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نسخه کامل مشاهده نسخه کامل : مقالات زمين شناسي به انگليسي ( ويژه )



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15-03-2007, 16:19
Geology of petroleum
Sedimentary rocks Petroleum may occur in any porous rock, but it is usually found in sedimentary rocks such as sandstone or limestone. Sedimentary rocks are grouped into three major classes: clastic, carbonate, and evaporitic.

Clastic rocks are those that are formed by the accumulation and cementation of sedimentary particles derived from weathered fragments of preexisting rocks. Weathering processes, such as freezing and thawing, rain, wind, and other similar events, break down the parent rock into small particles that can then be transported by wind and rain runoff. Streams carry the mud, sand, and gravel from the source area down to its final resting place, be that a stream channel, floodplain, lake, or ultimately the sea. There it accumulates, is buried and compacted by later-arriving sediments, and cemented to form sedimentary rocks. The mud compacts to shale or mudstone, the sands are cemented by silica or calcite to form sandstones, and the gravels become conglomerates. Sandstones, because of the inherent porosity between their grains, often become excellent reservoirs for oil or natural gas. In oil-field terminology, any potentially productive sandstone is called a "sand" (fig. 2a).

Figure 2a--A greatly magnified image of a sandstone as seen in a thin section of the rock under the microscope. The scale is equal to one millimeter. The rock sample was injected with blue-colored epoxy that is seen here filling pores which are interconnected (permeable). After plastic is injected and solidified, the rock sample is cut and polished on a glass slide to a thickness of 35 thousandths-of-an-inch. The "thin section" of the rock is thin enough to permit light to be transmitted through it as in this photomicrograph.

This particular sandstone contains grains of quartz (white), calcite, and feldspar (shades as brown). The grains originally came from other rocks that had been eroded. The sample is exceedingly porous and permeable. Thegrains are loosely packed and there is very little cement filling the space between the grains. The arrow indicates possible pathways for fluid movement.

large number of interconnected pores means oil will move easily through it
Carbonate rocks are limestones and dolomites. They usually form in warm seawater at shallow depths, ankle deep to about 20 ft (6 m), where various plants and animals thrive. The hard, usually calcareous parts of the organisms pile up on the seafloor over time, forming beds of lime particles. Algae, simple plants, are one of the greatest contributors of lime particles, but any shelled animal may contribute whole or fragmented shells to the pile. Reefs, banks of lime mud, and lime sand bars are commonly found preserved in rocks (figs. 2b and c).

Figure 2b--A thin-section photomicrograph of a Pennsylvanian limestone taken from a core sample of a producing zone in Victory field, haskell County, Kansas. This particular sample comes from an interval that is not a good reservoir rock. Circular grains composed of calcite (finely crystalline, reddish-stained areas in a grain) and dolomite (clear, coarse crystals) are completely cemented by medium crystalline calcite. No porosity is visible.

this rock, with very little pore space, is not a good reservoir

Figure 2c--A thin-section photomicrograph of a Pennsylvanian limestone. The scale bar equals one millimeter. These well-rounded carbinate grains consist of broken shells and other skeletal remains of marine organisms. The rounding is produced by coatings of dense, dark, finely crystalline calcite which formed rims around the particles as they were agitatated by current action in a shallow marine setting. The rounded particles are completely cemented together with finely crystalline calcium carbonate (calcite), and consequently no porosity is present.

calcite cement completely fills pores
Carbonate sediments are subject to many processes in becoming a rock. If lime mud is exposed to the air, it simply dries out and almost overnight becomes a natural "concrete," and lime sands become cemented by the evaporation of lime-rich seawater to form "beach rock." Rainwater, however, begins to destroy the rock and forms porosity in the process. If not exposed to the air, lime sediments continue to accumulate, perhaps to great thicknesses. Under these conditions, they compact under the weight of new sediments and eventually are cemented to form limestone. These rocks are rarely porous unless other processes become involved.

Limestone is composed of calcium carbonate (calcite or aragonite), thus the general rock term "carbonate" is used. Magnesium, a common element in seawater, can replace some of the calcium within the crystal structure of calcite. This often happens by various processes that are not fully understood; the resulting rock is known as "dolomite" (calcium-magnesium carbonate). The process of changing limestone to dolomite produces somewhat smaller crystals, so the resulting rock has tiny pores between the new crystals. This kind of porosity, much like that in sandstone, often contains oil and natural gas (fig. 2d).

Figure 2d--This thin-section photomicrograph came from a sample of a core taken 1 ft (.3 m) below the one shown in figure 2b. The scale bar equals one millimeter. This sample is representative of an excellent carbonate reservoir rock with pore space contributing nearly one-third of the total volume of the rock. In fact, this zone is one of the main reservoirs of Victory field. The carbonate grains artificially stained red on this thin section are poorly preserved remains of coated fossil fragments. Permeable porosity (indicated again by the blue epoxy) occurs within these particles as well as between them. The arrows trace possible avenues of migration for fluid such as oil and gas that now are found in this reservoir rock.

calcite that used to fill pores has been replaced and permeability has increased
Evaporites are formed by the direct precipitation of minerals by evaporation of seawater. Resulting rocks are ordinary salt (halite-sodium chloride), gypsum (calcium sulfate with some water), and various forms of potash salts. When gypsum is buried to considerable depths, the water is expelled from the crystals and "anhydrite" (meaning simply "without water"), a harder crystalline rock, results. Evaporites are not porous, although they are readily dissolved by water and are not source rocks for petroleum. However, they may be formed in highly stagnant water where black mud, rich in organic matter, may also be deposited, and so are commonly associated with good source rocks. Because they are impermeable, evaporates often form seals on other reservoir rocks. Evaporites of the Sumner Group form the upper seal of Chase Group carbonate reservoirs in the giant Hugoton gas area in southwestern Kansas.

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15-03-2007, 16:22
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ممنون

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15-03-2007, 16:44
Structure
Once formed, sedimentary rocks are subject to various kinds of deformation, such as folding and faulting. Three general types of folds are anticlines, synclines, and monoclines.
Folds
Anticlines are upfolds in the layered rocks. They are usually long, high wrinkles in the rocks that may extend for hundreds of feet, but normally they are miles or tens of miles long and may have numerous prominences. Anticlines are much like the "up-wrinkles" produced in a rug or sheet of paper when pushed or squeezed from side to side and are formed in much the same way as the Earth's crust was compressed or shortened by lateral forces. Circular upfolds in the rocks are called "domes." Anticlines are important types of "structural traps" in petroleum geology, as petroleum migrating up the dip along a flank of the fold is trapped at the crest. It can't rise any farther up the tilted strata and can't go back down the other flank, at least until the fold is full of oil and/or gas. A good example in Kansas is the El Dorado anticline that is a major producing oil field. The Central Kansas uplift is a large "antiform" with numerous smaller anticlines that collectively have produced in excess of 2.5 billion barrels of oil.

Synclines are the opposite of anticlines. A syncline is a downfold, usually occurring between two anticlines. Every upfold on our wrinkled rug or sheet of paper has one or two adjacent downfolds. Synclines, like their associated structures the anticlines, are elongate, perhaps extending for many miles. More or less circular depressions in the layered rocks are called "basins," but that term is usually reserved for very large depressions, tens or hundreds of miles wide, in the Earth’s crust. Such large basins are natural centers for thick accumulations of sedimentary rocks. Unlike anticlines, synclines only form structural traps for petroleum when the depressed strata occur above the water table in dry rocks and oil gathers in the bottom by gravity flow. Such synclinal oil fields are rare, although the first oil produced west of the Mississippi River was from a syncline at the Florence-Canyon City field in central Colorado (fig. 5).

Figure 5--Layered rocks of the Earth's crust are often folded when the crust is shortened by intense compressional forces. Upfolds are called "anticlines," downfolds are called "synclines," and broad downfolded area are known as "basins."

Faults
Faults are breaks, or fractures, in rocks along which one side has moved relative to the other side. There are many kinds of faults, some of which are important as structural traps for petroleum in Kansas. Faulting, for example, is important to entrapment and migration of oil at Salina-Lindsborg fields in Saline County. The most common type of fault is the "normal fault' (fig. 6a). In this case, rocks along one side of the break simply drop down relative to the other side. An example is the Humboldt fault zone, a series of normal faults which can be traced from Nebraska southwestward across the state of Kansas along the east side of the Nemaha ridge. This happens when the Earth's crust is stretched.

Figure 6a--Fractures in the Earth's crust along which movement has taken place are called "faults." Where one side of the fault is dropped down by gravity relative to the other side, it is called a "normal fault."

Another kind of fault occurs when one block of rock is faulted upward and over another. If the plane of the fault is steep, it is called a "reverse fault" (fig. 6b) and if it is low angle, it is called a "thrust fault" (fig. 6c). The fault at Salina-Lindsborg fields is a reverse fault, and the Humboldt fault zone includes some reverse faults. Reverse and thrust faults occur when the Earth's crust is compressed, or shortened. When this occurs, folds usually form first, only to break into thrust faults when the strength of the strata involved is exceeded by the compressional forces.

Figure 6b--Where one side of the fault is pushed up and over the opposite side along a steep fracture, it is called a "reverse fault."

Figure 6c--A "thrust fault" occurs where a sheet of rock is forced up and over the opposite side of the fault along a low-angle break. Rocks are sometimes displaced many miles along large thrust faults.

We are only now learning that the most important kind of faulting is when one block of the Earth's crust is forced to move laterally (horizontally) in relation to the other side. Such faults, known technically as "strike-slip faults," and rather colloquially as "wrench faults," form when lateral stresses (twisting in the horizontal plane) act on large expanses of the Earth (fig. 6d). Wrench faults usually form in broad bands, or swarms of many faults, that may be tens of miles wide and hundreds of miles long. Such extreme friction occurs that the rocks literally are shattered along a wide path and movement occurs along dozens or perhaps hundreds of individual faults and drag folds. The many faults that are active today in southern California, the San Andreas and related faults, constitute a wrench-fault zone. In that case, the western, or seaward, block is moving northward relative to the eastern, or continental side along hundreds of active faults.

Figure 6d--This block diagram of a wrench-fault zone shows that vertical movement is often very complex. Faults may appear to be normal or reverse along the fault zone, and fault reversals and scissoring are common; horizontal displacement is greater than these vertical complications.

eologists are now finding numerous wrench-fault zones, especially in rocks of younger Precambrian age, on every continent, and the midcontinent of North America is no exception. Structures associated with the Central Kansas uplift occur in patterns and trends which resemble those involved in wrench-fault zones. The Midcontinent Rift System that traverses from northeast to southwest across eastern Kansas is believed by some geologists to be an ancient, billion-year-old, wrench-fault zone.

Figure 6e--"Wrench faults" occur where one side of the fault moves slong several, often sinuous, faults, such as shown here along the Nemaha or Humboldt fault zone in eastern Kansas.

Basically, faulting of any kind makes structural traps for petroleum. Porous layers are commonly faulted against rocks with low porosity and permeability, stopping the updip migration of oil or natural gas; huge accumulations may result. The inherent complexities of wrench-fault zones may localize dozens or hundreds of oil or gas fields in large linear trends. Southern California is a well-known example; some geologists think that the Central Kansas uplift may be another.

Fractures in otherwise tight, nonporous rocks can themselves be open, providing "fracture porosity" that may contain petroleum. Thus a shale or dense limestone may be fractured and contain oil, forming another type of structural trap. Fractures commonly break through porous rocks and increase the permeability greatly by providing pathways that interconnect rock pores. Fracturing may be much more important in forming reservoirs in Kansas than we realize. Recent research on porosity and permeability development in shallow Pennsylvanian sandstones of southeastern Kansas and northeastern Oklahoma indicates a clear link between production and fracture patterns as mapped at the surface. Fracture porosity is also a component of the pore space in reservoirs in the Hugoton gas area. Ancient weathering along fractures has enhanced reservoir development in fields producing from the Arbuckle Group in the midcontinent.

An important characteristic of all structures, but of wrench-fault zones in particular, is that once a fold or fault begins to move, it is a zone of weakness for all remaining geologic time. Movement will recur each time properly oriented stresses are generated in the crust of the Earth for whatever reason. Consequently, structures originating in Precambrian basement rocks may have been rejuvenated repeatedly throughout geologic history. Each time there is renewed movement on a structure, be it ever so slight, overlying rocks are shuffled up or down, perhaps only by inches or a few feet. Every foot of topographic relief on the seafloor affects the nature of the sediments being deposited, especially in the case of carbonate sediments. Consequently, shoals may develop on the seafloor on and around high structures, and structural depressions become sedimentary basins. Either situation changes the environment of deposition to a degree.

As we have seen, different types of sediments eventually produce different porosity/permeability relationships in the rocks. If the rock type varies due to water depth that is controlled by structural movement during deposition, local variations in porosity/permeability will result. Thus a definite relationship exists between geologic structure and the kind of sedimentary rock that is produced, and stratigraphic traps result.

Petroleum reservoirs produced by structural growth during deposition of sediments are common in Kansas. The myriad oil/gas reservoirs in Pennsylvanian rocks of the Central Kansas uplift are examples, and more are being discovered by drilling every day. A prominent anticline, formed over deep-seated faulting in Haskell County, exhibits recurrent growth which helped develop a series of major oil and gas fields along this structure. The Cahoj field in Rawlins County in northwest Kansas was a topographic high during deposition of the Lansing-Kansas City reservoirs leading, in part, to the stacking of 11 reservoir units in that field. It is still high today. McClain field in Nemaha County produces from Simpson and Viola reservoirs. Both were influenced by ancient topography similar to present-day structure. Other Viola fields along the Pratt anticline in south-central Kansas exhibit early structural growth of this anticline which extends southward from the Central Kansas uplift.
Unconformities
Whenever the sea withdraws and the landscape is exposed to the elements, erosional processes take command. Physical weathering, such as rainfall, the resulting runoff as streams, wind action, and perhaps glacial scouring, work to lower and level the lands. Chemical processes form soils and dissolve soluble rocks such as limestones and evaporates. Structurally formed topography can be beveled to a near plain, exposing the eroded edges of formations that may have been tilted in the process. When the sea returns and new sediments are deposited on the old eroded land surface, the surface of contact is called an "unconformity" (fig. 7). If the old rocks have been tilted and beveled before burial by near-horizontal beds, the surface is called an "angular unconformity."

Figure 7--Uncomformity is a surface between rock layers that shows the effects of a period of erosion or nondeposition. In this case, the rocks below the wavy line (uncomformity) were deposited, folded to form an anticline, and then eroded to a plain before the rocks above the unconformity were deposited. Petroleum migrating along any permeable bed may be trapped when it rises to the eroded surface

The presence of an unconformity in the layered sequence of rocks indicates that some increment of time is missing in the rock record. It is estimated that the sedimentary rocks deposited in Kansas represent only a small part of geologic time. The remaining time is incorporated in the unconformities. These gaps in the record are at least as important as the rocks and markedly affect their distribution.

Oil and gas migrating upward along inclined rock layers may be trapped at an unconformity if the beds overlying the eroded surface are impermeable. Oil and gas may also have migrated along the unconformity. The major uplifts of Kansas, and some smaller folds and faults, have been elevated, and the resulting tilted strata beveled by erosion at different times during the geologic past. Excellent unconformity traps have resulted, notably along the flanks of the Central Kansas and Nemaha uplifts. Mississippian limestones along the western flank of the Central Kansas uplift contain vast amounts of petroleum beneath the Pennsylvanian/Mississippian unconformity.

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20-03-2007, 06:24
Tree of Life Turns Out to Have Complex Roots
By NICHOLAS WADE

From Yellowstone Park to the ocean's abysses, researchers are in hot pursuit of the universal ancestor. Not the sort that is painted in oils and hung proudly in the hallway, but a single-celled creature with few distinctive features save a fondness for living in near-boiling water.

Though the universal ancestor probably lived more than 3.5 billion years ago and was too small to be seen, it was far from contemptible. From this Abraham of microbes sprang the three great kingdoms of evolution, the bacteria, the archaea and the eukarya. All the world's visible forms of life are slender shoots at the tip of the eukaryan branch.

Biologists have long aspired to paint a genetic portrait of the ancestor by running the tree of evolution backward, going from its leaves -- the living creatures of today -- down to the point where all its branches coalesce in a single trunk. Defining the organism that existed at this point, and when and where it lived, might help toward one of biology's major goals, understanding the origin of terrestrial life.

The longstanding road map for finding the universal ancestor, however, turns out in the light of new data to have given misleading directions, and the road map's chief author, Dr. Carl Woese of the University of Illinois, is proposing a new theory about the earliest life forms.

Working back to the ancestor, an exercise based on the sequence of DNA letters in genes, resembles the way that linguists reconstruct the words of vanished mother-tongues from their living descendant languages.

Genes that perform the same role in human cells and in bacterial cells, say, may have a recognizably similar spelling of their DNA letters, reflecting the genes' descent from a common ancestor. In one such gene the human-bacterium similarity is as high as 45 percent.

Hope of reconstructing the ancestor from its inferred genes received new impetus three years ago when the first full DNA, or genome, of a bacterium was decoded. Since then, the genomes of a dozen microbes have been sequenced, including at least one from each of the three main branches of the evolutionary tree.

The three kinds of genome offered a broad basis for triangulating back to the ancestral genome. But the emerging picture is far more complicated than had been expected, and the ancestor's features remain ill-defined though not wholly elusive. "Five years ago we were very confident and arrogant in our ignorance," said Dr. Eugene Koonin of the National Center for Biotechnology Information. "Now we are starting to see the true complexity of life."

Despite the quagmire in which their present efforts have landed them, biologists have not in any way despaired of confirming the conventional thesis, that life evolved on earth from natural chemical processes. But a ferment of rethinking and regrouping is under way.

Until now, searchers in the universal-ancestor treasure hunt have followed a hallowed chart known as the ribosomal RNA phylogenetic tree. This is a family tree drawn up by Woese and based on a gene used by all living cells to specify ribosomal RNA, or ribonucleic acid, a component of the machinery that translates genetic information into working parts.

It was this tree that led Woese to recognize the tripartite division of living things and to realize that one of the three kingdoms belonged to the archaea, previously assumed to be a weird sort of bacteria.

Many of the deepest branches in Woese's tree, those that join nearest to the three-way junction of the kingdoms, turned out to belong to organisms that live at high temperatures, as in the fuming springs in Yellowstone Park or the volcanic vents that gash the ocean floor. That clue fit well with new ideas holding that life originated at volcanolike temperatures.

With the new ability to decode the full DNA of a microbe, it is these high-temperature microbes that biologists have chosen for some of their first targets. Aquifex aeolicus, a denizen of Yellowstone Park that lives at 5 degrees below the boiling point of water, is the deepest branching of all known bacteria.

In the light of evidence suggesting that the oldest region of the ribosomal RNA tree lies on the branch leading into the bacterial kingdom, Aquifex provided grounds for the claim that it was the nearest living cousin of the universal ancestor.

But the sequence of the Aquifex genome, reported last month in the journal Nature, has yielded only disappointments. For one thing, the microbe appears to have only one gene, called a reverse gyrase, that is not found in organisms that live at ordinary temperatures.

That suggests it may be quite easy for microbes to switch between high and normal temperatures, said Dr. Ronald Swanson, a member of the Aquifex team who works at Diversa Corp. of San Diego.

A second blow is that with the full genome sequence in hand, for Aquifex and a dozen other microbes, biologists can draw up family trees based on other genes besides the ribosomal RNA gene that provided the original map. And the trees based on other genes show different maps that do not agree with the ribosomal RNA map. "Each picture is different, so there is tremendous confusion," Woese said.

A basic source of the confusion is that in the course of evolution whole suites of genes have apparently been transferred sideways among the major branches. Among animals, genes are passed vertically from parent to child but single-celled creatures tend to engulf each other and occasionally amalgamate into a corporate genetic entity.

It has long been argued that mitochondria, the tiny organelles that handle the energy metabolism of eukaryotic cells, were once free-living bacteria that were enslaved by an early eukaryote. Mitochondria still possess their own bacteriumlike DNA but many of their genes have emigrated into the eukaryotic cell's own DNA in the nucleus.

Horizontal transfer of genes between kingdoms would severely tangle up the lines in family trees. "What impresses me is that the pattern of genes we see among organisms is not reduced to total chaos," said another member of the Aquifex team, Gary Olsen of the University of Illinois.

Presumably because of sideways gene traffic in the distant past, both archaea and eukarya seem to rely on bacterial-type genes to manage much of their general chemical metabolism. (The eukarya, thought to be descended from the archaea, rely on archaean-type genes to manage their DNA and to translate its genetic information into protein products.)

"It's possible that bacterial genes have swept all over the world and replaced everything else that existed, so some of the features of the last common ancestor may have been erased from the face of the planet," Koonin said.

But no one is abandoning the search for the ancestor. "My biggest fear is that evolution would be indecipherable because of all the random changes that took place," said Craig Venter of the Institute for Genomic Research in Rockville, Md. "The good news is that that is clearly not the case. I think it will be completely decipherable but because of horizontal transfer the tree may look more like a neural network," he said, referring to the criss-cross pattern of a neural computing circuit.

Venter, who pioneered the sequencing of microbial genomes, estimated that 50 to 100 more genomes needed to be sequenced to help triangulate back to the last common ancestor.

Evolutionary biologists are working on several approaches for seeing beyond the confusion caused by lateral transfer. Computational biologists like Koonin believe that it is already possible to identify 100 or so genes that the common ancestor must have possessed -- mostly ones that manage DNA and its translation into proteins -- and that others can be added with varying degrees of certainty.

Most biologists still favor the standard view that the universal ancestor, already a quite sophisticated organism that had come a long way since the origin of life, first branched into the bacteria and the archaea.

Later the eukarya branched off from the archaea, but accepted many genes from the bacteria. Koonin describes the eukaryotic cell as a "palimpsest of fusions and gene exchanges," referring to a manuscript that has been written over with new text.

But some important eukaryotic genes have no obvious predecessors in either the archaean or the bacterial lines. The family of genes that make the stiff framework of eukaryotic cells, known as the cytoskeleton, seems to appear out of nowhere.

"The absence of sequences closely related to the slowly changing proteins of the eukaryotic cytoskeleton remains unsettling," Dr. Russell Doolittle of the University of California, San Diego, wrote in the March 26 issue of Nature.

Another evolutionary biologist, Dr. Ford Doolittle of Dalhousie University in Halifax, Nova Scotia, has an explanation, though one that he concedes does not yet enjoy the company of evidence. He argues there might have been many lost branches of the tree of life before the universal ancestor. One of these branches, a fourth kingdom of life, might have contributed the cytoskeleton genes to the eukarya before falling into extinction.

A new and far-reaching theory about the universal ancestor has been developed by Woese. Though he declined to discuss it, because his article is due to be published in the Proceedings of the National Academy of Sciences, colleagues said the theory envisages that all three kingdoms emerged independently from a common pool of genes.

The pool was formed by a community of cells that frequently exchanged genes among themselves by lateral transfer. The price of membership in the community was to use the same genetic code, according to Woese's theory, which is how the code came to be almost universal.

The community of proto-genomes quickly shared innovations among themselves, in Woese's new view, and the system evolved by producing more complicated proteins, the working parts of the cell. The genetic code was at first translated rather inaccurately, so the proteins it produced were short and limited in capability. But the code became more accurate, and the proteins more complex, driven by the advantage that more capable proteins conferred.

At a certain stage of complexity, design decisions may have limited cells' ability to exchange genes, and the ancestral pool would have split into the three kingdoms seen today, the new theory suggests.

It is possible, of course, that evolution's early traces have become too faint to decipher. And at the back of researchers' minds is another worry, one that makes them throw up their hands since it cannot be addressed scientifically: that life may have arrived on earth from elsewhere.

Life seems to have popped up on earth with surprising rapidity. The planet is generally thought to have become habitable only some 3.85 billion years ago, after the oceans stopped boiling off from titanic asteroid impacts. Yet by 3.5 billion years ago, according to the earliest fossil records, living cells were flourishing, and there are indirect signs of life even earlier, in rocks that are 3.8 billion years old.

"There's the gee-whiz point of view, how can life possibly have evolved in 300 million years, which I think is still a problem," said Doolittle of Halifax. But life arriving from outer space is a hypothesis, he said, that "leaves you stunned -- there is nothing more you can say after that."

This narrowing window of time may be less embarrassing than it seems. Biologists are warming to the view that the emergence of life from chemical precursors is a quite probable event which does not require billions of years to get under way.

"You put a selective hammer on it and it happens fast," said Norman Pace, an evolutionary biologist at the University of California, Berkeley, referring to the force of natural selection "It's shockingly fast, maybe just tens of millions of years."

Still, many more years of evolution presumably passed before the universal ancestor, a quite sophisticated genetic system, attained its final form.

If the ancestor was a pool of organisms as Woese suggests, and not a definable species, it may be even harder to capture its likeness. But knowledge about this distant era at the dawn of life is moving so fast that few biologists are troubled by setbacks like the Aquifex dead end or the discordant family trees. "I'm unwilling to say we'll never know about anything, because we have come so far in the last two decades," Pace said.

Some family-tree problems, after all, have exact solutions. For example, Doolittle of Halifax wrote recently in commenting on an article by Doolittle of San Diego that they had discovered the reason for their common name: They shared a common ancestor eight generations back.
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20-03-2007, 06:30
Molecular "Fossils" Of Early Life

Yale Scientists Recreate Molecular "Fossils," Now Extinct, That May Have Existed At The Beginning Of Life

Discovery Narrows Search For Precursor Of All Life Forms

New Haven, Conn. -- Yale scientists report they have synthesized molecules like those that probably gave rise to the earliest life forms on Earth nearly 4 billion years ago, thus creating a biochemist's version of "Jurassic Park" populated by exotic molecular "fossils" that have long since become extinct.

In the May 26 issue of the Proceedings of the National Academy of Sciences, the Yale biologists report the creation of one of these "fossils," an unusual hybrid molecule made up of a scaffold from deoxyribonucleic acid (DNA) with chemical "scissors" attached to it.

Ronald R. Breaker, who created the first DNA enzymes in 1994 with colleagues at The Scripps Research Institute, said he "looted the tool box of proteins" to get the amino acid "scissors," which destroy messenger ribonucleic acid (RNA) in humans and many other organisms. The feat was accomplished using a technique known as test-tube evolution.

Breaker's tailor-made enzyme is the first known nucleic acid enzyme that uses an amino acid to trigger chemical activity, and it brings scientists a step closer to finding the precursor of all life -- a single molecule containing both genetic code and an enzyme capable of triggering self-replication.

"If we can raid a protein's tool box to take one of its favored chemical groups -- in this case, a key amino acid called histidine found in a protein called RNase A -- then we should be able to raid the entire tool box and make use of anything we find there to make highly sophisticated DNA or RNA enzymes," said Breaker, who collaborated with Yale postdoctoral associate Adam Roth.

Which Came First -- DNA, RNA Or Proteins?

The discovery provides important clues to the chicken-or-egg dilemma of which came first -- DNA, RNA or proteins. Most scientists agree life as we know it cannot exist without DNA as the storehouse of genetic code, RNA as the genetic messenger, and proteins to carry out the chemistry of reproduction. Can any one of these three key molecules have existed as the precursor of the other two, serving as both chicken and egg?

Evidence is mounting that "it was an RNA World at the dawn of life as the Earth began to cool," said Breaker, who added that he and his colleagues can create dual-purpose genetic enzymes in the laboratory out of either RNA or DNA. "These genetic enzymes have the chemical sophistication, the full catalytic ability, to do many of the fundamental reactions we see in biology today. I am confident one will be created soon that can replicate itself."

He added that the new DNA enzyme he crafted destroys RNA with impressive efficiency at a rate 10 million times faster than it would decay naturally, although the protein the enzyme mimics acts much faster still.

No naturally occurring DNA enzymes have been found to date, but such a discovery would not surprise Breaker. The discovery nearly two decades ago of naturally occurring RNA enzymes, or ribozymes, earned Yale biochemist Sidney Altman and University of Colorado researcher Thomas Cech the 1989 Nobel Prize in Chemistry. In separate experiments, Altman and Cech exploded the myth that RNA is merely a passive carrier of genetic code incapable of triggering cell activity.

Referring to the dozen or more DNA and RNA enzymes created in his laboratory in recent months, Breaker said, "We believe these are like ancient molecular 'fossils' that might have been found stomping around the planet -- or more likely floating in the seas -- during the Archean Era between 3.8 and 4 billion years ago."

RNA Identified As Strongest Candidate For Precursor To All Life

While the Yale biologists created the versatile protein mimic from DNA, Breaker theorizes that a similar enzyme could be created with RNA, which many scientists believe is the strongest candidate for being the precursor of all other life forms. In addition to RNA's dual function as genetic molecule and as enzyme, RNA serves important roles in all living systems as the carrier of genetic instructions from DNA and as the orchestrator of all protein synthesis.

"This is exactly what you would expect if RNA invented these processes during the 'RNA World,'" Breaker said. "Because DNA is about a million times more stable than RNA, DNA most likely evolved later as a safe storehouse for the genetic code first found in RNA. Similarly, proteins probably evolved that were more efficient chemical catalysts, eventually driving most RNA enzymes extinct and relegating RNA to a more limited role."

The discovery that nucleic acids can raid the tool box of proteins means "the RNA World could have been a very sophisticated place," Breaker said. "The earliest RNA could have had access to all of these chemical helpers now used by proteins. Instead of working from a very primitive palette, varieties of RNA could have evolved that had a very rich chemical capability early on."

Tailoring Nucleic Enzymes To Fight Disease

Besides elucidating how life might have evolved, DNA and RNA enzymes show great promise as powerful medications. In fact, some RNA enzymes already have been developed to function as precision scissors that can snip out flawed gene segments and splice in corrected versions -- a method that has potential for treating diseases ranging from cystic fibrosis to muscular dystrophy and sickle cell anemia.

Because DNA lends itself well to test-tube evolution techniques, it can be synthesized readily in the laboratory, and different strains of enzymes can be genetically engineered for specific purposes, Professor Breaker said. For example, he and his colleagues have created self-cleaving DNA enzymes that can fold into chemically active molecules and cut themselves or other DNAs into segments. The next step is to genetically engineer a DNA enzyme that can shred the genetic code of a harmful organism like the HIV virus, rendering it harmless.

Specific DNA enzymes also could be tailor-made to break down only in the presence of target molecules, making them effective as biosensors for detecting toxic chemicals in the environment or for medical diagnostics. Working in collaboration with a Jerusalem-based firm called IntelliGene Ltd., Breaker plans to create biosensors for detecting biological or chemical warfare agents with funding from the Defense Advanced Research Projects Agency (DARPA).

"Test-Tube Evolution" Mimics Nature

Breaker sets up a system of natural selection through test-tube evolution to produce DNA sequences with the characteristics he desires. Typically, Breaker and his colleagues begin crafting an enzyme by synthesizing more than 10 trillion random DNA sequences using a computerized DNA synthesizer. Then they wash a grid containing the sequences with various compounds, in this case histidine. Rare DNA molecules that by chance fold into enzymes will break themselves free from the grid.

By cloning the DNA sequences that are washed away by the amino acid and then repeating the process several times, the Yale biochemists isolate desired enzymes. "Our latest findings not only improve our understanding about the origins of life, they also expand our skills in molecular evolution," he said. "While we may not be able to resurrect fossilized creatures like they did in 'Jurassic Park,' we very well may be able to recreate many of the ancient enzymes that were needed at the very beginning of life nearly 4 billion years ago."

Funding for this research was from the Arnold and Mabel Beckman Foundation Young Investigator Award.

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Note to Editors: Ronald R. Breaker, (203) 432-9389, is a member of the American Association for the Advancement of Science and the American Chemical Society. He received his Ph.D. from Purdue University in 1992 and completed postdoctoral studies at The Scripps Research Institute in La Jolla, Calif., before joining the Yale faculty in 1995.

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20-03-2007, 06:34
Introduction

Humans are a young species, in geological terms. The average "lifespan" of a mammal species, measured by its duration in the fossil record, is around 10 million years. While hominids have followed a separate evolutionary path since their divergence from the ape lineage, around 7 million years ago, our own species (Homo sapiens) is much younger. Fossils classified as archaic H. sapiens appear about 400,000 years ago, and the earliest known modern humans date back only 170,000 years.

Our knowledge of human evolution is changing rapidly, as new fossils are discovered and described every year. Thirty years ago, it was generally accepted that humans and the great apes last shared a common ancestor perhaps 16-20 million years ago, and that the separate human branch was occupied by only a few species, each evolving from the one before. Now we know, through a combination of new fossil finds and molecular biology, that humans and chimpanzees diverged as little as 7 million years ago, and that our own lineage is "bushy", with many different species in existence at the same time.

Our view of our evolutionary past has changed as social attitudes have changed. Darwin was remarkably prescient when he wrote, in 1871 "The Descent of Man", that humans had evolved in Africa and were closely related to the great apes (gorilla, chimpanzee, and orang-utan). But at that time this view was anathema to many, since the majority of people still accepted the concept of special creation.

This is why the first fossil hominid material to be discovered, that of Neandertal Man, attracted even more controversy than the later discoveries of Australopithecus africanus and Homo erectus. Rather than accept the fossil as the remains of a human ancestor, the distinguished German scientist R. Virchow described it as the skeleton of a diseased Cossack cavalryman. And even once the antiquity of the remains was established, many scientists refused to accept that Neandertals could be closely related to modern humans, depicting them instead as brutish and apelike. This interpretation reflected the prevailing prejudices about human ancestry, and was supported by misinterpretation of the remains of the "Old Man of La Chapelle", whose skeleton was warped by arthritis.

Even when the idea that apes and humans shared a common ancestor became more widely accepted, the concept of an African origin was not. The scientist Ernst Haeckel, for example, was convinced that humanity's nearest common ancestor was the orang-utan, and that humans evolved in Asia. Though wrong in this, he was a persuasive writer and many people came to accept his view.

This is why Eugene Dubois sought the "missing link" between humans and apes in Indonesia (then the Dutch East Indies). However, he met with considerable disbelief - and some ridicule - when he named his Solo River fossils Pithecanthropus (now Homo) erectus and described them as belonging to a human ancestor. This rejection reflected the prevailing view that our large brain had evolved while the skeleton was still ape-like, and Dubois' suggestion that the reverse was true was sidelined.

The "large brain first" view received further support when the Piltdown fossils were presented to the world. While we now know that they are fraudulent, at the time (1911) they seemed to demonstrate quite clearly that early humans had a modern cranium atop an ape-like body. And since the Piltdown remains were found in England, they conveniently supported the prevailing idea that modern humans had evolved in Europe, rather than in Africa.

Consequently, when in 1924 Raymond Dart recognised the position of the Taung baby (Australopithecus africanus) on the human family tree, his ideas initially faced considerable opposition. Not until more australopithecine fossils were discovered did his recognition of A. australis as a hominid gain credence. However, it is now accepted that the ancestors of modern humans evolved in Africa and remained there until perhaps 1.5 million years ago, when Homo erectus populations left Africa and moved rapidly across Europe and Asia.

This diaspora was the reverse of a movement that occurred in the late Miocene, when the ancestors of the African apes migrated from Eurasia into Africa. Here they underwent another adaptive radiation, culminating in the divergence of ancestral chimp and hominid populations from their last common ancestor, 7 million years ago.


Miocene Apes

Apes evolved in Africa at least 20 million years ago, when the continent was a separate land mass. The best known of these early apes was Proconsul. Proconsul was recognisably an ape, but retained some monkey-like characteristics of the backbone, pelvis, and forelimbs that suggest it was quadrupedal, rather than a brachiator

Lowered sea levels 17 - 16.5 million years ago provided a land bridge between Africa and Eurasia, and some of these early apes used it to enter Eurasia, along with elephants, pigs and antelopes, and rodents. By this stage the apes had developed a thick coating of enamel on their teeth, which enabled them to eat the harder foods (such as nuts and tough-coated seeds) that weren't available to Proconsul. This evolutionary innovation was significant, as within 1.5 million years of apes moving into Eurasia they had diversified into at least eight different forms.

By 13 million years ago apes were found throughout Eurasia, including the lineages of Dryopithecus (in Europe) and Sivapithecus (in Asia). Both had very similar anatomy to modern great apes. These two lineages survived the major climate changes that marked the end of the Miocene, while the many other Eurasian ape species became extinct. They survived by moving into Southeast Asia (Sivapithecus) and back into Africa (Dryopithecus). The living great apes are descended from these two lineages. Phylogenetic analyses indicate that Sivapithecus is the likely ancestor of the orang-utan, while Dryopithecus is probably the forebear of African apes and humans.


The Earliest Hominids

Evidence from molecular biology strongly suggests that humans and chimpanzees last shared a common ancestor no more than 5-8 million years ago, and in recent years researchers have focused on finding fossils close to this divergence. The descriptions of Orrorin tugenensis (in 2001) and Sahelanthropus tchadensis (in 2002) have added to our knowledge of this period in our history. In addition, publication of the chimpanzee genome has allowed scientists to compare chimp and human genetic sequences, and to use the differences between them to estimate the date of divergence of the two species. The result suggests humans and chimps diverged "no more than 6.3 million years ago and perhaps even more recently than 5.4 million years ago" (Pennisi 2006). Interestingly, the data also raise the possibility that the two new species may have hybridised for some time after their initial separation (Patterson et al. 2006).

Orrorin tugenensis

Orrorin tugenensis, from Kenya, is dated at 6 million years old. Its remains are fragmentary, consisting of some limb bones, partial jaw material, and a few teeth. Its discoverers place it in the hominid family tree, and describe it as bipedal. This suggests that bipedalism in hominids evolved very early indeed. Not all researchers agree that Orrorin is a hominid, on the basis that its canine teeth are extremely ape-like. However, its lower limb bones are those of a bipedal organism. Recent examination (Galik et al. 2004) of the neck of the femur shows that the bone is thickest on the underside of the neck, as seen in humans. In chimpanzees the neck is of uniform thickness.

Sahelanthropus tchadensis

Sahelanthropus tchadensis was described in 2002 from an extremely well preserved cranium, a partial mandible and some teeth, dated at 6-7 million years old. This is very close indeed to the likely human-chimpanzee split. Michel Brunet's team describe Sahelanthropus as a hominid, for reasons including the shape and angle of the face and skull, and its dentition. Not all scientists agree with this, saying that the position of the foramen magnum suggests it was not a true biped, and that features of its dentition and skull are reminiscent of chimpanzees. However, a recent reconstruction of the cranium (Zollikofer et al., 2005) places the foramen magnum well under the skull, suggesting Sahelanthropus was indeed bipedal. Zollikofer et al. also suggest that comparisons of the reconstructed cranium with those of both modern apes and other fossil hominins demonstrate that it belongs on the hominin lineage, although other researchers disagree with this interpretation.

If Sahelanthropus is a hominid, it broadens the geographic range from which hominids are known: Lake Chad is well outside the region where previous fossil hominids have been found, and 7 million years ago the environment there would have been forested.

Ardipithecus ramidus

Ardepithecus ramidus is a third ancient hominid, which some scientists place in the genus Australopithecus. The oldest remains of this species, belonging to the subspecies kadabba, are from Ethiopian rocks dated at between 5.2 and 5.8 million years old. More recent Ardepithecus ramidus remains are dated at 4.4 million years. Most of the fossil material for this species consists of skull fragments and some teeth, and possibly a toe bone (which belonged to a bipedal organism).

Again, evidence from other fossils suggests that Ardipithecus lived in a forested environment. This is quite different from the open savannah conditions in which hominids were thought to have become bipedal.

Importance That all these species existed so close to the origin of hominids suggests that even then our family tree could be described as bushy, rather than having the single linear progression from species to species that is so often presented in images of human evolution.


The Australopithecines

This large group of species comprises both the gracile and the robust australopithecines. Recently some scientists have suggested that some species presently assigned to the Homo clade would be better placed in Australopithecus - an example of how rapidly our understanding of our evolutionary past is changing, and of the reviews, discussion and disagreements that characterise scientific research.

Australopithecus anamensis

The earliest known australopithecine is Australopithecus anamensis, which lived between 4.2 and 3.9 million years ago. This has teeth and jaws that strongly resemble those of older fossil apes. However, they were very likely bipedal (based on the structure of the tibia) and had human-like upper limbs. Maeve Leakey's research team suggests that anamensis may be ancestral to all later hominids.

Australpithecus afarensis

The best-known member of this species is "Lucy" , discovered in 1974 by Don Johanson & Tom Gray and estimated to be around 3.2 million years old (afarensis lived from 3.9 to 3 million years ago). This is an important find as the skeleton is remarkably complete for its age (40% complete by some estimates, but this does not include the bones of the hands and feet), providing a wealth of data about her size, posture, and gait. A range of other finds, including the 13 individuals of the "First Family", give supporting information, and the famous Laetoli footprints have also been attributed to this species.

Afarensis remains indicate that the species was strongly sexually dimorphic, with males much larger than females. The remains indicate that afarensis heights ranged from 107 to 152 cm, and cranial capacity from 375 cc to 550cc (AL 444-2, a large adult male). This may give us some clues about social behaviour in anamensis, since modern apes with a high degree of sexual dimorphism are polygynous.

The face and cranium of afarensis was ape-like: a prominent brow ridge, low forehead, and a prognathous muzzle that lacked a chin. The teeth are intermediate between ape and human: the molars are large and the canines, though much smaller than those of living apes, are larger and more pointed than those of humans. The shape of the dental arcade lies between the human parabolic form and the apes' rectangular shape, and the foramen magnum, while further forward than in apes, is not directly under the cranium as in humans.

However, their postcranial skeleton is far closer to that of modern humans. The pelvic, leg, and foot bones clearly show that this species was bipedal, though not well adapted for running. While the finger & toe bones are curved and longer than in humans, a feature that most scientists consider to be evidence that afarensis still spent time in the trees, their hands are otherwise human-like. (A recent study suggests that afarensis' wrist bones still show some adaptations for knuckle-walking.)

"Lucy's child"

Our knowledge of Australopithecus afarensis has been extended with the description of a juvenile afarensis (Alemseged et al. 2006). The complete skull and partial skeleton (around 50% complete) are probably those of a female who was around 3 years old when she died.

The find is particularly exciting in that it yields information lacking in other afarensis remains: an endocranial cast of the cranium; shoulder blades and collarbones - permitting an estimate of the extent of arm movement in this species; and a hyoid bone, which shows that the voice box had an ape-like structure.

Scientists have always wondered how much time afarensis spent in the trees. The form of the shoulder blade, the fact that the arms could be swung above the head, and the presence of long, curved fingers all suggest that the species was at least partly aboreal.

Kenyanthropus platyops

Until recently our knowledge of early hominids suggested that there was a single early-middle Pliocene lineage, of which A. afarensis is the best example. However, in 2001 Maeve Leakey's research team reported the find of a well-preserved cranium that they placed in a new genus: Kenyanthropus platyops.

This fossil is described as a mosaic, with a combination of ape-like and hominid features. On the ape side, it has a small ear opening, thick enamel on its molar teeth, a cranial capacity of about 400cc (the same as a chimp's), and a flat nose. However, its face has a number of novel features not seen in the other gracile australopithecines: a flat face, vertical cheek region, and small brow ridge and cheek teeth.

Some researchers dispute the classification of this specimen into a new genus, noting that the cranium is severely distorted and that many of the features used to define this genus are simply a result of the distortion.
Australopithecus garhi

This species, Australopithecus garhi, which its discoverers felt could be intermediate between A. afarensis & early Homo, was described in 1999 from fossils found in the Awash region of Ethiopia. The 2.5 million-year-old fossils were found in association with animal bones - which had marks on them that appeared to be from stone tools. Very simple stone tools were found in a nearby site of the same age.

The fossils of Australopithecus garhi comprise a partial cranium and a fragment of another, partial skeletons and other postcranial bones, and two mandibles. (The remains may or may not be all from the same species.) Many features of the skull, including the small cranial capacity of 450cm3, are very similar to A. afarensis. There was a sagittal crest and an ape-like dental arcade. The molars and canines were extremely large - an unexpected feature if garhi is to be regarded as ancestral to Homo. The proportions of the limb bones are of interest: the femur-to-humerus ratio was like that of modern humans, but the ratio of forearm-to-humerus was like that of a chimpanzee.

Australopithecus africanus

Raymond Dart's "Taung child", consisting of teeth, jaws, a complete set of facial bones, and an endocranial cast, was the first australopithecine fossil to be found. The fact that all its milk teeth are present, and the state of its cranial sutures, suggests that this individual was about 3 years old when it died. Although his description of the Taung infant as a hominid was originally questioned, the subsequent discovery of many adult africanus fossils confirmed his classification. As a species, africanus lived between 3.3 and 2 million years ago. Like afarensis, it showed strong sexual dimorphism, and bones of the feet, legs, pelvis and spine show that it was bipedal. However, both body size and cranial capacity (420 - 500cc) were slightly larger in africanus, which also had larger molar teeth, smaller canines, and a fully parabolic dental arcade.

Australopithecus anamensis, afarensis, and africanus, and Kenyanthropus platyops are collectively known as gracile australopithecines, because of their relatively light, slender build. This is by comparison to the "robust" australopithecines: all the gracile species were still more robust than modern H. sapiens.

Australopithecus robustus

Together with A. aethiopicus and boisei, robustus is one of the "robust" australopithecines. (Some authors have placed these three species in the genus Paranthropus.) All of them had large jaws, heavily built skulls, sagittal crests, and thick enamel on their molar teeth.

Robustus lived between 2 and 1.5 million years ago. While its body size was similar to that of A. africanus, it had a larger, more robust cranium (average capacity 530cc) and very large molars in its large lower jaw. Its face was also large, with no forehead, and many specimens had sagittal crests in addition to their big brow ridges. The combination of these ridges and crests with the large jaws and molar teeth suggest that this species must have eaten coarse, tough food requiring much chewing.

Interestingly, while tool use was regarded for many years as a characteristically human feature, robustus may have been one of the first hominids to use tools. This interpretation was placed on bones found with robustus fossils as the worn ends of these bones suggest they may have been used for digging.

Australopithecus aethiopicus

This is the oldest of the three robust australopith species, living between 2.6 and 2.3 million years ago. There is one major fossil, the "Black Skull" , so named because it had been stained by minerals in the soil. Some researchers consider it an ancestor of both robustus and boisei (see Figure 1). At 410cc its cranial capacity is little more than that of a chimpanzee, and posterior parts of the skull are similar to those of A. afarensis. But it also has the very heavily built face and jaws of the other robust species, and the largest sagittal crest ever seen in a hominid.

Australopithecus boisei

A. boisei, originally named Zinjanthropus boisei, is the most robust of all the robust australopithecines. Louis Leakey nicknamed it "Nutcracker Man" because of its huge molar teeth - some up to 2cm across. Its cranial capacity is similar to that of robustus, around 530cc, while its face and jaws are even more massively built. The "hyper-robust" nature of this species suggests it was highly specialised to chew hard, low quality foods. It's been suggested that boisei became extinct because it was so highly adapted to a specific ecological niche, and could not evolve fast enough to adapt when the environment changed.


Homo Species

Homo habilis

Until Jane Goodall's pioneering studies of chimpanzees most palaeoanthropologists believed that tool use was a hallmark of humanity. Consequently, when Louis Leakey's team found very simple stone tools closely associated with hominid remains, in Olduvai Gorge, he named the hominid Homo habilis. The associated tools are assigned to the Oldowan tool culture.

Homo habilis lived from 2.4 until 1.5 million years ago, and closely resembles the australopithecines. In fact, recent papers have suggested that habilis would be more appropriately classified in Australopithecus. The face still projects forwards but the facial angle is less than in A. africanus. Average cranial capacity in habilis is about 650cc, and the range is 500 - 800cc - this overlaps both the australopithecines (at the lower end) and H. erectus (at the upper limit). Analysis of wear patterns on the teeth suggest that habilis was adding meat to its diet - probably as a scavenger as there is no evidence that hunting was a common practice.

Postcranial remains are fragmentary, and in fact only one set of limb bones has been securely assigned to habilis. This fragmentary skeletal material suggests that the average height of Homo habilis was around 127cm, and they were probably about 45kg in weight. They were also obviously bipedal.

There is some argument about the taxonomic status of the habilis specimens. Recent papers have made the suggestion that at least some should be reclassified with the australopithecines, on the basis of features of the limbs. For example, the "dik-dik hominid" (OH 62) has arms that are considerably longer than its legs, an australopithecine characteristic.

Homo erectus or Homo ergaster

Homo erectus lived between 1.8 million and 300,000 years ago, and was probably the first hominid species to move out of Africa and colonise Europe and Asia. This significant event must have happened early in the species' history, as fossils that may belong to erectus but which are dated at around 1.8 million years ago have been found in Dmanisi, Georgia.

Note that some authors recognise two sister species: erectus is assigned to the Eurasian specimens while Homo ergaster is reserved for those from Africa. Ergaster has a smaller cranial capacity, and the two differ in some features of the skull, such as the shape of the brow ridges.

Erectus had a long, low skull, with little forehead and a cranial capacity of between 750 and 1225cc. The smaller brain sizes are associated with older specimens. The face was prognathous, and the protruding jaws supported large molar teeth but lacked a chin. This was the first hominid to have a projecting, rather than a flattened, nose.

The post-cranial skeleton of Homo erectus was robust, suggesting they were stronger than modern humans. Members of this species, at least in Africa, were tall; some estimates place them in the upper quartile of the height range for H. sapiens. However, the few remains from China ("Peking man") are from shorter individuals. This probably reflects adaptation to the local climate. Tall, slender individuals are well adapted to lose heat in hot climates, as their bodies have a high surface area to volume ratio (SA:V). Those living in colder regions need to conserve heat, and heat loss is reduced in short, stocky individuals with a lower SA:V.

Studies of erectus pelvic bones, particularly those of the Turkana (Nariokotome) Boy, show that members of this species had a narrower pelvis and pelvic canal than ours. This implies that their babies were smaller-brained at birth; it also suggests that erectus may have been more efficient at walking than sapiens.

Erectus was a competent toolmaker, and scientists have found large numbers of their tools, which are classified in the Acheulean tool culture. There is good evidence, in the form of scratch marks on bones, that these tools were used to butcher animal carcases; meat made up a significant portion of the erectus diet. There is also evidence that this species was the first to use fire. The first support for this hypothesis came from charcoal deposits from the Choukoutien caves near Beijing, where the fossils of "Peking man" were found. At least one researcher now suggests that these "hearths" are natural deposits. However, palaeontological and experimental evidence does support the idea of widespread use of fire among African erectus populations.

Homo floresiensis

On 27 October 2004, one of the most exciting discoveries in human evolution in recent years was announced to the world: Homo floresiensis. Found on the Indonesian island of Flores, this new hominin species was named on the basis of the partial remains - including the skull, jaw, and teeth - of an adult female, and fragments from several other individuals. What makes this find unique is its age - only 18,000 years - and its tiny size: the adult female stood only a metre tall, and had a cranial capacity of just 380cm3. Up till now, scientists had understood there to be only two hominin species in Asia: our own Homo sapiens, and H.erectus. This is yet another piece of evidence for the bushy nature of the human family tree, and evidence, too, that our present status as the only living hominin was only recently acquired.

The Flores skull shows a mix of primitive and advanced features: a low cranium, and prominent brow ridges, combined with a small & relatively flat face. Interestingly, although this hominin was bipedal, the pelvis is more similar to that of australopithecines than more modern hominins. Various features of the skull, including the shape of the brain itself, suggest that floresiensis was a dwarfed species that evolved from H. erectus (erectus was present on the island of Java from as long as 1.6 million years ago). Evolution of dwarfed island forms is known in other mammals: Malta had a dwarf elephant and hippopotamus, and floresiensis was found in association with the bones of a dwarfed species of elephant.

Despite its tiny brain, Homo floresiensis was probably a toolmaker & tool-user: a number of stone tools were found with the remains. Tools found earlier, and dated at up to 800,000 years ago, are attributed to a founding population of H. erectus. In addition, since Flores is separated from the larger island of Java by a deep ocean channel, it seems likely that the ancestors of this new species must have arrived by sea, perhaps on a primitive raft.

Read Carl Zimmer's excellent article on [ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ]
The Dmanisi fossils

Between 1999 and 2001 three hominin skulls aged around 1.8 million years were discovered at Dmanisi, in Georgia. Additional material comprised jawbones and some facial bones. The cranial capacity of these skulls ranged from 600 cm3 to 780 cm3. The skull of the smallest individual was the smallest, most primitive hominin skull found outside Africa. Although the crania are small and resembled habilis in some features, the scientists who described them felt that the fossils were more closely related to H. erectus/ergaster than to H. habilis.

However, stone tools also found at Dmanisi are essentially the same as those from the Oldowan culture associated with H. habilis. This, combined with the small cranial capacity of the skulls, has led some scientists to suggest that the Dmanisi individuals belonged to H. habilis or a related species. If correct, this will require a revision of the standard view that H. erectus was the first hominin species to venture out from Africa. The Dmanisi remains have since been placed in their own species, Homo georgicus.

Homo heidelbergensis

This is an alternative name for fossils that are also classified as "archaic Homo sapiens". Archaic H. sapiens first appears in the fossil record about half a million years ago. These fossils appear intermediate between Homo erectus and fully modern humans. Skulls attributed to archaic sapiens have an average cranial capacity of 1200cc, which is larger than erectus but less than the average value for modern sapiens. The vault of the skull is more rounded than in erectus, and many of the fossils have large brow ridges, receding foreheads, and weak chins.

The Petralona, Steinheim, and Swanscombe remains are also regarded as "archaic" Homo sapiens.

Homo neanderthalensis

Neandertals (or Neanderthals) lived between 230,000 and 30,000 years ago, during the last Ice Age, and were found only in Europe and the Middle East, where they coexisted with modern humans for the later part of their existence. This species gets its name from the Neander valley, or Tal, in Germany, where the type specimen was found in 1856.

All Neandertals are heavily built but those from Western Europe are particularly robust. Their heavy physique was probably an adaptation to the extremely cold conditions in which they lived. Neandertal men averaged only 168cm in height, but their bones are thick and heavy, and the scars of muscle attachment indicate that they were very heavily muscled.

However, the key differences between Neandertals and modern humans lie in features of the skull. The average cranial capacity is 1450cc, larger than the modern norm, although this may be a reflection of their greater bodily bulk. The skull is notably longer than that of modern humans, with a lower vault and an occipital bulge at the rear. The face was prognathous, with a receding forehead and weak chin. The cheekbones are swept back and the midfacial area protrudes (as if someone had grabbed the nose & pulled it forwards) - this feature may also be an adaptation to a cold environment as it is associated with a markedly larger nasal volume than in either erectus or modern sapiens. Two different explanations have been given for this large nose: it may have ensured that the cold air was warmed & moistened on its way to the lungs; alternatively it could have acted as a radiator, to lose heat generated by exertion while hunting.

Neandertals made a wider range of more complex tools - belonging to the Mousterian tool culture - than those used by erectus although, like erectus, they do not appear to have been particularly innovative until late in the species' existence, when Chatelperronian tools appear at some sites in France. Many researchers believe that they buried their dead, with the oldest known burial dating to about 100,000 years ago. However, not all scientists agree with this interpretation.

Recently scientists have been able to extract mitochondrial DNA from Neandertal bones. This has allowed them to compare DNA sequences from Neandertals and modern humans, an interesting experiment considering that in the past Neandertals have been viewed as direct ancestors of modern sapiens. The multiregional hypothesis of human origins also takes this stance. While there are problems with this technique, the data appear to show that Neandertals were not closely related to modern humans, but belonged to a separate species.

Homo sapiens (modern)

A very recent find provides good evidence that the earliest known recognisably modern humans lived in Africa, around 160,000 years ago. These fossils come from Herto, in the Middle Awash of Ethiopia, and "are morphologically and chronologically intermediate between archaic African fossils and later anatomically modern Late Pleistocene humans" (White et al. 2003). The fact that the Herto fossils are so old supports the argument that fully modern humans first arose in Africa, later migrating into Europe & Asia to displace the other hominid species already living there (the "out of Africa" hypothesis).

The average cranial capacity of modern humans is around 1350cc, with a range for normal individuals of from 800 to close to 2000cc. The brain is enclosed in a high, vaulted skull with a high forehead, and brow ridges are absent or, if present, very small. The relatively delicate jaw has small teeth and a prominent chin, and the post-cranial skeleton is gracile.

We think of complex culture as a hallmark of humanity. However, art works, such as jewellery, carving, and cave paintings do not appear in the record until 30-40,000 years ago. This follows the development of the extremely sophisticated Aurignacian tool kits associated with Cro-Magnon culture. Some authors suggest that the use of highly sophisticated language accompanied this flowering of culture. This is not to say that earlier humans, and hominids, were not capable of speech.

Over the last 100,000 years there has been a continuation of the trend towards smaller molar teeth and a more gracile skeleton, such that the Upper Palaeolithic humans of 30,000 years are described as being 20-30% more robust than present-day people. This demonstrable trend in tooth size is probably linked to the use of food-processing techniques that reduce the need for prolonged chewing, and thus provides a good example of the results of natural selection in human populations.


Trends in Human Evolution

Examination of hominid remains indicates several trends, including changes in posture, cranial capacity (brain size), and facial angle. Such trends are often misused, e.g. in popular illustrations, to give the impression that evolution has proceeded in a linear manner, from some primitive ancestor through a series of descendants, to culminate in our own species. It's important to remember that the evolutionary history of humans, as of most organisms, is best reconstructed as a bush, where there are often several related species in existence at any one time.

Having said that, these trends do give a useful overview of the evolutionary changes that have occurred in our biological history.

Trends in cranial capacity

Early workers in the field of human evolution expected that the first hominids would have an ape-like physique with a modern cranium. This reflected the attitude that, since our intelligence and large brain size set us apart from all other species, these would be the first human characteristics to evolve. The Piltdown Man fraud exploited these expectations. It was almost 50 years before the "fossils" were recognised as a modern human braincase and orang-utan jaw.

We now know that the actual trend is the reverse of this early expectation. There has been a gradual increase in cranial capacity over the course of human evolution. Thus Sahelanthropus and the early australopithecines had cranial capacities within the range of modern chimpanzees (average around 400cc), with the later australopithecines reaching 550cc. Skulls attributed to early Homo begin at around 510cc, and there was a marked increase with Homo erectus, where later specimens had brain sizes of up to 1225cc, well within the modern range.

The average cranial capacity of the Neandertals was larger than that of modern humans (1450cc and 1350cc respectively), but this may simply reflect the larger body mass of neanderthalensis. There is a strong positive correlation between body size and brain size, even within species e.g. male humans have larger body mass than females, and correspondingly larger cranial capacity. Equally importantly, the brain size in hominids, particularly Homo species, is greater than would be predicted for animals of their body mass.

Bipedalism

Bipedalism appeared very early in our evolutionary history. Until recently there was disagreement over the posture of Sahelanthropus (c. 7 million years ago). However, a computer-assisted reconstruction of this fossil shows a foramen magnum beneath the cranium, and relatively small nuchal crest, indicating that this species was bipedal (Zollikofer et at. 2005).

This is not to say that their posture was fully erect. For example, while the pelvic, leg, and foot bones of Australopithecus afarensis clearly show that this species was bipedal, it was not well adapted for running. In addition, the position of the foramen magnum (intermediate between that of apes and humans) suggests that afarensis did not hold its head fully erect.

In contrast, Homo erectus was possibly an even more efficient biped than modern humans, due to the narrower pelvic outlet in erectus. The wider pelvic outlet in sapiens, an adaptation permitting the birth of large-brained infants, places the hip joints further apart than required for optimum locomotory efficiency. (This is a good example of how evolution produces compromise solutions, rather than perfection.)

Trends in general morphology of the skull

Dental arcades: in an ape, the teeth are arranged in a rectangular dental arcade, where the left and right cheek teeth are in two parallel lines. Australopith dental arcades tend to be more rectangular than parabolic, but in Homo species the dental arcade is a full parabola, broader at the back than at the front.

There is also a strong trend in tooth size, such that the cheek teeth (in particular) of modern humans are smaller than those of australopithecines. And even within H. sapiens there has been a marked decrease in tooth size over the last 30,000 years.

Crests and ridges: both the great apes and early hominids have obvious crests and ridges on their skulls. The most obvious are the sagittal and nuchal crests and the brow ridges.

Where present, the sagittal crests provide anchorage for large chewing muscles, and are thus most prominent in species where the diet comprises hard, tough material requiring a lot of chewing. (They are also larger in males than in females, an example of sexual dimorphism.) Brow ridge development in hominids may also be related to diet, as large brow ridges help to redirect the considerable stresses placed on the skull by a diet of coarse vegetable matter.

The presence of a pronounced nuchal crest provides information about a species' posture, together with the position of the foramen magnum. The crest provides anchorage for neck muscles in those species where the skull is not balanced vertically atop the spine. Thus, modern humans have a completely upright posture: the foramen magnum is centrally placed beneath the skull and a nuchal ridge is absent. Early australopithecines such as "Lucy" (A. afarensis) have a foramen magnum position intermediate between that of humans and apes, and a small nuchal ridge. This tells us that their posture was not completely upright.

Facial angle:

There is a general trend towards a flatter facial angle with the appearance of more recent hominids, culminating in the vertical (orthognathous) face of Homo sapiens. Note, though, that there is considerable variation even among the older members of our lineage: Kenyanthropus platyops is named for its relatively flat face - its name means "flat-faced ape-man from Kenya".

Other morphological features Reduced sexual dimorphism:

All hominoids show some differences in size between the sexes, as well as in such features as the shape of the pelvis and in crests on the skull. Thus male gorillas weigh perhaps twice as much as females. This size difference is much less in chimpanzees and even less pronounced in modern humans, where on average males are 1.2 times as heavy as females.

This trend towards a lesser degree of sexual dimorphism can be traced in hominin fossils. The skeletons of the australopithecines show a marked degree of sexual dimorphism, which is reduced in the early hominids.

Changes in size of ribcage:

"Lucy" (Australopithecus afarensis) has a funnel-shaped ribcage, which is narrow at the top and expands towards the base above wide, flaring hipbones. In comparison, Homo erectus has a barrel-shaped ribcage, indistinguishable from our own, and with a waist separating ribcage and hips.

In his excellent discussion of the significance of the Nariokotome (Turkana) boy, Allan Walker (1996) relates these changes in ribcage to a significant change in diet. Gorillas, which are herbivores, have a ribcage similar to Lucy's. This flaring shape accommodates the extensive gut needed to process the gorillas' rough diet and extract sufficient nutrients. The barrel-shaped ribcage, and the presence of a waist, in erectus suggest that significant quantities of meat were being eaten. Weight for weight, meat is much higher in calories, and easier to digest, than an all-vegetable diet. This means that an omnivore, or a carnivore, has a much shorter gut than a complete vegetarian.

An increase in the amount of meat in the diet, with its greater fat content and higher calories, could also fuel the higher energy demands of a larger brain. Significantly, average cranial capacity increases markedly in Homo erectus.



Human Cultural Evolution

| Tools and Tool Use | Fire | Domestication of Plants and Animals |

There are many examples of human cultural evolution. They include: tool making, the controlled use of fire, manufacture of shelters and clothing, appearance of art and other non-utilitarian products, development of cooperative hunting behaviour, and domestication of plant and animal species (leading to settled agricultural societies). All of these features allowed humans to have greater control of their environment, rather than responsive to it. Thus, the development of these skills would directly contribute to the survival of individuals (& groups) practising these behaviours. (Cultural evolution is also described as non-biological evolution, since what is transmitted to new generations is changes in learned behaviour patterns. However, any genetic underpinnings to these behaviours would also be passed on.)

Some aspects of cultural evolution are easier to trace than others. Examples of stone tools made by hominin species are relatively common and easily recognised. Tools made of other substances, such as wood or bone, do not survive so well in the stratigraphic record. Changes in behaviour, such as the development of cooperative hunting groups or changes in social structure, leave no direct traces at all and their presence must be inferred from other evidence.

Evidence of developing human culture appears far back in time. Homo habilis was named for its association with the crude cobble tools of the Oldowan culture, and it's possible that Australopithecus garhi and one of the robust australopithecines, A. robustus , were also tool users. What differentiates these very simple, ancient tool-making cultures from the tool manufacture and use practised by modern chimpanzees? In fact, how do we define "culture" in the evolutionary sense?

At the time that H. habilis was discovered, manufacture and use of tools was generally viewed as an exclusively human activity. The Oldowan tools marked the earliest hard evidence of culture in our ancestors. We now know that many different animals use tools. Perhaps the best-known example is that of chimpanzees. Jane Goodall first documented this in her studies of wild chimpanzees in Africa's Gombe Reserve. Not only did her animals use rocks, twigs and vegetation as simple tools, but they modified them: for example, stripping a twig of leaves, and breaking it to the right length, so that they could "fish" for termites in the insects' tunnels. Young chimps learn these skills by observing their elders, an example of cultural transmission. And chimpanzees from different areas have distinctly different tool-making cultures.

However, one of the differences between chimp and human culture is that chimps seldom carry tools, or the raw materials for tool making, for any distance. In addition, chimps make tools only immediately before using them. Tools used by early humans were typically worked and reworked at different locations

So is it the complexity of culture that sets humans apart? We think of complex culture as a hallmark of humanity. However, art works, such as jewellery, carving, and cave paintings, do not appear in the record until 30-40,000 years ago. This follows the development of the sophisticated Aurignacian tool kits associated with Cro-Magnon culture. Some authors suggest that the use of highly sophisticated language accompanied this flowering of culture, and marked the appearance of a significant capacity for abstract thought. (This is not to say that earlier humans, and hominins, were not capable of speech.)

Cultural evolution has occurred in different times in different places. This is a reflection both of the time at which different regions of the globe were settled, and also the nature of the biology & geology of an area, which poses constraints on, for example, the domestication of plants & animals. This has had far-reaching consequences on later geopolitical history. (Guns germs & steel)

Tools and tool use

At present the earliest-known evidence of the manufacture and use of tools comes from a 2.5 million-year-old site, possibly associated with Australopithecus garhi. This site contains primitive stone tools, but no hominin remains. Animal bones recovered together with garhi remains, from a nearby site of the same age, appear to show cut marks from stone tools.

These tools predate the better-known Oldowan tool culture associated with Homo habilis. These are often described as "cobble tools", and comprise two main types, core tools and flake tools. Core tools are stones with one or more flakes knocked off one end to give a jagged edge. Flake tools are the flakes removed in producing core tools, and were not modified any further before being used. It's possible that the core "tools" are simply what remained after flake tools had been produced, and that they weren't used to any great extent.

The Oldowan tool culture persisted in Africa for almost a million years. With Homo erectus came the more sophisticated Acheulean toolkit. These tools were more highly modified than the earlier cobble and flake tools, with sharper and straighter edges formed by careful removal of more and smaller flakes. Perhaps the best-known Acheulean tool is the so-called hand axe, a teardrop-shaped implement with a pointed end and sharp sides. We have no way of knowing just how these hand axes were used, but they were probably put to a wide range of uses. Other Acheulean tools included hammers, cleavers, and flake-based tools such as knives (probably held directly in the hand, rather than hafted to a handle).

Erectus was probably the first hominin to leave Africa. Acheulean tools are found in both Europe and Asia. Until recently it was believed that Chinese erectus populations continued to use Oldowan tools, but Acheulean tools dating back 1.3 million years were found in China in 2001.

Along with more sophisticated tools came a change in the foods eaten, and how these foods were obtained. While the australopithecines, and perhaps H. habilis , were essentially vegetarian, meat was a regular part of the erectus diet. Remains from many sites, including Zhoukoudian in China, show that erectus was eating meat on a large scale and from a range of animal species, in addition to a wide variety of plant foods. These animals may have been both scavenged (from other predators) and hunted.

The year-round available of calories from meat would have made it possible for erectus to move from its tropical homeland into temperate regions. Parts of China, for example, experience cold winters, when fresh plant foods are not readily available and meat would be the primary source of calories.

There is also a possible causal link between the marked increase in cranial capacity of Homo erectus - especially the rapid rate of growth of the brain after birth - compared to its predecessors, and the regular presence of meat in erectus diets. The brain is a very fatty organ, and meat is a much better source of the necessary fats than plant foods. The high calorie content of meat is also important, as the brain is a very energy-hungry organ. (And of course, breastfeeding an infant with a rapidly growing brain is energetically very expensive.)

Another leap in tool development came with the Mousterian tool culture, associated with both Neandertals and archaic Homo sapiens . In a significant advance over the Acheulean culture, a stone core was carefully shaped before flakes were struck off it: different core shapes gave different flakes. These flakes could then be further modified for a range of different tasks, and some have a tang at the end that suggested that they were hafted to a wooden or bone handle.

The appearance of modern Homo sapiens saw further innovation with a new group of tool-making styles, collectively known as the Upper Palaeolithic industry. The earliest such tools date from Africa, around 90,000 years ago. The Upper Palaeolithic industry spanned the period 40,000 to 12,000years ago and included the Aurignacian (associated with Neandertals and modern humans), Chatelperronian (used largely by declining European Neandertal groups), Gravettian, Solutrean, and Magdalenian industries. These tools are far more complex than those of the earlier Mousterian culture, and are made of a wider range of materials. They show both regional variation and adaptation to particular needs: fishhooks & harpoon points were first manufactured by Upper Palaeolithic toolmakers, as were needles of ivory and bone.

Other cultural artefacts are associated with the later Gravettian, Solutrean, and Magdalenian tool industries. Ivory beads and "Venus" figurines are associated with Gravettian sites, while necklaces, animal figurines, and symbolic art (you need to click on the title after opening the front page) appeared during the Magdalenian, 18,000 to 12,000 years ago.

This hard evidence of human cultural evolution can be used to infer something about the nature of the human societies producing these artefacts. Needles suggest the manufacture of relatively sophisticated clothing, as does the use of huge quantities of beads to decorate these clothes (found in some grave sites). Palaeoanthropologists have linked the nature of many cave paintings and carvings to the development of various rituals - and also to the development of fluent abstract language. They argue that the complex and often abstract nature of much cave art could not have been developed without an equal ability to communicate. Similarly, the appearance of complex burials at some Upper Palaeolithic sites may imply concerns or beliefs about an afterlife.

Fire

Bones found in the Swartkrans Cave in South Africa, and dating back perhaps 1.5 million years ago, provide some of the earliest evidence for the use of fire. Analysis of the bones showed that they had been heated to the high temperatures normally associated with hearths. (Bush fires reach lower temperatures and do not generate the same changes to the bone.) Two hominins were present in Swartkrans at this time: Homo erectus and Paranthropus robustus , and it's not known which species burnt the bones. However, later sites where fire was used are definitely associated with erectus . Hearth sites 790,000 years old, found in Israel, also contain the Acheulean tools produced by erectus.

Prior to these discoveries in Africa and Israel, the earliest site with evidence of regular use of fire was Zhoukoudian (Choukoudian), or "Dragon Bone Hill", near Beijing. Here researchers studying "Peking Man" ( Homo erectus ) found charcoal, charred bones, and rocks cracked by exposure to fire. Many of the bones belonged to large game animals, which may mean that the local erectus population was engaging in organised hunts.

Learning to use fire in a controlled manner was a major step for our ancestors, because it gave them greater control over their environment and also had the potential to make available a far greater range of foods. Fire would not only offer protection from predators, but would also allow its users to survive in much colder environments. In addition, the controlled use of fire is evidence of the ability to plan ahead, and would also have aided social interactions as people gathered round the hearth.

Domestication of Plants and Animals

Both plants and animals were first domesticated by humans in Europe and western Asia. Dogs may have been domesticated as early as 13000 years ago, followed by goats, sheep, pigs and cows (8-10,000 years ago), and horses around 6,000 years ago). Animals suitable for domestication had to be easy to fed, grow fast and breed easily in captivity, have a tractable nature, be unlikely to panic, and have the sort of social hierarchy where humans could slot in as the leaders of the group. A lack of large animals meeting these criteria helps to explain why widespread use of animals for food, fibres, or beasts of burden did not occur in Africa, Australia, or the Americas. (In fact, donkeys are the only domesticated mammal to come from Africa.) This in turn gave European cultures an advantage when they began to move into the other major landmasses and, ultimately, the Pacific.

Domestication of plants appears to have begun in the Fertile Crescent (the region lying between the Tigris and Euphrates rivers, in what is now Iraq and Iran), about 10,000 years ago. This saw the beginnings of agriculture, and also of settled civilisations. A hunter-gatherer lifestyle can support only a small number of people in a given area. However, the surpluses of food offered by agriculture can support a larger, settled population, and also allow a division of labour whereby individuals are freed for tasks other than food gathering. Paradoxically, while agriculture allowed more people to settle in one place, this was accompanied by a reduction in their overall health. Skeletons recovered from early cemeteries show that townsfolk were often smaller, and less-well nourished, than hunter-gatherers. This is because, while agriculture certainly provided more calories, the overall quality of the diet was less.

The Middle East was particularly conducive to the development of agriculture because of the large number of plant species with the potential for domestication. The first plants to be domesticated would have been annual plants which bore large seeds or fruits (and so were more attractive to humans), including peas and other legumes, and cereals (derived from wild grasses). Fruits such as apples and olives came later. Rice was domesticated in Asia, while squash, maize and beans were key crops in the Americas. No plants were domesticated in Australia, despite humans having lived there for perhaps 60,000 years (and the only domesticated mammal, the dingo, was brought from Asia).

A useful link: [ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ]


Mitochondrial DNA

Not all of the genes in a eukaryote cell are found on its chromosomes. Both mitochondria, found in all eukaryote cells, and the chloroplasts of green plants and the algae have their own DNA. These organelles reproduce independently of the cell's nucleus and pass their genes on to their daughter organelles.

For the mitochondria and chloroplasts of multicellular organisms, In multicellular organisms the DNA of both mitochondria (mtDNA) and chloroplasts is inherited almost exclusively down the maternal line. This is because zygotes generally inherit all of their organelles from the ovum, rather than from the sperm or pollen. Just as for nuclear DNA, mtDNA can be used to examine phylogenetic relationships.

Organisms whose DNA sequence for a particular gene differs by only a few bases are likely to be closely related. This seems straightforward, but different parts of the genome mutate at different rates, and so scientists must select which region they wish to use. Ribosomal DNA (rDNA) mutates relatively slowly, and so can be used to examine the relationships between species that last shared a common ancestor hundreds of millions of years ago. However, mtDNA accumulates changes in the base sequence relatively rapidly, up to 10 times as fast as nuclear DNA. This means that it can be useful in studying the evolutionary history of species that diverged only recently, or to look at populations of the same species.

mtDNA and the "African Eve" hypothesis

mtDNA has been used to examine our own recent history. A number of studies have tried to put a date to the time when various human populations diverged. They have all found that the mtDNA of humans from a range of different geographical origins (i.e. "races") is relatively uniform. This indicates a very recent date for the populations to have separated. However, they have also shown that the mtDNA from African populations is more diverse than for any other group, suggesting that these populations have a relatively longer history. The overall conclusion is that the common origin for all modern human populations lies in Africa - the so-called "African Eve" hypothesis.

Dates for this origin range from around 60,000 to 400,000 years ago. However, more recent studies have placed the founding population at 200,000 years or less. These younger dates are supported by the discovery of modern human skulls dating back 160,000 years ago, from the Middle Awash of Ethiopia.

mtDNA and the history of Polynesian migrations

This section is based on material kindly provided by Dr Geoff Chambers and Adele Whyte of the Institute of Molecular Systematics at Victoria University, Wellington, NZ.

Studies of genomic DNA have shown that, in the NZ population as a whole, Maori and Polynesians have lower heterozygosity than the rest of the population. This fits with the idea that NZ was colonised by a series of "island-hopping" migrations, each of which would have led to a founder effect, with the result of inbreeding and decreased heterozygosity.

More detailed information on the history of these migrations can be obtained by studying mitochondrial DNA (mtDNA). This is because mtDNA is inherited almost exclusively down maternal lines. Studies of mtDNA lineages from the NZ population have confirmed earlier findings that the ancestors of NZ's indigenous population followed the Austronesian migration route, from Taiwan, into the Philippines and Indonesia, and then across the Pacific and finally to New Zealand. And like the studies of genomic DNA, they show a decrease in genetic diversity along this migration route.

The concept of a Taiwanese homeland is also supported by studies of genes coding for enzymes involved in the metabolism of alcohol in the liver. Many NZ Maori and Polynesians have a variant form of an enzyme that speeds this process up -- a trait that they share with the indigenous tribespeople of Taiwan.

The mtDNA data also make it possible to estimate the number of female colonists on the migration from Eastern Polynesia to New Zealand. There may have been more than 100 female settlers, which suggests that the migration was planned rather than the result of voyagers becoming lost between islands.

Interestingly, studies of Y chromosome DNA, which is passed exclusively from fathers to sons, indicate that male genetic lineages have different origins from female lineages. This is an outcome of gender-biased migration following contact between Austronesian and Papuan groups.

mtDNA and recent human evolution

A recent study (Ruiz-Pesini et al. 2004) of mtDNA has demonstrated that gene frequencies have changed over the last 50,000 years i.e. human populations have still been subject to evolution.

Some mutations in mtDNA may make aerobic respiration less efficient, so that the mitochondria generate more heat and less ATP. These mutations will be selected for if they are beneficial to the person carrying them - and they would certainly be advantageous for humans living in the cold climates that prevailed during the Ice Age.

Examination of the mtDNA from over 1,000 people has found that such a mutation is present in populations of Northern Europeans, East Asians, and Amerindians. Of those in the sample that live in Arctic regions, 75% had the mutation, which was also found in the 14% of the sample living in temperate zones. Some of the ancestors of these groups would have lived in Siberia, and all would have experienced the Ice Age's glacial conditions. However, the mutation is not found at all in people of African ancestry.

The study concludes that the correlation between habitat and presence of the beneficial mutation is evidence of positive selection for the changed gene sequence. That is, the mutation was selected for because those people who had them were able to generate more body heat in an extremely cold climate.

Other examples of ongoing human evolution

Obesity and all its related health problems, such as adult-onset (type II) diabetes, and cardiovascular disease, are frequently in the news these days. They are most common in populations of people who have only recently taken up westernised lifestyles e.g. Nauru islanders, and the Pima Indians of North America. In both these groups, 70% of 60-year-olds have type II diabetes. In both populations, many people die before 60 of diseases related to diabetes and/or obesity.

Because there are genotypes - beneficial for hunter-gatherer populations - that can predispose to these "western" diseases (Jared Diamond, 2002), then it should be possible to see natural selection working upon them. This is especially true for populations where individuals of reproductive age are affected, such as the Nauruans and Pima Indians. In such populations we can predict strong selection against the genotypes that predispose individuals to "western" health problems. When Europeans and non-Europeans are matched for diet and lifestyle, the Europeans have a lower frequency of type II diabetes. In Diamond's words, this "suggests that natural selection had already reduced European frequencies of those genotypes in previous centuries, as the western lifestyle was developing in Europe" (Diamond, 2002: 706).
Hominins Diagram


Figure 1 Possible evolutionary relationships of the hominins, indicating the five major genera, with Kenyanthropus in red, Homo in blue, Paranthropus in green, Australopithecus in black and Ardipithecus in yellow. Question marks indicate hypothetical or conjectural relationships; horizontal bars indicate uncertainty in the species' temporal spans.

With kind permission of Daniel Lieberman & Nature Publishing Group.

This link takes you to the Homepage of the science journal 'Nature': [ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ]

Reference Books Reference Books

Leslie C. Aiello & Mark Collard (2001) Our newest oldest ancestor? Nature 410: 526-527

David R. Begun (2003) Planet of the Apes Scientific American 289(2): 64-73

P. Brown, T. Sutikna, M. J. Morwood, R. P. Soejono, Jatmiko, E. Wayhu Saptomo & Rokus Awe Due (2004) A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia Nature 431, 1055 - 1061

Michel Brunet et al. (2002) A new hominid from the Upper Miocene of Chad, Central Africa Nature 418: 145-151

Jared Diamond (1997) Guns, germs and steel: a short history of everybody for the last 13,000 years pub. Vintage

Jared Diamond (2002) Evolution, consequences and future of plant and animal domestication Nature 418: 700-706

K. Galik, B. Senut, M. Pickford, D. Gommery, J. Treil, A. J. Kuperavage, R. B. Eckhardt (2004) External and Internal Morphology of the BAR 1002'00 Orrorin tugenensis Femur Science 305 (5689):1450-1453

Henry Gee (2001) Return to the planet of the apes Nature 412:131-132

Jeff Hecht (2004) Donkey domestication began in Africa New Scientist on-line: newscientist.com accessed 17 June 2004

Meave G. Leakey, Fred Spoor, Frank H. Brown, Patrick N. Gathogo, Christopher Kiarie, Louise N. Leakey, Ian McDougall (2001) New hominin genus from eastern Africa shows diverse middle Pliocene lineages Nature 410, 433 - 440

Meave G. Leakey, Craig S. Feibel, Ian McDougall, Alan Walker (2002) New four-million-year-old hominid species from Kanapoi and Allia Bay, Kenya Nature 376: 565-571

Michael Lemonick & Andrea Dorfman (1999) Up from the apes Time August 23 1999: 36-44 (a very good overview of recent work in human palaeontology)

Daniel E. Lieberman (2001) Another face in our family tree Nature 410: 419-420

John McCrone (2000) Fired up New Scientist 20 May 2000: 30-34 (use of fire by H. erectus in Africa)

Brian G. Richmond & David S. Strait (2002) Evidence that humans evolved from a knuckle-walking ancestor Nature 404: 382-385

Eduardo Ruiz-Pesini, Dan Mishmar, Martin Brandon, Vincent Procaccio, and Douglas C. Wallace (2004) Effects of Purifying and Adaptive Selection on Regional Variation in Human mtDNA Science 303(5655): 223 - 225

James Shreeve (1995) The Neandertal Enigma: solving the mystery of modern human origins, Morrow

Chris Stringer & Clive Gamble (1993) In Search of the Neanderthals: solving the puzzle of human origins, Thames & Hudson.

Alan Walker & Pat Shipman (1996) The Wisdom of Bones: in search of human origins Weidenfeld & Nicolson, UK

Tim White, Berhane Asfaw, David Degusta, Henry Gilbert, Gary Richards, Gen Suwas & F. Clark Howell (2003) Pleistocene Homo sapiens from Middle Awash, Ethiopia Nature 423: 742-747

Bernard Wood (2002) Hominid revelations from Chad Nature 418: 133-135

Christopher Zollikofer, Marcia Ponce de Leon, Daniel Lieberman, Frank Guy, David Pilbean, Andossa Likius, Hassane Mackaye, Patrick Vignaud and Michel Brunet (2005) Virtual reconstruction of Sahelanthropus tchadensis. Nature 434: 755-759

Reference Websites Reference Websites

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ] - an excellent website with a wealth of information and links to other sites and sources

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ] - this site provides good information on the workings of natural selection and genetic drift

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ] - proceedings of a conference organised by RSNZ; contains an excellent article by Colin Groves on human physical & cultural evolution

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ] - discusses changes in tool-making techniques, & tool-kits characteristic of various species

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ]

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ] - mentions various evolutionary trends in a discussion of the evolutionary relationships of Australopithecus garhi

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26-03-2007, 06:58
USING MICROFOSSILS
IN PETROLEUM EXPLORATION
BRIAN J. O'NEILL
WHEN I meet new people and they find out that I'm a paleontologist working for an oil company, the second question they ask (after "What is a paleontologist?") is usually "Why would an oil company hire one?" Most people think of dinosaurs when they think of paleontology, or at the very least trilobites and other invertebrate fossils. However, most of the rock samples available to those engaged in finding and developing hydrocarbon resources are in the form of "cuttings." Cuttings (Baker, 1979) are the small pieces of rock broken up by the drill bit and brought to the surface by the fluid which lubricates the drill bit and removes the cut rock from the bottom of the drill hole. If the bit encounters dinosaur bones or clam shells, they are so broken up in the process as to be almost unusable. Microfossils on the other hand, by virtue of their small size, can be recovered whole. Microfossils also happen to be abundant, especially in marine rocks which are the most common form of sedimentary rock in the crust of the Earth.

Microfossils have many applications to petroleum geology (Fleisher and Lane, in press, Ventress, 1991, LeRoy, 1977). The two most common uses are: biostratigraphy and paleoenvironmental analyses. Biostratigraphy is the differentiation of rock units based upon the fossils which they contain. Paleoenvironmental analysis is the interpretation of the depositional environment in which the rock unit formed, based upon the fossils found within the unit. There are many other uses of fossils besides these, including: paleoclimatology, biogeography, and thermal maturation.

There are a great number of different types of microfossils available for use. There are three groups which are of particular importance to hydrocarbon exploration. (The uses of microfossils in developing oil fields are analogous to those in exploration and so for brevity I will use the term exploration, which is looking for new resources, without the addition "development" or "exploitation" which refer to the drilling of wells to develop a field found by exploration.) The three microfossil groups most commonly used are: foraminifera, calcareous nannofossils, and palynomorphs. A brief introduction to each of these groups is included below. Many texts provide more detailed discussions of these and other microfossil groups (Haq and Boersma, 1978).

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Figure 1

Foraminifera (Figure 1) are protists that make a shell (called a "test") by secreting calcium carbonate or gluing together grains of sand or silt. Most species of "forams" are bottom- dwellers (benthic), but during the Mesozoic Era a group of planktonic foraminifera arose. These forms (Figure 2) were (and are) free-floating in the oceans and as a result are more widely dispersed than benthic species. After death, the planktonic foraminifera settle to the bottom and can be fossilized in the same rocks as contemporaneous benthic species.

Benthic foraminifera tend to be restricted to particular environments and as such provide information to the paleontologist about what the environment was like where the rock containing the fossils formed. For example, certain species of foraminifera prefer the turbid waters near the mouths of rivers while others live only in areas of very clear water.

Figure 2
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These preferences are recognized by two methods: (1) studies of the distribution of modern foraminifera and (2) analysis of the sediments containing ancient microfossils. In the first case, if the modern species has a fossil record, one can reasonably assume that the fossil ancestors had similar modes of life as the living organism. However if the species in question is extinct, then one examines modern forms, inferring that the fossil forms had similar environmental preferences. In thelatter case, studies of the rock containing the fossils (sandstone, shale, limestone, etc.) give further clues to the environment of deposition. If a given species is always found in sandstones deposited in river deltas, it is not too much of a guess to suggest that this species preferred to live in or near ancient river deltas. If a company is drilling for oil in deltaic reservoirs, then such information can be very useful by helping to locate ancient deltas both in time and space. For instance, the delta for the ancestral Mississippi River during the late Pliocene was not southeast of New Orleans as it is today, but rather far to the west, south of the Texas-Louisiana border (Galloway et al., 1991).


Planktonic foraminfera provide less information concerning the environment of deposition, since they lived floating in the water column; but they have other advantages. Whereas benthic foraminifera are restricted to certain environments, planktonic foraminifera are dispersed over a much broader part of the world oceans and often are found in large numbers. On a geologic time-scale, events such as the first appearance of a given species or its extinction can happen very quickly. For the paleontologists, these correlate points in time and space across a depositional basin (like the Gulf of Mexico) or even across whole oceans. However, local conditions may exclude a species from one area while it persists somewhere else. This gives a "suppressed" extinction point (i.e. the species disappears locally earlier in geologic time than it does in other parts of its range.)

[ برای مشاهده لینک ، لطفا با نام کاربری خود وارد شوید یا ثبت نام کنید ] Figure 3

Calcareous nannofossils are extremely small objects (less than 25 microns) produced by planktonic unicellular algae (Figure 3). As the name implies, they are made of calcium carbonate. Nannofossils first appeared during the Mesozoic Era and have persisted and evolved through time. The function of the calcareous "plates", even in living forms, is uncertain. One extant group that produces "nannofossils" is the Coccolithophorans, planktonic golden-brown algae that are very abundant in the world's oceans. The calcareous plates accumulate on the ocean floor, become buried beneath later layers, and are preserved as nannofossils. Some chalks, such as those comprising the White Cliffs of Dover, are composed almost entirely of nannofossils. Figure 4 illustrates the tremendous size difference between the foraminifera discussed above and the calcareous nannofossils. Like the planktonic foraminifera, the planktonic mode of life and the tremendous abundance of calcareous nannofossils makes them very useful tools for biostratigraphy.


Figure 4
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The third and final group of microfossils to be discussed here are the palynomorphs (Figure 5). These are organic walled fossils and include fossil pollen and spores, as well as certain marine organisms such as dinoflagellates (the red algae which make up the "red tides" in modern oceans). Pollen and spores are transported by wind and water and can travel long distances before final deposition. They are surprisingly resistant to decay and are common as fossils. Because of the long transport before deposition, they usually tell us little about the environment of deposition, but they can be used for biostratigraphy. Fossil pollen and spores can also give us information about ancient climates. For example during the Ice Ages, the distribution of plant species on the North American continent was much different during glacial and inter-glacial times. These variations are apparent in the palynomorphs found in sediments deposited in the Gulf of Mexico during that time period (Davies and Bujak, 1987). Additionally, the organic chemicals which comprise palynomorphs get darker with increased heat. Because of this color change they can be used to assess the temperature to which a rock sequence was heated during burial. This is useful in predicting whether oil or gas may have formed in the area under study, because it is h eat from burial in the Earth that makes oil and gas from
original organic rich deposits.

Figure 5
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Biostratigraphy plays a critical role in the building of geologic models for hydrocarbon exploration and in the drilling operations that test those models. The fundamental principal in stratigraphy is that the sedimentary rocks in the Earth's surface accumulated in layers, with the oldest on the bottom and the youngest on the top (Figure 6). The history of life on Earth has been one of creatures appearing, evolving, and becoming extinct (Figure 7). Putting these two concepts together, we observe that different layers of sedimentary rocks contain different fossils. When drilling a well into the Earth's crust in search of hydrocarbons, we encounter different fossils in a predictable sequence below the point in time where the organism became extinct. In our simplified case (Figure 6), the extant species C is present in the uppermost layers. Species B is only found in lower layers. The well does not penetrate any layers containing fossil A. The point at which you last find a particular fossil is called its LAD (Last Appearance Datum) (Figure 7). In a simplified case, the LAD in one sequence of rock represents the same geologic moment as the LAD in another sequence. These are our points of correlation between wells. Another well drilled in this area should penetrate the same sequence, but most likely at different depths than the original well.

Figure 6
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In addition to the LAD, another useful event is the First Appearance Datum (FAD). This may be difficult to recognize in a well, because rock from higher in the well bore may slough off the wall and mix with rock from the bottom of the hole. However, in studies of rock units exposed at the surface of the Earth and in some cases from well bores, these FADs are extremely useful biostratigraphic events. Lastly from Figure 7, one can recognize that the range of the three fossils overlap for only a relatively short period of geologic time. As a consequence, if a sample of rock contains all three (A, B, and C), it must have been deposited during this interval of time (Concurrent Range Zone). This is yet another "event" which can be used to subdivide geologic time into biostratigraphic units.

By studying the fossils in many wells, a geologic model for the area can be built up. Around Denver, the mountains contain uplifted sediments equivalent to those buried beneath the adjacent plains. In this area one can study the rocks that crop out at the surface and predict what will be penetrated by drilling. In the Gulf of Mexico basin, where I work, the rocks we drill for oil and gas do not crop out at the surface. However, micro-paleontologists have been active in examining well cuttings for over 70 years and thousands of data points have been recorded. The database is good, but as we drill deeper wells and in greater water depths, we find new events. Micropaleontology continues to play a critical role in Gulf of Mexico drilling.


Figure 7
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Figure 8 shows an example of biostratigraphy's role in constraining geologic models. It is a seismic profile from the Gulf of Mexico offshore from Texas. The profile represents a line trending northwest to southeast, from near shore to deeper waters. These profiles are made by sending sound waves into the Earth and recording the echoes reflected back from the layers of rock. Analyzing these echoes using computers, profiles such as this are produced. The large dark line running diagonally through Figure 8, from the upper left to the lower right, is known as the Corsair fault. It is a large geologic feature, a normal fault that was active during the deposition of the surrounding sediments. The sediments to the right of the fault slipped downward, creating space for more sediment to be deposited than on the left side. The difference in thickness of layers along one of these growth faults can be more than a thousand meters. Because of the large variation in thickness across growth faults, microfossils are extremely useful in correlating time equivalent horizons from one side to the other. In the illustration, layers known to contain natural gas in the near-by well were projected into the proposed well using seismic correlation of biostratigraphically constrained horizons.

Nearby wells have been drilled through the Corsair fault and the section beneath the fault is easily recognizable by distinctive benthic foraminiferal "marker species". The proposed well was drilled, but unfortunately did not find hydrocarbons. A micro-paleontologist on the drilling rig examined cuttings samples collected every ten meters during the drilling of the bottom 470 meters of the well. His workwas used to calibrate the small faults encountered while drilling near the large Corsair fault. The micropaleontologist was charged with ordering a halt to drilling if he observed fossils indicating that the Corsair fault was penetrated. The stopping point for the well was in fact determined using the observed microfossils.


Figure 8
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For paleoenvironmental analyses of Gulf of Mexico exploration, studies of the distribution of living benthic foraminifera (Poag, 1981; Pflum and Frerichs, 1976, Phleger and Parker, 1951) provide an excellent database. Using these studies and others, paleontologists constructed models for interpreting past Gulf of Mexico environments using fossil benthic foraminifera (Breard, Callender and Nault, 1993: Culver, 1988, Tipsworth et al., 1966). Wells drilled in Pleistocene and Pliocene age sediments encounter fossils of many extant species of benthic foraminifera and consequently paleoenvironmental interpretations are made with reasonable confidence. However, as wells are drilled deeper into older sediments, the percentage of extinct species encountered rises rapidly. In the older sediments paleoenvironments are more speculative, but can be inferred.


Commonly in Gulf Coast paleontology, ancient marine environments are related to interpreted water depths (paleobathymetry). This is an oversimplification because benthic foraminifera often respond to water conditions (temperature, salinity, dissolved oxygen, etc.) rather than to depth. However, there are over 40,000 wells drilled in the Gulf. By combining data from existing wells, it is possible to reconstruct the profile of the continental shelf and slope at various points in geologic time. Such paleogeographic maps, combined with seismic profiles and other geologic data sets, are the tools used in the search for hydrocarbons. It is paleontology that uniquely explains the element of geologic time and depositional environment to petroleum geology.

ACKNOWLEDGMENTS
The author is grateful for help from Anne Hill (Shell Offshore Inc.) for preparation of the figures and to Dennis Greig (Chevron USA, Inc.) for use of his fine SEM photomicrographs. Thanks also to Mike Styzen and Al DuVernay of Shell Offshore Inc. for review of the manuscript.

REFERENCES
Baker, R. 1979. A Primer of Oilwell Drilling. Petroleum Extension Service, the Univ. of Texas at Austin, Austin. 94 pp.

Breard, S.Q., A.D. Callender and M.J. Nault. 1993. Paleoecologic and biostratigraphic models for Pleistocene through Miocene foraminiferal assemblages of the Gulf Coast basin. Gulf Coast Association of Geological Societies, Transactions 43: 493-502.

Culver, S.J. 1988. New foraminiferal depth zonation of the Northwestern Gulf of Mexico. Palaios, 3: 69-86.

Davies. E.H. and J.P. Bujak. 1987. Petroleum exploration applications of palynological assemblage successions in the flexure trend, Gulf of Mexico. In Innovative biostratigraphic approaches to sequence analysis: New exploration opportunities. Gulf Coast Section Society of Economic Paleontologists and Mineralogists. p. 47-51.

Fleisher, R.L. and H.R. Lane. (eds.). In press. Applied Paleontology, In E.A. Beaumont and N.H. Foster (eds.), Exploring for Oil and Gas Traps, Handbook No. 3, Treatise of Petroleim Geology. American Association of Petroleum Geologists.

Galloway, W.E., D.G. Bebout, W.L. Fisher, J.G. Dunlap, Jr., R. C. Cabrera-Castro, J. E. Lugo-Rivera and T.M. Scott. 1991. Cenozoic. In A. Salvador (ed.). The Gulf of Mexico Basin. The Geology of North America Vol. J. p. 245-324.

Haq, B.U. and A. Boersma, (eds.). 1978. Introduction to Marine Micropaleontology. Elsevier, New York. 376 pp.

LeRoy, D.O. 1977. Economic Microbiostratigraphy. In L.W. LeRoy, D.O.LeRoy and J.W. Raese. Subsurface Geology - Petroleum - Mining - Construction. Colorado School of Mines. p.212-233.

Pflum, C.E. and W.E. Frerichs. 1976. Gulf of Mexico Deep-Water Foraminifers. Cushman Foundation for Foraminferal Research, Special Publication No. 14, 125 pp.

Phleger, F.B. and F.L. Parker. 1951. Ecology of foraminifera, northwest Gulf of Mexico. Geological Society of America. Memoir 46, Pt 1. 1-88, Pt. 2, 1-64.

Poag, C.W. 1981. Ecologic Atlas of Benthic Foraminfera of the Gulf of Mexico. Hutchinson Ross Publishing Co. 174 pp.

Tipsworth, H.L., F.M. Setzer and F.L. Smith. 1966. Interpretation of depositional environment in Gulf Coast petroleum exploration from paleoecology and related stratigraphy. Gulf Coast Association of Geological Societies, Transactions 16: 119-130.

Ventress, W.P.S. 1991. Paleontology and its application in South Louisiana Hydrocarbon Exploration, In D. Goldthwaite. (ed.). An Introduction to Central Gulf Coast Geology. New Orleans Geological Society p. 85-97.

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