A large proportion of functional sequence within mammalian genomes falls outside 
protein-coding exons and can be transcribed into long RNAs. However, the roles 
in mammalian biology of long noncoding RNA (lncRNA) are not well understood. Few 
lncRNAs have experimentally determined roles, with some of these being 
lineage-specific. Determining the extent by which transcription of lncRNA loci 
is retained or lost across multiple evolutionary lineages is essential if we are 
to understand their contribution to mammalian biology and to lineage-specific 
traits. Here, we experimentally investigated the conservation of lncRNA 
expression among closely related rodent species, allowing the evolution of DNA 
sequence to be uncoupled from evolution of transcript expression. We generated 
total RNA (RNAseq) and H3K4me3-bound (ChIPseq) DNA data, and combined both to 
construct catalogues of transcripts expressed in the adult liver of Mus musculus 
domesticus (C57BL/6J), Mus musculus castaneus, and Rattus norvegicus. We 
estimated the rate of transcriptional turnover of lncRNAs and investigated the 
effects of their lineage-specific birth or death. LncRNA transcription showed 
considerably greater gain and loss during rodent evolution, compared with 
protein-coding genes. Nucleotide substitution rates were found to mirror the in 
vivo transcriptional conservation of intergenic lncRNAs between rodents: only 
the sequences of noncoding loci with conserved transcription were constrained. 
Finally, we found that lineage-specific intergenic lncRNAs appear to be 
associated with modestly elevated expression of genomically neighbouring 
protein-coding genes. Our findings show that nearly half of intergenic lncRNA 
loci have been gained or lost since the last common ancestor of mouse and rat, 
and they predict that such rapid transcriptional turnover contributes to the 
evolution of tissue- and lineage-specific gene expression.