Penguins are Aussies: Or are they Kiwis?
First genome comparison gives insight into penguin origins, evolution


Date:
August 17, 2020
Source:
University of California - Berkeley
Summary:
Researchers sequenced the genomes of all 18 recognized species of
penguin to assemble a family tree, showing that the largest of the
penguins - king and emperor - split off from all other penguins
not long after penguins arose 22 million years ago in Australia
and New Zealand. Other penguins diversified after Drake's Passage
opened, revving up the circumpolar current and allowing penguins
to spread throughout the southern hemisphere.



FULL STORY ==========================================================================
From the four-foot-tall emperor penguin to the aptly named foot-long
little penguin, these unique flightless birds have invaded habitats from Antarctica to the equator, not to mention the hearts of the public.


==========================================================================
A comparison of the full genomes of 18 recognized species of penguins
provides clues to how they achieved this success -- though not their adorability -- over tens of millions of years, through warm and cold
climate swings. It also cautions that today's rapidly changing climate
may be too much for them.

"We are able to show how penguins have been able to diversify to occupy
the incredibly different thermal environments they live in today,
going from 9 degrees Celsius (48 F) in the waters around Australia and
New Zealand, down to negative temperatures in Antarctica and up to 26
degrees (79 F) in the Gala'pagos Islands," said Rauri Bowie, professor
of integrative biology at the University of California, Berkeley, and
curator in the Museum of Vertebrate Zoology (MVZ) at Berkeley. "But we
want to make the point that it has taken millions of years for penguins to
be able to occupy such diverse habitats, and at the rate that oceans are warming, penguins are not going to be able to adapt fast enough to keep
up with changing climate." The researchers established conclusively that penguins arose in the cool coastal regions of Australia and New Zealand,
not frigid Antarctica, as many scientists thought, and they pinpoint
the origin of penguins at about 22 million years ago.

Despite their success in spreading widely throughout the Southern
Hemisphere, many penguin populations are now threatened. Breeding colonies
of emperor penguins in Antarctica have had to relocate because of receding
sea ice, while last year saw mass mortality of Ade'lie penguin chicks
on the continent.

Gala'pagos penguin populations are declining as warm El Nin~o events
become more common. In New Zealand, populations of little and yellow-eyed penguins must be fenced off to protect them from the depredations of
feral cats, while African penguin populations are declining drastically
as the waters off southern Africa warm.

"We saw, over millions of years, that the diversification of penguins
decreased with increasing temperature, but that was over a longtime
scale," said Juliana Vianna, associate professor of ecosystems
and environment at the Pontifical Catholic University of Chile in
Santiago. "Right now, changes in the climate and environment are going
too fast for some species to respond to the climate change." Vianna is
first author of a paper with Bowie and other colleagues describing
their findings that will be published online this week in the journal Proceedings of the National Academy of Sciences.



========================================================================== Where did penguins come from? For the study, Vianna, Bowie and colleagues
at museums and universities around the world gathered blood and tissue
samples from 22 penguins representing 18 species and then sequenced and analyzed their whole genomes to chart penguin movement and diversification
over the millennia.

Their conclusions resolve several long-standing questions: in particular,
where penguins originated -- along the coasts of Australia, New Zealand
and nearby islands of the South Pacific -- and when -- 22 million years
ago. The genetic evidence indicates that the ancestors of the king and
emperor penguins, the two largest species, soon split off from the other penguins and moved to sub- Antarctic and Antarctic waters, respectively, presumably to take advantage of abundant food resources. This scenario
is consistent with the contested hypothesis that the emperor and king
penguins -- the only two species in the genus Aptenodytes -- are the
sister group to all other penguin lineages.

"It was very satisfying to be able to resolve the phylogeny, which has
been debated for a long time," Bowie said. "The debate hinged on where, exactly, the emperor and king penguins were placed in the family tree,
whether they are nested inside the tree closer to other lineages
of penguins or whether they are sisters to all the other penguins,
which is what our phylogeny showed and some other previous studies
had suggested. And it fits with the rich fossil history of penguins."
The other penguins diversified and spread widely across the southern
oceans, after the Drake's Passage between Antarctica and the southern tip
of South America fully opened about 12 million years ago. The opening
revved up the clockwise-moving Antarctic Circumpolar Current allowed
these flightless birds to swim with the ocean currents throughout the
southern ocean, populating both the cold sub-Antarctic islands and the
warmer coastal areas of South America and Africa, where they populated to coastlines and remote islands with cold, upwelling, nutrient-rich water.



========================================================================== Today, penguins are found in Australia and New Zealand (yellow-eyed,
little and other crested penguins), Antarctica (emperor, Ade'lie, gentoo
and chinstrap), the tropical west coast of South America (Gala'pagos and Humboldt), the southern coasts of South America (Magellanic and southern rockhopper), the South Atlantic (Magellanic and Macaroni), southern Africa (African) and some in the sub-Antarctic (king, gentoo and Macaroni),
Indian Ocean islands (eastern rockhopper) and sub-tropical regions
(northern rockhopper).

Using powerful analysis techniques, some developed recently to analyze historical interactions among humans and our Neanderthal and Denisovan relatives, the researchers were able to determine that several groups
of penguins have interbred over the course of their evolutionary
history. Through exchange of genetic material, penguins may have shared
genetic traits that facilitated the diversification of penguins across
the steep thermal and salinity gradients encountered in the southern
oceans. The most hybridized are the rockhopper penguins and their close relatives, which experienced at least four introgressions, or transfers
of genetic information, over the course of millions of years.

The team also pinpointed genetic adaptions that allowed penguins to
thrive in new and challenging environments, including changes in genes responsible for regulating body temperature, which allowed them to adapt
to subzero Antarctic temperatures, as well as tropical temperatures
near the equator; oxygen consumption that permitted deeper dives; and osmoregulation, so they could survive on seawater without the need to
find fresh water.

New analytical tools helped the researchers to infer the sizes of
ancient penguin populations going back about 1 million years. Most
penguin species, they found, increased to their greatest numbers as the
world cooled 40,000 to 70,000 years ago during the last glaciation --
many species prefer to breed on snow and ice -- and some had a bump in population during the previous glaciation period 140,000 years ago.

Two species -- the gentoo and the Gala'pagos -- seem to have been
declining in populations for at least the past 1 million years.

DNA from the most isolated birds on Earth Vianna has long-running
research projects on penguins in Chile and Antarctica and, for this study, obtained blood samples from many species in those areas.

Colleagues in France, Norway, Brazil, Australia, the United States
and South Africa supplied blood from some remote species -- Norwegian colleagues provided blood from the chinstrap penguin of the Bouvet
islands, for example -- while Vianna and Bowie obtained blood samples
from an African penguin in a colony at the California Academy of Sciences
in San Francisco.

But some species were harder to locate. The researchers were forced to
rely on tissue from a preserved specimen of the yellow-eyed penguin in
UC Berkeley's MVZ, while the American Museum of Natural History in New
York supplied tissue from preserved erect-crested and Fiordland penguins.

Each genome was sequenced 30 times by Illumina shotgun sequencing, which produced tiny pieces -- about 150 base pairs long -- of the entire genome.

Vianna, who at the time was working with Bowie at UC Berkeley on a
sabbatical, painstakingly aligned each piece along a reference genome
that had previously been sequenced -- that of the emperor penguin --
as a scaffold.

"Having a reference genome is like using the cover of a puzzle box to
assemble a jigsaw puzzle: You can take all your super little pieces and
align them to that reference genome," Bowie said. "We did that with each
of these penguin genomes." The genome comparisons told them that penguins arose between 21 million and 22 million years ago, narrowing down the 10-to-40-million-year window determined previously from fossil penguins.

They also disproved a paper published last year that suggested that
the closely related king and emperor penguins were a sister group to
the gentoo and Ade'lie penguins. Instead, they found that the king and
emperor penguins are the sister group to all other penguins.

Vianna and Bowie now have genome sequences of 300 individual penguins
and are diving more deeply into the genetic variations within and among disparate penguin populations. They recently discovered a new lineage
of penguin that awaits scientific description.

"Penguins are very charismatic, certainly," Vianna said. "But I hope
these studies also lead to better conservation." The work was supported
by the Chilean Antarctic Institute, Fondecyt Project, GAB PIA CONICYT (ACT172065) and the U.S. National Science Foundation (DEB- 1441652). Among
the paper's co-authors are Ke Bi and Cynthia Wang-Claypool of UC Berkeley
and Daly Noll of Pontifical Catholic University of Chile.


========================================================================== Story Source: Materials provided by
University_of_California_-_Berkeley. Original written by Robert
Sanders. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Juliana A. Vianna, Fla'via A. N. Fernandes, Mari'a Jose' Frugone,
Henrique V. Figueiro', Luis R. Pertierra, Daly Noll, Ke Bi,
Cynthia Y.

Wang-Claypool, Andrew Lowther, Patricia Parker, Celine Le Bohec,
Francesco Bonadonna, Barbara Wienecke, Pierre Pistorius, Antje
Steinfurth, Christopher P. Burridge, Gisele P. M. Dantas, Elie
Poulin, W.

Brian Simison, Jim Henderson, Eduardo Eizirik, Mariana F. Nery,
Rauri C.

K. Bowie. Genome-wide analyses reveal drivers of penguin
diversification.

Proceedings of the National Academy of Sciences, 2020; 202006659
DOI: 10.1073/pnas.2006659117 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200817191739.htm

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