April 17th, 2009
New evidence gleaned from CT scans of fossils locked inside rocks may flip the order in which two kinds of four-limbed animals with backbones were known to have moved from fish to landlubber.
Both extinct species, known as Ichthyostega and Acanthostega, lived an estimated 360-370 million years ago in what is now Greenland. Acanthostega was thought to have been the most primitive tetrapod, that is, the first vertebrate animal to possess limbs with digits rather than fish fins.
But the latest evidence from a Duke graduate student's research indicates that Ichthyostega may have been closer to the first tetrapod. In fact, Acanthostega may have had a terrestrial ancestor and then returned full time to the water, said Viviane Callier, who is the first author of a report on the findings to be published in today's issue of the journal Science.
"If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved," Callier said.
Co-author Jennifer Clack of the University Museum of Zoology in Cambridge, England -- where she supervised Callier's work for a master's degree -- found the fossils embedded in rocks collected from East Greenland.
Rather than trying to remove them -- an action that would have destroyed much of the evidence -- the researchers studied the fossils inside the stone with computed tomography (CT) scanning. Callier "reconstructed" the animals using imaging software (Amira and Mimics) to analyze the CT scans, focusing on the shapes of the two species' upper arm bones, or humeri.
The CT slices revealed that Clack had found the first juvenile forms of Ichthyostega. Previously known fossils of Ichthyostega had come from adults.
Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.
In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said
Because the shapes of its adult limbs seemed the most fin-like, scientists had previously concluded that Acanthostega was "more primitive," Callier said. "But now, if we look at the details of the humeri, Ichthyostega's are actually more similar to earlier fishes."
Ironically, the shape of Acanthostegas limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."
"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle."
Per Ahlberg, a Swedish paleontologist who was previously Clack's graduate student, also joined Clack in a comparative analysis of other more fish-like species living at about the same time as Ichthyostega and Acanthostega.
Those include Tiktaalik, another animal that has made the news because of scientists' deductions that it was in transition from water to land.
"It seems like there were different species evolving the same or similar traits independently -- evidence of parallel evolution," Callier said. "The terrestrial environment posed new challenges like feeding and moving on land and breathing air, to which the first tetrapods had to evolve solutions. Sometimes different lineages stumbled upon similar solutions."
Ahlberg, now professor at the University of Uppsala in Sweden, is corresponding author of the new Science report. The research was funded by the Winston Churchill Foundation and the Swedish Research Council.
Source: Duke University (news : web)
http://www.physorg.com/news159190294.html
Tuesday, May 19, 2009
Fossils suggest earlier land-water transition of tetrapod
April 17th, 2009
New evidence gleaned from CT scans of fossils locked inside rocks may flip the order in which two kinds of four-limbed animals with backbones were known to have moved from fish to landlubber.
Both extinct species, known as Ichthyostega and Acanthostega, lived an estimated 360-370 million years ago in what is now Greenland. Acanthostega was thought to have been the most primitive tetrapod, that is, the first vertebrate animal to possess limbs with digits rather than fish fins.
But the latest evidence from a Duke graduate student's research indicates that Ichthyostega may have been closer to the first tetrapod. In fact, Acanthostega may have had a terrestrial ancestor and then returned full time to the water, said Viviane Callier, who is the first author of a report on the findings to be published in today's issue of the journal Science.
"If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved," Callier said.
Co-author Jennifer Clack of the University Museum of Zoology in Cambridge, England -- where she supervised Callier's work for a master's degree -- found the fossils embedded in rocks collected from East Greenland.
Rather than trying to remove them -- an action that would have destroyed much of the evidence -- the researchers studied the fossils inside the stone with computed tomography (CT) scanning. Callier "reconstructed" the animals using imaging software (Amira and Mimics) to analyze the CT scans, focusing on the shapes of the two species' upper arm bones, or humeri.
The CT slices revealed that Clack had found the first juvenile forms of Ichthyostega. Previously known fossils of Ichthyostega had come from adults.
Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.
In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said
Because the shapes of its adult limbs seemed the most fin-like, scientists had previously concluded that Acanthostega was "more primitive," Callier said. "But now, if we look at the details of the humeri, Ichthyostega's are actually more similar to earlier fishes."
Ironically, the shape of Acanthostegas limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."
"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle."
Per Ahlberg, a Swedish paleontologist who was previously Clack's graduate student, also joined Clack in a comparative analysis of other more fish-like species living at about the same time as Ichthyostega and Acanthostega.
Those include Tiktaalik, another animal that has made the news because of scientists' deductions that it was in transition from water to land.
"It seems like there were different species evolving the same or similar traits independently -- evidence of parallel evolution," Callier said. "The terrestrial environment posed new challenges like feeding and moving on land and breathing air, to which the first tetrapods had to evolve solutions. Sometimes different lineages stumbled upon similar solutions."
Ahlberg, now professor at the University of Uppsala in Sweden, is corresponding author of the new Science report. The research was funded by the Winston Churchill Foundation and the Swedish Research Council.
Source: Duke University (news : web)
http://www.physorg.com/news159190294.html
New evidence gleaned from CT scans of fossils locked inside rocks may flip the order in which two kinds of four-limbed animals with backbones were known to have moved from fish to landlubber.
Both extinct species, known as Ichthyostega and Acanthostega, lived an estimated 360-370 million years ago in what is now Greenland. Acanthostega was thought to have been the most primitive tetrapod, that is, the first vertebrate animal to possess limbs with digits rather than fish fins.
But the latest evidence from a Duke graduate student's research indicates that Ichthyostega may have been closer to the first tetrapod. In fact, Acanthostega may have had a terrestrial ancestor and then returned full time to the water, said Viviane Callier, who is the first author of a report on the findings to be published in today's issue of the journal Science.
"If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved," Callier said.
Co-author Jennifer Clack of the University Museum of Zoology in Cambridge, England -- where she supervised Callier's work for a master's degree -- found the fossils embedded in rocks collected from East Greenland.
Rather than trying to remove them -- an action that would have destroyed much of the evidence -- the researchers studied the fossils inside the stone with computed tomography (CT) scanning. Callier "reconstructed" the animals using imaging software (Amira and Mimics) to analyze the CT scans, focusing on the shapes of the two species' upper arm bones, or humeri.
The CT slices revealed that Clack had found the first juvenile forms of Ichthyostega. Previously known fossils of Ichthyostega had come from adults.
Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.
In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said
Because the shapes of its adult limbs seemed the most fin-like, scientists had previously concluded that Acanthostega was "more primitive," Callier said. "But now, if we look at the details of the humeri, Ichthyostega's are actually more similar to earlier fishes."
Ironically, the shape of Acanthostegas limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."
"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle."
Per Ahlberg, a Swedish paleontologist who was previously Clack's graduate student, also joined Clack in a comparative analysis of other more fish-like species living at about the same time as Ichthyostega and Acanthostega.
Those include Tiktaalik, another animal that has made the news because of scientists' deductions that it was in transition from water to land.
"It seems like there were different species evolving the same or similar traits independently -- evidence of parallel evolution," Callier said. "The terrestrial environment posed new challenges like feeding and moving on land and breathing air, to which the first tetrapods had to evolve solutions. Sometimes different lineages stumbled upon similar solutions."
Ahlberg, now professor at the University of Uppsala in Sweden, is corresponding author of the new Science report. The research was funded by the Winston Churchill Foundation and the Swedish Research Council.
Source: Duke University (news : web)
http://www.physorg.com/news159190294.html
Monday, May 18, 2009
Humans, chimps may have bred after split
By Gareth Cook, Globe Staff | May 18, 2006
Boston scientists released a provocative report yesterday that challenges the timeline of human evolution and suggests that human ancestors bred with chimpanzee ancestors long after they had initially separated into two species.
The researchers, working at the Cambridge-based Broad Institute of Harvard and MIT, used a wealth of newly available genetic data to estimate the time when the first human ancestors split from the chimpanzees. The team arrived at an answer that is at least 1 million years later than paleontologists had believed, based on fossils of early, humanlike creatures.
The lead scientist said that this jarring conflict with the fossil record, combined with a number of other strange genetic patterns the team uncovered, led him to a startling explanation: that human ancestors evolved apart from the chimpanzees for hundreds of thousands of years, and then started breeding with them again before a final break.
''Something very unusual happened," said David Reich, one of the report's authors and a geneticist at the Broad and Harvard Medical School.
The suggestion of interbreeding was met with skepticism by paleontologists, who said they had trouble imagining a successful breeding between early human ancestors, which walked upright, and the chimpanzee ancestors, which walked on all fours. But other scientists said the work is impressive and will probably force a reappraisal of the story of human origins. And one leading paleontologist said he welcomed the research as a sign that new genetic information will yield more clues to our deep history than once thought.
''I find this terrifically exciting and important work," said David Pilbeam, a Harvard paleontologist who was not part of the Broad team.
Pilbeam helped discover an early human ancestor known as Toumai, which walked on two legs and is thought to have lived in present-day Chad 6.5 million to 7.4 million years ago. The new report, published in today's issue of the journal Nature, estimates that final break between the human and chimpanzee species did not come until 6.3 million years ago at the earliest, and probably less than 5.4 million years ago.
This contradiction could be resolved, Reich said, if early creatures like Toumai then interbred with chimpanzee ancestors, leaving a population of hybrids that developed into today's humans. (In this scenario, the line of Toumai creatures then went extinct.) But it is also possible, he said, that the dating of the early human fossils is wrong, or that the dating of other, older fossils used in his calculations is wrong, which would partially undercut the interbreeding theory. Scientists said that the report will probably bring intense scrutiny, as researchers look for potential flaws in the work or other explanations for its findings.
The work will also probably inspire biologists to devote more attention to hybrids, the term for offspring with parents of different species, and the role that they may play in fueling evolution. Biologists have long known about hybrids -- a half-grizzly bear, half-polar bear was recently discovered in Canada -- but it has been assumed that these were generally lone animals that had had little impact on the story of evolution. The Nature paper joins a wave of work showing that the lines between species are hazy, according to James Mallet, a biologist who studies hybrids at University College London.
As two species evolve, they can develop new abilities. Some hybrids could combine the best of both species, Mallet said, though the biological barriers to the creation of hybrids increase the longer the species are apart. It is thought that human ancestors were adapting to life on the savannah instead of the forest, where chimpanzees still live today. It is not known why human ancestors would have begun mating with chimpanzee ancestors again, or why they would have stopped.
To understand how long ago humans split from chimpanzees, Reich and his colleagues did a close study of DNA from the two. This technique rests on the idea that once the populations separate, the DNA will slowly drift apart as natural mutations accumulate. If they can count the number of changes, and determine how quickly the changes happened, then they can calculate how long the two populations have been separate, according to Nick Patterson, a scientist who was part of the Broad team.
Previous studies have used this idea and found that the two species split between about 5 million and 8 million years ago.
The Broad team sought to get a more precise answer by looking at how different the DNA of chimps and humans is at many locations, instead of calculating an average difference. The DNA of humans and chimpanzees is quite similar, meaning that scientists can readily identify many segments of DNA that are so similar they must have been handed down by a common ancestor, deep in the past. Scientists can then use a computer to put the segments of human and chimp DNA into alignment, placing side by side the segments that are very similar.
For each pair of segments, they then calculated how long it would have taken to accumulate all the differences. The team used sophisticated statistical techniques to calculate these ''divergence times."
This analysis brought surprises that the team could explain only by suggesting human ancestors and chimpanzee ancestors interbred. First, they found that the divergence times varied widely. Some parts of the DNA seemed to indicate the human and chimpanzee species had been apart much longer than others, by millions of years. If humans split from chimps and then interbred before splitting again, the more divergent DNA sequences could date to before the first split, while the less divergent sequences could date to just before the second split.
The other surprise was that sequences from the X chromosome, one of two chromosomes that determine gender, gave consistently more recent divergence times, instead of the range seen on other chromosomes. This, too, would be explained by the idea of interbreeding, according to the report. The X chromosome is thought to be the focus of fertility problems in hybrids, and population models suggest that all of the X chromosomes in a hybrid population would quickly come to match those of one of the parent species. This would explain why the human and chimpanzee X chromosomes are so similar.
Although the idea is controversial, there will soon be a wealth of more information to test it. Part of the Broad team's analysis relied on using DNA sequences from the gorilla and other primates as a kind of baseline to interpret their results. Only a relatively small amount of DNA has been sequenced from gorillas, limiting the amount of data the team could use. By the end of 2007, there should be a full sequence of the gorilla, allowing the scientists to do a much fuller analysis, Reich said.
The team also plans on looking at genetic data for other groups of closely related species to try to determine whether those species split apart fairly abruptly, or whether there is evidence that hybridization is a common part of evolution, bringing together the best of two species.
Gareth Cook can be reached at cook@globe.com.
© Copyright 2006 Globe Newspaper Company.
http://www.boston.com/news/science/articles/2006/05/18/humans_chimps_may_have_bred_after_split/
Boston scientists released a provocative report yesterday that challenges the timeline of human evolution and suggests that human ancestors bred with chimpanzee ancestors long after they had initially separated into two species.
The researchers, working at the Cambridge-based Broad Institute of Harvard and MIT, used a wealth of newly available genetic data to estimate the time when the first human ancestors split from the chimpanzees. The team arrived at an answer that is at least 1 million years later than paleontologists had believed, based on fossils of early, humanlike creatures.
The lead scientist said that this jarring conflict with the fossil record, combined with a number of other strange genetic patterns the team uncovered, led him to a startling explanation: that human ancestors evolved apart from the chimpanzees for hundreds of thousands of years, and then started breeding with them again before a final break.
''Something very unusual happened," said David Reich, one of the report's authors and a geneticist at the Broad and Harvard Medical School.
The suggestion of interbreeding was met with skepticism by paleontologists, who said they had trouble imagining a successful breeding between early human ancestors, which walked upright, and the chimpanzee ancestors, which walked on all fours. But other scientists said the work is impressive and will probably force a reappraisal of the story of human origins. And one leading paleontologist said he welcomed the research as a sign that new genetic information will yield more clues to our deep history than once thought.
''I find this terrifically exciting and important work," said David Pilbeam, a Harvard paleontologist who was not part of the Broad team.
Pilbeam helped discover an early human ancestor known as Toumai, which walked on two legs and is thought to have lived in present-day Chad 6.5 million to 7.4 million years ago. The new report, published in today's issue of the journal Nature, estimates that final break between the human and chimpanzee species did not come until 6.3 million years ago at the earliest, and probably less than 5.4 million years ago.
This contradiction could be resolved, Reich said, if early creatures like Toumai then interbred with chimpanzee ancestors, leaving a population of hybrids that developed into today's humans. (In this scenario, the line of Toumai creatures then went extinct.) But it is also possible, he said, that the dating of the early human fossils is wrong, or that the dating of other, older fossils used in his calculations is wrong, which would partially undercut the interbreeding theory. Scientists said that the report will probably bring intense scrutiny, as researchers look for potential flaws in the work or other explanations for its findings.
The work will also probably inspire biologists to devote more attention to hybrids, the term for offspring with parents of different species, and the role that they may play in fueling evolution. Biologists have long known about hybrids -- a half-grizzly bear, half-polar bear was recently discovered in Canada -- but it has been assumed that these were generally lone animals that had had little impact on the story of evolution. The Nature paper joins a wave of work showing that the lines between species are hazy, according to James Mallet, a biologist who studies hybrids at University College London.
As two species evolve, they can develop new abilities. Some hybrids could combine the best of both species, Mallet said, though the biological barriers to the creation of hybrids increase the longer the species are apart. It is thought that human ancestors were adapting to life on the savannah instead of the forest, where chimpanzees still live today. It is not known why human ancestors would have begun mating with chimpanzee ancestors again, or why they would have stopped.
To understand how long ago humans split from chimpanzees, Reich and his colleagues did a close study of DNA from the two. This technique rests on the idea that once the populations separate, the DNA will slowly drift apart as natural mutations accumulate. If they can count the number of changes, and determine how quickly the changes happened, then they can calculate how long the two populations have been separate, according to Nick Patterson, a scientist who was part of the Broad team.
Previous studies have used this idea and found that the two species split between about 5 million and 8 million years ago.
The Broad team sought to get a more precise answer by looking at how different the DNA of chimps and humans is at many locations, instead of calculating an average difference. The DNA of humans and chimpanzees is quite similar, meaning that scientists can readily identify many segments of DNA that are so similar they must have been handed down by a common ancestor, deep in the past. Scientists can then use a computer to put the segments of human and chimp DNA into alignment, placing side by side the segments that are very similar.
For each pair of segments, they then calculated how long it would have taken to accumulate all the differences. The team used sophisticated statistical techniques to calculate these ''divergence times."
This analysis brought surprises that the team could explain only by suggesting human ancestors and chimpanzee ancestors interbred. First, they found that the divergence times varied widely. Some parts of the DNA seemed to indicate the human and chimpanzee species had been apart much longer than others, by millions of years. If humans split from chimps and then interbred before splitting again, the more divergent DNA sequences could date to before the first split, while the less divergent sequences could date to just before the second split.
The other surprise was that sequences from the X chromosome, one of two chromosomes that determine gender, gave consistently more recent divergence times, instead of the range seen on other chromosomes. This, too, would be explained by the idea of interbreeding, according to the report. The X chromosome is thought to be the focus of fertility problems in hybrids, and population models suggest that all of the X chromosomes in a hybrid population would quickly come to match those of one of the parent species. This would explain why the human and chimpanzee X chromosomes are so similar.
Although the idea is controversial, there will soon be a wealth of more information to test it. Part of the Broad team's analysis relied on using DNA sequences from the gorilla and other primates as a kind of baseline to interpret their results. Only a relatively small amount of DNA has been sequenced from gorillas, limiting the amount of data the team could use. By the end of 2007, there should be a full sequence of the gorilla, allowing the scientists to do a much fuller analysis, Reich said.
The team also plans on looking at genetic data for other groups of closely related species to try to determine whether those species split apart fairly abruptly, or whether there is evidence that hybridization is a common part of evolution, bringing together the best of two species.
Gareth Cook can be reached at cook@globe.com.
© Copyright 2006 Globe Newspaper Company.
http://www.boston.com/news/science/articles/2006/05/18/humans_chimps_may_have_bred_after_split/
Thursday, May 14, 2009
Microbial Ocean Study Reels In RNA Surprise
By News Staff | May 13th 2009 01:00 AM
To study small RNA, snippets of RNA that act as switches to regulate gene expression in single-celled creatures, you need lab-cultured microorganisms but a new method of obtaining marine microbe samples while preserving the microbes' natural gene expression has shown the presence of many varieties of small RNAs.
The discovery of its presence in a natural setting may make it possible finally to learn on a broad scale how microbial communities living at different ocean depths and regions respond to environmental stimuli.
Microbes are ultra-sensitive environmental sensors that respond in the blink of an eye to minute changes in light, temperature, chemicals or pressure and modify their protein expression accordingly. But that sensitivity creates a quandary for the scientists who study them. Sort of like the observer effect in quantum physics, by entering the environment or removing the microbes from it, the observer causes the microbes to change their protein expression. That same sensitivity makes some of these creatures exceedingly difficult to grow in lab cultures.
"Microbes are exquisite biosensors," said Edward Delong, a professor of civil and environmental engineering (CEE) and biological engineering. "We had developed this methodology to look at protein-encoding genes, because if we know which proteins the microbes are expressing under what conditions, we can learn about the environmental conditions and how these microbes influence those. The unexpected presence and abundance of these small RNAs, which can act as switches to regulate gene expression, will allow us to get an even deeper view of gene expression and microbial response to environmental changes.
DeLong and co-authors Yanmei Shi, a graduate student in CEE, and postdoctoral associate Gene Tyson describe this work in the May 14 issue of Nature. The team used a technique called metatranscriptomics, which allows them to analyze the RNA molecules of wild microbes, something that previously could be done only with lab-cultured microbes.
To overcome the hurdle of quickly collecting and filtering microbial samples in seawater before the microbes change their protein expression, the research team — collaboratively with CEE Professor Sallie (Penny) Chisholm and her research team, which has successfully grown and studied the photosynthetic microbe, Prochlorococcus, in the lab — created a method for amplifying the RNA extracted from small amounts of seawater by modifying a eukaryotic RNA amplification technique.
When Shi began lab studies of the RNA in their samples, she found that much of the novel RNA they expected to be protein-coding was actually small RNA (or sRNA), which can serve as a catalyst or regulator for metabolic pathways in microbes.
"What's surprising to me is the abundance of novel sRNA candidates in our data sets," said Shi. "When I looked into the sequences that cannot be confidently assigned as protein-coding, I found that a big percentage of those sequences are non-coding sequences derived from yet-to-be-cultivated microorganisms in the ocean. This was very exciting to us because this metatranscriptomic approach — using a data set of sequences of transcripts from a natural microbial community as opposed to a single cultured microbial strain — opens up a new window of discovering naturally occurring sRNAs, which may further provide ecologically relevant implications."
"We've found an incredibly diverse set of molecules and each one is potentially regulating a different protein encoding gene," said DeLong. "We will now be able to track the protein expression and the sRNA expression over time to learn the relevance of these little switches."
If we think of marine bacteria and their proteins as tiny factories performing essential biogeochemical activities — such as harvesting sunlight to create oxygen and synthesize sugar from carbon dioxide — then the sRNAs are the internal switches that turn on and off the factories' production line. Their discovery in the ocean samples opens the way to learning even more detailed information in the lab: the researchers can now conduct lab experiments to look at the effects of environmental perturbation on microbial communities. These new sRNAs also expand our general knowledge of the nature and diversity of these recently recognized regulatory switches.
"Being able to track the dynamics of small RNA expression in situ provides insight into how microbes respond to environmental changes such as nutrient concentration and physical properties like light and pressure," said Shi. "A very interesting question to follow up in the lab is how much fitness advantage a small RNA confers to microbes. Can the microbes with a specific small RNA perform better in competing for nutrients in a tough situation, for instance? The discovery of naturally occurring small RNAs is a first step towards addressing such questions."
This work was supported by the Gordon and Betty Moore Foundation, the National Science Foundation and the U.S. Department of Energy.
http://www.scientificblogging.com/news_articles/microbial_ocean_study_reels_rna_surprise
To study small RNA, snippets of RNA that act as switches to regulate gene expression in single-celled creatures, you need lab-cultured microorganisms but a new method of obtaining marine microbe samples while preserving the microbes' natural gene expression has shown the presence of many varieties of small RNAs.
The discovery of its presence in a natural setting may make it possible finally to learn on a broad scale how microbial communities living at different ocean depths and regions respond to environmental stimuli.
Microbes are ultra-sensitive environmental sensors that respond in the blink of an eye to minute changes in light, temperature, chemicals or pressure and modify their protein expression accordingly. But that sensitivity creates a quandary for the scientists who study them. Sort of like the observer effect in quantum physics, by entering the environment or removing the microbes from it, the observer causes the microbes to change their protein expression. That same sensitivity makes some of these creatures exceedingly difficult to grow in lab cultures.
"Microbes are exquisite biosensors," said Edward Delong, a professor of civil and environmental engineering (CEE) and biological engineering. "We had developed this methodology to look at protein-encoding genes, because if we know which proteins the microbes are expressing under what conditions, we can learn about the environmental conditions and how these microbes influence those. The unexpected presence and abundance of these small RNAs, which can act as switches to regulate gene expression, will allow us to get an even deeper view of gene expression and microbial response to environmental changes.
DeLong and co-authors Yanmei Shi, a graduate student in CEE, and postdoctoral associate Gene Tyson describe this work in the May 14 issue of Nature. The team used a technique called metatranscriptomics, which allows them to analyze the RNA molecules of wild microbes, something that previously could be done only with lab-cultured microbes.
To overcome the hurdle of quickly collecting and filtering microbial samples in seawater before the microbes change their protein expression, the research team — collaboratively with CEE Professor Sallie (Penny) Chisholm and her research team, which has successfully grown and studied the photosynthetic microbe, Prochlorococcus, in the lab — created a method for amplifying the RNA extracted from small amounts of seawater by modifying a eukaryotic RNA amplification technique.
When Shi began lab studies of the RNA in their samples, she found that much of the novel RNA they expected to be protein-coding was actually small RNA (or sRNA), which can serve as a catalyst or regulator for metabolic pathways in microbes.
"What's surprising to me is the abundance of novel sRNA candidates in our data sets," said Shi. "When I looked into the sequences that cannot be confidently assigned as protein-coding, I found that a big percentage of those sequences are non-coding sequences derived from yet-to-be-cultivated microorganisms in the ocean. This was very exciting to us because this metatranscriptomic approach — using a data set of sequences of transcripts from a natural microbial community as opposed to a single cultured microbial strain — opens up a new window of discovering naturally occurring sRNAs, which may further provide ecologically relevant implications."
"We've found an incredibly diverse set of molecules and each one is potentially regulating a different protein encoding gene," said DeLong. "We will now be able to track the protein expression and the sRNA expression over time to learn the relevance of these little switches."
If we think of marine bacteria and their proteins as tiny factories performing essential biogeochemical activities — such as harvesting sunlight to create oxygen and synthesize sugar from carbon dioxide — then the sRNAs are the internal switches that turn on and off the factories' production line. Their discovery in the ocean samples opens the way to learning even more detailed information in the lab: the researchers can now conduct lab experiments to look at the effects of environmental perturbation on microbial communities. These new sRNAs also expand our general knowledge of the nature and diversity of these recently recognized regulatory switches.
"Being able to track the dynamics of small RNA expression in situ provides insight into how microbes respond to environmental changes such as nutrient concentration and physical properties like light and pressure," said Shi. "A very interesting question to follow up in the lab is how much fitness advantage a small RNA confers to microbes. Can the microbes with a specific small RNA perform better in competing for nutrients in a tough situation, for instance? The discovery of naturally occurring small RNAs is a first step towards addressing such questions."
This work was supported by the Gordon and Betty Moore Foundation, the National Science Foundation and the U.S. Department of Energy.
http://www.scientificblogging.com/news_articles/microbial_ocean_study_reels_rna_surprise
'Hobbit' Skull Study Finds Hobbit Is Not Human
ScienceDaily (Jan. 21, 2009) — In a an analysis of the size, shape and asymmetry of the cranium of Homo floresiensis, Karen Baab, Ph.D., a researcher in the Department of Anatomical Scienes at Stony Brook University, and colleagues conclude that the fossil, found in Indonesia in 2003 and known as the “Hobbit,” is not human.
They used 3-D shape analysis to study the LB1 skull of the hobbit and found the shape of the skull to be consistent with a scaled down human ancestor but not modern humans. Their findings, reported in the current online edition of the Journal of Human Evolution, add to the evidence that the hobbit is a new species.
The question as to whether the hobbit was human or another species remains controversial. Some scientists claim the hobbit was a diminutive human that suffered from some type of disease that causes microcephaly, which results in abnormal growth of the brain and causes the cranium to be much smaller than the normal human cranium. But Dr. Baab and co-author Kieran McNulty, Professor of Anthropology at the University of Minnesota, believe their findings counter the microcephaly theory.
“A skull can provide researchers with a lot of important information about a fossil species, particularly regarding their evolutionary relationships to other fossil species,” explains Dr. Baab. “The overall shape of the LB1 skull, particularly the part that surrounds the brain (neurocranium) looks similar to fossils more than 1.5 million years older from Africa and Eurasia, rather than modern humans, even though Homo floresiensis is documented from 17,000 to 95,000 years ago.”
To carry out the study, Dr. Baab and colleagues collected 3D landmark data on the LB1 skull and a large sample of fossils representing other extinct hominin species, as well as a comparative sample of modern humans and apes. They performed several analyses of different regions of the skulls. Taken together, these analyses indicated that the LB1 skull shape is that of a scaled down Homo fossil not a scaled down modern human.
The results of the analysis of the asymmetry of the skulls, which refers to differences between the right and left sides of the skull, refutes the suggestion that the LB1 skull was that of a modern human with a diagnosis of microcephaly. In modern humans, a high degree of asymmetry may indicate that the individual was diseased. At least one scientific study on the asymmetry of LB1 supported the argument that this individual had microcephaly. Conversely, Dr. Baab and colleagues found the degree of asymmetry of the LB1 skull was not unexpectedly high and therefore not supportive of the diagnosis of microcephaly.
“The degree of asymmetry in LB1 was within the range of apes and was very similar to that seen in other fossil skulls,” says Dr. Baab. “We suggest that the degree of asymmetry is within expectations for this population of hominins, particular given that the conditions of the cave in Indonesia in which the skull was preserved may have contributed to asymmetry.”
Dr. Baab recognizes that the controversy as to the evolutionary origins of Homo floresiensis will continue, perhaps without an answer. However, all the evidence that she and colleagues illustrate in their article “Size, shape, and asymmetry in fossil hominins: The status of the LB1cranium based on 3D morphometric analyses,” suggest that Homo floresiensis was most likely the diminutive descendant of a species of archaic Homo.
The results of this study are also in line with what other researchers in the Department of Anatomical Sciences at Stony Brook University have found regarding the rest of the hobbit skeleton. Drs. William Jungers and Susan Larson have documented a range of primitive features in both the upper and lower limbs of Homo floresiensis, highlighting the many ways that these hominins were unlike modern humans.
Adapted from materials provided by Stony Brook University Medical Center.
http://www.sciencedaily.com/releases/2009/01/090120144508.htm
They used 3-D shape analysis to study the LB1 skull of the hobbit and found the shape of the skull to be consistent with a scaled down human ancestor but not modern humans. Their findings, reported in the current online edition of the Journal of Human Evolution, add to the evidence that the hobbit is a new species.
The question as to whether the hobbit was human or another species remains controversial. Some scientists claim the hobbit was a diminutive human that suffered from some type of disease that causes microcephaly, which results in abnormal growth of the brain and causes the cranium to be much smaller than the normal human cranium. But Dr. Baab and co-author Kieran McNulty, Professor of Anthropology at the University of Minnesota, believe their findings counter the microcephaly theory.
“A skull can provide researchers with a lot of important information about a fossil species, particularly regarding their evolutionary relationships to other fossil species,” explains Dr. Baab. “The overall shape of the LB1 skull, particularly the part that surrounds the brain (neurocranium) looks similar to fossils more than 1.5 million years older from Africa and Eurasia, rather than modern humans, even though Homo floresiensis is documented from 17,000 to 95,000 years ago.”
To carry out the study, Dr. Baab and colleagues collected 3D landmark data on the LB1 skull and a large sample of fossils representing other extinct hominin species, as well as a comparative sample of modern humans and apes. They performed several analyses of different regions of the skulls. Taken together, these analyses indicated that the LB1 skull shape is that of a scaled down Homo fossil not a scaled down modern human.
The results of the analysis of the asymmetry of the skulls, which refers to differences between the right and left sides of the skull, refutes the suggestion that the LB1 skull was that of a modern human with a diagnosis of microcephaly. In modern humans, a high degree of asymmetry may indicate that the individual was diseased. At least one scientific study on the asymmetry of LB1 supported the argument that this individual had microcephaly. Conversely, Dr. Baab and colleagues found the degree of asymmetry of the LB1 skull was not unexpectedly high and therefore not supportive of the diagnosis of microcephaly.
“The degree of asymmetry in LB1 was within the range of apes and was very similar to that seen in other fossil skulls,” says Dr. Baab. “We suggest that the degree of asymmetry is within expectations for this population of hominins, particular given that the conditions of the cave in Indonesia in which the skull was preserved may have contributed to asymmetry.”
Dr. Baab recognizes that the controversy as to the evolutionary origins of Homo floresiensis will continue, perhaps without an answer. However, all the evidence that she and colleagues illustrate in their article “Size, shape, and asymmetry in fossil hominins: The status of the LB1cranium based on 3D morphometric analyses,” suggest that Homo floresiensis was most likely the diminutive descendant of a species of archaic Homo.
The results of this study are also in line with what other researchers in the Department of Anatomical Sciences at Stony Brook University have found regarding the rest of the hobbit skeleton. Drs. William Jungers and Susan Larson have documented a range of primitive features in both the upper and lower limbs of Homo floresiensis, highlighting the many ways that these hominins were unlike modern humans.
Adapted from materials provided by Stony Brook University Medical Center.
http://www.sciencedaily.com/releases/2009/01/090120144508.htm
Neandertals Sophisticated And Fearless Hunters
ScienceDaily (May 14, 2009) — Neandertals, the 'stupid' cousins of modern humans were capable of capturing the most impressive animals. This indicates that Neandertals were anything but dim. Dutch researcher Gerrit Dusseldorp analysed their daily forays for food to gain insights into the complex behaviour of the Neandertal. His analysis revealed that the hunting was very knowledge intensive.
Although it is now clear that Neandertals were hunters and not scavengers, their exact hunting methods are still something of a mystery. Dusseldorp investigated just how sophisticated the Neandertals' hunting methods really were. His analysis of two archaeological sites revealed that Neandertals in warm forested areas preferred to hunt solitary game but that in colder, less forested areas they preferred to hunt the more difficult to capture herding animals.
The Neandertals were not easily intimated by their game. Rhinoceroses, bisons and even predators such as the brown bear were all on their menu. Dusseldorp established that just as for modern humans, the environment and the availability of food determined the choice of prey and the hunting method adopted. If the circumstances allowed it, Neandertals lived in large groups and even the most attractive and difficult to catch prey were within their reach.
Coordination and communication
Although herding animals are difficult to surprise and isolate, many such game lived on the open steppes. This large supply attracted large groups of Neandertals. That the Neandertals were capable of hunting down such elusive game demonstrates that they had good coordination skills and could communicate well with each other.
Each prey has a specific cost-benefit scenario. For example, game that are more difficult to catch yield more calories and have a more usable, thick fleece. Dusseldorp used these data to examine the Neandertal's preferences. He also analysed the prey of hyenas in the same manner. Hyenas were important competitors of Neandertals as they had a similar dietary pattern.
Dusseldorp demonstrated that Neandertals, thanks to their intelligence, even surpassed hyenas at capturing the strongest game. All things being considered, the Neandertals were skilled and highly intelligent hunters. So the idea that Neandertals were brute musclemen can be dismissed.
This study was part of NWO project Thoughtful Hunters? The Archaeology of Neandertal Communication and Cognition. Dusseldorp is continuing his research with a postdoc position in
Adapted from materials provided by Netherlands Organization for Scientific Research, via AlphaGalileo.
http://www.sciencedaily.com/releases/2009/05/090514084115.htm
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