Penguin Genomes Shed Light on Their Evolutionary History and Adaptations

Humans have always been in awe of birds: their beautiful feathers, their graceful flight, and their sweet songs. These are just some of the features that distinguish them from other animals. Birds are extremely diverse—with over 10,000 living species on Earth—and are found in all kinds of environments, from extremely hot and dry deserts, to the frigid Antarctic. 

Penguins are particularly interesting for scientists as they are flightless birds that can swim and have evolved to thrive in the hostile Antarctic environment where few animals can survive. Now, we are a step closer to understanding their evolutionary history, population sizes in response to historical climate change, as well as the genes involved in their ability to adapt to such extreme climates, with an exciting new study published last month in GigaScience, an online open-access BGI-BioMed Central journal.

In a massive pioneering study, known as the avian phylogenomics project—the largest among four-limbed vertebrates to date—a consortium of international researchers sequenced the genomes of 45 bird species covering a wide range of bird groups. Birds such as pigeons, parrots, flamingoes, eagles, owls, ostriches, pelicans, and penguins, were included, among others. 

The sequencing was carried out at the research centre of Beijing Genomic Institute, known as BGIin Hong Kong, and the data is freely available at GigaScience database. The exciting findings from this project are reported in eight papers published in a special Dec 12 issue of Science (with free full-text) and another 15 are published in the open-access journals, GigaScience, BMC Genomics, Genome Biology, and others.

Combined with existing bird genomes available for the chicken, turkey, zebra finch, and a few others, the wealth of data generated from the sequencing unravels the mysteries behind how such an amazingly large array of bird species evolved, their common ancestor, and how they are related to each other. Scientists have been able to resolve the avian family tree using this data to better understand the relationships between bird species. 

The project also reveals how birds evolved feathers, how they lost their teeth giving rise to beaks around 116 million years ago, how they evolved vocal learning independently, how they have adapted to their environments, and how they are vulnerable to climate change. An effort to probe the genomic signatures of near-extinct birds such as the crested ibis in Northeast Asia will also help understand genetic elements that may make some species more vulnerable to extinction. This will help in conserving endangered bird species—almost two thousand species are threatened due to human activities.

The genomic data indicate a burst of bird diversity arose after the land dinosaurs were wiped out 65 million years ago. Scientists think that birds evolved from a clade of feathered dinosaurs that developed the ability to fly. Some bird lineages survived the mass extinction and birds are the only living ancestors of the dinosaurs we have with us today. The common ancestor of most of the land birds were found to be top predators. When non-bird dinosaurs went extinct, they evolved to exploit niches left by them giving rise to the huge diversity of birds seen on Earth. 

One of the papers from the project outlines the evolutionary history of two species of penguins, Adélie and emperor, from their DNA. Analysis of their genomes suggests that penguins arose 60 million years ago when they split from their closest relatives. Around 60 million to 50 million years ago, the Earth experienced a period of global warming; temperatures rose by 6°C and this resulted in a rise in sea levels and a large extinction of small marine organisms living at the bottom of the sea floor. This, the scientist suggest, may have opened up avenues for birds to colonize the seas by developing the ability to swim, giving rise to early penguins.

The populations of the two penguin species differ in their response to climate change. Adélie penguin populations rose when the climate got warmer 150,000 years ago, and dropped by 40 percent when it got cooler around 60,000 years ago. Emperor penguin populations, however, remained relatively stable during the period of cooling. Better adaptations to the cold are thought to favor the emperor penguins during the penultimate glacial period. These include incubating their eggs on their feet and having an abdominal fold of skin to insulate their eggs from the extreme cold.

Left: Adélie penguin with chicks. Credit Yvette Wharton - The University of Auckland Right: Adelie's on Pack Ice. Credit David Lambert

Left: Adélie penguin with chicks.
Credit Yvette Wharton – The University of Auckland
Right: Adelie’s on Pack Ice.
Credit David Lambert

Future warming may be detrimental to emperor penguins because they did not undergo a population boom like Adélie penguins did during the warming at the end of the penultimate glacial period, according to the team lead, Cai Li, at BGI, Shenzhen.

Peering into their genes provided clues on how they have adapted to cope with the extreme cold in the Antarctic where most animals would perish. Their feathers, composed mainly of Beta (β)-keratins, are short, stiff and spread evenly over the body to reduce heat loss. Compared to all avian species, keratinocyte β-keratin genes were found to be the highest in both penguin species. A gene, DSG1, known to cause a skin disease in humans that manifests as thick skin in the soles of the feet and palms, was found to be positively selected for in penguins and may have a role in producing the unique skin in penguins.

Profound changes in daylight in the Antarctic—where it can be dark for several months during the winter to having almost 24 hours of daylight in the summer—may require different visual adaptations in penguins compared with other bird species. They can also see underwater. Comparing the genomes of 48 bird species, the team found that penguins have only three classes of cone opsin genes as opposed to four in most other birds. Opsin genes code for light sensitive receptors found in the retina involved in converting light into electrical signals, known as light transduction. Moreover, Adélie and emperor penguins have different sets of genes involved in light transduction, implying they have developed different visual adaptations. The differing sets of genes, the scientists surmise, might be related to their contrasting breeding seasons: Adélie penguins breed in spring and summer when daylight is longer, as opposed to emperor penguins, which breed in the winter when days are short.

Researcher with Adélie penguins. Credit Yvette Wharton - The University of Auckland

Researcher with Adélie penguins.
Credit Yvette Wharton – The University of Auckland

Developing thick fat deposits are crucial for penguins to insulate themselves from the cold—temperatures in the Antarctic can plunge to -60°C in the winter months. Both species of penguins have evolved differing strategies for lipid formation and metabolism. Adélie penguins have eight genes found to be involved in lipid metabolism while emperor penguins have only three.

Penguin wings (forelimbs) have evolved to act as flippers for propelling themselves underwater. The team found 17 forelimb-related genes that underwent changes in penguins and may be involved in forming forelimbs. Among them, one gene of interest, EVC2, harbored the most changes. In humans, mutations in this gene have been known to cause Ellis-van Creveld syndrome, a rare bone growth disorder, which results in abnormally short forearms and lower legs. Further research to understand the role of EVC2 may help people with this syndrome.

Comparative genomics can show which species are better adapted to changes in climate as opposed to others and what adaptations make them more resilient by looking at their past population history. Despite being closely related, the two penguin species showed different genes, and therefore diverse adaptations in light transduction and lipid metabolism.

Recently, the genome of a midge native to Antarctica had been sequenced. It turned out to be the smallest insect genome sequenced, which scientists believe to be an adaptation to the harsh climate of Antarctica.

Even in the most optimistic scenario, global temperatures are projected to rise by almost 2°C by the end of the century, according to the IPCC. The effects of such a temperature change are hard to predict on bird species such as penguins but understanding their ability to cope with climate change in the past can help us predict risk factors for the future. 

Reference

Cai Li et al. (2014). Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment, GigaScience, 3:27

 

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