Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala
Abstract
Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved betweenmore »
- Authors:
-
- Fudan Univ., Shanghai (China)
- Northeast Normal University, Changchun (China)
- McGill University and Genome Quebec Innovation Center, Montreal, QC (Canada)
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; National Natural Science Foundation of China (NSFC); Fudan University
- OSTI Identifier:
- 1625345
- Grant/Contract Number:
- 31670382; JIH1322105
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genome Biology and Evolution
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 3; Journal ID: ISSN 1759-6653
- Publisher:
- Society for Molecular Biology and Evolution
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; evolutionary biology; genetics & heredity; Aquilegia; adaptation; ecological specialization; selection; speciation
Citation Formats
Li, Ming-Rui, Wang, Hua-Ying, Ding, Ning, Lu, Tianyuan, Huang, Ye-Chao, Xiao, Hong-Xing, Liu, Bao, and Li, Lin-Feng. Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala. United States: N. p., 2019.
Web. doi:10.1093/gbe/evz038.
Li, Ming-Rui, Wang, Hua-Ying, Ding, Ning, Lu, Tianyuan, Huang, Ye-Chao, Xiao, Hong-Xing, Liu, Bao, & Li, Lin-Feng. Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala. United States. https://doi.org/10.1093/gbe/evz038
Li, Ming-Rui, Wang, Hua-Ying, Ding, Ning, Lu, Tianyuan, Huang, Ye-Chao, Xiao, Hong-Xing, Liu, Bao, and Li, Lin-Feng. Thu .
"Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala". United States. https://doi.org/10.1093/gbe/evz038. https://www.osti.gov/servlets/purl/1625345.
@article{osti_1625345,
title = {Rapid Divergence Followed by Adaptation to Contrasting Ecological Niches of Two Closely Related Columbine Species Aquilegia japonica and A. oxysepala},
author = {Li, Ming-Rui and Wang, Hua-Ying and Ding, Ning and Lu, Tianyuan and Huang, Ye-Chao and Xiao, Hong-Xing and Liu, Bao and Li, Lin-Feng},
abstractNote = {Elucidating the mechanisms underlying the genetic divergence between closely related species is crucial to understanding the origin and evolution of biodiversity. The genus Aquilegia L. has undergone rapid adaptive radiation, generating about 70 well-recognized species that are specialized to distinct habitats and pollinators. In this study, to address the underlying evolutionary mechanisms that drive the genetic divergence, we analyzed the whole genomes of two ecologically isolated Aquilegia species, A. oxysepala and A. japonica as well as their putative hybrid. Our comparative genomic analyses reveal that while the two species diverged only recently and experienced recurrent gene flow, a high level of genetic divergence is observed in their nuclear genomes. In particular, candidate genomic regions that show signature of selection differ dramatically between the two species. Given that the splitting time of the two species is broadly matched with the decrease in effective population sizes, we propose that allopatric isolation together with natural selection have preceded the interspecific gene flow in the process of speciation. The observed high genetic divergence is likely an outcome of combined effects of natural selection, genetic drift and divergent sorting of ancestral polymorphisms. Our study provides a genome-wide view of how genetic divergence has evolved between closely related species.},
doi = {10.1093/gbe/evz038},
journal = {Genome Biology and Evolution},
number = 3,
volume = 11,
place = {United States},
year = {Thu Feb 21 00:00:00 EST 2019},
month = {Thu Feb 21 00:00:00 EST 2019}
}
Works referenced in this record:
Fast model-based estimation of ancestry in unrelated individuals
journal, July 2009
- Alexander, D. H.; Novembre, J.; Lange, K.
- Genome Research, Vol. 19, Issue 9
Genetics of ecological divergence during speciation
journal, June 2014
- Arnegard, Matthew E.; McGee, Matthew D.; Matthews, Blake
- Nature, Vol. 511, Issue 7509
Genetic Revolutions, Founder Effects, and Speciation
journal, November 1984
- Barton, N. H.; Charlesworth, B.
- Annual Review of Ecology and Systematics, Vol. 15, Issue 1
Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations
journal, December 2009
- Bastida, Jesús M.; Alcántara, Julio M.; Rey, Pedro J.
- Plant Systematics and Evolution, Vol. 284, Issue 3-4
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
journal, January 2011
- Chen, Hanbo; Boutros, Paul C.
- BMC Bioinformatics, Vol. 12, Issue 1
Genetic Variation at Nuclear Loci Fails to Distinguish Two Morphologically Distinct Species of Aquilegia
journal, January 2010
- Cooper, Elizabeth A.; Whittall, Justen B.; Hodges, Scott A.
- PLoS ONE, Vol. 5, Issue 1
Conflictual speciation: species formation via genomic conflict
journal, January 2013
- Crespi, Bernard; Nosil, Patrik
- Trends in Ecology & Evolution, Vol. 28, Issue 1
The variant call format and VCFtools
journal, June 2011
- Danecek, P.; Auton, A.; Abecasis, G.
- Bioinformatics, Vol. 27, Issue 15
Hybridization and the build-up of genomic divergence during speciation
journal, January 2013
- Feder, J. L.; Flaxman, S. M.; Egan, S. P.
- Journal of Evolutionary Biology, Vol. 26, Issue 2
The genomics of speciation-with-gene-flow
journal, July 2012
- Feder, Jeffrey L.; Egan, Scott P.; Nosil, Patrik
- Trends in Genetics, Vol. 28, Issue 7
A hot topic: the genetics of adaptation to geothermal vents inMimulus guttatus
journal, November 2016
- Ferris, Kathleen G.
- Molecular Ecology, Vol. 25, Issue 22
Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions
journal, February 2013
- Fior, Simone; Li, Mingai; Oxelman, Bengt
- New Phytologist, Vol. 198, Issue 2
Floral isolation between
Aquilegia formosa
and
Aquilegia pubescens
journal, November 1999
- Fulton, Michelle; Hodges, Scott A.
- Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 266, Issue 1435
The Genetic Architecture of Reproductive Isolation During Speciation-With-Gene-Flow in lake Whitefish Species Pairs Assessed by rad Sequencing: Special Section
journal, March 2013
- Gagnaire, Pierre-Alexandre; Pavey, Scott A.; Normandeau, Eric
- Evolution, Vol. 67, Issue 9
Geographic genetic structure of Iberian columbines (gen. Aquilegia)
journal, June 2017
- Garrido, Jose L.; Alcántara, Julio M.; Rey, Pedro J.
- Plant Systematics and Evolution, Vol. 303, Issue 9
circlize implements and enhances circular visualization in R
journal, June 2014
- Gu, Zuguang; Gu, Lei; Eils, Roland
- Bioinformatics, Vol. 30, Issue 19
Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
journal, April 2017
- Han, Fan; Lamichhaney, Sangeet; Grant, B. Rosemary
- Genome Research, Vol. 27, Issue 6
Adaptation to Climate Across the Arabidopsis thaliana Genome
journal, October 2011
- Hancock, A. M.; Brachi, B.; Faure, N.
- Science, Vol. 334, Issue 6052
Columbines: a geographically widespread species flock.
journal, May 1994
- Hodges, S. A.; Arnold, M. L.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 11
Adaptive radiations: From field to genomic studies
journal, June 2009
- Hodges, S. A.; Derieg, N. J.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue Supplement_1
Genetics of Floral Traits Influencing Reproductive Isolation between Aquilegia formosa and Aquilegia pubescens
journal, March 2002
- Hodges, Scott A.; Whittall, Justen B.; Fulton, Michelle
- The American Naturalist, Vol. 159, Issue S3
Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax
journal, April 2018
- Jiang, Peng; Shi, Feng-Xue; Li, Ming-Rui
- Frontiers in Plant Science, Vol. 9
Chromosome Inversions, Local Adaptation and Speciation
journal, October 2005
- Kirkpatrick, Mark; Barton, Nick
- Genetics, Vol. 173, Issue 1
Aquilegia : A New Model for Plant Development, Ecology, and Evolution
journal, June 2009
- Kramer, Elena M.
- Annual Review of Plant Biology, Vol. 60, Issue 1
Aquilegia as a model system for the evolution and ecology of petals
journal, February 2010
- Kramer, Elena M.; Hodges, Scott A.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1539
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016
- Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
- Molecular Biology and Evolution, Vol. 33, Issue 7
Evolution of Darwin’s finches and their beaks revealed by genome sequencing
journal, February 2015
- Lamichhaney, Sangeet; Berglund, Jonas; Almén, Markus Sällman
- Nature, Vol. 518, Issue 7539
Rapid hybrid speciation in Darwin’s finches
journal, January 2018
- Lamichhaney, Sangeet; Han, Fan; Webster, Matthew T.
- Science, Vol. 359, Issue 6372
Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010
- Li, Heng; Durbin, Richard
- Bioinformatics, Vol. 26, Issue 5
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
Phenotypic and genetic evidence for ecological speciation of Aquilegia japonica and A. oxysepala
journal, August 2014
- Li, Lin-Feng; Wang, Hua-Ying; Pang, Di
- New Phytologist, Vol. 204, Issue 4
Signatures of adaptation in the weedy rice genome
journal, April 2017
- Li, Lin-Feng; Li, Ya-Ling; Jia, Yulin
- Nature Genetics, Vol. 49, Issue 5
Genomic and EST microsatellite markers for Aquilegia flabellata
and cross-amplification in A. oxysepala
(Ranunculaceae)
journal, August 2011
- Li, Lin-Feng; Liao, Qiang-Lan
- American Journal of Botany, Vol. 98, Issue 8
Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer)
journal, August 2017
- Li, Ming-Rui; Shi, Feng-Xue; Li, Ya-Ling
- Genome Biology and Evolution, Vol. 9, Issue 9
Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex
journal, December 2017
- Ma, Tao; Wang, Kun; Hu, Quanjun
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 2
Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
journal, December 2015
- Malinsky, M.; Challis, R. J.; Tyers, A. M.
- Science, Vol. 350, Issue 6267
Genome-wide evidence for speciation with gene flow in Heliconius butterflies
journal, September 2013
- Martin, Simon H.; Dasmahapatra, Kanchon K.; Nadeau, Nicola J.
- Genome Research, Vol. 23, Issue 11
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing
journal, February 2012
- Nadeau, Nicola J.; Whibley, Annabel; Jones, Robert T.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 367, Issue 1587
Genomic scans for selective sweeps using SNP data
journal, October 2005
- Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob
- Genome Research, Vol. 15, Issue 11
Genomic divergence during speciation: causes and consequences
journal, February 2012
- Nosil, Patrik; Feder, Jeffrey L.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 367, Issue 1587
Tipping points in the dynamics of speciation
journal, January 2017
- Nosil, Patrik; Feder, Jeffrey L.; Flaxman, Samuel M.
- Nature Ecology & Evolution, Vol. 1, Issue 2
Divergent selection and heterogeneous genomic divergence
journal, February 2009
- Nosil, Patrik; Funk, Daniel J.; Ortiz-Barrientos, Daniel
- Molecular Ecology, Vol. 18, Issue 3
Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and betweenAquilegia formosaandA. pubescens
journal, November 2014
- Noutsos, C.; Borevitz, J. O.; Hodges, S. A.
- Molecular Ecology, Vol. 23, Issue 22
Genic analysis for the sterility of hybrids between distantly related varieties of cultivated rice
journal, December 1957
- Oka, Hiko-Ichi
- Journal of Genetics, Vol. 55, Issue 3
The population genetics of speciation: the evolution of hybrid incompatibilities.
journal, April 1995
- Orr, H. A.
- Genetics, Vol. 139, Issue 4
SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes
journal, June 2013
- Pavlidis, Pavlos; Živković, Daniel; Stamatakis, Alexandros
- Molecular Biology and Evolution, Vol. 30, Issue 9
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
journal, November 2012
- Pickrell, Joseph K.; Pritchard, Jonathan K.
- PLoS Genetics, Vol. 8, Issue 11
Genomic islands of divergence are not affected by geography of speciation in sunflowers
journal, May 2013
- Renaut, S.; Grassa, C. J.; Yeaman, S.
- Nature Communications, Vol. 4, Issue 1
SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.): GENOMICS OF SPECIATION IN WHITEFISH
journal, December 2010
- Renaut, SÉBastien; Nolte, Arne W.; Rogers, Sean M.
- Molecular Ecology, Vol. 20, Issue 3
Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers
journal, December 2013
- Renaut, Sebastien; Owens, Gregory L.; Rieseberg, Loren H.
- Molecular Ecology, Vol. 23, Issue 2
Transitions between phases of genomic differentiation during stick-insect speciation
journal, February 2017
- Riesch, Rüdiger; Muschick, Moritz; Lindtke, Dorothea
- Nature Ecology & Evolution, Vol. 1, Issue 4
The Genetic Architecture of Ecological Speciation and the Association with Signatures of Selection in Natural Lake Whitefish (Coregonus sp. Salmonidae) Species Pairs
journal, March 2007
- Rogers, S.; Bernatchez, L.
- Molecular Biology and Evolution, Vol. 24, Issue 6
Genomics and the origin of species
journal, February 2014
- Seehausen, Ole; Butlin, Roger K.; Keller, Irene
- Nature Reviews Genetics, Vol. 15, Issue 3
Sub‐ and neo‐functionalization ofAPETALA 3paralogs have contributed to the evolution of novel floral organ identity inAquilegia(columbine, Ranunculaceae)
journal, December 2012
- Sharma, Bharti; Kramer, Elena
- New Phytologist, Vol. 197, Issue 3
Understanding the development and evolution of novel floral form in Aquilegia
journal, February 2014
- Sharma, Bharti; Yant, Levi; Hodges, Scott A.
- Current Opinion in Plant Biology, Vol. 17
Isolation by Distance in Equilibrium and Non-Equilibrium Populations
journal, February 1993
- Slatkin, Montgomery
- Evolution, Vol. 47, Issue 1
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
Robust and scalable inference of population history from hundreds of unphased whole genomes
journal, December 2016
- Terhorst, Jonathan; Kamm, John A.; Song, Yun S.
- Nature Genetics, Vol. 49, Issue 2
Quality control of next-generation sequencing data without a reference
journal, May 2014
- Trivedi, Urmi H.; Cézard, Timothée; Bridgett, Stephen
- Frontiers in Genetics, Vol. 5
Genomic analyses suggest parallel ecological divergence in
Heliosperma pusillum
(Caryophyllaceae)
journal, August 2017
- Trucchi, Emiliano; Frajman, Božo; Haverkamp, Thomas H. A.
- New Phytologist, Vol. 216, Issue 1
Pollinator shifts drive increasingly long nectar spurs in columbine flowers
journal, June 2007
- Whittall, Justen B.; Hodges, Scott A.
- Nature, Vol. 447, Issue 7145
Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia
journal, September 2006
- Whittall, Justen B.; Voelckel, Claudia; Kliebenstein, Daniel J.
- Molecular Ecology, Vol. 15, Issue 14
Making sense of genomic islands of differentiation in light of speciation
journal, November 2016
- Wolf, Jochen B. W.; Ellegren, Hans
- Nature Reviews Genetics, Vol. 18, Issue 2
The genic view of the process of speciation: Genic view of the process of speciation
journal, November 2001
- Wu, Chung-I
- Journal of Evolutionary Biology, Vol. 14, Issue 6
Molecular basis for three-dimensional elaboration of the Aquilegia petal spur
journal, March 2015
- Yant, Levi; Collani, Silvio; Puzey, Joshua
- Proceedings of the Royal Society B: Biological Sciences, Vol. 282, Issue 1803
Natural Selection: It’s a Many-Small World After All
journal, October 2014
- Roesti, Marius; Salzburger, Walter
- Current Biology, Vol. 24, Issue 19
Understanding the development and evolution of novel floral form in Aquilegia
journal, February 2014
- Sharma, Bharti; Yant, Levi; Hodges, Scott A.
- Current Opinion in Plant Biology, Vol. 17
The genomics of speciation-with-gene-flow
journal, July 2012
- Feder, Jeffrey L.; Egan, Scott P.; Nosil, Patrik
- Trends in Genetics, Vol. 28, Issue 7
Conflictual speciation: species formation via genomic conflict
journal, January 2013
- Crespi, Bernard; Nosil, Patrik
- Trends in Ecology & Evolution, Vol. 28, Issue 1
Pollinator shifts drive increasingly long nectar spurs in columbine flowers
journal, June 2007
- Whittall, Justen B.; Hodges, Scott A.
- Nature, Vol. 447, Issue 7145
Robust and scalable inference of population history from hundreds of unphased whole genomes
journal, December 2016
- Terhorst, Jonathan; Kamm, John A.; Song, Yun S.
- Nature Genetics, Vol. 49, Issue 2
Signatures of adaptation in the weedy rice genome
journal, April 2017
- Li, Lin-Feng; Li, Ya-Ling; Jia, Yulin
- Nature Genetics, Vol. 49, Issue 5
Genomics and the origin of species
journal, February 2014
- Seehausen, Ole; Butlin, Roger K.; Keller, Irene
- Nature Reviews Genetics, Vol. 15, Issue 3
Adaptive radiations: From field to genomic studies
journal, June 2009
- Hodges, S. A.; Derieg, N. J.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue Supplement_1
Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex
journal, December 2017
- Ma, Tao; Wang, Kun; Hu, Quanjun
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 2
Columbines: a geographically widespread species flock.
journal, May 1994
- Hodges, S. A.; Arnold, M. L.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 11
Genetics of Floral Traits Influencing Reproductive Isolation between Aquilegia formosa and Aquilegia pubescens
journal, March 2002
- Hodges, Scott A.; Whittall, Justen B.; Fulton, Michelle
- The American Naturalist, Vol. 159, Issue S3
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
The variant call format and VCFtools
journal, June 2011
- Danecek, P.; Auton, A.; Abecasis, G.
- Bioinformatics, Vol. 27, Issue 15
Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer)
journal, August 2017
- Li, Ming-Rui; Shi, Feng-Xue; Li, Ya-Ling
- Genome Biology and Evolution, Vol. 9, Issue 9
The Genetic Architecture of Ecological Speciation and the Association with Signatures of Selection in Natural Lake Whitefish (Coregonus sp. Salmonidae) Species Pairs
journal, March 2007
- Rogers, S.; Bernatchez, L.
- Molecular Biology and Evolution, Vol. 24, Issue 6
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016
- Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
- Molecular Biology and Evolution, Vol. 33, Issue 7
Molecular basis for three-dimensional elaboration of the Aquilegia petal spur
journal, March 2015
- Yant, Levi; Collani, Silvio; Puzey, Joshua
- Proceedings of the Royal Society B: Biological Sciences, Vol. 282, Issue 1803
Aquilegia as a model system for the evolution and ecology of petals
journal, February 2010
- Kramer, Elena M.; Hodges, Scott A.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1539
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing
journal, February 2012
- Nadeau, Nicola J.; Whibley, Annabel; Jones, Robert T.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 367, Issue 1587
Genomic divergence during speciation: causes and consequences
journal, February 2012
- Nosil, Patrik; Feder, Jeffrey L.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 367, Issue 1587
Fast model-based estimation of ancestry in unrelated individuals
journal, July 2009
- Alexander, D. H.; Novembre, J.; Lange, K.
- Genome Research, Vol. 19, Issue 9
Genome-wide evidence for speciation with gene flow in Heliconius butterflies
journal, September 2013
- Martin, Simon H.; Dasmahapatra, Kanchon K.; Nadeau, Nicola J.
- Genome Research, Vol. 23, Issue 11
Genomic scans for selective sweeps using SNP data
journal, October 2005
- Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob
- Genome Research, Vol. 15, Issue 11
The genetic mosaic suggests a new role for hitchhiking in ecological speciation
journal, October 2008
- Via, Sara; West, Joan
- Molecular Ecology, Vol. 17, Issue 19
Hybridization and the build-up of genomic divergence during speciation
journal, January 2013
- Feder, J. L.; Flaxman, S. M.; Egan, S. P.
- Journal of Evolutionary Biology, Vol. 26, Issue 2
The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus
journal, August 2016
- Hendrick, Margaret F.; Finseth, Findley R.; Mathiasson, Minna E.
- Molecular Ecology, Vol. 25, Issue 22
Sub‐ and neo‐functionalization ofAPETALA 3paralogs have contributed to the evolution of novel floral organ identity inAquilegia(columbine, Ranunculaceae)
journal, December 2012
- Sharma, Bharti; Kramer, Elena
- New Phytologist, Vol. 197, Issue 3
Phenotypic and genetic evidence for ecological speciation of Aquilegia japonica and A. oxysepala
journal, August 2014
- Li, Lin-Feng; Wang, Hua-Ying; Pang, Di
- New Phytologist, Vol. 204, Issue 4
Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
journal, December 2015
- Malinsky, M.; Challis, R. J.; Tyers, A. M.
- Science, Vol. 350, Issue 6267
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
journal, January 2011
- Chen, Hanbo; Boutros, Paul C.
- BMC Bioinformatics, Vol. 12, Issue 1
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
journal, November 2012
- Pickrell, Joseph K.; Pritchard, Jonathan K.
- PLoS Genetics, Vol. 8, Issue 11
Genetic Variation at Nuclear Loci Fails to Distinguish Two Morphologically Distinct Species of Aquilegia
journal, January 2010
- Cooper, Elizabeth A.; Whittall, Justen B.; Hodges, Scott A.
- PLoS ONE, Vol. 5, Issue 1
Chromosome Inversions, Local Adaptation and Speciation
journal, October 2005
- Kirkpatrick, Mark; Barton, Nick
- Genetics, Vol. 173, Issue 1
Isolation by Distance in Equilibrium and Non-Equilibrium Populations
journal, February 1993
- Slatkin, Montgomery
- Evolution, Vol. 47, Issue 1
Quality control of next-generation sequencing data without a reference
journal, May 2014
- Trivedi, Urmi H.; Cézard, Timothée; Bridgett, Stephen
- Frontiers in Genetics, Vol. 5
Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax
journal, April 2018
- Jiang, Peng; Shi, Feng-Xue; Li, Ming-Rui
- Frontiers in Plant Science, Vol. 9