Crop-to-wild introgression in the European wild apple Malus sylvestris in Northern Britain 2 3 MARKUS RUHSAM

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Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae)

ACKNOWLEDGEMENTS We thank the management of the National Parks Board and Singapore Botanic Gardens for providing continuous support, facilities and fieldwork approval in Singapore’s nature reserves. We appreciate the digital research team at the University of Aberdeen and the research/scientific computing teams at The James Hutton Institute and NIAB for providing technical support while using the computational resources on the respective HPC clusters, “Maxwell” and the “UK Crop Diversity Bioformatics HPC” (BBSRC grant BB/S019669/1), which have contributed to the results within this paper. We thank numerous staff at the Singapore Botanic Gardens, particularly Khoo-Woon Mui Hwang and Neo Wei Ling for strong technical support in the molecular lab, Matti Niissalo for generous sharing of lab protocols and bioinformatics tips, Choo Le Min for patient help with lab troubleshooting, Chong Kwek Yan and Chan Pin Jia for forest survey expertise, and Louise Neo for thoughtful field and R advice. Our sincere thanks are due to Herbarium staff at the Royal Botanic Garden Edinburgh, including Lesley Scott, for efficient assistance in sending silica-dried samples to the Singapore Botanic Gardens. We also thank Camille Christe at the Conservatoire et Jardin botaniques de la Ville de Genève for kind advice related to the taxon-specific baits’ setup and purchase FUNDING We are grateful to the Lady Yuen Peng McNeice Charitable Foundation for financial support of this study.Peer reviewedPublisher PD

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns

Evolutionary diversification of new caledonian Araucaria

New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a ‘museum’ for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island for the radiation of the Pacific Araucaria sect. Eutacta clade.Mai Lan Kranitz, Edward Biffin, Alexandra Clark, Michelle L. Hollingsworth, Markus Ruhsam, Martin F. Gardner, Philip Thomas, Robert R. Mill, Richard A. Ennos, Myriam Gaudeul, Andrew J. Lowe, Peter M. Hollingswort

Evolutionary consequences of hybridyzation between Guem urbanum and G. rivale

Theoretical considerations predict that hybridization between plants with different breeding systems could potentially be a powerful evolutionary force but very few studies have been carried out to investigate hybridization among outcrossing and selfing species in natural populations. The objective of this thesis was to use G. urbanum and G. rivale, two freely hybridizing species with putatively different breeding systems, and study the processes that take place when the two different mating systems meet. To establish the extent of the morpholofical and genetic marker differences, the breeding system and levels of inbreeding depression in these two species, I examined reference populations from various locations in Great Britain using morphological (nine phenotypic traits) and genetic analyses of a long standing hybrid swarm between G. urbanum and G. rivale, the results revealed that the two parental species differed signigicanly in all nine traits measured and were clearly separated by 616 AFLP markers, of which 8% were species-specific. The breeding system analysis confirmed the highly selfing nature of G. urbanum and the outcrossing nature of G. rivale. No inbreeding depression was discovered in G. urbanum and very low levels in G. rivale. The AFLP analysis (203 loci) of the hybrid swarm showd that four distinct genetic groups can be distinguished (1) a parental G. urbanum life group (2) an F1 like group (3) a Backcross Rivale group and (4) a parental G. rivale like group. No Backcross Urbanum individuals were detected. Morphological data were hightly correlated with genetic data (Spearman Rank Order Correlation = 0.08,p<0.0001) but less informative as morphological data could not separate the Backcross Rivale samples from G. rivale. Analysis of seed progeny from the hybrid swarm showed that there were clear differences in the genotypic composition of the seed porgeny and the plants from which they were collected, revealing additional genetic classes such as Backcross Urbanum individuals which were not represented in the adult plant state. The Backcross Rivale parental group was the only one in which the average offspring position did not differ signigicantly from the mean parental psition in a PCO plot using 203 AFLP markers, indicating that this group might be reporductively isolated from other groups in the hybrid swarm. Taken together the results suggest that hybridization between G. urbanum and G. rivale results in the production of a range of genotypic and phenotypic classes, some of which are selected against. There is evidence for introgression between these two species, and tentative evidence for partial reporduction isolation of some hybrids suggestion that hybridisation between these outcrossing and selfing Geum species may represent a creative evolutionary force

Evolutionary consequences of hybridization between Geum urbanum and G. rivale

Theoretical considerations predict that hybridization between plants with different breeding systems could potentially be a powerful evolutionary force but very few studies have been carried out to investigate hybridization among outcrossing and selfing species in natural populations. The objective of this thesis was to use G. urbanum and G. rivale, two freely hybridizing species with putatively different breeding systems, and study the processes that take place when the two different mating systems meet. To establish the extent of the morpholofical and genetic marker differences, the breeding system and levels of inbreeding depression in these two species, I examined reference populations from various locations in Great Britain using morphological (nine phenotypic traits) and genetic analyses of a long standing hybrid swarm between G. urbanum and G. rivale, the results revealed that the two parental species differed signigicanly in all nine traits measured and were clearly separated by 616 AFLP markers, of which 8% were species-specific. The breeding system analysis confirmed the highly selfing nature of G. urbanum and the outcrossing nature of G. rivale. No inbreeding depression was discovered in G. urbanum and very low levels in G. rivale. The AFLP analysis (203 loci) of the hybrid swarm showd that four distinct genetic groups can be distinguished (1) a parental G. urbanum life group (2) an F1 like group (3) a Backcross Rivale group and (4) a parental G. rivale like group. No Backcross Urbanum individuals were detected. Morphological data were hightly correlated with genetic data (Spearman Rank Order Correlation = 0.08,p<0.0001) but less informative as morphological data could not separate the Backcross Rivale samples from G. rivale. Analysis of seed progeny from the hybrid swarm showed that there were clear differences in the genotypic composition of the seed porgeny and the plants from which they were collected, revealing additional genetic classes such as Backcross Urbanum individuals which were not represented in the adult plant state. The Backcross Rivale parental group was the only one in which the average offspring position did not differ signigicantly from the mean parental psition in a PCO plot using 203 AFLP markers, indicating that this group might be reporductively isolated from other groups in the hybrid swarm. Taken together the results suggest that hybridization between G. urbanum and G. rivale results in the production of a range of genotypic and phenotypic classes, some of which are selected against. There is evidence for introgression between these two species, and tentative evidence for partial reporduction isolation of some hybrids suggestion that hybridisation between these outcrossing and selfing Geum species may represent a creative evolutionary force.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Evolutionary consequences of hybridization between Geum urbanum and G. rivale

Theoretical considerations predict that hybridization between plants with different breeding systems could potentially be a powerful evolutionary force but very few studies have been carried out to investigate hybridization among outcrossing and selfing species in natural populations. The objective of this thesis was to use G. urbanum and G. rivale, two freely hybridizing species with putatively different breeding systems, and study the processes that take place when the two different mating systems meet. To establish the extent of the morpholofical and genetic marker differences, the breeding system and levels of inbreeding depression in these two species, I examined reference populations from various locations in Great Britain using morphological (nine phenotypic traits) and genetic analyses of a long standing hybrid swarm between G. urbanum and G. rivale, the results revealed that the two parental species differed signigicanly in all nine traits measured and were clearly separated by 616 AFLP markers, of which 8% were species-specific. The breeding system analysis confirmed the highly selfing nature of G. urbanum and the outcrossing nature of G. rivale. No inbreeding depression was discovered in G. urbanum and very low levels in G. rivale. The AFLP analysis (203 loci) of the hybrid swarm showd that four distinct genetic groups can be distinguished (1) a parental G. urbanum life group (2) an F1 like group (3) a Backcross Rivale group and (4) a parental G. rivale like group. No Backcross Urbanum individuals were detected. Morphological data were hightly correlated with genetic data (Spearman Rank Order Correlation = 0.08,p<0.0001) but less informative as morphological data could not separate the Backcross Rivale samples from G. rivale. Analysis of seed progeny from the hybrid swarm showed that there were clear differences in the genotypic composition of the seed porgeny and the plants from which they were collected, revealing additional genetic classes such as Backcross Urbanum individuals which were not represented in the adult plant state. The Backcross Rivale parental group was the only one in which the average offspring position did not differ signigicantly from the mean parental psition in a PCO plot using 203 AFLP markers, indicating that this group might be reporductively isolated from other groups in the hybrid swarm. Taken together the results suggest that hybridization between G. urbanum and G. rivale results in the production of a range of genotypic and phenotypic classes, some of which are selected against. There is evidence for introgression between these two species, and tentative evidence for partial reporduction isolation of some hybrids suggestion that hybridisation between these outcrossing and selfing Geum species may represent a creative evolutionary force.EThOS - Electronic Theses Online ServiceGBUnited Kingdo