Yosemite's Alpine Chipmunks Take Genetic Hit from Climate Change

ScienceDaily (Feb. 19, 2012) — Global warming has forced alpine chipmunks in Yosemite to higher ground, prompting a startling decline in the species' genetic diversity, according to a new study by researchers at the University of California, Berkeley.

The study, appearing Feb. 19, in the advance online publication of the journal Nature Climate Change, is one of the first to show a hit to the genetic diversity of a species because of a recent climate-induced change in the animals' geographic range. What's more, the genetic erosion occurred in the relatively short span of 90 years, highlighting the rapid threat changing climate can pose to a species.

With low genetic diversity a species can be more vulnerable to the effects of inbreeding, disease and other problems that threaten species survival, the researchers said.

"Climate change is implicated as the cause of geographic shifts observed among birds, small mammals and plants, but this new work shows that, particularly for mountain species like the alpine chipmunk, such shifts can result in increasingly fragmented and genetically impoverished populations," said study lead author Emily Rubidge, who conducted the research while a Ph.D. student at UC Berkeley's Museum of Vertebrate Zoology and the Department of Environmental Science, Policy and Management. "Under continued warming, the alpine chipmunk could be on the trajectory towards becoming threatened or even extinct."

Read on:  http://www.sciencedaily.com/releases/2012/02/120219143319.htm

Indian lesser flamingos compared to their African cousins in new genetic study

Are flamingos in India and Africa genetically birds of a feather?

Fenruary 2012. A University of Leicester conservation biologist - David Harper, from the Department of Biology - is leading a study which will establish whether lesser flamingos of India and Africa are genetically identical or not.

The Asian population of flamingos, which is the second largest in the world, is concentrated in Gujarat. However, the African flamingos are distributed in East, South and West Africa. The largest population is spread between Ethiopia and Tanzania, along the soda lakes of East Africa.

Dr David Harper is working with research scientist B M Parasharya and geneticist D.N. Rank of Anand Agricultural University (AAU) in Gujarat. The findings of this study will be compared with earlier results on African flamingos by Dr Harper's team of UK and Italian scientists from Insubria University, Varese. Then, they found that populations are distinct, but mix by about half a dozen individuals every generation who cross the thousands of kilometres between Botswana-Nabibia and Kenya-Tanzania.

Indian flamingos
Dr Harper recently attended the second Global Bird Watchers Conference at Ahmedabad - organised by Gujarat Tourism, in partnership with Federation of Indian Chambers of Commerce and Industry (FICCI) - where he made an invited presentation about lesser flamingos and their habitats. The study, which he carried out after the conference, will provide the only scientific evidence for inter-continental movement of flamingos.

David Harper says: "Lesser flamingos are fascinating birds for very many reasons. No other vertebrate on this planet can exist by filter feeding on bacteria alone. They have 4 distinct populations, thousands of miles apart, yet no birds have ever been seen moving between them. They breed in the most inhospitable regions of the earth where predators cannot survive - one in Tanzania and one in India. They are the origin of the fable of the Phoenix rising from the ashes, because until 1960 nobody knew where they bred, they just appeared from nowhere, a majestic ‘firebird'."

The study was originally funded by the Darwin Initiative and the British Council and more recently by the State of Gujarat Tourism Department as part of the 2nd Global Birdwatchers Conference.

http://www.wildlifeextra.com/go/news/lesser-flamingos.html

Birds of a Feather Don't Always Stick Together

ScienceDaily (Jan. 19, 2012) — Pigeons display spectacular variations in their feathers, feet, beaks and other physical traits, but a new University of Utah study shows that visible traits don't always coincide with genetics: A bird from one breed may have huge foot feathers, while a closely related breed does not; yet two unrelated pigeon breeds both may have large foot feathers.

"Most people think of pigeons as rats of the sky, but in fact they're really incredibly diverse," says Michael Shapiro, an assistant professor of biology and senior author of the study published online Jan. 19 in the journal Current Biology.

More than 350 breeds of pigeons differ in color, color pattern, body size, beak size and shape, structure of the skeleton, posture, vocalizations, feather placement and flight behavior. With help from pigeon breeders worldwide, the researchers studied the genetic relationships and visible traits of 361 pigeons from 70 domestic breeds and two free-living populations, one from Salt Lake City and the other on Scotland's Isle of Skye.

"What we found through this study is that birds that are only distantly related to each other can have very similar traits, and others that are very closely related to each other can look quite different in terms of their traits," Shapiro says.

In some cases, birds of a feather don't stick together -- genetically: The old German owl pigeon and English trumpeter both have head feathers known as a head crest, yet the two pigeon breeds aren't closely related. Another case: English trumpeters have feathers on their feet instead of scales. So do English pouters. Yet they are not closely related.

A few more examples of traits not matching genetics: Pigeon breeds known as the African owl and Budapest short-faced tumbler both have very short beaks, but they are not closely related. The African owl and old German owl pigeon breeds both have short beaks and are closely related, yet the African owl pigeon has a plain head, while the German owl has a head crest. And the English pouter and Brunner pouter are closely related, yet the former has foot feathers and the latter does not.

In other findings from the study:

-- Free-living pigeons -- including the common city pigeons known as "rats of the sky" -- carry the DNA of escaped or lost racing pigeons. Feral rock pigeons living in Salt Lake City are substantially related to a breed known as racing homers. Feral and perhaps wild pigeons from Scotland "are similar to an old domestic breed called the Modena, which used to be a racing pigeon but now is exclusively a show pigeon," Shapiro says.

-- Genetic analysis bolsters the idea that most of these pigeons studied have roots in the Middle East, and some with more recent origins in India.

-- Since birds with similar traits may be only distantly related (with no shared ancestors), it means certain traits in pigeons were selected by breeders repeatedly.

"Pigeons are a remarkable example of how selection and heredity work," Shapiro says. "These breeds are all members of the same species, but look really different. This happened because pigeon fanciers over the ages favored particular traits. This happened in dogs, too. It also happens to animals and other living things in the wild, except the agents of selection and change are environmental factors rather than human preference."

Continued:  http://www.sciencedaily.com/releases/2012/01/120119133154.htm

Tasmanian devil genome holds secret to survival (Via Dawn Holloway)

Scientists have sequenced the complete genomes of two Tasmanian devils in the hope of finding clues to preserving this highly endangered marsupial. Devil populations have been decimated by a highly contagious facial cancer that is transferred when these aggressive animals bite each other.

Read on...

Francis Galton: The man who drew up the 'ugly map' of Britain

16 June 2011

One hundred years after the death of Francis Galton, the "father of eugenics", geneticists are increasingly baffled by the nature versus nurture debate, writes Professor Steve Jones.

Type the phrase "scientists find the gene for" into Google and 68,000 results appear. Most of the hits are about human beings - which is a pretty impressive number, given that we have only 20,000 genes altogether.

The hits include genes for depression, religiosity, insomnia, marital failure and, perhaps surprisingly, premature ejaculation.

Does what we are born with make us what we will become, or is it the way we live? Newspapers tend to believe in nature - DNA, while sociologists go for nurture - the environment.

As they learn more, geneticists are finding that they have less and less of an idea about which is more important, or whether the question means anything in the first place.

Charles Darwin had an equally brilliant, but less well-known, cousin. He died 100 years ago in 1911.

This year is Galton year - a celebration of Francis Galton, a genius - but a flawed genius. He did many surprising things. He was the first person to use fingerprints in detective work and the first to publish a weather map, in the Times newspaper in 1875.

Galton is best known for his interest in inheritance. His book Hereditary Genius is sometimes said to have founded human genetics, and Galton founded the science (if that is the right word) of eugenics.

Its main aim was "to check the birth rate of the Unfit and improve the race by furthering the productivity of the fit by early marriage of the best stock".

Beauty map

At his death, he left the then enormous sum of £45,000 to found the Laboratory of National Eugenics at University College London (UCL).

The term was soon abandoned by UCL, although we still have a Galton Professorship. Even so eugenical ideas of good genes, bad genes, and all the rest is still very much in the public mind.

In fact, the most important part of Galton's work had nothing to do with eugenics, for he was one of the first to realise that science - biology as much as physics - needs maths rather than words. He was one of the founders of the science of statistics, and he measured many things.

He made statistical inquiries into the efficacy of prayer - he got into trouble for that for he found that those people frequently prayed for, like monarchs, lived no longer than anyone else.

He even made a beauty map of Britain, based on a secret grading of the local women on a scale from attractive to repulsive (the low point was in Aberdeen).

In a letter to Nature in 1879 entitled The Average Flush of Excitement, Galton recounts a visit to the Derby. He noted that while he was there he was able to assess what he called "the average tint of the complexion of the British upper classes" by observing the distant crowd through his opera glass.

He observed that after the race started, the crowd became "suffused with a strong pink tint, just as though a sun-set glow had fallen upon it". Galton found that he could work out the mood of a mass of people even without being able to distinguish one person from the next.

Some of his work has a strong resonance in modern science. Everyone knows that tall parents tend to have tall children, but Galton was the first to do some measuring.

He noted that the children of two six-footers tended to be tall, but not quite as tall as their parents. He called that "regression to the mean" and we now know that it happens because lots of genes are involved, with some hidden by others.

Sex is a way of mixing those genes - of reshuffling the genetic cards - and the child tends to inherit a more average kind of hand than that received by either of their exceptionally tall parents.

Of course, the environment is involved too. Food, exercise, good health, all are important in deciding how tall one will become. For height, and for almost anything else, nature and nurture always work together. It makes no sense to try to separate them.

That has not percolated into the public mind, as the Google search for "scientists find the gene for" shows. The three letter word for - the gene FOR something - is the most dangerous word in genetics. As Galton did not realise and as headline writers still do not, it is almost entirely ambiguous.

'A gamble'

A few months ago, the press reported with impressive unanimity that "Attention Deficit Hyperactivity Disorder is genetic". To the rolling of publicists' drums (and geneticists' eyes) came the news that some children behave outrageously because they inherit damaged DNA.

The Daily Mail came out with a hand-wringing piece entitled "Are some children just born bad?", which claimed "previous thinking was flawed and that some children, through no fault of the parents, are simply bad seeds".

That's an outrageous statement. Geneticists need to remind the public how little the word "genetic" actually means. One gene can do very different things, and the same thing can be under the influence of many genes - and nurture nearly always gets a look-in.

With all the fantastic technology now available, within a year we should be able to read a whole human genome in 15 minutes. But the biggest problem faced by geneticists is that we are not finding the genes.

Take height. As Galton noticed, height is highly heritable. We can now reach the scene of crime - the DNA - with the greatest of ease. The mappers have used their molecular tape measures on about 30,000 people.

They have found more than 50 different genes associated with being tall or short but altogether they account for only one-twentieth of the total variation needed to explain the similarity of children to their parents.

Where are the missing genes? We do not know.

Take adult diabetes, now a major health problem, and one that certainly runs strongly in families. Genome scans reveal scores of different bits of chromosome as possible culprits but together they explain just one part in 20 of the overall inherited liability to the disease.

The chance of being born with a predisposition to a common illness such as diabetes or depression is a gamble with huge numbers of cards.

So many small cards can be shuffled that everyone who falls ill fails in their own fashion and no gene says very much about whether or not you will get the gene (although the number of cheeseburgers you eat certainly does).

Steve Jones is a professor of genetics at University College London

http://www.bbc.co.uk/news/magazine-13775520

West and Central African Lions Are Genetically Different from Those in East and Southern Africa (via Chad Arment)

Via Kevin Stewart:


ScienceDaily (Apr. 4, 2011) — Researchers from the Institute of Environmental Sciences and the Leiden Institute of Biology in the Netherlands have recently published the findings of their genetic research on lions, which reveals a remarkable difference between lions in West and Central Africa and lions in East and southern Africa.


The study, from which the results were published in the Journal of Biogeography, was conducted by a consortium of researchers from a number of different universities.

Genetically different
The outcome of their research suggests that lions from West and Central Africa are genetically different from lions in East and southern Africa. The researchers analysed a region on the mitochondrial DNA of lions from all over Africa and from India, including sequences from extinct lions such as the Atlas lions in Morocco. Surprisingly, lions from West and Central Africa seemed to be more related to lions from the Asiatic subspecies than to their counterparts in East and southern Africa.

Previous research has already suggested that lions in West and Central Africa are smaller in size and weight, have smaller manes, live in smaller groups, eat smaller prey and may also differ in the shape of their skull, compared to their counterparts in East and southern Africa. However, this research was not backed by conclusive scientific evidence. The present research findings show that the difference is also reflected in the genetic makeup of the lions.

Barriers for dispersal
The distinction between lions from West and Central Africa and individuals from East and southern Africa can partially be explained by the location of natural structures that may form barriers for lion dispersal. These structures include the Central African rain forest and the Rift Valley, which stretches from Ethiopia to Tanzania and from the Democratic Republic of Congo to Mozambique. Another aspect explaining the unique genetic position of the West and Central African lion is the climatological history of this part of the continent.

It is hypothesised that a local extinction occurred, following periods of severe drought 40,000 to 8,000 years ago. During this period, lions continuously ranged deep into Asia and it is likely that conditions in the Middle East were still sufficiently favourable to sustain lion populations. The data published in the Journal of Biogeography suggest that West and Central Africa was recolonised by lions from areas close to India, which explains the close genetic relationship between lions from these two areas.

Declining population
There are thought to be some 1,700 lions left in West and Central Africa, which is less than 10% of the total estimated lion population in Africa. Lions in West and Central Africa are declining and are under severe threat due to the fragmentation or even destruction of their natural savannah habitat, the depletion of prey and retaliatory killing by livestock owners. The West and Central African lion is currently categorised as 'Regionally Endangered', according to IUCN criteria. Recent surveys in a large number of Lion Conservation Units in this region were, in fact, not able to confirm the presence of lions.

Other carnivore species, such as the wild dog and the cheetah, have become almost extinct in the region, with small populations surviving in Niger, Benin and Burkina Faso. These populations also appears to be struggling, suffering primarily from habitat loss and degradation, and conflict with local people.

Conservation
To save the last remaining large carnivores in this region, a new initiative has been launched: the 'Large Carnivore Initiative for West and Central Africa'. This initiative is supported by a large number of conservation organisations. Insights into the geographic pattern of genetic variation within a species can contribute significantly to the field of wildlife conservation. The patterns described in this publication should have consequences not only for in situ wildlife management, but also for management of zoo populations and captive breeding programmes.

http://www.sciencedaily.com/releases/2011/04/110401085113.htm

Craig Venter’s Genetic Typo

David M. Ewalt
Mar. 14 2011 - 12:00 pm

In May 2010, geneticist J. Craig Venter and his team made news by creating the first “synthetic life form,” replacing the genetic code in a bacterium with DNA they’d composed on a computer.

But during a presentation delivered Monday morning at the South By Southwest convention in Austin, Texas, Venter talked about two ways the landmark innovation went wrong.

In order to distinguish their synthetic DNA from that naturally present in the bacterium, Venter’s team coded several famous quotes into their DNA, including one from James Joyce’s A Portrait of the Artist of a Young Man: “To live, to err, to fall, to triumph, to recreate life out of life.”

After announcing their work, Venter explained, his team received a cease and desist letter from Joyce’s estate, saying that he’d used the Irish writer’s work without permission. ”We thought it fell under fair use,” said Venter.

The synthetic DNA also included a quote from physicist Richard Feynman, “What I cannot build, I cannot understand.”

That prompted a note from Caltech, the school where Feyman taught for decades. They sent Venter a photo of the blackboard on which Feynman composed the quote –and it showed that he actually wrote, “What I cannot create, I do not understand.”

“We agreed what was on the Internet was wrong,” said Venter. “So we’re going back to change the genetic code to correct it.”

http://blogs.forbes.com/davidewalt/2011/03/14/craig-venters-genetic-typo/

Owls change colour as climate warms

The owls are evolving to cope with increasing temperatures

Tuesday, 22 February 2011
By Emma Brennand
Earth News reporter

Tawny owls turn brown to survive in warmer climates, according to scientists in Finland.

Feather colour is hereditary, with grey plumage dominant over brown. But the study, published in the journal Nature Communications, found that the number of brown owls was increasing.

As winters become milder, the scientists say, grey feathered tawny owls are likely to disappear.

This study indicates that the birds are evolving in response to climate change.

Dr Patrik Karell from the University of Helsinki, who led the study, gathered together data from long-term tawny owl studies carried out across Finland over the last 30 years.

The owls can be split into two plumage-based categories - brown or grey.

The colour of a tawny owl's plumage does not change throughout its lifetime, so Dr Karell and his colleagues were able to use the data to create "colour maps" of breeding pairs and their offspring.

The maps showed that plumage colour was hereditary; pairs with grey plumage had the grey "version" of the gene that coded for plumage colour, so they produced grey offspring.

In the case of mixed colour breeding pairs, the grey colour trait was "dominant", which meant that an owlet that inherited both grey genes and brown genes would be likely to have grey plumage.

Lighter shade

The team examined tawny owl data, which was compiled by amateur bird ringers from the Finnish Museum of Natural History.

This revealed that, in years when winter weather was particularly severe, there was a higher mortality rate in the brown owl population.

This could be because brown owls were more visible to predators when there was thick snow cover.

Previous genetic studies have also suggested that brown owls' may have other disadvantages compared to their grey counterparts, including weaker immune systems and higher metabolic rates - meaning they need to forage more in order to survive.

But as the winters have become warmer, and snow cover has been reduced, the brown tawny owl populations have greatly increased.

Dr Karell told BBC News that the brown owls, which used to form 30% of the tawny owl population in Finland, now make up 50%.

"Its survival has improved as winters have become warmer," he said. "In other words, climate-driven selection has led to an evolutionary change in the population."

The results also suggest that a changing climate could, in some species, reduce the number and variety of characteristics that can be inherited.

If the grey owls disappeared from the "gene pool", for example, there would be only one version of the colour gene to be found.

http://news.bbc.co.uk/earth/hi/earth_news/newsid_9401000/9401733.stm
(Submitted by Dawn Holloway)

The Salmon That Grew & Grew

30-Sep-2010


Sometimes science is wrong, and one example of this are Frankenfish: In order to grow bigger salmon that can feed more people, a genetically-modified Atlantic salmon has been created that grows twice as fast as wild ones. Its genes have been artificially augmented with DNA taken from two other fish in order to give it more growth hormone. 

Researcher Craig Altier says, "The fisheries of the world are being rapidly depleted and so advances in aquaculture will be needed to meet the growing demand for protein. Genetically engineered animals might help to feed the world, but they must first meet the most stringent requirements for human and environmental safety.

"Is the introduced growth hormone gene safe for the fish itself? The studies designed to determine this were flawed, and so we don't know yet whether this is true. The burden of proof here is on the producer of this fish, Aquabounty, to perform further research to establish safety for the fish.

"Is the fish safe for human consumption? Exhaustive analysis by the FDA showed no difference from conventional salmon. The growth hormone itself presents no specific risk, as we consume growth hormone in all meats we eat (but SHOULD we?) The FDA also found no increase in allergens, which is important, as fish is already a food that causes allergic reactions in many people.

"We advised the FDA on the possible environmental impacts of this fish. Containment of the fish is essential, as the release of this fast-growing animal could have devastating effects on native fish populations. We need to treat these fish as we would a potentially dangerous medicine or pharmaceutical, and apply all of the same security measures to its production and transport."


http://www.unknowncountry.com/news/?id=8606

The Salmon That Grew & Grew

30-Sep-2010


Sometimes science is wrong, and one example of this are Frankenfish: In order to grow bigger salmon that can feed more people, a genetically-modified Atlantic salmon has been created that grows twice as fast as wild ones. Its genes have been artificially augmented with DNA taken from two other fish in order to give it more growth hormone. 

Researcher Craig Altier says, "The fisheries of the world are being rapidly depleted and so advances in aquaculture will be needed to meet the growing demand for protein. Genetically engineered animals might help to feed the world, but they must first meet the most stringent requirements for human and environmental safety.

"Is the introduced growth hormone gene safe for the fish itself? The studies designed to determine this were flawed, and so we don't know yet whether this is true. The burden of proof here is on the producer of this fish, Aquabounty, to perform further research to establish safety for the fish.

"Is the fish safe for human consumption? Exhaustive analysis by the FDA showed no difference from conventional salmon. The growth hormone itself presents no specific risk, as we consume growth hormone in all meats we eat (but SHOULD we?) The FDA also found no increase in allergens, which is important, as fish is already a food that causes allergic reactions in many people.

"We advised the FDA on the possible environmental impacts of this fish. Containment of the fish is essential, as the release of this fast-growing animal could have devastating effects on native fish populations. We need to treat these fish as we would a potentially dangerous medicine or pharmaceutical, and apply all of the same security measures to its production and transport."


http://www.unknowncountry.com/news/?id=8606

Galapagos frigatebirds genetically unique

Published: Sept. 28, 2010

WASHINGTON, Sept. 28 (UPI) -- Galapagos Islands frigatebirds are a genetically distinct species from their mainland counterparts, warranting new conservation status, U.S. scientists say.

The equatorial Pacific Ocean islands boast a number of unique plant and animal species from tortoises to iguanas to penguins, but frigatebirds can fly hundreds of miles across open ocean, suggesting their gene flow should be widespread and their genetic makeup should be identical to those of the frigatebirds on the mainland coast of the Americas, researchers from the Smithsonian Conservation Biology Institute say.

But three different genetics tests all yielded the same result -- the Galapagos seabirds have been genetically different from the frigatebirds elsewhere for more than half a million years.

"This was such a surprise," Frank Hailer, a research associate at institute, said. "It's a great testimony to just how unique the fauna and flora of the Galapagos are. Even something that is so well-adapted to flying over open oceans is isolated there."

What is clear is that this small population of genetically unique frigatebirds is a vulnerable group.

Any catastrophic event or threats by humans could wipe out the approximately 2,000 frigatebirds that nest on the Galapagos Islands, researchers say.

"The magnificent frigatebirds on the Galapagos are a unique evolutionarily significant unit, and if the Galapagos population did go extinct, the area will not likely be recolonized rapidly by mainland birds," Robert Fleischer, head of the institute's Center for Conservation and Evolutionary Genetics, said. "This emphasizes the importance of protecting this small population of birds there."

http://www.upi.com/Science_News/2010/09/28/Galapagos-frigatebirds-genetically-unique/UPI-78601285723104/
(Submitted by Chad Arment)

Galapagos frigatebirds genetically unique

Published: Sept. 28, 2010

WASHINGTON, Sept. 28 (UPI) -- Galapagos Islands frigatebirds are a genetically distinct species from their mainland counterparts, warranting new conservation status, U.S. scientists say.

The equatorial Pacific Ocean islands boast a number of unique plant and animal species from tortoises to iguanas to penguins, but frigatebirds can fly hundreds of miles across open ocean, suggesting their gene flow should be widespread and their genetic makeup should be identical to those of the frigatebirds on the mainland coast of the Americas, researchers from the Smithsonian Conservation Biology Institute say.

But three different genetics tests all yielded the same result -- the Galapagos seabirds have been genetically different from the frigatebirds elsewhere for more than half a million years.

"This was such a surprise," Frank Hailer, a research associate at institute, said. "It's a great testimony to just how unique the fauna and flora of the Galapagos are. Even something that is so well-adapted to flying over open oceans is isolated there."

What is clear is that this small population of genetically unique frigatebirds is a vulnerable group.

Any catastrophic event or threats by humans could wipe out the approximately 2,000 frigatebirds that nest on the Galapagos Islands, researchers say.

"The magnificent frigatebirds on the Galapagos are a unique evolutionarily significant unit, and if the Galapagos population did go extinct, the area will not likely be recolonized rapidly by mainland birds," Robert Fleischer, head of the institute's Center for Conservation and Evolutionary Genetics, said. "This emphasizes the importance of protecting this small population of birds there."

http://www.upi.com/Science_News/2010/09/28/Galapagos-frigatebirds-genetically-unique/UPI-78601285723104/
(Submitted by Chad Arment)

Great Gray Owl

Great gray owl research provides evidence that the Sierra Nevada is home to a genetically distinct population, compared to great gray owls outside of California.

Scientists, in 2010, documented Yosemite's great gray owl (Strix nebulosa Yosemitensis) as genetically distinct from the great gray owl in western North America (Strix nebulosa nebulosa). In addition to genetic differences, behavioral differences appear to exist in the Yosemite subspecies. These include differences in migration patterns, prey preference, and nest site selection. Each of these genetic and behavioral characteristics indicates the Sierra Nevada population of great gray owls has been isolated from other populations for an extensive period of time.

Yosemite, today, is the southernmost range and last sanctuary of almost all of California's great gray owls, listed as California State Endangered Species. Researchers estimate there are only about 200 to 300 individuals in California, and about 65% of the state's population resides in Yosemite. Great gray owls nest in the middle elevations of the park where forests and meadows meet. They can be active at any time of the day or night, preferring to hunt in open meadows and clearings within the forest.Then, in winter, they move downslope to snow-free areas where they can more easily access their rodent prey.

This rare and endangered owl is the largest North American owl but also can be found in Asia and Europe. It stands as tall as 2 feet with a 5-foot wingspan and has distinctive piercing yellow eyes accented by large facial disks.

To gain a greater understanding of Yosemite's great gray owl and its genetic make-up, Yosemite joined with the U.S. Forest Service's Pacific Southwest Research Station and geneticists from University of California, Davis to assess genetics, ecological-limiting factors, and immediate management needs of the Sierra-wide population. Great gray owls, restricted to montane meadows, are threatened from mounting resource use in the broader Sierra Nevada. Threats outside the park include timber harvest, grazing, and development pressures.

National parks like Yosemite that provide nearly intact ecosystems are critically important to both identify new species of plants and animals and to provide a laboratory in which to conduct scientific study. Yosemite's research aims to develop a predictive GIS-based habitat model of great gray owl distribution and habitat associations; and design a long-term monitoring plan to assess population trends.

Future genetic research on the great gray owl in Yosemite would help develop a technique to identify individual owls from their molted feathers. This non-invasive research method would allow scientists to study survival rates, reproduction patterns, and other important information through the DNA found in the collected feathers. Additionally, this research method would mitigate negative impacts on the sensitive great gray owl population in the park.

• Learn more about Yosemite's birds, including the park's other special status bird species.
  

Read the 2010 citation naming the Strix nebulosa Yosemitensis:
 

Hull, J.M.; Keane, J.J.; Savage, W.K.; Godwin, S.A.; Shafer, J.A.; Jepsen, E.P.; Gerhardt, R.; Stermer, C.; Ernest, H.B. (2010, July). Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California. Molecular Phylogenetics and Evolution, 56(1), 212-221, DOI: 10.1016/j.ympev.2010.02.027

 

http://www.nps.gov/yose/naturescience/great-gray-owl.htm

 

Mol Phylogenet Evol. 2010 Jul;56(1):212-21. Epub 2010 Mar 1.

Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California.

Hull JM, Keane JJ, Savage WK, Godwin SA, Shafer JA, Jepsen EP, Gerhardt R, Stermer C, Ernest HB.

Abstract
Investigations of regional genetic differentiation are essential for describing phylogeographic patterns and informing management efforts for species of conservation concern. In this context, we investigated genetic diversity and evolutionary relationships among great gray owl (Strix nebulosa) populations in western North America, which includes an allopatric range in the southern Sierra Nevada in California. Based on a total dataset consisting of 30 nuclear microsatellite DNA loci and 1938-base pairs of mitochondrial DNA, we found that Pacific Northwest sampling groups were recovered by frequency and Bayesian analyses of microsatellite data and each population sampled, except for western Canada, showed evidence of recent population bottlenecks and low effective sizes. Bayesian and maximum likelihood phylogenetic analyses of sequence data indicated that the allopatric Sierra Nevada population is also a distinct lineage with respect to the larger species range in North America ; we suggest a subspecies designation for this lineage should be considered (Strix nebulosa yosemitensis). Our study underscores the importance of phylogeographic studies for identifying lineages of conservation concern, as well as the important role of Pleistocene glaciation events in driving genetic differentiation of avian fauna.

(Submitted by Chad Arment)

Great Gray Owl

Great gray owl research provides evidence that the Sierra Nevada is home to a genetically distinct population, compared to great gray owls outside of California.

Scientists, in 2010, documented Yosemite's great gray owl (Strix nebulosa Yosemitensis) as genetically distinct from the great gray owl in western North America (Strix nebulosa nebulosa). In addition to genetic differences, behavioral differences appear to exist in the Yosemite subspecies. These include differences in migration patterns, prey preference, and nest site selection. Each of these genetic and behavioral characteristics indicates the Sierra Nevada population of great gray owls has been isolated from other populations for an extensive period of time.

Yosemite, today, is the southernmost range and last sanctuary of almost all of California's great gray owls, listed as California State Endangered Species. Researchers estimate there are only about 200 to 300 individuals in California, and about 65% of the state's population resides in Yosemite. Great gray owls nest in the middle elevations of the park where forests and meadows meet. They can be active at any time of the day or night, preferring to hunt in open meadows and clearings within the forest.Then, in winter, they move downslope to snow-free areas where they can more easily access their rodent prey.

This rare and endangered owl is the largest North American owl but also can be found in Asia and Europe. It stands as tall as 2 feet with a 5-foot wingspan and has distinctive piercing yellow eyes accented by large facial disks.

To gain a greater understanding of Yosemite's great gray owl and its genetic make-up, Yosemite joined with the U.S. Forest Service's Pacific Southwest Research Station and geneticists from University of California, Davis to assess genetics, ecological-limiting factors, and immediate management needs of the Sierra-wide population. Great gray owls, restricted to montane meadows, are threatened from mounting resource use in the broader Sierra Nevada. Threats outside the park include timber harvest, grazing, and development pressures.

National parks like Yosemite that provide nearly intact ecosystems are critically important to both identify new species of plants and animals and to provide a laboratory in which to conduct scientific study. Yosemite's research aims to develop a predictive GIS-based habitat model of great gray owl distribution and habitat associations; and design a long-term monitoring plan to assess population trends.

Future genetic research on the great gray owl in Yosemite would help develop a technique to identify individual owls from their molted feathers. This non-invasive research method would allow scientists to study survival rates, reproduction patterns, and other important information through the DNA found in the collected feathers. Additionally, this research method would mitigate negative impacts on the sensitive great gray owl population in the park.

• Learn more about Yosemite's birds, including the park's other special status bird species.
  

Read the 2010 citation naming the Strix nebulosa Yosemitensis:
 

Hull, J.M.; Keane, J.J.; Savage, W.K.; Godwin, S.A.; Shafer, J.A.; Jepsen, E.P.; Gerhardt, R.; Stermer, C.; Ernest, H.B. (2010, July). Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California. Molecular Phylogenetics and Evolution, 56(1), 212-221, DOI: 10.1016/j.ympev.2010.02.027

 

http://www.nps.gov/yose/naturescience/great-gray-owl.htm

 

Mol Phylogenet Evol. 2010 Jul;56(1):212-21. Epub 2010 Mar 1.

Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California.

Hull JM, Keane JJ, Savage WK, Godwin SA, Shafer JA, Jepsen EP, Gerhardt R, Stermer C, Ernest HB.

Abstract
Investigations of regional genetic differentiation are essential for describing phylogeographic patterns and informing management efforts for species of conservation concern. In this context, we investigated genetic diversity and evolutionary relationships among great gray owl (Strix nebulosa) populations in western North America, which includes an allopatric range in the southern Sierra Nevada in California. Based on a total dataset consisting of 30 nuclear microsatellite DNA loci and 1938-base pairs of mitochondrial DNA, we found that Pacific Northwest sampling groups were recovered by frequency and Bayesian analyses of microsatellite data and each population sampled, except for western Canada, showed evidence of recent population bottlenecks and low effective sizes. Bayesian and maximum likelihood phylogenetic analyses of sequence data indicated that the allopatric Sierra Nevada population is also a distinct lineage with respect to the larger species range in North America ; we suggest a subspecies designation for this lineage should be considered (Strix nebulosa yosemitensis). Our study underscores the importance of phylogeographic studies for identifying lineages of conservation concern, as well as the important role of Pleistocene glaciation events in driving genetic differentiation of avian fauna.

(Submitted by Chad Arment)

Genomes of Two Separate Ant Species Sequenced

August 27th, 2010

An international collaboration of scientists has just released the results of a new investigation, which managed to sequence the full genomes of two socially-divergent ant species. The finding can be used to derive more data on the role of epigenetics in aging and behavior.

Generally, the concept of epigenetics is used to refer to the field of genetic sciences which deals with studying the inherited changes that a body exhibits in its appearance (phenotype) and gene expression.

Studying this concept is one of the main goal in biology today, but two researchers at the Arizona State University (ASU) are now taking a more unconventional approach to understanding its role/

They are part of a team that is using the fully-sequenced genome of ants from the species Camponotus floridanus and Harpegnathos saltator to understand epigenetics.

The group also contains researchers from research institutions and organizations in New York, China, Pennsylvania, and Denmark.

The ASU crew is made up of School of Life Sciences assistant professor Jurgen Liebig and postdoctoral fellow Navdeep Mutti, who works in the former's lab.

“With the genome sequences and gene expression analyses of our two ant species, we show the potential of ants as a new system to study the epigenetic foundations of aging and developmental, reproductive and behavioral plasticity,” explains Liebig.

He is also a researcher at the ASU Center for Social Dynamics and Complexity, in the university's College of Liberal Arts and Sciences.

The international research effort was led by Howard Hughes Medical Institute Investigator Danny Reinberg, who is a professor of biochemistry at New York University (NYU) Langone Medical Center.

Details of the work were published in the August 27 issue of the esteemed journal Science.

“Ants are extremely social creatures and their ability to survive depends on their community in a very similar way to humans. Whether they are workers, soldiers or queens, ants seem to be a perfect fit to study whether epigenetics influences behavior and aging,” explains Reinber.

He also holds an appointment as a member of the NYU Cancer Institute. “In studying the genomes of these two ants, we were fascinated by the different behaviors and different roles that the worker ants develop,” he adds.

“Since every ant in the colony starts with the same genetic information, the different neuronal connections that specify the behavior appropriate for each social rank, must be controlled by epigenetic mechanisms,” the researcher explains further.

“The findings could potentially help us learn more about the effect of epigenetics on brain function in humans,” Reinber concludes.

http://news.softpedia.com/news/Genomes-of-Two-Separate-Ant-Species-Sequenced-153968.shtml

'Artificial life' breakthrough announced by scientists

Thursday, 20 May 2010
By Victoria Gill
Science reporter, BBC News

Scientists in the US have succeeded in developing the first synthetic living cell.

The researchers constructed a bacterium's "genetic software" and transplanted it into a host cell.

The resulting microbe then looked and behaved like the species "dictated" by the synthetic DNA.

The advance, published in Science, has been hailed as a scientific landmark, but critics say there are dangers posed by synthetic organisms.

The researchers hope eventually to design bacterial cells that will produce medicines and fuels and even absorb greenhouse gases.

The team was led by Dr Craig Venter of the J Craig Venter Institute (JCVI) in Maryland and California.

He and his colleagues had previously made a synthetic bacterial genome, and transplanted the genome of one bacterium into another.

Now, the scientists have put both methods together, to create what they call a "synthetic cell", although only its genome is truly synthetic.

Dr Venter likened the advance to making new software for the cell.

The researchers copied an existing bacterial genome. They sequenced its genetic code and then used "synthesis machines" to chemically construct a copy.

Dr Venter told BBC News: "We've now been able to take our synthetic chromosome and transplant it into a recipient cell - a different organism.

"As soon as this new software goes into the cell, the cell reads [it] and converts into the species specified in that genetic code."

The new bacteria replicated over a billion times, producing copies that contained and were controlled by the constructed, synthetic DNA.

"This is the first time any synthetic DNA has been in complete control of a cell," said Dr Venter.

'New industrial revolution'

Dr Venter and his colleagues hope eventually to design and build new bacteria that will perform useful functions.

"I think they're going to potentially create a new industrial revolution," he said.

"If we can really get cells to do the production that we want, they could help wean us off oil and reverse some of the damage to the environment by capturing carbon dioxide."

Dr Venter and his colleagues are already collaborating with pharmaceutical and fuel companies to design and develop chromosomes for bacteria that would produce useful fuels and new vaccines.

But critics say that the potential benefits of synthetic organisms have been overstated.

Dr Helen Wallace from Genewatch UK, an organisation that monitors developments in genetic technologies, told BBC News that synthetic bacteria could be dangerous.

"If you release new organisms into the environment, you can do more harm than good," she said.

"By releasing them into areas of pollution, [with the aim of cleaning it up], you're actually releasing a new kind of pollution.

"We don't know how these organisms will behave in the environment."

Dr Wallace accused Dr Venter of playing down the potential drawbacks.

"He isn't God," she said, "he's actually being very human; trying to get money invested in his technology and avoid regulation that would restrict its use."

But Dr Venter said that he was "driving the discussions" about the regulations governing this relatively new scientific field and about the ethical implications of the work.

He said: "In 2003, when we made the first synthetic virus, it underwent an extensive ethical review that went all the way up to the level of the White House.

"And there have been extensive reviews including from the National Academy of Sciences, which has done a comprehensive report on this new field.

"We think these are important issues and we urge continued discussion that we want to take part in."

Ethical discussions

Dr Gos Micklem, a geneticist from the University of Cambridge, said that the advance was "undoubtedly a landmark" study.

But, he said, "there is already a wealth of simple, cheap, powerful and mature techniques for genetically engineering a range of organisms. Therefore, for the time being, this approach is unlikely to supplant existing methods for genetic engineering".

The ethical discussions surrounding the creation of synthetic or artificial life are set to continue.

Professor Julian Savulescu, from the Oxford Uehiro Centre for Practical Ethics at the University of Oxford, said the potential of this science was "in the far future, but real and significant".

"But the risks are also unparalleled," he continued. "We need new standards of safety evaluation for this kind of radical research and protections from military or terrorist misuse and abuse.

"These could be used in the future to make the most powerful bioweapons imaginable. The challenge is to eat the fruit without the worm."

The advance did not pose a danger in the form of bio-terrorism, Dr Venter said.

"That was reviewed extensively in the US in a report from Massachusetts Institute of Technology (MIT) and a Washington defence think tank, indicating that there were very small new dangers from this.

"Most people are in agreement that there is a slight increase in the potential for harm. But there's an exponential increase in the potential benefit to society," he told BBC's Newsnight.

"The flu vaccine you'll get next year could be developed by these processes," he added.

More at: http://news.bbc.co.uk/1/hi/science_and_environment/10132762.stm

Neanderthal genes 'survive in us'

Thursday, 6 May 2010 19:02 UK

By Paul Rincon
Science reporter, BBC News

Many people alive today possess some Neanderthal ancestry, according to a landmark scientific study.

The finding has surprised many experts, as previous genetic evidence suggested the Neanderthals made little or no contribution to our inheritance.

The result comes from analysis of the Neanderthal genome - the "instruction manual" describing how these ancient humans were put together.

Between 1% and 4% of the Eurasian human genome seems to come from Neanderthals.

But the study confirms living humans overwhelmingly trace their ancestry to a small population of Africans who later spread out across the world.

The most widely-accepted theory of modern human origins - known as Out of Africa - holds that the ancestors of living humans (Homo sapiens) originated in Africa some 200,000 years ago.

A relatively small group of people then left the continent to populate the rest of the world between 50,000 and 60,000 years ago.

While the Neanderthal genetic contribution - found in people from Europe, Asia and Oceania - appears to be small, this figure is higher than previous genetic analyses have suggested.

"They are not totally extinct. In some of us they live on, a little bit," said Professor Svante Paabo, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Professor Chris Stringer, research leader in human origins at London's Natural History Museum, is one of the architects of the Out of Africa theory. He told BBC News: "In some ways [the study] confirms what we already knew, in that the Neanderthals look like a separate line.

"But, of course, the really surprising thing for many of us is the implication that there has been some interbreeding between Neanderthals and modern humans in the past."

John Hawks, assistant professor of anthropology at the University of Wisconsin-Madison in the US, told BBC News: "They're us. We're them.

"It seemed like it was likely to be possible, but I am surprised by the amount. I really was not expecting it to be as high as 4%," he said of the genetic contribution from Neanderthals.

The sequencing of the Neanderthal genome is a landmark scientific achievement, the product of a four-year-long effort led from Germany's Max Planck Institute but involving many other universities around the world.

The project makes use of efficient "high-throughput" technology which allows many genetic sequences to be processed at the same time.

The draft Neanderthal sequence contains DNA extracted from the bones of three different Neanderthals found at Vindija Cave in Croatia.

Retrieving good quality genetic material from remains tens of thousands of years old presented many hurdles which had to be overcome.

The samples almost always contained only a small amount of Neanderthal DNA amid vast quantities of DNA from bacteria and fungi that colonised the remains after death.

The Neanderthal DNA itself had broken down into very short segments and had changed chemically. Luckily, the chemical changes were of a regular nature, allowing the researchers to write software that corrected for them.

Writing in Science journal, the researchers describe how they compared this draft sequence with the genomes of modern people from around the globe.

"The comparison of these two genetic sequences enables us to find out where our genome differs from that of our closest relative," said Professor Paabo.

The results show that the genomes of non-Africans (from Europe, China and New Guinea) are closer to the Neanderthal sequence than are those from Africa.

The most likely explanation, say the researchers, is that there was limited mating, or "gene flow", between Neanderthals and the ancestors of present-day Eurasians.

This must have taken place just as people were leaving Africa, while they were still part of one pioneering population. This mixing could have taken place either in North Africa, the Levant or the Arabian Peninsula, say the researchers.

The Out of Africa theory contends that modern humans replaced local "archaic" populations like the Neanderthals.

But there are several variations on this idea. The most conservative model proposes that this replacement took place with no interbreeding between modern humans and Neanderthals.

Unique features

Another version allows for a degree of assimilation, or absorption, of other human types into the Homo sapiens gene pool.

The latest research strongly supports the Out of Africa theory, but it falsifies the most conservative version of events.

The team also identified more than 70 gene changes that were unique to modern humans. These genes are implicated in physiology, the development of the brain, skin and bone.

The researchers also looked for signs of "selective sweeps" - strong natural selection acting to boost traits in modern humans. They found 212 regions where positive selection may have been taking place.

The scientists are interested in discovering genes that distinguish modern humans from Neanderthals because they may have given our evolutionary line certain advantages over the course of evolution.

The most obvious differences were in physique: the muscular, stocky frames of Neanderthals contrast sharply with those of our ancestors. But it is likely there were also more subtle differences, in behaviour, for example.

Dr Hawks commented that the amount of Neanderthal DNA in our genomes seemed high: "What it means is that any traits [Neanderthals] had that might have been useful in later populations should still be here.

"So when we see that their anatomies are gone, this isn't just chance. Those things that made the Neanderthals apparent to us as a population - those things didn't work. They're gone because they didn't work in the context of our population."

Researchers had previously thought Europe was the region where Neanderthals and modern humans were most likely to have exchanged genes. The two human types overlapped here for some 10,000 years.

The authors of the paper in Science do not rule out some interbreeding in Europe, but say it was not possible to detect this with present scientific methods.

http://news.bbc.co.uk/1/hi/sci/tech/8660940.stm

Meet the Genetically Engineered Pig With Earth-Friendly Poop

Meet the Genetically Engineered Pig With Earth-Friendly Poop

Posted: 02 Apr 2010 12:05 PM PDT
Enviropig-ModelCanada has approved for limited production a genetically engineered, environmentally friendly pig.

The "Enviropig" has been genetically modified in such a manner that its urine and feces contain almost 65 percent less phosphorus than usual. That could be good news for lakes, rivers, and ocean deltas, where phosphorous from animal waste can play a role in causing algal blooms. These outbursts of algae rapidly deplete the water's oxygen, creating vast dead zones for fish and other aquatic life [National Geographic]. All living creatures need phosphorus, as the element plays an important role in many cellular and organ functions. Domesticated pigs get their daily dose from corn or cereal grains, but not without a struggle. These foods contain a type of phosphorus that is indigestible to the pigs, so farmers also feed their pigs an enzyme called phytase to allow the animals to break down and digest the phosphorus. But ingested phytase isn't as effective at breaking down phosphorus as phytase created inside the pig would be, so a fair amount of the element gets flushed out in pig waste. That waste, in turn, can make its way into the water supply [National Geographic].

To fix this problem, the scientists tinkered with the swine's genes to make the pig produce its own phytase in its salivary glands. When the cereal grains are consumed, they mix with the phytase in the saliva, and throughout the pig's digestive tract the enzyme works to break down the phosphorous in the food. With more phosphorus retained within the body, the amount excreted in waste is reduced by almost 65 percent, say researchers.
The researchers who created the Enviropig say it's not just eco-friendly, but it also cut farmers' feed-supplement costs. If the pigs eventually become common, they could also help U.S. farmers comply with "zero discharge" rules that forbid pork producers from releasing nitrogen or phosphorus runoff.

The Enviropigs will be raised only in controlled research settings in Canada for now, and experts say transgenic pork won't be landing on your late anytime soon; the new biotech pig will face years of safety trials to see if it should be approved for commercial production and consumption in the United States and Canada. No transgenic animal has been approved for consumption as of yet. But in 2008 the FDA announced approval of the first human health product made from a genetically engineered animal. The goat-derived anticoagulant, ATryn, is used for the prevention of blood clots in patients with a rare disease-causing protein deficiency

Fly Guys

A genetically engineered mosquito that vaccinates as it bites has been developed by Japanese scientists. A protein in its saliva protects against potentially fatal Leishmania, which is spread by sand flies. Although there is no known vaccine for malaria, which kills around 2million people a year, it is hoped it can eventually applied to that too.

http://e-edition.metroherald.ie/2010/03/19/ - p8.

Dogs domesticated in Middle East, not Asia

17 March 2010 19:37 GMT
By Steve Gorman

LOS ANGELES (Reuters) - From French poodles to German shepherds, domestic dogs likely trace most of their ancestry to the Middle East, as opposed to East Asian origins suggested by previous research, a genetic study reported on Wednesday.

The findings, published in the online edition of the scientific journal Nature, support an archaeological record that closely links the domestication of dogs in the Middle East with the rise of human civilization there, scientists said.

"It's significant because this is where civilization developed, and dogs were part of that," said Robert Wayne, professor of evolutionary biology at the University of California, Los Angeles, and a senior author of the study.

The region, often referred to as the Fertile Crescent, includes much of modern-day Iraq, Syria, Lebanon and Jordan --

"the same area where domestic cats and many of our livestock originated, and where agriculture first developed," he said.

The study is based on genetic comparisons between more than 900 dogs representing 85 breeds and over 200 wild gray wolves -- the closest living wild relative of dogs -- from around the globe, including North America, Europe, East Asia and the Middle East.

In the most extensive such analysis to date, scientists used molecular genetic techniques to examine more than 48,000 markers from across the entire genome -- or DNA sequence -- from each of the animals included in the study.

What they discovered was the vast majority of dogs share more unique genetic markers with gray wolves from the Mideast than with other wolf populations. A kinship to European wolves also was found, but to a lesser extent, Wayne said.

NUISANCE OR COMPANION?

One notable exception was the finding of a close genetic link between a small number of East Asian dog breeds and wolves from China, suggesting some intermingling between the two.

But the new research contradicts an earlier genetic study suggesting a close ancestry of all dogs to wolves from East Asia and China. That analysis was based on comparisons between a single, small DNA sequence taken from mitochondria -- tiny structures outside the nucleus of living cells that carry their own genes -- rather markers from entire genomes.

The newer research was far more comprehensive and "is much more consistent with the archaeological record," Wayne said.

"We know that dogs from the Middle East were closely associated with humans because they were found in human burial sites" there, he said. In one famous example, the remains of a puppy were found curled up in the arms of a human skeleton.

But the earliest bond between people and "man's best friend" was probably more often a love-hate relationship that persists in parts of the world to this day, and helps explain a cultural ambivalence towards dogs in the very region where they likely originated.

The archaeological record of dogs dates back 31,000 years to the remains of a Great Dane-like specimen found in Belgium. The first Mideast dogs appeared 12,000 to 13,000 years ago.

Although agriculture and animal husbandry go hand in hand, the first people to domesticate dogs from wild wolves probably were nomadic hunter-gatherers, who were followed at a distance by canine interlopers in search of scraps.

That relationship likely matured over thousands of years "to the point where these proto-dogs were living in close proximity with humans," and were often more of a nuisance than they were companions, Wayne said.

"Eventually dogs provided protection, an early warning system, maybe even helped out with the hunt, and then eventually, even closer in, provided companionship," he said.

While some dog breeds have ancient histories, 80 percent are modern varieties that have evolved since the explosion in dog breeding during the Victorian era, Wayne said.

(Editing by Dan Whitcomb and Vicki Allen)

http://news.stv.tv/oddly-enough/164262-dogs-domesticated-in-middle-east-not-asia/