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The Paleocene Epoch
66.4-57.8 MY Ago
Still isolated from influx of sediments (sands, silts and clays) derived from the lands to the North, bathed by warm northward-moving tropical waters, the Florida Platform continues to accumulate carbonates, as it did in the Cretaceous. After the hiatus in the early Paleocene, sea level remains generally high and the platform commmonly remains submerged.  While the pattern of rock accumulation might be the same as during the Cretaceous, there is a major difference in life in the Paleocene seas as the result of the great extinction that took place at the end of the Cretaceous. The ammonites are gone. The great reef builders of the past (like the rudists)  have either become extinct or, greatly reduced like the corals (although we do find evidence of patch reefs but not of massive reefs).  Clams and snails continue to be important, and bryozoans and echinoderms flourish. It is also worth noting that elsewhere this is the time when the first grasses appear on land, although not in Florida, where there is no land. The Cedar Keys Limestone is deposited from the Late Paleocene into the Early Eocene.

The Eocene Epoch
57.8-36.6 MY Ago
In the Early Eocene North America and Europe are still joined.  The Florida Platform is commonly submerged under a warm ocean and limestone deposition continues uninterrupted from the Paleocene as examplified by the Cedar Keys Limestone. 

In the Middle Eocene, the Oldsmar Limestone and overlying Avon Park Limestone are being put down in warm shallow seas where life still shows marked Tethyan (mediterranean) influences.  This is the first time that massive coral reefs re-appear on the platform, although they sill are uncommon. Echinoderms continue to branch out and sand dollars appear, as do sea turtles.  We also see the first appearance of archeocete whales, which still have large serrated teeth.  Two genera are relatively common; Zygorhiza reaches up to 20 feet  in length and the large Basilosaurus up to 70'. (More on fossil whales)

In Late Eocene, limestone continues to accumulate, only interrupted by occasional sea level fluctuations. The Ocala Limestone which succeeds the Avon Park, shows very little lithologic variation indicating that conditions are fairly uniform throughout that time. The sirenian Protosiren ancestor of the modern manatees and dugongs is found in the Ocala Ls. 

Some 40 Million Years ago, towards the end of the Eocene Epoch,  the global circulation patterns that prevailed since Cretaceous time begin to change and uniformly warm ocean temperatures become a thing of the past, especially in the ever widening Atlantic. Two events work together to bring about this change. Firstly, the eastern Tethys seaway almost completely closes. This shuts off the warm currents that once upon a time practically circled the globe from East to West. Secondly, as North America separates from Europe, the northern part of the Atlantic Ocean opens. As it becomes connected to the Arctic Ocean, cold arctic ocean waters spill into the North Atlantic. Consequently,  the abyssal (deepest part) of the ocean fills with cold water and cools significantly.  This injection of cold water may be the main cause of the extinction of many marine forms that occurs at the end of the Eocene. 

The Oligocene Epoch
36.6-23.7 MY Ago
Early Oligocene,
After a hiatus, carbonate deposition continues as the Suwannee Limestone is laid down and the Florida Platform persists as a subtropical carbonate bank, very similar to the present Bahamas. Massive coral reefs are now prominent.
Late Oligocene
In the Late Oligocene,  development of antarctic glaciers causes sea level to drop to near present levels and the oceans continue to cool. This drop will set the pattern for later sedimentation and erosion, and for life on the affected  peninsula as well. 

Up till this Late Oligocene sea level drop, a current flowed through the Suwanne Straights and blocked clastic sediments (namely sands silts and clays) from entering the Florida Peninsula. During this low stand, the platform emerges and the flow of the Suwannee current is interrupted.  The Suwannee Straights fill with sediments which are no longer being removed by the current. When sea level rises again, the Suwannee Current cannot reoccupy the straights because they are now filled.  Because there is no longer a barrier to southward sediment transport, the clastics now begin to gradually spread southward over the peninsula. 

At the same time, the peninsula is now exposed to weathering, erosion and karstification. West of Alachua Co., rocks are eroded to the Avon Park. In the cave area, erosion removes all the layers down into the Ocala Limestone which becomes intensely karstified.  As major portions of the peninsula are now land, the grasslands spread into Florida. This event is recorded by the oldest land vertebrate fauna in Florida, discovered in Alachua Co. as I-75 was being built.  The fauna was entombed some 25-30 MY ago in a solution feature and includes such diverse animals as horses, ungulates, carnivores and rodents. 
 

The Miocene Epoch
23.7-5.3 MY Ago
seals first appear in Miocene rocks, found in Hawthorn 
At the end of the Oligocene and the beginning of the Miocene, there is a warming trend that is the swan song of  tropical time in North Florida. On the platform, clastics, sands, silts and clays, are being deposited in increasing quantities as part of the Hawthorn Group, that includes several related formations. 
By Middle Miocene, Hawthorn deposition continues. Also, the Antarctic ice sheet begins to accumulate, leading to cooler conditions worldwide. 

By Late Miocene, clastics of the Hawthorn Formation have covered all the underlying limestones. Being rich in clays and silts, they protect them and interrupt karstification for a while. At the same time, the Antarctic ice sheet continues to grow, and the world enters a much cooler, more glacial mode, with much greater oscillations in climate and in sea levels. Towards the end of the Miocene, some 10 MY ago, sea level falls abruptly and dramatically to some 300' below present level and there is an associated large extinction episode in land mammals. This drop in sea level and its attendant erosional dominance, removes  the Hawthorn sediments exposing the Eocene carbonates. Denuded of the Hawthorn clay mantle, and subjected to active erosion both from running water, ground water and coastal processes. Ground water renews the karstification process begun in the Oligocene.  Running water reworks these sediments clays and clayey sands of the Hawthorn. Continuing episodically till today, this veneer of sediments, often called terrace deposits, is reworked and re-deposited on top of these carbonates, filling karst features and stream valleys.  Later, higher stands of sea level also rework these sediments and accumulate numerous sand-rich dune fields along these now "fossil" shorelines. It is one of these higher stands of sea level, when sea water stood some 90 feet above its present level that the sands of the Brooksville Ridge and the sands that we see overlying the limestone at Bat cave accumulated. There is little question that this reworking of sediments began in the Late Miocene. Whether the sands in the area are Late Miocene, is subject to some doubt. They more likely correspond to a Pliocene stand of the sea. 
We have no way of knowing when the solution processes that created the cave proper began. Undoubtedly they began at a time when the water table stood higher than it does now. But this could have been as early as Late Miocene and as late as  Late Pleistocene. 
The Miocene is reasonably represented in the vertebrate fossil record of Florida. Below is a partial list of sites in North Florida
Arikareean (29-20MY):Buda; Anthony-Martin; Live Oak (~21 MY) 
Hemingfordian (20-16MY): Thomas Farm Sinkhole fill 
Barstovian (16-11.5MY): 
Clarendonian (11.5-8MY): Love Bone Bed in Archer (fluvial to riparian) 
Hemphillian: Mixon's  in Williston 
Mc Gehee first invasion of S am sloths(8-9MY) 

The Pliocene Epoch
5.3 - 1.8 MY Ago
In the earlier part of the Pliocene, sea level rises again to levels that inundate much of the platform and clastics are the dominant sediments; by Mid Pliocene sands and clays cover almost the entire peninsula. 
Towards the latter part of the Pliocene, some 3.5 MY ago, climates once again become colder.  This may have been due to closing of the Panama Isthmus. Warm ocean currents can no longer flow from the Atlantic and Gulf  into the Pacific. The warm waters that pile up in the Gulf of Mexico now spill out into the Atlantic as a strong and warm Gulf Stream. This strengthened warm current now transports more warm water to the Arctic regions. Increased evaporation and precipitation off the warmer ocean waters of the North Atlantic feed glaciers on land, and by 2.5 MY ago, glaciation in the northern hemisphere continents is well established. 

For land animals, the closing of the Panama arc towards the end of the Pliocene leads to a major faunal exchange. Many marine mollusks become extinct because of the influx of cold water derived from glacier meltwater. 

Toward the end of the Pliocene, rising sea levels deposit shallow marine sediments on the coastal plains. In our area, vertebrate sinkhole deposits discovered in the Haile quarries and the Santa Fe River not only give us a glimpse of this past life but also indicate that ground water erosion and karstification are ongoing. 

The oldest of these is the Nebraskan glaciation which started some 700,000 yrs ago, followed by the Aftonian interglacial; the subsequent Kansan glacial is succeeded by the Yarmouth interglacial; then by the Illinoian glacial and Sangamon interglacial. The last, and perhaps the most intense glaciation is the Wisconsin that ends some 12,000 yrs ago and brings us into the Holocene or Recent interglacial, in which we now live. 

Just as glacial episodes affect climates, they also affect sea level.  During periods when water from the oceans accumulates on land as ice, sea level stands are low. The last glacial, the Wisconsin may have lowered sea level by as much as 450 feet below present level.  Conversely, as glaciers melt, sea level rises and parts of the peninsula become covered by the sea. 

While not affected directly, the land is still shaped by various agents influenced by changing sea levels. During lowered stands of sea level, recharge areas are more extensive and solution activity of ground water sculpts the landscape. Streams erode and redeposit sediments like they did in earlier times, redistributing the clays and sands. Because sea level is lower during glacial periods, streams have more energy and downcut their valleys more vigorously. These same valleys become backfilled with sediments during interglacials as streams become more sluggish and have less energy.  As before, since the Late Miocene, sand is blown inland creating dunes along higher sea level coastlines. However, because sea level probably never rose more than ~70' higher than it is now and the Bat Cave area was never covered by the sea, the sands that overlie the cave were deposited at an earlier time, during a higher stand episode either during the Late Miocene or, more likely, the Pliocene. 

The Pleistocene was also a time of major change in life on land and sea. In the oceans, many species are brought to extinction as the climate cools. In the Late Pleistocene, on land, among other great changes, people migrated into the New World and into Florida. The original migration that populated North America took place during the Wisconsin, ~17,000 yrs. ago when big game hunters and their dogs crossed the Bering Strait that had become dry land because the glaciers had lowered sea level. By 11,500 years ago, the Clovis culture had established itself all over the U.S. and hunted the megafauna (large, now extinct, mammals such as the mammoth and mastodon) and their spearpoints have been found all over N. Central Florida. By 10,900 BP (years before present) the Folsom culture supplants the Clovis culture. With the mammoth and mastodon gone, Folsom hunters focused on bison (the buffalo) as the major game animal. Clovis and Folsom cultures lived at a time when the exotic large mammal fauna disappeared, and the reign of the mammoth was replaced by the reign of the mouse. Some paleontologists believe that man was to blame for many of these extinctions. Others lay the blame on changing environments and climates. Whatever the reason for the extinctions, the differing styles of artefacts that were left by a rich succession of native cultures that populated this area from Clovis time to the last century, record the profound changes in lifestyle and techniques brought about by the changing environment and food supply. 

The Holocene or Recent Epoch
12,000 Years Ago to Now
As the climate warms and glaciers retreat in the Northern Hemisphere, sea level rises rapidly at first, and then slower to its present levels. The Florida Platform and shelves become large areas of shallow submarine plateaus where most of the sediments are being deposited along the coast. Commonly clastics dominate in the northern part of the peninsula, while the southern section, bathed by the warmer waters of the Gulf Stream is dominated by carbonate deposition and conditions ideal for reef growth (cf. the Florida Keys). Inland, Pleistocene and older sediments are being reworked in fluvial areas and affected by Karst. For native peoples,the demise of most of the large game leads toma more varied food base and, eventually, agriculture. The discovery of the Americas in 1492 and subsequent waves of European immigration and finally industrialization and urbanization have further led to profound changes in the land and the sea.