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Shadow Clans - R.A.G.E. (Rapid Ageing Genome)
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Large ground finch (Geospiza magnirostris) on Daphne Major island, Galpagos B. R. Grant

For more than four decades, the husband and wife team of Peter and Rosemary Grant travelled to the isolated Galapagos archipelago to watch evolution unfold in front of them.

They were studying some of the 15 species of Darwin's finches, so named because the famed naturalist observed them during the 1830s on his trip aboard the H.M.S. Beagle. Over the years, they noticed the beak size changed among species in response to its food supply - one species developed a smaller beak to take advantage of different seeds - which demonstrated evolution was happening much quicker than Darwin could ever have imagined.

Now, they have tapped the power of sequencing technology to understand the genetic underpinning of these changes. For the first time, scientists have sequenced the genomes of all the famous finches that inspired Charles Darwin's theory of natural selection.

In a study reported Thursday in Nature, the Grants, along with Leif Andersson of Uppsala University and several other authors, detailed the results from sequencing the genome of 120 birds from all of Darwin's finches.

For the DNA, the Grants provided drops of blood samples collected since 1987. They were especially interested in range of beak sizes, which had caught Darwin's eye because they were so much more diverse than the birds he had seen in Europe.

Comparing two species with blunt beaks and two with pointed beaks, they identified 15 regions of the genome as being very different. Six of these contained genes that previously have been associated with craniofacial and/or beak development.

Most significant, they found that genetic variation in the ALX1 gene is associated with variation in beak shape not only between species of Darwin's finches but also among individuals of the medium ground finch.

"This is a very exciting discovery for us since we have previously shown that beak shape in the medium ground finch has undergone a rapid evolution in response to environmental changes," Princeton University's Rosemary Grant said. "Now we know that hybridization (interbreeding between species) mixes the different variants of an important gene, ALX1."

The scientists also were able to show hybridization between a warbler finch and the common ancestor of tree and ground finches goes back more than 500,000 years and 800,000 years.

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Scientists sequence the genome of Darwin's finches

There's more to Darwin's finches than meets the eye. Famously, the 14 species found on the Galapagos islands are distinguished from one another largely by differences in beak shape. But the first full genome analysis of the birds shows the approach isn't foolproof, because some characteristic beak shapes appear to have evolved on two or three separate occasions.

The finches are named in Darwin's honour because he was the first to collect them during his time on the Beagle and later referred to them when he was formulating his theory of natural selection.

The Galapagos islands owe their reputation as a hotbed of adaptation to their geographical isolation and to the considerable changes in their climate and environments over the last few million years. The finches that inhabit the islands and which featured in Darwin's writings are generally distinguished from one another by the size and beak shape. Some species, for instance, have deep and blunt beaks for cracking nuts while others have long and pointed beaks for feeding on nectar.

Leif Andersson at Uppsala University, Sweden, and his colleagues, have now sequenced the full genomes of 120 birds, representing all 14 established species of Galapagos finch, a 15th species that lives on nearby Cocos Island, and two closely related species that live in the Caribbean. Theirs is the most comprehensive genetic analysis of the famous birds to date, says Andersson. Earlier studies have examined just the bird's mitochondrial DNA or small regions of the genome.

When comparing the full genetic sequences to build an evolutionary tree, the researchers found that what ornithologists going back to Darwin's time thought were just two species, based on their beak shape, may in fact be five separate species, based on their genomes.

One species of finch Geospiza difficilis pops up in three completely different branches of the family tree, so it should be counted as three separate species. Another species Geospiza conirostris sits on two separate evolutionary branches, so should be treated as two species.

That means there are 17 not 14 species of finch living on the Galapagos, says Andersson. "We hope that taxonomists will accept our suggestions."

The genetic evidence revealed something else. A single gene, ALX1, has played a vital role in shaping the evolution of beak shape in the finches in particular, whether they are long and pointed or deep and blunt, says Andersson. The find is remarkable because more often than not, important traits are encoded by hundreds of genes, each playing such a small role that linking single genes to a particular trait is very difficult.

"For instance, if you consider stature in humans, genetic studies have shown that there are hundreds of genes that each explain a very small part of the population variance," says Andersson.

So why was it easy to link ALX1 to beak shape? It may be down to the fact that the finch beak has been the focus of exceptionally strong natural selection during the evolutionary radiation of the finches, says Andersson. This means that any genes that are particularly important in its development will have evolved substantially, making them easier to spot in genetic studies.

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Genome reveals three more species of Darwin's finches

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Newswise ANN ARBOR, Mich. There are many reasons why people gain different amounts of weight and why fat becomes stored in different parts of their bodies. Now researchers are homing in on genetic reasons. Their findings, part of the largest genome-wide study to date, were published in two companion papers today in the journal Nature.

By analyzing genetic samples from more than 300,000 individuals to study obesity and body fat distribution, researchers in the international Genetic Investigation of Anthropometric Traits (GIANT) Consortium completed the largest study of genetic variation to date, and found over 140 locations across the genome that play roles in various obesity traits.

By applying novel computational methods to the genetic results, they discovered new biological pathways that are important in controlling body weight and fat distribution.

This work is the first step toward finding individual genes that play key roles in body shape and size. The proteins these genes help produce could become targets for future drug development.

Obesity is a global public health burden that affects millions of people. Yet, there are no long-term treatments.

Waist-to-hip ratios key for health risk One paper focused on where fat is stored in the body, one determinant of health risk. One of the observable traits linked to the genetic locations was waist-to-hip circumference ratio. People with waistlines larger than hip circumferences have more belly fat surrounding their abdominal organs. This makes them more likely to have metabolic conditions, such as type-2 diabetes, and cardiovascular problems than do people with body fat concentrated more in the hip area or distributed equally throughout the body.

We need to know these genetic locations because different fat depots pose different health risks, says Karen Mohlke, Ph.D., professor of genetics at the University of North Carolina School of Medicine and senior author of the paper that examined waist-to-hip ratio of fat distribution. If we can figure out which genes influence where fat is deposited, it could help us understand the biology that leads to various health conditions, such as insulin resistance/diabetes, metabolic syndrome, and heart disease.

The genetic locations associated with fat depots are associated with genes previously identified as being important for the creation of adipose tissue. Researchers also determined that 19 of the fat distribution genetic locations had a stronger effect in women; one had a stronger effect in men.

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Largest Ever Genome-Wide Study Strengthens Genetic Link to Obesity