AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change
At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assu...
| Autor principal: | |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
PeerJ
2021
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| Acceso en línea: | https://hdl.handle.net/10568/118075 |
| _version_ | 1855517734809370624 |
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| author | Kindt, R. |
| author_browse | Kindt, R. |
| author_facet | Kindt, R. |
| author_sort | Kindt, R. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at the population level. AlleleShift provides data sets with predicted frequencies and several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These visualizations include ‘dot plot’ graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot), ‘waffle’ diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these visualizations were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplemental videos. |
| format | Journal Article |
| id | CGSpace118075 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | PeerJ |
| publisherStr | PeerJ |
| record_format | dspace |
| spelling | CGSpace1180752023-09-08T16:03:26Z AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change Kindt, R. genetic resources genetic variation At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at the population level. AlleleShift provides data sets with predicted frequencies and several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These visualizations include ‘dot plot’ graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot), ‘waffle’ diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these visualizations were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplemental videos. 2021-06-15 2022-02-14T02:32:01Z 2022-02-14T02:32:01Z Journal Article https://hdl.handle.net/10568/118075 en Open Access PeerJ Kindt, R. 2021. AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change. PeerJ, 9, e11534 https://doi.org/10.7717/peerj.11534 |
| spellingShingle | genetic resources genetic variation Kindt, R. AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change |
| title | AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change |
| title_full | AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change |
| title_fullStr | AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change |
| title_full_unstemmed | AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change |
| title_short | AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change |
| title_sort | alleleshift an r package to predict and visualize population level changes in allele frequencies in response to climate change |
| topic | genetic resources genetic variation |
| url | https://hdl.handle.net/10568/118075 |
| work_keys_str_mv | AT kindtr alleleshiftanrpackagetopredictandvisualizepopulationlevelchangesinallelefrequenciesinresponsetoclimatechange |