Parrot Genomes Provide Insights Into Evolution Of Longevity And Cognition

Analysis of the genome of an Amazon parrot and 26 other birds revealed that long-lived birds share a large number of similar mutations in genes associated with longevity, larger brains and advanced cognitive abilities — and parrots evolved new genes associated with learning speech

by GrrlScientist for Forbes | @GrrlScientist

Wild adult turquoise-fronted (or blue-fronted) Amazon parrot (Amazona aestiva), in the Pantanal, Brazil.
(Credit: Charles J Sharp / Sharp Photography / CC BY-SA 4.0)

“[M]y dream as a researcher is to discover the processes that allowed us to evolve complex vocal behaviors — everything from human speech, to dolphin communication, to birdsong, parrot imitation, and even the songs of bats (I’ve worked in all of these systems!),” evolutionary neuroscientist and genomicist, Morgan Wirthlin, who is a Brainhub Postdoctoral Fellow in Computational Biology at Carnegie Mellon University, said in email. (She was a graduate student at Oregon Health & Science University when most of this research was done.)

Dr. Wirthlin was part of a large international team of researchers whose analysis of the genome of an Amazon parrot and 26 other bird species revealed that parrots and other long-lived birds share a large number of similar mutations in genes associated with longevity. Their analysis also identified changes that are similar to those in human genes associated with larger brains and more advanced cognitive abilities — and it also found that parrots evolved new genes associated learning speech and songs.

Parrots have an especially long lifespan, even amongst birds

For most animals, lifespan is correlated with body size — the bigger you are and the more you weigh, the longer you live. But birds are special because most species have a disproportionately long lifespan compared to mammals with the same body mass. And then there’s parrots: Even amongst birds, they have an especially long life span. Is their remarkable longevity due to genetics? This question inspired Dr. Wirthlin and a large international team of scientists at several institutions in Brazil and in the United States to investigate.

To better understand the longevity of parrots and several other traits that make them special, Dr. Wirthlin and her collaborators sequenced the genome of a blue-fronted amazon parrot, Amazona aestiva, named Moises. This involved fragmenting the parrot’s chromosomes, sequencing the pieces and then using computers to correctly reassemble them. This cutting-edge process, known as genome assembly, has created a massive increase in high-quality sequence data along with a decrease in time and cost compared to older sequencing technologies.

Researchers have sequenced the genome of the blue-fronted Amazon parrot (Amazona aestiva), and used it to perform the first comparative study of bird genomes.
(Credit: Glaucia Seixas)

Dr. Wirthlin and her collaborators compared the blue-fronted amazon genome assembly with those of 22 other bird species, including five additional parrot species, all which have reliable longevity data.

In their analysis, the researchers divided the bird species into two groups: those with high-longevity (HL; species with a maximum recorded longevity at least 20% higher than predicted by body mass) and regular-longevity (RL; those with a maximum recorded longevity corresponding to or lower than predicted by body mass) (Figure 1A), based upon estimated corrections for wild versus captive birds (Figures 1B and 1C). In addition to parrots, HL birds included several other notably long-lived species (rock dove, chimney swift, little egret, and barn owl). It is important to note that high longevity is most parsimoniously interpreted as having evolved independently in these avian groups, as is clearly seen when examining the distribution of this trait mapped onto the currently accepted avian phylogeny (red dots; Figure 1A).

Figure 1. Phylogenetic Relationships and Longevity of Parrots, Including Amazona aestiva, in Relation to Other Birds
 (A) This schematic phylogeny, derived from previously published studies, depicts the relationship between parrots and all other birds analyzed in the longevity analyses (ref & ref). Red nodes indicate the occurrence of high longevity and were used as branches to test for nonneutral sequence evolution in long-lived birds against a null model using a likelihood ratio test. The photo depicts Moises, the adult male blue-fronted Amazon whose genome was sequenced for this study. (B and C) The expected lifespan of the 23 bird species analyzed for genomic signatures of longevity in plotted as a solid line, based on calculations derived from Prinzinger (ref) that describe the relationship between mass (log weight) and longevity (log years) for wild (B) and captive ( C ) birds. Species falling outside of the dashed lines deviate significantly from expected lifespan based on mass and are indicated with an “*.”

Convergent selection in long-lived birds points to previously unknown longevity-influencing genes

Comparative genome analysis revealed that parrots and other long-lived avians share highly conserved mutations in gene sets that are responsible for their abnormally long lifespan. For example, the expected lifespan for a parrot the size of an amazon parrot should be between 15–20 years, but the blue-fronted amazon has been documented to live as long as 66 years. A comparable lifespan for humans would be in the hundreds of years.

Dr. Wirthlin and her collaborators searched for the largest possible set of genes that are unequivocally present in all 23 avian study species, and found 4,132 single gene clusters. Comprehensive genome analyses revealed that 344 genes (8%) showed differential rates of evolution between HL and RL avians. These genes, which extend lifespan by supporting DNA damage repair, slowing cell death due to stress, and limiting cell overgrowth and cancer, displayed increased variability that could lead to new functions, whereas others showed evidence of higher stabilizing selection, a process where the genes did not change drastically over time.

Previously, a small subset of these genes (n = 20; 6%) had been identified as influencing ageing in fruit flies, Drosophila melanogaster, and in Caenorhabditis elegans worms, both of which are common laboratory research organisms — a finding that highlighted the universality of genetic influence over ageing in all animals, not just in parrots and other long-lived birds. It also served as an important internal validation for this study.

“We also found a few hundred genes that have not been implicated in lifespan before, which are good candidates to study further,” said co-senior author and behavioral neuroscientist, Claudio Mello, a professor at Oregon Health & Science University.

Many of these remaining gene clusters (n = 324, or 94%) were related to cell division, cell-cycle regulation, and RNA splicing and processing, with a smaller number potentially being associated with DNA damage and repair, mitochondrial function, and oxidative metabolism.

Telomerase, an anti-aging enzyme, experienced strong selection in long-lived birds

The strongest evidence for selective pressure in HL birds was shown by a gene known as TERT (telomerase reverse transcriptase), a large enzyme complex that lengthens or maintains telomeres located at the ends of chromosomes (Figure 2CD). Lengthening telomeres increases the number of times individual cells can divide, thereby boosting cellular life span and slowing the ageing process.

Figure 2. Genes Under Positive Selection in Long-Lived Birds.
( C ) Comparative multiple sequence alignment of TERT proteins across avian species and humans, with sites under positive selection in long-lived birds indicated in red and metal binding sites in green, all occurring within the reverse transcriptase domain, in blue. Scales indicate amino acid position within alignments.
( D ) Crystal structure of TERT reverse transcriptase catalytic subunit. Positively selected residues are in red, which are in close physical proximity to metal binding sites critical for catalytic activity, in green. PDB: TERT, 3DU6.

It’s important to note that excess TERT activity has a downside, too: it can increase the risk of runaway cell division — cancer. But parrots evolved a solution to protect against that potential outcome, too: they’ve duplicated other genes that regulate genomic stability and cell senescence, thereby balancing telomerase activity and cell cycle regulation so increased cancer rates are prevented even whilst longevity is increased.

Similar changes in parrot and human genomes suggest convergent evolution of cognition

Other — apparently parrot-specific — changes were noted in genes associated with brain development. Similar gene mutations are located near comparable genes linked to neural development in humans, too.

“These define how the brain grows and how many cells are built,” Professor Mello explained. “We saw that regulatory elements of genes related to brain development and function had similar modifications in humans and parrots. That means that some cognitive abilities may have evolved convergently in both humans and parrots.”

“I like to make the analogy of a dolphin, a shark, and an ichthyosaur — all completely unrelated animals that had to solve the same problem of becoming an apex predator underwater,” said Dr. Wirthlin in email. “And there are certain phenotypic features — torpedo body shape, pointed fins, sharp teeth — that optimally solve that problem. This is what I’m always looking for — what are the fundamental organizing principles that show up in the brains and genes of these animals that gave them the incredible ability to sing?”

Pet turquoise-fronted amazon eats from a spoon. (Credit: Love2bird / Public domain.)

This discovery underscores the finding that convergent expansion of this gene family occurred in both primates and parrots, along with the evolution of the larger brains and more advanced cognitive abilities, suggesting intriguing parallels to evolutionary mechanisms that may have facilitated the emergence of these traits in humans.

“Humans ended up with bigger brains and more brain cells and more cognitive traits — including language — than primates,” Professor Mello explained.

Additionally, this study identified a set of several dozen parrot-specific genes that that may be important for their defining traits, such as their ability to imitate sounds. In view of what we’ve learned from songbirds, which have de novo genes devoted to vocal leaning behaviors (ref), these parrot-specific de novo genes are promising candidates for regulating brain regions involved in vocal learning, cognition, and other special parrot traits, particularly mimicry.

“Learning to imitate sounds is the basis of speech in birds and in humans as well,” Professor Mello said. “It’s actually a very complex process, and we don’t fully understand how it happens. We know that species incapable of vocal learning will still make sounds if you deafen or isolate them from birth, because their sounds are innate. But isolate or deafen a young parrot, as has been shown in budgerigars, and it will not learn to vocalize properly.”

Animals that have the ability to learn speech or songs are rare. A better understanding of how they evolved this capacity would give experts more insight into a convergent evolutionary process in humans.

“Unfortunately, we didn’t find as many speech-related changes as I had hoped,” Dr. Wirthlin added.

Why study parrots?

“Parrots are fascinating and we can learn a lot, even about ourselves, by studying them and trying to understand their unique traits,” Professor Mello said in email. “Parrots have bigger brains than other birds and more communication skills, and they have similar conserved elements that set them apart.”

Wild adult turquoise-fronted amazon (Amazona aestiva), in the Pantanal, Brazil.
(Credit: Charles J Sharp / Sharp Photography / CC BY-SA 4.0)

Wild parrots live in family or social groups, which may have driven the evolution of traits such as complex social behaviors, the ability to imitate sounds and other cognitive abilities. Further, complex social structures are thought to have been a driving force behind the evolution of language in humans, too.

Professor Mello added that the blue-fronted Amazon parrot “is one of the most vocal, best imitator parrot species, and also particularly long-lived, with typical life span exceeding that predicted by its body weight by 2.5–3 fold. Also it is the quintessential tropical parrot, and we obtained funding to sequence and analyze its genome though a consortium funded by a Brazilian government agency, to help characterize the avian tropical biodiversity in Brazil.”

Their special traits should make parrots important model systems for researchers who study cognition, learning and ageing.

“Biomedical research is being held back by our dependence on bored, overweight, socially deprived, behaviorally abnormal, overfed inbred mice,” Dr. Withlin pointed out in email. “We need to remember that we share the planet with a vast array of species with incredibly diverse phenotypes. Many of the traits we most want to understand about ourselves — the mysteries of speech, resistance to cancer, the ability to regenerate tissue following injury, etc — are met and excelled by non-mouse members of the animal kingdom (I’m thinking of parrots, naked mole-rats, and axolotls with those examples in particular, but examples could be picked out for any trait).”

“Whether you’re interested in the evolution of speech and intelligence or the genetic keys to increasing lifespan, I hope to encourage researchers, funders, and the public alike that the best path forward is the ‘ethological’ approach of picking the unique animal model that best fits their particular biological question, rather than trying to attack every nail with a mouse-shaped hammer,” Dr. Withlin said in email.

And of course, parrots will benefit from focussed field studies and creative conservation efforts.

“[M]uch more effort is needed,” Professor Mello added. “I also think it is important to try to understand them better in their own natural environment, so I am hoping to also help boost efforts in conservation.”


Morgan Wirthlin, Nicholas C.B. Lima, Rafael Lucas Muniz Guedes, Andre E.R. Soares, Luiz Gonzaga P. Almeida, Nathalia P. Cavaleiro, Guilherme Loss de Morais, Anderson V. Chaves, Jason T. Howard, Marcus de Melo Teixeira, Patricia N. Schneider, Fabrício R. Santos, Michael C. Schatz, Maria Sueli Felipe, Cristina Y. Miyaki, Alexandre Aleixo, Maria P.C. Schneider, Erich D. Jarvis, Ana Tereza R. Vasconcelos, Francisco Prosdocimi, and Claudio V. Mello (2018). Parrot Genomes and the Evolution of Heightened Longevity and Cognition, Current Biology, published online on 6 December 2018 ahead of print | doi:10.1016/j.cub.2018.10.050

Originally published at Forbes on 21 December 2018.