Determining population structure and hybridization for two iris species

Abstract

Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species.

Multiple hydroxyphenethyl glucosinolate isomers and their tandem mass spectrometric distinction in a geographically structured polymorphism in the crucifer Barbarea vulgaris

“…Empirical results confirm that such hybrid zones can be surprisingly narrow (Barton and Hewitt, 1989). However, extended 'mosaic zones' with both parental types as well as hybrids occurring can also form (Arnold, 1996;Nordström and Hedrén, 2008;Hamplin and Arnold, 2014). Judged from the random sampling of European populations studied in this report, the transition from a P-type dominated area to a G-type dominated area may seem to be quite sharp in Finland, while the expected transition further south is poorly defined because of lack of sampling (Fig.…”

Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone

“…However, because F 1 genotypes are viable, fertile and often reveal fitness measures higher than those of pure‐species parents regardless of the interspecific cross (Taylor et al., ), these individuals can persist across multiple flowering seasons and facilitate the production of extensive genetically and phenotypically diverse hybrid zones (Arnold, ; Riley, ; Viosca, ). A broad suite of traits are known to influence both prezygotic and postzygotic isolation between Louisiana Iris species, and a number of quantitative genetic studies have been performed that describe the genetic architecture of these traits (Arnold, ; Arnold, Tang, Knapp, & Martin, ; Ballerini et al., ; Hamlin & Arnold, ; Martin et al., , , ; Tang, Okashah, Knapp, Arnold, & Martin, ; Taylor et al., ; Taylor, Rojas, et al. ).…”

Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii

“…GBS is a reduced representation library strategy that has been used to generate SNPs in plant species with complicated genomes (Myles et al, 2010; Elshire et al, 2011; Poland et al, 2012), including polyploids, for which lack of clarity about paralogs can lead to ambiguity (Dufresne et al, 2013). Genotyping by sequencing has been particularly valuable for species with complex genomes in part because of the development of a reference‐free bioinformatic pipeline, the Universally Enabled Analysis Kit (UNEAK; Lu et al, 2013), which has been used to generate SNP markers for nonmodel species (White et al, 2013; Hamlin and Arnold, 2014) and polyploid taxa (Arruda et al, 2013; Lu et al, 2013; Matthews et al, 2013). In this study, we used GBS data to generate two SNP data sets for population genetic analysis of A. gerardii using distinct bioinformatics pipelines: (1) the UNEAK bioinformatic pipeline (the reference‐free pipeline) and (2) a reference‐guided pipeline based on the sequenced Sorghum bicolor genome.…”