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Incongruent patterns of nuclear and chloroplast variation in Correa (Rutaceae): introgression and biogeography in south-eastern Australia

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Abstract

Correa (family Rutaceae) is a genus endemic to southern Australia, in which chloroplast introgression between species has previously been inferred. The current study aimed to document the extent of incongruence between molecular markers and taxonomy, describe patterns of geographic variation, and infer genetic and biogeographic processes important in the history of the genus. Sampling focused on subg. Correa (nine species) and included 166 samples from 95 localities. Samples were genotyped at the chloroplast loci trnL-trnF and trnK and the nuclear ITS regions, either by direct sequencing or by restriction digests of PCR products. Both chloroplast and ITS datasets resolved subg. Persistens (two species mostly from wet forests) as distinct from those of subg. Correa. Within subg. Correa chloroplast and ITS lineages were largely incongruent with each other and with current taxonomy, but both datasets showed similar geographic patterns. In each dataset there was one lineage mostly restricted to western South Australia and Western Australia, and one lineage widespread in eastern South Australia, Victoria, Tasmania, New South Wales and Queensland. The split between these geographic lineages occurs in South Australia, on the western side of the Murray basin; it is sharply defined in the chloroplast results, whereas the distributions of ITS lineages overlap. The geographic patterns and incongruence exhibited by both ITS and chloroplast markers provide evidence for substantial chloroplast and nuclear introgression between species. Geographic distributions of genetic lineages are consistent with divergence caused by a historical vicariance event across the lower Murray basin and subsequent reconnection of populations.

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Acknowledgments

For assistance with fieldwork or provision of specimens we thank Asher Warren, Miranda Weir, Ruby Wilson, Ramadhanil Pitopang, Will Neal, Tom Hans, Ron Taylor, Daniel Ohlsen, Paul Forster, Mike Mathieson, Alison Kellow, the La Trobe University Herbarium and the National Herbarium of Victoria. Plant collecting permits were provided by the Department of Sustainability and Environment (Victoria), the Department of Primary Industries, Parks, Water and Environment (Tasmania) and the Department for Environment, Water & Natural Resources (South Australia). This work was partly supported by an Early Career Researcher grant to MJB from The University of Melbourne.

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    Philippa A. French, Gillian K. Brown & Michael J. Bayly

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Handling editor: Christian Parisod.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

606_2016_1277_MOESM1_ESM.jpg

Online Resource 1. Map showing locations of collecting sites for this study. Details for each numbered locality are given in Table 1 (JPEG 8993 kb)

606_2016_1277_MOESM2_ESM.jpg

Online Resource 2. Proof of principle restriction digests. A. trnK restriction digest with Hpy188I: lane 1 contains Easyladder (Bioline), lanes 2-4 contain samples from haplotype Group 3 and lanes 5-7 contain samples from haplotype Groups 1 and 2. B. trnK restriction digest with ApoI: lane 1 contains Easyladder (Bioline), lanes 2-3 contain samples from haplotype Group 1 and lanes 4-5 contain samples from haplotype Group 2. C. ITS2 restriction digest with ApoI: lane 1 contains Hyperladder (Bioline), lanes 2-4 contain samples from ITS Clade 2 and lanes 5-7 contain samples from ITS Clade 3 (JPEG 157 kb)

606_2016_1277_MOESM3_ESM.pdf

Online Resource 3. Strict consensus tree from MP analysis of combined cpDNA markers. This tree was used as input for the program Haploviewer to generate the haplotype network shown in Fig. 3. Bootstrap support is shown above branches and PP from Bayesian analysis is shown below branches. * = species not identified to variety due to lack of reproductive material (PDF 512 kb)

606_2016_1277_MOESM4_ESM.jpg

Online Resource 4. Sequencing chromatograms of putative hybrid (PAF160) and typical chromatograms of the ITS Clades 2 and 3. At bases which differentiate Clades 2 and 3, the putative hybrid has two peaks, representing both alternative bases and indicating the presence of two types of ITS copies in the genome of this individual (JPEG 146 kb)

Information on Electronic Supplementary Material

Information on Electronic Supplementary Material

Online Resource 1. Map showing locations of collecting sites for this study.

Online Resource 2. Proof of principle restriction digests.

Online Resource 3. Strict consensus tree from MP analysis of combined cpDNA markers.

Online Resource 4. Sequencing chromatograms of putative hybrid (PAF160) and typical chromatograms of the ITS Clades 2 and 3.

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French, P.A., Brown, G.K. & Bayly, M.J. Incongruent patterns of nuclear and chloroplast variation in Correa (Rutaceae): introgression and biogeography in south-eastern Australia. Plant Syst Evol 302, 447–468 (2016). https://doi.org/10.1007/s00606-016-1277-7

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