Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

Abstract

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

“…However, since the RAxML analysis already revealed a quite robust tree topology, we used this time-consuming coalescence approach only for the subclade data. Our results confirmed that the coalescent approach using RAD sequencing data is suitable for species delimitation, as recently shown by Brandrud et al (2019) on Dactylorhiza .…”

“…The authors summarized the available analytical tools for SNP calling in polyploids, however, these tools were mainly developed for model plants like crop species, where the parental lineages are previously known. Thus, only few studies using RAD sequencing on polyploid species are published so far (Mastretta-Yanes et al 2014; Qi et al 2015; Brandrud et al 2017, 2019; Feng et al 2018). Here we present a phylogenomic study on diploid and polyploid willow species by using a de-novo assembly of RAD sequencing data as implemented in ipyrad.…”

“…Furthermore, the thousands of biallelic SNPs harvested by RAD sequencing are generally well suited to resolve reticulate relationships, reconstruct species trees and to analyse polyploid species in a phylogenetic scope (Bryant et al 2012; Dufresne et al 2014; Clevenger et al 2015). However, there are only few studies using reduced representation libraries like RAD sequencing data, when dealing with polyploid non-model plants (Chen et al 2013; Mastretta-Yanes et al 2014; Qi et al 2015; Brandrud et al 2019). While many independent loci are advantageous for the reconstruction of the polyploid origin, phasing of many unlinked short loci as generated by RAD sequencing will not reveal enough information if treated separately.…”

“…The calling of biallelic SNPs based on likelihoods can overcome biases associated with genotype uncertainty (Blischak et al 2018b). Recently, Brandrud et al (2019) presented a workflow based on SNP data to deal with polyploids in a recently evolved orchid species complex ( Dactylorhiza ). It points out the ability of SNPs to analyse polyploid taxa.…”

Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status ofCorybas dowlingii

“…Hence, these approaches provide critical genomic data to evaluate taxonomic concepts in species complexes and to inform the development of effective conservation strategies for threatened species. Reduced representation library sequencing approaches, such as RADseq, ddRADseq and genotypingby-sequencing (GBS), have proven to be powerful tools for disentangling complex relationships and delimiting taxonomic boundaries in orchids (Ahrens et al 2017;Bateman et al 2018;Brandrud et al 2019a). Here, we present a study using more than 13,000 SNPs to unravel the complex relationships in the C. aconitiflorus complex containing three morphologically similar orchid species endemic to Australia.…”