The fossils of the Burgess Shale, like the Burgess Shale itself, are fossils that formed around 505 million years ago in the mid-Cambrian period. They were discovered in Canada in 1886, and Charles Doolittle Walcott collected over 65,000 specimens in a series of field trips up to the alpine site from 1909 to 1924. After a period of neglect from the 1930s to the early 1960s, new excavations and re-examinations of Walcott's collection continue to reveal new species, and statistical analysis suggests that additional discoveries will continue for the foreseeable future. Stephen Jay Gould's 1989 book Wonderful Life describes the history of discovery up to the early 1980s, although his analysis of the implications for evolution has been contested.

The fossil beds are in a series of shale layers, averaging and totalling about in thickness. These layers were deposited against the face of a high undersea limestone cliff. All these features were later raised up above current sea level during the creation of the Rocky Mountains.

These fossils have been preserved in a distinctive style known as Burgess Shale-type preservation, which preserves fairly tough tissues such as cuticle as thin films, and soft tissues as solid shapes, quickly enough that decay has not destroyed them. Moderately soft tissues, such as muscles, are lost. Scientists are still unsure about the processes that created these fossils. While there is little doubt that the animals were buried under catastrophic flows of sediment, it is uncertain whether they were transported by the flows from other locations, or lived in the area where they were buried, or were a mixture of local and transported specimens. This issue is closely related to whether conditions around the burial sites were anoxic or had a moderate supply of oxygen. Anoxic conditions are generally thought the most favourable for fossilization, but imply that the animals could not have lived where they were buried.

In the 1970s and early 1980s the Burgess fossils were largely regarded as evidence that the familiar phyla of animals appeared very rapidly in the Early Cambrian, in what is often called the Cambrian explosion. This view was already known to Charles Darwin, who regarded it as one of the greatest difficulties for the theory of evolution he presented in The Origin of Species in 1859. However, from the early 1980s the cladistics method of analysing "evolutionary family trees" has persuaded most researchers that many of the Burgess Shale's "weird wonders", such as Opabinia and Hallucigenia, were evolutionary "aunts and cousins" of present-day types of animal rather than a rapid proliferation of separate phyla, some of which were short-lived. Nevertheless, there is still debate, sometimes vigorous, about the relationships between some groups of animals.

Discovery, collection, and re-examinations

The first Burgess Shale fossils were found on Mount Stephen in Canada's Rocky Mountains by a construction worker, whose reports of them reached Richard McConnell of the Geological Survey of Canada. McConnell found trilobite beds there in 1886, and some unusual fossils that he reported to his superior. These were misdiagnosed as headless shrimps with unjointed appendages, and were named Anomalocaris because of their unusual appendages – but turned out to be pieces of a puzzle that took 90 years to solve.

Similar fossils were reported in 1902 from nearby Mount Field, another part of the Stephen Formation. These may have been why Charles Doolittle Walcott visited Mount Field in 1909. While taking photographs there Walcott found a slab of fossils that he described as "Phyllopod crustaceans". From late August to early September 1909, his team, including his family, collected fossils there, and in 1910 Walcott opened a quarry that he and his colleagues re-visited in 1911, 1912, 1913, 1917 and 1924, bringing back over 60,000 specimens in total. Walcott was Secretary of the Smithsonian Institution from 1907 to his death in 1927, and this kept him so busy that he was still trying to make time for analyzing his finds two years before his death. Although he drew attention to the exceptional detail of the specimens, which were the first known fossils of soft-bodied animals from the Cambrian period, he also had other research interests: the Early Paleozoic stratigraphy of the Canadian Rockies, which took up the great majority of his time there; and Precambrian fossils of algae and bacteria, to which he assigned as much importance as to the fossils of animals. He managed to publish four "preliminary" papers on the fossil animals in 1911 and 1912, and further articles in 1918, 1919 and 1920. Four years after Walcott's death his associate Charles Resser produced a package of additional descriptions from Walcott's notes. Walcott's classifications of most of the fossils are now rejected, but were supported at the time, and he accepted a change for one of the few where his conclusion was disputed. Many of the later comments were made with the benefits of hindsight, and of techniques and concepts unknown in Walcott's time.

Although in 1931 Percy Raymond opened and briefly excavated another quarry about above Walcott's "Phyllopod bed", there was very little interest in the Burgess Shale fossils from the 1930s to the early 1960s, and most of those collected by Walcott were stored on high shelving in back rooms at the Smithsonian Institution. Between 1962 and the mid-1970s Alberto Simonetta re-examined some of Walcott's collection and suggested some new interpretations. Beginning in the early 1970s Harry Whittington, his associates David Bruton and Christopher Hughes, and his graduate students Derek Briggs and Simon Conway Morris began a thorough re-examination of Walcott's collection. Although they assigned groups of fossils to each member of the team, they all decided for themselves which fossils to investigate and in what order. Their publications and Stephen Jay Goulds' popularization of their work in his book Wonderful Life aroused enduring scientific interest and some public interest in the Cambrian explosion, the apparently rapid appearance of moderately complex bilaterian animals in the Early Cambrian.

The continuing search for Burgess Shale fossils since the mid-1970s has led to the description in the 1980s of an arthropod Sanctacaris and in 2007 of Orthrozanclus, which looked like a slug with a small shell at the front, chain mail over the back and long, curved spines round the edges. Recent digs have discovered species yet to be formally described and named. They have also unearthed more and sometimes better fossils of animals that were discovered earlier, for example Odontogriphus was for many years known from just one poorly preserved specimen, but the discovery of a further 189 formed the basis for a detailed description and analysis in 2006. A full pre-publication draft, free but without pictures, may be available at Re-examination of Walcott's collection also continues, and has led to the reconstruction of the large marine animal Hurdia in 2009.

Geology

The Burgess Shale is a series of sediment deposits spread over a vertical distance of hundreds of metres, extending laterally for at least . The deposits were originally laid down on the floor of a shallow sea; during the Late Cretaceous Laramide orogeny, mountain-building processes squeezed the sediments upwards to their current position at around elevation in the Rocky Mountains.

The rocks containing the fossils are on the border between two partially overlapping bands of rock that run along the western face of the Canadian Rockies. On the eastern side of this border is the Cathedral Formation, a platform of limestone formed by algae. The western surface of the Cathedral Formation is steep and consists of the resistant rock dolomite, which was originally part of the limestone platform, but between the Mid Silurian and Late Devonian was transformed by hydrothermal flows of brine at up to , which replaced much of the limestone's calcium with magnesium. A layer of shale lies partly on top of and partly to the west of the Cathedral Formation. This shale layer used to be called the "thin" Stephen Formation where it lies above the Cathedral Formation and the "thick" Stephen Formation where it lies to the west; but the "thick" Stephen Formation is now generally known as the Burgess Formation.

The shale is made of alternating fine-grained layers of siliceous mudstone (compressed, hardened mud originally made of ground-up silicate rock) and calcisiltite originally animal shells. The calcisiltite layers contain relatively unremarkable shells and occasional non-biomineralized fossils (such as priapulid tubes). The soft-bodied organisms for which the Burgess Shale is famous are fossilized in the mudstone layers, which are between thick, averaging , and have well-defined bases. Opinions vary about how the mudstone layers were produced: perhaps by mudslides from the top of the "Cathedral" limestone platform, when its edge collapsed occasionally; or possibly by storms that created back-currents that abruptly washed large volumes of mud off the platform. Each mudstone layer is the result of one such catastrophe. The Greater Phyllopod Bed, a thick sequence consisting of Walcott's famous "Phyllopod Bed" plus the below that, contains at least 36 layers, deposited over 10 to 100 thousand years, during which the environment was essentially stable.

Fossil preservation

The processes responsible for preserving the exceptional quality of the Burgess Shale fossils are unclear, due partly to two related issues: whether the animals were buried where they lived (or may have been carried long distances by sediment flows), or whether the water at the burial sites was anoxic, limiting the effect of oxygen on degradation. The traditional view is that soft bodies and organs could only be preserved in anoxic conditions, otherwise oxygen-breathing bacteria would have made decomposition too rapid for fossilization. This would imply that the sea-floor organisms could not have lived there. However, in 2006 Caron and Jackson concluded that the sea-floor animals were buried where they lived. One of their main reasons was that many fossils represented partially decayed soft-bodied animals such as polychaetes, which had already died shortly before the burial event, and would have been fragmented if they had been transported any significant distance by a storm of swirling sediment. Other evidence for burial where the animals had lived includes the presence of tubes and burrows, and of assemblies of animals preserved while they fed – such as a group of carnivorous priapulids clustered round a freshly moulted arthropod whose new cuticle would not yet have hardened. Fossilized swimming organisms were also buried immediately below where they lived.

Fossil tracks are rare and no burrows under the sea-floor have so far been found in the Burgess Shale. These absences have been used to support the idea that the water near the sea-floor was anoxic. However it is possible that the water just above the sea-floor was oxygenated while the water in the sediment below it was anoxic, and also possible that there simply were no deep-burrowing animals in the Burgess Shale. Some fossils, such as Marrella, are almost always the right way up, which suggests they were not transported far if at all. Others, such as Wiwaxia, are often at odd angles, and some fossils of animals with shelly or toughened components very rarely contain remains of soft tissues. This suggests that the distances over which corpses were transported may have varied between genera, although most were buried where they had lived.