Parrot Genomes and the Evolution of Heightened Longevity and Cognition

Abstract

Summary Parrots are one of the most distinct and intriguing group of birds, with highly expanded brains [1], highly developed cognitive [2] and vocal communication skills [3], and a long lifespan compared to other similar-sized birds [4]. Yet the genetic basis of these traits remains largely unidentified. To address this question, we have generated a high-coverage, annotated assembly of the genome of the Blue-fronted Amazon (Amazona aestiva), and carried out extensive comparative analyses with 30 other avian species, including 4 additional parrots. We identified several genomic features unique to parrots, including parrot-specific novel genes and parrot-specific modifications to coding and regulatory sequences of existing genes. We also discovered genomic features under strong selection in parrots and other long-lived birds, including genes previously associated with lifespan determination as well as several hundred new candidate genes. These genes support a range of cellular functions, including telomerase activity, DNA damage repair, control of cell proliferation, cancer, immunity, and anti-oxidative mechanisms. We also identified brain-expressed, parrot-specific paralogs with known functions in neural development or vocal learning brain circuits. Intriguingly, parrot-specific changes in conserved regulatory sequences were overwhelmingly associated with genes that are linked to cognitive abilities and have undergone similar selection in the human lineage, suggesting convergent evolution. These findings bring novel insights into the genetics and evolution of longevity and cognition, as well as provide novel targets for exploring the mechanistic basis of these traits.

Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

“…Several recent studies suggested that molecular convergence may be widespread in nature ( 51, 58, 60 ). However, while most previous examples were restricted to a few genes ( 55, 60, 64, 65 ) or to closely related species ( 61, 66 ), our results suggest that molecular convergence can be pervasive in clades separated by >650 million years of evolution and can affect hundreds of gene families.…”

Molecular specializations of deep cortical layer analogs in songbirds

“…SLIT1 is a target of FOXP2, a transcription factor linked to speech developmental disorder 90 , and it is differentially regulated during vocal development 76 , possibly contributing to the establishment of the RA to brainstem connection. PLXNC1 has undergone a partial duplication unique to parrots, and has been suggested as potentially linked to the expanded vocal and imitative abilities of that taxon 91 . Other axon guidance genes shown here to be differentially expressed in RA but not AId include RELN and PLNXA4 , both of which also contribute to neuronal migration 92 , 93 , and RTN4R and LINGO1 , both key components of the Nogo receptor complex and known regulators of axonal growth and myelination 94 , 95 .…”

The Genetics of Aging: A Vertebrate Perspective

“…Naked mole rats have genetic variants under positive selection in telomeric repeat factor 1 (TRF1)-interacting nuclear factor 2 (TINF2), a gene that protects telomere integrity (Morgan et al, 2013). Long-lived species, such as myotis bats and parrots, also evolved mechanisms of telomere maintenance throughout lifespan (Foley et al, 2018;Wirthlin et al, 2018). The long-lived giant tortoise has unique variants in the DNA repair gene X-ray repair cross complementing 6 (XRCC6) (Quesada et al, 2019).…”