TY - BOOK

T1 - The evolutionary significance of incomplete lineage sorting (ILS) in animals

AU - Li, Fang

PY - 2021

Y1 - 2021

N2 - Understanding the evolutionary history of species and individual genes are important for our study on the origin and evolution of phenotypic trait. It is very common that gene trees disagree with the species tree in phylogenetic analysis. This incongruence poses challenges on tree of life construction and further biology character research. The reason behind such incongruence includes incomplete lineage sorting (ILS) and introgression.Randomly inheritance of polymorphism in the ancestor population by descendant species in ILS or gene flow by hybridization after speciation would lead to closer relationship for distant species. ILS and introgression have frequently been reported in some closely related species but the investigation in a broad phylogenetic range is still rare.This PhD thesis is an attempt to systematically explore ILS and introgression in two animal groups, the genus Drosophila and the order Primate. In the first chapter, I compared the genomes of 47 Drosophila species, including 15 newly sequenced by us and 20 which we have improved with additional sequence data. Based on these genomes, we resolve several previously ambiguous relationships, especially among subgroups in the melanogaster species group. We also found extensive incomplete lineage sorting could explain many previously ambiguous relationships in subgenus Sophophora, while high level of asymmetric introgression contributed to the difficult node of subgenus Drosophila.In the second chapter, I reconstructed the phylogeny of 49 primate species using the full genomes, including 29 newly sequenced by us and 20 released before. Based on these genomes, we re-construct the species tree that resolved the long-standing controversial relationships within the gibbon lineage and the diversification process of the New World Monkeys. The phylogenetic analysis for individual genes revealed a high proportion of gene tree and species tree discordance in primate species. We inferred that most of this discordance is best explained by incomplete lineage sorting (ILS) rather than introgression.In the third chapter I further explored if ILS contribute to the functional diversification and adaptive selection across species. Firstly the Gene Ontology analysis showed that the genes include high proportion of ILS signal cover broad functions, implying broad impact of ILS to the biological functions. Secondly there is no significant correlation between ILS and gene expression on whole genome scale, however, some genes include high proportion of ILS signal in their regulatory regions also show higher similar expression pattern between the lineages inherited same ancestral loci.Finally, I sought to identify ILS sites that are under positive selection in both lineages that inherited the same genotypes. Using the lineage of great apes as an example, I discovered ten genes contain loci with same genotypes between human and gorilla and are under positive selection in the ancestral population. The presence of these genes highlighted the possibility that the genomic sequences affected by ILS might introduce genetic materials that favored by natural selection in distance species.

AB - Understanding the evolutionary history of species and individual genes are important for our study on the origin and evolution of phenotypic trait. It is very common that gene trees disagree with the species tree in phylogenetic analysis. This incongruence poses challenges on tree of life construction and further biology character research. The reason behind such incongruence includes incomplete lineage sorting (ILS) and introgression.Randomly inheritance of polymorphism in the ancestor population by descendant species in ILS or gene flow by hybridization after speciation would lead to closer relationship for distant species. ILS and introgression have frequently been reported in some closely related species but the investigation in a broad phylogenetic range is still rare.This PhD thesis is an attempt to systematically explore ILS and introgression in two animal groups, the genus Drosophila and the order Primate. In the first chapter, I compared the genomes of 47 Drosophila species, including 15 newly sequenced by us and 20 which we have improved with additional sequence data. Based on these genomes, we resolve several previously ambiguous relationships, especially among subgroups in the melanogaster species group. We also found extensive incomplete lineage sorting could explain many previously ambiguous relationships in subgenus Sophophora, while high level of asymmetric introgression contributed to the difficult node of subgenus Drosophila.In the second chapter, I reconstructed the phylogeny of 49 primate species using the full genomes, including 29 newly sequenced by us and 20 released before. Based on these genomes, we re-construct the species tree that resolved the long-standing controversial relationships within the gibbon lineage and the diversification process of the New World Monkeys. The phylogenetic analysis for individual genes revealed a high proportion of gene tree and species tree discordance in primate species. We inferred that most of this discordance is best explained by incomplete lineage sorting (ILS) rather than introgression.In the third chapter I further explored if ILS contribute to the functional diversification and adaptive selection across species. Firstly the Gene Ontology analysis showed that the genes include high proportion of ILS signal cover broad functions, implying broad impact of ILS to the biological functions. Secondly there is no significant correlation between ILS and gene expression on whole genome scale, however, some genes include high proportion of ILS signal in their regulatory regions also show higher similar expression pattern between the lineages inherited same ancestral loci.Finally, I sought to identify ILS sites that are under positive selection in both lineages that inherited the same genotypes. Using the lineage of great apes as an example, I discovered ten genes contain loci with same genotypes between human and gorilla and are under positive selection in the ancestral population. The presence of these genes highlighted the possibility that the genomic sequences affected by ILS might introduce genetic materials that favored by natural selection in distance species.

M3 - Ph.D. thesis

BT - The evolutionary significance of incomplete lineage sorting (ILS) in animals

PB - Department of Biology, Faculty of Science, University of Copenhagen

ER -