1
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Nosil P, Gompert Z, Funk DJ. Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species. Nat Commun 2024; 15:2273. [PMID: 38480699 PMCID: PMC10937975 DOI: 10.1038/s41467-024-46294-9] [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: 03/02/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in fits and bursts, rather than being uniform and gradual. We show in Timema stick insects that one component of reproductive isolation evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum, and thus exhibits similar dynamics to morphological traits not implicated in reproductive isolation. The results show different evolutionary dynamics for different components of reproductive isolation and highlight a special relevance for species status in the process of speciation.
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Affiliation(s)
- Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Daniel J Funk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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2
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Gompert Z, Feder JL, Nosil P. Natural selection drives genome-wide evolution via chance genetic associations. Mol Ecol 2021; 31:467-481. [PMID: 34704650 DOI: 10.1111/mec.16247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
Understanding selection's impact on the genome is a major theme in biology. Functionally neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here, we use field experiments and genomic data in stick insects, deer mice and stickleback fish to show that widespread statistical associations with genes known to affect fitness cause many genetic loci across the genome to be impacted indirectly by selection. This includes regions physically distant from those directly under selection. Then, focusing on the stick insect system, we show that statistical associations between SNPs and other unknown, causal variants result in additional indirect selection in general and specifically within genomic regions of physically linked loci. This widespread indirect selection necessarily makes aspects of evolution more predictable. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations. This process has implications for the application of evolutionary principles in basic and applied science.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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3
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Buerkle CA. Inconvenient truths in population and speciation genetics point towards a future beyond allele frequencies. J Evol Biol 2017; 30:1498-1500. [DOI: 10.1111/jeb.13106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 11/28/2022]
Affiliation(s)
- C. A. Buerkle
- Department of Botany; University of Wyoming; Laramie WY USA
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4
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Kingston SE, Parchman TL, Gompert Z, Buerkle CA, Braun MJ. Heterogeneity and concordance in locus‐specific differentiation and introgression between species of towhees. J Evol Biol 2017; 30:474-485. [DOI: 10.1111/jeb.13033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/13/2016] [Accepted: 12/19/2016] [Indexed: 12/24/2022]
Affiliation(s)
- S. E. Kingston
- Program in Behavior, Ecology, Evolution, and Systematics University of Maryland College Park MD USA
- National Museum of Natural History Vertebrate Zoology Smithsonian Institution Washington DC USA
- Department of Biology and Coastal Studies Center Bowdoin College Brunswick ME USA
| | | | - Z. Gompert
- Department of Biology Utah State University Logan UT USA
| | - C. A. Buerkle
- Department of Botany University of Wyoming Laramie WY USA
| | - M. J. Braun
- Program in Behavior, Ecology, Evolution, and Systematics University of Maryland College Park MD USA
- National Museum of Natural History Vertebrate Zoology Smithsonian Institution Washington DC USA
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5
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Manel S, Perrier C, Pratlong M, Abi-Rached L, Paganini J, Pontarotti P, Aurelle D. Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Mol Ecol 2015; 25:170-84. [DOI: 10.1111/mec.13468] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Affiliation(s)
- S. Manel
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier -EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - C. Perrier
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier -EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - M. Pratlong
- Aix Marseille Université; CNRS; IRD; Avignon Université, IMBE UMR 7263; Station Marine d'Endoume, 13007; Marseille France
- Aix Marseille Université; CNRS; Centrale Marseille; I2M UMR 7373; Evolution Biologique Modélisation; 3 Place Victor Hugo, 13331 Marseille Cedex Case 19 France
| | - L. Abi-Rached
- Equipe ATIP; URMITE UM 63 CNRS 7278 IRD 198 Inserm U1095; IHU Méditerranée Infection; Aix-Marseille Université; 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05 France
| | - J. Paganini
- XEGEN SAS; 15 Rue de la République 13420 Gemenos France
| | - P. Pontarotti
- Aix Marseille Université; CNRS; Centrale Marseille; I2M UMR 7373; Evolution Biologique Modélisation; 3 Place Victor Hugo, 13331 Marseille Cedex Case 19 France
| | - D. Aurelle
- Aix Marseille Université; CNRS; IRD; Avignon Université, IMBE UMR 7263; Station Marine d'Endoume, 13007; Marseille France
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6
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Lindtke D, Buerkle CA. The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact. Evolution 2015; 69:1987-2004. [DOI: 10.1111/evo.12725] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/08/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Dorothea Lindtke
- Department of Botany and Program in Ecology; University of Wyoming; Laramie Wyoming 82071
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN United Kingdom
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology; University of Wyoming; Laramie Wyoming 82071
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7
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Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015; 16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023] Open
Abstract
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1618-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - David W Coltman
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
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Buehler D, Holderegger R, Brodbeck S, Schnyder E, Gugerli F. Validation of outlier loci through replication in independent data sets: a test on Arabis alpina. Ecol Evol 2014; 4:4296-306. [PMID: 25540691 PMCID: PMC4267868 DOI: 10.1002/ece3.1300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/11/2014] [Accepted: 10/01/2014] [Indexed: 12/25/2022] Open
Abstract
Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.
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Affiliation(s)
- Dominique Buehler
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland ; Department of Environmental Systems Science, ETH Zürich Universitätsstrasse 16, CH-8092, Zürich, Switzerland
| | - Sabine Brodbeck
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Elvira Schnyder
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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9
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Gompert Z, Lucas LK, Buerkle CA, Forister ML, Fordyce JA, Nice CC. Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants. Mol Ecol 2014; 23:4555-73. [DOI: 10.1111/mec.12811] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/27/2014] [Accepted: 04/29/2014] [Indexed: 12/16/2022]
Affiliation(s)
| | - Lauren K. Lucas
- Department of Biology; Utah State University; Logan UT 84322 USA
- Department of Biology; Texas State University; San Marcos TX 78666 USA
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology; University of Wyoming; Laramie WY 82071 USA
| | | | - James A. Fordyce
- Department of Ecology & Evolutionary Biology; University of Tennessee; Knoxville TN 37996 USA
| | - Chris C. Nice
- Department of Biology; Texas State University; San Marcos TX 78666 USA
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10
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Ellegren H. Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol 2014; 29:51-63. [DOI: 10.1016/j.tree.2013.09.008] [Citation(s) in RCA: 392] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/02/2013] [Accepted: 09/16/2013] [Indexed: 12/20/2022]
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11
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Restrepo S, Tabima JF, Mideros MF, Grünwald NJ, Matute DR. Speciation in fungal and oomycete plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:289-316. [PMID: 24906125 DOI: 10.1146/annurev-phyto-102313-050056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.
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Affiliation(s)
- Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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12
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Shahin A, Smulders MJM, van Tuyl JM, Arens P, Bakker FT. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars. FRONTIERS IN PLANT SCIENCE 2014; 5:567. [PMID: 25368628 PMCID: PMC4202788 DOI: 10.3389/fpls.2014.00567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/01/2014] [Indexed: 05/19/2023]
Abstract
Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.
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Affiliation(s)
- Arwa Shahin
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Jaap M. van Tuyl
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Freek T. Bakker
- Biosystematics Group, Wageningen UniversityWageningen, Netherlands
- *Correspondence: Freek T. Bakker, Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6700 AP Wageningen, Netherlands e-mail:
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13
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Gompert Z, Buerkle CA. Analyses of genetic ancestry enable key insights for molecular ecology. Mol Ecol 2013; 22:5278-94. [DOI: 10.1111/mec.12488] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 08/05/2013] [Accepted: 08/08/2013] [Indexed: 12/15/2022]
Affiliation(s)
| | - C. Alex Buerkle
- Department of Botany; University of Wyoming; Laramie WY 82071 USA
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14
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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15
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Hohenlohe PA, Day MD, Amish SJ, Miller MR, Kamps-Hughes N, Boyer MC, Muhlfeld CC, Allendorf FW, Johnson EA, Luikart G. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol Ecol 2013; 22:3002-13. [PMID: 23432212 DOI: 10.1111/mec.12239] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/05/2012] [Accepted: 12/11/2012] [Indexed: 12/14/2022]
Abstract
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300-400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences, Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844-3051, USA.
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16
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Lindtke D, Buerkle CA, Barbará T, Heinze B, Castiglione S, Bartha D, Lexer C. Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in Populus. Mol Ecol 2012; 21:5042-58. [PMID: 22989336 DOI: 10.1111/j.1365-294x.2012.05744.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 06/26/2012] [Accepted: 07/11/2012] [Indexed: 12/01/2022]
Abstract
The maintenance of species barriers in the face of gene flow is often thought to result from strong selection against intermediate genotypes, thereby preserving genetic differentiation. Most speciation genomic studies thus aim to identify exceptionally divergent loci between populations, but divergence will be affected by many processes other than reproductive isolation (RI) and speciation. Through genomic studies of recombinant hybrids sampled in the wild, genetic variation associated with RI can be observed in situ, because selection against incompatible genotypes will leave detectable patterns of variation in the hybrid genomes. To better understand the mechanisms directly involved in RI, we investigated three natural 'replicate' hybrid zones between two divergent Populus species via locus-specific patterns of ancestry across recombinant hybrid genomes. As expected, genomic patterns in hybrids and their parental species were consistent with the presence of underdominant selection at several genomic regions. Surprisingly, many loci displayed greatly increased between-species heterozygosity in recombinant hybrids despite striking genetic differentiation between the parental genomes, the opposite of what would be expected with selection against intermediate genotypes. Only a limited, reproducible set of genotypic combinations was present in hybrid genomes across localities. In the absence of clearly delimited 'hybrid habitats', our results suggest that complex epistatic interactions within genomes play an important role in advanced stages of RI between these ecologically divergent forest trees. This calls for more genomic studies that test for unusual patterns of genomic ancestry in hybridizing species.
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Affiliation(s)
- Dorothea Lindtke
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland.
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17
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Gompert Z, Buerkle CA. bgc: Software for Bayesian estimation of genomic clines. Mol Ecol Resour 2012; 12:1168-76. [DOI: 10.1111/1755-0998.12009.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 07/19/2012] [Accepted: 07/28/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Z. Gompert
- Department of Botany and Program in Ecology University of Wyoming Laramie WY 82071 USA
- Department of Biology Texas State University San Marcos TX 78666 USA
| | - C. A. Buerkle
- Department of Botany and Program in Ecology University of Wyoming Laramie WY 82071 USA
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18
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Magalhães S, Matos M. Strengths and weaknesses of experimental evolution. Trends Ecol Evol 2012; 27:649-50; author reply 650-1. [PMID: 22917849 DOI: 10.1016/j.tree.2012.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 02/03/2023]
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Abstract
Admixture and introgression have varied effects on population viability and fitness. Admixture might be an important source of new alleles, particularly for small, geographically isolated populations. However, admixture might also cause outbreeding depression if populations are adapted to different ecological or climatic conditions. Because of the emerging use of translocation and admixture as a conservation and wildlife management strategy to reduce genetic load (termed genetic rescue), the possible effects of admixture have practical consequences (Bouzat et al. 2009; Hedrick & Fredrickson 2010). Importantly, genetic load and local adaptation are properties of individual loci and epistatic interactions among loci rather than properties of genomes. Likewise, the outcome and consequences of genetic rescue depend on the fitness effects of individual introduced alleles. In this issue of Molecular Ecology, Miller et al. (2012) use model-based, population genomic analyses to document locus-specific effects of a recent genetic rescue in the bighorn sheep population within the National Bison Range wildlife refuge (NBR; Montana, USA). They find a subset of introduced alleles associated with increased fitness in NBR bighorn sheep, some of which experienced accelerated introgression following their introduction. These loci mark regions of the genome that could constitute the genetic basis of the successful NBR bighorn sheep genetic rescue. Although population genomic analyses are frequently used to study local adaptation and selection (e.g. Hohenlohe et al. 2010; Lawniczak et al. 2010), this study constitutes a novel application of this analytical framework for wildlife management. Moreover, the detailed demographic data available for the NBR bighorn sheep population provide a rare and powerful source of information and allow more robust population genomic inference than is often possible.
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Affiliation(s)
- Zachariah Gompert
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, WY 82071, USA.
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Gompert Z, Lucas LK, Nice CC, Fordyce JA, Forister ML, Buerkle CA. GENOMIC REGIONS WITH A HISTORY OF DIVERGENT SELECTION AFFECT FITNESS OF HYBRIDS BETWEEN TWO BUTTERFLY SPECIES. Evolution 2012; 66:2167-81. [DOI: 10.1111/j.1558-5646.2012.01587.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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