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Welcome to Gateway School of Real Estate
Established in June of 1990, Gateway School of Real Estate is a state licensed school that is dedicated to providing the very best real estate educational courses. Primarily teaching Sales Associate , Brokers Courses, & Continuing Education Credits. Jennifer G. Segala a Massachusetts approved Instructor (#004) & Florida Permitted instructor # ZH1003078 is the owner and principal teacher of all classes. Classes consist of live instruction by Jennifer. Lessons are taught by association, practical use and from much of Jennifer's own experience having been in real estate for the past 30 years. If you are interested in obtaining a real estate license.
All candidates must first successfully complete a pre-licensing course. Gateway School of Real Estate offers courses every other month in a variety of days and times covering all state mandatory topics.Once you have completed the required course you are then eligible to take the State real estate exam. When you have passed the exam you are then eligible to receive a license (currently this is all done in one step, you are now issued a license at the testing center the same day.)
Gateway School of Real Estate continues to holds one of the highest student passing scores for real estate tests in MA and hopes to bring that legacy to Florida.The School maintains the policy that in the event any student does not pass the licensing exam after completing the required courses, they may return to any future classes within a 1 year period to review or brush up on any of the course topics,at NO additional fee.
In addition to offering you a fun educational experience Gateway School of Real Estate is still also able to offer you these course at a fair cost to you.
Testing Centers
The testing center website
Massachusetts : https://candidate.psiexams.com
Florida : www.pearsonvue.com
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Baltimore Police have charged a Baltimore man with murder in connection with the stabbing death of another man in McElderry Park early on Saturday morning.
Todd Pollard, 28, of the 400 block of N. Montford Avenue was charged with first-degree murder, second-degree murder, first-degree assault, second-degree assault, concealing a dangerous weapon and using a dangerous weapon with the intent to injure. He had no lawyer listed in online court records for this charge.
Police said Pollard and another man, 38-year-old Miles Ringgold of the 1300 block of Crofton Street, were arguing at 12:15 a.m. Saturday in the 400 block of N. Montford Avenue when the victim was stabbed in the chest.
He died at a local hospital.

subset: commoncrawl


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NASHVILLE, Tenn. – Camouflage and duck calls will be the theme of the 5thAnnual Don Meyer Evening of Excellence hosted by Lipscomb Athletics as Phil, Kay and Si Robertson, stars of the A&E reality show Duck Dynasty, headline the event on April 27, 2013.
Known for their down-home values and Christian beliefs on their hit television show, the Robertsons are currently starring in their second season on the show that airs on Wednesday nights at 9 p.m CST on A&E.
A college quarterback at Louisiana Tech, Phil started his own business in 1972 making duck calls and patented his now famous Duck Commander line of products. The family business has thrived across the country with hunters and eventually led to a series of Duckmen videos that teach the proper techniques to bring ducks right into the hunter's blinds.
The A&E show began in 2011 and reaches into millions of homes each week with the finale of season one drawing 2.6 million viewers. The Robertson family is active in the White's Ferry Road Church of Christ in their hometown of West Monroe, La.
Tickets for the event are on sale now at http://www.BeHerdLU.com or by emailing firstname.lastname@example.com or calling 615-966-HERD (4373). Admission for adults is $20 and $10 for children 12 and under.


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THE AUDIENCE, Starring Helen Mirren, Draws Advance of £2 Million But Must End June 15
According to the Daily Mail, Helen Mirren has begun rehearsals for Peter Morgan's The Audience, about Elizabeth II. The play has already drawn a box office advance of £2 million, but regardless of popularity, The Audience must end its engagement on June 15 due to the Chichester Festival Theatre production of Private Lives, set to begin at the Gielgud Theatre on June 22.
Read the original report here.
In addition, now that The Audience is in rehearsals, the creative team is still mulling over whether to include the Queen's corgis or leave them out of the show.
Joining Helen Mirren as The Queen in this world premiere are Michael Elwyn as Anthony Eden, Haydn Gwynne as Margaret Thatcher, Robert Hardy as Winston Churchill, Richard McCabe as Harold Wilson, Nathaniel Parker as Gordon Brown, Paul Ritter as John Major and Rufus Wright as David Cameron. The Equerry is Geoffrey Beevers and the role of Young Elizabeth will be played by Bebe Cave, Maya Gerber and Nell Williams.
The Audience will preview at the Gielgud Theatre from 15 February 2013, with press night on 5 March 2013 and is currently booking to 15 June 2013. Designs are by Bob Crowley with lighting by Rick Fisher, sound by Paul Arditti, music by Paul Englishby and video by Ian William Galloway.
For sixty years Elizabeth II has met each of her twelve Prime Ministers in a weekly audience at Buckingham Palace - a meeting like no other in British public life - it is private. Both parties have an unspoken agreement never to repeat what is said. Not even to their spouses.
The Audience breaks this contract of silence and imagines a series of pivotal meetings between the Downing Street incumbents and their Queen. From Churchill to Cameron, each Prime Minister has used these private conversations as a sounding board and a confessional - sometimes intimate, sometimes explosive. In turn, the Queen can't help but reveal her own self as she advises, consoles and, on occasion, teases.
From young mother to grandmother these private audiences chart the arc of the second Elizabethan Age. Politicians come and go through the revolving door of electoral politics, while she remains constant, waiting to welcome her next Prime Minister.
The Audience is produced in the West End by Matthew Byam Shaw for Playful Productions, Robert Fox and Andy Harries.


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Bierwagen's annual pumpkin patch brings families back out to the farm
Special to The Union
This time of year, it's difficult to get Chris Bierwagen to sit still longer than five minutes.
"October is a nutty time. We're planting cover crops and running the pumpkin patch at the same time," he said as he hunted for a missing elbow for an irrigation line.
Chris Bierwagen is a fourth-generation farmer, working the same land in the community of Chicago Park that his great-grandfather, Ludwig Bierwagen, first developed in 1902. For more than two decades, the Bierwagen family has offered a pumpkin patch and the chance to come out to the farm for a real, no-frills rural agricultural experience good for the whole family.
It started with two hay bales and a bin full of pumpkins in front of the family's restaurant, "Happy Apple Kitchen," located on the other side of the Colfax Highway. But after a few years of screeching tires and traffic jams, the Bierwagens decided for safety's sake it was best to move the patch onto the farm.
"It's really turned more into an agritourism event down here," said Debbie Bierwagen, Chris' sister-in-law, who has witnessed an increasing number of folks in recent years who come to the farm with the intent of getting to know where their food comes from.
Five days a week throughout the month of October, busloads of school kids arrive at the farm. Debbie Bierwagen leads the youngsters out to the apple orchard where they learn the how-tos of picking an apple. They visit the packing area to learn how apples arrive out of the field and, from there, venture to meet farm animals: turkeys, chickens, two heifers and a longhorn steer named "Leroy." After running wild in the pumpkin patch, they conclude with a glass of fresh apple juice under the sprawling walnut tree.
Farm to School programs in the area seem to be making an impact on young people's understanding of how food gets to the dinner table, the Bierwagens say.
"Our kids in Nevada County are extremely knowledgeable about food and farming," Debbie Bierwagen said.
On the weekends, many people from out of the area are drawn to the pumpkin patch, too.
Anabelle Williams, 2, proudly cradled a pumpkin in her arms and set it into a wagon. She was visiting the Bierwagen Farm for the first time with her family from Auburn.
Her dad, who works in the town of Colfax, spotted the pumpkin patch signs en route back and forth to Grass Valley.
"It's great. It's mellow. The kids had a good time," said Carey Williams.
In addition to pumpkins and other seasonal squash, the farm's Harvest Festival, open 10 a.m. to 5 p.m. seven days a week, offers a museum, fresh pressed cider and juice, apples and other local foods like Calolea Olive Oil, McClaughry honey and Snow's mandarin salad dressings. The snack shack is open only on weekends and offers lunch items, including the popular apple fritter nuggets.
Families can enter their favorite photos in the annual Family Pumpkin Photo Contest on the Bierwagen's Facebook page. The photo with the most likes will win a half of a bushel of apples.
October's pumpkin patch is an important aspect of the Bierwagen farm's economic sustainability, representing about 20 percent of the overall revenue stream. Even with what appears to be a robust turnout on weekends, the farm has struggled in recent years.
"We all have a day job now," said Chris Bierwagen, who prunes trees in winter and helps run the farm's market stand in summer months. He was a full-time farmer up until three years ago when changes to the climate adversely impacted his peach crops.
Family members, local youth and interns work the farm to keep employee costs down.
For seven to eight years in the 1990s, Chris Bierwagen farmed during the "pinnacle of peach time," regularly shipping his highly sought-after peaches to San Francisco and Monterey.
Alice Waters featured the fruit in dishes at her internationally known Berkeley restaurant, Chez Panisse.
In 1998, the weather changed, and the Bierwagens began losing crops. The farm hasn't shipped outside the area since 2009.
Peach growing has dropped off, but apples remain strong, and the introductory year of boysenberries was "awesome."
Chris Bierwagen grows a diverse array of vegetables from his organic "truck garden" for sale at the family's farmer's market, next to the Happy Apple Kitchen during the warmer months.
The Bierwagens grow food on about 20 acres of the family's 125-acre farm.
Despite the ups and downs of farming, Chris Bierwagen's love for his trade remains steadfast. His eyes light up when he talks about the beauty of eggplants and the natural wonders of nitrogen-fixing cover crops. He has a particular affinity for harvesting tomatoes. Though he has farmed the family land much of his life, it wasn't until he turned 40 that his passion and romance for farming bloomed.
"When you see buckets of peaches, it's all worth it," he said.
To learn more, visit https://www.facebook.com/bierwagensfarm or call 530-477-5992
Contact freelance writer Laura Brown at email@example.com or 530-913-3067.
Start a dialogue, stay on topic and be civil.
If you don't follow the rules, your comment may be deleted.


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The choice, as they say, is yours.
Today is gameday in South Carolina – SC is traveling to Clemson for the biggest rivalry in these parts. Families are torn today. Friends are on opposite sides of the divide. One side will be unhappy tonight – and, I hope, they'll be mostly wearing orange. Some folks will be mad. Some will be mouthy, whiney, offended – and that'll be on both sides, win/lose/draw.
It happens in politics (if you're on Facebook, you know what it was like just a few short weeks ago, and still on some walls today). It happens in Christian circles, and I'm sure in other faith communities as well. It happens at work, at home, in the midst of family members, and in juts about anything we do together.
People disagree.
I don't like conflict. Lots of people think I do. I'm the one who asks the "devil's advocate" queries often, asking the counter-question in order to get to something other than the status quo. But that doesn't mean I like to be at odds with the room.
It happens, though – and sometimes it makes folks angry that I don't stay on the dotted line very well.
Or rather, they choose to be angry. Or if not actually mad, then to still treat me and my questions/statements as a hostile, as someone coming along with heresy and blasphemy at worst, with stupidity and childishness and in need of education at best.
Different ideas, different opinions, different expectations does not an enemy make.
But I choose to be offended. I choose to be angry. I choose to let someone else hold sway over how I feel about myself, about them, about life, the universe and everything.
But you choose to be offended. You choose to be angry. You choose to let someone else hold sway over how you feel about yourself, about them, about life, the universe and everything.
Or, I choose to not.
I choose today to not be angry, to not be offended, to not give someone else the keys to my emotional state.
We get to choose. Yes, it's harder when the folks closest to you are the ones choosing to be offended, to be mad, to label you as the opposition. But it's still your choice. It's still my choice.


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Country Club 101: What To Wear To Master The Dress Code
While we adore analysing the runways and poring over designer mood boards, we spend a considerable amount of time pondering a more prosaic question: what should we wear? Whether it's a wedding, work affair, or weekend brunch, getting dressed for specific occasions is a constant conundrum. In the hopes of outfit enlightenment--for us and for you!--we're delighted to present What To Wear, our weekly wardrobe guide for every occasion. This week, we'll be covering what to wear to a country club.
The Goal: Create a polished outfit that feels conservative, yet summery.
Nothing feels more on-point for a preppy environment than classic navy stripes.
Joie Tyson Top ($198) in Blue Violet
It's helpful to have a blazer on hand, especially if you move from outside to the more formal realm of the clubhouse.
Topshop Collarless Panel Jacket ($100)
Dressier fabrics like this silk skirt are always a safe bet. Unless you're dressed in sporting attire, leave the cotton and jersey at home!
Carven Shantung-Silk Paisley-Print Skirt ($155)
Low chunky heels feel more elevated than a flat, but are still comfortable for walking.
Campbell Favour Sandal ($130)
Leave your slouchy bags at home, and opt for a smart structured purse instead.
Pour La Victoire Aline Purse Lemon ($245)
Channel American icon Jacqueline Kennedy with these affordable round sunnies.
Fantas Eyes Round Sunglasses ($12) in Matte Tortoise
The light green tea and dandelion scent of this hand cream is an excellent summer alternative to heavier perfume.
Tokyo Milk Honey & The Moon No. 10 Hand Cream ($20)
These rings are just begging for a monogram. We would get one initial engraved on each, so when stacked together they make a complete monogram.
Gorjana Fatima Ring Set ($50)
- Explore More:
- sunglasses
- Sandals
- skirt
- What To Wear
- outfit
- dressy outfit
- country club
- outfit idea


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Teacher resources and professional development across the curriculum
Teacher professional development and classroom resources across the curriculum
Evaluating Communication
|Make a Lesson Plan | Summing Up the Session | Final Journal
Use the processes you learned in this session to plan a lesson for one of your own classes, using a problem that you currently teach, or plan to teach, in your subject area and grade level. Remember that students can communicate about mathematics by using words, pictures, symbols, tables, and functions. They can work individually, in pairs, in small or large groups, or as a whole class. Make sure that your lesson plan addresses these questions:
After you have created your lesson plan, use the Classroom Checklist (an Adobe PDF document) to evaluate it.
|Teaching Math Home | Grades 6-8 | Communication | Site Map | © |
© Annenberg Foundation 2017. All rights reserved. Legal Policy


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Buy a knife that will be a favorite for years to come.
Hand-wash is recommended. Oil handle to maintain quality.
Designed and manufactured in Germany.
From the Sarah Weiner collection, these knives are of the finest quality. Hand-made using a process including over 90 steps. Set includes knife, leather pouch and conditioning oil.
Design awards: Red Dot - Best of the Best 2012, Interior Innovation Award 2012, Universal Design Award 2012, Universal Design Consumer Favorite 2012.
Kaufmann Mercantile is committed to help you live a conscious and inspired life.
Many of the items you discover here are exclusive to Kaufmann Mercantile, which is what makes our community of designers and artisans so special.
If you find one of our products anywhere else for less than it's being sold on our site, we will match it.
Our dedicated Support Team is here to help. Reach out any time at:


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ARLINGTON, Texas -- After nearly 70 minutes of football, and nearly 40 minutes after the Dallas Cowboys finally started acting like the game had begun, the Cowboys lined up for the game-winning field goal. Kicker Dan Bailey narrowed his vision, went through his routine and booted a 38-yarder through the uprights. And like that, it was over.
How did Dallas celebrate a hard-fought 23-20 win over the Cleveland Browns at Cowboys Stadium? A few handshakes. A couple of low-fives. And a slow walk into the locker room.
NFL Replay
will re-air the Dallas Cowboys' 23-20 overtime victory over the Cleveland Browns in Week 11 on Tuesday, Nov. 20 at 9:30 p.m. ET.
» NFL Network schedule
For the first time since Week 12 of last season, the Cowboys have back-to-back victories. Unbelievably, despite the roller coaster they've ridden this season, they are just one game behind the New York Giants in the NFC East -- and the rest of their opponents this season have a combined record of 27-33.
The Cowboys won thanks to a tough-minded effort from quarterback Tony Romo, a career day from Dez Bryant (12 catches for 145 yards and a touchdown) and a resilient goal-line stand from the defense. And they did it despite having one foot in the grave in each of the past two weeks, ever since Bryant broke his fall and the Giants broke their hearts in Week 8.
Owner Jerry Jones summed up his thoughts outside an emptying Cowboys locker room on Sunday.
"We can't go out and rest on this, what we did out here," Jones said. "The facts are, we're 5-5. Sure we know that. We know the numbers. But we gotta play better."
Jones had praised his team's grit, its fight, its ability to come back from a 13-0 deficit in the first half. He'd lauded coach Jason Garrett for engineering a turnaround that included Romo completing 25 of 33 passes for 239 yards and a touchdown after halftime. And he'd smiled about revenge-minded defensive coordinator Rob Ryan's unit allowing just one play -- a 17-yard touchdown by Browns tight end Ben Watson that gave Cleveland a 20-17 lead with 1:07 left -- in the game's final 40 minutes.
But Jones' real message? That the way Dallas played against the bargain-basement Browns will not cut it. That if there was any euphoria over the victory, it should fade away pretty quickly.
"You can talk about these great character-builders," Jones said, "and all that's great. I'm proud of it. I need more of it. All that kinda thing. But it's time that we gotta get out here and have players that are committed professionals to be skilled and play and make plays and we gotta have game plans that -- when we come out on the field -- that we're not down before we're up."
Jones called Sunday's win "bass-ackwards from the antidote that we needed to play these Cleveland Browns."
The blame game is a Dallas staple, as it is in towns that are home to intense fan bases, high expectations and a fiery media market. Romo is at fault because of his 13 interceptions. No, Garrett's at fault for his late-game management. No, it's Jones himself, for building this roster. No, it's everyone around Jones, for their inability to evaluate talent.
The reality?
"You'll say, 'Was that your coach, was that your quarterback, was that (your) receiver?' " Jones said. "That is not the point. It's everybody. When it's good, it's everybody. And when it's not, it's everybody. So, we gotta do that right there, or we will find ourselves sucking our last breath against a team that our expectations were to come in here and play better against."
Of course, like everything else that revolves around Dallas, it's not simple. The angst about missed chances? About having to hang on for dear life against the Browns? It all comes with this backdrop.
The Cowboys still have a chance to accomplish everything they've wanted and more.
"I'm not going to make any excuses for winning," said Romo, who completed 11 straight passes at one point on Sunday. "I know it's hard no matter who you play. At the same time, we need to play better if we are trying to do things we hope to accomplish. ... We just need to be better, I don't know how else to explain it."
What did the Cowboys fight through? They fell behind, 13-0. Romo was sacked a whopping seven times. They punted seven times. Just 63 of their yards came rushing. By the end of the game, with star Tyron Smith having suffered a high-ankle sprain, their left tackle was Jermey Parnell, a former University of Mississippi basketball player. With the game on the line, Garrett had no choice but to hand the ball to undrafted rookie running back Lance Dunbar, thanks to injuries to DeMarco Murray and Felix Jones.
While the Cowboys overcame those obstacles, there was a sense that they created all of them. There was also a sense that -- 10 games into a key campaign for Garrett and this squad's stars -- no one actually knows what kind of team the Cowboys are. No wonder cornerback Brandon Carr said, "I'm not really satisfied with our record. I'm not really satisfied with anything. That's the way I feel. We won, but it's over. Time to move on to the next game."
It will come quickly: the Cowboys face the Washington Redskins on Thursday.
"The biggest thing we learned," tight end Jason Witten said, "is that you're not going to beat the Redskins by playing poorly early on. Hopefully, we build on this and don't let it happen again."
To be sure, there were positives on Sunday. Like a big-time, fumble-causing hit that Gerald Sensabaugh delivered on star Browns running back Trent Richardson when he was 1 yard away from converting a crucial first down with 12:54 left in the fourth quarter. The Browns recovered the ball but had to punt, setting up Dallas' second touchdown drive, which ended with a 28-yard scoring catch by Bryant.
Bryant's play overall, in fact, provided a massive dose of positivity.
"This is how I'm going to be," he announced.
There was also the goal-line stand later in the fourth quarter, with Richardson kept out of the end zone despite getting three carries inside the 6-yard line. Then, with 9:57 to go in overtime, safety Danny McCray stopped Browns receiver Josh Gordon in his tracks when he was 4 yards short of the first-down marker. The stop set the stage for Bailey's winning boot.
Plenty of positives. Just as many negatives. Five wins. Just as many losses.
"I think we'll benefit from it," Jones said. "I think there was enough here, enough feel-good, when we come out of here with a win. It gives us a mathematical chance."
******What else is going on? Here is a rundown:
Brady 1, Luck 0
A shootout between superstar quarterbacks Tom Brady of the New England Patriots and Andrew Luck of the Indianapolis Colts never materialized. If we learned one thing on Sunday, when Luck surrendered three picks while Brady casually passed for 331 yards and three touchdowns in a 59-24 beatdown, it's that the No. 1 overall pick of the 2012 NFL Draft -- and the likely Offensive Rookie of the Year -- isn't ready to go head-to-head with Brady. He isn't ready to recreate the classic duels between the Patriots' veteran and the Colts' former leader, Peyton Manning.
That's nothing to be ashamed of. When Brady and Manning were rookies, they wouldn't have been ready to battle a quarterback as good as their veteran selves, either.
What shouldn't be overlooked is the gamesmanship Brady unleashed, subtle as it was.
Though Brady has told the story of his first encounter with Manning -- with the veteran delivering a friendly "Hey Tom, I'm Peyton," greeting -- several times, Brady did not say hello to Luck before Sunday's matchup. "We didn't have a chance," Luck said, sounding like he was covering for Brady. "Schedules, whatever."
And then Brady played like he was furious about the hype his counterpart was getting, giving a performance that was reminiscent of what he did against the Denver Broncos last season -- when Brady's disdain for the publicity surrounding Tim Tebow was captured in a vicious spike. Brady notices when he's not the most-discussed quarterback, and he doesn't seem to like it. Perhaps that's why he stayed on the field for almost all of the blowout, scoring until the final whistle. It's almost like No. 12 wants upstart quarterbacks to earn their stripes.
Luck isn't quite there yet. He will be, though.
What is Bart Scott doing?
Attempting a media boycott, Bart Scott? Berating defensive teammates who talked to reporters after what should have been a feel-good, 27-13 victory for the New York Jets over the St. Louis Rams and former Jets offensive coordinator Brian Schottenheimer? Walking back and forth between the trainers' room and the locker room, loudly and immaturely telling players such as Yeremiah Bell and Bryan Thomas to answer media questions by simply saying "both teams played hard?"
I feel like I speak for players and reporters when I say, "Grow up."
After a tumultuous week that included anonymous players criticizing Tim Tebow in a New York Daily News article, Scott decided to rally the team against the media. Or something. I don't know what his point was, because he apparently talked to reporters himself later in a calm fashion, as if nothing happened.
This is the third inappropriate incident for Scott since January. At the conclusion of the 2011 season, he flipped off a reporter, earning a $10,000 fine. In September, he had to be separated from a reporter because the reporter took a picture. This time, thankfully, teammates such as Bell and Thomas told Scott to knock it off.
So while some in the Jets organization are grinding, trying to get it right, trying to save jobs, Scott is trying to fight media members. The over-the-hill linebacker is likely in his final season in New York, and he's only on the roster because of a $4.2 million guaranteed salary. At what point do the Jets step in and take control? At what point does Scott, with his one assisted tackle, become too much of a distraction? If the Jets do want to take back their team, eliminating such useless troubles would be a good place to start.
Patience, my dear Raiders
The frustration is understandable. The Oakland Raiders, boasting a new coach in Dennis Allen and plenty of talented players like running back Darren McFadden, seemed like a possible contender this season. Ten games into their campaign, the Raiders are anything but: Oakland is 3-7, and has lost three in a row. The latest defeat, Sunday's woeful 38-17 loss to the Saints, was never very close.
Does this ugly display mean Allen is in trouble? It shouldn't. The Raiders have salary-cap issues. The Al Davis era recently ended, and the franchise is still remaking itself from the inside out. The Raiders need a foundation. It all takes time. The key to getting back to what the Raiders used to be? Hide those quick instincts.
"You can't blame it on the salary cap," owner Mark Davis told the San Francisco Chronicle. "I am disappointed with the regression. But they'll fight and hopefully they'll fix it. ... I am patient, but I want to see progress."
When it comes to clear rebuilding situations like Oakland's, my thoughts are simple. If Allen is the guy -- and it appears many think he is -- chill. Relax. Don't make any rash decisions. Swallow your pride for a year or two while the organization shapes up.
Good to see Davis said he'll be patient. There will be a pull, particularly from fans, to make changes. If you believe in rebuilding, there must be growing pains. They aren't fun. The rewards are.
Some rapid-fire takes
» I talked to a scout this week who wondered what had happened to Houston Texans wide receiver Andre Johnson. He doesn't look like himself, the scout said. The thinking was, maybe Johnson had gotten old fast. Well, all he did Sunday was put up 273 yards and 14 catches, including the game-winner against the Jacksonville Jaguars. Afterward, Johnson said, "I've been telling you guys I've been feeling better and better every week. Maybe you guys will believe me after that."
NFL Replay
will re-air the Houston Texans' 43-37 overtime win over the Jacksonville Jaguars in Week 11 on Tuesday, Nov. 20 at 8 p.m. ET.
» NFL Network schedule
» Wow, the Saints are suddenly quite real, getting back to 5-5 and into the NFC playoff mix. How long ago does it seem like they were 0-4? Just try to keep them from the playoffs, even with their brutal schedule.
» Watching Arizona Cardinals receiver Larry Fitzgerald break free into the end zone, only to have quarterback John Skelton overthrow him by 5 yards in the first quarter, was depressing. How many scores has this still-productive receiver missed out on over the years thanks to poor quarterback play?
» That's four in a row for the hard-charging Tampa Bay Buccaneers, who are watching quarterback Josh Freeman grow up before their eyes. Eighty yards in 50 seconds with no timeouts? Whew. The throw into triple coverage that wound up in receiver Vincent Jackson's hands at the end of regulation was nice. The smooth play-fake on the two-point conversation was better.
» The Browns have deficiencies, and their talent base is fair at best. But if you're going to build, do it like they have. Cleveland's offensive line, led by left tackle Joe Thomas, is its best unit, and quarterback Brandon Weeden looked poised and relaxed all day behind it. On the other side, the Browns' physical front four helped sack Romo seven times. Cleveland CEO Joe Banner does, in fact, have some material to work with.
» One wonders, given the kicking issues that the Green Bay Packers had, if Nate Kaeding might be getting a call. How can Green Bay stand by and allow Mason Crosby to miss seven of his last 13? Not many weak links in Green Bay, but that's one.
» The Atlanta Falcons are the strangest one-loss team ever. Quarterback Matt Ryan throws five interceptions ... and wins?
» If Jacksonville Jaguars coach Mike Mularkey keeps his job for another year, games like Sunday's will be part of the reason. A lost season is winding down, his team was on enemy turf against the NFL's best -- and the Jags nearly pulled off a win. This team looks very far away from packing it in. Of course, Penn State coach Bill O'Brien refusing to publicly commit to 2013 does raise eyebrows, considering he was previously linked to Jacksonville. But Mularkey had his team ready Sunday ... thanks in part to backup quarterback Chad Henne.
» It took 10 weeks, but Cincinnati Bengals running back BenJarvus Green-Ellis finally gained more than 100 yards. If Cincy gets its ground game cranking, all it does is buy Andy Dalton and A.J. Green just a little more freedom. It's how they envisioned it.
» What a sad sight to see Arrowhead Stadium nearly empty with minutes to go in the Kansas City Chiefs' loss to the Bengals. A proud football town in shambles. The lack of fan support is a development that should shake those in the organization to their core.
» I can't laugh at the media coverage, because I'm still curious, every week, about what Jets quarterback Tim Tebow will do. I'm one of the people served by the frenzy; I can't help it. But 10 games in, he's simply a non-factor. On Sunday, he touched the ball three times and accounted for negative-6 yards.
» How many rookies would have survived an environment like FedExField? That's unclear. But Nick Foles did not. Interceptions on his first two drives on the road against the Washington Redskins likely triggered some changes in the Philadelphia Eagles' game plan, especially after they fell behind, making it hard to judge the Eagles rookie. Foles might be back at the helm this week.
» Sunday's road matchup with the Denver Broncos sure seemed like the San Diego Chargers' last hope. When even quarterback Philip Rivers is looking unsure and lost, things aren't good.
» Baltimore Ravens defensive backs Bernard Pollard and Corey Graham hit the way they were supposed to in the final seconds of their win over the Pittsburgh Steelers: hard, fast and legal. See, everyone -- it can be done. No head-hunting required.
» Detroit Lions wide receivers coach Shawn Jefferson and offensive coordinator Scott Linehan argued on the sideline on Sunday. According to the Detroit Free Press, the disagreement was over Jefferson's frustration with receiver Titus Young. One wanted him off the field. Trouble seems to find Young. And his production (33 catches for 383 yards) has been underwhelming. Tick, tock. ...
Follow Ian Rapoport on Twitter @RapSheet.


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Hello BBOS members and guests, it's time for our Weekly Recap for 10/9 - 10/15, 2011. The links below are the "in a nutshell" of what happened in everything BlackBerry last week. Leave us a comment on what you thought was the most memorable moment of the BlackBerry weekly recap!
NOTICE: We are also currently looking for outgoing writers to join the BBOS team - Click here for more information on how to join.
- White BlackBerry Bold 9900 Coming Soon?
- RIM announces BlackBerry Tag - Coming Soon to a BlackBerry Smartphones near you
- Official: OS 22.214.171.1248 for BlackBerry Bold 9700/9780 via Swisscom
- BlackBerryOS.com Weekly Recap 10/2 - 10/8
- RIM Releases BlackBerry Analytics Service 1.0
- BlackBerry Internet Service (BIS) Outage Day 2
- RIM Launches O7 Devices In Taiwan
- RIM Responds To ElcomSoft Encryption Exploits
- Accessory Review: BodyGuardz BlackBerry Bold 9900/9930 Armor Carbon Fiber
- BlackBerry Internet Service outage in EMEA [Update]
- Leaked: 126.96.36.1998 OS for BlackBerry Bold 9780
- Official: OS 22.214.171.1249 for BlackBerry Bold 9900 via Wind Mobile
- Official: OS 220.127.116.113 for BlackBerry Curve 9360 & Bold 9900 via Vidéotron
- Pearl 3G 9100 OS 184.108.40.2066 Officially Released By SK Telecom
- Service Update from Research In Motion CIO Robin Bienfait
- Research In Motion hosts conference call in reference to outages
- The RIMpocalypse Outage of 2011 now affecting all of North America
- BBM Music v126.96.36.199 comes and gets pulled just as quickly
- BlackBerry Simulators for Curve 9380 and Bold 9790 Available
- Bell Mobility To Get White Curve 9360
- Research In Motion: "Global BlackBerry Internet Services are restored"
- A Message From RIM's Co-CEO Mike Lazaridis Regarding Outage
- Things Slowly Starting To Improve With BlackBerry Service
- Former Sr. Director of Global Developer Relations, Mike Kirkup, Talks "Lessons Learned" Leaving RIM
- Colin Farrell a BlackBerry User?
- Groupon HD now available for PlayBook in BB App World
- A Deeper Look: BBM Connected Apps Access
- Foursquare for BlackBerry gets new icon and more with new alpha v3.2.8
- Tribute to Steve Jobs (Animated slideshow) Theme
- Gameloft Releases N.O.V.A 2 HD, Modern Combat 2, And More On PlayBook
- BeBuzz Beta updated to v4.0.87
- BlackBerry App World Updated To Version 220.127.116.11 In Beta Zone
- Ticketmaster For BlackBerry v220.127.116.11 Beta Update Now Available In Beta Zone
- Kik Messenger updated to 5.2.2
- Citrix Receiver For PlayBook Updated To Version 0.9.2
- BEJEWELED 2 Now Available for PlayBook
- E! News Now for BlackBerry PlayBook
- Digital Musician Theme
- FishLoader for BlackBerry - App Utility
- Camera Timer for BlackBerry Let your phone take the pictures for you!
- BBOS Gear Now Available - Win a BlackBerryOS.com T-Shirt! Winner Announced!
- Device Giveaway: Enter to Win a Unlocked BlackBerry Bold 9650!
- Enter to Win a Unlocked BlackBerry Storm 2 9550! Winner Announced!
- Enter to Win a BlackBerry PlayBook from Developer S4BB Limited


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Sidehill leveling system
The Hillco 3700S Sidehill Leveling System for 5088, 6088 and 7088 Case IH Axial-Flow combines provides up to 18% slope compensation. The new system features a direct-drive drivetrain design that uses original Case IH drivetrain components and is compatible with both single- and dual-drive tires. The electrohydraulic lateral header tilt control fully integrates with the combine's Terrain Tracker electronics, providing full automated header height and lateral tilt control for excellent ground-contouring performance. The 3700S can be easily installed on new or existing Case IH combines using Hillco's Near-Factory Installation program or by an authorized Case IH dealership. The Hillco/CNH Category IV warranty agreement ensures that all original combine warranties remain in full effect after installation of a Hillco Leveling System.
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Waste oil heaters and boilers
Used oil is a free fuel source in Lanair Waste Oil Heaters and Boilers. The Lanair Complete Value Package includes the heater, tank and chimney. Installation is simple and saves money. The products are EPA friendly and UL listed. The new MXD200 and MXD300 ductable models allow for heat distribution where needed. Free telephone and Web-based support is available.
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ParaDyme from Ag Leader and AutoFarm is a full-featured automated steering system with integrated wireless and cellular communication capabilities for remote diagnostics. A patented, dual-antenna roof module provides operators automatic steering control with sub-inch accuracy, improving product placement and fuel efficiency while significantly reducing operator fatigue. ParaDyme uses Logic 7D technology with the dual-antenna roof module to track pitch, roll and yaw as well as vehicle position and heading at all times, even when the vehicle is not moving. Once ParaDyme is installed, its Auto Calibration routine allows it to learn machine-specific steering characteristics.
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Remote bin monitoring
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For more information, visit www.TsgcInc.com, or call 800/438-8367 for a free quote.
Brandt Agricultural Products recently unveiled the GrainVac 7500 HP, a fast and simple way for busy grain growers to empty a bin. The GrainVac 7500 HP is capable of moving up to 8,000 bu. of wheat/hr. from a full bin with a straight hose, for example. Maximum grain movement can be achieved with only 120 hp, allowing growers to match the GrainVac 7500 HP with mid-sized tractors. Exclusive cone separator technology uses no moving parts to direct the grain into the auger or air into the fan. No adjustments are needed crop to crop.
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Ball valves
Green Leaf Inc. introduces the Side Load 3-Way Ball Valves and Bottom Load 3-Way Ball Valves in 1- to 2-in. sizes. Features include stainless steel bolts, Viton O-rings and a maximum operating pressure of 100 psi. The self-aligning ball moves freely against Teflon seats for smooth operation. The ball is diamond-turned after molding to make it spherically perfect, providing precise contact between the ball and seats.
For more information, call 800/654-9808 or visit www.green-leaf.us.
Grain auger steering
Large grain augers and conveyors are hard to maneuver, but the new Auger Steer makes auger steering and positioning easy.
The Auger Steer, distributed by Central City Scale Inc. and manufactured by Triple Steer Manufacturing Ltd. installs as an add-on kit for axles. It allows the axle and whatever it supports to be fully steered from the tractor cab with a set of steering knuckles activated by a new hydraulic cylinder.
Auger Steer can be installed on either an auger or conveyor with fixed wheels in about an hour. The kit includes a steering knuckle for each wheel. The wheel comes off, a 9-in. knuckle is bolted on, and the wheel is replaced. A small hydraulic cylinder is fitted against the axle and connected to each knuckle. New hoses are extended to the hydraulic remotes at the back of the tractor. Hydraulic pressure enables existing control levers or switches in the cab to turn the wheels left or right.
The Auger Steer comes in sizes and fittings for most makes of augers.
For more information, call Central City Scale at 308/946-3591 or visit www.ccscales.com.
Precision tillage system
Krause introduces the innovative Gladiator precision tillage system for strip-till farming with exclusive ST-PRO row units, available in 12- and 16-row pull-type configurations. Changing from field operation to transport is quick and easy, and the durable, fixed frame design with flip-and-fold toolbar provides a balanced, safe transport — even for 16-row machines. The design allows for easy maintenance and replacement of points or knives without crawling under the machine. The robust frames have the capacity to carry a 1,000-gal. liquid tank and tow an anhydrous tank to accommodate a variety of fertilizer placement options.
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This is the Cadillac CTS-V Sport Wagon. It is a staggeringly irrelevant ball of horsepower and excellence wrapped up in the coolest shape to come out of Detroit in years. We love it. You should, too.
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Mmm, fuzzy hot wagon love. Mmm, LSA hoonage. Mmm, flagship D-town mom-mobile. It gets no better than this.


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- Research article
- Open Access
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
- Liang Liu1Email author,
- Lili Yu2 and
- Scott V Edwards3
© Liu et al; licensee BioMed Central Ltd. 2010
- Received: 29 December 2009
- Accepted: 11 October 2010
- Published: 11 October 2010
Several phylogenetic approaches have been developed to estimate species trees from collections of gene trees. However, maximum likelihood approaches for estimating species trees under the coalescent model are limited. Although the likelihood of a species tree under the multispecies coalescent model has already been derived by Rannala and Yang, it can be shown that the maximum likelihood estimate (MLE) of the species tree (topology, branch lengths, and population sizes) from gene trees under this formula does not exist. In this paper, we develop a pseudo-likelihood function of the species tree to obtain maximum pseudo-likelihood estimates (MPE) of species trees, with branch lengths of the species tree in coalescent units.
We show that the MPE of the species tree is statistically consistent as the number M of genes goes to infinity. In addition, the probability that the MPE of the species tree matches the true species tree converges to 1 at rate O(M -1). The simulation results confirm that the maximum pseudo-likelihood approach is statistically consistent even when the species tree is in the anomaly zone. We applied our method, Maximum Pseudo-likelihood for Estimating Species Trees (MP-EST) to a mammal dataset. The four major clades found in the MP-EST tree are consistent with those in the Bayesian concatenation tree. The bootstrap supports for the species tree estimated by the MP-EST method are more reasonable than the posterior probability supports given by the Bayesian concatenation method in reflecting the level of uncertainty in gene trees and controversies over the relationship of four major groups of placental mammals.
MP-EST can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.
- Species Tree
- Gene Tree
- Horizontal Gene Transfer
- Branch Length
- Internal Branch
Empirical studies on the evolutionary history of sequences from multiple loci show strong evidence of incongruent gene trees across loci [1–3]. Such incongruence challenges the appropriateness of traditional methods for estimating phylogenies, such as supermatrix approaches, which are based on the assumption that all loci have the same gene tree [4, 5]. Several methods have been developed to accommodate the variability among gene trees when estimating species trees [6–11]. Consensus tree methods are commonly used to summarize a collection of gene trees [12–15] and can be easily adapted for the purpose of estimating species trees. Other approaches for combining multiple gene trees include supertree [16–18] and reconciliation [19–22] methods, which may capture important biological details through parameters without modelling it explicitly [23, 24]. We here focus on species tree reconstruction methods developed in the context of the multispecies coalescent model [10, 25–27], which assumes that gene trees are generated from the coalescent processes occurring in each branch of a species tree.
The relationship between gene coalescence times and species divergence times under the multispecies coalescent model has motivated several approaches for estimating species trees based on summary statistics of gene coalescence times [6, 28–32]. Although the likelihood function of the species tree under the multispecies coalescent model has already been derived by Rannala and Yang [25], research on the maximum likelihood (ML) estimation of species trees under the coalescent remains limited [7, 33, 34]. Under a simplified multispecies coalescent model in which population sizes are assumed constant across populations, Liu et al. [32] have shown that the Maximum Tree, a species tree with the largest possible branch lengths under the constraint that gene coalescence times across loci always predate species divergence times, is the maximum likelihood estimate (MLE) of the species tree.
Here coalescence time intervals s are fixed because gene trees G are given. In addition, b i is bounded because the branch length τ i in the species tree is restricted due to the assumption that gene coalescence times always predate species divergence times.
As an example, we calculate the likelihood scores of species trees for three fixed gene trees ((A:0.01, B:0.01):0.01, C:0.02), ((A:0.015, C:0.015):0.01, B:0.025), and ((A:0.02, B:0.02):0.01, C:0.03) (Figure 1b). The species tree is ((A:X, B:X):W, C:Y) where X is the divergence time of species A and B and Y is the height of the species tree. Note that Y = X+W because the species tree is ultrametric (Figure 1b). Branch lengths in the species tree and gene trees are in mutation units. Let θ1 be the population size of the root population and θ1 be the population size on the branch with length W in the species tree. Due to the constraint that gene coalescence times should be strictly larger than species divergence times, we have X < 0.01 and Y < 0.015. Let 0.01 < Y < 0.015. The likelihood of the species tree is
The second part of the likelihood, , is bounded because Y < 0.015. The first part of the likelihood, , goes to infinity as X increases towards 0.01 (but not equal to 0.01) and W decreases towards 0, while θ2 = 0.01-X + 2W. Note that 0.01-X+2W >0 because X < 0.01 and W > 0. Thus we can set θ2 = 0.01-X + 2W (all population sizes are always positive). The likelihood approaches to infinity at θ2 = 0, but because population size θ2 must be strictly positive, the MLE of the species tree for the three gene trees does not exist. Moreover, for a species tree of an arbitrary size, we can always find a rooted triple in the species tree such that the likelihood of the population indicated by the internal branch in the triple goes to infinity as the length (W in the previous example) of the internal branch decreases to 0 and species divergence time (X in the previous example) approaches to the minimum gene coalescence time (0.01 in the previous example) and thus the MLE of the species tree under the likelihood function f(G|S) does not exist. For this reason, we develop a pseudo-likelihood approach for estimating species trees from gene tree topologies. As we describe below, our method delivers MLEs for species trees, yet it is a pseudo-likelihood approach because the likelihoods of different rooted triples in the gene trees are not independent of one another. Nonetheless, we show that this method yields robust results that account for gene tree heterogeneity.
The arguments in the previous section imply that the Rannala and Yang formula f(G|S) can go to infinity as we change the values of branch length τ and population size θ. To overcome this problem, the species tree S is reparameterized such that branch lengths are measured in coalescent units, T = 2τ/θ [27, 37]. For the rest of this paper, branch lengths in the species tree are in coalescent units unless otherwise noted. We here develop a pseudo-likelihood to estimate the reparameterized species tree S* using topologies of gene trees. Since this method involves only topologies of gene trees, the term gene tree will be used to refer to the topology of the gene tree (without branch lengths) unless otherwise noted. The construction of the pseudo-likelihood is based on the fact that a species tree is characterized by a set of rooted triples for all subsets of three taxa [38]. Thus, estimating species tree S* is equivalent to estimating the set of rooted triples derived from S*. It motivates the rooted triple consensus method, an approach that utilizes rooted triples in gene trees to estimate the topology of the species tree [12, 13, 15]. Following the suggestion of Degnan et al. [39], we develop a pseudo-likelihood approach to estimate the species tree S*, including the topology and branch lengths, from a set of gene trees.
Throughout we assume that the species tree and gene trees are rooted trees. It is also assumed that the topologies of gene trees are known without error, although we show how to incorporate uncertainty in gene tree estimation into the estimate of the species tree. We assume that a single lineage is sampled from each species, as is common in phylogenetic studies [1, 40]. Since coalescence occurs for at least two lineages in a population in the species tree, the lengths of the external branches (terminal populations) in the species tree are not estimable for the case of single lineage per species. Missing lineages in some gene trees are allowed if lineages are missing randomly, but a lot of missing lineages may dramatically reduce the performance of the pseudo-likelihood approach. For simplicity, we assume no missing lineages in gene trees. The theory developed in this paper can be easily extended to the cases where lineages in gene trees are missing randomly.
Pseudo-likelihood of the Specie Tree
where , B j is the length of the internal branch of triple j in the species tree, and xj1, xj2, and xj3 are the frequencies of three types of triples in gene trees. The estimate of the species tree, including topology and internal branch lengths, is obtained by maximizing the pseudo-likelihood L(S*|G). Since w is a function of x and has no effect on the procedure of maximizing L(S*|G), it can be ignored from the likelihood function L(S*|G). We employ a heuristic search technique; nearest-neighbor interchanges (NNI), to find the maximum pseudo-likelihood estimate (MPE) of the species tree. We call this method Maximum Pseudo-likelihood for Estimating Species Trees, or MP-EST. When N = 3, (8) becomes (5) and the MP-EST tree is the most frequent gene tree triple with an internal branch of length described in (6). Note that the length B j of the internal branch of triple j in the species tree is the sum of one or several internal branch lengths {T i , i = 1,...,(N-1)} in the species tree. Because the length T i of internal branch i in the species tree involves in many species tree triples, it is estimated by the combination of the frequencies of the gene tree triples corresponding to the species tree triples that involve T i . Equation (6) implies that the estimate of the length of the internal branch in the species tree triple increases to infinity as the proportion x/M of the most frequent gene tree triple approaches to 1. Thus the length of an internal branch in the species tree is not estimable if all relevant triples in gene trees support the same topology. In this case, we assign "99" as the length of the branch to indicate that this branch length is not estimable.
Similarly, we can calculate the likelihoods of the other three triples in the species tree.
where y1, y2, y3 and y4 are the counts of gene tree triples ab|c and ab|d, cd|a, and cd|b. The estimate of T2 is 0 because the proportions of gene tree triples cd|a and cd|b matching the species tree triples CD|A and CD|B are equal to 1/3. The log-likelihood of the species tree with T1 = 0.693 and T2 = 0 is -11.797. There are 15 possible topologies for a four-taxon species tree. Similarly, we can calculate the log-likelihoods for the other 14 topologies and choose the one with the maximum log-likelihood score as the estimate of the species tree (topology and branch lengths).
Statistical Consistency
which shows that the MP-EST method is statistically consistent in estimating species trees (topology and branch lengths in coalescent units) as the number of genes increases.
This shows that the probability of matching the true species tree S T converges to 1 at O(M-1).
Robustness to Horizontal Gene Transfer (HGT)
It follows that the proportion of gene trees containing triple ab|c converges to the quantity specified in (15) and the MP-EST estimate of the length of the internal branch in triple AB|C does not converge to the true length B j when the rate λ of HGT is not 0. It implies that some estimates s of the lengths of internal branches in the species tree do not converge to the true lengths T i s. Otherwise if all estimated lengths s converge to the true lengths T i s, then all s will converge to B j s (because B j s are the sums of one or several T i s), which contradicts the previous conclusion that the MP-EST estimate of the length of the internal branch in triple AB|C does not converge to the true length B j . Inconsistency of the MP-EST estimates s of the lengths of internal branches in the species tree is due to the HGT events occurring among species A, B, and C. Because an internal branch in the species tree is estimated by the combination of the proportions of the gene tree triples corresponding to the species tree triples that involve this branch, the effect of the biased proportion of gene tree triples (due to the HGT events occurring among species A, B, and C) on the estimation of branch lengths is alleviated by the proportions of other gene tree triples that are not affected by HGT, especially when HGT events only occur in a small group of species.
where xj1 is the count of the most frequent gene tree triple. We know that the proportion xj1/M converges to (equation (15)) when HGT occurs at rate λ. It implies that for any δ > 0, there exists a large M such that , i.e., . Thus (16) holds if 1-e-2λL< ε because α becomes very small and negligible when M is large. We conclude that (16) holds if . It shows that if the rate (λ) of horizontal gene transfer is smaller than , the MP-EST method is still statistically consistent in estimating the topology of the species tree.
Estimating species trees from multilocus sequences
The proof for the consistency of the MP-EST method is based on the assumption that gene trees are known without error. In fact, gene trees are usually unknown and must be estimated from multilocus sequences. Under general conditions, the ML gene tree estimated from sequence data is a consistent estimator of the true gene tree G [45]. Thus the MPE of the species tree based on the estimated gene tree is a consistent estimator of the species tree S*. The procedure of estimating species trees from multilocus sequences includes two steps; gene trees are first independently estimated from mutlilocus sequences using the ML method [46] or any other method that is consistent, and rooted by an outgroup (we assume that the outgroup is known). Although gene trees can be rooted by multiple outgroups, it requires that the outgroup sequences must form a monophyletic clade consistently in all gene trees, which rarely occurs in reality. Thus when the appropriate outgroup includes multiple species and is comprised of a monophyletic group, then one must drop some sequences in order to estimate gene trees with a single sequence as the outgroup. However, multiple outgroups can be accommodated partially if they do not comprise a monophyletic group. In this case a single outgroup sequence is again used, and the additional outgroups are estimated as if they were part of the ingroup. Multiple species cannot simultaneously be designated as outgroups (for rooting gene trees) using MP-EST.
The rooted gene trees are then used to construct the MP-EST tree as the estimate of the species tree. Although ML gene trees are usually binary trees, there may be some cases in which some internal nodes and relevant rooted triples in gene trees are unresolved (polytomy). For an unresolved triple (a,b,c) in gene trees, we assign 1/3 to each of the three possible topologies ab|c, ac|b, and bc|a. The estimation error in gene trees can be incorporated into the analysis using bootstrapping techniques [47, 48]. Specifically, columns (or sites) in the aligned sequences are resampled with replacement for each gene sampled (with replacement) from the multilocus dataset [48, 49]. The MP-EST trees constructed for the bootstrapped samples are summarized by a consensus tree.
To evaluate the performance of MP-EST, we simulated 10 ten-taxon species trees from a birth and death process with birth rate of 10 and death rate of 0.1 from the phylogenetic program Mesquite [50]. The population sizes (θ) in the species tree were generated from a uniform distribution (0.005, 0.01). Branch lengths in the 10 species trees vary in the range of 0.00029 and 0.01832. To convert it to coalescent units, the branch length must be divided by the population size θ. Gene trees were generated from the ten species trees using the phylogenetic program Phybase [51] and then used as data to estimate species trees by MP-EST, STAR [11], and Rooted Triple consensus (RT) [12]. We repeated the simulation 100 times. The performance of each method was evaluated based on the proportion of trials yielding the true species trees. We also evaluated the mean square error (MSE) [52] of the branch length between the true species tree and the MP-EST estimate of the species tree. When calculating the MSE of the branch length, we discarded the branches with length "99" because the lengths of these branches are not estimable.
In the second simulation, we investigate the performance of MP-EST, STAR, and RT in estimating species trees in the anomaly zone. The anomaly zone is a region of species tree space, one with very short branches in the species tree, in which the most common gene tree is different from the species tree [37]. One would not expect estimation of species trees in this case to be straightforward. Gene trees were simulated from an anomalous species tree ((((A:0.5, B:0.5):0.025, C:0.525):0.025, D:0.55):1, E:1.55) (in coalescence units). The most probable gene tree has the topology (((A,B),(C,D)),E) and the RF distance between the true species tree and the most probable gene tree is 2. The generated gene trees were then used as data to infer the species tree using MP-EST, STAR, and RT. The simulation was repeated 100 times and we calculated the proportion of trials yielding the true species tree for each species tree reconstruction method. We also calculated the MSE of the branch length between the MP-EST tree and the true species tree. The result for the MP-EST method shows that the proportion of trials yielding the true species tree increases to 1, while the MSE of the branch length appears to decrease to 0, as the number of genes increases (Figure 4c and 4d). This confirms that MP-EST can consistently estimate the true species tree even in the anomaly zone, as expected from the theory we developed above. Similarly, the proportions of the STAR and RT trees matching the true species tree approach 1 as the number of genes increases. In this simulation, MP-EST appears to outperform STAR and RT at 100 and 500 genes (Figure 4c). In addition, the result suggests that all three methods require a large number of genes to accurately estimate anomalous species trees (Figure 4c).
We next investigated estimation of species trees from alignments of DNA sequences. In this simulation, a species tree was generated from a birth and death process: (A:0.019, (((B:0.01, C:0.01):0.0017, ((D:0.00003, E:0.00003): 0.00666, F:0.0067):0.005004):0.00312,((G:0.0043,(H:0.0003,I:0.0003):0.004):0.0034,J:0.0077):0.007):0.0038) with population sizes generated from a uniform distribution (0.005, 0.01). The branches in the species tree are in mutation units. Gene trees were generated from this species tree assuming a molecular clock and then used to simulate DNA sequences of 500 bp under the Jukes-Cantor model in Phybase [51]. The average height and branch length of the simulated gene trees are 0.0243 and 0.0072 in substitutions per site. Another set of DNA sequences were simulated from the gene trees generated from a non-clocklike species tree model which assumes that the substitution rate is the same for all genes and sequences in the same population in the species tree, but the rates may differ across populations [6]. The terminal and internal branches (terminal and ancestral populations) of the species tree were assigned with relative mutation rates generated from a Dirichlet distribution with the shape parameter β = 0. The branches of the gene tree entering a particular population in the species tree are multiplied by the relative mutation rate of that population. The simulated DNA sequences were used to estimate the species tree. ML gene trees were first estimated independently and without a molecular clock for each gene in the phylogenetic program PHYML [54] with the Jukes-Cantor model (we used the default for other parameters in PHYML) and rooted by species A. The MP-EST, STAR, and RT trees were constructed from the estimated gene trees. The simulation was repeated 100 times. For the MP-EST method, the proportion of trials yielding the true species tree appears to approach 1, while the MSE of the branch length goes towards 0, as the number of genes increases (Figure 4e and 4f), which suggests that MP-EST is statistically consistent in estimating species trees from multilocus sequences, not just when gene trees are given as in the first simulation. Overall, STAR slightly outperforms MP-EST and RT (Figure 4e). In addition, STAR, MP-EST, and RT perform better for the sequences generated from the clocklike species tree than those generated from the non-clocklike species tree, especially when the number of genes is small (10 genes in Figure 4e). Nevertheless, the proportions of STAR, MP-EST, and RT trees matching the true species tree increase to 1 as the number of genes increases to 100, regardless the sequences were generated from a clocklike species tree or a non-clocklike species tree. It suggests that MP-EST, STAR, and RT can consistently estimate the species tree in the absence of a molecular clock. The robustness of the methods to violating the clock is due to the fact that all three methods use only the topologies of gene trees to estimate species trees. In this simulation, we have demonstrated that MP-EST is statistically consistent for the cases of violating the clock randomly throughout the species tree and gene trees. There might be other ways of violating the clock for which MP-EST may not be consistent. For instance in long-branch attraction types of scenarios where gene trees can not be consistently estimated from molecular sequences, MP-EST may consistently estimate a wrong species tree due to the bias in the gene tree reconstruction. We observed that nearly half (49%) of the gene trees generated from the species tree across replicates were rooted incorrectly and species A was not located on the branch between (BCDEF) and (GHIJ). Yet in these cases and in the simulation generally, the correct species tree was always consistently estimated. This result suggests that MP-EST (STAR and RT) can consistently recover the true species tree even when estimated gene trees are misrooted frequently. The theory we developed assumes that the roots of the gene trees are known without error, yet our simulation suggests that this assumption can be violated and still yield a solid result under the coalescent model.
Although all results suggest that MP-EST is statistically consistent in estimating species trees, the ranges of genes required for MP-EST to recover the true species tree with a high probability are largely different across simulations. In the first simulation (Figure 4a), it requires at least 100 genes for the proportion of trials yielding the true species tree to reach 0.9. It increases to 1000 genes in the second simulation (Figure 4c), but decreases to 50 genes in the third simulation (Figure 4e). The number of genes needed depends on the true species tree. In general, it requires more genes to accurately estimate the species tree with short internal branches (in coalescent units) than to accurately estimate the species tree with long internal branches (in coalescent units). This explains why it needs a large number of genes in the second simulation where the species tree is in the anomaly zone and has very short internal branches (in coalescent units).
Mammal data analysis
Since the MP-EST method can accommodate only a single outgroup sequence (opossum), it suffers from of its inability to utilize multispecies outgroups, which are widely thought to help stabilize the roots of the estimated gene trees [59]. To investigate the problem of multispecies outgroups, we repeated the MP-EST analysis for the original mammal data set including the four marsupial outgroups (opossum, diprotodontian, monitor del monte, shrew opossum). ML gene trees were still rooted with outgroup opossum. The phylogenetic relationships of placental mammals in the MP-EST consensus tree for the full mammal data set are consistent with those constructed from the reduced data set (Additional file 2: Figure 2). In addition, the other 3 outgroup species (diprotodontian, monitor del monte, shrew opossum) in the MP-EST consensus tree form a basal clade with a high bootstrap proportion 0.98 (Additional file 2: Figure 2). However, we note that if the opossum outgroup is included, this results in a lack of monophyly for marsupials, which is clearly incorrect. Ultimately MP-EST is unable to accommodate multiple outgroups when the outgroup clade is monophyletic. Therefore we are forced to use a single outgroup and to drop other species that are more closely related to that outgroup than to the ingroup.
Unlike the highly supported Bayesian concatenation tree, most bootstrap proportions in the MP-EST consensus tree are less than 0.5 (Figure 6). It may be inappropriate to compare bootstrap supports with posterior probabilities because the relation between bootstrap values and posterior probabilities are highly variable [60, 61] and no studies have been conducted to assess the correlation between bootstrap supports and posterior probabilities at the species tree level. Neither bootstrap values nor posterior probabilities are measures of accuracy of the estimated phylogenetic trees. However, separate analyses for 20 gene segments of the mammal data set produced poorly supported gene trees (Additional file 3: Figure S3). Approximately 80% of the bootstrap values in the estimated gene trees are less than 0.5. In addition, most bootstrap values for deep phylogenetics relationships are less than 0.2. The poorly supported gene trees suggest that the mammal data set does not contain much information about the phylogenetic relationship of placental mammals. Nevertheless, most posterior probabilities in the Bayesian concatenation tree are equal to 1.0, indicating that the Bayesian concatenation method may have overestimated the posterior probabilities. In contrast, the low bootstrap supports in the MP-EST consensus tree have reasonably reflected uncertainty in the estimated gene trees. There are in general two types of genetic variations among multilocus sequences; genetic variation among loci and genetic variation within each locus. In the MP-EST analysis, both variations are considered in the nonparametric bootstrap technique. As a result, the bootstrap supports in the MP-EST consensus tree reflect the level of uncertainty of clades within and among gene trees. For example, the MP-EST consensus tree for the mammal data set has high bootstrap supports for the branches close to the terminal tips and low bootstrap supports for the branches close to the tree root, which is consistent with the pattern of bootstrap values in gene trees (Additional file 3: Figure S3). In contrast, the Bayesian concatenation method assumes congruent gene trees. The spuriously high posterior probabilities, as those in the Bayesian concatenation tree for the mammal data set, are probably due to the assumption of congruent gene trees, along with the fact that bootstrap values are more conservative than posterior probabilities as the measure of the reliability of phylogenetic trees [61].
Despite the molecular and genomic consensus of the four-clade classification of placental mammals (Xenarthra, Laurasiatheria, Euarchontoglires and Afrotheria), the relationship among the four major groups is highly controversial. Three different hypotheses regarding the topology of the four clades were supported by different phylogenetic markers [62]. Morphological markers and retroposons data favored the topology (Xenarthra, (Afrotheria, (Laurasiatheria, Euarchontoglires))) [63, 64]. The second topology ((Xenarthra, Afrotheria), (Laurasiatheria, Euarchontoglires)) was supported by phylogenetic studies of the full mitochondrial genome [62, 65], while the analyses of protein-coding and non-coding sequences supported the topology (Afrotheria, (Xenarthra, (Laurasiatheria, Euarchontoglires))) [57, 66]. More recently, the genome-wide analysis and large scale sequence data provided evidence for a clear trifurcation at the root of placentals [67, 68]. Nishihara et al [69] came to the same conclusion based on the retroposon analysis and recent geological data. The ancestral relationship for the four major groups in the MP-EST consensus tree is ((Xenarthra, Afrotheria), (Laurasiatheria, Euarchontoglires)) with bootstrap support 0.47, while the second most supported relationship is (Afrotheria, (Xenarthra, (Laurasiatheria, Euarchontoglires))) with support 0.37. Moreover, the bootstrap support for the relationship (Xenarthra, (Afrotheria, (Laurasiatheria, Euarchontoglires))) is 0.013. The very low support at the deep branches may be caused by the lack of information about deep relationships of placental mammals in the molecular dataset. It may also be caused by an unreliable placement of outgroup opossum. This unsolved relationship reflects the controversies over the relationship of four major groups of placental mammals. In contrast, the Bayesian concatenation tree predominantly favors the hypothesis (Afrotheria, (Xenarthra, (Laurasiatheria, Euarchontoglires))) with a support of 0.93 [57]. The MP-EST consensus tree contains a highly improbable group of Human and Strepirrhines to the exclusion of Tarsius. Because the bootstrap support for this group is just 0.42, adding more data may be able to more accurately resolve the relationship among Human, Strepirrhines, and Tarsius.
Our maximum pseudo-likelihood method, MP-EST, can consistently estimate the topology and branch lengths (in coalescent units) of the species tree including those in the anomaly zone. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), we have shown that the MP-EST method is robust to a small number of HGT events. Unlike HGT, in which only one or a few genes might be affected, gene flow between species necessarily affects all genes in the genome, and hence potentially all trees in a data set. Thus gene flow will likely have a bigger impact on species tree estimation than will HGT. However, this situation is no different from traditional phylogenetic analysis, in which HGT and gene flow are both complicating factors [70].
Execution times for running MP-EST as the number of genes increases.
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Execution times and memory consumption for running MP-EST as the number of species increases.
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Since MP-EST can estimate both the topologies and branch lengths of species trees, gene trees simulated from the MP-EST tree can be used to approximate the distribution of gene trees expected from the multispecies coalescent model. By comparing the lineage patterns in the estimated gene trees with those in the distribution of gene trees expected from the coalescent model, we can identify the lineages in the estimated gene trees that significantly deviate from the lineage patterns expected from the multispecies coalescent model. For example, if HGT occurs in the dataset, the distances among the lineages from distant species in the estimated gene trees should be significantly smaller than those expected from the multispecies coalescence model which assumes no HGT.
With regards to branch lengths, MP-EST is unable to estimate the lengths of external branches in the species tree because only one allele is sampled from each species. In addition, the internal branch length of a triple in the species tree is not estimable when all gene triples support the same topology. These internal branches are indicated with length of "99". Users should be cautious about the interpretation of length "99". It is not the actual length of the branch. The value "99" suggests that the corresponding branch length is not estimable due to the lack of topological variation among gene triples. In the cases where all genes support a single tree, MP-EST will fail to estimate any branch length.
Strategies for sampling genes are important for all species tree reconstruction methods. Biased representation of genes on the genome may introduce systematic error in species tree estimation. For example, if we would split mitochondrial genomes of placental mammals in single genes and use only these genes to estimate the species tree, MP-EST would find with bootstrap support 1.0 a species tree placing the flying lemur within primates, challenging this group paraphyletic. The MP-EST method assumes that given the species tree, the evolutionary histories of genes, i.e., gene trees, follow a coalescence process, but in practice this assumption may not always be satisfied. Although MP-EST is, to some extent, robust to the violation of the coalescent assumption, serious divergence from coalescent can certainly result in inaccurate MP-EST estimates of species trees.
Our algorithm is able at this stage to accept only a single allele per species. In addition, our algorithm yields species trees whose branch lengths are in coalescent units, rather than substitutions per site as most with most phylogenetic trees. However, such trees are still of practical use in phylogenetics. The topology of phylogenies is usually of primary interest and we have shown that the topology is consistently estimated by MP-EST. Even when we recover species trees with branch lengths in coalescent units, under certain assumptions we can obtain reasonable estimates of species divergence times in generations or years. Working in units of mutations, for example, if we assume that ancestral population sizes (θ) of lineages in our estimated species tree are similar to those of extant species (as estimated, for example, from multilocus genetic data), we can easily convert coalescent units in a species tree to branch lengths in units of substitutions per site (τ = μ). Or, when faced with variation in θ among extant species, one could reconstruct ancestral population sizes using any number of algorithms for phylogenetic comparative methods. Despite the fact that branch lengths are estimated in coalescent units, our algorithm is able to accommodate branch length variation in gene trees and can yield non-ultrametric species trees. In contrast, most species tree methods either ignore branch lengths in gene and/or species trees [8] or estimated ultrametric species trees [71]. Although it would be highly desirable to estimate branch lengths of species trees directly in units of substitutions per site as in traditional phylogenies and some species tree algorithms (STEM [33] and BEST [9]), such an estimation procedure would require properly modelling the mutation rate variation within and among genes. Our efforts are currently directed toward this end.
Availability and Requirements
Project name: A maximum psudo-likelihood approach for estimating species trees under the coalescent model (MP-EST)
Project home page: http://code.google.com/p/mp-est/
Operating system: platform independent.
Programming language: C
Other requirements: No
Licence: GNU GPL.
We thank Dennis Pearl for the helpful suggestion on the first draft of the manuscript. We thank Bruce Rannala for constructive discussion on the likelihood function of the species tree. We thank four anonymous reviewers for their constructive comments on the manuscript. This research is supported by the grant NSF DEB-0743616.
Authors' Affiliations
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Liam Hemsworth doesn't seem all that torn up about his recent breakup with twerking sensation Miley Cyrus.
Well, that's a relief...
Instead, the hunky "Hunger Games" star made it seem that things were quite amicable between himself and his former fiancée while he was promoting "The Hunger Games: Catching Fire" with costar Woody Harrelson in one of the first interviews in which he addressed the split.
"I'm extremely happy for all of her success," Hemsworth told Extra when asked where things stood with the "Wrecking Ball" singer.
The former couple met on the set of "The Last Song" in 2009 and got engaged in 2012. But they called it quits in September soon after Cyrus received a rash of press following her controversial MTV Video Music Awards performance in August and upon news that Hemsworth had been spotted kissing model Eiza González.
However, that relationship appears to be over.
"I don't have a lady at the moment," the 23-year-old Aussie actor said just as Harrelson hijacked the interview to save his costar. (Harrelson also said that "the perfect woman for Liam" is Oprah Winfrey, to which Hemsworth replied, "she's a wonderful woman" and he'd consider "all possibilities.")
Cyrus, appearing on "The Ellen DeGeneres Show" in October to promote her latest album, "Bangerz," said she wasn't really seeing anyone at the moment either because things had "been like so crazy busy."
"I'm just letting that chapter kind of close and just looking forward to that new one," the 20-year-old said. "I want to be really clear and determined with everything I'm doing in my life right now, and I have been. ...
"I keep saying I'm the happiest I've ever been, and that's not even a dig. That's just me because I really am genuinely happy finally with myself, which I think sometimes it takes you separating yourself from someone else to really be happy with who you are. I've never been able to just be alone, and I'm obsessed with being alone and like hearing my thoughts."
Well, Miley, we're hearing his thoughts loud and clear now too.
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