Federica Di Palma

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature. A reference genome sequence for threespine sticklebacks, and re-sequencing of 20 additional world-wide populations, reveals loci used repeatedly during vertebrate evolution; multiple chromosome inversions contribute to marine-freshwater divergence, and regulatory variants predominate over coding variants in this classic example of adaptive evolution in natural environments. Threespine sticklebacks have become a powerful model for studying the molecular basis of adaptive evolution. This paper presents a high-quality reference genome sequence, along with genomes of 20 further individuals from a global set of marine and freshwater populations. Genomic analysis reveals that reuse of globally shared standing genetic variation plays an important part in repeated evolution of distinct stickleback populations, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. The data are consistent with an important role for regulatory changes during parallel evolution of marine and freshwater sticklebacks.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease. This comparative genomics study, comparing the complete human genome sequence with those of 29 placental mammals, including chimpanzees, mice and dogs, identifies 4.2% of the human genome as constrained by evolutionary selection, and ascribes a potential function to about 60% of these constrained bases. A series of evolutionary signatures emerges, providing insights into coding and non-coding functional genomic elements, candidate RNA structural families and aspects of genome organization and evolution. Overlap with disease-associated variants indicates that the findings will be relevant for studies of human disease.

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification. Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification. The 2,000 or so species of cichlid fish, to be found in the lakes and rivers of Africa's Rift Valley, provide the classic example of adaptive radiations. This large-scale international collaboration has sequenced and analysed the genomes and transcriptomes of five distinct lineages of African cichlids. The data reveal an excess of gene duplications in comparison to other fish species. There is an abundance of non-coding element divergence; accelerated coding sequence evolution; expression divergence associated with transposable element insertions in orthologous gene pairs; and regulation by novel miRNAs. Sequencing data from sixty individuals from six closely related Lake Victoria species point to rapid cichlid speciation associated with genome-wide diversifying selection on coding and regulatory variants, and imply that ancient periods of relaxed purifying selection enabled the accumulation of standing variation, which may have been important in facilitating diversification.

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution. Genome sequencing and phylogenomic analysis show that the lungfish, not the coelacanth, is the closest living relative of tetrapods, that coelacanth protein-coding genes are more slowly evolving than those of tetrapods and lungfish, and that the genes and regulatory elements that underwent changes during the vertebrate transition to land reflect adaptation to a new environment. The African coelacanth (Latimeria chalumnae) attracted international attention when a specimen was netted off the South African coast in 1938, as coelacanths were thought to have gone extinct 70 million years ago. Now its genome has been sequenced. Phylogenomic analysis resolves the long-standing question of which lobe-finned fish is the closest living relative of the land vertebrates — it is the lungfish, and not the coelacanth. The protein-coding genes of the coelacanth are slowly evolving, which perhaps explains how similar today's coelacanth looks to its 300-million-year-old fossil ancestors. Examination of changes in genes and regulatory elements shows the importance of factors including brain and fin development, immunity and nitrogen excretion in the adaptation of vertebrates to land.