Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNA molecules that function in a wide range of biological processes, including the inactivation of sex chromosomes, imprinting and the regulation of gene expression. Despite their obvious biological importance, lncRNAs are the least understood class of genomic transcripts. Little is known about how they originate, how they acquire and evolve regulatory capacity, and how they function. Not surprisingly then, little is also known about the role that lncRNAs have played in the evolution of lineage-specific mammalian traits.This proposal combines molecular biology and evolutionary genetics tools to study the evolution and function of lncRNAs, and to evaluate their potential role in the specification of mammalian phenotypes. In this project I propose to generate a comprehensive and well-annotated set of mammalian long intergenic non-coding RNAs (lincRNAs) that – importantly – will include their regulatory regions. With this dataset, I aim to address the two main objectives of this proposal. Objective 1 is to identify the molecular mechanisms that generate novel lincRNAs, including how novel lincRNAs evolve their transcriptional regulation. By studying lncRNAs across 13 species that represent all major mammalian lineages, I will also investigate differences between lineages/species in the types of lncRNAs that they posses. Objective 2 is to identify networks of genes regulated by lincRNAs that underlie novel mammalian traits, and to investigate differences between species/lineages in these gene networks.This proposal will significantly advance the scientific community’s understanding of lncRNAs, including how these molecules have contributed to the functional evolution of mammalian genomes.