HybPhaser identifies hybrid evolution in Australian Thelypteridaceae

Bloesch, Zoë, Nauheimer, Lars, Almeida, Thais Elias, Crayn, Darren, and Field, Ashley Raymond (2022) HybPhaser identifies hybrid evolution in Australian Thelypteridaceae. Molecular Phylogenetics and Evolution, 173. 107526.

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Hybridisation has been proposed to play an important role in fern evolution, but has been difficult to investigate. This study explores the utility of target sequence capture and read-to-reference phasing of putative hybrids to investigate the role of evolutionary reticulation in ferns using Australian Thelypteridaceae as a model. The bioinformatics workflow HybPhaser was used to assess divergence between alleles, phase sequence reads to references and construct accessions resembling parental haplotypes. These accessions were included in phylogenetic and network analyses to detect hybrids and infer their parentage. This approach identified two novel hybrid lineages in Thelypteridaceae, one occurring between two different genera (Abacopteris and Christella), and another as part of a complex of Christella. In addition, hybrid phasing successfully reduced conflicting data and improved overall resolution in the Thelypteridaceae phylogeny, highlighting the power of this approach for reconstructing evolutionary history in reticulated lineages.

Item ID: 75766
Item Type: Article (Research - C1)
ISSN: 1095-9513
Keywords: Ferns, Hybridisation, HybPhaser, Reticulate evolution, Target capture sequencing
Copyright Information: © 2022 Published by Elsevier Inc.
Date Deposited: 17 Aug 2022 08:39
FoR Codes: 31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310203 Computational ecology and phylogenetics @ 50%
31 BIOLOGICAL SCIENCES > 3104 Evolutionary biology > 310410 Phylogeny and comparative analysis @ 50%
SEO Codes: 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 50%
18 ENVIRONMENTAL MANAGEMENT > 1806 Terrestrial systems and management > 180606 Terrestrial biodiversity @ 50%
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