Blue-fronted Amazon parrot genome studied


This 2015 video shows a blue-fronted parrot, Amazona aestiva, eating guaritá, Astronium graveolens, flowers in Mato Grosso do Sul in Brazil.

From Carnegie Mellon University in the USA:

Parrot genome analysis reveals insights into longevity, cognition

Genome of blue-fronted Amazon parrot compared with 30 other long-lived birds

December 6, 2018

Parrots are famously talkative, and a blue-fronted Amazon parrot named Moises — or at least its genome — is telling scientists volumes about the longevity and highly developed cognitive abilities that give parrots so much in common with humans. Perhaps someday, it will also provide clues about how parrots learn to vocalize so well.

Morgan Wirthlin, a BrainHub post-doctoral fellow in Carnegie Mellon University’s Computational Biology Department and first author of a report to appear in the Dec. 17 issue of the journal Current Biology, said she and her colleagues sequenced the genome of the blue-fronted Amazon and used it to perform the first comparative study of parrot genomes.

By comparing the blue-fronted Amazon with 30 other long- and short-lived birds — including four additional parrot species — she and colleagues at Oregon Health and Science University (OHSU), the Federal University of Rio de Janeiro and other entities identified a suite of genes previously not known to play a role in longevity that deserve further study. They also identified genes associated with longevity in fruit flies and worms.

“In many cases, this is the first time we’ve connected those genes to longevity in vertebrates,” she said.

Wirthlin, who began the study while a Ph.D. student in behavioral neuroscience at OHSU, said parrots are known to live up to 90 years in captivity — a lifespan that would be equivalent to hundreds of years for humans. The genes associated with longevity include telomerase, responsible for DNA repair of telomeres (the ends of chromosomes), which are known to shorten with age. Changes in these DNA repair genes can potentially turn cells malignant. The researchers have found evidence that changes in the DNA repair genes of long-lived birds appear to be balanced with changes in genes that control cell proliferation and cancer.

The researchers also discovered changes in gene-regulating regions of the genome — which seem to be parrot-specific — that were situated near genes associated with neural development. Those same genes are also linked with cognitive abilities in humans, suggesting that both humans and parrots evolved similar methods for developing higher cognitive abilities.

“Unfortunately, we didn’t find as many speech-related changes as I had hoped,” said Wirthlin, whose research is focused on the evolution of vocal behaviors, including speech. Animals that learn songs or speech are relatively rare — parrots, hummingbirds, songbirds, whales, dolphins, seals and bats — which makes them particularly interesting to scientists, such as Wirthlin, who hope to gain a better understanding of how humans evolved this capacity.

“If you’re just analyzing genes, you hit the end of the road pretty quickly,” she said. That’s because learned speech behaviors are thought be more of a function of gene regulation than of changes in genes themselves. Doing comparative studies of these “non-coding” regulatory regions, she added, is difficult, but she and Andreas Pfenning, assistant professor of computational biology, are working on the computational and experimental techniques that may someday reveal more of their secrets.

This work was supported through the Brazilian Avian Genome Consortium and by the National Institutes of Health/National Institute on Deafness and Other Communication Disorders.

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Goffin’s cockatoos making tools, new study


This 7 November 2018 video says about itself:

Goffin’s cockatoos create and use cardboard tools

Goffin’s cockatoos (Cacatua goffiniana) adjust the lengths but not the widths of their tools, according to a study published in the open-access journal PLOS ONE.

Goffin’s cockatoos can tear cardboard into long strips as tools to reach food, but fail to adjust strip width to fit through narrow openings.

Credits: Goffin Lab, University of Veterinary Medicine Vienna.

From PLOS:

Goffin’s cockatoos can create and manipulate novel tools

Cockatoos adjust length, but not width, when making their cardboard tools

November 7, 2018

Goffin’s cockatoos can tear cardboard into long strips as tools to reach food — but fail to adjust strip width to fit through narrow openings, according to a study published November 7, 2018 in the open-access journal PLOS ONE by A.M.I. Auersperg from the Medical University of Vienna, Austria, and colleagues.

The Goffin’s cockatoo (Cacatua goffiniana) is a type of parrot. Captive Goffins are capable of inventing and manipulating tools, even though they aren’t known to use tools habitually. The authors of the present study investigated two questions: do Goffins adjust tool properties to save effort, and if so, how accurately can they adjust tool dimensions for the task? The authors supplied six adult cockatoos with large cardboard sheets to tear into strips as tools for the testing apparatus: a food platform with a food reward set at varying distances (4-16cm) behind a small opening which also varied in width (1-2cm).

They found that the Goffins were capable of adjusting the length of their cardboard strip tools to account for variations in food distance, making shorter tools when the reward was closer than when it was set farther away. In every case, if a first-attempt tool was too short, the second-attempt tool would be significantly longer. On average, all six birds made significantly longer tools than were required to reach the reward in all test conditions, with the birds tending to make increasingly long tools as the study progressed — perhaps as a risk-avoidance strategy.

However, only one bird was able to make a sufficiently-narrow tool to successfully reach the food reward when the opening was at its narrowest. The authors hypothesize that the shearing technique the birds use to tear the cardboard limits the narrowness of the resulting strips. The authors suggest that future studies provide less restrictive materials to assess whether Goffins are cognitively capable of adjusting tool width in this situation.

Alice Auersperg adds: “The way they inserted and discarded manufactured pieces of specific lengths differently depending on condition suggests that the cockatoos could indeed adjust their tool making behavior in the predicted direction but with some limits in accuracy.”

How macaws communicate


This 2014 video says about itself:

Macaw in the nest, Blue-and-yellow Macaw, Ara ararauna, Wild birds, Brazilian fauna, Mato Grosso do sul, Brazil.

From PLOS:

Macaws may communicate visually with ‘blushing’, ruffled feathers

Facial feathers and blushing may signal positive social interactions

August 22, 2018

Parrots — highly intelligent and highly verbal — may also ruffle their head feathers and blush to communicate visually, according to a new study published August 22 in the open-access journal PLOS ONE by Aline Bertin of the INRA Centre Val de Loire, France and colleagues. The study extends the understanding of the complex social lives of these remarkable birds.

The authors studied five hand-reared captive blue-and-yellow macaws (Ara ararauna) interacting with one another and with their human caretakers. They assessed the feather position (ruffled or sleeked) on the crown, nape, and cheek, as well as the presence or absence of blushing on the bare skin of the cheek. They found that feather ruffling was more common when the birds were not in motion, such as during social interactions and resting periods. Crown feather ruffling and blushing were both more common when the human caretaker was actively interacting with the parrot by talking and maintaining eye contact than when the keeper was in the room but ignoring and turning their backs to the bird. Together, these results suggest that head feather ruffling is associated with states of lower arousal and positive social interactions, the authors concluded.

“How birds use facial displays and whether they communicate their inner subjective feelings is a question that is crucial to deepening our understanding of bird sentience,” say Bertin et al. “Although caution must be exercised when interpreting these data due to the small sample size, we argue that crown ruffling and skin color variation may provide facial indicators of birds’ inner subjective feelings. On a practical level, parrots are popular companion animals, with millions of parrots being kept as pets, and understanding visual communication in parrots may help to assess their well-being in captive conditions.”

Bertin summarizes: “Blushing may not be a characteristic unique to humans: the featherless cheek of the blue-and-yellow macaw parrot reveals rapid skin color changes in situations associated with emotion. The macaw’s particularly complex face may enable communication of emotion via color and feather displays.”

I saw and heard blue-and-yellow-macaws in Suriname.

Scarlet macaws, new research


This 2014 video says about itself:

Scarlet MacawsCosta Rica

Videos from Scarlet Macaw conservation projects in Costa Rica.

I saw scarlet macaws in Costa Rica.

From Penn State university in the USA:

Scarlet macaw DNA points to ancient breeding operation in Southwest

August 13, 2018

Somewhere in the American Southwest or northern Mexico, there are probably the ruins of a scarlet macaw breeding operation dating to between 900 and 1200 C.E., according to a team of archaeologists who sequenced the mitochondrial DNA of bird remains found in the Chaco Canyon and Mimbres areas of New Mexico.

Remains of a thriving prehistoric avian culture and breeding colony of scarlet macaws exist at the northern Mexican site of Paquimé, or Casas Grande. However, this community existed from 1250 to 1450, well after the abandonment of Chaco Canyon, and could not have supplied these birds to Southwest communities prior to the 13th century, said Richard George, graduate student in anthropology, Penn State.

Historically, scarlet macaws lived from South America to eastern coastal Mexico and Guatemala, thousands of miles from the American Southwest. Previously, researchers thought that ancestral Puebloan people might have traveled to these natural breeding areas and brought birds back, but the logistics of transporting adolescent birds are difficult. None of the sites where these early macaw remains were found contained evidence of breeding — eggshells, pens or perches.

“We were interested in the prehistoric scarlet macaw population history and the impacts of human direct management”, said George. “Especially any evidence for directed breeding or changes in the genetic diversity that could co-occur with different trade networks.”

The researchers sequenced the mitochondrial DNA of 20 scarlet macaw specimens, but were only able to obtain full sequences from 14. They then directly radiocarbon-dated all 14 birds with complete or near complete genomes and found they fell between 900 and 1200 CE.

“We looked at the full mitochondrial genome of over 16,000 base pairs to understand the maternal relationships represented in the Chaco Canyon and Mimbres regions,” said George.

Mitochondrial DNA exists separate from the cell nucleus and is inherited directly from the mother. While nuclear DNA combines the DNA inherited from both parents, mitochondrial DNA can show direct lineage because all siblings have the same mtDNA as their mother, and she has the same mtDNA as her own siblings and mother, all the way back through their ancestry.

Scarlet macaws in Mexico and Central America have five haplogroups — genetically similar, but not identical mitochondrial DNA lines — and each haplogroup has a number of haplotypes containing identical DNA lines. The researchers found that their scarlet macaws were all from haplogroup 6 and that 71 percent of the birds shared one of four unique haplotypes. They report the results of this analysis today (Aug 13) in the Proceedings of the National Academy of Sciences.

The researchers found that the probability of obtaining 14 birds from the wild and having them all come from the same haplogroup, one that is small and isolated, was extremely small. A better explanation, especially because these specimens ranged over a 300-year period, is that all the birds came from the same breeding population and that this population existed somewhere in the American Southwest or northern Mexico.

“These birds all likely came from the same source, but we don’t have any way to support that assumption without examining the full genome”, said George. “However, the genetic results likely indicate some type of narrow breeding from a small founder population with little or no introgression or resupply.”

However, no one has found macaw breeding evidence dating to the 900 to 1200 period in the American Southwest or northern Mexico.

“The next step will be to analyze macaws from other archaeological sites in Arizona and northern Mexico to narrow down the location of this early breeding colony,” said Douglas Kennett, professor and head of anthropology, Penn State, and co-director or the project.

Parrot intelligence, new study


This 2015 video says about itself:

Alex the Smart Parrot – Talking bird distinguishes colors, shapes, sizes, numbers

Due to repeated concerns regarding the empty cage shown in the video, it is my impression, after having read her book, that this is where Alex sleeps, like a bed, and that he is mostly perched outside the cage when he is not sleeping. Also, had Dr. Pepperberg taken Alex home with her every night or hung toys in his cage, it would have compromised the study. Enjoy the Genius of Birds.

From the University of Alberta in Canada:

Neuroscientists uncover secret to intelligence in parrots

Study shows evidence of convergence in bird and primate evolution

July 3, 2018

University of Alberta neuroscientists have identified the neural circuit that may underlay intelligence in birds, according to a new study. The discovery is an example of convergent evolution between the brains of birds and primates, with the potential to provide insight into the neural basis of human intelligence.

“An area of the brain that plays a major role in primate intelligence is called the pontine nuclei,” explained Cristian Gutierrez-Ibanez, postdoctoral fellow in the Department of Psychology. “This structure transfers information between the two largest areas of the brain, the cortex and cerebellum, which allows for higher-order processing and more sophisticated behaviour. In humans and primates, the pontine nuclei are large compared to other mammals. This makes sense given our cognitive abilities.”

Birds have very small pontine nuclei. Instead, they have a similar structure called the medial spiriform nucleus (SpM) that has similar connectivity. Located in a different part of the brain, the SpM does the same thing as the pontine nuclei, circulating information between the cortex and the cerebellum. “This loop between the cortex and the cerebellum is important for the planning and execution of sophisticated behaviours,” said Doug Wylie, professor of psychology and co-author on the new study.

Not-so-bird brain

Using samples from 98 birds from the largest collection of bird brains in the world, including everything from chickens and waterfowl to parrots and owls, the scientists studied the brains of birds, comparing the relative size of the SpM to the rest of the brain. They determined that parrots have a SpM that is much larger than that of other birds.

“The SpM is very large in parrots. It’s actually two to five times larger in parrots than in other birds, like chickens”, said Gutierrez. “Independently, parrots have evolved an enlarged area that connects the cortex and the cerebellum, similar to primates. This is another fascinating example of convergence between parrots and primates. It starts with sophisticated behaviours, like tool use and self-awareness, and can also be seen in the brain. The more we look at the brains, the more similarities we see.”

Next, the research team hopes to study the SpM in parrots more closely, to understand what types of information go there and why.

“This could present an excellent way to study how the similar, pontine-based, process occurs in humans”, added Gutierrez. “It might give us a way to better understand how our human brains work.”