Birds-of-paradise genomes target sexual selection

New genomic data from 5 birds-of-paradise reveal genes that are shaped by selection and help explain the origin of their spectacular plumage

Date:  January 28, 2019

Source:  GigaScience

A new study published in the open access journal GigaScience explores the genomes of a fascinating group of birds, birds-of-paradise, with work providing genome sequences from 5 birds-of-paradise species: 3 that did not have available genome sequences. Birds-of-paradise, with their elaborate and colorful feathers as well as complex courtship displays, have a special place in natural history. They serve as a school-book example of sexual selection, which is the outcome of generations of female mate choice of males that have "attractive" features. The result is an unparalleled radiation of species where males exhibit extreme morphological features and behaviors with no other evolutionary meaning than to attract females for mating. However, very little is known about the genetic variants that distinguish the lavishly colored birds-of-paradise from their less conspicuous relatives, such as the collared flycatcher. Whole genome availability of multiple species provides a rich resource for molecular evolutionary to identify genes that came under the influence of sexual selection, and a way to assess how these genes transformed the males' plumage into a colorful asset for mating purposes.

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Bird migration and conservation clues in robin and Turtle dove genomes

December 21, 2018, Wellcome Trust Sanger Institute

The European robin and Turtle dove have had their genetic codes sequenced and assembled for the first time by scientists at the Wellcome Sanger Institute and their collaborators. The genomes, completed today (21 December) will enable researchers to explore the genetic switches controlling bird migration and give insight into the magneto receptors that help robins 'see' the Earth's magnetic fields for navigation. The Turtle dove genome will help conservation efforts to save one of the UK's fastest declining bird species.

European robins live throughout Europe, Russia and western Siberia. While most British robins reside in the UK over winter, some birds will migrate to southern Europe to overwinter in warmer climates. Simultaneously in winter, migrant robins from Scandinavia, continental Europe and Russia head to the UK to avoid the harsh weather back home.

Turtle doves also migrate, visiting their breeding grounds in Europe and spending the winter months in Africa. However, since 1995, 94 per cent of Turtle doves have been lost and there are fewer than 5,000 breeding pairs left in the UK. The Turtle dove is the UK's fastest-declining bird species, and as a result, they are listed as vulnerable on the International Union for Conservation of Nature (IUCN) Red List.

Migration patterns and behaviours vary across species, but also within species. Similarly, environmental pressures such as disease and limited food resources affect various bird species differently. To fully understand the genetic components of complex traits, such as migration and breeding, the whole genetic code must be read and analysed.

The European robin and Turtle dove's genomes were read by the Sanger Institute and its partners, in celebration of Sanger's 25th anniversary.

Collaborators at the University of Lincoln sent robin and Turtle dove samples to the Sanger Institute near Cambridge. The sequencing teams extracted DNA from the samples and used PacBio SMRT Sequencing technology to generate the first reference genomes for robins and Turtle doves.

The European robin genome will enable researchers to explore the genetic switches underpinning migration, which tell robins when to leave and where to go. The robin's role as a model of bird migration will help in understanding the magneto receptors in birds' eyes that allow them to use the Earth's magnetic fields for navigation and also unpick migratory behaviour in other bird species.

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Parrot genome analysis reveals insights into longevity, cognition

December 6, 2018, Carnegie Mellon University

Parrots are famously talkative, and a blue-fronted Amazon parrot named Moises—or at least its genome—is telling scientists volumes about the longevity and highly developed cognitive abilities that give parrots so much in common with humans. Perhaps someday, it will also provide clues about how parrots learn to vocalize so well.

Morgan Wirthlin, a BrainHub post-doctoral fellow in Carnegie Mellon University's Computational Biology Department and first author of a report to appear in the Dec. 17 issue of the journal Current Biology, said she and her colleagues sequenced the genome of the blue-fronted Amazon and used it to perform the first comparative study of parrot genomes.

By comparing the blue-fronted Amazon with 30 other long- and short-lived birds—including four additional parrot species—she and colleagues at Oregon Health and Science University (OHSU), the Federal University of Rio de Janeiro and other entities identified a suite of genes previously not known to play a role in longevity that deserve further study. They also identified genes associated with longevity in fruit flies and worms.

"In many cases, this is the first time we've connected those genes to longevity in vertebrates," she said.

Wirthlin, who began the study while a Ph.D. student in behavioral neuroscience at OHSU, said parrots are known to live up to 90 years in captivity—a lifespan that would be equivalent to hundreds of years for humans. The genes associated with longevity include telomerase, responsible for DNA repair of telomeres (the ends of chromosomes), which are known to shorten with age. Changes in these DNA repair genes can potentially turn cells malignant. The researchers have found evidence that changes in the DNA repair genes of long-lived birds appear to be balanced with changes in genes that control cell proliferation and cancer.

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Newly sequenced golden eagle genome will help its conservation

September 3, 2018, Wellcome Trust Sanger Institute

Conservation and monitoring efforts for the golden eagle will benefit from the newly-completed golden eagle genome sequence – the first of 25 species' genomes sequenced by the Wellcome Sanger Institute, in collaboration with the University of Edinburgh.

The golden eagle genome, released today (31 August), will help scientists and conservationists understand the diversity and viability of the species worldwide. It will ultimately aid the monitoring of existing, reinforced and reintroduced populations of golden eagles, such as those in the South of Scotland Golden Eagle translocation project, which aims to bolster the protected species' population.

There are around 300,000 golden eagles worldwide, with between 9,300-12,300 pairs living in Europe. Despite being listed as 'least concern' by the IUCN Red List of Threatened Species and having widespread populations worldwide, the 508 breeding pairs of golden eagles in the UK are largely restricted to the Scottish Highlands and Islands.

The Scottish population is on the edge of the global range, and many existing world populations are small and declining.

For the first time, the golden eagle has had its genome sequenced by the Sanger Institute and its partners, in celebration of Sanger's 25th anniversary.

The genome will enable additional studies of golden eagles and will help in the conservation and monitoring of the species. The genetic information will aid in identifying populations or individuals that might be best involved in any reintroduction or other conservation projects.

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Flightless bird extinct for more than 700 years can be brought back to life, say scientists

The little bush moa inhabited parts of New Zealand and went extinct in the late 13th century as a result of overhunting.

By : Pinaz Kazi

February 28, 2018 19:00 IST

Scientists are a step closer to bringing back a species of flightless bird that has been extinct for almost 700 years. The little bush moa that inhabited parts of New Zealand went abruptly extinct as a result of overhunting in the late 13th century.

A team of researchers from Harvard University has assembled a nearly-complete genome of the extinct moa by extracting ancient DNA from the toe bone of a moa specimen held at the Royal Ontario Museum in Toronto, Canada.

The scientists now believe that they are closer to the goal of "de-extinction" — the vanished species can be brought back to life by slipping the genome into the egg of a living species, Statnews reported.

"High throughput sequencing has revolutionized the field of ancient DNA (aDNA) by facilitating recovery of nuclear DNA for greater inference of evolutionary processes of extinct species than is possible from mitochondrial DNA alone," according to the study.

The little bush moa was a part of the palaeognathae clade of birds and birds, and those like the kiwi, ostrich, and emu were considered its cousins. There were nine species of the moa but all of them are extinct now.

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Genome of threatened northern spotted owl assembled

Genome completion will help researchers better measure interbreeding among hybrid owls and guide conservation priorities in the West

Date:  September 5, 2017

Source:  California Academy of Sciences

Summary:

A charismatic owl iconic to Pacific Coast forests is no longer ruling the roost, and scientists now have another tool for understanding its decline. Researchers have assembled the California Academy of Sciences' first-ever animal genome after sequencing the DNA of the northern spotted owl (Strix occidentalis caurina). Academy scientists and collaborators extensively mapped the bird's genetic material to better understand how this threatened forest dweller is interacting with non-native owls invading its habitat.

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Warbler genomes look to be 99.97 percent alike

Date: August 23, 2016

Source: Cornell University

For decades, conservationists have considered blue-winged warblers to be a threat to golden-winged warblers, a species being considered for federal Endangered Species protection. Blue-winged warbler populations have declined 66 percent since 1968, according to the North American Breeding Bird Survey.

The two species are known to frequently interbreed where they co-occur, and scientists have been concerned that the more numerous blue-winged warblers would genetically swamp the rarer golden-wing gene pool.

New research from the Cornell Lab of Ornithology's Fuller Evolutionary Biology Program shows that, genetically speaking, blue-winged and golden-winged warblers are almost identical. Scientists behind the research say the main differences between the two species are in feather color and pattern, in some cases just a simple matter of dominant or recessive pairings of gene variants, or alleles.

"We think we have finally pinpointed the proverbial genomic 'needle in the haystack' between these taxa," said study co-author David Toews, adding the findings suggest conservationists should be less concerned with hybridization and primarily focused on preserving habitat for both species. "This is something that conservation practitioners have wanted for a very long time."

The research is published in the September issue of the journal Current Biology. Toews' collaborators include fellow Cornell Lab postdoctoral researcher Scott Taylor, along with partners from Cornell University's Department of Biological Statistics and Computational Biology, the University of California at Riverside and Environment and Climate Change Canada.

The team investigated the genetic architecture behind the differences between the two warblers by analyzing the genomes of 10 golden-winged and 10 blue-winged warblers from New York, with birds sampled from the Sterling Forest along the New Jersey border to the St. Lawrence River Valley. Across their analysis of the entire genomes of both species, they found only six regions (or less than .03 percent) that showed strong differences. In other words, blue-winged and golden-winged warblers are 99.97 percent alike genetically.

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Songbird's reference genome illuminate key role of epigenetics in evolution of memory and learning

Smart songbird's reference genome is milestone for ecological research

Date:January 25, 2016

Source:Netherlands Institute of Ecology (NIOO-KNAW)

A well-known songbird, the great tit, has revealed its genetic code, offering researchers new insight into how species adapt to a changing planet. Their initial findings suggest that epigenetics -- what's on rather than what's in the gene -- may play a key role in the evolution of memory and learning. And that's not just true for birds. An international research team led by the Netherlands Institute of Ecology (NIOO-KNAW) and Wageningen University will publish these findings in Nature Communications on Monday.

"People in our field have been waiting for this for decades," explain researchers Kees van Oers and Veronika Laine from the Netherlands Institute of Ecology. The reference genome of their favourite model species, the great tit, is "a powerful toolbox that all ecologists and evolutionary biologists should know about."

Coming from a single Dutch bird, the genetic code of the assembled reference genome will help to reveal the genetic basis of phenotypic evolution. This is essential for understanding how wild species adapt to our changing planet.

In addition to looking at the genome, the research team have also determined the so-called transcriptome and methylome. The latter belongs to the field of epigenetics: the study of what you can inherit not in but 'on' your genes. Specific DNA sequences in the genome can be 'methylated': methyl groups are added to them, modifying how the genes function.

The research team sequenced the complete genomes of a further 29 great tit individuals from different parts of Europe. This enabled them to identify regions in the great tit's genome that have been under selection during recent evolution of the bird. These regions appeared to be overrepresented for genes related to learning and cognition.

"The great tit has evolved to be smart," says Van Oers. "Very smart." It's not your average bird, as it belongs to the top 3% smartest birds when it comes to learning new behaviour. That makes it a perfect candidate for research into the evolution of learning, memory and cognitive processes.

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March of the penguin genomes

Date:

December 11, 2014

Source:

BioMed Central

Summary:

Two penguin genomes have been sequenced and analyzed for the first time. The study reveals insights into how these birds have been able to adapt to the cold and hostile Antarctic environment.

Antarctic penguins are subject to extremely low temperatures, high winds, and profound changes in daylight. They have developed complicated biological systems to regulate temperature and store energy for long-term fasting. Most studies have focused on the physiological and behavioral aspects of their biology, but an international team of researchers has now analyzed the DNA of two Antarctic penguins (Adélie and emperor) relative to other bird species, revealing the genetic basis of their adaptations and their evolutionary history in response to climate change.

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Genome Shows Mutant Gene Gives Pigeons Fancy Hairdos

Jan. 31, 2013 — University of Utah researchers decoded the genetic blueprint of the rock pigeon, unlocking secrets about pigeons' Middle East origins, feral pigeons' kinship with escaped racing birds, and how mutations give pigeons traits like a fancy feather hairdo known as a head crest.

"Birds are a huge part of life on Earth, and we know surprisingly little about their genetics," especially compared with mammals and fish, says Michael D. Shapiro, one of the study's two principal authors and an assistant professor of biology at the University of Utah. "There are more than 10,000 species of birds, yet we know very little about what makes them so diverse genetically and developmentally."

He adds that in the new study, "we've shown a way forward to find the genetic basis of traits -- the molecular mechanisms controlling animal diversity in pigeons. Using this approach, we expect to be able to do this for other traits in pigeons, and it can be applied to other birds and many other animals as well."

The study appears Jan. 31 on Science Express, the website of the journal Science. Shapiro led the research with Jun Wang of China's BGI-Shenzhen (formerly Beijing Genomics Institute) and other scientists from BGI, the University of Utah, Denmark's University of Copenhagen and the University of Texas M.D. Anderson Cancer Center in Houston.

This is a rock pigeon of the breed old Dutch capuchine, which has a kind of head crest known as a mane. More than 80 breeds out of some 350 breeds of rock pigeon have head crests, which form when head and neck feathers grow upward instead of downward. Scientists from the University of Utah, BGI-Shenzen in China and other institutions decoded the genome or genetic blueprint of the rock pigeon, then found that a single gene mutation linked to the head crest trait. 

(Credit: Michael D. Shapiro, University of Utah.)

Continued:  http://www.sciencedaily.com/releases/2013/01/130131144059.htm

Flycatchers’ genomes explain how one species became two

Why are hybrids sterile?

October 2012. Just how new species are established is still one of the most central questions in biology. In an article in the leading scientific journal Nature, researchers at Uppsala University in Sweden describe how they mapped the genomes of the European pied flycatcher and the collared flycatcher and found that it is disparate chromosome structures rather than separate adaptations in individual genes that underlies the separation of the species.

"We were surprised that such a large part of the genome was nearly identical in the two species," says Hans Ellegren, professor of evolutionary biology and director of the research team behind the new findings.

Interbreeding
The big question in species-differentiation research today involves the genetic background of how two evolutionary lines gradually come to diverge from each other and ultimately cannot produce fertile young. Horses and donkeys, for instance, can crossbreed and produce mules and hinnies, but something in the genome of the latter makes them infertile. There must therefore be DNA sequences from diverging evolutionary lines that are not compatible.

Genome sequence of flycatchers

Researchers at the Evolutionary Biology Centre, Uppsala University, are now presenting the genome sequence for the two flycatchers, which are the first organisms apart from so-called model organisms, to have their genome sequenced. They are also the first DNA sequences for a vertebrate to have been determined entirely by Swedish researchers and at a Swedish laboratory. 

Continued:  http://www.wildlifeextra.com/go/news/flycatcher-genome.html