Bar headed goose (Anser indicus) in a V formation.
| Photo Credit: K.V.S. Giri

Nearly all birds with bright red, orange, and yellow feathers or bills use a group of pigments called carotenoids to produce their colours.
| Photo Credit: Shutterstock

Across the animal kingdom, birds are some of the most colourful creatures of all. But how did all the amazingly coloured different bird species arise?

Nearly all birds with bright red, orange, and yellow feathers or bills use a group of pigments called carotenoids to produce their colours. However, these animals can’t make carotenoids directly. They must acquire them through their diets from the plants they eat. Parrots are the exception to this rule, having evolved an entirely new way to make colourful pigments, called psittacofulvins.

Although scientists have known about these different pigments for some time, understanding the biochemical and genetic basis behind how birds use them to vary in colour has been less clear. But two recent separate studies about parrots and finches have provided vital insight into this mystery.

One study, published in Current Biology, was led by one of us (Daniel Hooper), and the other was led by Portuguese biologist Roberto Abore and published in Science. Together, they advance our understanding of how birds produce their colourful displays – and how these traits have evolved.

A single enzyme

The two new studies involved large teams of international researchers. They used recent advances in genetic sequencing to examine which regions of the genome (an animal’s complete set of DNA) determine natural yellow-to-red colour variation in parrots and finches.

Remarkably, even though these two groups of birds produce their colourful displays using different types of pigments, scientists found they have evolved in similar ways.

Arbore’s study looked at the dusky lory (Pseudeos fuscata), a parrot native to New Guinea with bands of feathers that may be coloured yellow, orange or red. The research found that shifts between yellow and red feather colouring were associated with an enzyme called ALDH3A2. This enzyme converts red parrot pigments to yellow ones. When developing feathers contain large amounts of the enzyme, they end up yellow; when they have less, they end up red.

Scientists found the ALDH3A2 enzyme also explains colour variation in many other species of parrots which have independently evolved yellow-to-red colour variation.

Two special genes

The long-tailed finch (Poephila acuticauda) is a species of songbird native to northern Australia. There are two hybridising subspecies with different coloured bills. One is yellow-billed while the other is red-billed.

Most carotenoid pigments that birds might consume from their diet are yellow or orange, so birds’ bodies must somehow change the chemistry of the pigments after eating them to produce red colours.

Hooper’s study examined variation in this trait across the whole distribution of the long-tailed finch in the wild, and variation in the genomes of the measured birds. It turned out bill colour in these finches was mostly linked to two genes, CYP2J19 and TTC39B.

Together, these two genes drive the conversion of yellow dietary carotenoids to red ones.

In the long-tailed finch, yellow coloration appears to result from mutations that turn these genes off in the bill specifically while keeping them on in other parts of the body, such as the eyes.

By comparing the DNA code of these colour genes to other finch species, the researchers also found the ancestors of the modern long-tailed finch had red bills, but mutant yellow bills have slowly been growing more common.

Like a lightbulb dimmer

Together these studies show how colours can evolve in natural populations.

In both parrots and finches, the mutations responsible for yellow-to-red colour variation did not change the function of the enzymes involved. Instead they influenced where and when these enzymes were active. Think of it as changing the lighting in a room by installing a dimmer on an existing light switch, rather than removing an entire light fitting.

The scientists also showed that in wild populations of both parrots and finches, mutations to just a few genes can alter the chemical structure of the pigments profoundly – enough to make the difference between red and yellow.

The key genes change the chemical structure of the pigment molecule through the actions of an enzyme which adds just one atom of oxygen to the pigment. This changes it from a bright red to a bright yellow in parrots, and the opposite in finches, from bright yellow to bright red.

The wonder of nature

The evolution of colour in birds has been the focus of attention since Charles Darwin used them in outlining his theory of evolution by natural selection. The most obvious difference between the closely related species of birds that we see around us is their colour.

These two new studies have shown us how a few genes and the addition of that single oxygen atom can change the course of evolution, creating a new form that looks so dramatically different. If this improves the animal in an evolutionary sense – perhaps they look more attractive to potential partners or stand out more – it can lead to the origin of a new species.

This work reminds us of the wonder of nature and shows that evolution is an ongoing process.

To conserve species we need to protect as much of their genetic complexity as possible. Every individual in a population contains a unique genome and every small bit of variation is the product of millions of years of evolution in the past. It could also be the key to the development of a new species in the future.

This article is republished from The Conversation under a Creative Commons license. Read the original article here.

Part of the answer about how birds fly in a coordinated and effortless way lies in precise, and previously unknown, aerodynamic interactions, mathematicians have found. The researchers found that flow-mediated interactions between neighbours are, in effect, spring-like forces that hold each member in place. However, these ‘springs’ act in only one direction — a lead bird can exert force on its follower, but not vice versa — and this non-reciprocal interaction means that later members tend to resonate or oscillate wildly.

To replicate the columnar formations of birds, in which they line up one directly behind the other, the researchers created mechanized flappers that act like birds’ wings. The wings were 3D-printed from plastic and driven by motors to flap in water, which replicated how air flows around bird wings during flight. This ‘mock flock’ propelled through water and could freely arrange itself within a line or queue. The flows affected group organisation in different ways — depending on the size of the group. For small groups of up to about four flyers, the researchers discovered an effect by which each member gets help from the aerodynamic interactions in holding its position relative to its neighbours. For larger groups, the flow interactions cause later members to be jostled around and thrown out of position, typically causing a breakdown of the flock due to collisions among members. This means that the very long groups seen in some types of birds are not at all easy to form, and the later members likely have to constantly work to hold their positions and avoid crashing into their neighbours.

The largest-ever study of bird genomes has produced a remarkably clear picture of the bird family tree. 
| Photo Credit: Special Arrangement

The largest-ever study of bird genomes has produced a remarkably clear picture of the bird family tree. Published in the journal Nature today, our study shows that most of the modern groups of birds first appeared within 5 million years after the extinction of the dinosaurs.

Birds are a large part of our lives, a sign of nature even in cities. They are popular among the general public and well studied by scientists. But placing all of these birds into a family tree has been frustratingly difficult.

By analysing the genomes of more than 360 bird species, our study has identified the fundamental relationships among the major groups of living birds.

The new family tree overturns some previous ideas about bird relationships, while also revealing some new groupings.

Resolving a messy relationship

Previous studies showed the bird family tree has three major branches. The first branch contains the tinamous and ratites, which include flightless birds such as the emu, kiwi and ostrich.

The second branch holds the landfowl and waterfowl – chickens, ducks and so on. All other birds sit on the third branch, known as the Neoaves, which include 95% of bird species.

The Neoaves branch includes ten groups of birds. Most of these are what biologists have named the “Magnificent Seven”: landbirds, waterbirds, tropicbirds, cuckoos, nightjars, doves and flamingos. The other three groups are known as the “orphans” and include the shorebirds, cranes and hoatzin, a species from South America.

The relationships among these ten groups, especially the orphans, have been incredibly difficult to resolve. Our genome study shows a resolution is within reach.

Meet the ‘Elementaves’

Our genome study revealed a new grouping of birds we have named “Elementaves”. With a name inspired by the four ancient elements of earth, air, water and fire, this group includes birds well adapted for success on land, in the sky and in the water. Some of the birds have names relating to the sun, representing the element of fire. The Elementaves group includes hummingbirds, shorebirds, cranes, penguins and pelicans.

Our study also confirms a close relationship between two of the most familiar groups of birds in Australia, the passerines (songbirds and relatives) and parrots. These popular birds dominate the Australian Bird of the Year polls.

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Songbirds make up nearly 50% of all bird species and include birds like magpies, finches, honeyeaters and fairywrens. They had their humble beginnings in Australia about 50 million years ago, then spread across the globe to become the most successful group of birds.

When did birds really emerge?

A further goal of our study was to place a timescale on the bird family tree. We did this by modelling the evolution of genomes using a tool known as the “molecular clock”. By drawing on information from nearly 200 fossils, we were able to constrain the ages of some of the branches in the bird family tree.

Our study shows all living birds share an ancestor that lived just over 90 million years ago. But most groups of modern birds emerged about 25 million years later, within a small window of just a few million years after the end of the Cretaceous period around 66 million years ago.

This coincides with the mass extinction of dinosaurs and other organisms caused by an asteroid striking Earth. So it seems birds made the most of the opportunities that became available after these other dominant life forms were wiped out.

One mystery remains

The genome study is the product of nearly a decade of research, conducted as part of the Bird 10,000 Genomes Project. The ultimate goal of this project is to sequence the genomes of all 10,000 living bird species.

The current phase of the project focused on including species from every major group, or family, of birds. The study of these 363 genomes was a truly international effort led by researchers at the University of Copenhagen, University of California San Diego and Zhejiang University in China.

Even with such a huge amount of genome data, one branch of the bird family tree remains a mystery. Our analysis could not confidently determine the relationships of one of the orphans, the hoatzin. Found in South America, the hoatzin is a highly distinctive bird and the sole survivor of its lineage.

Our study shows that some relationships in the tree of life can only be determined using huge amounts of genome data. But our study also demonstrates the power of studying genomes and fossils together to understand the evolutionary history of life on Earth.