HybPhaser identifies hybrid evolution in Australian Thelypteridaceae

Bloesch, Zoë; Nauheimer, Lars; Almeida, Thaís Elias; Crayn, Darren M.; Field, Ashley R.

doi:10.1016/j.ympev.2022.107526

Cited by 10 publications

(6 citation statements)

References 48 publications

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“…In comparison, these values were 52.3% and 0.21%, respectively, across all non-hybrid natural accessions of pitcher plants ( Nepenthes spp. ; Nauheimer et al 2021), and 60.7% and 0.85% across a family-wide sampling of Australian Thelypterid ferns (Bloesch et al 2022). This indicates the abundant presence of paralogs in our Brassicaceae dataset, likely caused by ample hybridisation and gene duplication events (fig.…”

Section: Discussionmentioning

confidence: 99%

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

Hendriks

Kiefer

Al‐Shehbaz

et al. 2022

Preprint

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The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

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Section: Discussionmentioning

confidence: 99%

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

Hendriks

Kiefer

Al‐Shehbaz

et al. 2022

Preprint

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“…This is commonly achieved in target-capture data through HybPhaser (Nauheimer et al 2021), and has been shown to be highly effective in cases of neoallopolyploidy (e.g. Bloesch et al 2022;Bradican et al 2023); however the method requires careful selection of the presence of diploid references for putative parental clades, and is often unsuitable for groups with complex or ancient reticulation (e.g. McLay et al 2023).…”

Section: Reticulationmentioning

confidence: 99%

“…In the Australian flora, conflict has been attributed to likely WGD events in target capture datasets of Adenanthos , Pomaderris (Nge, Kellermann, et al 2021), Calytrix (Nge et al 2022), Cryptandra (Nge et al 2024), Senecio , Celmisiinae (Nicol et al 2024) and many lineages in Sapindales (Joyce et al 2023). Conflict due to reticulation has been detected in Adansonia (Karimi et al 2020) and Thelypteridaceae (Bloesch et al 2022), and reticulation in concert with deep coalescence in Adenanthos and Eucalyptus (McLay et al 2023). As illustrated by these examples, conflict in target capture data, if handled carefully, can actually give novel insight into key biological processes in the evolutionary history of plants.…”

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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“…This study also demonstrates the utility of target-capture DNA sequence data obtained with the GoFlag 408 probe set for characterizing hybrid origins in ferns. At least one other study used the same type of data and approach to detect hybrids in Australian Thelypteridaceae (Bloesch et al 2022). Although our phylogeny resolves one subgenome of the hybrid as sister to a clade comprising Goniopteris oroniensis and multiple accessions of G. nicaraguensis , we exclude G. oroniensis as a candidate progenitor, as it is very rare and only known from a few localities in far southeastern Costa Rica (Gomez 1978).…”

Section: Taxonomic Treatmentmentioning

confidence: 99%

Goniopteris ×tico (Thelypteridaceae), a New Hybrid Fern from Costa Rica

Sorojsrisom,

Alvarado-Rodríguez,

Testo

2023

Systematic Botany

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Abstract— Goniopteris ×tico, a new hybrid fern from La Selva Biological Station in Heredia Province, Costa Rica, is described based on morphology and analysis of target-capture DNA sequence data. The hybrid co-occurs with its two putative progenitors, Goniopteris mollis and Goniopteris nicaraguensis, and is readily recognizable by its intermediate leaf dissection and venation. It is also intermediate in pinnae size and shape, and presents irregularly lobed pinnae. Despite the broad overlap in the geographic distribution of its parental taxa, Goniopteris ×tico is only known from two collections from a single area of the La Selva Biological Station, highlighting the importance of close observation of ferns from even well-collected areas.

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HybPhaser identifies hybrid evolution in Australian Thelypteridaceae

Cited by 10 publications

References 48 publications

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

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

Goniopteris ×tico (Thelypteridaceae), a New Hybrid Fern from Costa Rica

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