An introduction to biodiversity bioinformatics using

Biodiversity Bioinformatics

An introduction to biodiversity bioinformatics using 1

Table of contents

Quantify coral reef biodiversity patterns using 2 Quantify coral reef ecological changes using 3

Lesson and materials developed by Ross Nehm, CUNY, and Ann Budd, University of Iowa, 2004.

©2004

National Science Education Standards (National Research Council, 1996) Life Science

CONTENT STANDARD C Life Science

BIOLOGICAL EVOLUTION BIOLOGICAL EVOLUTION

Species evolve over time. Evolution is the consequence of the interactions of (1) the potential for a species to increase its numbers, (2) the genetic variability of offspring due to mutation and recombination of genes, (3) a finite supply of the resources required for life, and (4) the ensuing selection by the environment of those offspring better able to survive and leave offspring.

Students gather data that demonstrate patterns of evolutionary change through time.

Natural selection and its evolutionary consequences provide a scientific explanation for the fossil record of ancient life forms, as well as for the striking molecular similarities observed among the diverse species of living organisms.

Students use the fossil record of ancient and living species and note their similarities and differences to develop biological hypotheses.

The millions of different species of plants, animals, and microorganisms that live on earth today are related by descent from common ancestors.

Students trace living species back through geological time.

Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.

Students use taxonomic information that represents the evolutionary relationships of the corals in their samples.

THE INTERDEPENDENCE OF ORGANISMS THE INTERDEPENDENCE OF ORGANISMS

Organisms both cooperate and compete in ecosystems. The interrelationships and interdependencies of these organisms may generate ecosystems that are stable for hundreds or thousands of years.

Students quantify changes in coral reef ecosystems over millions of years.

Human beings live within the world's ecosystems. Increasingly, humans modify ecosystems as a result of population growth, technology, and consumption. Human destruction of habitats through direct harvesting, pollution, atmospheric changes, and other factors is threatening current global stability, and if not addressed, ecosystems will be irreversibly affected.

Students compare species richness patterns in modern coral reef ecosystems to species richness patterns in ancient ecosystems in order to establish a baseline for assessing human impact.

Earth and Space Science Earth and Space ScienceCONTENT STANDARD D

THE ORIGIN AND EVOLUTION OF THE EARTH SYSTEMTHE ORIGIN AND EVOLUTION OF THE EARTH SYSTEM

Geologic time can be estimated by observing rock sequences and using fossils to correlate the sequences at various locations. Current methods include using the known decay rates of radioactive isotopes present in rocks to measure the time since the rock was formed.

Students observe and use fossils from sedimentary rock layers of differing ages to establish evolutionary patterns.

Interactions among the solid earth, the oceans, the atmosphere, and organisms have resulted in the ongoing evolution of the earth system. We can observe some changes such as earthquakes and volcanic eruptions on a human time scale, but many processes such as mountain building and plate movements take place over hundreds of millions of years.

Students document patterns that take millions of years to occur.

Science and Technology Science and TechnologyCONTENT STANDARD E

UNDERSTANDINGS ABOUT SCIENCE AND TECHNOLOGYUNDERSTANDINGS ABOUT SCIENCE AND TECHNOLOGY

Science often advances with the introduction of new technologies. Solving technological problems often results in new scientific knowledge. New technologies often extend the current levels of scientific understanding and introduce new areas of research.

Students use new technologies to answer questions that could not be addressed previously without computer technology.

Technological knowledge is often not made public because of patents and the financial potential of the idea or invention. Scientific knowledge is made public through presentations at professional meetings and publications in scientific journals.

Students become aware that the scientific data in NMITA is for public access.

Science in Personal and Social Perspectives Science in Personal and Social PerspectivesCONTENT STANDARD F

SCIENCE AND TECHNOLOGY IN LOCAL, NATIONAL, AND GLOBAL CHALLENGES SCIENCE AND TECHNOLOGY IN LOCAL, NATIONAL, AND GLOBAL CHALLENGES

Understanding basic concepts and principles of science and technology should precede active debate about the economics, policies, politics, and ethics of various science- and technology-related challenges. However, understanding science alone will not resolve local, national, or global challenges.

Students become aware that answering questions about human-induced changes in biodiversity require scientific knowledge of natural variation in ecosystems.

NYS Learning Standards employed in this lesson

New York State standards (Standard 1, Scientific Inquiry)Key Idea: The central purpose of scientific inquiry is to develop explanations of natural phenomena in a continuing, creative process.Performance indicator : Learn to ask "why" questions to seek greater understanding concerning objects and events they have observed and heard about

New York State standards (Standard 2, Information systems)Key Idea: Information technology is used to retrieve, process, and communicate information and as a tool to enhance learning.Performance indicator: Use a variety of equipment and software packages to enter, process, display and communicate information in different forms using text, pictures, and sound.

Performance indicator : Access needed information from media, electronic data bases and community resources.New York State standards (Standard 4, Living Environment)

Key Idea 1: Living things are both similar to and different from each other and nonliving things.Performance indicator : Explain how diversity of populations within ecosystems relates to the stability of ecosystems.Key idea 3: Individual organisms and species change over time.Performance indicator: Explain the mechanisms and patterns of evolution.Key Idea 6: Plants and animals depend on each other and their physical environment.Performance indicator : Explain the importance of preserving diversity of species and habitats.Performance indicator : Explain how the living and nonliving environments change over time and respond to disturbances.

Key idea 7: Human decisions and activities have had a profound impact on the physical and living environment.Performance indicator : Describe the effects of environmental changes on humans and other populations.Performance indicator : Explain the impact of technological development and growth in the human population on the living and nonliving environment

New York State standards (Standard 5, Computer technology)Key Idea: Key Idea: Computers, as tools for design, modeling, information processing, communication, and system control, have greatly increased human productivity and knowledge.

Lesson 2: Gather data to test hypotheses about biodiversity change through time

This lesson is designed to help you learn how to use a biodiversity bioinformatics

database known as NMITA to test hypotheses about coral reef biodiversity change through time. Lesson 1 reviewed the overall structure and data contained in NMITA. Lesson 2 takes you on a virtual journey to the Dominican Republic, a country located on the island of Hispañola in the Caribbean Sea. On the island you will explore the marine fossil corals and coral reefs that occur in different sedimentary rock layers that were formed when parts of the island were under the Caribbean Sea. You will also explore the diversity of living coral reefs from the southwestern part of the country. You will collect coral reef biodiversity data from six different time periods in order to determine if coral reef biodiversity has increased, decreased, or stayed the same over the past 20 million years in the Dominican Republic. You will collect 3 samples from each of the 6 time periods. An additional lesson (Lesson 3) is provided that builds upon what you learn here. It explores ecological patterns of biodiversity change in the same coral reef samples that you study here.

Key Terms: Key Concepts: Hypothesis Holocene Evolution Biodiversity Database Extinction Coral reef Sedimentary rock Speciation Species Pliocene Sampling Miocene Pleistocene Dating rock Directions:

1. Go to NMITA http://porites.geology.uiowa.edu/index.htm 2. Click Maps & Faunal Lists 3. Click Dominican Republic

1. 2. 3.

Quantify coral reef biodiversity patterns using 2

4. Note the map of the Dominican Republic. You will be collecting coral reef

biodiversity data from four major regions: (a) Jaragua National Park (Recent); (b) Lago Enriquillo (Holocene); (c) Santo Domingo (Pleistocene coastal terraces); (d) Rio Cana (Middle Pliocene, Early Pliocene, and Late Miocene). Be sure that you can find all four localities on the map.

5. Take out the lesson 2 data worksheets. You will notice that we are studying 3 samples from each time period (e.g., Holocene). Data for some samples are already filled in for you and the total number of species for that sample has been tabulated.

6. To finish this activity you will need to sum the total number of species for 18 data

points.

7. In order to gather data, click on the name of each region (e.g., Jaragua National Park) and then click on the sample number or locality listed on the data worksheets (e.g., region Jaragua National Park locality “Cabo Falso.”) Detailed visual instructions are shown on the next page.

8. Copy the list of species that occur at the locality to your worksheet.

9. Count the total number of species and write it at the bottom of the data cell.

10. Repeat step 9 until you have filled in all of the coral species that occur in all of

the samples.

11. When you are finished, you should know the number of coral species that occur in 3 samples from 6 different time periods (Recent, Holocene, Pleistocene, Middle Pliocene, Early Pliocene, and Upper Miocene). You will therefore have 18 total data points.

12. Take out your Lesson 2 analysis worksheet. On this worksheet you will plot the

data points on coral reef biodiversity in the Dominican Republic from the Miocene to today.

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Go to: http://porites.geology.uiowa.edu Click on: Maps & Faunal Lists Click on: Dominican Republic A map of the Dominican Republic will appear.

Note the rivers west of the city of Santiago. These rivers have exposed sedimentary rock rich in coral and mollusk fossils. Click on the river Rio Cana

A detailed map of the Rio Cana will appear along with small tributaries. Note the three main regions of the river. Click on Cana Gorge.

A detailed map of the Cana Gorge locality will appear along with sample localities. We will be studying three localities from Cana Gorge Click on locality AB03-3

A data screen will appear with information on the sample and the coral reef species that occur in the sample. Next to each genus and species is the shape of the coral species. You may click on each species to learn more about it.

For one of the lessons you will be comparing the number of coral reef species through time. Take out your Data Worksheet and transfer the data for Rio Cana sample “Cana Gorge AB03-3” to the worksheet.

Take out the Analysis Worksheet. You will plot the number of species that you found at Cana Gorge AB03-3 on the graph. You will repeat this process in order to determine how coral reef biodiversity has changed from the Late Miocene to Recent.

How to use NMITA to gather biodiversity data

Los Carraplanes (2) Cabo Falso (5) Bahia Honda en Cabo Rojo (8)

Jaragua National Park Jaragua National Park Jaragua National Park

1 Acropora palmata Acropora cervicornis2 Acropora cervicornis Undaria agaricites3 Undaria agaricites Undaria pusilla4 Undaria pusilla Agaricia lamarcki5 Helioseris cucullata Agaricia grahamae6 Agaricia lamarcki Agaricia fragilis7 Agaricia grahamae Helioseris cucullata8 Agaricia fragilis Porites porites9 Helioseris cucullata Porites astreoides10 Porites porites Madracis decactis11 Porites astreoides Madracis mirabilis12 Madracis decactis Madracis pharensis13 Madracis pharensis Diploria strigosa14 Madracis formosa Diplora labyrinthyformis15 Diploria strigosa Colpophyllia natans16 Diploria clivosa Colpophyllia breviserialis17 Diplora labyrinthyformis Colpophyllia amaranthus18 Colpophyllia natans Meandrina meandrites19 Colpophyllia breviserialis Montastraea "annularis"20 Colpophyllia amaranthus Montastraea faveolata21 Meandrina meandrites Montastraea franksi22 Montastraea "annularis" Montastraea cavernosa23 Montastraea faveolata Solenastrea bournoni24 Montastraea franksi Siderastrea siderea25 Montastraea cavernosa Dichocoenia stokesi26 Siderastrea siderea Dichocoenia stellaris27 Siderastrea radians Eusmilia fastigiata28 Dichocoenia stokesi Manicina aerolata29 Dichocoenia stellaris Manicina mayori30 Eusmilia fastigiata Mycetophyllia aliciae31 Mycetophyllia aliciae Mycetophyllia lamarckiana32 Mycetophyllia lamarckiana Mycetophyllia danaana33 Mycetophyllia danaana Mycetophyllia ferox34 Mycetophyllia ferox Mycetophyllia reesi35 Scolymia cubensis Scolymia cubensis36 Scolymia lacera Scolymia lacera37 Scolymia wellsi Scolymia wellsi38 Isophyllastrea rigida Isophyllastrea rigida39 Mussa angulosa Isophyllia sinuosa40 Stephanocoenia intersepta Mussa angulosa41 Stephanocoenia interseptaTOTAL SPECIES: TOTAL SPECIES: 40 TOTAL SPECIES: 41

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Lesson 2Data WorksheetName:

Sample 1 Sample 3 Sample 4

Lago Enriquillo Lago Enriquillo Lago Enriquillo

1. Acropora cervicornis 1 12. Undaria agaricites 2 23. Colpophyllia natans 3 34. Eusmilia fastigata 4 45. Favia fragum 5 56. Helioseris cucullata 6 67. Manicina areolata 7 78. Oculina diffusa 8 89. Porites astreoides 9 910. Porites divaricata 10 1011. Porites furcata 11 1112. Porites porites 12 1213. Scolymia lacera 13 1314. Siderastrea siderea 14 1415. Stephancoenia intersepta 15 1516 16 1617 17 1718 18 1819 19 1920 20 20TOTAL SPECIES: 15 TOTAL SPECIES: TOTAL SPECIES:

Santo Domingo (JK 5) Santo Domingo (JK 6) Santo Domingo (JK 8)

Pleistocene Coastal Terraces

Pleistocene Coastal Terraces

Pleistocene Coastal Terraces

1. Acropora cervicornis 1 Acropora cervicornis2. Acropora palmata 2 Acropora palmata3. Colpophyllia natans 3 Colpophyllia natans4. Dendrogyra cylindricus 4 Diploria labrynthiformis5. Diploria labrynthiformis 5 Diploria strigosa6. Diploria strigosa 6 Isophyllia sinuosa7. Montastraea "annularis" 7 Montastraea "annularis"8. Montastraea faveolata 8 Montastraea faveolata9. Montastraea franksi 9 Montastraea "organ pipe"10. Montastraea "organ pipe" 10 Montastraea cavernosa11. Montastraea cavernosa 11 Siderastrea siderea12. Siderastrea siderea 12 Stephanocoenia intersepta13. Stephanocoenia intersepta 13 Undaria agaricites14 14 15 15 16 16 17 17 18 18 19 19 20 20 TOTAL SPECIES: 13 TOTAL SPECIES: TOTAL SPECIES: 13

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Cana Gorge (AB03-3) Cana Gorge (AB03-4) Cana Gorge (JK-03-6)

Rio Cana Rio Cana Rio Cana1. Caulastrea portoricensis 1 1

2. Diploria zambensis 2 23. Favia maoadentrensis 3 34. Montastraea-II canalis 4 45. Montastraea-II cavernosa 5 56. Placocyathus variabilis 6 67. Porites-I macdonaldi 7 78. Porites-I portoricensis 8 89. Porites-I waylandi 9 910. Porites-II baracoaensis 10 1011. Stephanocoenia duncani 11 1112. Stylophora granulata 12 1213. Stylophora minor 13 1314. Undaria agaricites 14 1415 15 1516 16 1617 17 1718 18 1819 19 1920 20 20TOTAL SPECIES: 14 TOTAL SPECIES: TOTAL SPECIES:

Canada de Zamba (AB03-2) Canada de Zamba (JK03-10) Canada de Zamba (JK03-5)

Rio Cana Rio Cana Rio Cana

1. Agaricia lamarcki Caulastrea portoricensis 1

2. Favia dominicensis Favia maoadentrensis 23. Goniopora hilli Leptoseris gardineri 34. Isophyllia sp.A Montastraea-I limbata 45. Madracis cf.herricki Porites-I macdonaldi 56. Madracis decactis Porites-I portoricensis 67. Madracis decaseptata Porites-I waylandi 78. Madracis mirabilis Porites-II baracoaensis 89. Madracis sp.A Siderastrea siderea 910. Manicina grandis Stephanocoenia duncani 1011. Montastraea-I limbata Stylophora affinis 1112. Montastraea-II cavernosa Stylophora granulata 1213. Placocyathus variabilis Stylophora minor 1314. Porites-I macdonaldi Undaria agaricites 1415. Porites-I waylandi 1516. Porites-I baracoaensis 1617. Stylophora granulata 1718. Stylophora minor 1819 1920 20TOTAL SPECIES: 18 TOTAL SPECIES: 14 TOTAL SPECIES:

Mid

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Arroyo Bellaco (BEL-1) Arroyo Bellaco (BEL-3) Arroyo Bellaco (BEL-6)

Rio Cana Rio Cana Rio Cana

1. Agaricia lamarcki 1 Favia dominicensis2. Dichocoenia sp.A 2 Goniopora imperatoris3. Gardinerseris planulata 3 Madracis mirabilis4. Goniopora hilli 4 Montastraea-I limbata5. Goniopora imperatoris 5 Montastraea-II endothecata6. Montastraea-I limbata 6 Pocillopora crassoramosa7. Pocillopora crassoramosa 7 Porites-I portoricensis8. Porites-I waylandi 8 Stylophora affinis9. Siderastrea siderea 9 Undaria agaricites10. Solenastrea bournoni 10 11. Stephanocoenia duncani 11 12. Stephanocoenia spongiformis 12 13. Stylophora affinis 13 14 14 15 15 16 16 17 17 18 18 19 19 20 20 TOTAL SPECIES: 13 TOTAL SPECIES: TOTAL SPECIES: 9

Late

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Recent

Holocene

Recent

Pleistocene

Early Pliocene

Late Miocene

Middle Pliocene

Holocene

Pleistocene

Middle Pliocene

Early Pliocene

Late Miocene

Species richness (# of species)

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Discussion questions

1. How many samples do we need to take in order to obtain an accurate estimate of coral reef biodiversity in one time period (e.g., Late Miocene)? How do we know if three samples are sufficient?

2. Is it important to know if all species of corals have been collected, named and accurately identified from the Dominican Republic? Could this influence our results?

3. Is it possible to determine the impact of human activity on Caribbean coral reef biodiversity without using the fossil record? Explain.

4. Which of the following scenarios would be more accurate for estimating coral reef biodiversity: (a) Take three samples from the same place within each time period; or (b) take three samples from different places within each time period. Defend your choice.

5. Would it be better to estimate biodiversity using species or genera? Does it make a difference? Explain.

Lesson 3: Gather data to test hypotheses about ecological changes in reef corals over millions of years

This lesson is designed to help you learn how to use a biodiversity bioinformatics

database known as NMITA to test hypotheses about Caribbean coral reef ecological changes over the past several million years. Lesson 1 reviewed the overall structure and data contained in NMITA. Lesson 2 had you collect coral reef biodiversity data from six different time periods in order to determine if coral reef biodiversity has changed over the past several million years in the Dominican Republic. Lesson 3 builds upon lessons 1 and 2 and explores ecological and morphological patterns of biodiversity change in the same coral reef samples that you studied previously. In this lesson you will use NMITA to gather data on the morphology, or shape, of the living and fossil coral species and plot these changes through time.

Key Terms: Key Concepts: Hypothesis Database Evolution Biodiversity Miocene Extinction Coral reef Pliocene Speciation Morphology Pleistocene Coral morphotype Ecology Holocene Coral nutrition Directions:

1. Go to NMITA http://nmita.geology.uiowa.edu/ 2. Click Maps & Faunal Lists 3. Click Dominican Republic

1. 2. 3.

Quantify reef coral ecological patterns using 3

4. Note the map of the Dominican Republic. You will be collecting reef coral data from four major regions: (a) Jaragua National Park (Living); (b) Lago Enriquillo (Holocene); (c) Santo Domingo (Pleistocene coastal terraces); and (d) Rio Cana (Middle Pliocene, Early Pliocene, and Late Miocene). Be sure that you can find all four localities on the map (shown below).

5. Take out the lesson 3 data worksheets. 6. On the data worksheets you will notice that we are studying 3 samples from each

time period (e.g., Holocene, Pleistocene, Pliocene, etc).

7. For each sample you need to determine the morphotype, or shape, of each coral species. We will then use these data to determine if the reef coral morphotypes in the four regions of the Dominican Republic have changed over the past several million years.

8. Each coral species in the database has been identified as one of four

morphotypes: branching, massive, platy, or free-living.

9. The morphotypes for some species have already been filled in for you on the data worksheets and the percentages of the morphotypes in the sample have been calculated for you.

10. To finish this activity you will need to determine the percentages of branching,

massive, platy, or free-living morphotypes in all 18 samples.

11. In order to gather coral morphotype data for each sample, you will need to click on the name of each region (e.g., Jaragua National Park) and then click on the sample number listed on the data worksheets (e.g., region Jaragua National Park, locality “Cabo Falso.”) Detailed visual instructions are shown on the next page.

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Go to: http://nmita.geology.uiowa.edu Click on: Maps & Faunal Lists Click on: Dominican Republic A map of the Dominican Republic will appear.

Note the rivers west of the city of Santiago. These rivers have exposed sedimentary rock rich in coral and mollusk fossils. Click on the river Rio Cana

A detailed map of the Rio Cana will appear along with small tributaries. Note the three main regions of the river. Click on Cana Gorge.

A detailed map of the Cana Gorge locality will appear along with sample localities. We will be studying three localities from Cana Gorge Click on locality AB03-3

A data screen will appear with information on the sample and the coral reef species that occur in the sample. Next to each genus and species is the morphotype, or shape, of the coral species.

How to use NMITA to gather morphotype data

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The morphotype is listed after the name of each species in parentheses, e.g. [branching]. Transfer the morphotype data to the data worksheet. You may look at pictures of each species by clicking on the species name.

12. For each sample, determine the morphotype of each coral species. This information is shown after the scientific name of each species. Follow the instructions shown on the previous page.

13. Transfer the morphotype data to the data worksheets. Be sure that you are

placing the morphotype data in the correct sample box for the correct species.

14. When you are finished transferring all of the coral morphotype data to the data worksheet, calculate the percentage of each morphotype in each sample. To perform this calculation, divide the number of species of a given morphotype by the total number of species in the sample (e.g, 8 branching species/16 total species = 50% branching species in the sample).

15. Repeat steps 13 and 14 until you are finished with all 18 samples.

16. When you are finished, you should know the percentage of branching, massive,

platy, and free-living coral species in all 18 samples.

17. Now plot the percentage data on the graphs on the analysis worksheet. You will be completing 2 graphs, one for platy morphotypes and one for branching morphotypes. When you are finished you will have documented patterns of coral morphotype change over the past 6 million years in the Dominican Republic.

Data interpretation: Has the percentage of platy or branching coral morphotypes changed over the past 6 million years in the Dominican Republic? If one were to travel back in time to the Pliocene, would coral reefs in the Dominican Republic have similar percentages of branching species as there are today? What would be the advantages or disadvantages of plotting the average morphotype percentage value for each time period? Would this change the patterns that we observe? Why would this be significant? Discussion questions: Corals have different morphotypes because of genetic differences and environmental differences. What environmental factors might contribute to different coral morphotypes? Could changes in coral morphotypes through time be a product of changes in the environmental conditions in the Caribbean? Explain.

Los Carraplanes (2) Morphology Cabo Falso (5) Morphology Bahia Honda en Cabo Rojo (8) Morphology

Jaragua National Park

Branching

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Jaragua National Park

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1 Acropora palmata Acropora palmata X Acropora cervicornis X 2 Undaria agaricites Acropora cervicornis X Undaria agaricites X3 Undaria pusilla Undaria agaricites X Undaria pusilla X4 Helioseris cucullata Undaria pusilla X Agaricia lamarcki X5 Porites porites Helioseris cucullata X Agaricia grahamae X6 Porites astreoides Agaricia lamarcki X Agaricia fragilis X7 Diploria strigosa Agaricia grahamae X Helioseris cucullata X8 Colpophyllia natans Agaricia fragilis X Porites porites X9 Montastraea "annularis" Helioseris cucullata X Porites astreoides X10 Montastraea faveolata Porites porites X Madracis decactis X11 Montastraea franksi Porites astreoides X Madracis mirabilis X12 Montastraea cavernosa Madracis decactis X Madracis pharensis X13 Siderastrea siderea Madracis pharensis X Diploria strigosa X14 Siderastrea radians Madracis formosa X Diplora labyrinthyformis X15 Manicina areolata Diploria strigosa X Colpophyllia natans X16 Isophyllastrea rigida Diploria clivosa X Colpophyllia breviserialis X17 Isophyllia sinuosa Diplora labyrinthyformis X Colpophyllia amaranthus X18 Colpophyllia natans X Meandrina meandrites X19 Colpophyllia breviserialis X Montastraea "annularis" X20 Colpophyllia amaranthus X Montastraea faveolata X21 Meandrina meandrites X Montastraea franksi X22 Montastraea "annularis" X Montastraea cavernosa X23 Montastraea faveolata X Solenastrea bournoni X24 Montastraea franksi X Siderastrea siderea X25 Montastraea cavernosa X Dichocoenia stokesi X26 Siderastrea siderea X Dichocoenia stellaris X27 Siderastrea radians X Eusmilia fastigiata X28 Dichocoenia stokesi X Manicina aerolata X29 Dichocoenia stellaris X Manicina mayori X30 Eusmilia fastigiata X Mycetophyllia aliciae X31 Mycetophyllia aliciae X Mycetophyllia lamarckiana X32 Mycetophyllia lamarckiana X Mycetophyllia danaana X33 Mycetophyllia danaana X Mycetophyllia ferox X34 Mycetophyllia ferox X Mycetophyllia reesi X35 Scolymia cubensis X Scolymia cubensis X36 Scolymia lacera X Scolymia lacera X37 Scolymia wellsi X Scolymia wellsi X38 Isophyllastrea rigida X Isophyllastrea rigida X39 Mussa angulosa X Isophyllia sinuosa X40 Stephanocoenia intersepta X Mussa angulosa X41 Stephanocoenia intersepta XTOTAL SPECIES: 17 TOTAL SPECIES: 40 7 18 12 3 TOTAL SPECIES: 41 6 22 12 1

Percent of total species: Percent of total species: 18 45 30 8 Percent of total species: 15 54 29 2

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Sample 1 Morphology Sample 3 Morphology Sample 4 Morphology

Lago Enriquillo

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Lago Enriquillo

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Lago Enriquillo

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1. Acropora cervicornis X Undaria agaricites X Acropora cervicornis 2. Undaria agaricites X Agaricia lamarcki X Agaricia lamarcki 3. Colpophyllia natans X Colpophyllia breviserialis X Undaria agaricites4. Eusmilia fastigata X Colpophyllia natans X Colpophyllia natans5. Favia fragum X Dichocoenia stokesi X Dichocoenia stokesi6. Helioseris cucullata X Helioseris cucullata X Eusmilia fastigata7. Manicina areolata X Montastraea "annularis" X Helioseris cucullata8. Oculina diffusa X Madracis mirabilis X Montastraea "annularis"9. Porites astreoides X Mussa angulosa X Madracis mirabilis10. Porites divaricata X Montastraea cavernosa X Manicina areolata11. Porites furcata X Mycetophyllia lamarckiana X Mussa angulosa12. Porites porites X Oculina diffusa X Montastraea cavernosa13. Scolymia lacera X Porites astreoides X Oculina diffusa14. Siderastrea siderea X Porites divaricata X Porites astreoides15. Stephancoenia intersepta X Scolymia lacera X Porites divaricata16 Siderastrea siderea X Porites furcata17 Stephancoenia intersepta X Porites porites18 Siderastrea siderea19 Stephancoenia intersepta20 TOTAL SPECIES: 15 6 6 2 1 TOTAL SPECIES: 17 4 9 4 0 TOTAL SPECIES: 19

Percent of total species: 40 40 13 7 Percent of total species: 24 53 24 0 Percent of total species:

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Santo Domingo (JK 5) Morphology Santo Domingo (JK 6) Morphology Santo Domingo (JK 8) Morphology

Pleistocene Coastal Terraces

Branching

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Pleistocene Coastal Terraces

Branching

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Pleistocene Coastal Terraces

Branching

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Platy

Free-living

1. Acropora cervicornis X Acropora cervicornis Acropora cervicornis X 2. Acropora palmata X Acropora palmata Acropora palmata X 3. Colpophyllia natans X Dendrogyra cylindricus Colpophyllia natans X4. Dendrogyra cylindricus X Dichocoenia stokesi Diploria labrynthiformis X5. Diploria labrynthiformis X Diploria clivosa Diploria strigosa X6. Diploria strigosa X Diploria strigosa Isophyllia sinuosa X7. Montastraea "annularis" X Favia fragum Montastraea "annularis" X8. Montastraea faveolata X Isophyllia sinuosa Montastraea faveolata X9. Montastraea franksi X Montastraea "annularis" Montastraea "organ pipe" X10. Montastraea "organ pipe" X Montastraea faveolata Montastraea cavernosa X11. Montastraea cavernosa X Montastraea "organ pipe" Siderastrea siderea X12. Siderastrea siderea X Siderastrea siderea Stephanocoenia intersepta X13. Stephanocoenia intersepta X Stephanocoenia intersepta Undaria agaricites X14 15 16 17 18 19 20 TOTAL SPECIES: 13 2 11 0 0 TOTAL SPECIES: 13 TOTAL SPECIES: 13 2 10 1 0

Percent of total species: 15 85 0 0 Percent of total species: Percent of total species: 15 77 8 0

Plei

stoc

ene

page 3Name:

Cana Gorge (AB03-3) Morphology Cana Gorge (AB03-4) Morphology Cana Gorge (JK-03-6) Morphology

Rio Cana

Branching

Massive

Platy

Free-living

Rio Cana

Branching

Massive

Platy

Free-living

Rio Cana

Branching

Massive

Platy

Free-living

1. Caulastrea portoricensis X Caulastrea portoricensis X Caulastrea portoricensis 2. Diploria zambensis X Montastraea-I limbata X Diploria zambensis 3. Favia maoadentrensis X Montastraea-II cylindrica X Isophyllia sp.A4. Montastraea-II canalis X Porites-I portoricensis X Madracis decactis5. Montastraea-II cavernosa X Porites-I waylandi X Montastraea-I limbata6. Placocyathus variabilis X Porites-II baracoaensis X Montastraea-II cavernosa7. Porites-I macdonaldi X Stephanocoenia spongiformis X Mussismilia sp.A8. Porites-I portoricensis X Stylophora granulata X Mussismilia sp.B9. Porites-I waylandi X Undaria agaricites X Porites-I portoricensis10. Porites-II baracoaensis X Porites-I waylandi11. Stephanocoenia duncani X Porites-II baracoaensis12. Stylophora granulata X 13. Stylophora minor X 14. Undaria agaricites X 15 16 17 18 19 20 TOTAL SPECIES: 14 5 5 2 2 TOTAL SPECIES: 9 4 4 1 0 TOTAL SPECIES: 11

Percent of total species: 36 36 14 14 Percent of total species: 44 44 11 0 Percent of total species:

Mid

dle

Plio

cene

Name: page 4

Canada de Zamba (AB03-2) Morphology Canada de Zamba (JK03-10) Morphology Canada de Zamba (JK03-5) Morphology

Rio Cana

Branching

Massive

Platy

Free-living

Rio Cana

Branching

Massive

Platy

Free-living

Rio Cana

Branching

Massive

Platy

Free-living

1. Agaricia lamarcki Caulastrea portoricensis Diploria zambensis 2. Favia dominicensis Favia maoadentrensis Favia dominicensis 3. Goniopora hilli Leptoseris gardineri Isophyllia sp.A4. Isophyllia sp.A Montastraea-I limbata Madracis mirabilis5. Madracis cf.herricki Porites-I macdonaldi Montastraea-I limbata6. Madracis decactis Porites-I portoricensis Mussismilia sp.A7. Madracis decaseptata Porites-I waylandi Pocillopora crassoramosa8. Madracis mirabilis Porites-II baracoaensis Porites-I macdonaldi9. Madracis sp.A Siderastrea siderea Porites-I waylandi10. Manicina grandis Stephanocoenia duncani Siderastrea siderea11. Montastraea-I limbata Stylophora affinis Stephanocoenia duncani12. Montastraea-II cavernosa Stylophora granulata Stylophora affinis13. Placocyathus variabilis Stylophora minor Stylophora minor14. Porites-I macdonaldi Undaria agaricites Undaria agaricites15. Porites-I waylandi 16. Porites-I baracoaensis 17. Stylophora granulata 18. Stylophora minor 19 20 TOTAL SPECIES: 18 TOTAL SPECIES: 14 TOTAL SPECIES: 14

Percent of total species: Percent of total species: Percent of total species:

Early

Plio

cene

Name: page 5

Arroyo Bellaco (BEL-1) Morphology Arroyo Bellaco (BEL-3) Morphology Arroyo Bellaco (BEL-6) Morphology

Rio Cana

Branching

Massive

Platy

Free-living

Rio Cana

Branching

Massive

Platy

Free-living

Rio Cana

Branching

Massive

Platy

Free-living

1. Agaricia lamarcki Gardinerseris planulata X Favia dominicensis X 2. Dichocoenia sp.A Goniopora hilli X Goniopora imperatoris X 3. Gardinerseris planulata Goniopora imperatoris X Madracis mirabilis X4. Goniopora hilli Montastraea-I limbata X Montastraea-I limbata X5. Goniopora imperatoris Montastraea-II canalis X Montastraea-II endothecata X6. Montastraea-I limbata Montastraea-II endothecata X Pocillopora crassoramosa X7. Pocillopora crassoramosa Porites-I waylandi X Porites-I portoricensis X8. Porites-I waylandi Stephanocoenia duncani X Stylophora affinis X9. Siderastrea siderea Stephanocoenia spongiformis X Undaria agaricites X10. Solenastrea bournoni Stylophora affinis X 11. Stephanocoenia duncani Undaria agaricites X 12. Stephanocoenia spongiformis 13. Stylophora affinis 14 15 16 17 18 19 20 TOTAL SPECIES: 13 TOTAL SPECIES: 11 1 9 1 0 TOTAL SPECIES: 9 4 4 1 0

Percent of total species: Percent of total species: 9.1 82 9 0 Percent of total species: 44 44 11 0

Late

Mio

cene

Name: page 6

Recent

Holocene

Recent

Pleistocene

Early Pliocene

Late Miocene

Middle Pliocene

Holocene

Pleistocene

Middle Pliocene

Early Pliocene

Late Miocene

% Platy species

Name:

Tim

eTi

me

A.

B.

10 20 30 40

Mill

ions

of y

ears

ago

0

1

5

3

4

7

6

8

2

Mill

ions

of y

ears

ago

0

1

5

3

4

7

6

8

2

% Branching species10 20 30 40

Lesson 4: Use NMITA to determine when modern reef corals originated. This lesson is designed to help you learn how to use a biodiversity bioinformatics database known as NMITA to determine when modern reef corals from the Dominican Republic originated. Did all the living genera and species of corals appear recently, or many millions of years ago? Did the modern genera and species appear together or randomly through time? NMITA’s data on fossil reef corals, combined with data from living reefs, can be used to answer these questions.

Lesson 4 takes you on a virtual journey to the Dominican Republic, a country located on the island of Hispañola in the Caribbean Sea. On the island you will explore the marine fossil corals and coral reefs that occur in different sedimentary rock layers that were formed when parts of the island were under the Caribbean Sea. You will also explore the diversity of living coral reefs from the southwestern part of the country. You will collect coral reef biodiversity data from six different time periods in order to determine when, in geological time, modern reef coral biodiversity originated in the Dominican Republic. You will collect data from 3 samples from each of the 5 time periods. Key Terms: Key Concepts: Origination Holocene Evolution Biodiversity Database Extinction Coral reef Sedimentary rock Speciation Geological time Pliocene Sampling Miocene Pleistocene Dating rock Directions:

1. Go to NMITA http://nmita.geology.uiowa.edu/ 2. Click Maps & Faunal Lists 3. Click Dominican Republic

1. 2. 3.

When did modern reef corals originate? 4

4. Note the map of the Dominican Republic. You will be collecting coral reef biodiversity data from four major regions: (a) Jaragua National Park (Recent); (b) Lago Enriquillo (Holocene); (c) Santo Domingo (Pleistocene coastal terraces); and (d) Rio Cana (Middle Pliocene, Early Pliocene, and Late Miocene). Be sure that you can find all four localities on the map.

5. You will record data on these four regions on the lesson 4 data worksheet. 6. Take out the data worksheet. You will notice that we are gathering data on the

number of modern genera and species that have been found in samples from previous time periods (e.g., Holocene, Pleistocene, etc.). The total number of genera and species in each sample has already been tabulated on the data worksheet. You will be calculating the percentage of modern genera and species that have been found in each sample.

7. In order to gather data, you will need to find out if any of the modern genera or

species are present in the fossil record. A list of all the modern genera and species is provided as an appendix to this lesson. You will need to use this list to complete the lesson.

8. Use NMITA to explore all the regions of the Dominican Republic that have

samples of fossil corals (e.g., Lago Enriquillo, Pleistocene coastal terraces, and Rio Cana). Compare the genera and species that occur in these samples to the list of modern coral species.

9. Record the number of modern genera and species from each fossil sample on

the data worksheet. Repeat step 8 until you have filled in all the boxes.

10. When you are finished, you should know the number of modern corals that occur in all the fossil samples. Calculate the percentage of modern corals in each sample by dividing the number of modern species by the total number of species and multiplying by 100: [(#Modern / Total # ) x 100].

11. Plot the percentage results on the Lesson 4 graph.

1

2

3

4

1

2

3

4

5

6

Go to: http://nmita.geology.uiowa.edu Click on: Maps & Faunal Lists Click on: Dominican Republic A map of the Dominican Republic will appear.

Note the rivers west of the city of Santiago. These rivers have exposed sedimentary rock rich in coral and mollusk fossils. Click on the river Rio Cana

A detailed map of the Rio Cana will appear along with small tributaries. Note the three main regions of the river. Click on Cana Gorge.

A detailed map of the Cana Gorge locality will appear along with sample localities. We will be studying three localities from Cana Gorge Click on locality AB03-3

Compare the list from your sample to the list of living coral species Determine if any of the genera or species found in the sample also occur in the living fauna. Record the number of genera or species from the sample that occur in the modern fauna in the data worksheet

How to gather data for lesson 4

Data interpretation

1. Describe how the percentages of modern reef coral genera change through geologic time. 2. Describe how the percentages of modern reef coral species change through geologic time. 3. Are the two patterns similar? Explain why or why not. 4. Which time period, or epoch, had the least modern species? 5. Which time period, or epoch, had the most modern species? 4. If you wanted to conduct further studies to better understand modern reef coral origination, which time period, or epoch, would you investigate? Explain why.

Discussion questions

1. Corals are marine animals. What environmental variables could have possibly influenced the patterns of coral extinction or origination that you documented?

2. Why is studying changes in biodiversity through geologic time important?

3. How could such data influence conservation efforts or environmental policies?

1 Acropora palmata2 Acropora cervicornis3 Acropora palmata4 Agaricia fragilis5 Agaricia grahamae6 Agaricia lamarck i7 Colpophyllia amaranthus8 Colpophyllia breviserialis9 Colpophyllia natans

10 Dichocoenia stellaris11 Dichocoenia stokesi12 Diplora labyrinthyformis13 Diploria clivosa14 Diploria strigosa15 Eusmilia fastigiata16 Helioseris cucullata17 Isophyllastrea rigida18 Isophyllia sinuosa19 Madracis decactis20 Madracis formosa21 Madracis mirabilis22 Madracis pharensis23 Manicina aerolata24 Manicina mayori25 Meandrina meandrites26 Montastraea "annularis"27 Montastraea cavernosa28 Montastraea faveolata29 Montastraea franksi30 Mussa angulosa31 Mycetophyllia aliciae32 Mycetophyllia danaana33 Mycetophyllia ferox34 Mycetophyllia lamarck iana35 Mycetophyllia reesi36 Porites astreoides37 Porites porites38 Scolymia cubensis39 Scolymia lacera40 Scolymia wellsi41 Siderastrea radians42 Siderastrea siderea43 Solenastrea bournoni44 Stephanocoenia intersepta45 Undaria agaricites46 Undaria pusilla

List of living coral species

Age of sample Region Locality # liv

ing

gene

ra in

this

sam

ple

# liv

ing

spec

ies

in

th

is s

ampl

e

tota

l gen

era

in th

is

sam

ple

tota

l spe

cies

in th

is

sam

ple

% li

ving

gen

era

in

this

sam

ple

% li

ving

spe

cies

in

this

sam

ple

Sample 1 12 15Sample 3 15 17Sample 4 16 19

Santo Domingo (JK 5) 7 13Santo Domingo (JK 6) 9 13Santo Domingo (JK 8) 8 13Cana Gorge (AB03-3) 9 14Cana Gorge (AB03-4) 6 9Cana Gorge (JK-03-6) 7 11

Canada de Zamba (AB03-2) 10 18Canada de Zamba (JK03-10) 9 14Canada de Zamba (JK03-5) 12 14

Arroyo Bellaco (BEL-1) 11 13Arroyo Bellaco (BEL-3) 7 11Arroyo Bellaco (BEL-6) 8 9

%

Holocene Lago Enriquillo

Modern species in

sample

Total genera and species in

sample

Pleistocene Pleistocene coral terraces

Middle Pliocene Rio Cana

Early Pliocene Rio Cana

Late Miocene Rio Cana

Recent

Holocene

Recent

Pleistocene

Early Pliocene

Late Miocene

Middle Pliocene

Holocene

Pleistocene

Middle Pliocene

Early Pliocene

Late Miocene

% Modern genera

Name:

Tim

eTi

me

A.

B.

Mill

ions

of y

ears

ago

0

1

5

3

4

7

6

8

2

Mill

ions

of y

ears

ago

0

1

5

3

4

7

6

8

2

% Modern species