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The Pennsylvania State University The Graduate School College of Earth and Mineral Sciences

DISTRIBUTION AND ABUNDANCE OF BENTHIC MARINE TAXA IN

SHELF MARGIN DEPOSITIONAL SEQUENCES OF THE SAN ANDRES

FORMATION, LAST CHANCE CANYON, NEW MEXICO

A Thesis in Geosciences by Garett M. Brown

Submitted in Partial Fulfillment of the Requirements for the Degree of

Masters of Science

December 2016

The thesis of Garett M. Brown was reviewed and approved* by the following

Mark E. Patzkowsky Professor of Geosciences Thesis Adviser

Elizabeth A. Hajek Assistant Professor of Geosciences

Michael A. Arthur Professor of Geosciences

Demian Saffer Professor of Geosciences Associate Head for Graduate Program

*Signatures are on file in the Graduate School.

Abstract The processes that control stratigraphic architecture also play an important role in the distribution and accumulation of fossil material. For example, abrupt changes in fossil occurrences and abundances occur at stratigraphic surfaces marking abrupt shifts in lithofacies and in stratigraphic intervals created by slow net accumulation of sediment. However, the exact controls governing the relationship between sequence stratigraphy and the distribution and accumulation of fossils are not fully understood. The well exposed and well-defined sequence stratigraphic framework of the fossiliferous Middle Permian San Andres Formation within Last

Chance Canyon provides an opportunity to test these controls. This study examines the fossiliferous shell beds of the San Andres Formation in Last Chance Canyon through two depositional sequences about 180 m in thickness across approximately 700 meters along depositional dip to characterize the distribution and accumulation of fossil material. Major changes in biofacies from molluscan dominated assemblages in a channelized pelloidal sandstone to brachiopod-sponge-echinoid dominated assemblages in a heavily bioturbated sandstone occur at the maximum flooding surface. In addition, high density shell beds accumulated near the maximum flooding surface. While this implies the sedimentation rates are influencing the abundance of these fossiliferous beds, sedimentary structures indicate transport is the dominant factor within these facies. An additional biofacies and shell density change from brachiopod-sponge dominated sandstones to very dense Parafusulina dominated carbonates occurs within the depositional sequence. However, no major stratigraphic surfaces were observed at this transition, most likely indicating a shift in environments favorable to

Parafusulina. These biofacies changes and high shell densities result from sediment transport or changes in productivity, rather than the processes that control the stratigraphic architecture of

Last Chance Canyon.

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TABLE OF CONTENTS

List of Figures iv List of Tables x Acknowledgements xi

INTRODUCTION 1

GEOLOGIC SETTING 4

METHODS 9

RESULTS 18

DISCUSSION 56

CONCLUSIONS 64

Bibliography 67

Appendix A: Appendix Introduction 76

Appendix B: Fossil Counts Matrix 77

Appendix C: Sample Attributes Matrix 89

Appendix D: R Codes for Statistical Analyses 99

LIST OF FIGURES

Figure 1 3 Diagram showing where fossil material is expected to accumulate within a progradational sequence. A high density of fossil material is expected to occur near the toplap and downlap surfaces as the result of low net sedimentation given a constant rate of shell input (Kidwell 1986). Modified from Kidwell (1991a). Figure 2 5

Chronostratigraphic chart of the Permian formations within the Delaware Basin and the Northwestern Shelf. Modified from Sonnenfeld and Cross (1993) and Barnaby and Ward (2007). Figure 3 6

A) Last Chance Canyon is located in the Guadalupe Mountains of SE New Mexico and is part of the Northwestern Shelf of the Permian Basin. B) Last Chance Canyon is located NW of the Capitan Reef Escarpment and is close to the edge of the furthest progradation of the San Andres shelf margin. Modified from Sonnenfeld (1993) and Barnaby and Ward (2007). Figure 4 7

Regional stratigraphic setting of the Permian strata from the Northwestern Shelf to the Delaware Basin. Detailed are the 3rd and 4th order cycles identified in each formation as well as the higher order cycles identified by Sonnenfeld (1991, 1993). The box represents the study area in Last Chance Canyon. Modified from Sonnenfeld and Cross (1993). Figure 5 10

Satellite image of study area in Last Chance Canyon. Locations of all the LIDAR scan positions and GigaPan image positions are represented by circles and triangles respectively. Measured sections are denoted by a dotted line. A third measured section is located near LIDAR Scan Position 2. Figure 6 12

Two GigaPan panoramic images of the north face of the canyon wall within Last Chance Canyon. Figure 6A encompasses between measured sections 1 and 2. Figure 6B encompasses area between measured sections 2 and 3. These two view will be used in the rest of the document.

Figure 7 14

Various images of the fossil preservation found within Last Chance Canyon. A) Shell bed where skeletal material has been completely silicified and morphological features are obscured. B) Silicified shell bed where some morphological features are identifiable. C) A complete Enteletes individual and D) silicified sponge showing excellent preservation. Figure 8 19-20

A) Lithologic log and faunal log for Measured Section 1. The width of the bars on the faunal log corresponds to relative abundance. B) Lithologic log and faunal log for Measured Section 2. C) Lithologic log and faunal log for Measured Section 3. The width of the bars on the faunal log corresponds to relative abundance. Figure 9 21

Location of facies and major stratigraphic surfaces on the north face of canyon wall. Figure 9A shows all 8 identified facies whereas Figure 9B only shows Facies 3 through Facies 8. Figure 10 23, 24

A) Angular carbonate breccia from Facies 1. B) Nodular carbonate mudstone preserved in Facies 1. C) Image showing the contact between the carbonate breccia of Facies 1 at base, the light gray thin bedded, carbonate mudstones of Facies 2 in the middle, and the channelized peloidal sandstones of Facies 3 at the top. Figure 11 26

A) Chert filled Thalassinoides burrows in the carbonate mudstones from Facies 2. Notice the thin chert cap at the top of the bed. B) Contact between the carbonate mudstones of Facies 2B and the bioturbated sandstones of Facies 4. Figure 12 28-30

A) Truncating beds of the channelized peloidal sandstone of Facies 3. B) Annotated image of Figure 12A highlighting the truncating beds common within Facies 3. C) Subplanar laminations and soft sediment deformation commonly found within this facies. D) Annotated image of Figure 12C highlighting the subplanar laminations and soft sediment deformation. E). Shell beds from Facies 3 containing bivalves, gastropods and Parafusulina.

Figure 13 32

A) Facies 4 is generally massive and slope forming with little bedding features and no sedimentary structures. B) Bedded members of Facies 4 have sharp contacts and can have planar to subplanar laminations. C) Annotated image of Figure 13B highlighting the planar laminations (black dotted lines). Figure 14 34

A) Sharp contact between the sloping, massive bedded sandstone of Facies 4 and the thinly bedded sandstones of Facies 5. B) Chert nodules frequently preserved within Facies 5. C) Shell beds are dominated by well-preserved sponges and Parafusulina. Figure 15 36

A) Thin bedded, sandy carbonate packstones of Facies 6. B) Parafusulina rich chert layers typically found within Facies 6, right above the contact with Facies 5. Figure 16 37

Thick bedded, cliffy carbonate beds of Facies 7.

Figure 17 39

A) Block representing Facies 8. B) Close up showing the lack of fossiliferous material.

Figure 18 43, 44

A) Cluster analysis depicting the 4 major clusters. B) Cluster analysis coded by sample lithology show that only clusters 1 and 2 group well by lithology. C) Two-way cluster analysis shows cluster1 is defined by molluscan taxa, cluster 2 by brachiopod, sponge and echinoid taxa and clusters 3 and 4 are defined by varying degrees of Parafusulina dominance. Figure 19 46

DCA showing the spread of both samples (black) and taxa (red) along axes 1 and 2. Figure 20 46

DCA showing the spread of both samples (black) and taxa (red) along axes 2 and 3.

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Figure 21 47

DCA Axes 1 and 2 coded by lithology. Carbonate rich samples are in red, sandstone rich samples are in blue. There is a gradient along Axis 1 from more sandstone rich samples to more carbonate rich samples. Figure 22 47

DCA Axes 1 and 2 coded by biofacies. Brachiopod-sponge-echinoid samples in blue are located in the negative values of Axis 1. Molluscan samples in red plot in the positive values of Axis 1. This indicates that these two biofacies represent two end members of an environmental gradient. Parafusulina samples in green plot in the center of the ordination. Figure 23 48

DCA Axes 2 and coded by lithology. Carbonate rich samples are in red, sandstone rich samples are in blue. Unlike Axis 1, there is no gradation in lithology along either axis. Figure 24 48

DCA Axes 2 and 3 coded by biofacies. Brachiopod-sponge-echinoid samples in blue plot in two distinct groups on Axes 2 and 3. Molluscan and Parafusulina samples in red and green respectively plot in the center of the ordination. Figure 25 49

DCA Axes 2 and 3 coded by percent sponge abundance. The size of the circle represents the percent abundance of sponges in the sample. Figure 26 49

DCA Axes 2 and 3 coded by percent echinoid abundance. The size of the circle represents the percent abundance of echinoids in the sample. Figure 27 50

NMDS of samples coded by lithology. Carbonate samples are coded red, and sandstone samples are coded in blue. There is a gradation from carbonate to sandstone lithologies on both axes. Figure 28 51 NMDS of samples coded by biofacies. Molluscan samples are coded red, brachiopod- sponge-echinoid samples are blue, and Parafusulina samples are green.

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Figure 29 53 Biofacies as coded in the two-way cluster analysis are overlain onto an image of the outcrop. Molluscan biofacies only occurs in Facies 3 beneath the MFS, and the brachiopod-sponge-echinoid and Parafusulina biofacies occur in Facies 4-7 above the MFS. There are two different Parafusulina dominated zones. The first Parafusulina zone is separated from the brachiopod-sponge-echinoid zone by a section ~ 30m thick devoid of fossils. Figure 30 54 Fossil density of samples drawn as contour lines onto the face of the outcrop. Warmer colors indicate higher densities (individuals/cm2), whereas cooler colors indicate lower density samples. Areas without fossils were colored gray. Figure 31 62 Comparison of fossil densities found within the HST of the San Andres at Last Chance Canyon with expectations set forth by Kidwell’s model. High densities of shell material were found at the downlap surface in Last Chance Canyon, which is congruent with the model, but no shell material was found near the toplap surface. High fossil densities occurred instead within the foresets of the prograding clinoforms.

LIST OF TABLES Table 1 56 Summary of results identifying the major biofacies, their respective lithofacies, depositional environments, and systems tracts. Also describes whether or not these biofacies were found in areas with evidence of transport or in condensed sections. Table 1 also summarizes the shell density and sedimentation rates relative to the other biofacies.

ACKNOWLEDGEMENTS

I would like to thank my advisor Mark Patzkowsky for his guidance, instruction, and patience throughout this project. I would also like to thank my committee members Elizabeth Hajek and

Michael Arthur for their help and suggestions on this project. I would like to thank Judith

Sclafani for her assistance with lithologic and taxonomic identifications during the 2015 and

2016 field seasons and Sheila Trampush for her assistance with the LIDAR and GigaPan imaging and processing. I would also like to thank the Carbonate Sequence Stratigraphy May

2016 class for their helpful and insightful discussions on the sequence stratigraphy of Last

Chance Canyon. Finally, I would like to thank the Patzkowsky lab group for their advice and critics as this project evolved over the last two years.

Funding for this project was provided for by the Geological Society of America Student

Research Grants, American Association of Petroleum Geologists Grants in Aid Program, the

Shell Geosciences Energy Research Facilitation Awards, the Petroleum Research Fund of the

American Chemical Society, and the Penn State Department of Geosciences.

Introduction

Paleobiologists use the fossil record primarily to understand long-term changes in diversity, ecology, past environments, mass extinctions, preservation and sampling biases

(Valentine, 1969; Raup, 1972; Sepkoski et al, 1981; Alroy et al, 2008). Just as important are studies that examine the fossil record through the lens of sequence stratigraphic architecture

(Kidwell, 1986, 1991 a, b; Holland, 1995, 2000; Brett, 1995; Holland and Patzkowsky, 1999,

2002, and 2015; Scarponi and Kowalewski, 2004, 2007; and Patzkowsky and Holland, 2012) because the processes controlling sequence stratigraphy (i.e. sedimentation rates, relative sea level changes, changes in accommodation space) also impact fossil distribution and thus our interpretation of the fossil record.

For example, Holland (1995, 2000) and Scarponi and Kowalewski (2007) examined the relationship between sequence stratigraphy and the distribution of fossil assemblages. Holland

(1995) modeled occurrences of marine taxa through a series of depositional sequences and found that first and last occurrences of taxa clustered around flooding surfaces and sequence boundaries, recording abrupt changes in fossil assemblages. Scarponi and Kowalewski (2007) found that the diversity and taxon abundances can vary among the systems tracts preserved within a given sequence. For samples from the Pleistocene and Holocene of western Italy, they found that fossil assemblages from the transgressive systems tract were more diverse and more even than those from the highstand systems tract. These differences in diversity and abundances were attributed to both taphonomic (i.e. sedimentation rates, time averaging, reworking) and environmental (i.e. changes in water depth) factors intrinsic to each systems tract.

Fossil shell beds accumulate as the result of shell input rate and sedimentation rate within a system (Kidwell, 1986; Tomašových et al, 2006a, 2006b, Brady, 2016). The shell input rate is a

1 function of shell material produced within-habitat (productivity) as well as the amount of shells transported into and out of the assemblage. Sedimentation rate is a function of sediments that are deposited into the system and transported away through erosion. Typically, shell input rates and sedimentation rates are viewed as net rates, or the amount of shell material and sediment that remains in the system (R-hardpart and R-sediment; see Kidwell, 1986). While several studies have shown that shell concentrations can form as the result of an intense or variable amount of shell input (Allmon, 1993; Tomašových et al, 2006a, 2006b, Brady, 2016), dense shell beds are typically interpreted to be the result of low net sedimentation rates given a constant, background rate of shell input (Kidwell, 1986; Brett, 1995). This background rate of shell input usually infers a constant rate of productivity as the only source of shell input into a system without any addition through transport. Low net sedimentation rates will then concentrate the shell material into fossiliferous beds (Kidwell, 1986). Kidwell (1991a, b) found that fossiliferous beds form around stratigraphic surfaces (i.e. flooding surfaces and sequence boundaries) with toplap, downlap, and onlap geometries (Figure 1). These fossiliferous beds are within units that are volumetrically smaller relative to units up or down depositional dip, yet preserve the same amount of time. Called condensed sections, these units form as the result of lower rates of net sedimentation (Loutit et al, 1988; Kidwell, 1991a; Posamentier and Allen, 1999; Catuneanu,

2006).

Figure 1- Diagram showing where fossil material is expected to accumulate within a progradational sequence. A high density of fossil material is expected to occur near the toplap and downlap surfaces as the result of low net sedimentation given a constant rate of shell input (Kidwell 1986). Modified from Kidwell (1991a).

Despite these models showing that the processes controlling stratigraphic architecture have a significant, non-random impact on fossil accumulation, the sequence stratigraphic controls on fossil occurrence are not completely understood. This lack of understanding results from few field studies specifically testing these models. This study analyzes the distribution and abundance fossil assemblages in relation to the stratigraphic architecture of the Middle Permian

San Andres Formation in Last Chance, New Mexico. The well-exposed progradational clinoforms at Last Chance Canyon preserve condensed sections resulting from sediment starvation during relative highstands with toplap and downlap surfaces easily identifiable at outcrop scale (Sonnenfeld, 1993). The San Andres Formation serves as a prime candidate to assess how low sedimentation rates in condensed sections impacts the accumulation and distribution of fossils and the changes in biofacies through the depositional sequence. Fossil

3 assemblages are expected to follow patterns that directly correlates to their position within the depositional sequence. This study addresses the following questions: 1) do biofacies change predictably across stratigraphic surfaces that reflect environmental shifts? 2) does fossil density increase at positions of low net sedimentation?

Geologic Setting

The San Andres Formation is a Lower to Middle Permian (Leonardian-Guadalupian, 279-

265 Mya; Gradstein et al, 2012) mixed siliciclastic and carbonate shelf margin succession. It extends from the San Andres and Sacramento Mountains in south-central New Mexico to the

Permian Basin in Western Texas (Figure 3A). It overlays older Leonardian shelf margin successions of the Yeso, Victorio Peak, and Bone Spring formations, and is capped by the mixed siliciclastic and carbonate Grayburg Formation (Figure 4). The San Andres Formation is also an oil-producing reservoir in the Delaware and Central Basins of west Texas (Boyd, 1958; Kerans and Fitchen, 1995, Galloway, 1983). Fossils previously found from the San Andres Formation include brachiopods, molluscs, crinoids, corals, echinoderms, fusulinids, and sponges (Girty,

1909; Boyd, 1958).

Figure 2- Chronostratigraphic chart of the Permian formations within the Delaware Basin and the Northwestern Shelf. Modified from Sonnenfeld and Cross (1993) and Barnaby and Ward (2007).

Figure 3- A) Last Chance Canyon is located in the Guadalupe Mountains of SE New Mexico and is part of the Northwestern Shelf of the Permian Basin. B) Last Chance Canyon is located NW of the Capitan Reef Escarpment and is close to the edge of the furthest progradation of the San Andres shelf margin. Modified from Sonnenfeld (1993) and Barnaby and Ward (2007).

Figure 4- Regional stratigraphic setting of the Permian strata from the Northwestern Shelf to the Delaware Basin. Detailed are the 3rd and 4th order cycles identified in each formation as well as the higher order cycles identified by Sonnenfeld (1991, 1993). The box represents the study area in Last Chance Canyon. Modified from Sonnenfeld and Cross (1993).

Last Chance Canyon is located in the Guadalupe Mountains of southeastern New Mexico approximately 20 km northwest of the Capitan Escarpment (Figure 3B) and exposes the upper

San Andres Formation that was deposited during the middle of the Guadalupian (~ 267Mya;

Gradstein et al, 2012) (Sarg and Lehmann, 1986; Sonnenfeld, 1993; Sonnenfeld and Cross,

1993). At this time, Last Chance Canyon was ± 5° from the paleoequator in an arid environment

(Scotese et al, 1979; Fischer and Sarnthein, 1988). Here, the upper San Andres Formation overlies the mixed siliciclastic and carbonate Cutoff Formation of the Delaware Mountain Group and is overlain by the Grayburg Formation (Figure 4).

Previous studies of Last Chance Canyon examined the distribution of lithologies and fossils and correlated the San Andres Formation to other units surrounding the Delaware Basin

(King, 1942; 1948; Boyd, 1958; Newell et al, 1972). Sonnenfeld (1991, 1993), and Sonnenfeld and Cross (1993) examined the San Andres Formation within Last Chance Canyon in the context 7 of sequence stratigraphy. Sonnenfeld (1991, 1993) identified and analyzed two complete fourth order (2-4myr) depositional cycles: upper San Andres sequence 3 (uSA3) and 4 (uSA4). In addition, Sonnenfeld found 5th order (less than 100 kyr) progradational clinoform sequences preserved within uSA4 (Figure 4). These sequences record the change from carbonate depositional environments on the shelf to siliciclastic depositional environments on the slope and basin. Sonnenfeld (1993) and Sonnenfeld and Cross (1993) named these siliciclastic deposits the

Cherry Canyon Sandstone Tongue as they are equivalent to the Cherry Canyon Sandstone

Formation of the Delaware Mountain Group located within the Delaware Basin.

This change in sedimentation is common within the Delaware Basin, leading to a sedimentation model for the basin called “reciprocal sedimentation” (Wilson, 1967; Meissner,

1972; Sonnenfeld and Cross, 1993; Olseger, 1998; Tinker, 1998; Kerans et al, 2013). Under this model, carbonate facies dominate the shelf and slope environments during relative highstands

(i.e. when sea level is relatively high and sediment supply is greater than the creation of accommodation space through sea level rise and subsidence). The carbonate facies are interpreted to be autochthonous deposits formed from local carbonate materials. The sandstone facies formed during periods of relative lowstand (i.e. when sea level is relatively low and sediment supply is greater the creation of accommodation space through sea level rise and subsidence) as the result of terrestrial sediments bypassing the shelf margin and being deposited in slope and basin environments.

Within Last Chance Canyon, fluvial runoff was limited during highstands due to an arid climate (Fischer and Sarthein, 1988) associated with the equatorial paleolattitude. Clastic sediments were deposited on the shelf proximal to the paleo-shoreline and negligible amounts of hemipelagic clays made their way past the shelf margin. In addition, calcareous and siliceous

8 planktonic organisms are absent at this time since they do not originate until the Triassic (Bown et al, 2004; Falkowski et al, 2004). These two factors created a sediment starved slope and basin during highstands, which should form condensed sections (Loutit et al, 1988, Posamentier and

Allen, 1999; Catuneanu, 2006). This makes the progradational clinoforms at Last Chance

Canyon prime candidates to assess how low sedimentation rates in condensed sections impacts the accumulation and distribution of fossils and the changes in biofacies through the depositional sequence.

Methods Imaging

Two panoramic photographs of the north face of the canyon were taken using a Nikon

D700 DSLR camera and a GigaPan Epic Pro camera mount. One was taken along the hiking trail near the overflow parking for the Sitting Bull Falls Recreational Area (Figure 5). The other was taken on top of a peloidal sandstone bench near the junction of Wilson and Last Chance Canyon

(Figure 5). Both sets of images were processed using the program GigaPan Stitch to produce high resolution photographs. These panoramic photos were then uploaded to the GigaPan website (http://gigapan.com/gigapans/155238; http://gigapan.com/gigapans/178468).

Additionally, Last Chance Canyon was imaged using Lidar equipment to produce a three- dimensional digital model of the canyon. A total of fifteen scans were collected using a Riegel

VZ-1000 scanner at 0.5 m resolution (Figure 5), and compiled and processed using Riscan Pro v.

2.0.3.

Figure 5- Satellite image of study area in Last Chance Canyon. Locations of all the LIDAR scan positions and GigaPan image positions are represented by circles and triangles respectively. Measured sections are denoted by a dotted line. A third measured section is located near LIDAR Scan Position 2.

Measured Sections Three stratigraphic sections were measured along the north face of the canyon (Figure 6).

The westernmost section (Measured Section 1, Figure 6A) was a 100 m section that began at the maximum flooding surface identified by Sonnenfeld (1993) and ended at the contact between the

San Andres and Grayburg formations. A second measured section (Measured Section 2, Figures

6A and 6B) was located 100m east of the previous measured section. Measured Section 2 encompassed 170 m of section that began at the base of the canyon wall and ended within the

Grayburg Formation. The final measured section (Measured Section 3, Figure 6B) was conducted approximately 500 m east of the first. It was 20 m in height and focused on the beds bounding the maximum flooding surface. Each section was measured using a 1.5 m Jacob’s staff 10 demarcated in 0.1 m increments and a Brunton compass to aid in line of sight. Field descriptions of lithofacies included lithology, sedimentary structures, amount of bioturbation and trace fossils, amount of fossil fragmentation, and the relative amount and types of chert preserved. Rock samples were collected along the measured sections for thin sections to corroborate field identifications of lithology. Thin sections were not examined at this time.

In addition, fossil logs tied to measured sections recorded the occurrence and abundance of taxa. Abundances were recorded on the rank scale of rare (1-2 individuals), common (3-6 individuals), abundant (7-12 individuals) and very abundant (> 12 individuals). GPS coordinates were collected in lateral transects between the measured sections to identify areas of extremely low fossil density (< 1 individual/m2) or areas that were fossil barren.

Figure 6-Two GigaPan panoramic images of the north face of the canyon wall within Last Chance Canyon. Figure 6A encompasses between measured sections 1 and 2. Figure 6B encompasses area between measured sections 2 and 3. These two view will be used in the rest of the document.

Fossils Counts

The fossil material preserved within Last Chance Canyon is heavily silicified (Figure 7).

As a result, most morphological characters used to identify species were obscured. A few specimens were preserved well enough for genus level identification, but the vast majority had to be identified at higher taxonomic levels. Unidentifiable chert material was found on the outcrop among the silicified fossil material. The unidentifiable chert material appears to be of similar size and shape as the fossil material. Boyd (1958) and Newell et al (1972) also noted that silicified fossils and the unidentifiable chert material tend to co-occur in the San Andres Formation, and suggested that some of the amorphous chert was completely replaced fossil material. Based on this suggestion, the varieties of chert material observed (i.e. vugs, nodules, bands) as well as their abundances and distributions on the outcrop were recorded as another method for understanding the distribution of fossil material at Last Chance Canyon.

Figure 7- Various images of the fossil preservation found within Last Chance Canyon. A) Shell bed where skeletal material has been completely silicified and morphological features are obscured. B) Silicified shell bed where some morphological features are identifiable. C) A complete Enteletes individual and D) silicified sponge showing excellent preservation.

Forty-six surface counts were made to determine biofacies and fossil density changes

through the stratigraphic sequence. Sample sizes range from 21 to 334 individuals. The median

sample size is 52.5 individuals. The majority of samples contained a minimum of two taxa, with.

the exception of 11 samples comprised solely of Parafusulina. These 11 samples were included

in the analyses due to the dramatic increase in fossil density and the sudden drop in diversity.

Fossil specimens were identified to genus when possible. However, the overall poor preservation

and silicification of the fossil material required many individuals to be identified to higher

taxonomic levels. GPS coordinates, elevation, surface area, and lithology for each count was also

14 recorded. The fossil density was calculated from the number of individuals divided by the surface area of each count.

Statistical Analyses Fossil counts were used to create a 46 sample by 30 taxon matrix (Appendix B). Cluster analysis, detrended correspondence analysis (DCA), and nonmetric multidimensional scaling

(NMDS) were performed on this matrix using the statistical program R to identify biofacies and the environmental gradients driving the changes in biofacies. After the initial analyses, the original matrix was modified to remove all occurrences of the taxon Parafusulina. This second matrix contained 35 samples and 29 taxa. The same statistical analyses were also performed on this new matrix to determine the effect of the Parafusulina-dominated samples on the results.

A third matrix defining attributes of each sample was created to complement the sample by taxon matrix (Appendix C). This sample attributes matrix contained information such as sample lithology, elevation, GPS coordinates, sample area (cm2), and biofacies identified from cluster analyses. These sample attributes were used to identify environmental gradients in the cluster analysis, DCA, and NMDS.

Cluster Analysis

Q-mode cluster analysis was performed to identify samples with similar taxonomic compositions. For each sample, the proportional abundance of each taxon was calculated relative to the sample total. This removes any variation between samples caused by differences in sample size and allows for easier comparison between samples. The cluster analysis was performed on a

Bray- Curtis distance matrix. Bray-Curtis distances are used for ecological datasets because they better reflect the distance between variables with discrete values (McCune and Grace, 2002).

Ward’s Method was used as the linkage method for all of the cluster analyses presented here because it minimizes the increase of error in the sum of squares of distances between samples, and has the major benefit of producing well-defined and compact clusters (McCune and Grace,

2002).

An R-mode cluster analysis was performed on the taxa within this dataset to determine which taxa tend to co-occur. For this analysis, the data set was transformed by first calculating the proportional abundance of each taxon relative to the sample total, followed by dividing each taxon’s proportional abundance by the maximum percentage of that taxon. This multiple transformation accounts for differences in both sample size and taxon abundance. The matrix was then transposed. Bray-Curtis Distances were calculated, and linked using Ward’s Method.

The R-mode analysis was combined with the Q-mode analysis to produce a two-way cluster diagram used to define biofacies.

Detrended Correspondence Analysis Detrended correspondence analysis (DCA) was performed to identify any environmental gradients driving patterns found within the dataset. To prepare the data for DCA, the proportional abundance of each taxon was calculated relative to the sample total to account for differences in sample size and then relativized to the column maximum to account for differences in abundance. The DCA was then run in R using the program’s default parameters.

To identify environmental gradients driving sample distributions, samples were coded by lithology and biofacies. This information was overlain on the DCA plot of sample scores to see how lithology and biofacies contribute to the variation in scores among samples.

Eigenvalues from a Correspondence Analysis (CA) were used to calculate the amount of variance explained by each axis of the DCA. A CA is calculated very similar to a DCA, but does

16 not “detrend” and remove the arch that can result from this analysis (Hill and Gauch, 1980). By not detrending the ordination, the eigenvalues from the CA accurately reflect the variation explained by each axis (Økland 1999; McCune and Grace 2002). The variation explained by each axis was calculated by taking the proportion of the respective axis’s eigenvalue to the sum of all the eigenvalues. This value represents what is called the “relative inertia” of an eigenvalue.

Relative inertia differs from the eigenvalues of other ordinations such as PCA because it does not directly represent the proportion of variance explained. However, relative inertia can be used to give a sense of the amount of variation explained by a particular environmental factor and is frequently reported in CAs and DCAs (Økland 1999).

Nonmetric Multidimensional Scaling A Nonmetric Multidimensional Scaling ordination (NMDS) was also calculated to identify environmental gradients and to determine the robustness of the DCA. To prepare the data for NMDS, the data was transformed using the proportional abundance of each taxon relative to sample total. Percent sample transformation was used for consistency between the

DCA and NMDS results. Bray-Curtis Distances were used to calculate the distance matrices, and the NMDS was set to run over 20 iterations over multiple dimensions (k) to find the best solution. The “best” solution is the value of k where the addition of subsequent dimensions yields diminishing returns on the reduction of stress. A general rule for choosing the best solution is that the stress value for the chosen solution should be less than 0.10 (McCune and Grace, 2002).

As with the DCA, the ordination scores for each sample were taken, coded by lithology and biofacies, and plotted within ordination space to determine any patterns within the ordination.

Results

Facies Description

Figure 8 depicts the lithology and faunal logs for each measured section. Eight facies were identified and their occurrence on the canyon wall is shown in Figure 9.

Figure 8A: Lithologic log and faunal log for Measured Section 1. The width of the bars on the faunal log corresponds to relative abundance.

Figure 8 B- Lithologic log and faunal log for Measured Section 2. The width of the bars on the faunal log corresponds to relative abundance.

Figure 8 C: Lithologic log and faunal log for Measured Section 3. The width of the bars on the faunal log corresponds to relative abundance.

Figure 9- Location of facies and major stratigraphic surfaces on the north face of canyon wall. Figure 9A shows all 8 identified facies whereas Figure 9B only shows Facies 3 through Facies 8.

Facies 1 – Matrix-supported carbonate breccia (Figure 10)

Description- Facies 1 is a cliff forming, dark gray, matrix-supported carbonate breccia containing cobble sized (10 + cm) carbonate mudstone clasts. Minimal effervescence after the application of hydrochloric acid suggests that these carbonates are dolomitic. Silt was found in very low abundance within this facies. Bedding is typically medium (10 – 30 cm) to thick (30 –

100 cm), and beds truncate and pinch out into one another. Clasts grade from angular to rounded, and are supported by a carbonate mudstone matrix. No internal sedimentary structures were observed, and some beds showed some moderate bioturbation (ii3; ichnofabric index of Droser and Bottjer, 1986). This facies is fossil poor, with brachiopods in rare abundance. The brachiopods are well-preserved, such that some individuals are articulated and still have delicate morphological features such as spines. Facies 1 is located at the base of the outcrop, and a sharp, erosive contact separates Facies 1 from Facies 2 (Figure 10 C).

Interpretation- The size, shape, and grading of the clasts suggests a carbonate debris flow

(Playton et al, 2010). The condition of the brachiopod fossils indicates that the source for the flow was nearby. Truncated beds and occasional bioturbation indicate multiple, episodic debris flows and suggest that this facies was not the result of a single event. Since carbonate mud is the dominant sediment, this facies is interpreted to have been deposited in the lower slope to distal ramp depositional environment (Playton et al, 2010). While dolomitized carbonate breccias could also indicate a supratidal environment (Pratt, 2010), the lack of evaporite crystals and presence of fossil material make such an interpretation unlikely. Sonnenfeld (1991) interpreted this facies as a lower to toe of slope carbonate megabreccia resulting from debris flows. Phelps and Kerans (2007) also interpreted this facies as a debris flow, and suggested this facies formed as the result of channel-levee collapse.

Figure 10- A) Angular carbonate breccia from Facies 1. B) Nodular carbonate mudstone preserved in Facies 1.

Figure 10 (Continued)- C) Image showing the contact between the carbonate breccia of Facies 1 at base, the light gray thin bedded, carbonate mudstones of Facies 2 in the middle, and the channelized peloidal sandstones of Facies 3 at the top.

Facies 2 – Cherty carbonate mudstones (Figure 11)

Description- Facies 2 is a resistant, ledge forming, light gray, moderately bioturbated (ii 3

– 4) medium bedded (10 - 30 cm) sandy carbonate mudstone rich with chert-filled

Thalassinoides burrows (Figure 11A). These burrows can form discontinuous, red colored chert caps approximately 1 cm thick at the tops of the beds. The siliciclastic component of these

Thalassinoides-rich beds range from silt to very-fine sand. Interbedded with these sandy,

Thalassinoides-rich beds are light gray, medium-bedded (10-30 cm) Thalassinoides-poor carbonate mudstones with chert vugs and nodules and no siliciclastic material. The contacts between these beds are sharp and distinct. Facies 2 is fossil poor, with only rare fusulinids

24 observed. However, chert vugs (~ 1 – 3 cm) are present and may represent heavily altered fossil material. Two sets of beds belonging to Facies 2 were identified in the measured sections. Facies

2A overlays Facies 1 with a sharp, undulatory contact (Figure 10C). The carbonate mudstone beds from Facies 2 fill in the undulations, but do not truncate at the contact. Facies 2A is overlain by Facies 3. The contact between Facies 2A and Facies 3 is predominately within a covered interval, but is sharp and undulatory where it is expressed. Facies 2B overlays Facies 3, but the nature of this contact is hard to determine due to the amount of cover. The contact between

Facies 2B and Facies 4 is predominately covered, but it is sharp where exposed near the easternmost measured section. The surface of Facies 2B is heavily burrowed at this contact.

These burrows are filled with siliciclastics that are piped down from Facies 4.

Interpretation- The fine grained carbonate matrix, the abundance of Thalassinoides and lack of sedimentary structures suggest that Facies 2 was created from hemipelagic silts and carbonate muds in a quiet environment that was not affected by wave action. These hemipelagic are derived from sediments washed in from shallower environments and are not biogenic in origin since calcareous nannoplankton had not evolved in the Permian (Bown et al, 2004;

Falkowski et al, 2004). The alternation from Thalassinoides-rich and Thalassinoides-poor beds may reflect changes in the sedimentation rates of these hemipelagic sediments, with the chert caps representing periods of minimal sedimentation (Phelps and Kerans, 2007). It is possible that the alternation from Thalassinoides-rich to Thalassinoides-poor beds may reflect shifts from aerobic to dysaerobic conditions (Sonnenfeld, 1991; Sonnenfeld and Cross, 1993), but episodic sedimentation seems most likely. Typically, hemipelagic sourced carbonate mudstones and lack of sedimentary structures are associated with distal, deep water environments and as such, Facies

2 is interpreted to be a lower slope to distal environment that was below storm wave base. Both

Sonnenfeld (1991) and Phelps and Kerans (2007) interpret this facies to be below storm wave base on the lower slope as well.

Figure 11- A) Chert filled Thalassinoides burrows in the carbonate mudstones from Facies 2. Notice the thin chert cap at the top of the bed. B) Contact between the carbonate mudstones of Facies 2B and the bioturbated sandstones of Facies 4.

Facies 3- Channelized peloidal sandstone (Figure 12)

Description- Facies 3 is a ledge forming, white, medium (10 – 30 cm) to thick bedded (30

– 100 cm) unit where individual beds fine upward from a fossiliferous peloidal grainstone to a very fine grained sandstone. This facies shows minimal bioturbation (ii1), with burrows found primarily at the top of this facies. Contacts between beds are easily identifiable. Channel structures were observed at outcrop scale where the beds of Facies 3 truncate and onlap onto one another (Figure 12A). Planar laminations and soft sediment deformation (Figure 12C &D) such as flame and loading structures were observed within this facies. Whole fossils and coarse fragments formed shell beds in the peloidal grainstone portions of this facies. Fossils include bivalves, gastropods, cephalopods, and fusulinids (Figure 12E). Fusulinids in these assemblages were oriented in an East-West direction. Fossils are well preserved compared to other facies, and genus level identifications were possible. Facies 3 overlies Facies 2A with a sharp, undulatory contact that appears erosive. The contact between Facies 3 and Facies 2B lies within a covered interval and could not be observed.

Facies 12- A) Truncating beds of the channelized peloidal sandstone of Facies 3. B) Annotated image of Figure 12A highlighting the truncating beds common within Facies 3.

Facies 12 continued- C) Subplanar laminations and soft sediment deformation commonly found within this facies. D) Annotated image of Figure 12C highlighting the subplanar laminations and soft sediment deformation.

Figure 12 (continued) - E). Shell beds from Facies 3 containing bivalves, gastropods and Parafusulina.

Interpretation- The channel structures and graded beds preserved in this facies all indicate that Facies 3 was deposited by a channelized flow. Soft sediment deformation indicates that the sediments were deposited quickly. The molluscan fauna, peloids, and fine grained sands indicate a proximal, shelf source for the sediment that was ultimately transported to a lower to toe of slope depositional environment. This interpretation is consistent with that of Sonnenfeld (1991), who interpreted this facies as a turbidite succession characterized by Bouma ABC sequences.

Phelps and Kerans (2007) also identified a similar facies that was interpreted as a channelized skeletal packstone in the lower slope to distal depositional environments.

Facies 4- Heavily bioturbated sandstone (Figure 13)

Description- Facies 4 represents a massively bedded (>3 m), very fine grained sandstone.

This facies is very heavily bioturbated (ii5-6), with burrows and feeding traces present and sedimentary structures are absent. Grains are well sorted and rounded. Occasionally, thin (3 – 10 cm) to medium (10 – 30 cm), less bioturbated (ii3) beds with planar laminations are exposed.

Fusulinids within these bedded intervals may also be oriented along an approximately 110° -

190° azimuth. This facies grades from fossiliferous at its base, to fossil poor for the majority of its thickness (~80 m), to fossiliferous again at its top. Echinoid spines and plates, and fusulinids dominate the fossil assemblages at the base, whereas the top of the facies is dominated by brachiopods and sponges. Silicification of fossils has destroyed morphological detail in most cases, making identifications at the genus level difficult. The fossil poor middle zone is characterized by sparse occurrences of chert vugs that are on average less than 3 cm in diameter.

Discontinuous chert layers also form around the planar laminations. Facies 4 overlies Facies 2B.

A sharp contact separates Facies 4 from Facies 5.

Figure 13- A) Facies 4 is generally massive and slope forming with little bedding features and no sedimentary structures. B) Bedded members of Facies 4 have sharp contacts and can have planar to subplanar laminations. C) Annotated image of Figure 13B highlighting the planar laminations (black dotted lines)

Interpretation- Within the Permian Basin, siliciclastic dominated lithologies are typically associated with either proximal, nearshore environments or distal basins. The intense bioturbation, lack of sedimentary structures, and intact sponges and in-life-position articulated brachiopods with intact spines found within the massive beds of Facies 4 indicate a quiet environment that was not influence by wave action. These massive beds likely formed as the result of hemipelagic siliciclastics that were bypassing shelf environments. As such, Facies 4 is interpreted to have been deposited in the lower slope or basinal environment. Oriented

Parafusulina tests, fragmented fossil material, and laminations within the medium beds indicate periods of transport controlled deposition in this deep water environment. While fossils are for the most part absent in the majority of Facies 4, the rare small chert vugs may represent fossils replaced by chert. Fossil material at the base and top of this facies are also heavily silicified.

Sources for the silica replacement in Facies 4 were either sponges (Pufahl, 2010), as sponge spicules can be identified throughout the facies, or the large amount of siliciclastics entering this environment.

Facies 5- Thin bedded fossiliferous sandstone (Figure 14)

Description- Facies 5 represents a tan colored, thin (3 – 10cm) to medium (10 – 30 cm) bedded very fine grained sandstone. This facies corresponds to the silty brachiopod/ sponge wackstone facies of Sonnenfeld (1991). This work found Facies 5 to have a higher amount of siliciclastic grains than carbonate grains and therefore identifies Facies 5 as a sandstone. This facies is moderately bioturbated (ii3-4). Skeletal material is very dense, with brachiopods, sponges and fusulinids abundant. Fossil assemblages change from brachiopod and sponge dominant at the base of Facies 5 to fusulinids dominant at the top of Facies 5. These fusulinids dominated assemblages occur in laterally continuous, nodular chert bands several centimeters

33 thick. The fusulinids are not oriented, unlike Facies 3 and 4. Fossils here were heavily silicified, making identification to genus level difficult. Although Facies 4 and Facies 5 have similar grain composition, they are separated by the change in bedding, bioturbation and faunal assemblage.

Facies 5 overlies Facies 4, and interfingers with Facies 6.

Figure 14- A) Sharp contact between the sloping, massive bedded sandstone of Facies 4 and the thinly bedded sandstones of Facies 5. B) Chert nodules frequently preserved within Facies 5. C) Shell beds are dominated by well-preserved sponges and Parafusulina.

Interpretation- The intact sponges, well-preserved articulated brachiopods, and non- oriented Parafusulina tests does not indicate transport of skeletal material. Increase in non- transported Parafusulina tests indicates a shift to a shallower environment that would allow these 34 photosynthetic organisms to thrive. However, similar grain size and composition to Facies 4 indicates a similar depositional process, and therefore not a dramatic change in depositional environments. Therefore, Facies 5 likely represents a middle slope depositional environment.

Facies 6- Thin bedded sandy skeletal packstone (Figure 15)

Description- Facies 6 represents a dark grey, thin bedded (3 – 10 cm) sandy skeletal packstone. This facies is bioturbated (ii3-4), and form more resistant beds than those found in

Facies 5. Skeletal grains are form dense shell beds made up almost exclusively of Parafusulina, with rare brachiopods. Additionally, these shell beds form within nodular chert beds like Facies

5. As with Facies 5, Parafusulina tests are not oriented and do not show evidence for transport.

This facies is consistent with the cherty brachiopod-fusulinid wackstone of Sonnenfeld (1991).

Facies 6 interfingers with Facies 5 laterally, but overlies Facies 5 with either a sharp or gradational contact. Parafusulina density is highest where these two facies interfinger. Facies 6 is overlain by Facies 7.

Interpretation- Facies 6 is very similar to Facies 5. The gradational relationship and interfingering between these two facies makes it difficult to differentiate them. The only difference is the introduction of more carbonate grains, and the decrease in faunal diversity.

Facies 6 could represent an upper shelf environment due to the increased abundance of carbonate grains and the dominance of photosynthetic Parafusulina. Its close association with Facies 5, however, might indicate that Facies 6 represents a middle slope environment experiencing more carbonate input. Therefore, I would place Facies 6 within the transition between the upper and middle slope depositional environments. Sonnenfeld (1991, 1993), Sonnenfeld and Cross (1993), and Kerans et al (2013), however, all identify this facies as a fusulinid-rich- packstone entirely within an upper slope depositional environment.

Figure 15- A) Thin bedded, sandy carbonate packstones of Facies 6. B) Parafusulina rich chert layers typically found within Facies 6, right above the contact with Facies 5.

Facies 7- Carbonate skeletal-peloidal packstones/ peloidal wackstones (Figure 16)

Description- Facies 7 represents a cliff forming, thick bedded (30 – 100 cm) skeletal peloidal packstone that grades into peloidal wackstone due to decreases in the amount of skeletal grains up section. Parafusulina make up the entirety of fossil material and skeletal grains within the packstone. Parafusulina abundance decreases upward from dense shell beds containing complete tests to sparse fusulinid molds to completely absent. Parafusulina do not have an orientation. The matrix appears to be dolomitic. This facies is heavily bioturbated (ii5-6) and sedimentary structures are absent. Fossil material was silicified, but chert vugs and nodules were not observed. Facies 7 overlies both Facies 5 and Facies 6, and the face of the outcrop is more recessed at their contact. The top of Facies 7 is overlain by a covered interval, and the nature of the contact between Facies 7 and 8 is uncertain.

Figure 16- Thick bedded, cliffy carbonate beds of Facies 7.

Interpretation- The presence of peloids and non-oriented Parafusulina tests indicate within habitat deposition of the carbonate grains. The abundance of Parafusulina also indicates that this was a shallow water environment within the photic zone, such as within the shelf to upper slope depositional environment. The gradation from packstone to wackstone is the result of a decrease in fusulinids abundances. Fusulinids grade upward from whole silica-replaced tests to fusulinid molds to complete absence of fusulinids. This dissolution of fusulinids tests could indicate that geochemical conditions gradually became unfavorable to preservation of fusulinids.

Alternatively, the gradual decrease in fusulinids may simply indicate a slight change in sea level such that environmental conditions were no longer favorable for a large population of fusulinids.

Such a shift would be expected to preserve different carbonate lithologies- grainstones would be expected with an onshore shift, and carbonate mudstones with an offshore shift. However, it is unlikely that the fluctuation in Parafusulina abundance within Facies 7 represents an onshore or offshore shift in facies as the lithology remains a peloidal packstone/wackstone throughout

Facies 7.

Facies 8- Sandy Pelloidal Grainstone (Figure 17)

Description- Facies 8 represents a thick (30 – 100 cm) bedded pelloidal sandy grainstone that is mildly bioturbated (ii1-2) and planar laminations are observed throughout. Facies 8 has a similar lithology as Facies 3, but differs due to the lack of fossiliferous material, graded bedding, and soft sediment deformation. No chert nodules or vugs were observed within this facies. Facies

8 overlies Facies 7, but is separated by a covered interval so the nature of the contact between

Facies 7 and 8 is unclear. Facies 8 is overlain by a covered interval, and the relationship of this facies with overlying beds is uncertain. Above this covered interval are well sorted, fine to medium grained beds of tan sandstone with large scale cross-trough beds that are typically

38 associated with the Grayburg Formation (Boyd, 1958; Barnaby and Ward; 2007; Kerans et al.,

2013)

Figure 17- A) Block representing Facies 8. B) Close up showing the lack of fossiliferous material.

Interpretation- Carbonate grainstones typically reflect shallow marine, higher energy shelf environments (Pratt, 2010) Peloidal grains and planar laminations suggest that Facies 8 is a subtidal, shelf environment near fair weather wave base where frequent wave action provided the energy required to transport away the smaller grains and matrix.

Sequence Interpretation – (Figure 9)

A sequence boundary is interpreted to occur at the contact between Facies 2A and Facies

3. Large scale channel scours cut into Facies 2A and are subsequently filled by Facies 3. A relative decrease in sea level during a lowstand would expose the shelf where the siliciclastics, peloids, and molluscan faunas of Facies 3 were likely sourced, and provide the conditions that transported these sediments into a lower slope and basinal environment.

The maximum flooding surface is interpreted to be located at the contact between Facies

2B and Facies 4 as the result of basinal siliciclastics overlying slope carbonates. Stratal geometries also suggest that this contact is a maximum flooding surface. Facies 4 appears to have a slight dip angle where beds thin down depositional dip and downlap onto the top of

Facies 2B. Also, the top of Facies 2B is heavily burrowed, which would be expected at a hiatal surface. Conversely, Facies 2B could be interpreted as a maximum flooding zone, as the multiple beds of discontinuous caps of chert filled Thalassinoides burrows may represent multiple hiatal surfaces.

Another sequence boundary is interpreted to be in the covered interval above the sandy peloidal grainstone of Facies 8. Above this covered interval are the well sorted, fine to medium grained beds of tan sandstone with large scale cross-trough beds belonging to the Grayburg

Formation (Boyd, 1958; Barnaby and Ward; 2007; Kerans et al., 2013). These sandstones are interpreted to represent aeolian sand dunes (Barnaby and Ward; 2007; Kerans et al., 2013).

These terrestrial sand dunes are directly overlying subtidal peloidal grainstones, creating a non-

Waltherian relationship as the expected shallow subtidal and peritidal carbonates are not present.

Two distinct stratigraphic sequences can be inferred from the locations of these three surfaces. Facies 1 and 2A are below the first sequence boundary and therefore represent either transgressive systems tract (TST) or highstand systems tract (HST) of the first sequence. Facies 3 marks the beginning of the second sequence and represents the lowstand systems tract (LST) since it is bounded by both the sequence boundary and the maximum flooding surface. Facies 2B represents the TST of the second sequence. Facies 4- Facies 8 all represent the HST of this second sequence as they are all above the maximum flooding surface and beneath the upper

40 sequence boundary. These interpretations are consistent with the in-depth sequence stratigraphic analysis made by Sonnenfeld (1991) and Sonnenfeld and Cross (1993).

The inclusion of the siliciclastic Facies 4 and Facies 5 within the HST is inconsistent with the model of reciprocal sedimentation believed to govern deposition of the Permian Basin at this time (Wilson, 1967; Meissner, 1972; Sonnenfeld and Cross, 1993; Olseger, 1998; Tinker, 1998;

Kerans et al, 2013). Under this model, the carbonate lithologies are dominate during highstands, whereas large siliciclastic units are produced during lowstands. Sonnenfeld (1991, 1993) and

Sonnenfeld and Cross (1993) identified a series of progradational clinoforms within the HST.

These clinoforms are observable at outcrop scale (represented by gray lines in Figure 9), with the resistant medium-bedded sandstones within Facies 4 representing the clinoforms surfaces.

Sonnenfeld (1991, 1993) and Sonnenfeld and Cross (1993) proposed that these clinoforms represent higher order cycles within the overall HST that are the products of higher order cycles of reciprocal sedimentation. For example, the massive bedded sandstone of Facies 4 represents a higher order lowstand sequence where siliciclastic sediment was still being transported to the lower slope environments during this overall HST. Likewise, the carbonate Facies 6-8 all represent higher order relative highstands within the overall HST that allowed the carbonate platform to prograde out into the basin.

Biofacies Analysis

Four major clusters of samples were identified from the cluster analysis (Figure 18).

Cluster 1 contains samples that were collected from channelized peloidal sandstone lithofacies, and is defined as a molluscan dominated biofacies. The molluscan biofacies contains bivalves, gastropods and cephalopods to the exclusion of brachiopods, sponges, echinoids and fusulinids.

Cluster 2 contains samples that were collected from the heavily bioturbated sandstone

41 lithofacies, and is defined by the brachiopod-sponge echinoid biofacies. No molluscan taxa were found within these samples. Cluster 3 contains samples from both the channelized peloidal sandstone and the heavily bioturbated sandstone lithofacies, and is defined as the Parafusulina- echinoid biofacies. Samples within this biofacies contain mostly Parafusulina and echinoids, with other taxa being extremely rare. Cluster 4 contains samples from an assortment of carbonate and sandstone lithologies, and is defined as the Parafusulina dominated biofacies. While

Parafusulina is the dominant taxa in these assemblages, the occurrence of rare taxa divides

Cluster 4 into a series of subclusters. For example, Cluster 4a contains echinoids and sponges in addition to Parafusulina. Cluster 4b contains the 11 samples that are solely made up of

Parafusulina. Cluster 4c contains brachiopod and sponges. 4d contains sponges and mollusks. 4e contains bivalves.

Figure 18- A) Cluster analysis depicting the 4 major clusters. B) Cluster analysis coded by sample lithology show that only clusters 1 and 2 group well by lithology.

Facies 18 (continued)-. C) Two-way cluster analysis shows cluster1 is defined by molluscan taxa, cluster 2 by brachiopod, sponge and echinoid taxa and clusters 3 and 4 are defined by varying degrees of Parafusulina dominance.

DCA was performed to identify any environmental gradients based on the position of samples and taxa within the ordination space (Figures19 & 20). Eigenvalues calculated from the

CA for the first four axes are 0.8946, 0.7544, 0.5662, and 0.5418. Using the ratio of eigenvalue to “total inertia” for each of axis identifies that Axis 1 explains 32% of the variance, Axis 2 explains 27% of the variance and Axis 3 explains 21% of the variance. Samples grade along

Axis 1 from sandstone lithofacies in the more negative values to carbonate lithofacies in the positive values of Axis 1 (Figure 21). In addition, samples grade along Axis 1 from the brachiopod-sponge-echinoid biofacies in the negative values to Parafusulina dominate biofacies in the center to molluscan dominate biofacies in the positive values (Figure 22). Samples ordinate along Axis 2 with a group of sandstone lithofacies in the negative values, carbonate values in the center, and another group of sandstone lithofacies in the positive values (Figure 21

& 23).Samples also ordinate along Axis 2 with a group of brachiopod-sponge-echinoid dominated samples in the negative values, group of molluscan dominant and Parafusulina dominant samples in the center, and another group of brachiopod-sponge-echinoid dominant samples in the positive values (Figures 22 & 24). These same lithofacies and biofacies patterns hold up for Axis 3. To examine this pattern, samples were coded by percent abundances of sponges and echinoids (Figures 25 & 26). Samples grade along Axis 2 from high percent abundance in the negative values to low percent abundance of sponges in the positive values.

Sponges are also only present in samples located within the positive values of Axis 3. Percent abundance of echinoids does not appear to explain any variance in the dataset.

Figure 19-DCA showing the spread of both samples (black) and taxa (red) along axes 1 and 2.

Figure 20- DCA showing the spread of both samples (black) and taxa (red) along axes 2 and 3.

Figure 21- DCA Axes 1 and 2 coded by lithology. Carbonate rich samples are in red, sandstone rich samples are in blue. There is a gradient along Axis 1 from more sandstone rich samples to more carbonate rich samples.

Figure 22- DCA Axes 1 and 2 coded by biofacies. Brachiopod-sponge-echinoid samples in blue are located in the negative values of Axis 1. Molluscan samples in red plot in the positive values of Axis 1. This indicates that these two biofacies represent two end members of an environmental gradient. Parafusulina samples in green plot in the center of the ordination.

Figure 23- DCA Axes 2 and coded by lithology. Carbonate rich samples are in red, sandstone rich samples are in blue. Unlike Axis 1, there is no gradation in lithology along either axis.

Figure 24- DCA Axes 2 and 3 coded by biofacies. Brachiopod-sponge-echinoid samples in blue plot in two distinct groups on Axes 2 and 3. Molluscan and Parafusulina samples in red and green respectively plot in the center of the ordination.

Figure 25; DCA Axes 2 and 3 coded by percent sponge abundance. The size of the circle represents the percent abundance of sponges in the sample.

Figure 26- DCA Axes 2 and 3 coded by percent echinoid abundance. The size of the circle represents the percent abundance of echinoids in the sample.

NMDS was also performed to identify environmental gradients. These ordinations were created using a k value of 3 dimensions, which had a stress value equal to 0.013. Results from

NMDS were very similar to DCA. A gradient from carbonate lithology to siliciclastic lithology was identified along Axis 2 (Figure 27) A gradient from molluscan dominated biofacies to

Parafusulina dominated biofacies to brachiopod-sponge biofacies was also identified along Axis

2 (Figure 28).

Figure 27: NMDS of samples coded by lithology. Carbonate samples are coded red, and sandstone samples are coded in blue. There is a gradation from carbonate to sandstone lithologies on both axes.

Figure 28- NMDS of samples coded by biofacies. Molluscan samples are coded red, brachiopod-sponge-echinoid samples are blue, and Parafusulina samples are green.

Cluster analysis, DCA and NMDS were performed a second time after removing all

Parafusulina from the samples. This was because of the abundant and ubiquitous distribution of

Parafusulina and provided the opportunity to see if the ubiquitous occurrence of these taxa masked other structure in the data. However, patterns observed from analyses with Parafusulina removed are no different than the analyses above.

Biofacies Changes through the San Andres

Biofacies as defined by the two-way cluster (Figure 18C) are overlain on the outcrop to view how biofacies changes occur with respect to stratigraphy (Figure 29). The molluscan dominated samples occur in the channelized peloidal sandstones of Facies 3 beneath the maximum flooding surface. The samples from the heavily bioturbated sandstones of Facies 4 that downlap onto the maximum flooding surface are dominated by Parafusulina and echinoids.

Above the downlap surface is a zone that is devoid of fossil material for approximately 15m. The upper half of the heavily bioturbated sandstones contain samples dominated by brachiopods and sponges. The contact between the thin bedded sandstones of Facies 5 and the thin-bedded carbonates of Facies 6 contains Parafusulina dominated samples with some brachiopods and sponges or are comprised solely of Parafusulina. The samples close to the base of the thick bedded, cliffy carbonates of Facies 7 contain only Parafusulina.

Fossil Density

Fossil density calculated for each sample was also overlain on to the outcrop to determine how it changed with respect to stratigraphy (Figure 30). No fossil material was found in Facies 1 and Facies 2A beneath the first sequence boundary. High density of fossil material was found around the downlap surface separating the channelized peloidal sandstone of Facies 3 from the heavily bioturbated sandstones of Facies 4 (on the order of 10-1 individuals per cm2). Above this area of dense fossil material and along measured sections 1 and 2, is a zone approximately 30m thick that is devoid of fossil material. This barren zone slowly grades into an area of low fossil density where occurrences were equal to single individuals within several square meters. In the medium-bedded units of Facies 4 above measured section 3 are laterally discontinuous

Parafusulina shell beds that also have a density of 10-1 individuals per cm2. These shell beds are laterally equivalent to the fossil poor/ barren zone, and the beds above and below these medium bedded sandstones are fossil poor. Fossil density continues to increase up-section until the interface between the thin bedded sandstones and carbonates of Facies 5 and Faces 6, where density is the highest (100 individuals per cm2). Fossil material decreases through the cliffy carbonate packstones of Facies 7, and is completely absent in Facies 8. This pattern is repeated when Parafusulina is removed from analyses.

Figure 29- Biofacies as coded in the two-way cluster analysis are overlain onto an image of the outcrop. Molluscan biofacies only occurs in Facies 3 beneath the MFS, and the brachiopod-sponge-echinoid and Parafusulina biofacies occur in Facies 4-7 above the MFS. There are two different Parafusulina dominated zones. The first Parafusulina zone is separated from the brachiopod-sponge- echinoid zone by a section ~ 30m thick devoid of fossils.

Figure 30- Fossil density of samples drawn as contour lines onto the face of the outcrop. Warmer colors indicate higher densities (individuals/cm2), whereas cooler colors indicate lower density samples. Areas without fossils were colored gray.

Chert Density

Chert and silicification takes on several forms such as small chert vugs, discontinuous cherty fossiliferous material, and large nodules. Density of chert varies as well, ranging from isolated vugs to thick, laterally continuous beds. Overall, the distribution of chert appears to follow a similar pattern to the distribution of fossil density. Small chert vugs (~ 1-3 cm) occur in rare abundance in Facies 1. Within Facies 2, Thalassinoides trace fossils are either filled with sand or completely replaced by chert. Chert vugs are also common where Thalassinoides traces are not present. Within Facies 2B are thin (~3cm) beds of nodular chert. These chert layers extend past measured section 1 farther into the canyon, but pinch out between measured sections

2 and 3. Fossils within Facies 3 are silicified, and small chert vugs are more common at the base.

Silicified fossil material occurs in high abundance at the base and top of Facies 4. Sparse silicified material occurs in the middle fossil barren/poor zone of Facies 4 typically in the form of small chert vugs. They first appear as sparse (~1-3 vugs/m2) and very small (~1 cm), but increase in abundance (~5-10 vugs/m2) and size (~3-5 cm) up section. Thin discontinuous beds of silicified unidentifiable fossil material can occur where planar laminations are exposed within

Facies 4. These discontinuous beds of chert are parallel to bedding. Non-laterally continuous nodular chert bands (~3-5 cm thick) are sporadically located at the base of Facies 5 that increase in abundance up section. Interbedded between these chert bands are small chert vugs (1-3 cm).

The chert bands eventually grade into dense Parafusulina rich nodular beds (~ 5cm thick) at the top of Facies 6. No chert vugs or nodules were observed in Facies 6 or 7, but Parafusulina tests within Facies 6 are silicified.

Table 1: Summary of results identifying the major biofacies, their respective lithofacies, depositional environments, and systems tracts. Also describes whether or not these biofacies were found in areas with evidence of transport or in condensed sections. Table 1 also summarizes the shell density and sedimentation rates relative to the other biofacies.

Discussion

Biofacies Distribution Cluster analysis identified 4 major biofacies- molluscan dominated, brachiopod-sponge- echinoid dominated, Parafusulina-echinoid dominated, and Parafusulina dominated (Figure

18C; Table 1). These biofacies tend to occur in specific lithologies and are related to environmental gradients. When overlain onto ordination scores of DCA and NMDS, lithology

56 and biofacies identify environmental gradients. Since NMDS generated similar results to DCA, discussion of environmental gradients will focus on DCA results.

When coded by lithology (Figure 21), samples grade from siliciclastic rich in the negative values to more carbonate rich in the positive values along DCA Axis 1. Samples plotting around

-2 to -3 on Axis 1 were collected from the bioturbated sandstones (Facies 4) interpreted to represent lower slope to basinal sandstones. Samples plotting around 1 to 3 on Axis 1 were collected from the channelized peloidal sandstone (Facies 3) interpreted to represent lower slope channel deposits. Samples plotting in the middle of the ordination are a mixture of thin bedded slope siliciclastics and carbonates (Facies 5 and 6) and shelfal carbonate packstones/wackstones

(Facies 7). Since there are lower slope depositional environments in both the positive and negative values, Axis 1 cannot represent onshore-offshore gradient. This is surprising given that an onshore-offshore gradient frequently controls Axis 1 for data sets containing benthic marine faunas (Patzkowsky 1995, Holland et al 2001, Miller et al 2001, Scarponi and Kowalewski 2004,

Patzkowsky and Holland 2012). However, samples do appear to grade with respect to systems tracts. The samples plotting in the negative values and in the center of the ordination belong to the HST, whereas the samples plotting in the positive values belong to the LST.

When coded by biofacies, samples grade along Axis 1 from brachiopod-sponge-echinoid dominated in the negative values, Parafusulina dominated samples in the middle, to molluscan dominated in the positive values. It is expected for Parafusulina dominated samples plot in the center of the ordination as field observations noted Parafusulina to have a ubiquitous and abundant distribution across the outcrop. What is worth noting, however, is that the brachiopod- sponge-echinoid dominated samples and molluscan dominated samples do not overlap in ordination space. Olszewki and Patzkowsky (2001) found a similar separation of bivalves and

57 brachiopod biofacies within other Permian assemblages. This indicates that the brachiopod- sponge-echinoid dominated samples and the molluscan dominated samples possibly represent two endmembers of an environmental gradient.

Using faunal communities to make inferences about environment can lead to circular arguments however. Therefore, the sample ordination by biofacies was examined with respect to the sample ordination by lithology. Parafusulina dominated samples plot within the same ordination space as the overlap of sandstone and carbonate lithologies. The brachiopod-sponge- echinoid dominated samples plot within the same ordination space as the sandstones of Facies 4 and 5. Molluscan dominated samples only plot in the same ordination space as the Facies 3 channelized peloidal sandstones. Late Paleozoic benthic communities were structured such that brachiopods are typically most abundant in more slope and offshore settings, and molluscs are most abundant within nearshore and shelf settings (Sepkoski, 1991; Olszewski and Patzkowsky,

2001; Clapham and Bottjer, 2007). This suggests that molluscan communities may have occurred within nearshore, shelf environments whereas the brachiopod-sponge communities may have occurred within more offshore, slope environments. Additionally, this interpretation is corroborated by observation from Sonnenfeld (1993) and Sonnenfeld and Cross (1993) on the distribution of skeletal material. They found autochthonous molluscan material in shelf environments and autochthonous brachiopods and sponges were found along the shelf margin, slope and lower slope environments of Last Chance Canyon.

The lithofacies interpretations in this study indicate that many of these shell beds include transported material (see Table 1). The molluscan-dominated samples all occur within the channelized peloidal sandstone of Facies 3. Although the molluscan taxa occur within the peloidal grainstone laminations within this facies, which suggests that the material comes from

58 more onshore environments, the orientation of Parafusulina tests, graded bedding, soft sediment deformation and channel structures provide clear evidence this facies is the result of transported material. Some of the brachiopod-sponge-echinoid dominated samples come from the heavily bioturbated sandstone of Facies 4, where disarticulation of brachiopods and sponges at the base and the orientation of fusulinids within the medium beds all point to transported skeletal material as well.

Overlaying the biofacies onto an image of the outcrop puts the biofacies into a stratigraphic perspective (Figure 29). Molluscan dominated assemblages only occur within the channelized peloidal sandstones of Facies 3 beneath the maximum flooding surface.

Parafusulina-echinoid dominated samples are found just above this maximum flooding surface within the bioturbated sandstones of Facies 4. Above this is roughly 30 m of section where

Facies 4 is extremely fossil poor to essentially fossil barren. Fossil material begins to reappear as single sponges and brachiopods and increase in abundance until they become the dominant faunal members of samples towards the top of Facies 4. Samples then grade to Parafusulina dominated in the thin bedded sandstones of Facies 5and then to Parafusulina only samples as lithology transitions into the carbonates of Facies 6 and 7. Above the Parafusulina only samples, the carbonates are fossil barren through the sequence boundary.

This succession of faunal change suggests that DCA Axis 1 may also reflect the different systems tracts preserved in Last Chance Canyon. Molluscan taxa were found in the channelized peloidal grainstones of the LST below the maximum flooding surface. Brachiopods and sponges were found in the slope and basinal sandstones of the HST above the maximum flooding surface.

The maximum flooding surface marks a distinct shift from molluscan dominated to brachiopod- sponge dominated, which appears to support Holland’s (1995) findings that major biofacies

59 changes occur at stratigraphic surfaces. Even though a change in water depth is occurring, these shifts in biofacies are not occurring due to shifts in environment and faunal ecology, as would be expected under Holland’s mode, but is rather controlled by shell transport.

Parafusulina abundance increases from the top of Facies 4 through to Facies 7. As stated earlier, Facies 4-8 represent the HST of the second sequence, and preserve high frequency progradational clinoforms. Facies 5 and 6 interfinger, and it is at this interface where assemblages change from brachiopod-sponge-dominated to Parafusulina dominated. Although there may be a slight offlap/downlap relationship between Facies 5 and 6 (Sonnenfeld and Cross

1993), there are no higher order stratigraphic surfaces observed to link this biofacies change to sequence stratigraphic architecture.

DCA Axes 2 and 3 do not display a gradient when coded by biofacies or lithology.

Molluscan dominated carbonate samples and Parafusulina dominated carbonate/siliciclastic samples plot in the middle of the ordination, while brachiopod-sponge-echinoid dominated sandstones ordinate at both the positive and negative extremes of Axis 2 and Axis 3. Samples were coded by percent abundances of echinoids and sponges to identify a gradient. Percent abundance of echinoids did not show any gradation along Axis 2 or 3. However, the gradation of percent abundance of sponges along Axis 2, and presence – absence of sponges along Axis 3 reflects field observations. Sponges are not present at the base of Facies 4 and increase in abundance within the sandstone Facies 4 and 5 vertically through the measured section.

Sonnenfeld (1993) observed intact, autochthonous sponges to be preserved with shelf margin to mid slope facies of the higher order cycles of the HST, but not basinal. Therefore, the gradient from high sponge abundance to low sponge abundance along Axis 2 and the presence-absence

60 gradient of sponges along Axis 3 both represent an onshore-offshore gradient of the higher order cycles preserved within the HST.

Changes in Fossil Density High density of fossil material (on the order of 10-1 individuals per cm2) accumulated within the channelized peloidal sandstone of Facies 3 (Figure 30). The dense amount of skeletal material within Facies 3 is derived from transported materials given the graded bedding, orientation of Parafusulina tests, soft sediment deformation and channel structures. These shell beds in Facies 3 are condensed as the result of high input of transported skeletal material, and not as the result of and low sedimentation rates.

Located at the base of the prograding clinoforms of the HST, Facies 4 has a downlapping relationship with the maximum flooding surface that can be observed at outcrop scale.

Volumetric partitioning by Sonnenfeld and Cross (1993) clearly show that these bottomsets are condensed relative to their respective foresets. This is consistent with Kidwell’s (1991) conceptual model of shell accumulation (Figure 31). However, the orientation of Parafusulina tests, fragmentation of fossil material, and the lack of well preserved, delicate structures such as intact sponges and brachiopod spines at the base of Facies 4 indicate transport was also an important factor in the condensation of skeletal material.

Figure 31- Comparison of fossil densities found within the HST of the San Andres at Last Chance Canyon with expectations set forth by Kidwell’s model. High densities of shell material were found at the downlap surface in Last Chance Canyon, which is congruent with the model, but no shell material was found near the toplap surface. High fossil densities occurred instead within the foresets of the prograding clinoforms.

No fossils are found surrounding the sequence boundary where Facies 8 has a toplapping relationship to the overlying Grayburg Formation. Facies 8 was simply a non-fossiliferous depositional environment and therefore has a density value of zero. In this instance, our hypothesis of finding high density of shell material near toplap surfaces based upon Kidwell’s

(1991) model has to be rejected.

The highest accumulation of fossils occurs where shelf to upper slope carbonates of

Facies 6 interfinger with the lower slope siliciclastics of Facies 5 (Figures 30 & 31). Fossil material here is mostly comprised of Parafusulina with some productid brachiopods, and fossil density is on the order of 100 individuals per cm2. This zone of dense fossil material does not appear to be located near the major toplap or downlap surfaces of the high frequency progradational clinoforms within the HST. Therefore, one interpretation for this high accumulation of Parafusulina is a highly productive paleoenvironment. Water depths of 10-30 m

(Ross 1983) in the shallow subtidal environment would have been the preferred environment of these large photosymbiotic benthic foraminifera (Ross 1992, BouDagher-Fadel 2008). Our environmental interpretation of Facies 6 fits these criteria well, but would be at the shallow end for interpreted water depth of Facies 5. Therefore, it is plausible that this high density of

Parafusulina fossils simply reflects high input of shell material resulting high productivity, and not condensation as the result of low sedimentation rates.

We observed at outcrop scale, similar to Sonnenfeld and Cross (1993), what appear to be onlap and downlap surfaces where the Facies 5 sandstones and Facies 6 carbonates interfinger.

This indicates that there may be a relationship between these high density Parafusulina beds and higher order stratigraphic surfaces. However, these potential surfaces and their relationship to the high density Parafusulina shell beds could not be accessed due to the steepness of the outcrop where they were preserved. These surfaces could not be laterally followed to where it was safe to make the necessary observations, and the high resolution GigaPan images were not helpful in determining the nature of these surfaces either. As such, an argument connecting the controls of sequence stratigraphic to the formation of these Parafusulina beds cannot be made at this time.

Chert Density and Sequence Stratigraphy

A qualitative analysis on the distribution of chert may also add to the understanding of fossil density within Last Chance Canyon. The majority of the skeletal material preserved within

Last Chance Canyon is heavily silicified, with molluscs and Parafusulina just as likely to be altered as brachiopods. This indicates that skeletal material provides a nucleation point for silicification and growth of chert. Additionally, silica is in abundant supply in Last Chance

Canyon and is most likely derived from either sponge material or siliciclastic sediments.

Chert densities follow similar patterns to shell densities and sequence architecture. Chert vugs are sparse where fossil material is sparse as well, such as within the foresets of Facies 4 and the nonfossiliferous Facies 1 and 2. Chert vugs increase in density in beds where fossils are moderately dense, such as the base of Facies 3 and the base Facies 4 where the sequence boundary and maximum flooding surface are located. Discontinuous bands of chert are common where dense shell beds are present, such as the top of Facies 4 and the base of Facies 5. The densest occurrence of chert is within the dense Parafusulina shell beds within Facies 5 and

Facies 6.

While not directly associated with any shell beds, the densely packed chert filled

Thalassinoides burrows of Facies 2B also coincide with stratigraphic surfaces. These

Thalassinoides burrows and thin bedded chert cap are above the maximum flooding surface, and have a sharp contact with other beds. Additionally, these beds pinch out down depositional dip as they downlap onto Facies 3, implying condensation. Therefore, it is likely these chert filled

Thalassinoides burrows occur near minor flooding surfaces, and support the interpretation that

Facies 2B could represent a maximum flooding zone.

Conclusions

1) Biofacies were expected to change at stratigraphic surfaces that mark changes in

environment. Indeed, biofacies changes were found around the maximum flooding surface.

Biofacies changed from a molluscan dominated assemblage in the LST below the maximum

flooding surface to brachiopod-sponge and Parafusulina dominated assemblages in the

sandstones and carbonates in the HST. However, evidence for transported material was found

within the channelized peloidal grainstone (i.e. graded bedding, soft sediment deformation,

orientation of Parafusulina tests) and at the base of the heavily bioturbated sandstone (i.e.

orientation of Parafusulina tests, lack of well-preserved sponge material or brachiopod

spines that are found higher in the section) bounding the maximum flooding surface. This

indicates that the shift in biofacies is not driven by communities tracking their preferred

environment, but is being dominated by shell transport.

2) High density shell beds were expected to be found near stratigraphic surfaces as the result of

condensation by low sedimentation rates (R-sediment). Relatively high density of fossil

material was found near the maximum flooding surface. Fossil density decreased both up and

down section of the maximum flooding surface. High densities of chert were also located

near the maximum flooding surface The evidence for transport stated above indicates that

these dense shell beds formed resulting from variable rates of shell input (R-hardpart) and not

the low rates of sedimentation associated with the maximum flooding surface. Fossils were

not found at the sequence boundary between the San Andres and the Grayburg, creating a

barren zone near the toplap surface.

3) The highest densities of fossil material are from the Parafusulina shell beds within the

interfingering thin bedded carbonates and sandstones. No sequence stratigraphic surfaces

connected to low sedimentation rates were observed to connect these beds to any higher

order sequences. Lithologic characteristics indicate that these shell beds formed at shallow

water depths that were optimal for Parafusulina. These shell beds appear to be the result of

high productivity, not processes controlling stratigraphic architecture.

The results from this study do not support the original hypotheses. Biofacies changes across stratigraphic surfaces do not reflect a shift in ecological preferences of fossil taxa because these biofacies result from transport of fossils out of habitat. Shell density is likewise controlled by transport and productivity, and not low net sedimentation rates. These instances of transport

65 and productivity-dominated shell beds at Last Chance Canyon do not invalidate previous findings of the relationship between fossil accumulations and processes controlling stratigraphic architecture. Rather, this study demonstrates that these early models, while useful for forming predictions and initial hypotheses, can sometimes be too simplistic. This study serves as an example of how other processes in addition to the controls of stratigraphic condensation must be considered when examining fossiliferous shell beds.

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Appendix A: Appendix Introduction Included in the appendices below are the fossil counts matrix (Appendix B), the sample attributes matrix (Appendix C), and the R-codes (Appendix D) that were used to perform the statistical analyses. Appendix B is the first sample-by-taxon matrix described in the methods section with 46 samples and 30 taxa. It can be modified into the second sample-by-taxon matrix by removing all occurrences of Parafusulina. Appendix C contains all the identifying information regarding each sample (GPS coordinates, elevation, area, lithofacies, and biofacies) that were used to code the environmental attributes of the statistical analysis. Appendix D provides the lines of R-code used as well as some annotations. Not included in these appendices are the original lithologic logs and faunal logs from the three measured sections. These logs are available upon request.

Appendix B: Fossil Counts Matrix

Bivalve Brachiopod Astartella indet Ganiophora Modiomorph Nuculana Nuculavus Schizodus indet Strophomenid LCC-15- 01 1 14 0 0 0 0 0 1 0 LCC-15- 02 0 0 0 0 0 0 0 0 0 LCC-15- 03 0 0 0 0 0 0 0 0 0 LCC-15- 04 0 0 0 0 0 0 0 0 0 LCC-15- 05 0 0 0 0 0 0 0 0 0 LCC-15- 06 0 0 0 0 0 0 0 5 0 LCC-15- 07 0 0 0 0 0 0 0 0 0 LCC-15- 08 0 0 0 0 0 0 0 0 0 LCC-15- 09 0 0 0 0 0 0 0 8 1 LCC-15- 10 0 0 0 0 0 0 0 2 0 LCC-15- 11 0 0 0 0 0 0 0 0 0 LCC-15- 12 0 0 0 0 0 0 0 0 0 LCC-15- 13 0 0 0 0 0 0 0 0 0 LCC-15- 14 0 0 0 0 0 0 0 0 0 LCC-15- 15 0 0 0 0 0 0 0 0 0

Discotropis Encrusting Cephalopod Nautiliod Productid sp Enteletes Hustedia Neospirifer Bryozoan Bryozoan indet indet LCC-15- 01 0 0 0 0 0 0 0 3 0 LCC-15- 02 0 0 0 0 0 0 0 0 0 LCC-15- 03 0 0 0 0 0 0 0 0 0 LCC-15- 04 0 0 0 0 0 3 0 0 0 LCC-15- 05 0 0 0 0 0 0 0 0 0 LCC-15- 06 0 0 0 1 0 3 0 0 0 LCC-15- 07 0 0 0 0 0 0 0 0 0 LCC-15- 08 0 0 0 0 0 0 0 0 0 LCC-15- 09 0 0 1 1 0 0 0 0 0 LCC-15- 10 0 0 0 0 0 0 2 0 0 LCC-15- 11 0 0 0 0 0 0 0 0 0 LCC-15- 12 0 0 0 0 0 0 0 0 0 LCC-15- 13 0 0 0 0 0 0 0 0 0 LCC-15- 14 0 0 0 0 0 0 0 0 0 LCC-15- 15 0 0 0 0 0 0 0 0 0

Gastropod Gastropod Echinoid Goniasma indet planispiral Lophopyllidium Meekospira Parafusulina LCC-15- 01 0 1 8 0 1 0 1 LCC-15- 02 5 0 0 0 0 0 21 LCC-15- 03 10 0 0 0 0 0 25 LCC-15- 04 3 0 1 0 0 0 30 LCC-15- 05 2 0 0 0 1 0 36 LCC-15- 06 1 0 0 0 0 0 0 LCC-15- 07 2 0 0 0 0 0 45 LCC-15- 08 0 0 0 0 0 0 33 LCC-15- 09 17 0 0 0 0 0 6 LCC-15- 10 8 0 0 0 0 0 44 LCC-15- 11 5 0 0 0 0 0 56 LCC-15- 12 0 0 0 0 0 0 120 LCC-15- 13 0 0 0 0 0 0 334 LCC-15- 14 0 0 0 0 0 0 40 LCC-15- 15 0 0 0 0 0 0 30

Massive Parallel Spongey Spicule Tubular Sponge Sponge Sponge LCC-15- 01 0 0 0 LCC-15- 02 0 0 0 LCC-15- 03 0 0 0 LCC-15- 04 0 0 0 LCC-15- 05 0 0 0 LCC-15- 06 4 4 0 LCC-15- 07 2 0 0 LCC-15- 08 4 3 0 LCC-15- 09 1 0 0 LCC-15- 10 0 0 0 LCC-15- 11 0 0 0 LCC-15- 12 0 0 0 LCC-15- 13 0 0 0 LCC-15- 14 0 0 0 LCC-15- 15 0 0 0

Bivalve Brachiopod Astartella indet Ganiophora Modiomorph Nuculana Nuculavus Schizodus indet Strophomenid LCC-15- 16 0 0 0 0 0 0 0 0 0 LCC-15- 17 0 0 0 0 0 0 0 2 0 LCC-15- 18 0 0 0 0 0 0 0 0 0 LCC-15- 19 0 0 0 0 0 0 0 0 0 LCC-15- 20 0 0 0 0 0 0 0 0 0 LCC-15- 21 0 0 0 0 0 0 0 0 0 LCC-15- 22 0 0 0 0 0 0 0 0 0 LCC-15- 23 0 1 0 0 0 0 0 0 0 LCC-15- 24 0 1 0 0 0 0 0 0 0 LCC-15- 25 2 9 1 0 1 1 1 0 0 LCC-15- 26 1 2 0 0 0 0 0 0 0 LCC-15- 27 1 16 0 1 2 1 0 0 0 LCC-15- 28 0 5 0 0 0 0 0 0 0 LCC-15- 29 0 7 0 0 0 0 0 0 0 LCC-15- 30 1 16 0 0 0 0 1 0 0

Discotropis Encrusting Cephalopod Nautiliod Productid sp Enteletes Hustedia Neospirifer Bryozoan Bryozoan indet indet LCC-15- 16 0 0 0 0 0 0 0 0 0 LCC-15- 17 0 0 0 0 0 0 0 0 0 LCC-15- 18 0 0 0 0 0 0 0 0 0 LCC-15- 19 0 0 0 0 0 0 0 0 0 LCC-15- 20 0 0 0 0 0 0 0 0 0 LCC-15- 21 0 0 0 0 0 0 0 0 0 LCC-15- 22 0 0 0 0 0 0 0 0 0 LCC-15- 23 0 1 0 0 0 0 0 0 0 LCC-15- 24 0 0 0 0 0 0 0 0 0 LCC-15- 25 0 0 0 0 0 0 0 0 2 LCC-15- 26 0 0 0 0 0 1 0 0 0 LCC-15- 27 0 0 0 0 0 0 0 0 1 LCC-15- 28 0 0 0 0 0 0 0 0 0 LCC-15- 29 0 0 0 0 0 0 0 0 0 LCC-15- 30 0 0 0 0 0 3 0 1 0

Gastropod Gastropod Echinoid Goniasma indet planispiral Lophopyllidium Meekospira Parafusulina LCC-15- 16 0 0 0 0 0 0 30 LCC-15- 17 0 0 0 0 0 0 108 LCC-15- 18 0 0 0 0 0 0 44 LCC-15- 19 0 0 0 0 0 0 100 LCC-15- 20 0 0 0 0 0 0 63 LCC-15- 21 0 0 0 0 0 0 93 LCC-15- 22 0 0 0 0 0 0 55 LCC-15- 23 0 0 2 0 0 0 111 LCC-15- 24 7 0 0 0 0 2 19 LCC-15- 25 0 0 3 3 0 0 0 LCC-15- 26 0 0 1 0 0 0 199 LCC-15- 27 0 0 5 4 0 0 0 LCC-15- 28 0 0 0 0 0 0 21 LCC-15- 29 0 0 0 0 0 0 32 LCC-15- 30 0 0 12 0 0 0 0

Massive Parallel Spongey Spicule Tubular Sponge Sponge Sponge LCC-15- 16 1 0 0 LCC-15- 17 0 0 0 LCC-15- 18 1 0 0 LCC-15- 19 0 0 0 LCC-15- 20 0 0 0 LCC-15- 21 0 0 0 LCC-15- 22 0 0 0 LCC-15- 23 0 0 0 LCC-15- 24 0 0 0 LCC-15- 25 0 0 0 LCC-15- 26 0 0 0 LCC-15- 27 0 0 0 LCC-15- 28 0 0 0 LCC-15- 29 0 0 0 LCC-15- 30 0 0 0

Bivalve Brachiopod Astartella indet Ganiophora Modiomorph Nuculana Nuculavus Schizodus indet Strophomenid LCC-15- 31 0 7 0 0 0 0 1 0 0 LCC-15- 32 0 0 0 0 0 0 0 19 2 LCC-15- 33 0 0 0 0 0 0 0 0 0 LCC-15- 34 0 0 0 0 0 0 0 0 0 LCC-15- 35 0 0 0 0 0 0 0 0 0 LCC-15- 36 0 0 0 0 0 0 0 0 0 LCC-15- 37 0 0 0 0 0 0 0 0 0 LCC-15- 38 0 0 0 0 0 0 0 0 0 LCC-15- 39 0 0 0 0 0 0 0 2 0 LCC-15- 40 0 0 0 0 0 0 0 0 0 LCC-15- 41 0 0 0 0 0 0 0 0 0 LCC-15- 42 0 0 0 0 0 0 0 0 0 LCC-15- 43 0 0 0 0 1 0 0 1 0 LCC-15- 44 0 0 0 0 0 0 0 2 0 LCC-15- 45 0 0 0 0 0 0 0 1 0 LCC-15- 46 0 0 0 0 0 0 0 9 0

Discotropis Encrusting Cephalopod Nautiliod Productid sp Enteletes Hustedia Neospirifer Bryozoan Bryozoan indet indet LCC-15- 31 0 0 0 0 0 0 0 0 0 LCC-15- 32 0 0 0 0 0 0 0 0 0 LCC-15- 33 0 0 0 0 0 0 0 0 0 LCC-15- 34 0 0 0 0 0 0 0 0 0 LCC-15- 35 0 0 0 0 0 0 0 0 0 LCC-15- 36 0 0 0 0 0 0 0 0 0 LCC-15- 37 1 0 0 0 0 0 0 0 0 LCC-15- 38 0 0 0 0 0 0 0 0 0 LCC-15- 39 0 0 0 0 0 0 0 0 0 LCC-15- 40 4 0 0 0 0 0 0 0 0 LCC-15- 41 1 0 0 0 0 0 0 0 0 LCC-15- 42 2 0 0 0 0 0 0 0 0 LCC-15- 43 2 0 0 0 0 0 0 0 0 LCC-15- 44 0 0 0 0 0 0 0 0 0 LCC-15- 45 0 0 0 0 0 0 0 0 0 LCC-15- 46 0 0 0 0 1 0 0 0 0

Gastropod Gastropod Echinoid Goniasma indet planispiral Lophopyllidium Meekospira Parafusulina LCC-15- 31 0 0 0 0 0 0 42 LCC-15- 32 15 0 0 0 0 0 0 LCC-15- 33 0 0 0 0 0 0 122 LCC-15- 34 0 0 0 0 0 0 57 LCC-15- 35 0 0 0 0 0 0 103 LCC-15- 36 0 0 0 0 0 0 38 LCC-15- 37 0 0 0 0 0 0 82 LCC-15- 38 0 0 0 0 0 0 73 LCC-15- 39 4 0 0 0 0 0 275 LCC-15- 40 0 0 0 0 0 0 219 LCC-15- 41 0 0 0 0 0 0 176 LCC-15- 42 0 0 0 0 0 0 194 LCC-15- 43 0 0 0 0 0 0 68 LCC-15- 44 3 0 0 0 0 0 34 LCC-15- 45 48 0 0 0 0 0 13 LCC-15- 46 47 0 0 0 0 0 13

Massive Parallel Spongey Spicule Tubular Sponge Sponge Sponge LCC-15- 31 0 0 0 LCC-15- 32 1 1 0 LCC-15- 33 2 0 2 LCC-15- 34 0 1 0 LCC-15- 35 0 0 0 LCC-15- 36 0 0 0 LCC-15- 37 1 0 0 LCC-15- 38 0 0 0 LCC-15- 39 2 0 0 LCC-15- 40 0 0 0 LCC-15- 41 0 0 0 LCC-15- 42 0 0 0 LCC-15- 43 0 0 0 LCC-15- 44 0 0 0 LCC-15- 45 0 0 0 LCC-15- 46 0 0 0

Appendix C: Sample Attributes Matrix

Elevation length width Area Facies Lithology meters Northing Westing (cm) (cm) (cm2) LCC -15- Channelized Peloidal 01 Sandstone PSS 1399.03 32.25681 104.69941 127 45.72 5806.44 LCC-15- 02 VF HB SS VFHBSS 1423.72 32.25974 104.7011 101.6 81.28 8258.05 LCC-15- 03 VF HB SS VFHBSS 1438.05 32.25789 104.70101 228.6 190.5 43548.3

LCC-15- 04 VF HB SS VFHBSS 1429.82 32.25784 104.70108 162.56 121.92 19819.32

LCC-15- 05 VF HB SS VFHBSS 1434.69 32.25782 104.70113 129.54 50.8 6580.63

LCC-15- 06 VF HB SS VFHBSS 1481.94 32.25924 104.70073 698.5 236.22 164999.7

LCC-15- 07 VF HB SS VFHBSS 1502.05 32.25937 104.70054 15 15 225

LCC-15- 08 VF HB SS VFHBSS 1493.52 32.25949 104.70078 106.68 60.96 6503.21

LCC-15- 09 VF HB SS VFHBSS 1499.62 32.25961 104.70121 162.56 60.96 9909.66 LCC-15- Channelized Peloidal 10 Sandstone PSS 1385.32 32.25854 104.69734 90 90 8100

Cluster Percent Group Cluster Name Percent Echinoid Sponge LCC -15- 01 1 Molluscan 0 0 LCC-15- Parafusulina- 02 3 Echinoid 0.19230769 0 LCC-15- Parafusulina- 03 3 Echinoid 0.28571429 0 Parafusulina LCC-15- Dominate- 04 5 Echinoid 0.08108108 0 Parafusulina LCC-15- Dominate- 05 5 Echinoid 0.05128205 0 Echinoid- LCC-15- Brachiopod- 06 2 Sponge 0.04761905 0.380952381 Parafusulina LCC-15- Dominate- 07 5 Echinoid 0.04081633 0.040816327 Parafusulina LCC-15- Dominate- 08 5 Echinoid 0 0.175 Echinoid- LCC-15- Brachiopod- 09 2 Sponge 0.48571429 0.028571429 LCC-15- Parafusulina- 10 3 Echinoid 0.14285714 0

Elevation length width Area Facies Lithology meters Northing Westing (cm) (cm) (cm2)

LCC-15- 11 VF HB SS VFHBSS 1391.72 32.25854 104.69734 70 40 2800 LCC-15- Sandy Carbonate 12 Packstone SCP 1492 32.2594 104.70008 15.24 20.32 309.68 LCC-15- Sandy Carbonate 13 Packstone SCP 1492 32.2594 104.70008 10.16 22.86 232.26 LCC-15- 14 Carbonate Mudstone CP 1497.18 32.25941 104.70004 45.72 30.48 1393.55 LCC-15- 15 Carbonate Mudstone CP 1506.63 32.25944 104.7001 35.56 25.4 903.22 LCC-15- 16 Carbonate Mudstone CP 1503.58 32.5939 104.7001 76.2 17.78 1354.84 LCC-15- 17 Carbonate Packstone CP 1496.57 32.25938 104.70028 14 8 112 LCC-15- 18 VF SS thin VFtSS 1496.87 32.25949 104.70058 12 8 96 LCC-15- 19 Carbonate Packstone CP 1502.66 32.25953 104.70077 10 10 100 LCC-15- Sandy Carbonate 20 Packstone SCP 1509.98 32.25958 104.70088 88.9 35.56 3161.28

Cluster Percent Group Cluster Name Percent Echinoid Sponge Parafusulina LCC-15- Dominate- 11 5 Echinoid 0.08196721 0 LCC-15- Parafusulina 12 7 Only 0 0 LCC-15- Parafusulina 13 7 Only 0 0 LCC-15- Parafusulina 14 7 Only 0 0 LCC-15- Parafusulina 15 7 Only 0 0 LCC-15- Parafusulina 16 6 Dominate 0 0.032258065 LCC-15- Parafusulina 17 6 Dominate 0 0 LCC-15- Parafusulina 18 6 Dominate 0 0.022222222 LCC-15- Parafusulina 19 7 Only 0 0 LCC-15- Parafusulina 20 7 Only 0 0

Elevation length width Area Facies Lithology meters Northing Westing (cm) (cm) (cm2) LCC -15- 21 Carbonate Packstone CP 1493.52 32.25969 104.70104 9 6 54 LCC-15- 22 Carbonate Mudstone CP 1503.27 32.25977 104.70103 30.48 30.48 929.03 LCC-15- Channelized Peloidal 23 Sandstone PSS 1382.57 32.25863 104.69719 132.08 40.64 5367.73 LCC-15- Channelized Peloidal 24 Sandstone PSS 1379.52 32.25858 104.69732 76.2 30.48 2322.58 LCC-15- Channelized Peloidal 25 Sandstone PSS 1395.98 32.25676 104.6994 139.7 60.96 8516.11 LCC-15- Channelized Peloidal 26 Sandstone PSS 1400.56 32.25754 104.69919 182.88 60.96 11148.36 LCC-15- Channelized Peloidal 27 Sandstone PSS 1394.46 32.25652 104.70049 60.96 50.8 3096.77 LCC-15- Channelized Peloidal 28 Sandstone PSS 1401.47 32.25681 104.7009 45.72 25.4 1161.29 LCC-15- Channelized Peloidal 29 Sandstone PSS 1406.65 32.25714 104.70149 60.96 45.72 2787.09 LCC-15- Channelized Peloidal 30 Sandstone PSS 1398.73 32.25658 104.70074 91.44 20.32 1858.06

Cluster Percent Group Cluster Name Percent Echinoid Sponge LCC -15- Parafusulina 21 7 Only 0 0 LCC-15- Parafusulina 22 7 Only 0 0 LCC-15- Parafusulina 23 6 Dominate 0 0 LCC-15- Parafusulina- 24 3 Echinoid 0.23333333 0 LCC-15- 25 1 Molluscan 0 0 LCC-15- Parafusulina 26 6 Dominate 0 0 LCC-15- 27 1 Molluscan 0 0 LCC-15- Parafusulina- 28 4 Bivalve 0 0 LCC-15- Parafusulina- 29 4 Bivalve 0 0 LCC-15- 30 1 Molluscan 0 0

Elevation length width Area Facies Lithology meters Northing Westing (cm) (cm) (cm2) LCC -15- Channelized Peloidal 31 Sandstone PSS 1414.88 32.25743 104.70159 71.12 25.4 1806.45

LCC-15- 32 VF HB SS VFHBSS 1472.79 32.25917 104.69976 541.02 20.32 10993.53 LCC-15- 33 VF SS thin VFtSS 1503.58 32.2593 104.70028 38.1 7.62 290.32 LCC-15- 34 VF SS thin VFtSS 1505.71 32.2593 104.70028 10 10 100 LCC-15- 35 VF SS thin VFtSS 1503.27 32.2594 104.70046 10 6 60 LCC-15- 36 VF SS thin VFtSS 1506.93 32.25951 104.70045 50.8 25.4 1290.32 LCC-15- 37 VF SS thin VFtSS 1494.43 32.25948 104.70062 8 13 104 LCC-15- 38 VF SS thin VFtSS 1495.65 32.25952 104.70078 17.78 10.16 180.64 LCC-15- 39 VF SS thin VFtSS 1499.01 32.25953 104.7009 60.96 15.24 929.03 LCC-15- 40 VF SS thin VFtSS 1494.13 32.25954 104.70098 35.56 12.7 451.61

Cluster Percent Group Cluster Name Percent Echinoid Sponge LCC -15- Parafusulina- 31 4 Bivalve 0 0 Echinoid- LCC-15- Brachiopod- 32 2 Sponge 0.39473684 0.052631579 LCC-15- Parafusulina 33 6 Dominate 0 0.031746032 LCC-15- Parafusulina 34 6 Dominate 0 0.017241379 LCC-15- Parafusulina 35 7 Only 0 0 LCC-15- Parafusulina 36 7 Only 0 0 LCC-15- Parafusulina 37 6 Dominate 0 0.011904762 LCC-15- Parafusulina 38 7 Only 0 0 LCC-15- Parafusulina 39 6 Dominate 0.01413428 0.007067138 LCC-15- Parafusulina 40 6 Dominate 0 0

Elevation length width Area Facies Lithology meters Northing Westing (cm) (cm) (cm2) LCC -15- 41 VF SS thin VFtSS 1494.13 32.25954 104.70098 25.4 7.62 193.55 LCC-15- 42 VF SS thin VFtSS 1494.13 32.25954 104.70098 40.64 17.78 722.58 LCC-15- VF SS thin Carbonate 43 interfinger VFtSSC 1500.23 32.25969 104.70125 55.88 12.7 709.68

LCC-15- 44 VF HB SS VFtSS 1468.83 32.25906 104.70157 45 15 675

LCC-15- 45 VF HB SS VFHBSS 1433.17 32.25835 104.70206 508 279.4 141935.2

LCC-15- 46 VF HB SS VFHBSS N/A N/A N/A N/A N/A N/A

Cluster Percent Group Cluster Name Percent Echinoid Sponge LCC -15- Parafusulina 41 6 Dominate 0 0 LCC-15- Parafusulina 42 6 Dominate 0 0 LCC-15- Parafusulina 43 6 Dominate 0 0 Parafusulina LCC-15- Dominate- 44 5 Echinoid 0.075 0 Echinoid- LCC-15- Brachiopod- 45 2 Sponge 0.77419355 0 Echinoid- LCC-15- Brachiopod- 46 2 Sponge 0.66197183 0

Appendix D: R Codes for Statistical Analyses library(vegan)

#Import Fossil Counts Matrix

NewCountsMatrix<-read.csv("NewCountsMatrix.csv", header=TRUE, row.names=1) #Fossil Counts Matrix where all bivalve, brachiopod, and echinoid taxa were reduced to "bivalve indet", "brachiopod indet" and "echinoid" NewSampleTotals<-rowSums(NewCountsMatrix) #Determine the sample size of each fossil count mean(NewSampleTotals) median(NewSampleTotals)

#Import Sample Attributes Matrix SampleAttributes<-read.csv("SampleAttributes.csv", header=TRUE, row.names=1) #Create objects out of different categories of Sample Attributes Lithology<-SampleAttributes$Lithology Clusters<-SampleAttributes$New.Sample.Cluster PercentEchinoid<-SampleAttributes$PercentEchinoid PercentSponge<-SampleAttributes$PercentSponge

#NewCountsMatrix Standardizations Newpropsamp<-decostand(NewCountsMatrix,"total");Newpropsamp

#NewCountsMatrix Distance Matrix BrayNewpropsamp<-vegdist(Newpropsamp, method="bray", diag=TRUE);BrayNewpropsamp

#NewCountsMatrix Q- mode Cluster Analysis library(sparcl) library(cluster)

Newpropsampcluster<-agnes(BrayNewpropsamp, method="ward") plot(Newpropsampcluster, which.plots=2, cex=0.5, hang=-0.1)

#Colored Q-mode analysis myCols <- vector(length = nrow(NewCountsMatrix)) # this says that myCols is an object of class "vector". A vector is a series of values or characters that are referenced by a number. myCols[4] would return the 4th item in vector myCols. Here what we've done is created a vector with no values stored in it yet, but we set the length of the vector to be the number of rows in our original data matrix (corresponding to the number of samples. If you wanted more or less variables you'd just add or subtract the lines of code. x <- which(SampleAttributes$Lithology == "CM") # here we create an object x which stores the index of the rows where the column labeled "time" in "NewCountsMatrix" is equal to the string "CM". So if the 4th row had "CM", one of the values in x would be 4. myCols[x] <- "pink" # here we reference the new vector myCols with x, telling it that you want all of the values of x in myCols to be "pink". Because the agnes function keeps the same order of samples when it creates labels, we can use this information to map color onto our dendrogram. Below we'll repeat with all of the variables x <- which(SampleAttributes$Lithology == "CP") myCols[x] <- "red" x <- which(SampleAttributes$Lithology == "SCP") myCols[x] <- "orange" x <- which(SampleAttributes$Lithology == "PSS") myCols[x] <- "gold" x <- which(SampleAttributes$Lithology == "VFHBSS") myCols[x] <- "green2"

100

x <- which(SampleAttributes$Lithology == "VFtSS") myCols[x] <- "blue" x <- which(SampleAttributes$Lithology == "VFtSSC") myCols[X] <- "dodgerblue"

# method b uses a loop to go through all the values of NewCountsMatrix column time and record a value in myCols myCols <- vector(length = nrow(NewCountsMatrix)) for(i in 1:length(myCols)) { # when R sees a for loop it will perform the operations in the brackets after the for loop for the number of times you set (in this case from 1 to the number of items in the vector myCols or 1:length(myCols). the value i is used as a counter, every time the loop finishes, 1 is added to i, and the loop is run again until i is equal to myCols.

if(SampleAttributes$Lithology[i] == "CM") myCols[i] <- "pink" # an if statement asks the question, is the first part of the expression equal to the second part of the expression? In this case, is the ith value of NewCountsMatrix$Lithofacies equal to the character string "CM"? If this is true, it performs the second part, namely making the ith element of myCols equal to the character string "pink" else if(SampleAttributes$Lithology[i] == "CP") myCols[i] <- "red" #else if has to come after an if statement, but you don't have to use this expression if you don't want it. It says, if the previous if statement was false, look to see if this statement is true. So if the ith element equaled "CP" the statement would be false in the original if statement and R would look at this line of code and see that it was true, setting the ith element of myCols to the value "red" else if (SampleAttributes$Lithology[i] == "SCP") myCols[i] <- "orange" else if(SampleAttributes$Lithology[i] == "PSS") myCols[i] <- "gold" else if(SampleAttributes$Lithology[i] == "VFHBSS") myCols[i] <- "green2" else if(SampleAttributes$Lithology[i]== "VFtSS") myCols[i] <- "blue" else if (SampleAttributes$Lithology[i]=="VFtSSC") myCols[i] <- "dodgerblue"

101

else myCols[i] <- "black" # if you use "else if" you should end your statement with an else function. Else just says if none of these are true, do this (ie make the color black). You should do this so if there is some problem in your sample matrix (say, something is spelled wrong). You won't just get an error message and you'll be able to see that something is wrong on your dendrogram }

# THIS IS IMPORTANT # objects in R (ie anything you save using a <-) has something called a class. Vectors are of class vector, matricies can be of several different classes (matrix, data.frame, etc). You can tell the class of an item by typing class(x), where x is the object. There are several different classes of dendrograms, and different functions will produce different dendrograms. the function agnes() produces an object of the class "agnes" and "twins". We need to get our data in the form of class "hclust" if we want to produce a plot with colored dendrogram leaves. The general function for changing any class into any other class is as."class name". We'll use the function as.hclust() to change our agnes object into an hclust object.

NewmyHClust <- as.hclust(Newpropsampcluster)

#the function we want to use now is called ColorDendrogram(). In this function, the first parameter is the data, the second parameter "y" is the object we want to use to label the dendrogram.

ColorDendrogram(NewmyHClust, y = myCols) legend("topright", c("Carbonate Packstone","Sandy Carboante Packstone","Channelized Peloidal Sandstone","Bioturbated Sandstone","Thin Bedded Sandstone","Sandy Carbonate"), col=c("red","orange","gold","green2","blue","dodgerblue"), lty=1, lwd=2, bty="n")

#R Mode Cluster Analysis

102

NewCountsMatrixColMax<-decostand(Newpropsamp, method="max") RedoTaxaData<-t(NewCountsMatrixColMax) #This creates a taxon by sample matrix used for the R-mode cluster RedoTaxaDist<- vegdist(RedoTaxaData, "bray", diag=TRUE) RedoTaxaCluster<- agnes(RedoTaxaDist, method="ward") plot(RedoTaxaCluster, which.plots=2, cex=0.8, hang=-0.1)

#Create Two-way cluster analysis with colored cells myBreaks <- seq(0.05,1, by = .05) # you can set your breaks to any sequence you want, and they don't have to be the same length. You can do this manually too. myBreaks <- c(0,.000001, myBreaks) # here we added a 0 to .000001 bin to the heatmap, making this bin essentially 0. myColors <- topo.colors(20) # here we used the function rainbow to create a vector of colors. You can set these colors yourself too. It is important that this vector is one element less than the myBreaks vector myColors <- c("white", myColors) # now we can add "white" onto the vector, this will be the first color bin, which we're going to set to be (essentially) 0. pheatmap(Newpropsamp) # general function, with no custom colors. Note that values of '0' get a color on the color bar. This makes it difficult to distinguish a 0 from a non-zero, but small relative abundance value pheatmap(Newpropsamp, color = myColors, breaks = myBreaks) # general function using our breaks. This allows us to set the '0' cells to be white

103 pheatmap(Newpropsamp, color = myColors, breaks = myBreaks, clustering_method = "ward") #here we use ward's method using the argument clustering_method = "ward" and a bray- curstis distance by specifying the Q and R mode distance matricies pheatmap(Newpropsamp, color = myColors, breaks = myBreaks, clustering_method = "ward", clustering_distance_rows = BrayNewpropsamp, clustering_distance_cols = RedoTaxaDist) # here we fed the function a distance matrix we wanted to use. myDist and myTaxaDist both are distance matricies that were made by vegdist (bray-curtis distances).

#DCA with NewCountsMatrix Newpropsamp<-decostand(NewCountsMatrix,"total") Newpropsampstandmax<-decostand(Newpropsamp,"max") NewCountsMatrix.dca<-decorana(Newpropsampstandmax) summary(NewCountsMatrix.dca) #this will provide a summary of taxon and sample scores, as well and the eigenvalues of the first 4 axes. Eigenvalues here will not be accurate representations of % variance explained- will use the CA eigenvalues. plot(NewCountsMatrix.dca, choices=c(1,2)) #plots DCA of samples and taxa along Axes 1 and 2 plot(NewCountsMatrix.dca, choices=c(2,3)) #plots DCA of samples and taxa along Axes 2 and 3 plot(NewCountsMatrix.dca, choices=c(1,3)) #plots DCA of samples and taxa along Axes 1 and 3

#CA of NewCoutnsMatrix to explain variance NewCountsMatrix.ca<-decorana(Newpropsampstandmax, ira=1) summary(NewCountsMatrix.ca) #Will list the eigenvalues of the first four axes. % variance explained will use the total inertia of each axis (eigenvalue of the axis divided by the sum of all the eigenvalues) 104

#CA Axis 1 0.8946/(0.8946+0.7544+0.5662+0.5418) #0.3244831 #CA Axis 2 0.7544/(0.8946+0.7544+0.5662+0.5418) #0.2736308 #CA Axis 3 0.5662/(0.8946+0.7544+0.5662+0.5418) #0.2053682 #CA Axis 4 0.5418/(0.8946+0.7544+0.5662+0.5418) #0.196518 #DCA Sample Scores Newsamplescores1<-scores(NewCountsMatrix.dca, display=c("sites"),choices=1) Newsamplescores2<-scores(NewCountsMatrix.dca, display=c("sites"),choices=2) Newsamplescores3<-scores(NewCountsMatrix.dca, display=c("sites"),choices=3)

#DCA Sample Scores coded by lithology Newsamplescores1.split<-split(Newsamplescores1, Lithology) Newsamplescores2.split<-split(Newsamplescores2, Lithology) Newsamplescores3.split<-split(Newsamplescores3, Lithology)

#DCA Axes 1 and 2; samples coded by lithology plot(Newsamplescores1, Newsamplescores2, type="n", xlab="DCA Axis 1", ylab="DCA Axis 2") points(Newsamplescores1.split$CP, Newsamplescores2.split$CP, pch=16, col="red") points(Newsamplescores1.split$SCP, Newsamplescores2.split$SCP, pch=16, col="maroon") points(Newsamplescores1.split$PSS, Newsamplescores2.split$PSS, pch=16, col="violetred") points(Newsamplescores1.split$VFHBSS, Newsamplescores2.split$VFHBSS, pch=16, col="dodgerblue")

105 points(Newsamplescores1.split$VFtSS, Newsamplescores2.split$VFtSS, pch=16, col="blue") points(Newsamplescores1.split$VFtSSC, Newsamplescores2.split$VFtSSC, pch=16, col="purple2") legend("topright", c("Carbonate Packstone", "Sandy Carboante Packstone", "Channelized Peloidal Sandstone", "Bioturbated Sandstone", "Thin Bedded Sandstone", "Sandy Carbonate"), title="Lithology", col=c("red", "maroon", "violetred", "dodgerblue", "blue", "purple2"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.8, title.adj=0, bty="n")

#DCA Axes 1 and 3; samples coded by lithology plot(Newsamplescores1, Newsamplescores3, type="n") points(Newsamplescores1.split$CM, Newsamplescores3.split$CM, pch=16, col="pink1") points(Newsamplescores1.split$CP, Newsamplescores3.split$CP, pch=16, col="red") points(Newsamplescores1.split$SCP, Newsamplescores3.split$SCP, pch=16, col="maroon") points(Newsamplescores1.split$SPG, Newsamplescores3.split$SPG, pch=16, col="violetred") points(Newsamplescores1.split$VFHBSS, Newsamplescores3.split$VFHBSS, pch=16, col="dodgerblue") points(Newsamplescores1.split$VFtSS, Newsamplescores3.split$VFtSS, pch=16, col="blue") points(Newsamplescores1.split$VFtSSC, Newsamplescores3.split$VFtSSC, pch=16, col="purple2") legend("topright", legend=c("Carbonate Packstone", "Sandy Carboante Packstone", "Channelized Peloidal Sandstone", "Bioturbated Sandstone", "Thin Bedded Sandstone", "Sandy Carbonate"), title="Lithology", col=c("pink1", "red", "maroon", "violetred", "dodgerblue", "blue", "purple2"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.8,

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title.adj=0, bty="n")

#DCA Axes 2 and 3; samples coded by lithology plot(Newsamplescores2, Newsamplescores3, type="n", xlab="DCA Axis 2", ylab="DCA Axis 3") points(Newsamplescores2.split$CP, Newsamplescores3.split$CP, pch=16, col="red") points(Newsamplescores2.split$PSS, Newsamplescores3.split$PSS, pch=16, col="maroon") points(Newsamplescores2.split$SPG, Newsamplescores3.split$SPG, pch=16, col="violetred") points(Newsamplescores2.split$VFHBSS, Newsamplescores3.split$VFHBSS, pch=16, col="dodgerblue") points(Newsamplescores2.split$VFtSS, Newsamplescores3.split$VFtSS, pch=16, col="blue") points(Newsamplescores2.split$VFtSSC, Newsamplescores3.split$VFtSSC, pch=16, col="purple2") legend("topright", c("Carbonate Packstone", "Sandy Carboante Packstone", "Channelized Peloidal Sandstone", "Bioturbated Sandstone", "Thin Bedded Sandstone", "Sandy Carbonate"), title="Lithology", col=c("red","maroon","violetred","dodgerblue","blue","purple2"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.8, title.adj=0, bty="n") dev.off()

#DCA Sample Scores coded by Biofacies Newsamplescores1.split2<-split(Newsamplescores1, Clusters) Newsamplescores2.split2<-split(Newsamplescores2, Clusters) Newsamplescores3.split2<-split(Newsamplescores3 ,Clusters)

#DCA Axes 1 and 3, samples coded by Biofacies

107 plot(Newsamplescores1, Newsamplescores2,type="n", xlab="DCA Axis 1", ylab="DCA Axis 2") points(Newsamplescores1.split2$`1`, Newsamplescores2.split2$`1`, pch=16, col="red") points(Newsamplescores1.split2$`2`, Newsamplescores2.split2$`2`, pch=16, col="blue") points(Newsamplescores1.split2$`3`, Newsamplescores2.split2$`3`, pch=16, col="dodgerblue") points(Newsamplescores1.split2$`4`, Newsamplescores2.split2$`4`, pch=16, col="pink1") points(Newsamplescores1.split2$`5`, Newsamplescores2.split2$`5`, pch=16, col="green") points(Newsamplescores1.split2$`6`, Newsamplescores2.split2$`6`, pch=16, col="forestgreen") points(Newsamplescores1.split2$`7`, Newsamplescores2.split2$`7`, pch=16, col="black") legend("topright", legend=c("Molluscan", "Brachiopod-Sponge-Echinoid", "Parafusulina-Brachiopod-Sponge- Echinoid", "Parafusulina-Bivalve", "Parafusulina Dominate-Echinoid", "Parafusulina Dominate", "Parafusulina Only"), title="Biofacies", col=c("red","blue","dodgerblue","pink1","green","forestgreen","black"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.7, bty="n")

#DCA Axes 2 and 3; samples coded by biofacies plot(Newsamplescores2, Newsamplescores3, type="n", xlab="DCA Axis 2", ylab="DCA Axis 3") points(Newsamplescores2.split2$`1`, Newsamplescores3.split2$`1`, pch=16, col="red") points(Newsamplescores2.split2$`2`, Newsamplescores3.split2$`2`, pch=16, col="blue") points(Newsamplescores2.split2$`3`, Newsamplescores3.split2$`3`, pch=16, col="dodgerblue") points(Newsamplescores2.split2$`4`, Newsamplescores3.split2$`4`, pch=16, col="pink1") points(Newsamplescores2.split2$`5`, Newsamplescores3.split2$`5`, pch=16, col="green") points(Newsamplescores2.split2$`6`, Newsamplescores3.split2$`6`, pch=16, col="forestgreen") points(Newsamplescores2.split2$`7`, Newsamplescores3.split2$`7`, pch=16, col="black") legend("topright",

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legend=c("Molluscan", "Brachiopod-Sponge-Echinoid", "Parafusulina-Brachiopod-Sponge- Echinoid", "Parafusulina-Bivalve", "Parafusulina Dominate-Echinoid", "Parafusulina Dominate", "Parafusulina Only"), title="Biofacies", col=c("red","blue","dodgerblue","pink1","green","forestgreen","black"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.7, bty="n")

#DCA Axes 1 and 3; samples coded by biofacies plot(Newsamplescores1, Newsamplescores3, type="n") points(Newsamplescores1.split2$`1`, Newsamplescores3.split2$`1`, pch=16, col="red") points(Newsamplescores1.split2$`2`, Newsamplescores3.split2$`2`, pch=16, col="blue") points(Newsamplescores1.split2$`3`, Newsamplescores3.split2$`3`, pch=16, col="dodgerblue") points(Newsamplescores1.split2$`4`, Newsamplescores3.split2$`4`, pch=16, col="pink1") points(Newsamplescores1.split2$`5`, Newsamplescores3.split2$`5`, pch=16, col="green") points(Newsamplescores1.split2$`6`, Newsamplescores3.split2$`6`, pch=16, col="forestgreen") points(Newsamplescores1.split2$`7`, Newsamplescores3.split2$`7`, pch=16, col="black") legend("topright", legend=c("Molluscan", "Brachiopod-Sponge-Echinoid", "Parafusulina-Brachiopod-Sponge- Echinoid", "Parafusulina-Bivalve", "Parafusulina Dominate-Echinoid", "Parafusulina Dominate", "Parafusulina Only"), title="Biofacies", col=c("red","blue","dodgerblue","pink1","green","forestgreen","black"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.7, bty="n")

#DCA Axes 2 and 3; samples coded by Percent Echinoid abundanc plot(Newsamplescores2,Newsamplescores3,cex=(PercentEchinoid*3), main="% Echinoid", xlab="DCA Axis 2", ylab="DCA Axis 3")

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#cex (point size) was set 3 times the value of percent echinoid abundance to make the points visible in ordination space

#DCA Axes 2 and 3; samples coded by Percent Sponge abundance plot(Newsamplescores2, Newsamplescores3, cex=(PercentSponge*10),main="% Sponge",xlab="DCA Axis 2", ylab="DCA Axis 3") #Percent sponge was calculated by taking the percent abundances of each of the 3 sponge varieties identified in Lasts Chance Canyon. cex (point size) was set 10 times the value of percent sponge abundance to make the points visible in ordination space

#NMDS of NewCountsMatrix; samples transformed % sample total NMDSpk1<- metaMDS(comm= Newpropsamp, distance="bray",k=1, trymax=20, autotransform=FALSE);NMDSpk1 # “autotransform = FALSE” prevents R from preforming its own transformation based on the size of the data set and range of values in each sample. We account for this by inserting a transformed matrix into the “comm= “ function. In this case, the NewCountMatrix transformed by the percent sample totals was used. k=1 indicates the NMDS was run using 1 dimension. plot(NMDSpk4, type="t", main="k=1", sub="Stress=0.13")

NMDSpk2<- metaMDS(comm= Newpropsamp, distance="bray",k=2, trymax=20, autotransform=FALSE);NMDSpk2 #k=2 indicates the NMDS was run using 2 dimensions plot(NMDSpk2, type="t", main="k=2", sub="Stress=0.038")

NMDSpk3<- metaMDS(comm= Newpropsamp, distance="bray",k=3, trymax=20, autotransform=FALSE);NMDSpk3 #k=3 indicates the NMDS was run using 3 dimensions plot(NMDSpk3, type="t", main="k=3", sub="Stress=0.013")

NMDSpk4<- metaMDS(comm= Newpropsamp, distance="bray",k=4, trymax=20, autotransform=FALSE);NMDSpk4 #k=4 indicates the NMDS was run using 4 dimensions

110 plot(NMDSpk4, type="t", main="k=4", sub="Stress= 0.007")

NMDSpk5<- metaMDS(comm= Newpropsamp, distance="bray",k=5, trymax=20, autotransform=FALSE);NMDSpk5 #k=5 indicates the NMDS was run using 5 dimensions plot(NMDSpk5, type="t", main="k=5", sub="Stress= 0.005")

#Skree plot showing changes in stress values over multiple dimensions NMDSpStress<-c(0.13, 0.038, 0.013, 0.007, 0.005) plot(NMDSpStress) lines(NMDSpStress) #adds a trend line to the skree plot

#NMDS Sample Scores dim1Newpropsamp.NMDSpk3<-scores(NMDSpk3, display=c("sites"), choices=1) dim2Newpropsamp.NMDSpk3<-scores(NMDSpk3, display=c("sites"), choices=2) dim3Newpropsamp.NMDSpk3<-scores(NMDSpk3, display=c("sites"), choices=3)

#NMDS sample scores coded by lithology dim1NPS.split1<-split(dim1Newpropsamp.NMDSpk3, Lithology) dim2NPS.split1<-split(dim2Newpropsamp.NMDSpk3, Lithology) dim3NPS.split1<-split(dim3Newpropsamp.NMDSpk3, Lithology)

#NMDS samples scores coded by biofacies dim1NPS.split2<-split(dim1Newpropsamp.NMDSpk3, Clusters) dim2NPS.split2<-split(dim2Newpropsamp.NMDSpk3, Clusters) dim3NPS.split2<-split(dim3Newpropsamp.NMDSpk3, Clusters)

#NMDS Axes 1 and 2; samples coded by lithology

111 plot(dim1Newpropsamp.NMDSpk3,dim2Newpropsamp.NMDSpk3, type="n", xlab="NMDS 1", ylab="NMDS 2") points(dim1NPS.split1$CP,dim2NPS.split1$CP, pch=16, col="red") points(dim1NPS.split1$SCP,dim2NPS.split1$SCP, pch=16, col="maroon") points(dim1NPS.split1$PSS, dim2NPS.split1$PSS, pch=16, col="violetred") points(dim1NPS.split1$VFHBSS, dim2NPS.split1$VFHBSS, pch=16, col="dodgerblue") points(dim1NPS.split1$VFtSS, dim2NPS.split1$VFtSS, pch=16, col="blue") points(dim1NPS.split1$VFtSSC, dim2NPS.split1$VFtSSC, pch=16, col="purple2") legend("topleft", c("Carbonate Packstone", "Sandy Carboante Packstone", "Channelized Peloidal Sandstone", "Bioturbated Sandstone", "Thin Bedded Sandstone", "Sandy Carbonate"), title="Lithology", col=c("pink1","red","maroon","violetred","dodgerblue","blue","purple2"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.8, title.adj=0, bty="n")

#NMDS Axes 1 and 2; samples coded by biofacies plot(dim1Newpropsamp.NMDSpk3, dim2Newpropsamp.NMDSpk3, type="n", xlab="NMDS 1", ylab= "NMDS 2") points(dim1NPS.split2$`1`, dim2NPS.split2$`1`, pch=16, col="red") points(dim1NPS.split2$`2`, dim2NPS.split2$`2`, pch=16, col= "blue") points(dim1NPS.split2$`3`, dim2NPS.split2$`3`, pch=16, col="dodgerblue") points(dim1NPS.split2$`4`, dim2NPS.split2$`4`, pch=16, col= "pink1") points(dim1NPS.split2$`5`, dim2NPS.split2$`5`, pch=16, col="green") points(dim1NPS.split2$`6`, dim2NPS.split2$`6`, pch=16, col="forestgreen") points(dim1NPS.split2$`7`, dim2NPS.split2$`7`, pch=16, col="black") legend(x=-0.5, y=-0.3,

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legend=c("Molluscan","Brachiopod-Sponge-Echinoid","Parafusulina-Brachiopod-Sponge- Echinoid","Parafusulina-Bivalve","Parafusulina Dominate-Echinoid","Parafusulina Dominate","Parafusulina Only"), title="Biofacies", col=c("red","blue","dodgerblue","pink1","green","forestgreen","black"), pch=c(16,16,16,16,16,16,16,16,16,16,16), cex=0.8, bty="n")

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