Phylogenomics and diversification in subtribe Malinae

Hybridisation, polyploidy (the possession of more than two chromosome sets) and apomixis (asexual reproduction via seeds) constitute an evolutionary syndrome considered key for organismic diversification in several major plant families including the sunflower family, buttercup family, or rose family. We will study the consequences of this syndrome for organismic diversification in the subtribe Malinae (i.e. apple, pear and their about 25 related genera, all of which distributed in the Northern Hemisphere) and genus Crataegus (hawthorns including medicinally important species) as models. We address two main aims: (1) We expect that unintended sequencing of duplicated genes (leading to false placement of affected individuals in phylogenetic reconstructions), incomplete lineage sorting (the stochastic sorting of ancestral molecular variants into phylogenetic lineages), and reticulate events (i.e. hybridisation) all played a significant role in the evolution of the Malinae and Crataegus. We aim to identify the relative role of these processes and causes and to solve existing phylogenetic conflicts in the placement of genera and species. (2) We will study the origin of species diversity in Eurasian hawthorns. We are particularly interested to understand the role of ancient sexual species (so-called orthospecies) in the origin of derived, often asexual species (so-called nothospecies) and to clarify their validity as species of their own right. Traditional phylogenetic studies were hampered by low numbers of available and affordable markers, lack of knowledge of genomic location of markers, and in Malinae, by low sequence divergence and resolution of markers. Our study promises to overcome these limits in basing phylogenetic reconstructions on a dense sample of orthologs (markers which have a single and identical origin) covering the whole genome. We will use High-throughput sequencing to identify non-linear relationships using phylogenetic network techniques and build species phylogenies from mutually congruent gene trees. High-throughput sequencing revolutionized the methodological repertoire of DNA-molecular techniques available to biologists and provides access to unchallenged high levels of resolution and accuracy of data and analyses. Although extensive work has been attributed to taxonomic characterization, applications of modern approaches to study the systematics of Eurasian Crataegus are virtually missing. Here we make the theoretically and analytically important step from traditional morphology-based taxonomy to an integrative evolutionary approach for species delimitation based aside of classical morphology on molecular phylogenetics and cytological data (flow cytometry by which we estimate number of chromosome sets and reproductive mode of individuals).