Utetes lectoides (Gahan), an egg parasite, and Opius downesi Gahan, a larval parasite (both Braconidae). Eclosion of wasps should be timed with the presence of susceptible fly stages, but reports indicate U. lectoides ecloses in the absence of flies under no-chill conditions. Based on this, we tested the hypotheses that chill durations and no-chill temperatures both differentially regulate eclosion times of R. zephyria and its parasitic wasps. When fly puparia were chilled at ~3°C for 130-180 d, U. lectoides and O. downesi always eclosed on average later than flies. However, after 180-d chill, flies eclosed on average earlier than after 130- and 150-d chill, whereas eclosion times of U. lectoides and O. downesi were less or not affected by chill duration. When fly puparia were exposed to 20-22°C (no chill), U. lectoides eclosed before flies, with 88.9% of U. lectoides versus only 0.61% of flies eclosing. Taken together, findings show that eclosion times of flies are more sensitive to changes in chill duration than those of wasps. Flies are less sensitive than wasps to no-chill in that most flies do not respond by eclosing after no-chill while most wasps do. Our results suggest that shorter winters and longer summers due to climate change could cause mismatches in eclosion times of flies and wasps, with potentially significant evolutionary consequences.
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Affiliation(s)
- Wee L Yee
- USDA-ARS, Temperate Tree Fruit & Vegetable Research Unit, 5230 Konnowac Pass Road, Wapato, WA 98951, USA
| | - Robert B Goughnour
- Washington State University Extension, 1919 NE 78th Street, Vancouver, WA 98665, USA
| | - Andrew A Forbes
- Department of Biology, the University of Iowa, 434A Biology Building, Iowa City, IA 52242, USA
| | - Joshua M Milnes
- Washington State Department of Agriculture - Plant Protection Division, 21 North 1st Avenue, Suite 103, Yakima, WA 98902, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, Galvin Life Sciences Building, University of Notre Dame, Notre Dame, IN 46556, USA
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7
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Smith JJ, Brzezinski P, Dziedziula J, Rosenthal E, Klaus M. Partial Ribosomal Nontranscribed Spacer Sequences Distinguish Rhagoletis zephyria (Diptera: Tephritidae) From the Apple Maggot, R. pomonella. JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:647-661. [PMID: 35048980 PMCID: PMC9007244 DOI: 10.1093/jee/toab264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 06/14/2023]
Abstract
The apple maggot, Rhagoletis pomonella (Walsh), was introduced into the apple-growing regions of the Pacific Northwest in the U.S.A. during the past 60-100 yr. Apple maggot (larvae, puparia, and adults) is difficult to distinguish from its morphologically similar sister species, Rhagoletis zephyria Snow, which is native and abundant in the Pacific Northwest. While morphological identifications are common practice, a simple, inexpensive assay based on genetic differences would be very useful when morphological traits are unclear. Here we report nucleotide substitution and insertion-deletion mutations in the nontranscribed spacer (NTS) of the ribosomal RNA gene cistron of R. pomonella and R. zephyria that appear to be diagnostic for these two fly species. Insertion-deletion variation is substantial and results in a 49 base-pair difference in PCR amplicon size between R. zephyria and R. pomonella that can be scored using agarose gel electrophoresis. PCR amplification and DNA sequencing of 766 bp of the NTS region from 38 R. pomonella individuals and 35 R. zephyria individuals from across their geographic ranges led to the expected PCR fragments of approx. 840 bp and 790 bp, respectively, as did amplification and sequencing of a smaller set of 26 R. pomonella and 16 R. zephyria flies from a sympatric site in Washington State. Conversely, 633 bp mitochondrial COI barcode sequences from this set of flies were polyphyletic with respect to R. pomonella and R. zephyria. Thus, differences in NTS PCR products on agarose gels potentially provide a simple way to distinguish between R. pomonella and R. zephyria.
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Affiliation(s)
- J J Smith
- Department of Entomology, Michigan State University, 244 Farm Lane, Room 243, Michigan State University, East Lansing, MI 48825-1115, USA
- Lyman Briggs College, Michigan State University, 919 E. Shaw Lane, Room E-35, East Lansing, MI 48825-3804, USA
| | - P Brzezinski
- Lyman Briggs College, Michigan State University, 919 E. Shaw Lane, Room E-35, East Lansing, MI 48825-3804, USA
| | - J Dziedziula
- Lyman Briggs College, Michigan State University, 919 E. Shaw Lane, Room E-35, East Lansing, MI 48825-3804, USA
| | - E Rosenthal
- Lyman Briggs College, Michigan State University, 919 E. Shaw Lane, Room E-35, East Lansing, MI 48825-3804, USA
| | - M Klaus
- Plant Protection Division, Washington State Department of Agriculture, 21 North 1st Avenue Suite 103, Yakima, WA 98902, USA
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8
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The Build-Up of Population Genetic Divergence along the Speciation Continuum during a Recent Adaptive Radiation of Rhagoletis Flies. Genes (Basel) 2022; 13:genes13020275. [PMID: 35205320 PMCID: PMC8872456 DOI: 10.3390/genes13020275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 02/05/2023] Open
Abstract
New species form through the evolution of genetic barriers to gene flow between previously interbreeding populations. The understanding of how speciation proceeds is hampered by our inability to follow cases of incipient speciation through time. Comparative approaches examining different diverging taxa may offer limited inferences, unless they fulfill criteria that make the comparisons relevant. Here, we test for those criteria in a recent adaptive radiation of the Rhagoletis pomonella species group (RPSG) hypothesized to have diverged in sympatry via adaptation to different host fruits. We use a large-scale population genetic survey of 1568 flies across 33 populations to: (1) detect on-going hybridization, (2) determine whether the RPSG is derived from the same proximate ancestor, and (3) examine patterns of clustering and differentiation among sympatric populations. We find that divergence of each in-group RPSG taxon is occurring under current gene flow, that the derived members are nested within the large pool of genetic variation present in hawthorn-infesting populations of R. pomonella, and that sympatric population pairs differ markedly in their degree of genotypic clustering and differentiation across loci. We conclude that the RPSG provides a particularly robust opportunity to make direct comparisons to test hypotheses about how ecological speciation proceeds despite on-going gene flow.
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9
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Aguirre-Ramirez E, Velasco-Cuervo S, Toro-Perea N. Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature. INSECTS 2021; 12:1116. [PMID: 34940204 PMCID: PMC8704581 DOI: 10.3390/insects12121116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/23/2022]
Abstract
Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants-Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae-in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.
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Affiliation(s)
- Elkin Aguirre-Ramirez
- Grupo de Estudios Ecogenéticos y Biología Molecular, Departamento de Biología, Universidad del Valle, Cali 760032, Colombia; (S.V.-C.); (N.T.-P.)
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10
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Nickel J, Schell T, Holtzem T, Thielsch A, Dennis SR, Schlick-Steiner BC, Steiner FM, Möst M, Pfenninger M, Schwenk K, Cordellier M. Hybridization Dynamics and Extensive Introgression in the Daphnia longispina Species Complex: New Insights from a High-Quality Daphnia galeata Reference Genome. Genome Biol Evol 2021; 13:6448229. [PMID: 34865004 PMCID: PMC8695838 DOI: 10.1093/gbe/evab267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/02/2023] Open
Abstract
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further resequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.
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Affiliation(s)
- Jana Nickel
- Institute of Zoology, Universität Hamburg, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tania Holtzem
- Department of Ecology, University of Innsbruck, Austria
| | - Anne Thielsch
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Stuart R Dennis
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | | | | | - Markus Möst
- Department of Ecology, University of Innsbruck, Austria
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.,IoME, Gutenberg University, Mainz, Germany
| | - Klaus Schwenk
- Molecular Ecology, Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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11
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Calvert MB, Doellman MM, Feder JL, Hood GR, Meyers P, Egan SP, Powell THQ, Glover MM, Tait C, Schuler H, Berlocher SH, Smith JJ, Nosil P, Hahn DA, Ragland GJ. Genomically correlated trait combinations and antagonistic selection contributing to counterintuitive genetic patterns of adaptive diapause divergence in Rhagoletis flies. J Evol Biol 2021; 35:146-163. [PMID: 34670006 DOI: 10.1111/jeb.13952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 11/27/2022]
Abstract
Adaptation to novel environments can result in unanticipated genomic responses to selection. Here, we illustrate how multifarious, correlational selection helps explain a counterintuitive pattern of genetic divergence between the recently derived apple- and ancestral hawthorn-infesting host races of Rhagoletis pomonella (Diptera: Tephritidae). The apple host race terminates diapause and emerges as adults earlier in the season than the hawthorn host race, to coincide with the earlier fruiting phenology of their apple hosts. However, alleles at many loci associated with later emergence paradoxically occur at higher frequencies in sympatric populations of the apple compared to the hawthorn race. We present genomic evidence that historical selection over geographically varying environmental gradients across North America generated genetic correlations between two life history traits, diapause intensity and diapause termination, in the hawthorn host race. Moreover, the loci associated with these life history traits are concentrated in genomic regions in high linkage disequilibrium (LD). These genetic correlations are antagonistic to contemporary selection on local apple host race populations that favours increased initial diapause depth and earlier, not later, diapause termination. Thus, the paradox of apple flies appears due, in part, to pleiotropy or linkage of alleles associated with later adult emergence and increased initial diapause intensity, the latter trait strongly selected for by the earlier phenology of apples. Our results demonstrate how understanding of multivariate trait combinations and the correlative nature of selective forces acting on them can improve predictions concerning adaptive evolution and help explain seemingly counterintuitive patterns of genetic diversity in nature.
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Affiliation(s)
- McCall B Calvert
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, USA
| | - Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.,Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana, USA.,Advanced Diagnostics and Therapeutics Initiative, University of Notre Dame, Notre Dame, Indiana, USA
| | - Glen R Hood
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.,Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Peter Meyers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Scott P Egan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.,Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana, USA.,Advanced Diagnostics and Therapeutics Initiative, University of Notre Dame, Notre Dame, Indiana, USA.,Department of Biosciences, Rice University, Houston, Texas, USA
| | - Thomas H Q Powell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.,Department of Biological Sciences, Binghamton University (State University of New York), Binghamton, New York, USA
| | - Mary M Glover
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Cheyenne Tait
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Hannes Schuler
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Bozen, Italy
| | - Stewart H Berlocher
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - James J Smith
- Department of Entomology, Lyman Briggs College, Michigan State University, East Lansing, Michigan, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,CEFE, CNRS, EPHE, IRD, Univ Montpellier, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Daniel A Hahn
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.,Advanced Diagnostics and Therapeutics Initiative, University of Notre Dame, Notre Dame, Indiana, USA
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12
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Yee WL, Forbes AA, Feder JL. Contrast in Post-Chill Eclosion Time Strategies Between Two Specialist Braconid Wasps (Hymenoptera: Braconidae) Attacking Rhagoletis Flies (Diptera: Tephritidae) in Western North America. ENVIRONMENTAL ENTOMOLOGY 2021; 50:1173-1186. [PMID: 34387323 DOI: 10.1093/ee/nvab080] [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: 03/02/2021] [Indexed: 06/13/2023]
Abstract
Parasitoids comprise a speciose insect group, displaying a wide array of life history strategies. In the Pacific Northwest of the United States, the tephritid fruit flies Rhagoletis tabellaria (Fitch) and Rhagoletis indifferens Curran infest red osier dogwood, Cornus sericea L. (Cornaceae), and bitter cherry, Prunus emarginata (Douglas ex Hooker) Eaton (Rosaceae), respectively. The flies are parasitized by different braconid wasps at different life stages; Utetes tabellariae (Fischer) oviposits into R. tabellaria eggs, whereas Diachasma muliebre (Muesebeck) oviposits into R. indifferens larvae feeding in cherries. Because Rhagoletis only have one major generation a year and the wasps attack temporally distinct fly life stages, we predicted that eclosion times of U. tabellariae should more closely follow that of its host than the larval-attacking D. muliebre. As predicted, U. tabellariae eclosed on average 6.0-12.5 d later than R. tabellaria, whereas D. muliebre eclosed on average 32.1 d after R. indifferens. Unexpectedly, however, longer chill duration differentially affected the systems; longer overwinters minimally influenced eclosion times of R. tabellaria and U. tabellariae but caused earlier eclosion of both R. indifferens and D. muliebre. Results imply that in temperate regions, diapause timing in braconid wasps evolves in response to both host life stage attacked and fly eclosion characteristics, possibly reflecting differential effects of winter on host plant fruiting phenology. Differences in phenological sensitivity of the lower host plant trophic level to variation in environmental conditions may have cascading effects, sequentially and differentially affecting eclosion times in higher frugivore (fly) and parasitoid (wasp) trophic levels.
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Affiliation(s)
- Wee L Yee
- USDA-ARS, Temperate Tree Fruit and Vegetable Research Unit, 5230 Konnowac Pass Rd, Wapato, WA 98951, USA
| | - Andrew A Forbes
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Jeffrey L Feder
- Department Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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13
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Neven LG, Wakie T, Yee WL. The Eclosion of Rhagoletis pomonella (Diptera: Tephritidae) Under Different Chill Durations and Simulated Temperate and Tropical Conditions. ENVIRONMENTAL ENTOMOLOGY 2021; 50:706-712. [PMID: 33822024 DOI: 10.1093/ee/nvab018] [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: 10/27/2020] [Indexed: 06/12/2023]
Abstract
The apple maggot fly, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae), is a serious pest of apple in North America that is subject to quarantine measures to prevent its spread to currently pest-free regions, including the tropics. How the fly may survive in warmer climates is unclear. Here, we studied the effects of exposing postchill puparia to simulated temperate and tropical environmental conditions on eclosion of R. pomonella from Washington State, U.S.A. Puparia were chilled for 0-30 wk at 3°C and then held under four postchill conditions: A = 23°C, 16:8 L:D, 40% RH; B = 26°C, 12:12 L:D, 80% RH; C = 26°C, 16:8 L:D, 80% RH; and D = 23°C, 12:12 L:D, 40% RH, with B and D representing tropical conditions and A and C temperate conditions. Within each chill duration, total numbers of flies eclosed were equally high in tropical treatment B and temperate treatment C, while they were lower in treatments A and D. Mean weeks of the first eclosion in treatments B and C were earlier than in treatment D; mean week of peak eclosion and 50% eclosion in treatments A, B, and C were earlier than in treatment D. Eclosion spans in treatments A, B, and D were generally shorter than in treatment C. Results suggest that if introduced into a humid tropical country, R. pomonella puparia from Washington State could produce adult flies, regardless of chill duration or lack of chilling during the pupal stage, but whether flies could establish there would require further study.
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Affiliation(s)
- Lisa G Neven
- USDA-ARS, Temperate Tree Fruit and Vegetable Research Unit, Wapato, WA, USA
| | | | - Wee L Yee
- USDA-ARS, Temperate Tree Fruit and Vegetable Research Unit, Wapato, WA, USA
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14
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Yee WL, Goughnour RB, Feder JL. Distinct Adult Eclosion Traits of Sibling Species Rhagoletis pomonella and Rhagoletis zephyria (Diptera: Tephritidae) Under Laboratory Conditions. ENVIRONMENTAL ENTOMOLOGY 2021; 50:173-182. [PMID: 33247295 DOI: 10.1093/ee/nvaa148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 06/12/2023]
Abstract
Closely related phytophagous insects that specialize on different host plants may have divergent responses to environmental factors. Rhagoletis pomonella (Walsh) and Rhagoletis zephyria Snow (Diptera: Tephritidae) are sibling, sympatric fly species found in western North America that attack and mate on plants of Rosaceae (~60 taxa) and Caprifoliaceae (three taxa), respectively, likely contributing to partial reproductive isolation. Rhagoletis zephyria evolved from R. pomonella and is native to western North America, whereas R. pomonella was introduced there. Given that key features of the flies' ecology, breeding compatibility, and evolution differ, we predicted that adult eclosion patterns of the two flies from Washington State, USA are also distinct. When puparia were chilled, eclosion of apple- and black hawthorn-origin R. pomonella was significantly more dispersed, with less pronounced peaks, than of snowberry-origin R. zephyria within sympatric and nonsympatric site comparisons. Percentages of chilled puparia that produced adults were ≥67% for both species. However, when puparia were not chilled, from 13.5 to 21.9% of apple-origin R. pomonella versus only 1.2% to 1.9% of R. zephyria eclosed. The distinct differences in eclosion traits of R. pomonella and R. zephyria could be due to greater genetic variation in R. pomonella, associated with its use of a wider range of host plants than R. zephyria.
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Affiliation(s)
- Wee L Yee
- United States Department of Agriculture-Agricultural Research Service, Temperate Tree Fruit and Vegetable Research Unit, Wapato, WA
| | | | - Jeffrey L Feder
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN
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15
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Kaiser TS, von Haeseler A, Tessmar-Raible K, Heckel DG. Timing strains of the marine insect Clunio marinus diverged and persist with gene flow. Mol Ecol 2021; 30:1264-1280. [PMID: 33410230 DOI: 10.1111/mec.15791] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Genetic divergence of populations in the presence of gene flow is a central theme in speciation research. Theory predicts that divergence can happen with full range overlap - in sympatry - driven by ecological factors, but there are few empirical examples of how ecologically divergent selection can overcome gene flow and lead to reproductive isolation. In the marine midge Clunio marinus (Diptera: Chironomidae) reproduction is ecologically restricted to the time of the lowest tides, which is ensured through accurate control of development and adult emergence by circalunar and circadian clocks. As tidal regimes differ along the coastline, locally adapted timing strains of C. marinus are found in different sites across Europe. At the same time, ecologically suitable low tides occur at both full and new moon and twice a day, providing C. marinus with four nonoverlapping temporal niches at every geographic location. Along the coast of Brittany, which is characterized by a steep gradient in timing of the tides, we found an unusually large number of differentially adapted timing strains, and the first known instances of sympatric C. marinus strains occupying divergent temporal niches. Analysis of mitochondrial genotypes suggests that these timing strains originated from a single recent colonization event. Nuclear genotypes show strong gene flow, sympatric timing strains being the least differentiated. Even when sympatric strains exist in nonoverlapping temporal niches, timing adaptations do not result in genome-wide genetic divergence, suggesting timing adaptations are maintained by permanent ecological selection. This constitutes a model case for incipient ecological divergence with gene flow.
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Affiliation(s)
- Tobias S Kaiser
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.,Max Perutz Laboratories, University of Vienna, Vienna, Austria.,Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | | | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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16
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Dowle EJ, Powell THQ, Doellman MM, Meyers PJ, Calvert MB, Walden KKO, Robertson HM, Berlocher SH, Feder JL, Hahn DA, Ragland GJ. Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation. Proc Natl Acad Sci U S A 2020; 117:23960-23969. [PMID: 32900926 PMCID: PMC7519392 DOI: 10.1073/pnas.2002357117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many organisms enter a dormant state in their life cycle to deal with predictable changes in environments over the course of a year. The timing of dormancy is therefore a key seasonal adaptation, and it evolves rapidly with changing environments. We tested the hypothesis that differences in the timing of seasonal activity are driven by differences in the rate of development during diapause in Rhagoletis pomonella, a fly specialized to feed on fruits of seasonally limited host plants. Transcriptomes from the central nervous system across a time series during diapause show consistent and progressive changes in transcripts participating in diverse developmental processes, despite a lack of gross morphological change. Moreover, population genomic analyses suggested that many genes of small effect enriched in developmental functional categories underlie variation in dormancy timing and overlap with gene sets associated with development rate in Drosophila melanogaster Our transcriptional data also suggested that a recent evolutionary shift from a seasonally late to a seasonally early host plant drove more rapid development during diapause in the early fly population. Moreover, genetic variants that diverged during the evolutionary shift were also enriched in putative cis regulatory regions of genes differentially expressed during diapause development. Overall, our data suggest polygenic variation in the rate of developmental progression during diapause contributes to the evolution of seasonality in R. pomonella We further discuss patterns that suggest hourglass-like developmental divergence early and late in diapause development and an important role for hub genes in the evolution of transcriptional divergence.
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Affiliation(s)
- Edwina J Dowle
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217;
- Department of Anatomy, University of Otago, 9016 Dunedin, New Zealand
| | - Thomas H Q Powell
- Department of Biological Sciences, Binghamton University-State University of New York, Binghamton, NY 13902
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611
| | - Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637
| | - Peter J Meyers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - McCall B Calvert
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Stewart H Berlocher
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Environmental Change Initiative, University of Notre Dame, Notre Dame, IN 46556
| | - Daniel A Hahn
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217;
- Department of Entomology, Kansas State University, Manhattan, KS 66506
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17
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Powell THQ, Nguyen A, Xia Q, Feder JL, Ragland GJ, Hahn DA. A rapidly evolved shift in life‐history timing during ecological speciation is driven by the transition between developmental phases. J Evol Biol 2020; 33:1371-1386. [DOI: 10.1111/jeb.13676] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/08/2020] [Accepted: 06/29/2020] [Indexed: 01/02/2023]
Affiliation(s)
- Thomas H. Q. Powell
- Entomology and Nematology Department University of Florida Gainesville Florida USA
- Department of Biological Sciences Binghamton University (State University of New York) Binghamton New York USA
| | - Andrew Nguyen
- Entomology and Nematology Department University of Florida Gainesville Florida USA
| | - Qinwen Xia
- Entomology and Nematology Department University of Florida Gainesville Florida USA
| | - Jeffrey L. Feder
- Department of Biological Sciences University of Notre DameNotre Dame Indiana USA
| | - Gregory J. Ragland
- Department of Integrative Biology University of Colorado Denver Denver Colorado USA
| | - Daniel A. Hahn
- Entomology and Nematology Department University of Florida Gainesville Florida USA
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18
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Meyers PJ, Doellman MM, Ragland GJ, Hood GR, Egan SP, Powell THQ, Nosil P, Feder JL. Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190534. [PMID: 32654640 DOI: 10.1098/rstb.2019.0534] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether and how host-related selection on diapause timing associates with genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of Rhagoletis pomonella to their sibling species Rhagoletis mendax that attacks blueberries. The associations of 57 857 single nucleotide polymorphisms in a diapause genome-wide-association study (GWAS) on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three fly populations at a field site in Fennville, MI, USA. The apple race and R. mendax show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause GWAS on R. mendax revealed compensatory changes throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in Rhagoletis. The generality of this result is placed in the context of other similar systems. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Peter J Meyers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gregory J Ragland
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.,Environmental Change Initiative, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217, USA
| | - Glen R Hood
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Scott P Egan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Biosciences, Rice University, Houston, TX 77005, USA.,Advanced Diagnostics and Therapeutics Initiative, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Thomas H Q Powell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.,Department Biological Sciences, Binghamton University, Binghamton, NY 13902, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Centre d'Ecologie Fonctionnelle and Evolutive, Centre National de la Recherche Scientifique, Montpellier 34293, France
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.,Environmental Change Initiative, University of Notre Dame, Notre Dame, IN 46556, USA.,Advanced Diagnostics and Therapeutics Initiative, University of Notre Dame, Notre Dame, IN 46556, USA
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19
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Yurchenko AA, Masri RA, Khrabrova NV, Sibataev AK, Fritz ML, Sharakhova MV. Genomic differentiation and intercontinental population structure of mosquito vectors Culex pipiens pipiens and Culex pipiens molestus. Sci Rep 2020; 10:7504. [PMID: 32371903 PMCID: PMC7200692 DOI: 10.1038/s41598-020-63305-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the population structure and mechanisms of taxa diversification is important for organisms responsible for the transmission of human diseases. Two vectors of West Nile virus, Culex pipiens pipiens and Cx. p. molestus, exhibit epidemiologically important behavioral and physiological differences, but the whole-genome divergence between them was unexplored. The goal of this study is to better understand the level of genomic differentiation and population structures of Cx. p. pipiens and Cx. p. molestus from different continents. We sequenced and compared the whole genomes of 40 individual mosquitoes from two locations in Eurasia and two in North America. Principal Component, ADMIXTURE, and neighbor joining analyses of the nuclear genomes identified two major intercontinental, monophyletic clusters of Cx. p. pipiens and Cx. p. molestus. The level of genomic differentiation between the subspecies was uniform along chromosomes. The ADMIXTURE analysis determined signatures of admixture in Cx. p. pipens populations but not in Cx. p. molestus populations. Comparison of mitochondrial genomes among the specimens showed a paraphyletic origin of the major haplogroups between the subspecies but a monophyletic structure between the continents. Thus, our study identified that Cx. p. molestus and Cx. p. pipiens represent different evolutionary units with monophyletic origin that have undergone incipient ecological speciation.
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Affiliation(s)
- Andrey A Yurchenko
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, USA.,Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, USA
| | - Natalia V Khrabrova
- Laboratory of Ecology, Genetics, and Environment Protection, Tomsk State University, Tomsk, Russia
| | - Anuarbek K Sibataev
- Laboratory of Ecology, Genetics, and Environment Protection, Tomsk State University, Tomsk, Russia
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, USA
| | - Maria V Sharakhova
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, USA. .,Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia. .,Laboratory of Ecology, Genetics, and Environment Protection, Tomsk State University, Tomsk, Russia.
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20
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Walter GM, Abbott RJ, Brennan AC, Bridle JR, Chapman M, Clark J, Filatov D, Nevado B, Ortiz-Barrientos D, Hiscock SJ. Senecio as a model system for integrating studies of genotype, phenotype and fitness. THE NEW PHYTOLOGIST 2020; 226:326-344. [PMID: 31951018 DOI: 10.1111/nph.16434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Adrian C Brennan
- School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, UK
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Mark Chapman
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James Clark
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | | | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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21
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Hood GR, Powell THQ, Doellman MM, Sim SB, Glover M, Yee WL, Goughnour RB, Mattsson M, Schwarz D, Feder JL. Rapid and repeatable host plant shifts drive reproductive isolation following a recent human-mediated introduction of the apple maggot fly, Rhagoletis pomonella. Evolution 2019; 74:156-168. [PMID: 31729753 DOI: 10.1111/evo.13882] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 10/24/2019] [Accepted: 10/27/2019] [Indexed: 01/26/2023]
Abstract
Ecological speciation via host-shifting is often invoked as a mechanism for insect diversification, but the relative importance of this process is poorly understood. The shift of Rhagoletis pomonella in the 1850s from the native downy hawthorn, Crataegus mollis, to introduced apple, Malus pumila, is a classic example of sympatric host race formation, a hypothesized early stage of ecological speciation. The accidental human-mediated introduction of R. pomonella into the Pacific Northwest (PNW) in the late 1970s allows us to investigate how novel ecological opportunities may trigger divergent adaptation and host race formation on a rapid timescale. Since the introduction, the fly has spread in the PNW, where in addition to apple, it now infests native black hawthorn, Crataegus douglasii, and introduced ornamental hawthorn, Crataegus monogyna. We use this "natural experiment" to test for genetic differentiation among apple, black, and ornamental hawthorn flies co-occurring at three sympatric sites. We report evidence that populations of all three host-associations are genetically differentiated at the local level, indicating that partial reproductive isolation has evolved in this novel habitat. Our results suggest that conditions suitable for initiating host-associated divergence may be common in nature, allowing for the rapid evolution of new host races when ecological opportunity arises.
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Affiliation(s)
- Glen R Hood
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202
| | - Thomas H Q Powell
- Department of Biological Sciences, Binghamton University, Binghamton, New York, 13902
| | - Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Sheina B Sim
- USDA-ARS Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii, 96720
| | - Mary Glover
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Wee L Yee
- USDA-ARS Yakima Agricultural Research Laboratory, Wapato, Washington, 98951
| | | | - Monte Mattsson
- Environmental Services, City of Portland, Portland, Oregon, 97204
| | - Dietmar Schwarz
- Department of Biology, Western Washington University, Bellingham, Washington, 98225
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556.,Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, Indiana, 46556.,Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana, 46556
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22
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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23
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Goodman KR, Prost S, Bi K, Brewer MS, Gillespie RG. Host and geography together drive early adaptive radiation of Hawaiian planthoppers. Mol Ecol 2019; 28:4513-4528. [PMID: 31484218 DOI: 10.1111/mec.15231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022]
Abstract
The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.
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Affiliation(s)
- Kari Roesch Goodman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Frankfurt/Main, Germany
| | - Ke Bi
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.,Ancestry, San Francisco, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Michael S Brewer
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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24
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Doellman MM, Schuler H, Jean GS, Hood GR, Egan SP, Powell THQ, Glover MM, Bruzzese DJ, Smith JJ, Yee WL, Goughnour RB, Rull J, Aluja M, Feder JL. Geographic and Ecological Dimensions of Host Plant-Associated Genetic Differentiation and Speciation in the Rhagoletis cingulata (Diptera: Tephritidae) Sibling Species Group. INSECTS 2019; 10:E275. [PMID: 31470668 PMCID: PMC6780410 DOI: 10.3390/insects10090275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 11/17/2022]
Abstract
Ascertaining the causes of adaptive radiation is central to understanding how new species arise and come to vary with their resources. The ecological theory posits adaptive radiation via divergent natural selection associated with novel resource use; an alternative suggests character displacement following speciation in allopatry and then secondary contact of reproductively isolated but ecologically similar species. Discriminating between hypotheses, therefore, requires the establishment of a key role for ecological diversification in initiating speciation versus a secondary role in facilitating co-existence. Here, we characterize patterns of genetic variation and postzygotic reproductive isolation for tephritid fruit flies in the Rhagoletis cingulata sibling species group to assess the significance of ecology, geography, and non-adaptive processes for their divergence. Our results support the ecological theory: no evidence for intrinsic postzygotic reproductive isolation was found between two populations of allopatric species, while nuclear-encoded microsatellites implied strong ecologically based reproductive isolation among sympatric species infesting different host plants. Analysis of mitochondrial DNA suggested, however, that cytoplasmic-related reproductive isolation may also exist between two geographically isolated populations within R cingulata. Thus, ecology associated with sympatric host shifts and cytoplasmic effects possibly associated with an endosymbiont may be the key initial drivers of the radiation of the R. cingulata group.
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Affiliation(s)
- Meredith M Doellman
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Hannes Schuler
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
- Current Address: Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Gilbert Saint Jean
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
| | - Glen R Hood
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
- Current Address: Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Scott P Egan
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
- Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, IN 46556, USA
- Current Address: Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77088, USA
| | - Thomas H Q Powell
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
- Current Address: Department of Biological Sciences, Binghamton University, Binghamton, NY 13902, USA
| | - Mary M Glover
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
| | - Daniel J Bruzzese
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
| | - James J Smith
- Michigan State University, Department of Entomology and Lyman Briggs College, East Holmes Hall, E. Lansing, MI 48824, USA
| | - Wee L Yee
- United States Department of Agriculture, Agricultural Research Service, Temperate Tree Fruit and Vegetable Research Unit, 5230 Konnowac Pass Road, Wapato, WA 98951, USA
| | - Robert B Goughnour
- Washington State University Extension, 1919 NE 78th Street, Vancouver, WA 98665, USA
| | - Juan Rull
- PROIMI Biotecnología-CONICET, LIEMEN-División Control Biológico de Plagas, Av. Belgrano y Pje. Caseros, T4001MVB San Miguel de Tucumán, Tucumán, Argentina
| | - Martin Aluja
- Instituto de Ecología, A.C., Carretera Antigua a Coatepec no. 351, Congregación el Haya, C.P. 91070 Xalapa, Veracruz, México
| | - Jeffrey L Feder
- Department of Biological Sciences, Galvin Life Sciences Bldg., University of Notre Dame, Notre Dame, IN 46556, USA
- Advanced Diagnostics and Therapeutics, University of Notre Dame, Notre Dame, IN 46556, USA
- Environmental Change Initiative, University of Notre Dame, Notre Dame, IN 46556, USA
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25
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Shields GF, Procunier WS. Sympatric speciation in the Simulium arcticum s. l. complex (Diptera: Simuliidae): The Rothfels model updated. Ecol Evol 2019; 9:8265-8278. [PMID: 31380088 PMCID: PMC6662398 DOI: 10.1002/ece3.5402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/11/2019] [Accepted: 05/30/2019] [Indexed: 11/23/2022] Open
Abstract
ABSTRACT We tested the Rothfels sympatric speciation model for black flies by comparing all available data for sex-chromosome diversity with the geographic locations of larval collection sites within the Simulium arcticum complex of black flies (Diptera: Simuliidae). Five separate data sets equaling about 20,000 larvae were included from throughout the geographic range of this complex. We record a total of 31 taxa having unique sex chromosomes, all of which demonstrate linkage disequilibrium with most taxa sharing autosomal polymorphisms. All siblings share portions of their distributions with S. negativum, the presumed oldest member of the complex. Twenty-one of 22 cytotypes have distributions within the ranges of siblings thus supporting the sympatric speciation model of Rothfels. Chromosomally diverse sites may require analysis of as many as 200 larvae to be properly described. There is no effect of any inversions influencing the occurrence of other inversions. Finally, we report a new cytotype, Simulium arcticum IIL-6, which we originally discovered in Alaska. Aspects of future genomic research are discussed as they relate to the main chromosomal structural/functional tenants of the model. OPEN RESEARCH BADGE This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data are available at https://doi.org/10.6084/m9.figshare.7719398.
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Affiliation(s)
- Gerald F. Shields
- Department of Life and Environmental SciencesCarroll CollegeHelenaMontana
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26
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Oakeshott JG, Robin C, Gordon KH. Editorial overview: Revisiting Dobzhansky and the 'modern synthesis' in light of insect evolutionary genomics. CURRENT OPINION IN INSECT SCIENCE 2019; 31:iii-vi. [PMID: 31109682 DOI: 10.1016/j.cois.2019.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- John G Oakeshott
- CSIRO, Clunies Ross St, GPO Box 1700, Acton, ACT, 2601, Australia.
| | - Charles Robin
- School of Biosciences, University of Melbourne, Grattan St, Melbourne, VIC, 3010, Australia
| | - Karl Hj Gordon
- CSIRO, Clunies Ross St, GPO Box 1700, Acton, ACT, 2601, Australia
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27
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Doellman MM, Feder JL. Genomic transitions during host race and species formation. CURRENT OPINION IN INSECT SCIENCE 2019; 31:84-92. [PMID: 31109679 DOI: 10.1016/j.cois.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Darwin recognized species as discontinuous, yet considered them to be formed by an incremental process of natural selection. Recent theoretical work on 'genome-wide congealing' is bridging this gap between the gradualism of divergent selection and rapid genome-wide divergence, particularly during ecological speciation-with-gene-flow. Host races and species of phytophagous insects, displaying a spectrum of divergence and gene flow among member taxa, provide model systems for testing predicted non-linear transitions from 'genic' divergence at a few uncoupled loci to 'genomic' divergence with genome-wide coupling of selected loci and strong reproductive isolation. Integrating across natural history, genomics, and evolutionary theory, emerging research suggests a tipping point from 'genic' to 'genomic' divergence between host races and species, during both sympatric speciation and secondary contact.
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Affiliation(s)
- Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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28
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Hood GR, Zhang L, Hu EG, Ott JR, Egan SP. Cascading reproductive isolation: Plant phenology drives temporal isolation among populations of a host‐specific herbivore. Evolution 2019; 73:554-568. [DOI: 10.1111/evo.13683] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Glen R. Hood
- Department of BiosciencesAnderson Biological LaboratoriesRice University Houston Texas 77005
- Department of Biological SciencesWayne State University Detroit Michigan 48202
| | - Linyi Zhang
- Department of BiosciencesAnderson Biological LaboratoriesRice University Houston Texas 77005
| | - Elaine G. Hu
- Department of BiosciencesAnderson Biological LaboratoriesRice University Houston Texas 77005
| | - James R. Ott
- Population and Conservation Biology ProgramDepartment of BiologyTexas State University San Marcos Texas 78666
| | - Scott P. Egan
- Department of BiosciencesAnderson Biological LaboratoriesRice University Houston Texas 77005
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