publication . Article . 2016

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

Roux, Camille; Fraïsse, Christelle; Romiguier, Jonathan; Anciaux, Yoann; Galtier, Nicolas; Bierne, Nicolas;
Open Access English
  • Published: 01 Dec 2016 Journal: PLoS Biology, volume 14, issue 12 (issn: 1544-9173, eissn: 1545-7885, Copyright policy)
  • Publisher: Public Library of Science
Abstract
International audience; Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids-the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of specia...
Subjects
free text keywords: 576 Genetics and evolution, Gene Flow, Research Article, Population Metrics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Evolutionary Processes, Genetic Loci, Effective Population Size, Genetics, Evolutionary Biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], People and Places, Demography, Gene Pool, Animals; Genetic Variation; Genetics, Population; Hybridization, Genetic; Models, Biological, Population Genetics, Biology and Life Sciences, Heredity, Introgression, Population Size, QH301-705.5, Speciation, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population Biology, Biology (General)
Funded by
EC| POPPHYL
Project
POPPHYL
Population phylogenomics: linking molecular evolution to species biology
  • Funder: European Commission (EC)
  • Project Code: 232971
  • Funding stream: FP7 | SP2 | ERC
56 references, page 1 of 4

1. Coyne JA, Orr HA, Others. Speciation. 2004.

2. De Queiroz K. Species concepts and species delimitation. Syst Biol. 2007;56: 879-886.

3. Dettman JR, Sirjusingh C, Kohn LM, Anderson JB. Incipient speciation by divergent adaptation and antagonistic epistasis in yeast. Nature. 2007;447: 585-588.

4. Amato A, Kooistra WHCF, Ghiron JHL, Mann DG, Pröschold T, Montresor M. Reproductive isolation among sympatric cryptic species in marine diatoms. Protist. 2007;158: 193-207.

5. Mayr E. Animal species and evolution. Cambridge, Massachusetts; 1963.

6. Gavrilets S. Fitness landscapes and the origin of species (MPB-41). Princeton University Press Princeton; 2004.

7. Bolnick DI, Fitzpatrick BM. Sympatric Speciation: Models and Empirical Evidence. Annu Rev Ecol Evol Syst. Annual Reviews; 2007;38: 459-487.

8. Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M. Robust demographic inference from genomic and SNP data. PLoS Genet. 2013;9: e1003905.

9. McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Mol Phylogenet Evol. 2012;62: 397-406.

10. Emerson BC, Paradis E, Thébaud C. Revealing the demographic histories of species using DNA sequences. Trends Ecol Evol. 2001;16: 707-716.

11. Csilléry K, Blum MGB, Gaggiotti OE, François O. Approximate Bayesian Computation (ABC) in practice. Trends Ecol Evol. 2010;25: 410-418.

12. Barton N, Bengtsson BO. The barrier to genetic exchange between hybridising populations. Heredity; 1986;57: 357-376.

13. Sousa VMC, Carneiro M, Ferrand N, Hey J. Identifying Loci Under Selection Against Gene Flow in Isolation with Migration Models. Genetics. 2013; genetics.113.149211-.

14. Roux C, Tsagkogeorga G, Bierne N, Galtier N. Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species. Mol Biol Evol. 2013;30: 1574-1587. [OpenAIRE]

15. Roux C, Fraïsse C, Castric V, Vekemans X, Pogson GH, Bierne N. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. J Evol Biol. 2014;27: 1662-1675. [OpenAIRE]

56 references, page 1 of 4
Abstract
International audience; Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids-the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of specia...
Subjects
free text keywords: 576 Genetics and evolution, Gene Flow, Research Article, Population Metrics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Evolutionary Processes, Genetic Loci, Effective Population Size, Genetics, Evolutionary Biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], People and Places, Demography, Gene Pool, Animals; Genetic Variation; Genetics, Population; Hybridization, Genetic; Models, Biological, Population Genetics, Biology and Life Sciences, Heredity, Introgression, Population Size, QH301-705.5, Speciation, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population Biology, Biology (General)
Funded by
EC| POPPHYL
Project
POPPHYL
Population phylogenomics: linking molecular evolution to species biology
  • Funder: European Commission (EC)
  • Project Code: 232971
  • Funding stream: FP7 | SP2 | ERC
56 references, page 1 of 4

1. Coyne JA, Orr HA, Others. Speciation. 2004.

2. De Queiroz K. Species concepts and species delimitation. Syst Biol. 2007;56: 879-886.

3. Dettman JR, Sirjusingh C, Kohn LM, Anderson JB. Incipient speciation by divergent adaptation and antagonistic epistasis in yeast. Nature. 2007;447: 585-588.

4. Amato A, Kooistra WHCF, Ghiron JHL, Mann DG, Pröschold T, Montresor M. Reproductive isolation among sympatric cryptic species in marine diatoms. Protist. 2007;158: 193-207.

5. Mayr E. Animal species and evolution. Cambridge, Massachusetts; 1963.

6. Gavrilets S. Fitness landscapes and the origin of species (MPB-41). Princeton University Press Princeton; 2004.

7. Bolnick DI, Fitzpatrick BM. Sympatric Speciation: Models and Empirical Evidence. Annu Rev Ecol Evol Syst. Annual Reviews; 2007;38: 459-487.

8. Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M. Robust demographic inference from genomic and SNP data. PLoS Genet. 2013;9: e1003905.

9. McCormack JE, Maley JM, Hird SM, Derryberry EP, Graves GR, Brumfield RT. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Mol Phylogenet Evol. 2012;62: 397-406.

10. Emerson BC, Paradis E, Thébaud C. Revealing the demographic histories of species using DNA sequences. Trends Ecol Evol. 2001;16: 707-716.

11. Csilléry K, Blum MGB, Gaggiotti OE, François O. Approximate Bayesian Computation (ABC) in practice. Trends Ecol Evol. 2010;25: 410-418.

12. Barton N, Bengtsson BO. The barrier to genetic exchange between hybridising populations. Heredity; 1986;57: 357-376.

13. Sousa VMC, Carneiro M, Ferrand N, Hey J. Identifying Loci Under Selection Against Gene Flow in Isolation with Migration Models. Genetics. 2013; genetics.113.149211-.

14. Roux C, Tsagkogeorga G, Bierne N, Galtier N. Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species. Mol Biol Evol. 2013;30: 1574-1587. [OpenAIRE]

15. Roux C, Fraïsse C, Castric V, Vekemans X, Pogson GH, Bierne N. Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone. J Evol Biol. 2014;27: 1662-1675. [OpenAIRE]

56 references, page 1 of 4
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publication . Article . 2016

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence

Roux, Camille; Fraïsse, Christelle; Romiguier, Jonathan; Anciaux, Yoann; Galtier, Nicolas; Bierne, Nicolas;