Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia

Gunn, Bee F.; Murphy, Daniel J.; Walsh, N. G.; Conran, John G.; Pires, J. Chris; Macfarlane, Terry D.; Birch, Joanne L.

doi:10.1016/j.ympev.2020.106836

Cited by 14 publications

(13 citation statements)

References 79 publications

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“…This supports our hypothesis that the rate of biome shifting increases among high-ploidy lineages in our genera, suggesting that WGD could be important in facilitating biome shifts. WGD may influence the ability of lineages to shift into new biomes, through mechanisms such as greater adaptive potential [12,[33][34][35]41], improved ability to survive in small populations [27,28], increased stress tolerance [10,11,[21][22][23] and broader environmental niche [18,77,78]. The open biome is a key origin for both genera in NZ.…”

Section: Discussionmentioning

confidence: 99%

“…Globally, polyploids are more abundant at higher altitudes, higher latitudes and in post-glacial regions [5][6][7][8][9]. They have also been associated with arid/ drought-prone conditions [10][11][12], greater soil productivity [13,14], younger/ less stable environments [15][16][17][18][19] and isolated landmasses [1,2,20]. These patterns may be caused by increased stress tolerance [18,[21][22][23], reduced tolerance of nutrient limitation [14,[24][25][26], ability to persist in small populations [5,27,28] and correlation with perennial/herbaceous lifeforms [9,17,29].…”

Section: Introductionmentioning

confidence: 99%

“…Although the role of WGD in biome occupancy remains little understood, several studies have indicated strong niche shifts in high-ploidy lineages [12,34,41]. Lineage biome occupancy has previously been thought to be generally conserved, with rare biome shifts, reflecting phylogenetic niche conservatism [42][43][44].…”

Section: Introductionmentioning

confidence: 99%

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Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

et al. 2021

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The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open and alpine) were determined for indigenous species in both clades. The distribution of low-ploidy ( Coprosma : 2 x , Veronica : 6 x ) versus high-ploidy ( Coprosma : 4–10 x , Veronica : 12–18 x ) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and WGD was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high-ploidy lineages. We find support for a greater than random portion of high-ploidy species occupying multiple biomes. We also find strong support for high-ploidy lineages showing a three- to eightfold increase in the rate of biome shifts. These results suggest that WGD promotes ecological expansion into new biomes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

et al. 2021

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“…Target capture sequencing (also referred to as target enrichment and HybSeq) has rapidly become a preferred approach for phylogenetic inquiry. In Australian plant systematics, a multitude of data types are used (Nauheimer et al 2019;Fowler et al 2020;Gunn et al 2020Gunn et al , 2024Orel et al 2023a;Orel et al 2023b), but the ongoing trend points to a greater adoption of target capture sequencing (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Joyce,

Schmidt-Lebuhn,

Orel

et al. 2024

Preprint

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Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking a step-change in the generation of data for phylogenetic inference. While this advancement has facilitated the resolution of many phylogenetic relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, deep coalescence or rapid speciation – processes that are particularly common in plant evolution. The proliferation of methods designed to analyse target capture data in the presence of these processes can be overwhelming for many researchers, especially students. In this review, we guide researchers through the target capture bioinformatic workflow, with a particular focus on robust phylogenetic inference in the presence of conflict. Through the workflow, we highlight key considerations for reducing artefactual conflict, synthesise strategies for managing paralogs, explain the causes and measurement of conflict, and summarise current methods for investigating biological processes underlying conflict. While we draw from examples in the Australian flora, this review is broadly relevant for any researcher working with target capture data. We conclude that conflict is often inherent and inevitable in plant phylogenetic research, but when properly managed, target capture data can provide unprecedented insight into the extraordinary and complex evolutionary histories of plants.

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“…Epigenetic modifications, including DNA methylation and histone modification, affect gene expression and provide a broader range of adaptations in allopolyploid plants (Gunn et al., 2020; Wu et al., 2022). DNA methylation is conserved in the genome, and abnormal changes can cause developmental failure in plants and animals, as well as embryo lethality (Zhang et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

Genomic asymmetric epigenetic modification of transposable elements is involved in gene expression regulation of allopolyploid Brassica napus

Xiao,

Xi,

Wang

et al. 2023

The Plant Journal

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SUMMARYPolyploids are common and have a wide geographical distribution and environmental adaptability. Allopolyploidy may lead to the activation of transposable elements (TE). However, the mechanism of epigenetic modification of TEs in the establishment and evolution of allopolyploids remains to be explored. We focused on the TEs of model allopolyploid Brassica napus (AnAnCnCn), exploring the TE characteristics of the genome, epigenetic modifications of TEs during allopolyploidization, and regulation of gene expression by TE methylation. In B. napus, approximately 50% of the genome was composed of TEs. TEs increased with proximity to genes, especially DNA transposons. TE methylation levels were negatively correlated with gene expression, and changes in TE methylation levels were able to regulate the expression of neighboring genes related to responses to light intensity and stress, which promoted powerful adaptation of allopolyploids to new environments. TEs can be synergistically regulated by RNA‐directed DNA methylation pathways and histone modifications. The epigenetic modification levels of TEs tended to be similar to those of the diploid parents during the genome evolution of B. napus. The TEs of the An subgenome were more likely to be modified, and the imbalance in TE number and epigenetic modification level in the An and Cn subgenomes may lead to the establishment of subgenome dominance. Our study analyzed the characteristics of TE location, DNA methylation, siRNA, and histone modification in B. napus and highlighted the importance of TE epigenetic modifications during the allopolyploidy process, providing support for revealing the mechanism of allopolyploid formation and evolution.

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Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia

Cited by 14 publications

References 79 publications

Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Genomic asymmetric epigenetic modification of transposable elements is involved in gene expression regulation of allopolyploid Brassica napus

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