Tuesday, June 28, 2011

Ichnology Meeting and Field Work

For those who do not know, "Ichnology" means the study of trace fossils and that is what I am currently doing for my PhD Dissertation. In that vein I am going to Spain for the International Ichnofabric Workshop to give a presentation on what is essentially the start of my PhD prep. I am currently working on building up a trace fossil database for research purposes. After that I am going to be in the field at Zumaia, Spain to study a specific group of trace fossils called "graphoglyptids", which I will explain what are at some later time. Following that I am going to Krakow, Poland to take pictures in the geology museum of more graphoglyptids.

Following that I am coming back. So, since my schedule looks to be pretty full for the next couple of weeks I am going to have the blog be running on autopilot, posting GeoJeopardy! as well as some other posts automatically. I may have time for a new post here or there but I really don't know.  So I wanted to leave you with my abstract for the conference.


Internet databases in ichnology: The benefits and need for a dynamic Universal Ichnological Database

Lehane, J.R. and Ekdale, A.A.

Department of Geology and Geophysics, University of Utah, 115 South 1460 East,

Room 383 FASB, Salt Lake City, UT 84112-0102, U.S.A.


     Scientific research has been steadily progressing into the digital realm to the point that most, if not all, journals offer a digital means of obtaining their articles, and some journals now are exclusively digital, including Palaeontologia Electronica and PLoS ONE. This has created a tremendous advantage to researching scientists, because what used to take days or even weeks to obtain articles on some obscure subject can now take minutes with a careful search and appropriate access. Research tools like GeoRef, the American Geological Institute’s geoscience database, and Google Scholar make finding information extremely timely and most of the time relevant.

     In the case of paleontology, numerous databases have made attempts at synthesizing the information into one all-encompassing portal. These databases include FossilPlot (Tapanila, 2007), The Paleontology Portal (http://www.paleoportal.org/) and The Paleobiology Database (http://paleodb.org) (PBD). However, these resources currently have been of little use to ichnologists. There are also more specific databases that deal with ichnology in particular. These most commonly are collection-specific databases, which may or may not be widely, or personal online databases.

     It is to the benefit of current ichnologists that a Universal Ichnological Database (UID) be set up with all of the available ichnological information readily available to facilitate future research. Paleontology has often taken advantage of biostratigraphic and paleobiogeographic data to analyze data. With the advent of a UID, this could then be more readily applied to ichnology. The database could be used to help develop ichnological range charts and ichnobiogeographic maps for applications in ichnostratigraphy.

Literature Search Engines

     There are several literature search engines on the internet that may be used in ichnological research. The problem with these is that you still need to wade through the piles of information to find what you want. For example, if we search for the trace fossil Zoophycos within GeoRef and Google Scholar (as of March 2011), we get 467 published works returned in GeoRef, including abstracts and conference materials. This result can be narrowed down by limiting the search to just Zoophycos located within the title (94 results) or a number of other variables. While GeoRef confines its searches to titles, abstracts, and keywords, Google Scholar is a little more diverse, usually being able to search the entire document. A search of Zoophycos in Google Scholar returns about 2,480 results. Google Scholar though only has the option to limit the search to the entire article (if available) or the title. A title-only search of Zoophycos returns 137 results.

Paleontology Databases

Of all the available paleontology databases online, there are three primary ones which seem to be the most diverse and dynamic. The first one, FossilPlot, is an Excel-based spreadsheet of the Sepkoski Compendium, but it does not include trace fossils. So for a direct trace fossil analysis, this database is not useful. However, it does have tremendous value in listing the concurrent ranges of marine taxa body fossils that may be trace makers. The concurrent range charts which can be produced are useful in ichnology if the trace fossil maker is known, or at least assumed.

     The next paleontology database, The Paleontology Portal, is an educational resource that lists fossils by period. For example, it is possible to click on “Jurassic” and see what animals lived during that time period. The Paleontology Portal does contain some trace fossils, but they are extremely limited in their extent and contain almost no information other than a picture, the ichnogenus, and a general locality of the specimen. The available trace fossils on the site are divided roughly equally between vertebrate and invertebrate traces (46% to 54%). This is in contrast to what is actually seen in the fossil record, which is dominated by invertebrate traces. When working through The Paleontology Portal, there are two main ways to find information. The most straightforward way is to click on the “Trace Fossils” link, and then click on the time period, which will then give you an image list available for trace fossils from that time period. Unfortunately, there are only 39 individual trace fossils listed (as of March 2011) with 32 unique trace fossils. For example, when you click on the Devonian, you will get one result, which is Zoophycos. The information that is associated with that trace fossil also is limited. When you click on the link for the trace fossil, you get a larger image, the same one that was previously shown, as well as the state in which the trace fossil was found, but that is it. Another way is to search for trace fossils is through the search function. This basically just pulls up all available occurrences of that trace fossil in the database. If you type in “Zoophycos”, you will get back one result, the same one from the Devonian. If you type in another common trace fossil, “Thalassinoides”, you get no results at all, since that common ichnogenus is not in the database. So for use in ichnological research, The Paleontology Portal does not currently serve well.

     The third primary paleontology database is The Paleobiology Database (PBD). This is the paleontology database that has the most potential in ichnology. As of March 2011, it currently had over 180,000 species listed. However, the number of trace fossils in the database is not available, since there was no specific search function for trace fossils. If we are to search for Zoophycos again, it returns a list of 132 separate occurrences of Zoophycos, most of which are located in the Devonian of New York (94). When you click on the “Show More Details” tab, you learn that Zoophycos is a genus, and that is it. Since the database is primarily based on literature identifications, most of the links of the fossils point back to the primary sources. The database also is very helpful in identifying the locations of the fossils on a paleogeographic map, but it is not able to search for specific characteristics. So although this database has potential as a starting off point, it is not much better than doing more personalized research using Google Scholar or GeoRef.

Ichnology Databases

     There also are more ichnologically specific databases where one can search for data. One group of these are the collection-specific databases, including one used at the University of Utah and also one being developed for the Muséum national d’Histoire naturelle, Paris (Goldstein et al., 2010). Collection-specific databases can provide important information, since they often include many fossils that have not been reported in formal publications. Thus, such collection-specific tabulations include information that ordinarily would not make it to the online databases, since those are built primarily upon published information (either published in a journal or through an online forum). What can be gleaned from these databases are range and locality information. Usually there are no images associated with the databases, so if you are not in the actual presence of the trace fossils you have to rely solely on the database information. The main problem with this approach is that if you are not in the vicinity of the fossils, you need to rely on someone else’s knowledge of the trace fossil for identification, and you probably do not know that name of the identifier, since it is not usually listed.

     There is also the Trace Fossil Image Database , which is a website run by Anthony J. Martin at Emory University, who has catalogued the images of about 61 different trace fossils (as of March 2011) (http://www.envs.emory.edu/faculty/MARTIN/ichnology/images.htm). Unlike most of the other databases, this one includes a descriptive analysis of the trace fossil as well as an image with the age, formation, location, and collector information of each of the images. Although very useful, the main problem with this website is that there is no easy way to search through the database or update the information. You need to know what you are looking for to help find the information.

Developing a Universal Ichnological Database

At this time, there is no real one-stop-shopping location for all your ichnological database inquiries. There is no one place where you can find the range data as well as a photo and a description of each trace all in an easily searchable database. This means that a comprehensive, easily accessible database of ichnological information must be built. The best solution for accomplishing this objective may be a dataset that already has the infrastructure to handle the input and searching for information. The database should be dynamic and not reliant on any single contributor. The problem with most websites and institutional collection-specific databases is that they are run by individuals who are not only fallible but temporary. A database should transcend the temporary. Among the existing internet databases, FossilPlot is useful but not as widely used, is maintained by one individual, and does not contain any trace fossils. The Paleontology Portal seems to be an elementary introduction website that is not very useful in scientific research. The Trace Fossil Image Database and the institutional collection-specific databases may be used as building blocks for a Universal Ichnological Database (UID), but at this point they are not set up for easy input of information needed to build and maintain a universal database. The Paleobiology Database (PBD) has one of the largest online communities, who are daily adding new species or information to old species, so it holds promise as a possible vehicle to build a comprehensive internet-accessible UID. 

Since the PBD fits all of the criteria for a good starting point, it has been chosen as the repository for the UID. To start off, some information already has been included into the database. Roy Plotnick, the only current ichnological contributor to the PBD, has already entered most of the genus names from the Treatise on Invertebrate Paleontology, Volume W (Häntzschel, 1975). The only thing that was needed was to go back and supplement that information. The important information that should be included is the First Appearance Datum (FAD), the Last Appearance Datum (LAD), the diagnostic information, a photographic representation, and any identified species. The secondary information, which would sometimes be included if available, would be the possible trace maker, the inferred behavior, the paleoenvironment, and the ichnofacies. The PBD already has most of these columns setup prior to any input of information.

When the information of most available trace fossils is entered into the database, it then will be available for a variety of ichnological analyses. These analyses may include creating range charts to identify the age of rocks, studying behavioral evolution, producing a searchable diagnosis database for people to identify unknown trace fossils, and creating paleobiostratigraphic maps, to name just a few.


JRL thanks ExxonMobil for the ExxonMobil Science Grants for Students, which paid for the work on this project.

Literature Cited

Tapanila, L. 2007. FossilPlot, an Excel-based computer application for teaching stratigraphic paleontology using the Sepkoski Compendium of fossil marine genera. Journal of Geoscience Education, 55, 133-137.

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