Genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture

Abstract

Premise When divergent lineages come into secondary contact, reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (Iris, series Hexagonae) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. We estimated standing genetic variation to understand the current distribution of population structure in the Louisiana Irises. Methods We used genotyping‐by‐sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. We sampled 20 populations (n = 632 individuals) across 11,249 loci and used Entropy and PCA models to assess population genetic data. Results We discovered evidence for interspecific gene flow in parts of the range. Our analysis revealed patterns of population structure at odds with widely accepted nominal taxonomy. We discovered undescribed hybrid populations, designated as belonging to the I. brevicaulis lineage. Iris nelsonii shared significant ancestry with only one of the purported parent species, I. fulva, evidence inconsistent with a hybrid origin. Conclusions This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. Compared to the other nominal species, I. brevicaulis contains a large amount of genetic diversity. In addition, we discovered a previously unknown hybrid zone between I. brevicaulis and I. hexagona along the Texas coast. Finally, our results do not support the long‐standing hypothesis that I. nelsonii has mixed ancestry from three parental taxa.

Genomics of plant speciation

“…To date, genomic studies have confirmed the hybrid origin of the Oxford ragwort ( Senecio squalidus ) from the two Senecio species on Mt. Etna described above ( Nevado et al., 2020 ), identified several potential new cases of homoploid hybrid speciation (e.g., Grünig et al., 2021 ; Wang et al., 2021b ; Wang et al., 2022 ), suggested a difference in hybrid ancestry for two of the three well-studied sunflower homoploid hybrid species ( Owens et al., 2023 ), and failed to support several previously hypothesized examples of homoploid hybrid speciation, including Iris hexagona ( Zalmat et al., 2021 ) and two cases from Phlox ( Goulet-Scott et al., 2021 ).…”

A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi

“…Extracted DNA from the broader collection of mussels ( n = 378 [ 19 ]) was used to create a reduced-complexity genomic library. This library included the 14 tissue and 14 swab replicates utilized here and was generated following modified protocols commonly used in our laboratory group across a wide diversity of species [ 5 , 19 , 20 , 21 , 22 ]. Restriction enzymes EcoRI and MseI were used to digest extracted DNA; EcoRI adapters (i.e., 10–20 base-pair multiplex identifier sequences: MIDs) were ligated onto the resulting fragments, and the 14 swab and 14 tissue replicates were each assigned unique barcodes.…”

A first complete phylogenomic hypothesis for diploid blueberries (Vaccinium section Cyanococcus)

“…Homoploid hybrid speciation is the process by which a new species is formed through hybridization of divergent parent lineages, but without an increase in ploidy (Grant, 1981;Rieseberg, 1997). Although several potential homoploid hybrid species are known in various plant groups-for example, Carex (Hodel et al, 2022), Senecio (James and Abbott, 2005;Brennan et al, 2012), Iris (Arnold, 1993;Taylor et al, 2013;Zalmat et al, 2021), Pinus (Wang and Szmidt, 1994), Penstemon (Wolfe et al, 1998), and Paeonia (Pan et al, 2007)-they appear to be somewhat rare in nature (but see Nieto Feliner et al, 2017). Results of the present study suggest that V. pallidum is an additional example.…”