Genomics of Hybridization and Adaptation in Primates
Dissertation
Datum der mündl. Prüfung:2023-11-22
Erschienen:2023-12-07
Betreuer:Prof. Dr. Lutz Walter
Gutachter:Prof. Dr. Lutz Walter
Gutachter:Prof. Dr. Bernd Wollnik
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Zusammenfassung
Englisch
In chapter 1, we used high coverage (30X) whole genome sequences from 225 wild baboons (genus Papio) representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population, those from western Tanzania, with a genetic composition that is derived from three distinct lineages (yellow, olive and Kinda baboons). The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. In chapter 2, we conducted a phylogenomic analysis of macaques (genus Macaca) using 16 newly generated (30X) and eight published macaque genomes. First, we found strong support for the division of macaques into seven species groups. Second, we identified incomplete lineage sorting (ILS) as the primary factor contributing to the discordance observed among gene trees, but we also found evidence for hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages which resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, we used our phylogenomic results to establish a scenario for macaque radiation. Our findings provide insights into ILS and potential ancient introgression events involved in the radiation of macaques, which contribute to a better understanding of rapid speciation events in non-human primates. In chapter 3, we present a high-quality genome assembly (Tfra_5.0, N50 98.23 Mb) of a limestone langur (Trachypithecus francoisi) and genome resequencing data (30X) of 48 langurs representing 15 of the 22 recognized species. We found that genes related to ion channels (Na, Ca, K, Se, and others) exhibit significantly faster evolutionary rates in limestone langurs compared to other langurs. Limestone langur-specific mutations in ion channel proteins alter the inward ion current in cells in-vitro, and some mutations cause dysfunction of ion channels (channelopathies) in humans. Furthermore, a mutation (Glu94Asp) in the melanocortin 1 receptor (MC1R) results in increased levels of basal cyclic adenosine monophosphate (cAMP) production, which may be responsible for the dark coat color of limestone langurs. Our study reveals the adaptive evolution of ion channels and pelage color and provides insights into human channelopathies and vertebrate pigmentation. In chapter 4, we investigated the genetic load, adaptive potential and population history of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam’s famous Ha Long Bay and with ca. 70 living individuals one of the most threatened primates in the world. Using high-coverage (30X) whole genome data of four wild individuals, we revealed a 5-fold decline in effective population size Ne over the last 100 years. Compared to other primates and mammals, the Cat Ba langur showed extremely low levels of genetic diversity and long runs of homozygosity, but genetic diversity has been maintained in protein-coding genes and on chromosome 19, an autosome known for its unusual high gene density. Further, we found no evidence for an excess of either deleterious or loss-of-function mutations in a homozygous state. At the same time, the Cat Ba langur exhibits a large number of unique non-synonymous variants and genes under positive selection that are related to calcium and sodium metabolism, muscle contraction and the cardiovascular system, which may have improved adaptation to saltwater consumption and high calcium intake as well as climbing ability. This study provides important baseline data for conservation and evidence for unique adaptation to harsh environments. Finally, we show that species exhibiting low overall genetic diversity can still preserve diversity in functionally important regions.
Keywords: Genomic; Hybridization; Adaptation; Evolution