ACTIVITY NAME: Counting Critters: Using the Paleobiology Database to track fossil diversity through geologic time

AUTHOR AND INSTITUTION: Rowan Lockwood, Department of Geology, The College of William and Mary

EMAIL: rxlock@wm.edu

SUMMARY(overview of what students will do and the intended outcomes, no more than 1-2 very brief paragraphs.)Students learn how to use the Paleobiology Database (PBDB) to develop a diversity curve showing changes in global biodiversity through time. They then use this curve to explore major events in the history of life, including the Cambrian Explosion and end-Permian extinction. As an optional supplement, students can explore the effects of sampling and preservation on diversity curves.

GOALS(What concepts and content should students learn from this activity? Are there higher-order thinking skills (e.g. critical thinking, data analysis, synthesis of ideas, model development) that are developed by this activity? Are there other skills (writing, oral presentation, field techniques, equipment operation, etc.) that are developed by the activity.)Students will be able to:▪ Construct a diversity curve using data and tools from PBDB Navigator (Part 1)▪ Interpret graphical representations of diversity curves to identify possible increases and decreases in diversity (Part 1)▪ Identify a major origination (Cambrian Explosion) graphically and use internet sources to research its possible causes (Part 1)▪ Identify a major extinction (end-Permian Extinction) graphically and use internet sources to research a possible cause.▪ Assess the effects of sampling and preservation on quantifying diversity (Part 2)▪ Assess the extent to which diversity patterns are affected by the inclusion of singleton taxa (Part 2)▪ Determine the extent to which Pull of the Recent is influencing diversity patterns (Part 2)

CONTEXT FOR USEEducational level: To be used in an introductory or intermediate undergraduate course, including (but not limited to) physical geology, historical geology, paleontology, etc.

Class size: Students can work as individuals or in pairs and class size can range from a small seminar (< 10 students) to a large lecture (> 100), as long as sufficient computer facilities are available.

Institution type: Can be used with non-majors or majors from two or four year institutions. Each student or student pair will need access to a laptop or desktop computer connected to the internet, running both Microsoft Word and an internet browser.

Is it lab, lecture, or field exercise: This activity can be used as a lecture, lab, or homework activity.

How much time is needed: Part 1: Constructing a Diversity Curve (stand alone)(60 mins)Part 2: Sampling and Preservational Bias (must be completed after Part 1)(30 mins)

Skills or concepts that students should have already mastered before encountering this activityStudent is able to:- Define Linnaean taxonomy terms: family, genus (Part 1)- Define the terms “linear” and “exponential” (Part 1)- Understand that organisms (plants and animals) didn’t invade land (terrestrial ecosystems) until after the Cambrian (Part 1)- Think about two time intervals that have been particularly well sampled (e.g., intervals with population organisms like dinosaurs, intervals with major extinctions)(Part 2) - Think about two groups of organisms that are likely to have a well-preserved fossil record (e.g., organisms with bones or shells)(Part 2)- Define the term “taphonomy” (Part 2)- Use Microsoft Word to fill out answers in document (all parts)- Interpret basic graph features (all parts)

How is this activity situated in the course? Presented during unit focusing on fossil diversity and major events in the history of life (e.g., Cambrian Explosion, Permo-Triassic mass extinction).

How easy (or hard) would it be to adapt the activity for use in other settings?Very easy. It is divided into two parts and can be modified by picking and choosing which parts (and which questions within parts) to include.

Grade level:College (13-14)College (15-16)

ACTIVITY DESCRIPTION AND TEACHING MATERIALS

Narrative describing the mechanics of the activity and all the materials needed to implement the activity (or links and references to those materials).In this activity, students learn how to use the Paleobiology Database to develop a diversity curve showing changes in global biodiversity through time. They then use this curve to explore major events in the history of life, including the Cambrian Explosion and end-Permian mass extinction.

This activity is designed to be flexible and can be used as a lecture, lab, or homework activity. It is divided into two parts and can be modified by picking and choosing which parts (and which

questions within parts) to include. The duration of the activity ranges from 10 minutes to three hours, depending on which parts are assigned.

Students can work as individuals or in pairs and class size can range from a small seminar (< 10 students) to a large lecture (> 100), as long as sufficient computer facilities are available.

Each student or student pair will need access to a laptop or desktop computer connected to the internet, running both Microsoft Word and an internet browser. TEACHING NOTES AND TIPSThis section should include notes and tips for instructors who might use the activity (e.g., common areas of confusion, things that need reinforcement, safety guidelines, other practical tips)

ASSESSMENTThis section should describe how the author determines whether or not students (either individually or collectively) are achieving the learning goals outlined for the activity. Formative assessmentCan be accomplished in lecture or lab by observing student progress and trouble-shooting challenges. Can also doublecheck that the major tasks (i.e., constructing correct diversity curve, circling increases in diversity, starring decreases in diversity, researching the Cambrian Explosion, research the end-Permian extinction) are accomplished in a timely manner and are accurate.Summative assessmentKey summative assessment points include: the graph of diversity, identifying increases and decreases on this graph, describing two possible drivers of the Cambrian Explosion, and describing one possible cause of the end-Permian extinction. Instructors can use the answer key provided to assess students’ understanding of the main concepts. Summative assessment can also be included as midterm and final exam questions focusing on the key summative assessment points listed above.

RESOURCESThis section should include references and links to online resources that discuss the specific activity or will support faculty and/or students using the activity. How to interpret graphshttp://www.bbc.co.uk/bitesize/standard/maths_i/relationships/interpreting_graphs/revision/1/http://www.bbc.co.uk/skillswise/factsheet/ma37grap-l1-f-extracting-and-interpreting-data-from-line-graphshttp://serc.carleton.edu/mathyouneed/graphing/index.htmlhttps://www.khanacademy.org/math/ab-sixth-grade-math/al-statistics-probability/al-data/v/u08-l1-t2-we2-reading-line-graphs

What is a diversity curve?http://www.els.net/WileyCDA/ElsArticle/refId-a0001636.htmlhttp://simpson-carl.github.io/papers/2010%20Simpson.pdfhttp://serc.carleton.edu/NAGTWorkshops/paleo/activities/33101.html

http://www.indiana.edu/~g563/Handouts/Foote%20and%20Miller,%20Calculating%20Diversity%20Curves.pdf

Major events in the history of lifehttp://www.bbc.co.uk/nature/history_of_the_earthhttps://en.wikipedia.org/wiki/Timeline_of_the_evolutionary_history_of_lifehttp://evolution.berkeley.edu/evolibrary/article/evo_13

Cambrian Explosionhttps://en.wikipedia.org/wiki/Cambrian_explosionhttp://www.evolution.berkeley.edu/evosite/evo101/VIIB1cCambrian.shtmlhttp://www.pbs.org/wgbh/evolution/library/03/4/l_034_02.htmlhttp://www.bbc.co.uk/science/earth/earth_timeline/cambrian_explosion

End-Permian extinction eventhttps://en.wikipedia.org/wiki/Permian%E2%80%93Triassic_extinction_event#Microbeshttp://www.pbs.org/wgbh/evolution/library/03/2/l_032_02.html

How to develop hypotheseshttps://explorable.com/how-to-write-a-hypothesishttp://www.sciencebuddies.org/science-fair-projects/project_hypothesis.shtml#keyinfohttp://www.sciencebuddies.org/blog/2010/02/a-strong-hypothesis.php

SHORT DESCRIPTION (1-2 SENTENCES)Students learn how to use the Paleobiology Database to develop a diversity curve showing changes in global biodiversity through time. They then use this curve to explore major events in the history of life, including the Cambrian Explosion and end-Permian extinction.

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Counting Critters: Using the PBDB to track fossil diversity and extinction through geologic time

IntroductionOne of the most fundamental questions we can ask in geology is how the diversity of life has changed over time. Data on the diversity of organisms in the fossil record make it possible to identify intervals of mass extinction and origination, determine how climate change has affected diversity in the past, and gain perspective on the loss of biodiversity in modern ecosystems.

To do this, paleontologists track the occurrence of fossil organisms, in other words where a species occurs in space (geographically) and when a species occurs in time (stratigraphically). The Paleobiology Database (PBDB, https://paleobiodb.org/navigator/) is a huge online database that seeks to catalogue all fossil occurrences, across all geologic time, and across the whole tree of life. It’s the standard tool used by paleobiologists to create diversity curves—which are visual plots of the diversity of life over time.

Delving into the DatabaseOpen the PBDB Navigator and spend some time getting comfortable with how it works:https://paleobiodb.org/navigator/

The Navigator consists of three parts:1. Map (CENTER) showing continents with dots representing fossil occurrences. The color of

these dots represents their geologic age. If you click on the dots, you can see all of the information on each site and the fossil species that occur there.

2. Geologic time scale (BOTTOM) showing the major eras, periods, and stages. If you click on the timescale, the map will show you the location of all fossil occurrences from that time interval.

3. Tool bar (LEFT) showing the tools you can use to explore the database. These include:

zoom in/out on the map

reconstruct plate tectonic configurations for time interval (era or smaller) you are exploring

narrow down which taxonomic group is plotted on map

create a diversity curve for the occurrences currently plotted on map

download the data (lat/long, geologic age, etc.) for the occurrences plotted on map

Need help? Here’s a Youtube video to help you get started: https://www.youtube.com/watch?v=db2He3p-Jco

NOTE TO STUDENTS: Several of the questions asked in this activity are open-ended and do not have explicitly right or wrong answers. These questions give you the freedom to explore

this material and think about it creatively. ---------------------------------------------------------------------------------------------------------------------Part 1: Constructing a Diversity Curve1. Given what you know about the early history of life on Earth, predict how the number of

organisms would change over the past 500 million years.

(a) Would it increase, decrease, or stay the same?

(b) If you predicted it would change, would it change linearly (i.e., increasing or decreasing in a straight line) or exponentially (i.e., increasing or decreasing rapidly towards today) or in another pattern?

(c) Sketch the pattern you expect to see on the graph to the RIGHT.

Now, use the PBDB Navigator to develop a diversity curve—for all organisms, globally, throughout the past 500 million years. To do this,

- Make sure that the PBDB map is as zoomed out as far as possible- Click on the icon on the toolbar on the left side of the screen- For taxonomic level, choose “genus” - For temporal resolution, choose “Age” - Then click on “Use advanced diversity curve generator” button- WAIT. Please be patient, it can take 5-10 minutes to calculate all of life’s diversity

through time!- When a graph appears on the screen, check the box “Rangethrough diversity”- UNCHECK the boxes “Sampled-in-bin diversity” and “Include singletons”

2. (a) Does the general pattern (i.e., increasing, decreasing, staying the same, linear, exponential) match your predicted diversity curve from Question 1?

(b) If no, how is it different (in detail)?

3. Insert your diversity curve (using the “Save this image” button, then the Insert Pictures tool in Word) and make it as large as possible below. This curve displays “Rangethrough diversity”-- which assumes that each genus as present in the fossil record from its oldest occurrence to its youngest occurrence, regardless of whether or not it was actually found in the intervening intervals. Singletons are fossil genera that have only been found in one time interval. Your diversity curve does not include singletons.

4. (a) Do you see any evidence for rapid increases in diversity on your graph? If so, circle these on your graph above.

(b) How many did you circle?

5. (a) Do you see any evidence for rapid decreases in diversity on your graph? If so, mark these with a star on your graph above.

(b) How many did you mark with a star?

6. Examine the earliest increase in diversity that occurs on this diversity curve.

(a) In which geologic (i.e., time) period does it occur?

(b) Given this time interval, do you think this increase in diversity occurred in the ocean or on land or both?

(c) Why?

This sudden increase in diversity is called the “Cambrian Explosion.” Use internet sources to learn more about this particular event.

(d) Do you think this increase in diversity is due to an increase in origination rates or a decrease in extinction rates or both?

(e) Describe (in detail) two possible causes for this event.

7. Compare the decreases in diversity that occur throughout the Phanerozoic. Examine diversity from 400 to 0 million years ago. Find the interval of time in which diversity is at its lowest from 400 to 0 million years ago.

(a) Between which two geological time intervals does it occur? Need help figuring out geological periods? See the following link: https://www.geosociety.org/science/timescale/

This event is called the end-Permian mass extinction. Use internet sources to learn more about this particular event.

(b) When (approximately) did this extinction occur in millions of years?

(c) What percentage of species went extinct?

(d) Describe (in detail) one possible causal mechanism for this extinction.

---------------------------------------------------------------------------------------------------------------------Part 2: Sampling and Preservational BiasFiguring out how biodiversity has changed over time is complicated by a number of sampling and preservational issues.

1. Sampling issues occur when paleontologists study one time interval (or site or organism) more thoroughly than another. Poor sampling can artificially decrease estimates of diversity for a particular time interval (or site or organism).

(a) Given what you already know about the fossil record, can you identify two intervals of time that have been particularly well sampled?

(b) Why are these two well sampled?

2. Preservational issues occur because the likelihood that an organism gets preserved in the fossil record may vary occur to time interval, site, or organism. Preservation can artificially decrease estimates of diversity for a particular time interval (or site or organism).

(a) Given what you know about fossil preservation, identify at least two groups of organisms that are likely to have a well-preserved fossil record.

(b) Why did you choose these?

3. Several paleontologists have suggested that the number of singletons in a time interval should increase when sampling and preservational quality decrease. Experiment with the effects of singletons on your diversity curve by checking and unchecking the box labeled “Include singletons.”

(a) Does including singletons change the overall shape of your diversity curve? If so, how?

(b) Does including singletons change the increase in diversity at the Cambrian Explosion? If so, how?

(c) Does including singletons change the decrease in diversity at the end-Permian extinction? If so, how?

4. The term “Pull of the Recent” refers to the hypothesis that biodiversity estimates are artificially inflated during more recent time intervals because: (A) older fossils are more likely to have been destroyed by taphonomic processes and (B) younger strata and organisms are easier to sample. Re-examine the diversity curve you produced in Part 1.

(a) Do you think “Pull of the Recent” has affected this curve?

(b) Why or why not?

5. How could you control for “Pull of the Recent” when you develop diversity curves? Describe at least one solution that would allow you to solve this problem—either mathematically or otherwise.

6. Reflection:(a) Have you used the PBDB before this activity? (Check one) __ No __ Yes

If yes…:

How many times have you used it before? _______When did you use it? (Circle one)

a) previous lab/class activity

b) other: ________________________________________

(b) Now that you've used the database for this activity, how could you use this database to create your own research project?

(c) Would you want to use this database to create/conduct your own research project? Why or why not?

ANSWER KEY---------------------------------------------------------------------------------------------------------------------Part 1: Constructing a Diversity Curve1. Given what you know about the early history of life on Earth, predict how the number of

organisms would change over the past 500 million years.

(a) Would it increase, decrease, or stay the same?

Answers will vary according to student

(b) If you predicted it would change, would it change linearly (i.e., increasing or decreasing in a straight line) or exponentially (i.e., increasing or decreasing rapidly towards today) or in another pattern?

Answers will vary according to student

(c) Sketch the pattern you expect to see on the graph to the RIGHT.

Now, use the PBDB Navigator to develop a diversity curve—for all organisms, globally, throughout the past 500 million years. To do this,

- Make sure that the PBDB map is as zoomed out as far as possible- Click on the icon on the toolbar on the left side of the screen- For taxonomic level, choose “genus” - For temporal resolution, choose “Age” - Then click on “Use advanced diversity curve generator” button- WAIT. Please be patient, it can take 5-10 minutes to calculate all of life’s diversity

through time!- When a graph appears on the screen, check the box “Rangethrough diversity”- UNCHECK the boxes “Sampled-in-bin diversity” and “Include singletons”

2. (a) Does the general pattern (i.e., increasing, decreasing, staying the same, linear, exponential) match your predicted diversity curve from Question 1?

Answers should refer back to Question 1

(b) If no, how is it different (in detail)?

Answers should refer back to Question 1

3. Insert your diversity curve (using the “Save this image” button, then the Insert Pictures tool in Word) and make it as large as possible below. This curve displays “Rangethrough diversity”-- which assumes that each genus as present in the fossil record from its oldest occurrence to its youngest occurrence, regardless of whether or not it was actually found in the intervening intervals. Singletons are fossil genera that have only been found in one time interval. Your diversity curve does not include singletons.

We recommend that while students are completing the activity, instructors doublecheck that their diversity curve matches that one above. If student answers differ from above, check:

- That student zoomed out on the map as far as possible- That they chose “genus” for taxonomic level- That they chose “Age” for temporal resolution- That they checked the box “Rangethrough diversity”- That they unchecked the boxes “Sampled-in-bin diversity” and “Include singletons”

4. (a) Do you see any evidence for rapid increases in diversity on your graph? If so, circle these on your graph above.

Students should include at least three of the steepest increases (circled in red above).

(b) How many did you circle?

Could range from 3-16

5. (a) Do you see any evidence for rapid decreases in diversity on your graph? If so, mark these with a star on your graph above.

Students should include at least three of the steepest decreases (marked with stars above).

(b) How many did you mark with a star?

Could range from 3-17

6. Examine the earliest increase in diversity that occurs on this diversity curve.

(a) In which geologic (i.e., time) period does it occur? Need help figuring out geological periods? See the following link: https://www.geosociety.org/science/timescale/

Cambrian (Cm)

(b) Given this time interval, do you think this increase in diversity occurred in the ocean or on land or both?

In the ocean

(c) Why?

Because organisms (plants and animals) didn’t invade the land until AFTER the Cambrian.

This sudden increase in diversity is called the “Cambrian Explosion.” Use internet sources to learn more about this particular event.

(d) Do you think this increase in diversity is due to an increase in origination rates or a decrease in extinction rates or both?

Answers will vary according to student.

(e) Describe (in detail) two possible causes for this event.

Depending on internet sources, answer could include: Increase in oxygen levels● Ozone formation● Snowball Earth● Increase in the calcium concentration of the Cambrian seawater● Developmental explanations● End-Ediacaran mass extinction● Evolution of eyes● Arms races between predators and prey● Increase in size and diversity of planktonic animals● Ecosystem engineering● Complexity threshold (e.g., genetic threshold)

7. Compare the decreases in diversity that occur throughout the Phanerozoic. Examine diversity from 400 to 0 million years ago. Find the interval of time in which diversity is at its lowest from 400 to 0 million years ago.

(a) Between which two geological time intervals does it occur? Need help figuring out geological periods? See the following link: https://www.geosociety.org/science/timescale/

Permian and Triassic (or P and Tr)

This event is called the end-Permian mass extinction. Use internet sources to learn more about this particular event.

(b) When (approximately) did this extinction occur in millions of years?

Between 252 and 248 million years ago, depending on internet source used

(c) What percentage of species went extinct?

Between 96 and 72% of species, depending on internet source used

(d) Describe (in detail) one possible causal mechanism for this extinction.

Depending on internet source used, could include:● Impact event● Volcanism● Methane hydrate● Anoxia● Hydrogen sulfide emissions● The supercontinent Pangaea● Microbial methane production● Combination of causes

---------------------------------------------------------------------------------------------------------------------Part 2: Sampling and Preservational BiasFiguring out how biodiversity has changed over time is complicated by a number of sampling and preservational issues.

1. Sampling issues occur when paleontologists study one time interval (or site or organism) more thoroughly than another. Poor sampling can artificially decrease estimates of diversity for a particular time interval (or site or organism).

(a) Given what you already know about the fossil record, can you identify two intervals of time that have been particularly well sampled?

Answers will vary by student.

(b) Why are these two well sampled?

Answers will vary by student. Could include intervals represented by popular organisms (e.g., dinosaurs, trilobites) or intervals represented by big extinctions (like the end-Permian or end-Cretaceous) or intervals that are easy to access (e.g., exposed at the surface).

2. Preservational issues occur because the likelihood that an organism gets preserved in the fossil record may vary occur to time interval, site, or organism. Preservation can artificially decrease estimates of diversity for a particular time interval (or site or organism).

(a) Given what you know about fossil preservation, identify at least two groups of organisms that are likely to have a well-preserved fossil record.

Answers will vary by student.

(b) Why did you choose these?

Answers will vary by student. Could include organisms with hard parts (skeleton, shell), organisms that are abundant, organisms with broad geographic ranges, organisms with long stratigraphic ranges, organisms that live in environments that are favorable for preservation (e.g., marine, lake, etc.), organisms with behaviors that are favorable for preservation (e.g., burrowing).

3. Several paleontologists have suggested that the number of singletons in a time interval should increase when sampling and preservational quality decrease. Experiment with the effects of singletons on your diversity curve by checking and unchecking the box labeled “Include singletons.”

(a) Does including singletons change the overall shape of your diversity curve? If so, how?

Including singletons changes the diversity curve slightly (see below). It makes some peaks higher, and some troughs lower.

(b) Does including singletons change the increase in diversity at the Cambrian Explosion? If so, how?

Including singletons increases the peak in diversity at the Cambrian Explosion

(c) Does including singletons change the decrease in diversity at the end-Permian extinction? If so, how?

Including singletons doesn’t change the trough in diversity at the end-Permian extinction (although students could argue that the overall decrease in diversity is higher because diversity itself is higher before the end-Permian when singletons are included)

4. The term “Pull of the Recent” refers to the hypothesis that biodiversity estimates are artificially inflated during more recent time intervals because: (A) older fossils are more likely to have been destroyed by taphonomic processes and (B) younger strata and organisms are easier to sample. Re-examine the diversity curve you produced in Part 1.

(a) Do you think “Pull of the Recent” has affected this curve?

Answers will vary according to student

(b) Why or why not?

Answers will vary according to student, but should be logical explanations that demonstrate that the student understands the concept of Pull of the Recent.

5. How could you control for “Pull of the Recent” when you develop diversity curves? Describe at least one solution that would allow you to solve this problem—either mathematically or otherwise.

Answers will vary according to student. Could include:- Not including modern organisms in compiling diversity estimates- Not using a range-through approach - Mathematically model the likelihood of preservation and sampling and apply that to

diversity estimates