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Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa

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Title: Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa
Authors: Premachandra, Tharindu, Cauret, Caroline M. S., Conradie, Werner, Measey, John, Evans, Ben J.
Publisher Information: Oxford University Press
Publication Year: 2022
Collection: Stellenbosch University: SUNScholar Research Repository
Subject Terms: Gene flow, Xenopus laevis -- Africa, Southern, Phylogeography -- Africa, Polyploid ratchet, Population genetics -- Data processing, Frogs
Description: The original publication is available at https://academic.oup.com ; Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog—the African clawed frog (Xenopus laevis)—over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa. ; CITATION: Premachandra, T. et al .2022. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 Genes|Genomes|Genetics, 13(2), doi:10.1093/g3journal/jkac325. ; Natural Science and Engineering Research Council of Canada (RGPIN-2017-05770), a Resource Allocation Competition awards from Compute Canada, the Museum of Comparative Zoology at Harvard University, and The National Research Foundation (NRF) of South Africa (NRF grant no. 87759 to J.M.) provided financial support for the project sampling and sequencing. J.M. was supported by the DSI-NRF Centre of Excellence for Invasion Biology. Fieldwork by W.C. was supported by the Foundational Biodiversity Information Program, BioGaps, Bayworld, and the Eastern Cape Parks and ...
Document Type: article in journal/newspaper
File Description: 13 pages : illustrations, maps; application/pdf
Language: English
Relation: Premachandra, T. et al .2022. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 Genes%7CGenomes%7CGenetics, 13(2), doi:10.1093/g3journal/jkac325.; https://scholar.sun.ac.za/handle/10019.1/132972
DOI: 10.1093/g3journal/jkac325
Availability: https://doi.org/10.1093/g3journal/jkac325
https://scholar.sun.ac.za/handle/10019.1/132972
Rights: Authors retain copyright
Accession Number: edsbas.686F4642
Database: BASE
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  – Url: https://doi.org/10.1093/g3journal/jkac325#
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  Data: Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa
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  Data: <searchLink fieldCode="AR" term="%22Premachandra%2C+Tharindu%22">Premachandra, Tharindu</searchLink><br /><searchLink fieldCode="AR" term="%22Cauret%2C+Caroline+M%2E+S%2E%22">Cauret, Caroline M. S.</searchLink><br /><searchLink fieldCode="AR" term="%22Conradie%2C+Werner%22">Conradie, Werner</searchLink><br /><searchLink fieldCode="AR" term="%22Measey%2C+John%22">Measey, John</searchLink><br /><searchLink fieldCode="AR" term="%22Evans%2C+Ben+J%2E%22">Evans, Ben J.</searchLink>
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  Data: Oxford University Press
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  Data: 2022
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  Data: Stellenbosch University: SUNScholar Research Repository
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  Data: <searchLink fieldCode="DE" term="%22Gene+flow%22">Gene flow</searchLink><br /><searchLink fieldCode="DE" term="%22Xenopus+laevis+--+Africa%22">Xenopus laevis -- Africa</searchLink><br /><searchLink fieldCode="DE" term="%22Southern%22">Southern</searchLink><br /><searchLink fieldCode="DE" term="%22Phylogeography+--+Africa%22">Phylogeography -- Africa</searchLink><br /><searchLink fieldCode="DE" term="%22Polyploid+ratchet%22">Polyploid ratchet</searchLink><br /><searchLink fieldCode="DE" term="%22Population+genetics+--+Data+processing%22">Population genetics -- Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Frogs%22">Frogs</searchLink>
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  Data: The original publication is available at https://academic.oup.com ; Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog—the African clawed frog (Xenopus laevis)—over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa. ; CITATION: Premachandra, T. et al .2022. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 Genes|Genomes|Genetics, 13(2), doi:10.1093/g3journal/jkac325. ; Natural Science and Engineering Research Council of Canada (RGPIN-2017-05770), a Resource Allocation Competition awards from Compute Canada, the Museum of Comparative Zoology at Harvard University, and The National Research Foundation (NRF) of South Africa (NRF grant no. 87759 to J.M.) provided financial support for the project sampling and sequencing. J.M. was supported by the DSI-NRF Centre of Excellence for Invasion Biology. Fieldwork by W.C. was supported by the Foundational Biodiversity Information Program, BioGaps, Bayworld, and the Eastern Cape Parks and ...
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  Data: Premachandra, T. et al .2022. Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. G3 Genes%7CGenomes%7CGenetics, 13(2), doi:10.1093/g3journal/jkac325.; https://scholar.sun.ac.za/handle/10019.1/132972
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