Friday, September 06, 2013 5:57:59 AM
Convergent evolution seen in hundreds of genes
Bottlenose dolphins can detect prey with a sonar-like trick similar to that used by bats — and the similarity extends to the genetic underpinnings of this ability.
Doug Perrine/Nature Picture Library
Bats and dolphins may have developed echolocation via similar mutations.
By Erika Check Hayden
04 September 2013
A new analysis suggests that many genes evolved in parallel in bats and dolphins as each developed the remarkable ability to echolocate.
Different organisms often independently evolve similar observable traits such as anatomical or functional features, but the genetic changes underpinning such 'convergent evolution' are usually different. The new study [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )], published today in Nature, hints that evolution may be finding the same genetic solutions to a problem more often than previously thought.
“These results imply that convergent molecular evolution is much more widespread than previously recognized,” says molecular phylogeneticist Frédéric Delsuc at the The National Center for Scientific Research (CNRS) at the University of Montpellier in France, who was not involved in the study. What is more, he adds, the genes involved are not just the few, obvious ones known to be directly involved in a trait but a broader array of genes that are involved in the same regulatory networks.
Biologists have long debated how different animal species independently developed echolocation, the sonar-like mechanism in which animals listen to their own clicks and calls echoing back from obstacles or prey. In the study released today, biologists led by Stephen Rossiter and Joe Parker at Queen Mary University of London, drew upon the largest dataset ever to look for convergent evolution in 2,326 genes shared by 22 mammals, including six bats and the bottlenose dolphin.
Same difference
The team found a 'convergence signature' in nearly 200 regions of the genome. Genes involved in hearing were more likely to have evolved similarly across species than those involved in other biological traits. Some genes involved in vision were also among those bearing the strongest signal of convergence — a surprising result.
In earlier studies, scientists had found far fewer examples of genes clearly involved in convergent evolution of various traits, Parker says, because no one had taken a look across entire genomes before.
“This study is the first to examine genome-wide convergence at the level of protein sequences and connect it very explicitly to convergent phenotypes, which is very nice,” says evolutionary biologist Antonis Rokas at Vanderbilt University in Nashville, Tennessee.
The work would not have been possible without the genetic sequence data now available for dozens of different mammals — including four newly sequenced bat genomes — and the use of the Queen Mary GridPP High Throughput Cluster, a powerful computing grid. GridPP is normally used to churn through data from the Large Hadron Collider at CERN, Europe's particle-physics lab near Geneva in Switzerland. It took Rossiter and Parker’s team roughly a month to perform its analyses using the cluster; it would have taken years on a desktop computer, Parker says.
But finding out whether and how any of the 200 genes from this analysis are involved in echolocation will be a major challenge.
Rokas says that a statistical test of the kind used in the new analysis to check whether evolution has specifically favored particular genetic sequences has been shown to throw up many false positive results [ http://www.nature.com/hdy/journal/v99/n4/full/6801031a.html ]. He says that convergence — the evolution of similar genetic sequences — is a strong indication that natural selection does indeed favor these sequences. But, he adds, it would also help to know how selection influences changes in the types of amino acids within the proteins that the genes code for. If the convergent amino acids are physiochemically quite different than the ancestral amino acids, it's a stronger signal that they were favored by natural selection: such ”radical substitutions” are rarer, “because they tend to change the structure and function of proteins quite a bit,” he says.
Stronger evidence yet would come from showing that any of the specific amino-acid changes in the paper improve an animal's ability to use the sonar mechanism, says Sean Carroll, a geneticist at the University of Wisconsin–Madison and at the Howard Hughes Medical Institute in Chevy Chase, Maryland.
“The real test,” agrees Parker, “is to go into the most convergent genes and start elucidating their functions directly.”
Reference
Parker, J. et al., Genome-wide signatures of convergent evolution in echolocating mammals, Nature (2013)
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )
Nature
doi:10.1038/nature.2013.13679
*
Related stories and links
From nature.com
Hawkmoths zap bats with sonic blasts from their genitals
03 July 2013
http://www.nature.com/news/hawkmoths-zap-bats-with-sonic-blasts-from-their-genitals-1.13333 ( http://www.nature.com/doifinder/10.1038/nature.2013.13333 )
Poisonous platypuses confirm convergent evolution
12 October 2010
http://www.nature.com/news/2010/101012/full/news.2010.534.html ( http://www.nature.com/doifinder/10.1038/news.2010.534 )
Better sonar through dolphin teeth
19 March 2007
http://www.nature.com/news/2007/070319/full/news070319-2.html ( http://www.nature.com/doifinder/10.1038/news070319-2 )
Spider webs untangle evolution
01 November 2004
http://www.nature.com/news/2004/041101/full/news041101-4.html ( http://www.nature.com/doifinder/10.1038/news041101-4 )
From elsewhere
Stephen Rossiter
http://webspace.qmul.ac.uk/sjrossiter/
Queen Mary GridPP High Throughput Cluster
http://pprc.qmul.ac.uk/research/gridpp
*
© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited
http://www.nature.com/news/convergent-evolution-seen-in-hundreds-of-genes-1.13679 [with comments]
--
Study Sees Convergent Evolution at Hundreds of Echolocation Loci
September 04, 2013
http://www.genomeweb.com/sequencing/study-sees-convergent-evolution-hundreds-echolocation-loci
--
Echolocation's Convergent Evolution: Genetic Similarities Between Bats And Dolphins
By News Staff | September 4th 2013 01:25 PM
The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, and scientists who investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution, sought to examine the frequency of the process at a genomic level.
Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).
The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.
They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several 'hearing genes'.
a, For each locus, the goodness-of-fit of three separate phylogenetic hypotheses was considered: (left) H0, the accepted species phylogeny based on recent findings (for example, refs 14, 23, 24, 25); (top-right panel) H1, or ‘bat–bat convergence’, in which echolocating bat lineages (shown in brown) are forced to form a monophyletic group to the exclusion of non-echolocating Old World fruit bats (shown in orange); and (bottom-right panel) H2, or ‘bat–dolphin convergence’, in which the echolocating bat lineages and the dolphin (blue) form a monophyletic group to the exclusion of all non-echolocating mammals. See Methods for details of model fitting and topologies. b, The distribution of convergence signal across 2,326 loci in 14–22 representative mammalian taxa, as measured by locus-wise mean site-specific likelihood support for the species topology (H0) over (left) the ‘bat–bat’ hypothesis uniting echolocating bats (that is, ?SSLS (H1)) and (right) bat–dolphin hypothesis (that is, ?SSLS (H2)). Representative hearing and vision loci are shown in green and blue, respectively; for each locus significance levels based on simulation denote whether it had significant counts of convergent sites after correcting for expected counts in random (control) phylogenies (*), and additionally whether strength of positive selection (dN/dS) and convergence (?SSLS) at sites under selection in echolocators were correlated (**); see Supplementary Table 4 and Methods.
Credit and link: doi:10.1038/nature12511 [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )]
To perform the analysis, the team had to sift through millions of letters of genetic code using a computer program developed to calculate the probability of convergent changes occurring by chance, so they could reliably identify 'odd-man-out' genes.
Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.
"We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible," explains Dr. Joe Parker, first author on the paper. "We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing."
Dr. Georgia Tsagkogeorga, who undertook the assembly of the new genome data for this study, added, "We found that molecular signals of convergence were widespread, and were seen in many genes across the genome. It greatly adds to our understanding of genome evolution."
Group leader, Dr. Stephen Rossiter, said, "These results could be the tip of the iceberg. As the genomes of more species are sequenced and studied, we may well see other striking cases of convergent adaptations being driven by identical genetic changes."
Citation: Joe Parker, Georgia Tsagkogeorga, James A. Cotton, Yuan Liu, Paolo Provero, Elia Stupka& Stephen J. Rossiter, 'Genome-wide signatures of convergent evolution in echolocating mammals', Nature 4 September 2013 doi:10.1038/nature12511 [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )]
*
Related Articles on Science 2.0
The Robotic Mind
http://www.science20.com/gadfly/blog/robotic_mind-116014
What The Platypus Genome Is And Isn't
http://www.science20.com/adaptive_complexity/what_the_platypus_genome_is_and_isnt
Bat Echolocation May Have Evolved Multiple Times
http://www.science20.com/news_releases/bat_echolocation_may_have_evolved_multiple_times
Dolphins Retain Social Memories, Even After 20 Years
http://www.science20.com/news_articles/dolphins_retain_social_memories_even_after_20_years-117934
Of Bats, Flight And Immunity To Viruses
http://www.science20.com/another_incubation/blog/bats_flight_and_immunity_viruses-104375
*
© 2013 ION Publications LLC
http://www.science20.com/news_articles/echolocations_convergent_evolution_genetic_similarities_between_bats_and_dolphins-119741 [no comments yet]
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Bottlenose dolphins can detect prey with a sonar-like trick similar to that used by bats — and the similarity extends to the genetic underpinnings of this ability.
Doug Perrine/Nature Picture Library
Bats and dolphins may have developed echolocation via similar mutations.
By Erika Check Hayden
04 September 2013
A new analysis suggests that many genes evolved in parallel in bats and dolphins as each developed the remarkable ability to echolocate.
Different organisms often independently evolve similar observable traits such as anatomical or functional features, but the genetic changes underpinning such 'convergent evolution' are usually different. The new study [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )], published today in Nature, hints that evolution may be finding the same genetic solutions to a problem more often than previously thought.
“These results imply that convergent molecular evolution is much more widespread than previously recognized,” says molecular phylogeneticist Frédéric Delsuc at the The National Center for Scientific Research (CNRS) at the University of Montpellier in France, who was not involved in the study. What is more, he adds, the genes involved are not just the few, obvious ones known to be directly involved in a trait but a broader array of genes that are involved in the same regulatory networks.
Biologists have long debated how different animal species independently developed echolocation, the sonar-like mechanism in which animals listen to their own clicks and calls echoing back from obstacles or prey. In the study released today, biologists led by Stephen Rossiter and Joe Parker at Queen Mary University of London, drew upon the largest dataset ever to look for convergent evolution in 2,326 genes shared by 22 mammals, including six bats and the bottlenose dolphin.
Same difference
The team found a 'convergence signature' in nearly 200 regions of the genome. Genes involved in hearing were more likely to have evolved similarly across species than those involved in other biological traits. Some genes involved in vision were also among those bearing the strongest signal of convergence — a surprising result.
In earlier studies, scientists had found far fewer examples of genes clearly involved in convergent evolution of various traits, Parker says, because no one had taken a look across entire genomes before.
“This study is the first to examine genome-wide convergence at the level of protein sequences and connect it very explicitly to convergent phenotypes, which is very nice,” says evolutionary biologist Antonis Rokas at Vanderbilt University in Nashville, Tennessee.
The work would not have been possible without the genetic sequence data now available for dozens of different mammals — including four newly sequenced bat genomes — and the use of the Queen Mary GridPP High Throughput Cluster, a powerful computing grid. GridPP is normally used to churn through data from the Large Hadron Collider at CERN, Europe's particle-physics lab near Geneva in Switzerland. It took Rossiter and Parker’s team roughly a month to perform its analyses using the cluster; it would have taken years on a desktop computer, Parker says.
But finding out whether and how any of the 200 genes from this analysis are involved in echolocation will be a major challenge.
Rokas says that a statistical test of the kind used in the new analysis to check whether evolution has specifically favored particular genetic sequences has been shown to throw up many false positive results [ http://www.nature.com/hdy/journal/v99/n4/full/6801031a.html ]. He says that convergence — the evolution of similar genetic sequences — is a strong indication that natural selection does indeed favor these sequences. But, he adds, it would also help to know how selection influences changes in the types of amino acids within the proteins that the genes code for. If the convergent amino acids are physiochemically quite different than the ancestral amino acids, it's a stronger signal that they were favored by natural selection: such ”radical substitutions” are rarer, “because they tend to change the structure and function of proteins quite a bit,” he says.
Stronger evidence yet would come from showing that any of the specific amino-acid changes in the paper improve an animal's ability to use the sonar mechanism, says Sean Carroll, a geneticist at the University of Wisconsin–Madison and at the Howard Hughes Medical Institute in Chevy Chase, Maryland.
“The real test,” agrees Parker, “is to go into the most convergent genes and start elucidating their functions directly.”
Reference
Parker, J. et al., Genome-wide signatures of convergent evolution in echolocating mammals, Nature (2013)
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )
Nature
doi:10.1038/nature.2013.13679
*
Related stories and links
From nature.com
Hawkmoths zap bats with sonic blasts from their genitals
03 July 2013
http://www.nature.com/news/hawkmoths-zap-bats-with-sonic-blasts-from-their-genitals-1.13333 ( http://www.nature.com/doifinder/10.1038/nature.2013.13333 )
Poisonous platypuses confirm convergent evolution
12 October 2010
http://www.nature.com/news/2010/101012/full/news.2010.534.html ( http://www.nature.com/doifinder/10.1038/news.2010.534 )
Better sonar through dolphin teeth
19 March 2007
http://www.nature.com/news/2007/070319/full/news070319-2.html ( http://www.nature.com/doifinder/10.1038/news070319-2 )
Spider webs untangle evolution
01 November 2004
http://www.nature.com/news/2004/041101/full/news041101-4.html ( http://www.nature.com/doifinder/10.1038/news041101-4 )
From elsewhere
Stephen Rossiter
http://webspace.qmul.ac.uk/sjrossiter/
Queen Mary GridPP High Throughput Cluster
http://pprc.qmul.ac.uk/research/gridpp
*
© 2013 Nature Publishing Group, a division of Macmillan Publishers Limited
http://www.nature.com/news/convergent-evolution-seen-in-hundreds-of-genes-1.13679 [with comments]
--
Study Sees Convergent Evolution at Hundreds of Echolocation Loci
September 04, 2013
http://www.genomeweb.com/sequencing/study-sees-convergent-evolution-hundreds-echolocation-loci
--
Echolocation's Convergent Evolution: Genetic Similarities Between Bats And Dolphins
By News Staff | September 4th 2013 01:25 PM
The evolution of similar traits in different species, a process known as convergent evolution, is widespread not only at the physical level, but also at the genetic level, and scientists who investigated the genomic basis for echolocation, one of the most well-known examples of convergent evolution, sought to examine the frequency of the process at a genomic level.
Echolocation is a complex physical trait that involves the production, reception and auditory processing of ultrasonic pulses for detecting unseen obstacles or tracking down prey, and has evolved separately in different groups of bats and cetaceans (including dolphins).
The scientists carried out one of the largest genome-wide surveys of its type to discover the extent to which convergent evolution of a physical feature involves the same genes.
They compared genomic sequences of 22 mammals, including the genomes of bats and dolphins, which independently evolved echolocation, and found genetic signatures consistent with convergence in nearly 200 different genomic regions concentrated in several 'hearing genes'.
a, For each locus, the goodness-of-fit of three separate phylogenetic hypotheses was considered: (left) H0, the accepted species phylogeny based on recent findings (for example, refs 14, 23, 24, 25); (top-right panel) H1, or ‘bat–bat convergence’, in which echolocating bat lineages (shown in brown) are forced to form a monophyletic group to the exclusion of non-echolocating Old World fruit bats (shown in orange); and (bottom-right panel) H2, or ‘bat–dolphin convergence’, in which the echolocating bat lineages and the dolphin (blue) form a monophyletic group to the exclusion of all non-echolocating mammals. See Methods for details of model fitting and topologies. b, The distribution of convergence signal across 2,326 loci in 14–22 representative mammalian taxa, as measured by locus-wise mean site-specific likelihood support for the species topology (H0) over (left) the ‘bat–bat’ hypothesis uniting echolocating bats (that is, ?SSLS (H1)) and (right) bat–dolphin hypothesis (that is, ?SSLS (H2)). Representative hearing and vision loci are shown in green and blue, respectively; for each locus significance levels based on simulation denote whether it had significant counts of convergent sites after correcting for expected counts in random (control) phylogenies (*), and additionally whether strength of positive selection (dN/dS) and convergence (?SSLS) at sites under selection in echolocators were correlated (**); see Supplementary Table 4 and Methods.
Credit and link: doi:10.1038/nature12511 [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )]
To perform the analysis, the team had to sift through millions of letters of genetic code using a computer program developed to calculate the probability of convergent changes occurring by chance, so they could reliably identify 'odd-man-out' genes.
Consistent with an involvement in echolocation, signs of convergence among bats and the bottlenose dolphin were seen in many genes previously implicated in hearing or deafness.
"We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible," explains Dr. Joe Parker, first author on the paper. "We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing."
Dr. Georgia Tsagkogeorga, who undertook the assembly of the new genome data for this study, added, "We found that molecular signals of convergence were widespread, and were seen in many genes across the genome. It greatly adds to our understanding of genome evolution."
Group leader, Dr. Stephen Rossiter, said, "These results could be the tip of the iceberg. As the genomes of more species are sequenced and studied, we may well see other striking cases of convergent adaptations being driven by identical genetic changes."
Citation: Joe Parker, Georgia Tsagkogeorga, James A. Cotton, Yuan Liu, Paolo Provero, Elia Stupka& Stephen J. Rossiter, 'Genome-wide signatures of convergent evolution in echolocating mammals', Nature 4 September 2013 doi:10.1038/nature12511 [ http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12511.html ( http://dx.doi.org/10.1038/nature12511 )]
*
Related Articles on Science 2.0
The Robotic Mind
http://www.science20.com/gadfly/blog/robotic_mind-116014
What The Platypus Genome Is And Isn't
http://www.science20.com/adaptive_complexity/what_the_platypus_genome_is_and_isnt
Bat Echolocation May Have Evolved Multiple Times
http://www.science20.com/news_releases/bat_echolocation_may_have_evolved_multiple_times
Dolphins Retain Social Memories, Even After 20 Years
http://www.science20.com/news_articles/dolphins_retain_social_memories_even_after_20_years-117934
Of Bats, Flight And Immunity To Viruses
http://www.science20.com/another_incubation/blog/bats_flight_and_immunity_viruses-104375
*
© 2013 ION Publications LLC
http://www.science20.com/news_articles/echolocations_convergent_evolution_genetic_similarities_between_bats_and_dolphins-119741 [no comments yet]
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