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Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

(2020) PLOS GENETICS. 16(5).
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Abstract
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
Keywords
Genetics(clinical), Genetics, Cancer Research, Ecology, Evolution, Behavior and Systematics, Molecular Biology, GENE FLOW, ARABIDOPSIS-ARENOSA, GENOME EVOLUTION, TAXONOMIC STATUS, ANURA, TREE, SEQUENCE, CHROMOSOMES, ALIGNMENT, SUDELLI

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MLA
Novikova, Polina, et al. “Polyploidy Breaks Speciation Barriers in Australian Burrowing Frogs Neobatrachus.” PLOS GENETICS, vol. 16, no. 5, 2020, doi:10.1371/journal.pgen.1008769.
APA
Novikova, P., Brennan, I. G., Booker, W., Mahony, M., Doughty, P., Lemmon, A. R., … Donnellan, S. C. (2020). Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLOS GENETICS, 16(5). https://doi.org/10.1371/journal.pgen.1008769
Chicago author-date
Novikova, Polina, Ian G. Brennan, William Booker, Michael Mahony, Paul Doughty, Alan R. Lemmon, Emily Moriarty Lemmon, et al. 2020. “Polyploidy Breaks Speciation Barriers in Australian Burrowing Frogs Neobatrachus.” PLOS GENETICS 16 (5). https://doi.org/10.1371/journal.pgen.1008769.
Chicago author-date (all authors)
Novikova, Polina, Ian G. Brennan, William Booker, Michael Mahony, Paul Doughty, Alan R. Lemmon, Emily Moriarty Lemmon, J. Dale Roberts, Levi Yant, Yves Van de Peer, J. Scott Keogh, and Stephen C. Donnellan. 2020. “Polyploidy Breaks Speciation Barriers in Australian Burrowing Frogs Neobatrachus.” PLOS GENETICS 16 (5). doi:10.1371/journal.pgen.1008769.
Vancouver
1.
Novikova P, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, et al. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLOS GENETICS. 2020;16(5).
IEEE
[1]
P. Novikova et al., “Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus,” PLOS GENETICS, vol. 16, no. 5, 2020.
@article{8661865,
  abstract     = {Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.},
  articleno    = {e1008769},
  author       = {Novikova, Polina and Brennan, Ian G. and Booker, William and Mahony, Michael and Doughty, Paul and Lemmon, Alan R. and Moriarty Lemmon, Emily and Roberts, J. Dale and Yant, Levi and Van de Peer, Yves and Keogh, J. Scott and Donnellan, Stephen C.},
  issn         = {1553-7404},
  journal      = {PLOS GENETICS},
  keywords     = {Genetics(clinical),Genetics,Cancer Research,Ecology,Evolution,Behavior and Systematics,Molecular Biology,GENE FLOW,ARABIDOPSIS-ARENOSA,GENOME EVOLUTION,TAXONOMIC STATUS,ANURA,TREE,SEQUENCE,CHROMOSOMES,ALIGNMENT,SUDELLI},
  language     = {eng},
  number       = {5},
  pages        = {24},
  title        = {Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus},
  url          = {http://dx.doi.org/10.1371/journal.pgen.1008769},
  volume       = {16},
  year         = {2020},
}

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