Resolving fuzzy species limits: nuclear evidence for speciation by hybridisation in Amazonian Trichomanes ferns

Unclear species boundaries are a common challenge in ecological studies and species inventories, obscuring patterns of biodiversity and complicating inferences about ecological and evolutionary processes. One possible cause of fuzziness is hybridisation, but little information exists on hybridisation in the tropics. Here we aim to address the question of potential hybridisation in the tropical American fern genus Trichomanes (Hymenophyllaceae) and to clarify evolutionary relationships within the genus. We take advantage of nuclear target-capture sequencing, haplotype phasing and off-target plastid reads to detect phylogenetic relationships and reticulate histories. We sampled 303 individuals that represent 41 known Trichomanes species. Our analyses recovered a robust backbone for the genus, strongly supporting subgenus Trichomanes as sister to subgen. Feea, and subgen. Davalliopsis as sister to subgen. Lacostea. Trichomanes pinnatum proved to be a complex where six different unnamed morphs represent four different kinds of evolutionary history. Two morphs appear to be stabilised, relatively old hybrid-derived species, one represents a recent hybrid, one reflects repeated spontaneous hybridisation between the same parent species, and one represents within-species morphological variation without any obvious genomic signal. Excluding the four hybrids makes T. pinnatum s.s. morphologically and genetically much more uniform, but its geographic distribution still covers practically all tropical America, indicating that the species may be approaching panmixia.