Molecular systematic analysis of the genus Notelaea (Oleaceae): SNPs from high‐density DArT‐sequencing unravel the mystery of the species limits of threatened species of Notelaea

Abstract

Conservation decision‐making and prioritization of management actions for taxa at high risk of extinction require a clear understanding of systematic relationships and species boundaries. Taxonomic uncertainty surrounds two threatened species of native olive (genus Notelaea) endemic to Australia. Notelaea ipsviciensis is known from only one small population and is listed as critically endangered under Australian and Queensland legislation, while Notelaea lloydii is listed as vulnerable due to its restricted distribution in south‐east Queensland, Australia. Notelaea ipsviciensis occurs in sympatry with N. lloydii, at the only site where it is found, and exhibits intermediate morphology between N. lloydii and Notelaea ovata raising speculation that it is a natural hybrid of the two. To address this uncertainty, we have reconstructed the molecular phylogeny of the genus Notelaea using both single‐gene sequencing and single nucleotide polymorphism (SNP) data. While the chloroplast DNA markers were not found to be informative, the genome‐wide SNPs used in this study have unequivocally resolved the long‐standing question of the hybrid origin of N. ipsviciensis. Results of the phylogenetics and hybrid analyses of SNP data show that N. ipsviciensis is a natural hybrid of N. lloydii and N. ovata, and the taxon's circumscription needs to be re‐evaluated. Our results also revealed unclear species boundaries among numerous other Notelaea species, including the threatened N. lloydii, indicating that further investigation and taxonomic revision may be necessary.

Conservation genetics of Notelaea lloydii (Oleaceae) in south‐eastern Queensland, Australia

“…Furthermore, this study did not find reciprocal monophyly of N. lloydii and N. microcarpa, i.e., two clades of N. lloydii were nested within different parts of the N. microcarpa clade, but some phylogeographic structure was reported (Manawaduge et al, 2022). Moreover, N. lloydii populations are small, each with less than 30 individuals, and limited recruitment has been observed (Approved conservation advice for Notelaea lloydii, 2008); therefore, further population genetic analysis is required.…”

“…Hybridisation can reduce the viability of small populations through demographic and genetic swamping (Ellstrand & Elam, 1993 ; Ellstrand & Rieseberg, 2016 ) and may ultimately influence the time to local extinction (Wolf et al., 2001 ). Furthermore, this study did not find reciprocal monophyly of N. lloydii and N. microcarpa , i.e., two clades of N. lloydii were nested within different parts of the N. microcarpa clade, but some phylogeographic structure was reported (Manawaduge et al., 2022 ). Moreover, N. lloydii populations are small, each with less than 30 individuals, and limited recruitment has been observed ( Approved conservation advice for Notelaea lloydii , 2008 ); therefore, further population genetic analysis is required.…”

“…The results of our recent molecular systematics study indicate that N. lloydii and N. microcarpa do not show reciprocal monophyly (Manawaduge et al, 2022), but they do exhibit distinguishing growth forms and leaf morphologies (Guymer, 1987). Because leaf size and shape are functionally significant, adaptive traits (Nicotra et al, 2011;Read et al, 2014), even if N. microcarpa and N. lloydii constitute a single species, populations with different leaf form may be worthy of conservation.…”

“…A principal coordinate analysis (PoA) was performed on SNP data using DarTR to visualise the genetic relationship between N. lloydii and N. microcarpa. A phylogenetic tree was also constructed using the maximum likelihood method as described in Manawaduge et al (2022). Pairwise Wright's F st between N. lloydii populations were estimated using StAMPP (Pembleton et al, 2013) in R. Nei's pairwise F st (Nei, 1987) and D genetic distance (Nei, 1972) were also estimated using the hierfstat (Goudet, 2005) and StAMPP (Pembleton et al, 2013) packages in R, respectively.…”

“…Several other disjunct populations have since been identified within an area of approximately 3700 km 2 in SE-QLD (Approved conservation advice for Notelaea lloydii, 2008;Halford, 1998), resulting in N. lloydii being listed as vulnerable (Environment Protection and Biodiversity Conservation Act, 1999). A recent molecular systematics study of the genus Notelaea has revealed that another Notelaea species in the vicinity, N. ipsviciensis W. K. Harris, is a hybrid between N. lloydii and N. ovata (Manawaduge et al, 2022). Molecular data have revealed that hybrid backcrossing with N. lloydii is occurring at the site where they are sympatric.…”