A first look at sea-lavenders genomics – can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex?

Abstract

Background Sea-lavenders (Limonium Mill., Plumbaginaceae) are a cosmopolitan group of diploid and polyploid plants often adapted to extreme saline environments, with a mostly Tethyan distribution, occurring in the Mediterranean, Irano-Turanian, Euro-Siberian and in the New World. The halophylic Limonium vulgare polyploid complex in particular, presents a large distribution throughout extreme salt-marsh habitats and shows little morphological but high taximetric variation, frequently blurring species delimitation. In this work we pursue three main goals: assert whether SNP data from polyploid individuals has the resolution to distinguish the seven sampled species, to better understand how genetically structured Limonium vulgare is, and attempt to identify specific molecular mechanisms for the differentiation between L. maritimum and L. vulgare. For this purpose, 95 individuals were genotyped using Genotyping by Sequencing (GBS), which were assembled as two independent datasets using ipyrad. All analyses performed downstream of assembly were fully automated. Phylogenetic inference, PCA, and admixture plots were used to infer answers to the study’s main goals. Results Close to 10,000 SNPs were obtained for each dataset. Phylogenetic analyses reveal that polyploid data can be used to infer species relationships. Population structure analyses suggest a genetically structured L. vulgare. A set of 34 SNPs were found to be fully segregated between L. vulgare and L. maritimum, two of which are potentially linked to proteins that might be involved in the speciation process. Conclusion Despite polyploid data analyses shortcomings, GBS generated SNPs have the resolution to discern all seven included species. Limonium vulgare revealed pronounced genetic structure along a geographical north-south cline. L. maritimum always appears as a distinct genetic entity. Segregated SNPs between L. vulgare and L. maritimum indicate salinity response and morphological trait control genes as potentially interesting to follow up for studying these species’ divergence process.

Figure 1 from: Malekmohammadi M, Koutroumpa K, Crespo MB, Domina G, Korotkova N, Akhani H, von Mering S, Borsch T, Berendsohn WG (2024) A taxonomic backbone for the Plumbaginaceae (Caryophyllales). PhytoKeys 243: 67-103. https://doi.org/10.3897/phytokeys.243.122784

“…Only a few studies explore species limits and relationships in Limonium at shallow phylogenetic levels. A recent example is the phylogenomic investigation by Pina-Martins et al (2023) on seven representatives of Limonium sect. Limonium.…”

“…Limonium maritimum, represented by a single population although it is widely distributed along the Portuguese coast (Cortinhas et al 2015), differed from L. vulgare only by 34 out of 10,000 SNPs. Moreover, the populations of L. vulgare across its distributional range showed high genetic structure based on the phylogenetic and clustering analyses (Pina-Martins et al 2023). Limonium maritimum was described as separate species based on morphometric data, in which few diagnostic traits had slightly smaller yet largely overlapping size ranges compared to the closely related L. vulgare (Cortinhas et al 2015).…”

“…We used phylogenetic studies for the circumscription of taxa in Limonium, where available (e.g., Akhani et al 2013;Pina-Martins et al 2023). As many species are of restricted range, in the absence of such studies it was considered adequate to use morphological circumscriptions from regional floras (e.g., Erben 1993Erben , 2012, regional monographs (e.g., Brullo and Erben 2016, Limonium in Greece;Doğan et al 2020, Limonium in Turkey), taxonomic revisions of specific species groups (e.g., Bogdanović and Brullo 2015, Limonium cancellatum group), and protologues (Pignatti 1955(Pignatti , 1982…”

Correction: A first look at sea-lavenders genomics – can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex?

“…Following the publication of the original article [ 1 ], the authors would like to update the Funding section.…”

“…The correction does not have any effect on the results or conclusions of the paper. The original article [ 1 ] has been corrected.…”