Phylogenomic analyses reveal a history of hybridisation and introgression between Sophora sect. Edwardsia (Fabaceae) species in New Zealand

ABSTRACT

Past studies of Sophora sect. Edwardsia using traditional phylogenetic and population genetic markers have been unable to produce a resolved species phylogeny of this recent radiation of shrubs and trees. Here we examined the relationships within and between the New Zealand species of Sophora sect. Edwardsia using next-generation sequencing. We generated genome-wide SNP data with double-digest restriction site-associated DNA sequencing (ddRADseq). Sophora prostrata was resolved as sister to the remaining species in all analyses. Relationships between the remaining taxa exhibited a high level of conflict with many of the genetic clusters reflecting geography rather than species boundaries. This result contrasts with a previous study, which was able to differentiate most species using genotype data from nine microsatellite loci. Overall our ddRADseq results indicate a high level of interspecific hybridisation and introgression within the group, which blurs the taxonomic boundaries throughout the distributional ranges of most species. Hybridisation and introgression among regional metapopulations comprising closely related species may increase the adaptive potential to respond to changing local conditions, and at the same time selection acts to maintain their genetic identity in the face of ongoing gene flow.

KEYWORDS:

• Adaptive radiation
• ddRADseq
• hybridisation
• introgression
• kōwhai
• network
• paraphyly
• phylogeny

Acknowledgements

Samples were collected under Department of Conservation permits WA-23814-FLO, BOP- 23814-FLO, TT-23661-FLO and NO-233360-FLO. We would like to acknowledge all iwi and hapu who granted us permission to collect from within their rohe, in particular those who contacted and/or met with us in person: Ngāti Kuri, Tikakina te Taiao, Ngāi Tahu, Ngātiwai, Ngā Puhi, Ngā Rauru, Ngāti Hauiti, Rangitane, Ngāti Tama and Ngāti Mutanga. We thank Peter de Lange, Tina Mullins (Porirua City Council), Kevin Matthews, Graeme La Cock, Wendy Holland, Robin Atherton and Andrew Townsend for assistance with sampling. We thank two anonymous reviewers and the Associate Editor for their helpful comments.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

L.D.S. acknowledges support from a Rutherford Discovery Fellowship from the Royal Society of New Zealand [contract number RDF-MNZ1201] and P.B.H. thanks the Strategic Science Investment Funding (SSIF) for Crown Research Institutes from the Ministry of Business, Innovation and Employment’s Science and Innovation Group for funding.