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The mammalian family of bears (Ursidae) comprises eight extant species, occurring on four different continents. Among them are the iconic and well-known brown and polar bears, both widely distributed across the Northern hemisphere. Their intraspecific genetic structuring has been extensively investigated, albeit with a focus on genetic markers from maternally inherited parts of their genomes (mitochondrial DNA). The evolutionary relationship and divergence time between brown and polar bears have recently triggered an extensive debate, while less focus has been put on to other parts of the ursid phylogeny, particularly to a clade of three Asian bear species. To date, whole genomes of more than 100 bear individuals from four different species have been sequenced. Yet, one fundamental part of the genome has been largely omitted from specific analyses, in bears as well as in most other mammals: the Y chromosome.
The mammalian Y chromosome provides a unique perspective on the evolutionary history of organisms due to its distinct features, and specifically reflects the patriline because of its male-specific inheritance. The characteristics of this chromosome make it well suited to complement and contrast evolutionary inferences based on other genetic markers, and to uncover processes like sex-biased gene flow and hybridization. The unique insights that can be gained from analyses of Y-linked genetic variation made me utilize this part of the genome to investigate the evolution of male lineages in bears. Studying the patriline is particularly promising in this taxonomic group because of male-biased dispersal and a complex and fast radiation of bears. The analysis of Y-chromosomal genetic markers is thus the common theme of this dissertation: I present the identification of large amounts of Y-chromosomal sequence, the development of male-specific markers from such sequences, and the application of these markers to trace the evolution of male lineages of different bear species.
Specifically, I developed a molecular sex determination system based on the detection of two Y-linked fragments that allows to reliably discriminate between females and males from seven different bear species (Bidon et al. 2013). The approach is highly sensitive, bear-specific, and can be applied in standard molecular laboratories. This makes it valuable in conservation genetics and forensic applications, e.g. to analyze non-invasively collected samples.
Furthermore, I used Y-linked markers in a comprehensive and range-wide sample of brown and polar bears, and show that male-biased gene flow plays an important role in distributing genetic material throughout the ranges of both species (Bidon et al. 2014). In brown bears, I detected a lack of paternal population structuring which is in strong contrast to the detailed structuring of the matriline.
Analyzing Y-chromosomal sequences from all eight bear species, I present a phylogeny of the patriline that largely resembles the topology from other nuclear markers but is different from the topology of the mitochondrial gene tree (Kutschera et al. 2014). This discordance among loci generates interesting hypotheses about inter-species gene flow, particularly among American and Asiatic black bears.
With the identification of almost two million basepairs of Y-chromosomal sequence and the analysis of an unprecedented large male-specific dataset in polar bears, a high-resolution view on the distribution of their intraspecific variation was obtained (Bidon et al. 2015). In particular, two clades that are divergent but do not show pronounced phylogeographic structure were detected, confirming the great dispersal capacity of males of this high arctic species.
This dissertation thus represents a comprehensive investigation of Y-linked genetic variation on the intra- and interspecific level in a non-model organism. With my research, I contribute to an increased understanding of the complex evolutionary history of bears. In particular, I show that male-biased gene flow strongly influences the distribution of nuclear genetic variation, and that the contrast between phylogenies of differentially inherited markers can help to understand interspecific hybridization between closely related species. Moreover, my findings demonstrate the potential of Y-chromosomal markers to uncover unknown evolutionary patterns and processes. This applies not only to bears but to many species, even such that are generally well known and well described.