Blog from July, 2021

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 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 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 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.

WHAT'S NEW: Short version (scroll down for longer version)

More and better data

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.

Default user privileges have changed

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.

Web edits and redesign

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.

Increased offerings from our digital library

We've added thousands of new images.

Improved identification keys

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.

Improved species accounts

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.

More research and outreach products

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.

More citizen science opportunities

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.

WHAT'S NEW: Long version

More and better data

Specimen-vouchered

We process our data in “batches” that we call “Tracks”. 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:

• We identified over 2,500 records as spatial or temporal outliers and examined the specimens behind them. About 70% of these proved to be mis-identified and they have now been corrected.
• Over 550 records were re-georeferenced as a result of the verification process.
• Various other data problems were also fixed (users should check back to verify any data they downloaded previously).
• Although we continue to work on our Track 2 data, they are now available in this version for bulk download (see our documentation: Track 2 Data) though are not yet searchable via the site's query functions.

Non-specimen-vouchered data

(for details see our documentation: Addition of Literature and Other Non-vouchered Data Sources)

• Photo-vouchered: We've been developing a small database of photo-vouchered occurrences and recently we setup our own iNaturalist site to allow others to easily contribute their own observations.
• Literature-vouchered: We've long been building a database of occurrences documented in the literature for which supporting specimens are apparently not available. That nascent and evolving database is now available. We hope to expand this database greatly with the help of our community.

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).

Web edits and redesign

• Our original beta web content was distributed across four web servers leading to navigational and management difficulties. Content has now been integrated onto two servers (one with three subdomains) and we've improved how the websites interact to improve user experience.
• Our now greatly improved and expanded documentation continues to be hosted on Google Sites, but navigation between it and the rest of the site has been improved by nesting documentation within our 'About' tab.
• Tool tips, visible when one mouses over the icons strategically scattered throughout most content provide instant help.
• Our "Maps" tab has been improved by having what we consider to be 'suspect' records (geographical outliers or potentially erroneous identifications) now appear in red and verified identifications in green.
• Our redesigned specimen detail pages now have additional data fields and notes regarding data edits done by project staff (mostly related to specimen re-determinations and georeferencing).
• Added time-lapse distribution map videos on each of our species account (taxon) pages that allow users to view the changing specimen-based distributions over time and includes a link to specimen records so that users can easily peruse the data.
• Our 'checklist' tab has been redesigned to become a more comprehensive entry point to website content. Here users can not only get lists for the whole state or diverse political and natural sub-regions, but they can also search for any species (using [CTRL] + F and enter all or part of genus, species or common names). Most species in these lists are linked to species accounts.
• The old version of our website is still available and is now archived here.
• The "Donate" tab is totally new - please use it!

Increased offerings from our digital library

We have added lots more images including:

• 1,199 field notes.
• 414 live, in situ photos of species in natural habitats by Garold Sneegas.
• 723 magnified images of poeciliids including gonopodia by Brian Langerhans and F. Douglas Martin.
• 2,485 specimen images.
• 229 x-rays.

Improved identification keys

• New illustrated dichotomous key to Poeciliidae of Texas.
• Hubbs et al 2008 checklist key with hyperlinks.
• Interactive Lucid 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.

More research and outreach products

Species Distribution Models

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.

Bioassessment analyses

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.

More citizen science opportunities

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.

What to look for in future versions

• We continue working on our data and verifications of suspect records from track 1 and 2 are still underway.
• The track 3 data set is growing rapidly and currently includes well over 7,500 lots recently added by the Texas Natural History Collection (our own collection) by the Texas Parks and Wildlife Department and others, as well as collection growth at other institutions. Inquire with us if you are interested in this dataset.
• Track 2 data will be fully incorporated into our database and available via our query page.
• Improvements to appearance of some pages.
• Addition of locality photos.
• Improvement of species accounts.
• Inclusion of additional data including government aquatic biodiversity databases and stream water quality databases.
• Additional research and research products including.
  • Improved Species Distribution Models derived from occurrences linked to GIS-friendly NHDPlus flowlines.
  • Strategic Conservation Area Planning analyses in collaboration with TPWD and USFWS Landscape Conservation Cooperatives.

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.