A group of scientists in Princeton's Department of Ecology and Evolutionary Biology has uncovered a new biological mechanism that could provide a clearer window into a cell's inner workings.
What's more, this mechanism could represent an "epigenetic" pathway -- a route that bypasses an organism's normal DNA genetic program -- for so-called Lamarckian evolution, enabling an organism to pass on to its offspring characteristics acquired during its lifetime to improve their chances for survival. Lamarckian evolution is the notion, for example, that the giraffe's long neck evolved by its continually stretching higher and higher in order to munch on the more plentiful top tree leaves and gain a better shot at surviving.
The research also could have implications as a new method for controlling cellular processes, such as the splicing order of DNA segments, and increasing the understanding of natural cellular regulatory processes, such as which segments of DNA are retained versus lost during development. The team's findings will be published Jan. 10 in the journal Nature.
Princeton biologists Laura Landweber, Mariusz Nowacki and Vikram Vijayan, together with other members of the lab, wanted to decipher how the cell accomplished this feat, which required reorganizing its genome without resorting to its original genetic program. They chose the singled-celled ciliate Oxytricha trifallax as their testbed.
Ciliates are pond-dwelling protozoa that are ideal model systems for studying epigenetic phenomena. While typical human cells each have one nucleus, serving as the control center for the cell, these ciliate cells have two. One, the somatic nucleus, contains the DNA needed to carry out all the non-reproductive functions of the cell, such as metabolism. The second, the germline nucleus, like humans' sperm and egg, is home to the DNA needed for sexual reproduction.
When two of these ciliate cells mate, the somatic nucleus gets destroyed, and must somehow be reconstituted in their offspring in order for them to survive. The germline nucleus contains abundant DNA, yet 95 percent of it is thrown away during regeneration of a new somatic nucleus, in a process that compresses a pretty big genome (one-third the size of the human genome) into a tiny fraction of the space. This leaves only 5 percent of the organism's DNA free for encoding functions. Yet this small hodgepodge of remaining DNA always gets correctly chosen and then descrambled by the cell to form a new, working genome in a process (described as "genome acrobatics") that is still not well understood, but extremely deliberate and precise.
Landweber and her colleagues have postulated that this programmed rearrangement of DNA fragments is guided by an existing "cache" of information in the form of a DNA or RNA template derived from the parent's nucleus. In the computer realm, a cache is a temporary storage site for frequently used information to enable quick and easy access, rather than having to re-fetch or re-create the original information from scratch every time it's needed.
"The notion of an RNA cache has been around for a while, as the idea of solving a jigsaw puzzle by peeking at the cover of the box is always tempting," said Landweber, associate professor of ecology and evolutionary biology. "These cells have a genomic puzzle to solve that involves gathering little pieces of DNA and putting them back together in a specified order. The original idea of an RNA cache emerged in a study of plants, rather than protozoan cells, though, but the situation in plants turned out to be incorrect."
Through a series of experiments, the group tested out their hypothesis that DNA or RNA molecules were providing the missing instruction booklet needed during development, and also tried to determine if the putative template was made of RNA or DNA. DNA is the genetic material of most organisms, however RNA is now known to play a diversity of important roles as well. RNA is DNA's chemical cousin, and has a primary role in interpreting the genetic code during the construction of proteins.
First, the researchers attempted to determine if the RNA cache idea was valid by directing specific RNA-destroying chemicals, known as RNAi, to the cell before fertilization. This gave encouraging results, disrupting the process of development, and even halting DNA rearrangement in some cases.
In a second experiment, Nowacki and Yi Zhou, both postdoctoral fellows, discovered that RNA templates did indeed exist early on in the cellular developmental process, and were just long-lived enough to lay out a pattern for reconstructing their main nucleus. This was soon followed by a third experiment that "… required real chutzpah," Landweber said, "because it meant reprogramming the cell to shuffle its own genetic material."
Nowacki, Zhou and Vijayan, a 2007 Princeton graduate in electrical engineering, constructed both artificial RNA and DNA templates that encoded a novel, pre-determined pattern; that is, that would take a DNA molecule of the ciliate's consisting of, for example, pieces 1-2-3-4-5 and transpose two of the segments, to produce the fragment 1-2-3-5-4. Injecting their synthetic templates into the developing cell produced the anticipated results, showing that a specified RNA template could provide a new set of rules for unscrambling the nuclear fragments in such a way as to reconstitute a working nucleus.
"This wonderful discovery showed for the first time that RNA can provide sequence information that guides accurate recombination of DNA, leading to reconstruction of genes and a genome that are necessary for the organism," said Meng-Chao Yao, director of the Institute of Molecular Biology at Taiwan's Academia Sinica. "It reveals that genetic information can be passed on to following generations via RNA, in addition to DNA."
The research team believes that if this mechanism extends to mammalian cells, then it could suggest novel ways for manipulating genes, besides those already known through the standard methods of genetic engineering. This could lead to possible applications for creating new gene combinations or restoring aberrant cells to their original, healthy state
Saturday, February 23, 2008
Saturday, February 2, 2008
Oxygen: The Clue To First Appearance Of Large Animals
The sudden appearance of large animal fossils more than 500 million years ago – a problem that perplexed even Charles Darwin and is commonly known as “Darwin’s Dilemma” – may be due to a huge increase of oxygen in the world’s oceans.
In 2002 researchers found the world’s oldest complex life forms between layers of sandstone on the southeastern coast of Newfoundland. This pushed back the age of Earth’s earliest known complex life to more than 575 million years ago, soon after the melting of the massive “snowball” glaciers. New findings reported today shed light on why, after three billion years of mostly single-celled evolution, these large animals suddenly appeared in the fossil record.
A huge increase in oxygen following the Gaskiers Glaciation 580 million years ago corresponds with the first appearance of large animal fossils on the Avalon Peninsula in Newfoundland.
Now for the first time, geochemical studies have determined the oxygen levels in the world’s oceans at the time these sediments accumulated in Avalon. Studies show that the oldest sediments on the Avalon Peninsula, which completely lack animal fossils, were deposited during a time when there was little or no free oxygen in the world’s oceans. Immediately after this ice age there is evidence for a huge increase in atmospheric oxygento at least 15 per cent of modern levels, and these sediments also contain evidence of the oldest large animal fossils.
The close connection between the first appearance of oxygenated conditions in the world’s oceans and the first appearance of large animal fossils confirms the importance of oxygen as a trigger for the early evolution of animals, the researchers say. They hypothesize that melting glaciers increased the amount of nutrients in the ocean and led to a proliferation of single-celled organisms that liberated oxygen through photosynthesis. This began an evolutionary radiation that led to complex communities of filter-feeding animals, then mobile bilateral animals, and ultimately to the Cambrian “explosion” of skeletal animals 542 million years ago.
In 2002 researchers found the world’s oldest complex life forms between layers of sandstone on the southeastern coast of Newfoundland. This pushed back the age of Earth’s earliest known complex life to more than 575 million years ago, soon after the melting of the massive “snowball” glaciers. New findings reported today shed light on why, after three billion years of mostly single-celled evolution, these large animals suddenly appeared in the fossil record.
A huge increase in oxygen following the Gaskiers Glaciation 580 million years ago corresponds with the first appearance of large animal fossils on the Avalon Peninsula in Newfoundland.
Now for the first time, geochemical studies have determined the oxygen levels in the world’s oceans at the time these sediments accumulated in Avalon. Studies show that the oldest sediments on the Avalon Peninsula, which completely lack animal fossils, were deposited during a time when there was little or no free oxygen in the world’s oceans. Immediately after this ice age there is evidence for a huge increase in atmospheric oxygento at least 15 per cent of modern levels, and these sediments also contain evidence of the oldest large animal fossils.
The close connection between the first appearance of oxygenated conditions in the world’s oceans and the first appearance of large animal fossils confirms the importance of oxygen as a trigger for the early evolution of animals, the researchers say. They hypothesize that melting glaciers increased the amount of nutrients in the ocean and led to a proliferation of single-celled organisms that liberated oxygen through photosynthesis. This began an evolutionary radiation that led to complex communities of filter-feeding animals, then mobile bilateral animals, and ultimately to the Cambrian “explosion” of skeletal animals 542 million years ago.
Wednesday, January 23, 2008
Monday, January 21, 2008
Bones From French Cave Show Neanderthals, Cro-Magnon Hunted Same Prey
Finding: A 50,000-year record of mammals consumed by early humans in southwestern France indicates there was no major difference in the prey hunted by Neanderthal and Cro-Magnon.
Research findings counter the idea proposed by some scientists that Cro-Magnon, who were physically similar to modern man, supplanted Neanderthals because they were more skilled hunters as a result of some evolutionary physical or mental advantage.
The new study suggests Cro-Magnon were not superior in getting food from the landscape. Archeoligists could detect no difference in diet, the animals they were hunting and the way they were hunting across this period of time, aside from those caused by climate change.
The takeover by Cro-Magnon does not seem to be related to hunting capability. There is no significant difference in large mammal use from Neanderthals to Cro-Magnon in this part of the world. The idea that Neanderthals were big, dumb brutes is hard for some people to drop. Cro-Magnon created the first cave art, but late Neanderthals made body ornaments, so the depth of cognitive difference between the two just is not clear.
Bears, Caves, and Cro-magnon
The study also resurrects a nearly 50-year-old theory first proposed by Finnish paleontologist Björn Kurtén that modern humans played a role in the extinction of giant cave bears in Europe. Cro-Magnon may have been the original "apartment hunters" and displaced the bears by competing with them for the same caves the animals used for winter den sites.
The cave has a rich, dated archaeological sequence that extends from about 65,000 to about 12,000 years ago, spanning the time when Neanderthals flourished and died off and when Cro-Magnon moved into the region. Neanderthals disappeared from southwestern France around 35,000 years ago, although they survived longer in southern Spain and central Europe.
The researchers were most interested in the transition from the Middle to Upper Paleolithic, or Middle to Late Stone Age.
Neanderthals occupied Grotte XVI as far back as 65,000 years ago, perhaps longer. Between 40,000 and 35,000 years ago, people began making stone tools in France, including at Grotte XVI, that were more like those later fashioned by Cro-Magnon. However, human remains found with these tools at several sites, were Neanderthal, not Cro-Magnon. Similar tools but no human remains from this time period were found in Grotte XVI and people assumed to be Cro-Magnon did not occupy the cave until about 30,000 years ago.
The researchers examined more than 7,200 bones and teeth from large hoofed mammals that had been recovered from the cave. The animals – ungulates such as reindeer, red deer, roe deer, horses and chamois were the most common prey – were the mainstay of humans in this part of the world, according to Grayson.
He and Delpech found a remarkable dietary similarity over time. Throughout the 50,000-year record, each bone and tooth assemblage, regardless of the time period or the size of the sample involved, contained eight or nine species of ungulates, indicating that Neanderthals and Cro-Magnon both hunted a wide variety of game.
The only difference the researchers found was in the relative abundance of species, particularly reindeer, uncovered at the various levels in Grotte XVI. At the oldest dated level in the cave, reindeer remains accounted for 26 percent of the total. Red deer were the most common prey at this time, accounting for nearly 34 percent of the bones and teeth. However, as summer temperatures began to drop in Southwestern France, the reindeer numbers increased and became the prey of choice. By around 30,000 years ago, when Cro-Magnon moved into the region, reindeer accounted for 52 percent of the bones and teeth. And by around 12,500 years ago, during the last ice age, reindeer remains accounted for 94 percent of bones and teeth found in Grotte XVI.
Grayson and Delpech also looked at the cut marks left on bones to analyze how humans were butchering their food. They found little difference except, surprisingly, at the uppermost level, which corresponds to the last ice age.
It is possible that because it was so cold, people were hard up for food. The bones were very heavily butchered, which might be a sign of food stress. However, if this had occurred earlier during Neanderthal times, people would have said this is a sure sign that Neanderthals did not have the fine hand-eye coordination to do fine butchering.
In examining the Grotte XVI record, the researchers also found a sharp drop in the number of cave bears from Neanderthal to Cro-Magnon times.
Cave bears and humans may have been competing for the same living space and this may have led to their extinction. He added that it is not clear if the decline and eventual extinction of the bears was driven by an increase in the number of humans or increased human residence times in caves, or both.
If we can understand the extinction of any animal from the past, such as the cave bear, it gives us a piece of evidence showing the importance of habitat to animals. The cave bear is one of the icons of the late Pleistocene Epoch, similar to the saber tooth cats and mammoths in North America. If further study supports the argument, we finally may be in a position to confirm a human role in the extinction of a large Pleistocene mammal on a Northern Hemisphere continent.
Research findings counter the idea proposed by some scientists that Cro-Magnon, who were physically similar to modern man, supplanted Neanderthals because they were more skilled hunters as a result of some evolutionary physical or mental advantage.
The new study suggests Cro-Magnon were not superior in getting food from the landscape. Archeoligists could detect no difference in diet, the animals they were hunting and the way they were hunting across this period of time, aside from those caused by climate change.
The takeover by Cro-Magnon does not seem to be related to hunting capability. There is no significant difference in large mammal use from Neanderthals to Cro-Magnon in this part of the world. The idea that Neanderthals were big, dumb brutes is hard for some people to drop. Cro-Magnon created the first cave art, but late Neanderthals made body ornaments, so the depth of cognitive difference between the two just is not clear.
Bears, Caves, and Cro-magnon
The study also resurrects a nearly 50-year-old theory first proposed by Finnish paleontologist Björn Kurtén that modern humans played a role in the extinction of giant cave bears in Europe. Cro-Magnon may have been the original "apartment hunters" and displaced the bears by competing with them for the same caves the animals used for winter den sites.
The cave has a rich, dated archaeological sequence that extends from about 65,000 to about 12,000 years ago, spanning the time when Neanderthals flourished and died off and when Cro-Magnon moved into the region. Neanderthals disappeared from southwestern France around 35,000 years ago, although they survived longer in southern Spain and central Europe.
The researchers were most interested in the transition from the Middle to Upper Paleolithic, or Middle to Late Stone Age.
Neanderthals occupied Grotte XVI as far back as 65,000 years ago, perhaps longer. Between 40,000 and 35,000 years ago, people began making stone tools in France, including at Grotte XVI, that were more like those later fashioned by Cro-Magnon. However, human remains found with these tools at several sites, were Neanderthal, not Cro-Magnon. Similar tools but no human remains from this time period were found in Grotte XVI and people assumed to be Cro-Magnon did not occupy the cave until about 30,000 years ago.
The researchers examined more than 7,200 bones and teeth from large hoofed mammals that had been recovered from the cave. The animals – ungulates such as reindeer, red deer, roe deer, horses and chamois were the most common prey – were the mainstay of humans in this part of the world, according to Grayson.
He and Delpech found a remarkable dietary similarity over time. Throughout the 50,000-year record, each bone and tooth assemblage, regardless of the time period or the size of the sample involved, contained eight or nine species of ungulates, indicating that Neanderthals and Cro-Magnon both hunted a wide variety of game.
The only difference the researchers found was in the relative abundance of species, particularly reindeer, uncovered at the various levels in Grotte XVI. At the oldest dated level in the cave, reindeer remains accounted for 26 percent of the total. Red deer were the most common prey at this time, accounting for nearly 34 percent of the bones and teeth. However, as summer temperatures began to drop in Southwestern France, the reindeer numbers increased and became the prey of choice. By around 30,000 years ago, when Cro-Magnon moved into the region, reindeer accounted for 52 percent of the bones and teeth. And by around 12,500 years ago, during the last ice age, reindeer remains accounted for 94 percent of bones and teeth found in Grotte XVI.
Grayson and Delpech also looked at the cut marks left on bones to analyze how humans were butchering their food. They found little difference except, surprisingly, at the uppermost level, which corresponds to the last ice age.
It is possible that because it was so cold, people were hard up for food. The bones were very heavily butchered, which might be a sign of food stress. However, if this had occurred earlier during Neanderthal times, people would have said this is a sure sign that Neanderthals did not have the fine hand-eye coordination to do fine butchering.
In examining the Grotte XVI record, the researchers also found a sharp drop in the number of cave bears from Neanderthal to Cro-Magnon times.
Cave bears and humans may have been competing for the same living space and this may have led to their extinction. He added that it is not clear if the decline and eventual extinction of the bears was driven by an increase in the number of humans or increased human residence times in caves, or both.
If we can understand the extinction of any animal from the past, such as the cave bear, it gives us a piece of evidence showing the importance of habitat to animals. The cave bear is one of the icons of the late Pleistocene Epoch, similar to the saber tooth cats and mammoths in North America. If further study supports the argument, we finally may be in a position to confirm a human role in the extinction of a large Pleistocene mammal on a Northern Hemisphere continent.
Monday, January 14, 2008
Biogeographic distributions
I. Three important principles:
How do these principles support descent with modification?
A. Environment cannot account for either similarity or dissimilarity, since similar environments can harbor entirely different species groups
B. "Affinity" (=similarity) of groups on the same continent (or sea) is closer than between continents (or seas)
C. Geographical barriers usually divide these different groups, and there is a correlation between degree of difference and rate of migration or ability to disperse across the barriers.
Disjoint locations for the same extant species: Is this evidence for creation? Note that Evolution proposes Single Centers for the origins of species, so Discontinuous Distributions need to be explained.
A. this means that a method of dispersal must be proposed.
1. Changes in climate or geology must have affected migration (i.e., by first allowing migration and then preventing migration)
2. Darwin designed tests of a priori assumptions
3. Although "accidental", dispersal is not really random (and thus allows very specific predictions about distributions in some cases)
B. Case study: Similarity of flora and fauna at mountain summits (is this evidence for independent creations or something else?)
1. Evidence is clear for recent glaciation
2. Migrations are easily visualized in the gradual advances and retreats of glaciers
3. Because mountain tops retain a colder climate, some cold-adapted, northern species would be retained on mountain tops (and thus isolated during glacial retreat)
4. Also explains why such mountain-top species are most closely related to species living due north
5. Isolation poses an opportunity for change, esp. if it means a change in its interspecific associations
6. Assumption of the scenario: Circumpolar distribution is uniform (presently the case)
7. Secondary assumption: Similar situation for subarctic species
C. Many difficulties remain to be solved, esp. the very distinct, but distantly related forms in the Southern hemisphere (e.g., marsupial versus placental mammals)
1. These species are too distinct to be explained by the recent glaciation
2. Darwin postulates an earlier glaciation, because he did not know about plate tectonics
3. With plate tectonics, many (if not all) of these kinds of problems are soluble.
Fresh water distributions
Because freshwater is isolated, you might expect restricted ranges, however, this is not the case just the opposite, they often have distributions even broader than terrestrials: How can this be explained? Three cases to consider:
A. Distribution of Fish
B. Distribution of Shells (molluscs)
C. Distribution of Plants (often very wide ranges)
In all cases, dispersal of freshwater organisms depends largely on animal (esp. bird) transport
Distribution of species on oceanic islands
Darwin considered this evidence as especially strong in its support of descent with modification
A. The total number of species on oceanic islands is small compared to the number on an equal area of continent
B. Proportion of endemic species is very high
C. Oceanic islands are missing entire Classes
D. Endemic species often possess characters that are adaptive elsewhere, but are useless characters on the island
E. Endemic species often show (new) adaptive traits not possessed by any of their relatives
F. Batrachians are universally absent (except one frog in New Zealand)
G. Terrestrial mammals are not found on any island >300 miles from mainland
H. But arial mammals are found on such islands, and many of these are endemic
I. Also a correlation between the depth of the sea separating islands inhabited by mammals and the degree of "affinity" (classification) between these species
J. "The most striking and important fact" (p. 397) is the affinity of these island species to those of the nearest mainland, without being actually the same species
K. Within an archipelago, species are more closely related to each other than to those on the mainland (but still distinct from each other)
L. The principle applies widely that island inhabitants are most closely related to the inhabitants of a region from which colonization is possible
M. According to this principle, it must be the case that at some former time, a single parental species covered both ranges (i.e., the migration event itself)N. Darwin draws a parallel between Time and Space in the "Laws of Life"
How do these principles support descent with modification?
A. Environment cannot account for either similarity or dissimilarity, since similar environments can harbor entirely different species groups
B. "Affinity" (=similarity) of groups on the same continent (or sea) is closer than between continents (or seas)
C. Geographical barriers usually divide these different groups, and there is a correlation between degree of difference and rate of migration or ability to disperse across the barriers.
Disjoint locations for the same extant species: Is this evidence for creation? Note that Evolution proposes Single Centers for the origins of species, so Discontinuous Distributions need to be explained.
A. this means that a method of dispersal must be proposed.
1. Changes in climate or geology must have affected migration (i.e., by first allowing migration and then preventing migration)
2. Darwin designed tests of a priori assumptions
3. Although "accidental", dispersal is not really random (and thus allows very specific predictions about distributions in some cases)
B. Case study: Similarity of flora and fauna at mountain summits (is this evidence for independent creations or something else?)
1. Evidence is clear for recent glaciation
2. Migrations are easily visualized in the gradual advances and retreats of glaciers
3. Because mountain tops retain a colder climate, some cold-adapted, northern species would be retained on mountain tops (and thus isolated during glacial retreat)
4. Also explains why such mountain-top species are most closely related to species living due north
5. Isolation poses an opportunity for change, esp. if it means a change in its interspecific associations
6. Assumption of the scenario: Circumpolar distribution is uniform (presently the case)
7. Secondary assumption: Similar situation for subarctic species
C. Many difficulties remain to be solved, esp. the very distinct, but distantly related forms in the Southern hemisphere (e.g., marsupial versus placental mammals)
1. These species are too distinct to be explained by the recent glaciation
2. Darwin postulates an earlier glaciation, because he did not know about plate tectonics
3. With plate tectonics, many (if not all) of these kinds of problems are soluble.
Fresh water distributions
Because freshwater is isolated, you might expect restricted ranges, however, this is not the case just the opposite, they often have distributions even broader than terrestrials: How can this be explained? Three cases to consider:
A. Distribution of Fish
B. Distribution of Shells (molluscs)
C. Distribution of Plants (often very wide ranges)
In all cases, dispersal of freshwater organisms depends largely on animal (esp. bird) transport
Distribution of species on oceanic islands
Darwin considered this evidence as especially strong in its support of descent with modification
A. The total number of species on oceanic islands is small compared to the number on an equal area of continent
B. Proportion of endemic species is very high
C. Oceanic islands are missing entire Classes
D. Endemic species often possess characters that are adaptive elsewhere, but are useless characters on the island
E. Endemic species often show (new) adaptive traits not possessed by any of their relatives
F. Batrachians are universally absent (except one frog in New Zealand)
G. Terrestrial mammals are not found on any island >300 miles from mainland
H. But arial mammals are found on such islands, and many of these are endemic
I. Also a correlation between the depth of the sea separating islands inhabited by mammals and the degree of "affinity" (classification) between these species
J. "The most striking and important fact" (p. 397) is the affinity of these island species to those of the nearest mainland, without being actually the same species
K. Within an archipelago, species are more closely related to each other than to those on the mainland (but still distinct from each other)
L. The principle applies widely that island inhabitants are most closely related to the inhabitants of a region from which colonization is possible
M. According to this principle, it must be the case that at some former time, a single parental species covered both ranges (i.e., the migration event itself)N. Darwin draws a parallel between Time and Space in the "Laws of Life"
Monday, January 7, 2008
Greenland: Oldest DNA Shows Warmer Planet
Greenland: Scientists studying the glaciers probed two kilometers and recovered the oldest plant DNA. Their studies also showed that the earth was much warmer hundreds of thousands of years ago than is generally believed.
Using the DNA of trees, plants and a variety of insects from underneath the southern Greenland glacier estimated to date from 500,000 to 900,000 years ago.
So what is the prevailing view that a forest of this kind could only have existed in Greenland as recently as 2.4 million years ago. This means that if the area supported these plants and insects, it was warmer than previously thought.
The DNA samples showed that the temperature may have reached 50 degrees Fahrenheit in the summer and 1 degree F in the winter.
Another finding showed that during the last period between ice ages, between 116,000-130,000 years ago, temperatures were on average 9 degrees F higher than now, so the glaciers on Greenland did not completely melt away.
Using the DNA of trees, plants and a variety of insects from underneath the southern Greenland glacier estimated to date from 500,000 to 900,000 years ago.
So what is the prevailing view that a forest of this kind could only have existed in Greenland as recently as 2.4 million years ago. This means that if the area supported these plants and insects, it was warmer than previously thought.
The DNA samples showed that the temperature may have reached 50 degrees Fahrenheit in the summer and 1 degree F in the winter.
Another finding showed that during the last period between ice ages, between 116,000-130,000 years ago, temperatures were on average 9 degrees F higher than now, so the glaciers on Greenland did not completely melt away.
Monday, December 24, 2007
How trees changed the world
Finding: A nearly completly preserved tree dating 385 million years ago from the Gilboa Forests was found. It came from the first forests on Earth.
The Gilboa tree dates from the middle of the Devonian period (416 to 359 million years ago), a time of explosive evolutionary action among land plants. During this period trees evolved from small, primitive forms that would have barely brushed your ankle into genuine trees up to 30 metres tall. And with the evolution of trees, they and all the other plants - hitherto confined to marshy environments - went on to conquer the surface of the planet.
The First Forests
These first forests changed the face of the Earth. Early land plants had already started leaking oxygen into the atmosphere, creating soils and providing food and shelter for animals, and the evolution of trees upped the pace of change. They weathered rocks, made soils deeper and
richer, created complex habitats and changed the climate beyond recognition. By the end of the Devonian, an ecologically modern world had appeared. Discoveries such as the Gilboa tree are bringing stunning new insights into how the foresting of the world came about.
Plants in the Ordovician Period
Plants first colonised land in the Ordovician period, around 465 million years ago (see Chart). By the early Devonian they had developed many of the features of modern plants, including a protective waxy cuticle, vascular plumbing for transporting water and nutrients, and pores called stomata to draw in carbon dioxide. But there were many differences from modern plants too. Seeds had yet to evolve - early land plants instead reproduced by way of spores. Wood, large leaves and deep roots were unknown. Few plants were taller than a few centimetres.
The Rhynie ecosystem
The best place to catch a glimpse of this primitive terrestrial forest is in the hills around the village of Rhynie in Aberdeenshire, UK. Here the finely crystallized quartz of the Rhynie chert preserves in extraordinary detail an entire ecosystem that was engulfed and petrified by silica-rich waters from a volcanic spring 410 million years ago. The fossil plants still stand upright, and even their cells remain visible. Tiny creatures such as insects, centipedes, mites, harvestmen and spider-like trigonotarbids are preserved in great detail. Some still cling to the stems on which they lived and died.
Originally, Rhynie wouldn't have been recognisable as a modern environment. Every plant would have been on a small scale - knee height and lower. However, by the late Devonian, plants are on a scale that humans are used to. You can walk around a woodland and identify a tree canopy layer, a shrub layer and a herbaceous layer. Now the whole environment looks more modern.
Prototaxites
The Rhynie landscape was not entirely devoid of large living things, however. Dotted here and there were featureless columns standing up to 6 metres high and a metre wide at the base. When first described in 1857, from fossils found in Quebec, they were identified as conifer trunks and named Prototaxites. However, studies into the structure of their "wood" soon revealed that they were not trees. Various alternatives were proposed, including giant algae, lichen and fungi, but the identity of Prototaxites remained uncertain.
Last year a research team University of Chicago decided to settle matters. They measured the ratio of different carbon isotopes in Prototaxites fossils to reveal whether they were making a living from photosynthesis or by eating rotting matter as fungi do today. The results clearly showed that Prototaxites was a fungus. It was both tougher and stronger
And there was more. The isotopes also revealed that some Prototaxites were probably living off microbial crusts composed of bacteria, algae and lichens. These crusts still exist today but are confined to places where vascular plants can't grow, such as deserts. What Prototaxites shows is that there were large patches of the early Devonian landscape with no vascular plants. This means that plants didn't conquer the land as quickly and completely as scientists once assumed.
The Rise of the Forests
With large patches of land still free of vascular plants, clearly an upgrade of their plumbing and support systems was needed for the terrestrial conquest to continue. This was achieved through "secondary growth", the evolution of tougher and stronger tissues to carry water and nutrients up longer stems. Once these were in place, plants were able to grow much bigger. It was these advances that allowed the trees of the Gilboa forest to reach their full height of 8 meters or more. The foresting of the Earth had begun.
The appearance of trees changed the rules of the game, with evolutionary scramble for height, for light to power photosynthesis, and for prime positions to disperse spores. Once it became possible to be a tree, then the race is on for size and dominance. If you look at modern ecosystems, the trees that are dominant hog the light space of the environment. The goal is to be at the top and collect the most light.
The Gilboa Forest
So what was the Gilboa forest like? Its trees, known as cladoxylopsids, looked a bit like tree ferns, although they are not related. Their trunks were long and slender, with a bulbous base and shallow roots. They did not have leaves, instead sporting a goblet-shaped crown of branches and thread-like branchlets. These were probably green to carry out photosynthesis. In other words it must have looked like a strange, giant bottle brush.
Gilboa, 385 million years ago, was a warm, wet flood plain 10 degrees south of the equator. Since the cladoxylopsids lacked leaves, the forest would have been airier and brighter than any modern forest. There was a diverse understorey that included club mosses and ferns, but the only animal inhabitants were arthropods, including insects, centipedes and mites. It would also have been wet underfoot: as with today's ferns and mosses, cladoxylopsid spores could only be fertilised on wet surfaces, so the trees were confined to flood plains.
World Wide Representation
Cladoxylopsids achieved worldwide success: fossils of their crowns (which until the Gilboa tree were thought to be complete plants) have been found in Europe, China and the Americas. However, in many respects they were primitive, and lurking in their shadows was a group of plants that would soon put them in the shade.
Other Plant Developments
These were the archaeopterids, relatives of the conifers. At the time of the Gilboa forest, archaeopterids were no bigger than shrubs, but their lineage soon made some key evolutionary advances, including wood, deep roots and large leaves. By 370 million years ago, a fully fledged tree, Archaeopteris, had emerged from the archaeopterid ranks.
With the trunk of a conifer and fern-like leaves, Archaeopteris reached 30 metres - as tall as a mature oak - and dominated late Devonian forests all over the world. Its wooden trunk permitted it to grow much taller than the cladoxylopsids. There is a stronger material around, per mass, than wood says a leading researcher in the chemical make-up of fossil plants. Wood also led to the formation of the first complex soils. Soil humus is, by and large, lignin, the polymer that makes wood tough.
The Decline of CO2 Levels and the Rise of Deep Roots
Archaeopteris was also the first plant to evolve deep roots. Roots eat away at rocks, burrowing into and dissolving them with acids in pursuit of nutrients. Over an immense period of time the weathered material gets washed into the oceans, where it combines with dissolved CO2 to form sediments that are eventually subducted into the Earth's interior by tectonic activity. This process removed huge amounts of CO2 from the oceans and atmosphere, with profound consequences for the climate. Between the beginning and end of the Devonian, levels of the gas plummeted by up to 95 per cent. Greenhouse conditions vanished, to be replaced by an ice age that at its peak 300 million years ago saw glaciers approaching the tropics.
Deep Roots and Large Leaves
But oddly it was the climatic upheaval brought about by roots that appears to have driven the next great innovation - large leaves. These first appeared 390 million years ago, but only became widespread with Archaeopteris 15 million years later. The stripping of CO2 from the Devonian atmosphere helped to remove an obstacle that had been inhibiting the evolution of large leaves.
Although large, flat leaves are very efficient at capturing sunlight for photosynthesis, they are difficult to keep cool. To prevent overheating, leaves need to release water vapour through their pore-like stomata - the plant equivalent of sweating. The problem is the number of stomata is regulated by a genetic switch that responds to CO2 levels in the atmosphere: the more CO2, the lower the stomatal density. If that genetic switch was already in place in the Devonian, high CO2 levels would have prevented plants from evolving large leaves. If large leaves had appeared then they would have cooked.
Only with falling levels of CO2, and improvements in roots and vascular systems to supply cooling water, could plants evolve the high stomatal densities that make large leaves viable. Studies on fossil leaves have so far supported this idea: earlier leaves were smaller and had far fewer pores than later ones, and only after CO2 levels fell did large leaves become abundant.
The Rise of Seeds
Archaeopteris had one more innovation to offer. It evolved a method of reproduction that partially freed trees from the flood plains that had confined the cladoxylopsids. Male and female cladoxylopsid spores were the same size, and fertilisation could only occur on wet ground where nutrients were readily available to nourish the embryo. In contrast, female Archaeopteris spores were larger than male ones and stored a food supply for the embryo. From this beginning, seeds evolved.
Seed plants - the grasses, flowers, shrubs and trees that are everywhere today - are thought to have descended from Archaeopteris and its relatives. With the evolution of seeds, plants could now spread to all sorts of places that had previously been out of bounds. Seeding freed plants from a reproductive necessity on water. Seeds allow trees to occupy and colonise drier environments.
Where Do Trees Colonise?
One of the most difficult places for trees to colonise was the uplands. In 2003, scientists discovered the oldest-known fossils of mountain plants, in Blanche Brook, a remote river in Newfoundland. Hundreds of giant trees lying in the a remote part of the river bed. The trees turned out to be 305 million years old, from the late Carboniferous. Known as cordaitaleans and standing up to 50 metres tall, they were seed plants related to conifers and looked a bit like monkey puzzle trees.
What about the Carboniferous Sporing vs Seeds?
Elsewhere in the Carboniferous, however, sporing plants still held sway. In the swampy lowland rainforests, Archaeopteris and the cladoxylopsids were overshadowed by giant club moss and horsetail trees that towered above the seed plants jostling for space below. In modern forests the opposite is true, with seed-bearing trees dominating the sporing ferns, mosses and horsetails of the understorey. It's like the world was turned upside down. Spores prevailed over seeds for the last time.
Organic Carbon and Coal
These late Carboniferous lowlands are noted for the sheer fecundity of their tree and plant fossils. Much of Europe, Asia and North America were near the equator and were blanketed by huge tracts of rainforest. Tectonic forces meant that the basins where the rainforests grew were slowly subsiding. This process, coupled with regular flooding, led to colossal amounts of organic carbon being buried. Much of the world's coal reserves formed in this 20-million-year period.
Then around 300 million years ago, a catastrophic earthquake caused one coal forest in what is now Illinois to slump below sea level, where it was rapidly buried. Low-oxygen conditions preserved a 1000-hectare expanse of this forest floor in near-pristine condition. The forest floor now forms the ceiling of the Riola and Vermilion Grove coal mines in Illinois.
The Ancient Rainforest
Scientists conducted the largest ever study of this ancient forest. The coal that had been mined out used to be the soil of the ancient rainforest, so as you walked around looking up you could see roots hanging down just above your head, and you could see giant fallen trees complete with their roots, trunk and crown.
You can see the roots of an ancient rainforest hanging down just above your head.
Spectacular 40-metre club mosses and shorter tree ferns monopolised the Illinois forest. There is really nothing today that looks anything like the giant club mosses. They probably grew much closer together than do trees in a modern rainforest because they don't have large canopies, so you don't have a lot of shadow cast by the trees. The forest would also have been greener than its modern counterpart, as the abundant club mosses had green scale-like leaf cushions all over their trunks and branches.
Swampworld and Tectonic Forces
Swampworld was not to last. As tectonic forces dragged the world's landmasses together to form the supercontinent Pangaea, the climate changed. Dryer, harsher conditions set in, and by the end of the Carboniferous the coal swamps had disappeared from most of the world. The mighty sporing trees could no longer find the water they needed to reproduce, and seed plants gained the upper hand. The reign of modern plants had truly begun.
The Gilboa tree dates from the middle of the Devonian period (416 to 359 million years ago), a time of explosive evolutionary action among land plants. During this period trees evolved from small, primitive forms that would have barely brushed your ankle into genuine trees up to 30 metres tall. And with the evolution of trees, they and all the other plants - hitherto confined to marshy environments - went on to conquer the surface of the planet.
The First Forests
These first forests changed the face of the Earth. Early land plants had already started leaking oxygen into the atmosphere, creating soils and providing food and shelter for animals, and the evolution of trees upped the pace of change. They weathered rocks, made soils deeper and
richer, created complex habitats and changed the climate beyond recognition. By the end of the Devonian, an ecologically modern world had appeared. Discoveries such as the Gilboa tree are bringing stunning new insights into how the foresting of the world came about.Plants in the Ordovician Period
Plants first colonised land in the Ordovician period, around 465 million years ago (see Chart). By the early Devonian they had developed many of the features of modern plants, including a protective waxy cuticle, vascular plumbing for transporting water and nutrients, and pores called stomata to draw in carbon dioxide. But there were many differences from modern plants too. Seeds had yet to evolve - early land plants instead reproduced by way of spores. Wood, large leaves and deep roots were unknown. Few plants were taller than a few centimetres.
The Rhynie ecosystem
The best place to catch a glimpse of this primitive terrestrial forest is in the hills around the village of Rhynie in Aberdeenshire, UK. Here the finely crystallized quartz of the Rhynie chert preserves in extraordinary detail an entire ecosystem that was engulfed and petrified by silica-rich waters from a volcanic spring 410 million years ago. The fossil plants still stand upright, and even their cells remain visible. Tiny creatures such as insects, centipedes, mites, harvestmen and spider-like trigonotarbids are preserved in great detail. Some still cling to the stems on which they lived and died.
Originally, Rhynie wouldn't have been recognisable as a modern environment. Every plant would have been on a small scale - knee height and lower. However, by the late Devonian, plants are on a scale that humans are used to. You can walk around a woodland and identify a tree canopy layer, a shrub layer and a herbaceous layer. Now the whole environment looks more modern.
Prototaxites
The Rhynie landscape was not entirely devoid of large living things, however. Dotted here and there were featureless columns standing up to 6 metres high and a metre wide at the base. When first described in 1857, from fossils found in Quebec, they were identified as conifer trunks and named Prototaxites. However, studies into the structure of their "wood" soon revealed that they were not trees. Various alternatives were proposed, including giant algae, lichen and fungi, but the identity of Prototaxites remained uncertain.
Last year a research team University of Chicago decided to settle matters. They measured the ratio of different carbon isotopes in Prototaxites fossils to reveal whether they were making a living from photosynthesis or by eating rotting matter as fungi do today. The results clearly showed that Prototaxites was a fungus. It was both tougher and stronger
And there was more. The isotopes also revealed that some Prototaxites were probably living off microbial crusts composed of bacteria, algae and lichens. These crusts still exist today but are confined to places where vascular plants can't grow, such as deserts. What Prototaxites shows is that there were large patches of the early Devonian landscape with no vascular plants. This means that plants didn't conquer the land as quickly and completely as scientists once assumed.
The Rise of the Forests
With large patches of land still free of vascular plants, clearly an upgrade of their plumbing and support systems was needed for the terrestrial conquest to continue. This was achieved through "secondary growth", the evolution of tougher and stronger tissues to carry water and nutrients up longer stems. Once these were in place, plants were able to grow much bigger. It was these advances that allowed the trees of the Gilboa forest to reach their full height of 8 meters or more. The foresting of the Earth had begun.
The appearance of trees changed the rules of the game, with evolutionary scramble for height, for light to power photosynthesis, and for prime positions to disperse spores. Once it became possible to be a tree, then the race is on for size and dominance. If you look at modern ecosystems, the trees that are dominant hog the light space of the environment. The goal is to be at the top and collect the most light.
The Gilboa Forest
So what was the Gilboa forest like? Its trees, known as cladoxylopsids, looked a bit like tree ferns, although they are not related. Their trunks were long and slender, with a bulbous base and shallow roots. They did not have leaves, instead sporting a goblet-shaped crown of branches and thread-like branchlets. These were probably green to carry out photosynthesis. In other words it must have looked like a strange, giant bottle brush.
Gilboa, 385 million years ago, was a warm, wet flood plain 10 degrees south of the equator. Since the cladoxylopsids lacked leaves, the forest would have been airier and brighter than any modern forest. There was a diverse understorey that included club mosses and ferns, but the only animal inhabitants were arthropods, including insects, centipedes and mites. It would also have been wet underfoot: as with today's ferns and mosses, cladoxylopsid spores could only be fertilised on wet surfaces, so the trees were confined to flood plains.
World Wide Representation
Cladoxylopsids achieved worldwide success: fossils of their crowns (which until the Gilboa tree were thought to be complete plants) have been found in Europe, China and the Americas. However, in many respects they were primitive, and lurking in their shadows was a group of plants that would soon put them in the shade.
Other Plant Developments
These were the archaeopterids, relatives of the conifers. At the time of the Gilboa forest, archaeopterids were no bigger than shrubs, but their lineage soon made some key evolutionary advances, including wood, deep roots and large leaves. By 370 million years ago, a fully fledged tree, Archaeopteris, had emerged from the archaeopterid ranks.
With the trunk of a conifer and fern-like leaves, Archaeopteris reached 30 metres - as tall as a mature oak - and dominated late Devonian forests all over the world. Its wooden trunk permitted it to grow much taller than the cladoxylopsids. There is a stronger material around, per mass, than wood says a leading researcher in the chemical make-up of fossil plants. Wood also led to the formation of the first complex soils. Soil humus is, by and large, lignin, the polymer that makes wood tough.
The Decline of CO2 Levels and the Rise of Deep Roots
Archaeopteris was also the first plant to evolve deep roots. Roots eat away at rocks, burrowing into and dissolving them with acids in pursuit of nutrients. Over an immense period of time the weathered material gets washed into the oceans, where it combines with dissolved CO2 to form sediments that are eventually subducted into the Earth's interior by tectonic activity. This process removed huge amounts of CO2 from the oceans and atmosphere, with profound consequences for the climate. Between the beginning and end of the Devonian, levels of the gas plummeted by up to 95 per cent. Greenhouse conditions vanished, to be replaced by an ice age that at its peak 300 million years ago saw glaciers approaching the tropics.
Deep Roots and Large Leaves
But oddly it was the climatic upheaval brought about by roots that appears to have driven the next great innovation - large leaves. These first appeared 390 million years ago, but only became widespread with Archaeopteris 15 million years later. The stripping of CO2 from the Devonian atmosphere helped to remove an obstacle that had been inhibiting the evolution of large leaves.
Although large, flat leaves are very efficient at capturing sunlight for photosynthesis, they are difficult to keep cool. To prevent overheating, leaves need to release water vapour through their pore-like stomata - the plant equivalent of sweating. The problem is the number of stomata is regulated by a genetic switch that responds to CO2 levels in the atmosphere: the more CO2, the lower the stomatal density. If that genetic switch was already in place in the Devonian, high CO2 levels would have prevented plants from evolving large leaves. If large leaves had appeared then they would have cooked.
Only with falling levels of CO2, and improvements in roots and vascular systems to supply cooling water, could plants evolve the high stomatal densities that make large leaves viable. Studies on fossil leaves have so far supported this idea: earlier leaves were smaller and had far fewer pores than later ones, and only after CO2 levels fell did large leaves become abundant.
The Rise of Seeds
Archaeopteris had one more innovation to offer. It evolved a method of reproduction that partially freed trees from the flood plains that had confined the cladoxylopsids. Male and female cladoxylopsid spores were the same size, and fertilisation could only occur on wet ground where nutrients were readily available to nourish the embryo. In contrast, female Archaeopteris spores were larger than male ones and stored a food supply for the embryo. From this beginning, seeds evolved.
Seed plants - the grasses, flowers, shrubs and trees that are everywhere today - are thought to have descended from Archaeopteris and its relatives. With the evolution of seeds, plants could now spread to all sorts of places that had previously been out of bounds. Seeding freed plants from a reproductive necessity on water. Seeds allow trees to occupy and colonise drier environments.
Where Do Trees Colonise?
One of the most difficult places for trees to colonise was the uplands. In 2003, scientists discovered the oldest-known fossils of mountain plants, in Blanche Brook, a remote river in Newfoundland. Hundreds of giant trees lying in the a remote part of the river bed. The trees turned out to be 305 million years old, from the late Carboniferous. Known as cordaitaleans and standing up to 50 metres tall, they were seed plants related to conifers and looked a bit like monkey puzzle trees.
What about the Carboniferous Sporing vs Seeds?
Elsewhere in the Carboniferous, however, sporing plants still held sway. In the swampy lowland rainforests, Archaeopteris and the cladoxylopsids were overshadowed by giant club moss and horsetail trees that towered above the seed plants jostling for space below. In modern forests the opposite is true, with seed-bearing trees dominating the sporing ferns, mosses and horsetails of the understorey. It's like the world was turned upside down. Spores prevailed over seeds for the last time.
Organic Carbon and Coal
These late Carboniferous lowlands are noted for the sheer fecundity of their tree and plant fossils. Much of Europe, Asia and North America were near the equator and were blanketed by huge tracts of rainforest. Tectonic forces meant that the basins where the rainforests grew were slowly subsiding. This process, coupled with regular flooding, led to colossal amounts of organic carbon being buried. Much of the world's coal reserves formed in this 20-million-year period.
Then around 300 million years ago, a catastrophic earthquake caused one coal forest in what is now Illinois to slump below sea level, where it was rapidly buried. Low-oxygen conditions preserved a 1000-hectare expanse of this forest floor in near-pristine condition. The forest floor now forms the ceiling of the Riola and Vermilion Grove coal mines in Illinois.
The Ancient Rainforest
Scientists conducted the largest ever study of this ancient forest. The coal that had been mined out used to be the soil of the ancient rainforest, so as you walked around looking up you could see roots hanging down just above your head, and you could see giant fallen trees complete with their roots, trunk and crown.
You can see the roots of an ancient rainforest hanging down just above your head.
Spectacular 40-metre club mosses and shorter tree ferns monopolised the Illinois forest. There is really nothing today that looks anything like the giant club mosses. They probably grew much closer together than do trees in a modern rainforest because they don't have large canopies, so you don't have a lot of shadow cast by the trees. The forest would also have been greener than its modern counterpart, as the abundant club mosses had green scale-like leaf cushions all over their trunks and branches.
Swampworld and Tectonic Forces
Swampworld was not to last. As tectonic forces dragged the world's landmasses together to form the supercontinent Pangaea, the climate changed. Dryer, harsher conditions set in, and by the end of the Carboniferous the coal swamps had disappeared from most of the world. The mighty sporing trees could no longer find the water they needed to reproduce, and seed plants gained the upper hand. The reign of modern plants had truly begun.
Subscribe to:
Posts (Atom)