Tag Archives: Evolution

Understanding Evolution: Macroevolution & Major Transitions

May 2, 2015 antonio Leave a comment

Evolution is a fascinating topic that allows you to look at life through the lens of deep time. ‘Deep time’ are vast intervals that cannot be experienced in normal everyday life and it is studied through the science disciplines of geology and paleontology.

But what is ‘evolution’? Is it a fact? Is it a theory?

There are many variants on the definition of evolution, but in the most concise definition, evolution is change over time. More importantly, it is the observable change over time on generations. Changes in a single human individual is not evolution, but developmental. Evolution is concerned with changes on a population.

Evolution is often divided into microevolution and macroevolution. Microevolution refers to change within a species. Species are a group of organisms with shared traits, but a condensed definition of species is a closed gene pool. Macroevolution is when a species changes into another species – a process known as speciation.

Evolution is both a fact and theory. Across the scientific disciplines, evolution without an argument is a fact. The ‘fact’ stems from the overwhelming amount of evidence of the fossil records, transitional fossils, molecular clock, genetics, and so forth, which also includes facts from laboratory experiments and data from the observable real-world. The ‘theory’ part deals with how we think the fact of evolution has occurred.

In this post, we will be concerned with macroevolutionary transitions.

Macroevolution transitions are that of where some great leap happened, such as a novel mean of adapting to a radical environment. For some examples, think about transitions from sea to the land, the land to the air, the land back to the sea, or salt water to fresh water. Think about leaps in habitats that also forced additional leaps in reproduction. For example, think of the development on land of both plant seeds and enclosed animal eggs as adaptation to arid environments. Another example is live birth by dolphins, which is an adaptation to marine environments. Fruits with surrounding seeds that entice hungry animals is an adaptation to enhance plant reproduction.

In turn, some major evolutionary transitions actually changed environments, thus driving additional evolutionary transitions. Think of how the evolution of land plants changed landscapes, the evolution of coral reefs changed seascapes, and evolution flying pollinating insects that changed landscapes.

We can see these sorts of transitions all around us. For example, although modern seals and walruses are adapted to spend most of their lives in marine environments, they are descended from land dwelling animals. An opposite example are penguins which are in transition from terrestrial to marine environments. They descended from birds that originally flew in the air. They now use their flying ability to great advantage when flying under the water.

Here are some major evolutionary transitions:

Eukaryotic cells – the first major transition which happened more than 2 billion years ago.
Multi-celled animals – single cell eukaryotes evolved to become multi-celled animals ca. 600-550 ma
Skeletons – animals went from softbodied to hardbodied with the development of skeletons and other mineralized parts, whether these evolved with shells, bones or teeth. Animals with a backbone show up in the fossil record ca. 530 ma.
Life on land – This is an interesting transition that happened ca. 500 – 400 ma. Here, plants, fungi, and animals all evolved to live on land that descended from organisms that originally lived in marine environments.
Vertebrate origins – Vertebrate also became four-legged and started to walk on land ca. 400 ma.
Insect flight and coevolution with seed plants – While vertebrates were beginning to walk on four legs, insects also began to appear ca. 400 – 350 ma. The appearance of insects nearly coincided with the transition of plants with seeds and the first forest.
First eggs – The evolution of enclosed animal eggs happened ca. 340 – 310 ma. This was a huge transition. This freed reptiles from watery environments and led to the later evolution of mammals and dinosaurs, as well as flying and swimming reptiles.
First flowers – The evolution of flowering plants happened ca. 130 -125 ma. This changed the world as we know it. Not coincidentally, this major transition happened with an evolution of insects into pollinating insects.
Mammal origins and evolution – Their evolution originally from reptiles happened ca. 230 ma. Later, they underwent additional evolutionary leaps, such as from egg-laying to giving live birth, and from hoofed land-dwellers to whales.
Primate and human origins – There are several important transitions involved in their overall transitions; from tree dwelling primates to the eventual evolution of humans.

Four Factors that are Responsible for Macroevolutionary Change*

Geographic Isolation

Geographic isolation refers to how populations of a species may become isolated from one another. This include a physical barrier like a mountain chain, a river, or an ocean, that splits a species into different places. Geographic isolation is not restricted to physical barriers, it simply may be an unfavorable habitat between two populations that prevent them from mating with each other. With enough time, geographic isolation can result in a second factor responsible for macroevolutionary change: genetic drift.

Genetic Drift

This means that a species has drifted enough, genetically speaking, from its ancestral population that it then became a different species or even diversified into many species. We sometimes call this adaptive radiation. It is important to note that while we are speaking of genetic drift in a macroevolutionary sense, genetic drift can also operate on the microevolution level without directly attributing to a new species. Genetic drift on this level concerns itself with fluctuations in allele frequencies on a population due to chance. One example are the Amish people of Eastern Pennsylvania. They are a closed population that originated from a small number of German immigrants. They inherited rare concentrations of gene mutations from the German founders (hence, the founder effect) that is still active in their population. These mutations causes a number of disorders such as polydactyly (extra fingers) and forms of dwarfism. Because Amish people tend to marry within their population, the recessive genes have a high chance to come together during meiosis which requires two copies of the gene to trigger the disorders.

Environmental Change

Environmental change can be local or global. For example, lowering of sea levels during a time of global cooling would be advantageous for those organisms adapted to cool environment, or to an expansion of land environment.

Mass Extinctions

Mass extinctions are recognized as a factor in macro evolution. There has been 5 mass extinctions (a 6th is currently hypothesized) in the geologic past well before humans showed up. These extinctions occurred 440 ma, 360 ma, 250 ma, 200 ma, and 65 ma. We now suspect that these extinction events while also taking out a lot of species, also led to the opening of habitats and resources for those species that survived. One example is the evolution of dinosaurs from ancestral reptiles that occurred after an extinction event 200ma. Extinctions may have hastened some evolutionary transitions.

These four factors could be summarized by a little phrase coined by Charles Darwin: Natural Selection. After all, as environments change or mass extinctions take place, organisms in the right place, with the right stuff (genetically speaking), gets selected to pass on those genes to the next generation. Selection also includes the ‘artificial selection’ that we humans have done through the selective breeding and modification of domestic animals.

*Although we speak of four factors/natural selection that drive macroevolutionary change, it is important to note that there are other roles that attribute to evolutionary changes. We’ll examine a bit of these roles to understand how far science has progressed since Charles Darwin proposed the hypothesis of descent with modification via his 1859 book Origins of Species, which later turned into evolutionary theory.

New science roles that emerged since Darwin’s time include plate tectonics, which helps explain how populations have become geographically isolated in the geologic past. It also helps to explain how volcanism might have altered the atmosphere, how mountain building and how other earth processes change environments or even influence mass extinctions. Developmental biology examines how genes code for the development of growing organisms and how these genes might be switched on or off during evolution. Ecology is sophisticated science that looks closely and systematically at how organisms and communities interact with one another and how physical factors in their environments affect and guide their evolution. Modern genetic studies also examine genetic similarity and even help to explain sources of variation. One of the tools that are used in genetic studies include the molecular clock (the general idea is using calculated rates of change in RNA and DNA to estimate when major transitions may have happened.)

Time-permitting, I will come back to expand on a web series regarding evolution.

Archaeology, Geology

Analysis of the Sterkfontein Cave Site in South Africa

November 18, 2014 antonio 1 Comment

Microstratigraphic Analysis of the Sterkfontein Cave Site

by antonio kuilan

Abstract

Sterkfontein is an extremely complicated plio-pliestocene site. The cave formation process climaxed ca 25 Ma as the sea that it was submerged in retreated. Avens on the surface washed in debris that later cemented into breccia. In the late 1800s, an Italian miner dynamited the surface of Sterkfontein in search of lime which led to discovery of cave formations and put Sterkfontein on the map of the scientific world. Primate fossils appeared in the mid-30s in discarded breccia by the miners and this generated more interest that led to the discovery of Australopithecus by the late Robert Broom. This ignited archaeological interest that evolved an excavation program that continues to the present day. The site has produced thousands of fauna fossils and stone tools (including Oldowan and Acheulian industries), and hundreds of hominid remains and fragments of fossilized wood with notable hominins: Australopithecus, A. africanus, Paranthropus, P. robustus, and early Homo. Understanding the complex stratigraphy is still a work in progress and recent dating methods that includes magnetostratigraphy and uranium dating are arriving at more precise dates. One controversy was the discovery of blood residue of stone tools but studies by three researchers suggest that the clay-rich environment of Sterkfontein slows down the decay process that will give residues the appearance of being preserved tens of thousands of years later.

Sterkfontein Cave Site

To begin to understand the complexities of the Sterkfontein Cave site, one must start back at the beginning to have a working geological knowledge of its formation. The Plio-Pleistocene site of Sterkfontein is located in the Gauteng region about 50km northwest of Johannesburg, South Africa. Around 2.5 billion years ago, this region was submerged under a warm shallow sea that provided the conditions for the formation of sediments that later solidified as dolomitic limestone rock. Through hundreds of millions of years, extensive formations of quartzite and shale formed from other sediments that covered the dolomite as it rested beneath the seabed. Circa 25 million years ago, the sea retreated and geological processes altered the attitude of the strata to dip in a northwestern manner (Figure 1).

Around 50 m deep under the water table, cavern formations commenced with the calcium carbonate being dissolved out of the dolomite across horizontal planes by the weakly acidic ground water. Later, these cavern formations became sealed air-filled cavities as the water table dropped (Figure 2).

Slow seeping acidic groundwater continued to work the dolomite, dissolving minerals, and when each drop reached the cave’s ceiling, it precipitated back to limestone, forming elongated stalactites (figure 2) – a process that has taken thousands of years. Eventually, avens opened on the surface above, resulting from the prolonged dissolution of the dolomite along vertical cracks or joints (figure 3).

Some joints became exposed due to the surface being subjected to erosional processes, which also ended the sealed state of the air-filled cavities (Figure 3). Over thousands of years, earth and rock washed into the cave forming talus deposits that eventually became cemented by dripping lime. Some of the breccia, formed from talus, collapsed from the higher, mature, cave formations above, with some of it returning to returning to its natural, soft state, due to decalcification (Figure 4).

The excavation of these ancient infills is what yields hominid remains, flora, fauna, and stone artifacts .

In the 1890s, it was Italian miner Guglielmo Martinaglia that first started dynamiting the Sterkfontein surface to exploit the stalactites and stalagmites below for its lime.

Around the same time, Geologist David Draper from the South African Geological Society attempted to convince the miners to stop mining and preserve the main cave due to its rich geologic content but was unsuccessful. Mining continued throughout the decades, with the area becoming a local attraction. It was the initial blasting by Martinaglia that paved the path to later scientific exploration at Sterkfontein.

Various studies have shown that the Sterkfontein caves with its brecciated infills, talus deposits, surface debris deposited through avens, orientation of deposits, the dissolution of limestone, and the decalcification of lime-consolidated breccias, make the site extremely complex and its stratigraphy difficult to decipher.

Figure 5 shows an overall diagram of the complexity of the Sterkfontein Caves. The site is divided into the Lincoln Cave, Silberberg Grotto, Jakovec Cavern, Name Chamber, Elephant Chamber and Milner Hall. There are 6 members at Sterkfontein. Geologist Tim Partridge performed detailed studies on the stratigraphy of Sterkfontein and identified six geological divisions of the Sterkfontein Formation that he described as Members 1, 2, 3, 4, 5, and 6.

These members are shown in a simplified drawing by Ron Clarke in Figure 6; Members 4, 5, and 6 are based on the surface and Members 1, 2, and 3 are underground.

This Member naming structure continues to be used in scientific literature.

Archaeological Evolution and the Significant Finds at Sterkfontein

The mining at Sterkfontein since Martinaglia blasted the area in the 1890s changed evolved throughout the decades and by the early 1930s large amounts of blasted breccia removed by the lime workers started to reveal primate bones, from which Trever Jones, a student of Raymond Dart, obtained fossil monkeys in 1935 and published the first scientific study of fossils form the site in 1936. Interest kept increasing at Sterkfontein. Other students of Dart introduced Paleontologist Robert Broom, who was 70 years old at the time and searching for ape-man remains at nearby Pretoria, to Sterkfontein in August 1936. A few days later, George Barlow, the lime quarry manager at the time, handed Broom the first hominid fossil from the breccia, Australopithecus. This led to many other discoveries including the most complete skull of Australopithecus africanus in 1947.

Interest at Sterkfontein was at its maximum and in 1956 Charles K Brain and Anthony B.A. Brink discovered the first early Acheulian hominid stone stools in the breccia dumped by lime workers. After this discovery, archaeologist Revil Mason conducted the first test excavation with Charles Brain in 1956. John Robinson (the late Robert Broom’s trusted assistant) excavated Sterkfontein from 1957-1958 revealing an early Acheulian industry that was later analyzed by Revil Mason. Palaeoanthropologist Philip V Tobias created the full-time excavation program in 1966 at Sterkfontein that has run to the present day without interruptions. Ian Watt surveyed the Sterkfontein Caves and created a greatly extended grid system necessary to record the positions of finds at the site; this grid system was implemented in Tobias excavation program. Alun Hughes headed the Tobias excavation program from 1966 to 1991 and during this time the discovery of hundreds of Australopithecus fossils were credited to him.

Suspended Harris Matrix over excavation site.

Palaeoanthropologist Ronald Clarke has headed the excavation program since 1991, a few years later he was searching through stored boxes containing faunal remains that were excavated in early 1980 from the Silberberg Grotto section of Sterkfontein, discovering leg/foot bones that belonged to one individual. He predicted the rest were embedded in the breccia of that section and based on the cataloged information, he instructed this assistants to search the Member 2 breccia. A short time later in 1997, the rest of the bones (radius, lower legs, left humerus) were discovered, including the first complete skull ever found of Australopithecus, which was later dubbed “Little Foot.” Its species designation is an ongoing controversy.

Over 9,000 stone tools/flakes, thousands of faunal fossils, hundreds of fragments of fossil wood, and nearly 500 hominid fossils (skulls, jaws, teeth, and other skeletal remains) have been found in the entirety of the excavations at Sterkfontein. Members 1 through 3 are mostly partial remains of monkeys and carnivores. Analysis on fossilized wood fragments from the breccia in Member 4 reveal that the area was surrounded by tropical forest trees ca. 2.8 Ma. Australopithecus has been found in the breccias of Member 2 & 4 and in the lower cave, Jacovec Cavern. A. africanus is found in Member 4. Early Homo has been found in StW 53 (an infill between Members 4 and 5) and in Member 5. Paranthropus and P. robustus are also found in Member 5. Member 6 is dated < 200ka and produces primates of modern form. Oldowan and Acheulian tools are found in Member 5.

One Controversy at Member 5

In 1997, T.H. Loy claimed that he detected blood residues on Oldowan stone tools from the stratigraphic Member 5. This became controversial. It was stated that researchers are unable to describe the mechanism of residue decays, leading analysts who record data to make interpretations that are oversimplified or inaccurate. Peta Jane Jones (2009) conducted a study that directly assessed Loy’s blood residue claim. Jones performed an indepth microstratigraphic investigation into the Member 5 geological matrix that housed the stone tools from Loy’s claims. Jones conducted a battery of chemical tests, including petrographic analysis and pH analysis on the composition of the breccia burial matrix. Jones study suggested that a cave environment with a well-cemented, clay-rich burial matrix, a favorable alkaline pH, and a high soil cation exchange capacity, favors residue preservations over extreme timeframes. Jones summarized that:

Stone tools are used multiple times to butcher, leaving thick layer of blood residues on them; as it dries, it secretes into microcracks.
Through transport, residues later come in contact with clay and leads to a degree of binding that creates hydrophobic proteins.
The artifacts and sediment are transported, and may be deposited through avens, slopes, or other entrances.
Organic-mineral complexes are encouraged by large negatively charged surface area and swelling ability of clay sediment; the accumulated proteins with clay are more resistant to degradation.
Leaching occurs by rainfall releasing calcium ions from dolomitic rock on top and the solution filters through sediments below as calcite which cements deposits into brecciated infill.
Organic material absorbs calcium ions, weak bonds form between calcite and clay surfaces, and the precipitated calcite creates a well-cemented clay/calcite matrix that encloses and protects artifacts and blood residue.
A regulated environment is maintained by the breccia matrix that “…is not directly exposed to surficial water and was possibly buried with further compaction from overlying brecciated deposits, protected from detrimental conditions.”

A summary of Jones' work — A summary of Jones’ work

Geeske Langejans (2010) took a step further and performed experimental archaeology by leaving stone tools at 3 different sites for a year to test preservation. Sterkfontein was one site, along with Sibudu, and Zelhem, a site in the Netherlands that act as a control. At Sterkfontein, he left 80 samples; 40 samples inside the cave and 40 samples outside the cave (see Figure 7).

The 40 samples to be placed inside the cave were further divided: 20 left buried and 20 left on top of sediment. Langejans retrieved the residue samples in the cave 1 year later and found that those that were buried preserved best. Langejans stated that different residues preserve differentially, some better than others; though residue always undergo decomposition, those that are in a dry zone bioactivity undergo slow decay that can take tens of thousands of years, give residues the appearance of being permanently preserved – as long as the environment remains stable. This experiment and the work of Jones and Hopley provide evidence of preservation at Sterkfontein, but can also be used to make predictions of residue preservation at other and future sites.

Dating

Early dating of the Sterkfontein Caves was based on faunal correlation based on changes in dentition and anatomy, followed by later cosmogenic isotope burial ages, uranium-lead dating of speleothems, ESR, and magnetostratigraphy.

Uranium Dating

Pickering (2010) performed dating on young carbonates from open exposures at Sterkfontein, on boreholes that were drilled twenty-five years earlier by Partridge and Watt, and on underground deposits from the caves. Figure 8 shows updated stratigraphic logs with black arrows pointing to the uranium dating. Uranium dating gave the following estimates to the given members:

Member 1 = >2.8 Ma
Member 2 = 2.6 – 2.8 Ma
Member 3 = 2.6 – 2.0 Ma
Member 4 = 2.6 – 2.0 Ma
Member 5 = < 2.0 Ma

Interesting to note that Pickering argued for a revised stratigraphy at Sterkfontein, that Pickering “believe” no clastic sedimentation exist between Members 2 and 4 but instead separated by a massive flowstone layer. Most strongly, Pickering claims that there is no evidence that the present cave “…was ever wholly filled up with sediments.” Pickering also note that Sterkfontein is complex including the problem of past mining activity removing material, noting that his interpretation is not absolute, but that stratigraphy at Sterkfontein is “…likely to remain a contentious issue.”

Magnetostratigraphy

One recent palaeomagnetic analysis was published by Herries and Shaw in based on analysis from speleothems in Members 1 through 5. Figure 9 (Herries) depict the location of paleomagnetic samples based on the composite stratigraphy compiled by Partridge in 2000. Two methods of sampling were executed at Sterkfontein by Herries: block sampling and drill coring.

Figure 10 (Herries) illustrates the magnetostratigraphy for the Sterkfontein Cave. Palaeolatitude (degrees) versus depth (meters) are plotted against: archaeology, hominin fossils, polarity, Members, and the geomagnetic polarity timescale. Key: O = Olduvai event, R = Reunion event, HR = Huckleberry Ridge event.

Herries (2011) proposed a chart with suggested age ranges based on a combination of uranium, ESR, and magnetostratigraphy data (Figure 11).

Conclusion

The Sterkfontein Cave is an extremely complicated site. Although continuing work has been conducted since the late 30s at the site, there is much debate about its stratigraphy. Pickering even implied that the Member naming scheme may be limiting since he attempted to revise the stratigraphy without distorting the Member system. The complex infills and other deposition combined with collapsing cave mechanics and chemical weathering, leave the guts of Sterkfontein intertwined. Because of the topographic complexity, it had made earlier to recent dating slightly difficult. The accumulative work of researchers over the decades seem to be revealing precise dates but what is going on inside the cave still continues to be the subject of long arduous work. The site still continue to produce countless finds – perhaps the next one will add another clue to our evolutionary past.

References

Creighton, Gabel. Africa South: The Last 30,000 Centuries: Recent Investigations of Man’s Past in the Sub-Saharan Tropics. Journal of Field Archaeology. 2: 363-387. 1983

Herries, Andy I.R. and Shaw, John. Palaeomagnetic Analysis of the Sterkfontein Palaeocave Deposits: Implications for the Age of the Hominin Fossils and Stone Tool Industries. Journal of Human Evolution. 2010. 1-17.

Hopley, J. Philip, et al. Speleothem Preservation and Diagenesis in South African Hominin Sites: Implications for Paleoenvironments and Geochronology. Geoarchaeology. 24 (5): 519-547. 2009

Jones, Jane Peta. A Microstratigraphic Investigation into the Longevity of Archaeological Residues, Sterkfontein, South Africa. Archaeological Science Under a Microscope. 2009.

Kuman, Kathleen. The Archaeology of Sterkfontein – Past and Present. Journal of Human Evolution. 27:471-495. 1994.

Kuman, Kathleen, and Clarke Ron, J. Stratigraphy, Artefact Industries and Hominid Associations for Sterkfontein, Member 5. Journal of Human Evolution. 38: 827-847. 2000.

Langejans, H.J. Geeske. Remains of the Day-Preservation of Organic Micro-Residues on Stone Tools. Journal of Archaeological Science. 37: 971-985. 2010.

Pickering, Robyn. Re-Appraisal of the Stratigraphy and Determination of New U- Pb dates for the Sterkfontein Hominin Site, South Africa. Journal of Human Evolution. 59: 70-86. 2010.

Stratford, J. Dominic, et al. New Stratigraphic Interpretations of the Fossil and Artefact-Bearing Deposits of the Name Chamber, Sterkfontein. South African Archaeological Bulletin. 67 (196): 159-167. 2012.

Wilkinson, M. Justin. Geomorphic Perspectives on the Sterkfontein Australopithecine Breccias. Journal of Archaeological Science. 10: 515- 529. 1983.