Mineralogy of Petrified Wood from Costa Rica

Abstract

Costa Rica is located along the narrow isthmus that connected South America to North America beginning in the mid-Cenozoic. The exchange of vertebrates between the two continents has received considerable study, but paleobotanical aspects are less known. The Pacific coast “ring of fire” volcanoes produced abundant hyaloclastic material that provided a source of silica for wood petrifaction, and the tropical forests contained diverse taxa. This combination resulted in the preservation of petrified wood at many sites in Costa Rica. Fossil wood ranges in age from Lower Miocene to Middle Pleistocene, but Miocene specimens are the most common. Our research involved the study of 54 specimens, with the goal of determining their mineral compositions and interpreting the fossilization processes. Data came from thin-section optical microscopy, SEM images, and X-ray diffraction. Two specimens were found to be mineralized with calcite, but most of the woods contained crystalline quartz and/or opal-CT. The preservation of anatomical detail is highly variable. Some specimens show evidence of decay or structural deformation that preceded mineralization, but other woods have well-preserved cell structures. This preliminary study demonstrates the abundance and botanical diversity of fossil wood in Costa Rica, hopefully opening a door into future studies that will consider the taxonomy and evolutionary aspects of the country’s fossil forests.

1. Introduction

Fossil and subfossil woods are relatively abundant in Costa Rica, ranging in age from Miocene to Quaternary. These fossils have received little scientific attention; most reports simply mention petrified wood as an example of fossilization [1,2,3,4]. Some Costa Rican fossil woods have bright colors caused by the presence of trace metals. Petrified wood has long been prized by amateur collectors, and specimens have also been commercially exploited in less detail. Popular interest is evidenced using fossil wood for jewelry and ornamental purposes, with specimens displayed in homes, hotels, and parks.

Costa Rican petrified wood potentially provides information for understanding the paleoenvironment, paleoclimate, and paleogeography of the region. This report provides the first investigation that focus on the petrographic and taphonomic aspects of petrified wood from Costa Rica, using specimens from sites that span the length of the nation. The goal of our research study is to provide an analysis of the mineralogy of the fossil wood, setting the stage for future studies.

1.1. Geologic Setting

Costa Rica is part of the Central America terrestrial bridge that connects North America and South America, forming a natural barrier between the Pacific Ocean and the Caribbean Sea (Figure 1) This southern part of the Panama isthmus is of relatively young geologic age, created as a result of the oblique subduction of the former Farallón plate that, during the Lower Miocene, broke into the Cocos and Nazca plates, which were subducted below the Caribbean plate. For that reason, Costa Rica is characterized by complex geology and physiography. The geology has been mapped and described by several authors [5,6,7,8,9,10,11,12,13].

Costa Rica is characterized by complex geology (Figure 2). The oldest rocks are Mesozoic ophiolites (basalts, diabases, peridotites, rare picrites, and komatiites), and related sedimentary rocks (radiolarites, limestones, and hyaloclastic sediments) of Jurassic to Eoceneage. Late Cretaceous (Campanian) subalkaline volcanism and Cenozoic subalkaline volcanism produced volcanic islands and ranges that were created and destroyed several times. Younger deposits include deep sea marine sediments (shales and sandstones) and shallower marine sediments of Late Cretaceous to Pliocene age. These sediments include shales, sandstones, conglomerates, and limestone. Coetaneous fluvial and paralic volcaniclastic sediments became abundant beginning in the Neogene, when volcanic activity was a dominant geologic process in the islands of the ancestral archipelago. This deposition continued throughout the remainder of the Quaternary. The present physiography was largely shaped by Neogene and Quaternary volcanism [10,13].

This geologic setting is a favorable environment for the preservation of fossil wood. Neogene volcanism produced calderas with adjacent forested slopes. Most silicate minerals have low solubility, and Si in groundwater comes from two principal sources: volcanic glass and the weathering of feldspar [14,15]. In Costa Rica, felsic to intermediate volcanic rocks were a ready source for dissolved silica, preserving wood in two possible environments: trees or woody debris were buried by airfall tephra and pyroclastic flow deposits, or wood was fluvially transported to become driftwood along the margins of lakes or in shallow marine deposits near the continental coast. Taphonomy suggests that the dominant form of wood petrifaction involved transported wood fragments, explaining the relative scarcity of fossilized logs preserved in the growth position. The rapid burial of wood hindered microbial degradation. The durability of fossil wood allowed specimens to withstand fluvial transport, and good specimens can be found along rivers and in coastal cliffs (Figure 3).

1.2. Paleobiology of Central America

The separation of North and South America at ~525 Ma caused plants and animals of the two continents to have differing evolutionary histories. During the mid-Cenozoic, the Central American archipelago comprised a dispersed chain of small islands situated between the Pacific Ocean and the Caribbean Sea and the Pacific Ocean. Miocene tectonism resulted in an uplift that eventually created an isthmus between North and South America (Figure 4). A detailed history of this process can be found in [16]. The isthmus is known to have been in place by ~3 Ma (Late Pliocene/Early Pleistocene), but vertebrate fossils suggest that an emerging peninsula was present during the Miocene [17,18].

The development of a continuous land bridge led to the exchange of taxa between North and South America, a phenomenon referred to as the Great American Interchange. This episode is best known for the migration of animals. In North America, the opossum, armadillo, and porcupine all trace back to ancestors that came across the land bridge from South America. Likewise, bears, cats, dogs, horses, llamas, and raccoons all made the trek south across the isthmus. Plants were also part of the interchange. Migration rates for plants were different from animals that were capable of walking, flying, or swimming. However, plant rage expansion was directly related to animal migration because of the important role that vertebrates play in the transport of seeds. Published research includes three classic papers [19,20,21].

1.3. History of Paleobotany Research in Central America

The study of fossil plants in Central America dates back to the pioneering work of U.S. Geological Survey paleobotanist Edward S. Berry. His studies focused on fossil plants from Panama [22,23,24] (1914, 1919, 1921, 1928) but included Costa Rica [25] and the surrounding region [26] (1942). Later, paleobotany research focused on the paleoflora of Panama, reflecting geological discoveries that originated with the excavation of the Panama Canal [27,28,29,30,31,32]. Petrified wood from Guatemala was reported by Mustoe and Eberl [33].

The first mention of petrified wood in Costa Rica came from the southeastern part of San José (capital of Costa Rica) and from localities at Caldera and Pozo Azul de Candelaria [1,2]. There was a surprising silence in the mention of petrified wood until 1970, when Madrigal [3] reported isolated fragments of fossil wood south of Mata de Limón. This report was followed by cursory mentions of fossil wood [8,34,35,36]. Most of these reports lack detailed descriptions and/or precise locations.

Beginning in the 1980s, paleobotanical research in Costa Rica became focused on subfossil pollen diatoms and charcoal fragments collected from soils, lake sediments, and peat bogs, which span an age range from Late Pleistocene to Holocene [37,38,39,40,41]. These studies revealed that plant species migrated up and down mountain slopes in response to cyclic climate change. Other studies reported plant fossils preserved in shale, but again, this fossil record mostly comes from the Late Pleistocene [42,43]. Taxonomic descriptions are typically restricted to a single species [44,45,46,47,48,49,50,51]. These studies provide a fascinating look at environmental change that was largely controlled by climate fluctuations. A limitation is that these interpretations are applicable only to Pleistocene and Holocene phenomena.

The study of Costa Rican fossil wood potentially offers a means for studying botanical evolution and environmental change as far back as the Miocene. The goal of our research is to find diverse localities where fossil wood is preserved, to examine the mineralogy of this wood in the hope of understanding fossilization processes, and to evaluate the preservation of anatomic detail that could one day be useful for taxonomic studies and paleoenvironmental interpretation. Our research strategy is preliminary in nature, but it is work that will hopefully open a door to future investigations. This research has already begun, as evidenced by the recent publication of a study that described the taxonomy of five Miocene wood specimens, one each from locations in central and northern Costa Rica [52]. The challenge of interpreting the geographic dispersal and taxonomy of ancient plant communities is evidenced by the diversity of modern plant communities in Costa Rica, which include approximately 670 genera of trees and shrubs, distributed within 124 families that contain about 1800 species [53]. Another source [54] recognized 192 families of woody plants, with 860 indigenous genera and 181 introduced taxa. By any metric, the paleobotanical history of Costa Rica’s tropical forests will be a daunting task.

2. Methods and Materials

The 53 fossil woods specimens used in this study came from diverse locations (Figure 3, Table S1), but there are three principal localities: Salinas village near Caldera (central Costa Rica), Guapinol de la Cruz (northern Costa Rica), and San Vito de Coto Brus (southern Cost Rica). All of these sites are located on the Pacific flank of the central mountain axis. The Salinas–Caldera–Tivives localities contains Lower Miocene tuffaceous reddish to greenish fluvial and estuarine sandstones and pyroclastic deposits of the Mata de Limón Member [8,9,55]. The Guapinol locality occurs near an old volcanic caldera associated with the Monteverde volcanism of the Upper Pliocene to Lower Pleistocene age [56]. San Vito samples came from the contact of Late Miocene shallow estuarine/deltaic sediments (siltstones and sandstones with conglomerates), called the San Gerardo unit, that overlies the San Vito unit (volcanic debris avalanche and fluvial deposits) of the Lower Pleistocene age [5,55,57,58]. All fossils were surface collected near the outcrops. Specimens were selected to represent a range of colors and textures, recording the GPS location for each specimen. Age estimates are based on the geologic setting and regional stratigraphy.

Analytical methods included the measurement of density via hydrostatic weighing. Density values are useful for evaluating mineral composition; woods mineralized with opal commonly have densities of 1.9–21 g/cm³, compared to 2.3–2.6 g/cm³ for woods mineralized with chalcedony or quartz [59]. However, these density values may vary for woods that contain porosities or those that are only partially mineralized. Mineral identifications were, therefore, confirmed using a combination of data: XRD, SEM/EDS, and optical mineralogy.

Microscopy included low-power reflected light images obtained with a Bausch & Lomb StereoZoom binocular microscope (New York Microscope Company, Hicksville, NY, USA, https://microscopecentral.com, accessed on 7 January 2025). Thin-section images were made using two microscope systems: (1) a Zeiss petrographic microscope (Carl Zeiss Microscopy, White Plains, NY, USA) equipped with a Hayear 500B 5-megapixel CMOS camera (Shenzen Hayear Electronics Ltd., Shenzen, China. https://hayear.com, accessed on 24 February 2025) and (2) an Annlov digital microscope (https://www.tomlov.com (accessed on 23 February 2025)) equipped with a 16-megapixel camera (https://www.annlov.net/products/ (accessed on 16 January 2025)).

Thin sections were made at a standard 30-micron thickness, using Wards-Ingrahm equipment (Wards Science, Rochester, NY, USA. https://www.wardsci.com, accessed on 19 April 2025). System Three General Purpose Epoxy Resin was used for cementing rock blocks to frosted glass slides and for attaching coverslips (System Three, Seattle, WA, USA; https://www.systemthree.com, accessed on 19 April 2025).

SEM images came from a Tescan Vega III scanning electron microscope (Tescan, Brno, Czech Republic) that includes an Oxford energy-dispersive X-ray detector running AzTek 4.0 software. Freshly fractured specimens were mounted on 1 cm diameter aluminum stubs using epoxy adhesive and sputter-coated with Pd to provide electrical conductivity. SEM conditions were a 10 KV beam voltage, with the beam diameters and working distance optimized for each photomicrograph. The most common photographic conditions were a 9 mm working distance with a 90-s acquisition time.

X-ray diffraction patterns were made on packed powdered specimens using a Rigaku Miniflex diffractometer running SmartLab II software (Rigaku Corp., Tokyo, Japan). Samples were analyzed using Ni-filtered Cu-α radiation at 40 KV, 20 Ma over a 2-theta range of 5–55°.

3. Results

Fossil woods from Costa Rica localities show considerable variation in their mineral compositions. The samples typically show distinctive compositions in XRD patterns (Figure 5). Silicified woods are composed of opal-CT, microcrystalline quartz, and megacrystalline quartz. Specimens of each composition type are described in detail in an accessory file. The compositions are summarized in Figure 6.

3.1. Wood Fossilization Processes

Fossil woods from Costa Rica have a wide range of mineral compositions. Intermediate to felsic volcaniclastic rocks provided a source of dissolved silica. This diagenesis is evidenced by SEM images of the matrix that encloses silicified wood specimens. Diagenetic characteristics include the devitrification of volcanic glass and paragenesis of zeolites. The presence of intact phenocrysts of plagioclase suggests that Si was released from volcanic glass rather than the degradation of feldspar (Figure 7).

3.2. Evidence of Decay

Anatomical preservation varies among individual specimens. Some samples preserve excellent cell structures (Figure 8). Wood color variations have not been studied for Costa Rican specimens, but previous research suggests that petrified wood colors are commonly caused by trace levels of metallic elements, particularly iron. A wide range of colors can be produced by variations in the abundance and oxidation state of Fe. Brown and black colors may result from the presence of relict organic matter [60].

Some Costa Rican specimens show evidence of decay prior to the onset of petrifaction (Figure 9). Other woods were deformed or fragmented prior to petrifaction (Figure 10).

3.3. Silicified Woods: Microcrystalline Quartz

The most common form of wood petrifaction in Costa Rica is the result of the replacement of tissue quartz, both as microgranular crystals and chalcedony. Quartz formation occurs when dissolved silica concentrations are relatively low, with a precipitation rate that allows time for the development of well-ordered lattices. SEM images commonly show the microcrystallinity. These images may also show topographic aspects of anatomical features (Figure 11).

Transmitted light views of petrographic thin sections provide the identifications of fossil woods where void spaces have been filled with microcrystalline quartz (Figure 12). These features are indicative of multiple stages of silica precipitation, where cellular tissues were silicified, followed by coarser-textured quartz forming later in spaces that remained open.

3.4. Silicified Wood: Megacrystalline Quartz

A few Costa Rican fossil woods contain megacrystalline quartz crystals (Figure 13). In some specimens, euhedral quartz crystals are the predominant constituent. In other specimens, quartz crystals occur in open spaces (e.g., conductive vessels or rot pockets), representing a late stage in a mineralization sequence that occurred in multiple episodes.

3.5. Chalcedony Mineralization

Chalcedony is a form of quartz that has a fibrous morphology (Figure 14). The chalcedony group comprises three structural types. Length-fast and length-slow chalcedony can be recognized by optical properties under polarized light. Moganite (a monoclinic form of hydrous SiO₂) can be recognized via X-ray diffraction and infrared spectroscopy [61]. However, in our investigation, we have not attempted to identify individual members of the chalcedony family because our focus has been to determine whether or not petrified woods preserve anatomical details that would permit future taxonomic identifications.

3.6. Silicified Wood: Opal-CT

The mineralization of wood with opal occurs when high concentrations of dissolved silica result in rapid precipitation rates, when silica molecules lack the time needed to form well-ordered lattices. Wood opal can have two forms. Opal-A is an amorphous form of hydrous silica that consists of very small spherical masses (lepispheres). Most opal wood is composed of opal-CT, a material that has incipient crystal structure representing the structural transition of amorphous opal to crystobalite/tridymite. Less commonly, the composition is opal-C, which has an incipient cristobalite structure [62].

These hydrous silica polymorphs can be identified from X-ray diffraction patterns, thin-section petrography, and SEM images. The lack of crystallinity causes opal-A to show only a broad, low XRD pattern. Likewise, in thin sections, opal-A is isotropic under polarized light, while opal-C and opal-CT have weak birefringence. Under SEM examination, opal-A commonly appears as smooth-surfaced microspheres. In contrast, opal-C and opal-CT commonly consist of hemispherical shapes that have a distinctive “cornflake” texture [62].

In our study, opal wood from Costa Rican localities consisted of opal-CT. Photomicrographs of five specimens are shown in Figure 15 and Figure 16.

3.7. Opal and Quartz

A few specimens show intermixtures of quartz and opal-CT, as evidenced by transmitted light images of thin sections. Zonation patterns visible in specimen CR-29 suggest the possibility of diagenetic transformation (Figure 17A). For specimen CR-23, the precipitation of opal occurred during a late stage of mineralization when groundwater containing dissolved silica entered a complex fracture zone. The walls of the fracture are coated with a very thin layer of clear quartz, which is overlain by a thick layer of opal-CT. Open central areas became sites for second-stage quartz precipitation (Figure 17B,C). The angular outline of the fracture zone is evidence that the wood had been petrified prior to fracture.

3.8. Calcite Wood

After silica, calcium carbonate is the most common agent for wood petrifaction, but known examples are relatively rare. Indeed, woods mineralized with calcite have previously been reported from only 16 global locations [63], originating under a variety of geological conditions, with ages ranging from Jurassic to Pleistocene [64,65].

Several factors result in calcite mineralization of wood. Dissolved calcium needs to be at saturation levels, but this element can be present in groundwater in any region that contains limestone or other calcareous rocks. Wood petrified with calcite may occur in situations where there is a paucity of dissolved Si, but the predominant factor is the pH. Silicification is driven by the solubility of Si under basic conditions, with precipitation occurring when the pH becomes acidic (Figure 18). Calcite mineralization involves inverse condition, with acidity favoring Ca solubility and precipitation occurring at a basic pH.

The differing geochemical conditions between silicification and calcification have a bearing on the phenomenon of permineralization, which is defined as intact cellular tissue that becomes entombed within mineral matter. Contrary to longstanding commentary on wood petrifaction, most silicified only a small percentage of relict organic matter [66]. In contrast, the more gentle pH conditions that accompany calcite precipitation are favorable for the preservation of cellular material, and it is common for calcite-mineralized woods to be examples of true permineralization [65,66].

Figure 18. Stability diagram for silica and calcite. These geochemical limitations are evident in Costa Rican samples. Silicified woods do not contain calcite, and calcite-mineralized woods do not contain quartz. Data adapted from [67,68].

Figure 18. Stability diagram for silica and calcite. These geochemical limitations are evident in Costa Rican samples. Silicified woods do not contain calcite, and calcite-mineralized woods do not contain quartz. Data adapted from [67,68].

Examples of calcite mineralized woods from Costa Rica are shown in Figure 19.

3.9. Pyrite as an Accessory Mineral in Fossil Wood

The precipitation of pyrite requires the availability of dissolved iron and sulfur and appropriate pH and Eh conditions. The decomposition of plant tissue commonly produces reducing conditions, and pyrite may be found in fossil wood [60,61,62,63,64,65,66,67,68,69,70,71,72]. This is especially likely in Costa Rican wood because the volcanic deposits and anoxic sediments are sources of sulfur. The abundance of iron is evidenced by the widespread presence of lateritic soil, where deep weathering caused the removal of more soluble elements to create an excess of iron and aluminum [73]. Under reducing conditions, this iron may become soluble. Pyrite may precipitate over a wide pH range (Figure 20), explaining why the mineral may occur as an accessory mineral in both silicified and calcified wood (Figure 21).

3.10. Preservation of Relict Tissue

Wood that consists of original organic matter or altered variations is sometimes described as “carbonized wood”, but this terminology is ambiguous. There are three mechanisms that can cause ancient wood to remain unmineralized. One possibility is the burial wood in impermeable sediments, where mineral-bearing groundwater is unable to penetrate. This “mummified wood” typically occurs when wood is buried in a stratum of dense clay. Coalification is another mechanism, where organic constituents of plant tissues undergo metamorphic reactions in response the heat and pressure. The resulting material is arbitrarily categorized by “coal rank”, e.g., lignite, sub-bituminous, bituminous, and anthracite. Lignite (also known as brown coal) may preserve anatomical detail, but higher rank coals generally contain plant remains that have little, if any, structural fidelity. The third possibility is the conversion of wood to charcoal as a result of anaerobic heating. Although charcoalified wood may consist of pure carbon, its anatomical detail is commonly very good. Tissues composed of reduced carbon (charcoal and most coal) is likely to be resistant to silicification because that mineralization is commonly initiated by organic templating, where silicic acid molecules form hydrogen with functional groups in the cellulosic cell walls of buried wood. This bonding does not occur when the tissues have been thermally converted to carbonaceous alteration products. These processes were summarized by Mustoe [62].

The preservation of relict tissue in Costa Rica may have originated from more than one mechanism. The dark color of some specimens (Figure 22) is suggestive of localized charring that may have developed from contact with hot volcanic materials, and as discussed earlier in this report, the calcification of wood may be in the form of permineralization, where cell walls may remain intact within wood that was infiltrated with CaCO₃. This wood may retain a dark brown color, but wood with blackened areas commonly represents charcoalification.

4. Conclusions

Costa Rica has a multitude of petrified wood occurrences that originated in association with Neogene to Middle Quaternary volcanism. This fossil wood is potentially important as source of information regarding ancient environments, the distribution of trees and shrubs, and the migration of the plant taxa during the formation of the Central American land bridge. Our investigation is a preliminary study of the mineralization mechanisms and the degree of anatomical preservation. The latter characteristic is important for future taxonomic research.

At each locality, the fossilization of wood depended on a variety of physical and chemical parameters. The requirements were the availability of dissolved elements at concentrations that exceed the saturation point in an environment, with pH and Eh conditions that favored precipitation. Buried wood commonly retains hollow cells that allow for the permeation of mineral-bearing groundwater, but mineralization can only occur if the sediment that encloses the wood has permeability. Costa Rica volcanism had conditions that commonly met the above requirements. Pyroclastic materials and hyaloclastic alluvial sediments provided sources for dissolved silica. This solubilization was enhanced by the warm, moist tropical/subtropical climate.

The precipitation of minerals within buried wood was facilitated by the release of organic reducing agents during the degradation of tissue. Wood petrifaction may represent localized Eh and pH gradients, which explains why the mineralogical composition of buried wood may be different compared to the composition of the adjacent matrix. For example, wood may become mineralized because the pore spaces in the enclosing sediment initially remain open. This permeability allows for the entrance of mineral-bearing groundwater. Initial silicification may result from the affinity of cellulosic cell walls for silicic acid molecules, with mineralization continuing in successive events to produce complete silicification. Under different Eh and pH conditions, woods may be mineralized with calcite instead of silica. These fossilization processes are important for determining the degree of anatomical preservation. In general, wood petrifaction involves rate-competitive processes, where tissue is being degraded at the same time as it is becoming mineralized. If the rate of wood decomposition is rapid, cellular detail is not likely to be preserved. In extreme cases (e.g., wood buried by lava flows), the result may be a cast that preserves only the external shape. Conversely, a slow rate of wood degradation may mean that the wood becomes coalified rather than petrified. Our study of 53 specimens revealed a diversity of mineral compositions, with their anatomical preservation ranging from excellent to very poor. These results suggest that future taxonomic studies will require the careful selection of specimens and a search for localities that offer favorable geologic conditions.

Finding optimum collecting sites requires geological expertise because the occurrence of petrified wood specimens involves a multitude of factors. Although it may sometimes be possible to observe fossil wood in situ (e.g., limbs or logs preserved within pyroclastic fall deposits), most specimens are found at surface levels, where weathering and erosion released the fossil wood from the less-durable matrix. This process potentially allows for specimens to be transported by streams and rivers to downstream locations. Likewise, longshore processes may laterally move petrified wood once fluvially transported specimens arrive at the coast.

In summary, despite a paucity of past research, petrified wood occurs in abundance in Costa Rica. These specimens potentially provide a record of Neogene plant communities that span a temporal range that begins with the Miocene appearance of the Central American land bridge. This fossil record has the potential to widen our paleobotanical knowledge beyond the data that are obtainable from foliage fossils and palynology, which mostly provide information from the Pleistocene and Holocene, when the land bridge was well established. The complexity of this task is evidenced by the molecular clock data obtained from extant taxa, which suggest that 58 unambiguous migration events occurred across the Isthmus of Panama, determined from 16 phylogenetic events for plants and 27 for animals [75].