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Woolly mammoth populations were plentiful 45,000 years ago, but went into genomic freefall as their numbers dwindled around 4,000 years ago.

Isolated on an island in the Arctic Ocean, not only were woolly mammoths the last of a dying species but they were also swamped with bad genes that are likely to have stripped their sense of smell and saddled them with translucent coats.

A study1 published 2 March in PLOS Genetics gives a rare insight into how genomes change as a species dies out. Towards the end of the last Ice Age, around 11,700 years ago, woolly mammoths ranged through Siberia and into the colder stretches of North America. But by about 4,000 years ago, mainland mammoths had died out and only 300 remained on Wrangel Island off the Siberian coast.

In order to examine this disappearance at the genetic level, biologists Rebekah Rogers and Montgomery Slatkin at the University of California, Berkeley, compared the complete genome of a mainland mammoth (Mammuthus primigenius) that lived about 45,000 years ago with that of a Wrangel Island mammoth from about 4,300 years ago. The sequences were made available by Love Daln at the Swedish Museum of Natural History in Stockholm.

As I looked at the sequence data, says Rogers, it became very clear that the Wrangel mammoth had an excess of what looked like bad mutations.

Some of these changes are only visible to a geneticists eye. Compared with the mainland mammoth, the Wrangel Island specimen's genome was riddled with deletions and an abundance of sequences called stop codons which tell a cell when to stop transcribing a section of DNA among other changes to the DNA. But some of these changes would also have been visible in the mammoths behaviour and appearance.

Rogers and Slatkin found that genes related to smell and urinary proteins, which in modern elephants are important for eliciting mating behaviours or signalling social status were shut down by the mutations. These might be related, the researchers hypothesize, because a duller sense of smell may have been hitched in a feedback loop to the loss of urinary proteins, leading to the rapid loss of both. Changes to the Wrangel mammoths coats would have been even more obvious. Rogers and Slatkin propose that a mutation in a part of the genome called FOXQ1 would have given the mammoths a satin coat, marked by fur that is the same colour as normal but is shiny and translucent.

What happened on Wrangel wasnt a matter of inbreeding, Rogers says the genetic signal is different.

What did happen was that the population was simply small, she says, and under these circumstances any mammoth was better than no mammoth at all, so natural selection did not operate in the usual way. This allowed unhelpful mutations to rack up, following a previously identified phenomenon called nearly neutral genome evolution. Bad mutations that would normally be weeded out werent removed from the population because of reduced competition, says Rogers.

Isolation and reducing population size have long been recognized as important factors causing endangerment, says palaeontologist Ross MacPhee of the American Museum of Natural History in New York City, but the recognition of the mammoths genetic meltdown is a sign of how far studies of ancient DNA have come, and the work that still lies ahead.

The changes on Wrangel Island took place after mammoths had already been wiped out on the mainland. Tracking the downfall of the species is an ongoing effort, says MacPhee. With additional specimens, drawn from other times and parts of the woolly mammoths enormous range, we may get a better picture of the genetic load that this species was labouring under at the end of its tenure.

Still, MacPhee adds, the study is maybe telling us something very important about what happens in populations already under severe threat because of diminished range and numbers.

MacPhee cautions that no single animal or genome can tell the whole story for an entire species. But he notes that human hunting, climate change or any other external factor wasn't enough by itself to wipe out the woolly mammoth. There had to be some other element operating within the animals, driving them to extinction.

As dramatic as genetic meltdown sounds, Rogers says that its difficult to tell whether the increase in bad mutations contributed directly to the final extinction of the woolly mammoth. Yet the findings have implications for the survival of the mammoths elephant cousins and other endangered mammals. Rogers notes that its better to prevent a species from becoming endangered in the first place than to try to recover its genetic diversity after a sharp plummet.

Even though we can improve the number of individuals in endangered populations, she says, their genomes may still bear the hallmarks of genomic meltdown, which will be difficult to undo.

More here:
Dying woolly mammoths were in 'genetic meltdown' - Nature.com

Higher corn populations may be the way of the future, but seed companies are finding yield and economic benefits from high populations are both hybrid- and field-specific.

Myron Stine, president of Stine Seed Company, said his company began to see benefits in hybrids that performed well at high populations in the early 1990s. Over time, they started to identify the genetics responsible and developed a high-population growing system matched with specific genetics.

Genetics are fluid, but it takes a long time to change those, Stine said. We view (high-population corn) as a constantly evolving technology (and) management practice.

Honing in on higher populations

Stine said the number of growers in 2016 who saw a difference from higher population corn was fewer than in 2015, but those who did notice a difference saw a more dramatic improvement.

Like other management practices, farmers who use higher populations expect better yields on average across multiple years just as varying benefits are expected from fungicide or split-season nitrogen applications because of variable growing season conditions.

Stine said that in 2016 some high-population plantings had nitrogen left over, while the high-population fields with the biggest yield gains used up the available nitrogen.

The company developed a twin 20-inch-row planting system with John Deere and Great Plains. The twin rows can be harvested with a 20-inch corn header while halving the row spacing width. A twin 30-inch-row system is also possible.

This system is also being used with variable rate technology. Growers are varying populations from 30,000 to 45,000 seeds per acre and changing hybrid selection as they move from less productive to more productive ground.

Pairing populations and hybrids

Paul Carter, DuPont Pioneer senior agronomy sciences manager, said all Pioneer hybrids are tested at 20 to 30 locations over several years, plus hundreds of on-farm trials. Planting populations in some of these tests range from 18,000 to 50,000 seeds per acre on 30-inch rows.

In general, Pioneer has found the seeding rate required to maximize yield increases as yield level increases, Carter said.

The economic optimum seeding rate varies from about 30,000 seeds/acre for locations yielding 150 bu./acre to over 37,000 seeds/acre for yields of 240 bu./acre. Average responses vary by hybrid and local situations.

Brad Van Kooten, DuPont Pioneer senior marketing manager, said in studies looking at high seeding rates in 15-inch rows, they found about 80 percent of the germplasm worked well with 30-inch-row performance 20 percent responded differently. Of the total, 10 percent performed better in narrow row, high-population environments over a period of at least three years.

The benefits from these top-performing, high-population hybrids are incremental, Van Kooten said. While statistically better, they were not make or break differences.

Producers should review soil fertility levels to make sure they match their higher production goals, he said.

Pioneer also found a correlation between higher seeding rate advantages and shorter maturity corn.

Location is likely an important factor as higher planting densities may be better able to take advantage of a shorter growing season, Van Kooten explained.

Carter said that over the past 50 years, improved corn genetics have led to a gain of around 2 bushels per acre per year.

A lot of that gain has come from developing hybrids that can withstand the stress of plant to plant competition, he said.

Its important for growers to keep up with this gain, but the additional population required may be near an additional 250 plants per acre per year, he said.

So theres been a steady, a linear increase. We havent seen a step change, he said.

Van Kooten said theyve learned that the highest yielding genetics may not always benefit from higher populations. Population should be a hybrid-by-hybrid decision.

To find the sweet spot for each hybrid, Pioneer has a number of tools, including a Planting Rate Estimator app. Local seed reps likely are the best resource for farmers, Van Kooten said.

Understanding high populations

Becks Hybrids Practical Farm Research Agronomist Alexandra Knight said theyve seen a trend of high population seeding rate success in highly productive soils with high organic matter.

Knight said Becks participated in a multi-hybrid planting study from 2012 to 2015, testing offensive and defensive hybrids and corresponding seeding rates based on yield map history. It found a 7 bushel per acre benefit in corn.

Their Iowa 2016 High Yield Attempt PFR study a moonshot of sorts for highest yield also showed a yield advantage with a higher seeding rate.

Knight said some of the factors that seem to play a role in making a hybrid that performs best at high populations include uniform emergence and consistency of ear fill. Precise nitrogen placement, both timing and location, has also been key in high-yield attempts.

In 2017, PFR research will include testing hybrids at planting rates from 30,000 to 42,000, Knight said.

As they continue to develop their high population corn system, Stine said they are finding a number of traits are responsible for making a hybrid that performs well at high populations.

Generally, we are seeing shorter plant types with more upright leaves, he said.

On some high-population hybrids, they are beginning to see tassels below top leaves of the plant, he added.

Earlier flowering is also common observation with successful early season hybrids, Stine said.

More:
Genetics key with high corn populations - Missouri Farmer Today

New light shed on genetics and social mobility

KATHARINE CHILD | 2017-03-02 07:06:54.0

DNA molecule. File photo.

Scientists are learning the first few years of a child's life can be a good predictor of whether they will have a successful life or be condemned to poverty.

Now an international study conducted in South Africa shows that genetics can determine whether an underprivileged baby will respond to interventions to help them.

The study was published in the journal PLOS this week.

Peter Singer, CEO of Grand Challenges Canada, said: "This is a startling finding that changes the way I think about child development. Why is that important? Because child development is the ladder of social mobility to climb out the hole of inequity for millions of children all over this inequitable world."

The first study was conducted by Stellenbosch Professor Mark Tomlinson between 1999 and 2003 in which caregivers taught about 220 Khayelitsha mothers to communicate and engage with their babies to help them form good bonds, a process dubbed "attachment".

Attachment is a psychological measure of a child's bond with its mother and can predict future wellbeing.

Another 220 mothers received no training. Their children were assessed at 18 months and compared with babies whose mothers received training.

The trial was described as only "moderately" successful, registering a small improvement.

But researchers recently found 220 of the original children and analysed if they had a short or long form of SLC6A4 - the serotonin transporter gene, which is involved in nerve signalling, and which has been linked to anxiety and depression.

Children with the short form of the gene, and whose pregnant mothers were mentored, were almost four times more likely to be securely attached to their mothers at 18 months old than children carrying the short form whose mothers did not receive help.

Meanwhile, children with the long form of the serotonin transporter gene did equally well regardless of the mentoring.

Tomlinson told The Times they didn't want to genetically screen children as it would be "morally wrong".

"This raises more questions than answers," he said.

Link:
New light shed on genetics and social mobility - Times LIVE

For weeks, the market and certain sectors have been operating under uncertainty as doubts over the direction of President Trumps administration were growing. After Tuesday nights speech, investors are beginning to get some clarity, allowing a number of companies that have been locked in a range to begin showing signs that they are ready to move higher.

Todays three big stock charts look at Myriad Genetics, Inc. (NASDAQ:MYGN), Wal-Mart Stores Inc (NYSE:WMT) and Nucor Corporation (NYSE:NUE). These three companies have experienced recent technical trends that suggest they areready to shift back into rally mode.

Myriad, along with a large portion of the health care and biotechnology sectors, has been held back by uncertainty around the repeal and replacement of Obamacare. With this option becoming less likely, these stocks are starting to rally again.

MYGN shares recently broke above their 50- and 100-day moving averages as volume on the stock saw an increase. This suggests that the technical traders are now getting behind the shift in trends.

While breaking above the 50-day, this trendline has started to transition into a rising pattern for Myriad. Our stock modeling programs show that MYGNand other stocks are twice as likely to continue their trend when the 50-day is moving higher.

Myriad shares are coming off an overbought reading after the recent positive earnings results. This suggests that we may see a short-term decline in MYGNshares theres a catch here though.

From a long-term perspective, the market technicals view Myriad Genetics as an oversold, undervalued stock. This means that MYGNshares could more easily remain in short-term overbought territory as the crowd is only beginning to migrate into the stock.

Watch for a pause at $20, but from there the shares should find plenty of technical strength to rally higher.

The retail sector has taken a beating as of late, as the fourth-quarter earnings results have been underwhelming to say the least. One standout, at least from a technical perspective, is Walmart. The SPDR S&P Retail (ETF) (NYSEARCA:XRT) is trading 2.5% lower over the last 12 months compared to the 6% return for WMTshares.

Now, the technical picture for Walmart shares isimproving from an intermediate-term perspective.

Last week, WMT shares broke above the 200-day moving average on a positive earnings report. This move also broke Walmart stock into a technically overbought reading that we expected to see force a pullback, which is exactly what happened.

Now, WMT shares are consolidating around the 200-day trendline, just above $70. The support from this trendline suggests that the stock is now gaining technical strength. Supporting that theory is the fact that Walmarts 50-day trendline is now moving higher. This bullish transition improved the technical outlook for the largest retailer.

Weve seen overhead resistance at $75 for WMT shares since June 2016; however, the growing momentum looks to overtake this hurdle over the next few weeks.

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3 Big Stock Charts for Thursday: Myriad Genetics, Inc. (MYGN), Wal-Mart Stores Inc (WMT) and Nucor Corporation (NUE) - Investorplace.com

When most people think of potatoes, the word research does not usually follow. But with their Mr. Potato head mascot watching over the lab, the University of Nevada Reno's plant biology tag team, Dylan Kosma and Patricia Santos, are searching for ways to reduce potato crop losses during storage.

The University's Kosma-Santos lab, in the College of Agriculture, Biotechnology and Natural Resources, was recently awarded a $1.37 grant by the National Science Foundation to investigate the molecular-genetics and biochemistry that underlies potato crop losses during tuber storage. As the number one vegetable crop in the United States and a top five crop for the state of Nevada, potato crop losses can be economically devastating to farmers and the potato industry as a whole. A large proportion of these crop losses are due to factors such as rapid water loss and disease while in storage.

In 2013, approximately 33 percent of the U.S. crop was lost, which equated to $1.2 billion in lost profits for farmers. Kosma, assistant biochemistry professor, and Santos, assistant research professor, are focusing their research on reducing this number.

"Even a 5 percent reduction in potato losses during storage would improve the economic return for the producers and the potato industry by $170 million," Kosma said.

The research delves into comprehending how different potato varieties can have different storage lives. They are using one variety that stores very well and another that stores very poorly to understand the molecular basis of this differential storage capacity. From a basic science perspective, no one has yet figured this out.

Specifically, Kosma is interested in the corky lipid polymer that comprises a large proportion of the skin. This polymer is referred to as "suberin." Suberin can be found in nearly every plant, and although it is widespread, there is still little known about its makeup and function.

Kosma and Santos want people to know that potatoes do not just go straight from the field to the store. Potatoes are grown and harvested in the fall and kept in cold storage until sold and distributed. The problem occurs when potatoes are not stored properly, which then impacts profits.

When potatoes are harvested in the field, they tend to get damaged and form "scabs" or wound periderm that prevent the sugars and water from coming out and also keeps bacteria and fungi from getting in. This wound-healing tissue is made up of suberin. These are the rough raises we tend to see on potatoes from the supermarket. It is important for potatoes to form this wound-repairing tissue to prolong storage life.

The idea of this research is to ultimately improve how potatoes heal with this wound suberin deposition and how to, in turn, improve their lasting storability.

A native of Illinois, Kosma showed an interest in plant biology from a young age. Although he jokes that he was not tremendously influenced by potatoes growing up, he always enjoyed going outside to forage wild foods and plants for both fun and to satisfy his general curiosity about the natural world. He received both his bachelors and master's degrees in plant biology from Southern Illinois University, and furthered his education at Purdue University, where he received his doctorate degree. His post-doctorate work led him to Michigan State University where he met Santos, his wife and research partner. Santos, an assistant research professor, has an emphasis in plant pathology with specific interests in plant-microbe interactions.

Both are interested in plant stress tolerance in relation to the environment, and found that Nevada well suited those research interests. They have been a part of the Department of Biochemistry and Molecular Biology at the University of Nevada, Reno for two years, having moved here in January 2015.

The two are extremely passionate about their work, and this project is something that had been stewing in Kosma's thoughts well before their move to Nevada.

"In Michigan, two years prior to moving here Dylan was already talking about writing a project about potatoes and how cool it would be," Santos said.

Since then, their research team has grown to include: Professor Karen Sclauch, who specializes in bioinformatics at the University; Professor Dave Douches, a potato breeder out of Michigan State University; and Professor Ray Hammerschmidt, a plant pathologist also from Michigan State. They have one graduate student and numerous undergraduates working with them in their lab.

The $1.37 million National Science Foundation grant will keep this research going for the next four years.

Visit link:
Studying genetics of potatoes - Nevada Appeal

In March 2006, angler Edward Reid pulled a staggering 14.48 pound largemouth bass from the depths of Lake Conroe near Houston. On Feb. 10, nearly 11 years later and more than 234 miles away, angler Ryder Wicker caught the 13.07-pound offspring of that fish from Marine Creek Lake near Fort Worth.

The Lake Conroe fish, later called ShareLunker 410, was able to leave a legacy of her big-bass genetics to the state thanks to the Texas Parks and Wildlife Departments Toyota ShareLunker Program, which has been selectively breeding and stocking angler-caught largemouth bass over 13 pounds since 1986 with the goal of increasing the production of trophy-sized fish in Texas reservoirs.

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