Genomic Diversity And Comparative Phylogenomics In Malvales With A Focus On Dipterocarpaceae Using NGS Data

Evolutionary relationships in Malvales(with more than > 6000 spp)are of great interest as the order contains an exceptional number of ecologically and economically important families.However,many of these remain understudied and their evolutionary relationships unclear,as the historical classification is based entirely on morphological characters,many of which are now deemed highly confusing.Marker-based phylogenies have helped clear some patterns,but major uncertainties remain.In other groups,the application of genome-scale data has shown great promise at resolving intricate relationships in highly specious,recently evolved taxa.The absence of a fully resolved(sub-)family level phylogeny and inclusion of basal species in families such as the Dipterocarpaceae is prohibiting the construction of a global hypothesis for evolution in either.This has major consequences for our ability to sustainably utilize species,and conserve and assess genetic diversity.Dipterocarpaceae(and other species)in the order Malvales form the dominant structural components of Asian tropical wet lowland forest and are the economically most important native tree family for wood production.Increasing anthropogenic pressures on the family for wood production in tropical Asia make it essential to resolve their complex phylogenomic relationships and understand the distribution of genetic diversity across the range and between/within species.Here,we explored the distribution of genomic diversity within and between ecologically and economically import plant species in the Malvales order by using cutting edge NGS,bioinformatic and genomic tools,in order to understand and describe their classification,evolution,adaptation and divergence.We employed Maximum Likelihood and Bayesian phylogenetics of whole plastome and NRC datasets,and Bayesian molecular divergence time estimation to reconstruct evolutionary relationships in Malvales,with a focus on representatives from the nine subfamilies in Malvaceae s.l.and all genera in tribe Shoreae and over half of the genera in tribe Dipterocarpeae in subfamily Dipterocarpoideae,family Dipterocarpaceae.The chapter on the utility of genomic data in resolving the evolution of Malvaceae s.l.presents the first fully resolved phylogenomic backbone including representatives of all nine subfamilies.It resolves the placement of rare Brownlowioideae and presents a first hypothesis identifying morphological synapomorphies for the nine major subfamilies in the order.Stem groups of most subfamilies originated during humid and hot conditions during the Late Cretaceous(Helicteroideae,Sterculioideae,Bombacoideae,Malvoideae,and Brownlowioideae)or a subsequent warm phase in the Paleocene(Grewioideae,Bynttnerioideae,Dombeyoideae,Tilioideae)when tropical vegetation was globally widespread.We explored the complex relationship between geographic distribution and distribution of genomic diversity within Dipterocarpaceae occurring on the edge of the family's range(the northern limit running through southern China).Results describe low levels of genomic diversity(even between genera)among analyzed range-edge species,and phylogenomic incongruence in the signals provided by chloroplast vs nuclear DNA.This is of particular interest,as(sub-)tropical taxa at the edge of the distribution range are exposed to a wider extent of habitat-and climate conditions.As such,they are expected to have a different response to climate change from taxa occurring with the core of the tropical distribution area.These results lay the basis for future work in Dipterocarpaceae,needed to better understand the contrasting patterns between these groups.The chapter describing the evolution and newly proposed(sub-)sectional classification of the subfamily Dipterocarpoideae using chlorplost and nuclear DNA resolves the phylogenetic uncertainty in the placement and divergence time of species including all genera in tribe Shoreae and over half of the genera in tribe Dipterocarpeae.Our results are in agreement with previous studies but offer more resolution at lower taxonomic levels and provide evidence for previously doubtful placements of Parashorea and Neobalanocarpus heimii,sections and subsections of the genera Anisoptera,Hopea,Shorea and Vatica,and the position of Dipterocarpus and Dryobalanops.Parashorea is closely related to Shorea.Hypotheses of Neobalanocarpus heimii's origin by intergeneric hybridisation between Anthoshorea(maternally inherited)and Hopea(paternally inherited)species were corroborated.Results clarify a longstanding issue in the tribal and sectional distinction in the family,important not only for our understanding of the evolution and designation of taxa contained within,but also crucial for reconstruction of the temporal divergence and patterns of flower and fruit innovation.A new tribal classification of Dipterocarpoideae is proposed here,consisting of 4 tribes: 1/ Dipterocarpeae;2/ Dryobalaneae;3/ Shoreae;and 4/ Vaticeae.A further restructuring of sections and the elevation of some of these to generic rank is proposed,based in this molecular data and already available morphological data.Genomic data also describes the origin of Neobalanocarpus heimii by intergeneric hybridisation between Anthoshorea(maternally inherited)and Hopea(paternally inherited).Molecular dating results places the origin of the Dipterocarpoideae around 51.78 Ma which places it ca.40 Ma after the family's currently proposed origin(the Upper Cretaceous,ca.93 Ma).It is expected that development of genome-scale resources in these groups will finally resolve long-discussed puzzled patterns of flower and fruit evolution,ecological adaptation,historical biogeography and evolutionary relationships.In turn,these resources will prove invaluable in providing the basis for conservation of genetic resources and crop improvement of the many promising and valuable species in this order.Analyses of the plastome data provided well-resolved and supported phylogenetic trees largely clarifying phylogenetic relationships of analysed species.Nuclear-ribosomal cistron data congruently supported plastome derived phylogenies,but support of the backbone phylogeny was poor impeding further assessment of gene-tree incongruence.This work demonstrates that the application of genome-scale data is able to provide the muchneeded phylogenomic resolution and framework required in downstream genetic,evolutionary and biogeographic analyses.Furthermore,it is able to provide the baseline information needed in conservation assessments and ex-situ cultivation.NGS provides good resolution at hitherto poorly resolved relationships at both high and lower taxonomic levels.The provided data are a valuable genomic resource that can aid in further taxonomic revisions and evolutionary studies in Malvales.Data and results presented here provide resources for addressing urgent questions regarding the effects of species loss and climate change in a dominant tropical tree group.As of yet,no fully sampled classification based on molecular data has been presented,and our studies makes important progress towards resolving past uncertainties in both classification and evolutionary relationships.This serves as a basis for further completing our understanding of this enigmatic group.