Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae)

Background and Aims Tecticornia is the most species-rich genus within the tribe Salicornieae. These halophytes are distributed across the Australian continent along coastlines and inland salt lake shores, playing a key ecological role in these hostile habitats. However, species delimitation within the genus remains controversial and little is known about infrageneric phylogenetic relationships. Therefore, the primary aim of this study was to infer the evolutionary history of Tecticornia and to genetically assess the reliability of current species concepts. Methods We sampled multiple accessions per taxon from nearly all currently recognised species in Australia. We used a target enrichment approach with two bait sets: Angiosperms353 and a custom Salicornieae bait set (‘Salibaits’). Analyses were performed using HybPiper, and we addressed paralogy using a tree-based approach. In addition, we tested the potential influence of missing data and/or missing gene trees on the topology of the final phylogenetic tree. Key Results Despite extensive gene tree discordance and the presence of short branches, the customised Salibaits set consistently produced better-resolved trees than the Angiosperm353 bait set. Missing data were found to have a negligible effect on the final tree inference. These data highlight there is genetic support for lineages in line with observed morphological variation, suggesting markedly more taxon diversity than is currently circumscribed. While we have shown there is genetic evidence to support the characterisation of several new species awaiting formal description, it is clear further molecular and morphological investigation is required to resolve continent-wide species aggregates, each comprising multiple novel taxa. Conclusions The target enrichment method effectively addressed the challenges of species delimitation in Tecticornia posed by reduced morphology and high ecological plasticity. We have shown that while there are several complexes constituting variants widely distributed across the Australian continent, some well-defined taxa have highly restricted distributions, which may represent conservation priorities.