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Tree of Life in the Genes? Not Yet

first_imgNow that we have hundreds of animal genomes in the bank (the GenBank), is Darwin’s tree of life becoming visible?  If the image is present, it is extremely weak, said Michael J. Sanderson of the Department of Ecology and Evolutionary Biology at University of Arizona.  Writing for Science,1 he showed that only a small fraction of genomes show even minimal support for a phylogenetic (evolutionary) tree.    His report was accompanied by a circle diagram with 876 taxonomic orders represented by small rectangles along the rim.  He shaded blue those that contained a minimal phylogenetic signal, and yellow those that did not.  The entire circle was almost all yellow.  One has to look hard for blue rectangles.  This is after “improvements in algorithms and high-performance computing technology have dramatically increased the scale of feasible phylogenetic inference; and unconventional sources of data, including whole genomes, expressed sequence tag libraries, and barcode sequences, have altered the landscape of large-scale phylogenetics with an infusion of new evidence.”  The distribution of species in GenBank (the database of gene sequences) is remarkably broad, he said.  If there was ever a time to see Darwin’s tree of life come to light in the genes, it should be now.    In light of the flood of evidence, how can the phylogenetic signal be so weak?  “Construction of a high-resolution phylogenetic tree containing all eukaryotic species in the database is a grand challenge that is substantially more tractable than inferring the entire tree of life, but to succeed, strategies will have to overcome serious sampling impediments,” he said.  “Quantifying the distribution and strength of phylogenetic evidence currently in the database is a prerequisite for this effort.”  So that’s what he set out to do.  And that’s what turned out to look pretty weak.    Sanderson looked at 1127 higher taxa for evidence of a phylogenetic signal.  He had to set his standards pretty low.  He figured if there were at least four operational taxonomic units [OTUs] that were similar between two taxa, for instance, then an evolutionary relationship could be inferred.  His choice of tree-building software also was rigged to produce a “fast but conservative” result.  “Any clade in the resulting tree will have had at least 50% bootstrap support in maximum parsimony ‘fast’ bootstrap analyses with two different sequence alignment algorithms,” he explained.2  “Although this protocol biases the confidence assessment slightly downward, the bias is small.”  Is that a matter of human opinion?    There were more hints the standards were loose.  “For comparative purposes and to aid in the visualization of results, an arbitrary cutoff value of 1.5 was selected as minimal phylogenetic support,” he continued.  “This is equivalent, for example, to the information content of two independent loci, each resolving three-quarters of clades to at least a bootstrap value of 51%.”  This sounds close to the tipping point for inferring no relationship at all.    After manipulating his protocols, summing, and averaging, the evolutionary signal came out surprisingly low, even with the loose standards.  Here is the upshot:Among individual OTUs [operational taxonomic units], Homo sapiens had the maximum support value of 293.9, but the distribution of scores had a long tail leading to 6402 OTUs with no support at all (most of which, 6079, simply were not found in any phylogenetically informative clusters).  The top 10 were all mammals; the top 25 were mammals, angiosperms (tomato, potato, tobacco, rice, and wheat), Drosophila melanogaster, and Drosophila simulans, all with support scores above 60 units.  Of the 171,703 OTUs for which scores were calculated, only 12% achieved minimal phylogenetic support.  The mean support was 0.84, less than the equivalent of each taxon being found in at least one well-resolved and -supported phylogenetic tree.So only 12% reached the already-low bar for evolutionary signal – that means 88% did not.  At the level of orders, the scores were skewed even lower.  The maximum score was 10 in primates, and 0.0 in 75 other orders.  He tried to draw an inference between orders that were species-rich and species poor, but many of the orders outside of primates and arthropods did not even reach minimal phylogenetic support regardless of species richness.    So what did Sanderson conclude from his investigation of the strength of the signal of Darwin’s tree of life in the genes?  Basically, he said more work is needed.  “An accurate high-resolution phylogeny will require substantial increases in sequence data to bring that score to a level comparable to that of the best-supported higher taxa.”  He thinks more data targeted at the right clusters of genes might help.  Better algorithms in the tree-building software might help, too.  Maybe the signal will become clearer when genes from undiscovered species in poorly-resolved branches become available.  “In the meantime, sampling protocols guided by quantitative assessments of the phylogenetic distribution of data will improve the efficiency of emerging phylogenomic strategies for building the tree of life of known organisms.”  Translated, this almost sounds like he is claiming that better data-massaging methods might just begin to help develop strategies for beginning to find ways to begin to visualize Darwin’s tree.  In colloquial terms, it’s going to take a lot of work to fix this picture.1.  Michael J. Sanderson, “Phylogenetic Signal in the Eukaryotic Tree of Life,” Science, 4 July 2008: Vol. 321. no. 5885, pp. 121-123, DOI: 10.1126/science.1154449.2.  For more on the meanings of bootstrap, maximum parsimony and other phylogenetic tree-building terms, see the entries from 04/26/2008, 01/26/2008, 03/30/2004, 10/15/2003, and 11/06/2002.Charlie’s hanging from his own tree.  Why give him more rope?  It will only make the carcass horizontal instead of vertical.(Visited 23 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

Time to ignite the 2010 World Cup – Celebrating 365 days to kick off

first_imgCall to all South Africans to fly the flag, wear a football shirt, blow your vuvuzela and sing out the National Anthem on 11th June 2009.Thursday 11th June 2009 at 16h00 marks one year to the kick-off of the FIFA 2010 Soccer World Cup – it’s time for ignition! In a symbolic demonstration of national unity and pride, Brand South Africa calls on all South Africans to wear a football jersey (preferably a Bafana Bafana one) or a yellow shirt, on the day and fly the South African flag. And at exactly 16h00, to blow a vuvuzela and sing the National Anthem.A five-minute count-down will begin at 15h55 on radio stations across the country, to cue all citizens, wherever they are, to sing Nkosi Sikelele Afrika at 16h00. The intention behind this nation-wide activation is for South Africa to celebrate one year to kick-off, and to serve as a point of ignition for the tournament. “It is also an act of national pride in, and support to our country as Africa’s first host of this prestigious tournament,” says Paul Bannister, International Marketing Council of South Africa’s Chief Executive.“With the Bulls Super 14 victory fresh in our minds, the IPL cricketing extravaganza successfully behind us, the British and Irish Lions clash in play and the Confederations Cup literally only hours away, South Africa’s sports buzz is infectious,” says Bannister.There is however a subtle but vital difference between being a good host and a great one. “The magic underpinning being great lies in our people, who are able to provide event viewers and visitors with the contagious, edge-of-your-seat buzz and a taste of the competitive spirit to come whilst making them feel truly “at home” in South Africa,” he says.It is up to us all to rally together, as South Africans. “We encourage every South African, whether you are in Johannesburg, Cape Town, Sydney, Toronto or London to join us as we mark an important milestone in our Nation’s history,” concludes Bannister. “This is an easy and fun way for us to let the world know that we are lighting the touch paper for the 2010 World Cup .” Be a part of South Africa’s World Cup revolution!1.       South Africa’s national anthem2.       South Africa 2010: find out more About the International Marketing of South Africa (Brand South Africa)The International Marketing Council of South Africa was established in August 2002 to help create a positive and compelling brand image for South Africa. At that time, the world was unsure about what to think of South Africa, with many different messages being sent out by various sources. This did very little to build the country’s brand and it was evident that to attract tourism and investment there was a need to co-ordinate marketing initiatives to make them more effective. This led to the creation of the IMC, whose main objective is the marketing of South Africa through the Brand South Africa campaign.  There are many benefits to having a consolidated brand image, with the most important being that a consistent Brand South Africa message creates strategic advantages in terms of trade and tourism for the country in an increasingly competitive marketplace.For further information:Margaret DingaloDirector: Stakeholder RelationsInternational Marketing Council of South AfricaTel: +27 11 483 0122Web: www.brandsouthafrica.comYolande De NysschenAccount DirectorMS&L Worldwide | South AfricaTel: +27 11 235 4300Web: www.mslworldwide.comlast_img read more

All 67 MLAs in Himachal cast vote

first_imgAll 67 legislators of the Himachal Pradesh Vidhan Sabha, including Chief Minister Virbhadra Singh, Leader of the Opposition Prem Kumar Dhumal and Speaker Brij Bihari Lal Butail exercised their franchise in the presidential polls on Monday. The State has a 68-member Assembly but one seat is vacant following the death of Congress MLA Karan Singh.Independent membersSecretary of State Vidhan Sabha Sunder Lal Verma said that 35 Congress MLAs, 28 Bharatiya Janata Party MLAs and four Independent MLAs voted in the polls. Both the BJP and the Congress have claimed support of two Independent members each.Unicameral HouseIn the Unicameral House of the State, each MLA vote has a value of 51 votes and the State has four seats in the Lok Sabha — all occupied by the BJP. It also has three Rajya Sabha seats, one occupied by the BJP and the other two by the Congress. The Congress has a minor edge in the polls if no cross voting takes place.BJP meets GovernorRight after casting their votes, a delegation of the BJP met Governor Acharya Devvrat. Memo submittedThey submitted a memo urging him to dismiss the Virbhadra Singh-led government due to the “worsening law and order situation” in the State. Independent MLAs Balbir Verma and Manohar Dhiman, who recently joined the BJP, were part of the delegation.last_img read more