Welcome to the Fishes of Texas Project Documentation
If you have been to the Fishes of Texas website recently, you may have noticed some changes. On September 9, 2022, we released a major update, of both the website and the underlying data, to Version 3.0. More on that below, but before going there, with this milestone release and a formal end of direct external funding, we are trying to decide where to focus our future efforts at this transitional state. If you have not done so, please complete our quick online survey to help influence our direction.
Now, back to what’s changed since Version 2.0. Here is a summary with links to more information in our now extensively updated and improved documentation.
Please update your user profile, so we can keep you updated and please now use the updated citation below when referring to either the website or the data in all publications that use FoTX data:
Hendrickson, Dean A., and Adam E. Cohen. 2022. Fishes of Texas Project Database (Version 3.0). http://doi.org/10.17603/C3WC70. Accessed (insert date).
We thank the following people who have been critical for making this version update possible:
Texas Advanced Computing Center: Tomislav Urban and Chris Jordan
University of Texas: Gary Garrett, Melissa Casarez (now TPWD), Doug Martin, Roy Kleinsasser, Ben Labay, Bob Edwards, Colton Avila, Casey Hartsough, and Ryan Rash.
Texas Parks and Wildlife Department: Tim Birdsong, Stephen Curtis, Sarah Robertson, and Kevin Mayes
Valuable insights regarding native distributions and the flagging of suspect records were received from the following additional people: Doug Martin, Roy Kleinsasser, Gary Garrett, Chris Taylor, Megan Bean, Kevin Conway, Bob Edwards, Melissa Casarez, and Chris Hoagstrom (consulted for single species).
We would also like to acknowledge all original collectors, data managers, etc. who created the records in FoTX.
Thanks,
Dean Hendrickson and Adam Cohen
Contact us using the e-mail address below with any questions or comments.
--------------------------
Fishes of Texas Team
fishesoftexas@gmail.com
mailing address:
University of Texas, Biodiversity Collections
Texas Natural History Collections, PRC 176/R4000,
10100 Burnet Road, Austin, TX 78758-4445
We just presented a poster at the Texas Chapter of the American Fisheries Society meeting in Corpus Christi on Feb 23-25, 2023. The abstract is below:
Fish occurrence data are widely scattered and mostly not published as data readily utilizable by computers. Global biodiversity aggregating services (e.g. GBIF, iDigBio, Fishnet) now aggregate and serve whatever data are submitted to them in the standard Darwin Core format, but their data are often replete with errors, minimally normalized, lacking content across standard fields, and served via generic mapping services lacking linkages to local and aquatic ecology-relevant resources (i.e., for fishes, they are ignorant of hydrography). In contrast, Fishes of Texas (FoTX) includes the same data and much more, including unpublished data from more diverse sources. FoTX’s rigorous quality-control measures, including specimen-based ID verifications, checking of legacy georeferencing, and flagging suspicious records has combined to greatly reduce errors. The custom FoTX website provides interactive exploration and data summarization, within the context of geopolitical and, now geographically-expanded hydrographic coverages, thus facilitating visualization and discovery of conservation-relevant histories and trends over time. The site allows viewing of derivative products, such as niche models, estimates of native ranges, checklists, data dashboards, and Native Fish Conservation Areas. The site also serves extensive image collections, collectors’ field notes, and links to digitized, formerly inaccessible unpublished agency reports. Finally, core FoTX data fields are also published to GBIF as Darwin Core to make it available to the world.
If you want to take our digital survey to help direct future efforts please do so here before the end of March: https://docs.google.com/forms/d/e/1FAIpQLScMG92tdqwtmyNh8BzXxRY2_HoZrQVEVN9hyJ--XQ9TgqSCyA/viewform
See our poster here: https://repositories.lib.utexas.edu/bitstream/handle/2152/117536/FoTX_for_TCAFS_Corpus_FINAL.pdf?sequence=3&isAllowed=y
posted Oct 29, 2015, 5:15 PM by Dean A. Hendrickson [ updated Jan 13, 2016, 9:45 PM ]
We've embedded comprehensive metadata in both Google Scholar and Dublin Core formats to every page, and registered our database in DataCite. That will help the world find our site and now, we have a proper citation with permanent DOI ("Hendrickson, Dean A., and Adam E. Cohen. 2015. 'Fishes of Texas Project Database (Version 2.0)' doi:10.17603/C3WC70. Accessed (insert date)."). Thanks for helping us out by always citing us whenever you use our data. Doing so will not only help us get a better handle on who our data users are, but also provide us more credible usage and citation stats that will help us sustain this effort. You'll will find a link to more detailed citation instructions in the footer of every page.
posted Jun 14, 2015, 12:21 PM by Dean A. Hendrickson [ updated Jun 23, 2015, 9:05 AM ]
Labay, Benjamin J., Dean A. Hendrickson, Adam E. Cohen, Timothy H. Bonner, Ryan S. King, Leroy J. Kleinsasser, Gordon W. Linam, and Kirk. O. Winemiller. In press June 14, 2015. 'Can Species Distribution Models Aid Bioassessment When Reference Sites Are Lacking? Tests Based on Freshwater Fishes,' Environmental Management (link).
This one takes good advantage of all of our Species Distribution Models, applying them to help resolve complex and persistent practical issues in the real world realm of bioassessment (evaluating the relative environmental health of streams and rivers and setting quantifiable goals for management efforts). Here's the abstract:
Recent literature reviews of bioassessment methods raise questions about use of least-impacted reference sites to characterize natural conditions that no longer exist within contemporary landscapes. We explore an alternate approach for bioassessment that uses species site occupancy data from museum archives as input for species distribution models (SDMs) stacked to predict species assemblages of freshwater fishes in Texas. When data for estimating reference conditions are lacking, deviation between richness of contemporary versus modeled species assemblages could provide a means to infer relative biological integrity at appropriate spatial scales. We constructed SDMs for 100 freshwater fish species to compare predicted species assemblages to data on contemporary assemblages acquired by 4 independent surveys that sampled 269 sites. We then compared site-specific observed/predicted ratios of the number of species at sites to scores from a multimetric index of biotic integrity (IBI). Predicted numbers of species were moderately to strongly correlate with the numbers observed by the four surveys. We found significant, though weak, relationships between observed/predicted ratios and IBI scores. SDM-based assessments identified patterns of local assemblage change that were congruent with IBI inferences, however, modeling artifacts that likely contributed to over-prediction of species presence may restrict the stand-alone use of SDM-derived patterns for bioassessment and therefore warrant examination. Our results suggest that when extensive standardized survey data that includes reference sites are lacking, as is commonly the case, SDMs derived from generally much more readily available species site occupancy data could be used to provide a complementary tool for bioassessment.
posted Nov 1, 2013, 11:04 AM by Dean A. Hendrickson
Yesterday we submitted the final report on a project funded by Texas Parks and Wildlife Department (via US Fish and Wildllife Service's Section 6 funding). It was quickly approved by both TPWD and USFWS and we then archived it, and all data produced and used in this study, in the University of Texas Digital Repository for permanent public access:
Labay, Ben J., Adam E. Cohen, Dean A. Hendrickson, Blake Sissel, Sahotra Sarkar, and Melissa Casarez. 2013. 'Final Report: Data Compilation, Distribution Models, Conservation Planning, and Status Survey for Selected Fishes of Concern in Texas and Region'. Texas Parks and Wildlife Section 6 grant TX E-136-R, TPWD #416853. Austin, Texas: University of Texas at Austin. http://hdl.handle.net/2152/21837
We feel this is a good example of application of our extensive, high quality Fishes of Texas Project data, the Species Distribution Models that we have produced from it, and the power of Conservation Network Planning software. We will be doing more of this in the near future.
posted Mar 27, 2013, 3:09 PM by Adam Cohen [ updated Mar 28, 2013, 1:15 PM ]
We've been very busy and have made dramatic improvements in data content and website design resulting in great improvement in overall user experience. On November 14, 2013 our database and website (www.fishesoftexas.org) were updated to reflect those improvements and became version 1.10 of both the Fishes of Texas Project (FoTX) database and website. Users who downloaded data from version 1.00 beta are encouraged to query this new version for updated and new data not formerly available. Read the list of changes below carefully since many are substantial and could affect some users.The data quality is substantially improved in this version, as is site usability and documentation. Both the website and data will continue to evolve, and as we now start to more rigorously track versions of both, we also hope to expand in new directions to better serve our users and broaden the user community.
We've been working with our data and examining the specimens and have now updated our database to reflect those new discoveries as well as some other issues. Our track 2 data are now available. We are also now beginning to develop non-specimen based data and those are available as well.
All data are now visible to all users. But registration and login allows users to download data and participate by commenting on our data and providing images.
We've made numerous changes to the website that will improve the user experience and the utility of the data provided. Among the noteworthy improvements: expanded our documentation; consolidated our site to 2 servers (from 4); added helpful tooltips; and greatly improved the maps and specimens pages' presentation of data.
We've added thousands of new images.
We've been developing new keys including some based on character matrices that are extensively illustrated and function in innovative ways unlike traditional dichotomous keys.
Our species accounts are greatly improved with text now provided by Dr. Timothy Bonner and colleagues at Texas State University and new dynamic distribution maps.
We now provide our Species Distribution Models for many of the state's species and some of our findings based on the same data that we now make available to the public.
Users are encouraged to be active participants in improving our data and can now also assist us in georeferencing and by providing data to our growing photo-vouchered database.
We process our data in “batches†that we call “Tracksâ€. Each Track goes through extensive standardization, normalization and quality checking before addition to the online database. The only data available in the beta version were those in Track 1 (81,243 records). In this version the quality of Track 1 data is improved in many ways, and Track 2 (43,173 records) is made available for the first time (as a separate download, but soon to be added to the main database).
Track 1 data edits new to this version:
(for details see our documentation: Addition of Literature and Other Non-vouchered Data Sources)
Default user privileges have changed
Both non-registered and registered users are no longer restricted with regard to what data they can see and can now view all data approved for public distribution by our data donors. Registration and login are still required for downloads and to contribute comments or images, but registration is now immediate (users used to have wait on us to manually process their applications for registration).
Increased offerings from our digital library
We have added lots more images including:
Improved identification keys
Improved species accounts
Our previous species accounts had little information content, but are now nearly fully complete for many freshwater species. We are now collaborating with Dr. Timothy Bonner at Texas State University who has provided those accounts.
Our first generation (Class 1) species distribution models (n = 96) are now all available for download and we've added a section to our documentation ("Models") that comprehensively explains their creation and how to interpret them. Links to our use of these can also be found there.
We are collaborating with experts around the state to explore application of species distribution models to bioassessment of fish communities. See a summary of a working manuscript HERE.
Beyond our new iNaturalist site where users can submit their own occurrence data with photos, we now provide an easy way for users to assist us with georeferencing. We especially encourage users who may have contributed specimen records included in our database to take a look at how we've georeferenced them.
posted Jun 16, 2014, 1:05 PM by Dean A. Hendrickson
US Fish and Wildlife Service provided funding to support a fun clean-up of the occurrence data for minnows (Cyprinidae) from the Colorado River basin. We examined a huge proportion of all specimens of the family ever collected in this drainage with the primary objective of more rigorously assessing the hypothesis that the endangered Sharpnose Shiner (Notropis oxyrhynchus) might be native to the Colorado despite a long history of literature that contends it was introduced there from the adjacent Brazos basin. We focused our efforts on older specimens and turned up some formerly mis-identified specimens and other lines of evidence that strongly support it being native in the Colorado, though unfortunately, it seems likely extirpated there. We feel this product is a great case study that exemplifies the value of museum specimen databases and the specimens themselves. The report and associated data are permanently archived:
Cohen, Adam E., Dean A. Hendrickson, and F. Douglas Martin. Final Report: Verification of Identifications of Cyprinid Specimens from the Colorado River Basin, Texas. Austin, Texas: University of Texas at Austin, June 5, 2014. 16 pages + online data. (http://hdl.handle.net/2152/24627.
And we now note that we have been remiss in not mentioning other recent products here so here they are:
Martin, F. Douglas, Adam E. Cohen, Benjamin J. Labay, Melissa Casarez, and Dean A. Hendrickson. 2013. 'Persistence of a Landlocked Population of Gulf Pipefish, Syngnathus scovelli.' The Southwestern Naturalist 58(3):378-380. doi: 10.1894/0038-4909-58.3.376
Cohen, Adam E., Ben J. Labay, Dean A. Hendrickson, Melissa Casarez, and Sahotra Sarkar. 2013. Final Report: Data Provision and Projected Impact of Climate Change on Fish Biodiversity within the Desert LCC. Submitted to United States Department of the Interior, Bureau of Reclamation, Desert Landscape Conservation Cooperative; Agreement Number: R11AP81527. Austin, Texas: University of Texas at Austin, November 30, 2013. 109 pages + online data. http://hdl.handle.net/2152/22475.
posted Jan 29, 2021, 2:06:15 PM by Adam E. Cohen
The Fishes of Texas Project data and team have been assisting the Texas Parks and Wildlife Department to develop Native Fish Conseration Areas, which have become critical for conservation planning in Texas. To learn more visit the Texas Native Fish Conservation Network website.
posted Mar 14, 2011, 8:00 PM by Dean A. Hendrickson [ updated Mar 12, 2013, 2:49 PM by Adam Cohen ]
On Feb 11, 2011, in the following presentations given at the annual meeting of the Texas Chapter of the American Fisheries Society, we announced availability of the Fishes of Texas version 1.0 beta website serving all data contributed by our own collection, the Texas Natural History Collection at University of Texas. Data from other contributing collections will be added to the data available through the web search engine as permissions are obtained from those institutions. In our presentations we discussed the project's history, content, and evolution, and presented selected research we have done with the data:
Hendrickson, D. A.*, A. E. Cohen, B. Labay, F. D. Martin, S. Sarkar, B. Sissel, M. Ciarleglio, J. Harrison, M. Casarez, G. P. Garrett, and R. J. Edwards. The Fishes of Texas Project - Status of Compilation and Standardization of Museum-vouchered Fish Collection Data, Online Database, and Related Research
Labay, B. J.*, A. E. Cohen, F. D. Martin, D. A. Hendrickson, B. Sissel, and S. Sarkar. Assessing the Decline of Barton Creek Fish Community Using Classical Surveys, Historic Data, and Species Distribution Modeling
F. D. Martin*, A. E. Cohen, B. Labay, and D. A. Hendrickson. Combining Historical Data on the Fishes of Texas with Modeling to Evaluate Changes in Ranges of Fish Species in Texas Coastal Prairie Streams
These presentations are all now available from the Texas Chapter AFS website as podcasts.
Though the website had been available to select colleagues and testers prior to Feb 11, 2011, this is the date that we consider to represent the first public release of the website and its database. Much work remains to be done on many aspects of the project, but now many more people can make use of the data and start helping us further improve what we offer here.
posted Mar 20, 2011, 10:24 AM by Dean A. Hendrickson [ updated Feb 29, 2012, 9:43 AM by Ben Labay ]
Until now our database site lacked documentation. Though it will still evolve (comments welcome) today we made our extensive documentation maintained in Google Sites public. You're looking at one page of it now. In getting the documentation online, we tried to make navigation between it and the database as easy as possible.
We also linked, from both the documentation and the database, to our test "Sandbox" pages in Scratch Pad, where we are working on new and improved species accounts and where we will also soon publish new drafts of much-improved identification keys. Please have a look.
In summary, the overall project now consists of three separate, but inter-linked websites. The database is hosted on a high-speed database server that excels in providing such data, and our project is integrated into the University of Texas' Texas Advanced Computing Center (TACC) Supercomputer group's mission to provide high-security and long-term support for such services. Our team finds it much easier to maintain our documentation in Google Sites, where any of us can edit it at any time. Similarly, Scratch Pad's mission, and the services that well supported program provides, give us a comprehensive platform for distributed development (potentially expanding far beyond our immediate team) of improved species account content, keys, bibliography, and much more. Pending continued support for the project we hope to slowly move more content from our current species accounts to here.