How a Salamander Saved a City: the Politics and Science of Endangered Species

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How a Salamander Saved a City:

The Politics and Science of Endangered Species

Dr. David Hillis April 22, 2016

Produced by and for Hot Science - Cool T a lks by the Environmental Science Institute. We request that the use of these materials include an acknowledgement of the presenter and Hot Science - Cool T a lks by the Environmental Science Institute at UT Austin. We hope you find these materials educational and enjoyable.

How a Salamander Saved a City

The Politics and Science of
Endangered
Species
David M. Hillis
The University of

Texas at Austin

April 22, 2016

If you could return to 1990 from today,

how would you advise Austin’s City

Council about the future?

Economic development Population growth
Water supply protection Increase green spaces, parks & wild areas

“For fifth

year, 5-county

area is U.S.’s

fastest

growing…”

Austin American

Statesman (2016)

Why is Austin on nearly every

Top-Ten list as a place to live?

Quality of Life
Excellent entertainment

Strong economy
Great parks and

recreation
Vibrant diverse city

“Weirdness” factor

Image Courtesy of Save Our Springs (2016)

What are the top complaints about Austin?

. Traffic
. Weather

. Crowds
. Allergies

. Cost of living
. Water shortages

Colorado River drought
KUT (2014)

Austin

San Antonio

Settlement of Central Texas

Salado
Georgetown
Austin

San Marcos

Springs
Edwards aquifer

New Braunfels
San Antonio

Del Rio

Brackettville

Uvalde

Sharp (2003) Hot Science – Cool Talks

Then and Now…

Salado Springs Today
What Salado Springs looked like in the 1870s

Artesian Springs and Wells

The Edwards Aquifer

Drainage zone Recharge zone

Artesian zone

Musgrove (2000)

Musgrove et al. (2001)

Central Texas is a biodiversity hot spot

Typical Terrestrial
Salamander sent to

Salamander

Stejneger in 1896

Plethodon albagula,
Eurycea rathbuni,

White-throated Slimy Salamander
Texas Blind Salamander

Salamanders in Texas

Texas Spring
Salamander

Eurycea neotenes

Discovered in 1937 by Bishop & Wright

San Marcos

Salamander

Discovered in 1941 by Bishop

Eurycea nana

Barton Springs

Image Courtesy of

Save Our Springs

Barton Springs

Image Courtesy of

Save Our Springs (2016)

Ideal Model Organisms

Texas Spring and Cave
Salamanders

(e.g., fruit flies, yeast, bacteria)

. Abundant
. Endangered and rarely seen

. Difficult to raise
. Easily cultured

. Easy to collect and observe

. No permits required

. Difficult to collect & observe

. Many permits & regulations

. Rapid growth, short
. Slow growth, long

generation time
generation time

. Small, easily sampled
. Giant genome; no genome

genome
sequenced

Barton Springs

Image Courtesy of

Save Our Springs

What is an Endangered Species?

. Endangered Species Act
(ESA) created in 1973

. A species likely to become extinct throughout all or a large portion of its range

. Receives special protections by federal government to help it recover

. Must be evaluated and meet certain criteria to be listed

as “endangered”

Late 1980s…

. Pool cleaning methods nearly eliminate salamanders

. “Liaison Committee” created between city and UT to develop “salamander friendly” cleaning methods

Memorabilia from

conservation groups

New methods

adopted to clean Barton Springs Pool

Recommended publications

Profile of David M. Hillis

Proﬁle of David M. Hillis hilippe Padieu was called a mod- down through the maternal line. However, ern-day Casanova. Women said both types of analyses had their short- Pthey were drawn to him for his comings: chloroplast DNA analysis was sweet personality and charm. restricted to plants, and mtDNA evolves However, Padieu harbored a secret. In so quickly that it was best suited for 2009, he was found guilty of aggravated reconstructing relatively recent di- assault for purposefully infecting six vergence events. So Hillis looked to nu- women with HIV and sentenced to 45 clear ribosomal DNA, as well as nuclear- years in prison. Credit for Padieu’s guilty encoded proteins, to reconstruct the verdict goes partly to David Hillis, an evolutionary history of amphibians. The evolutionary biologist at the University results revealed enormous hidden di- of Texas at Austin. versity among morphologically similar Hillis, elected to the National Academy amphibians (2, 3). Rather than throwing of Sciences in 2008, has devoted his re- out centuries of morphological work, search career to phylogeny, the study of however, Hillis worked to integrate mo- evolutionary relationships. His work tack- lecular and morphological studies of les some of the greatest questions of evo- phylogeny (4). lutionary biology: How do species arise? Soon Hillis turned his attention to how How do genes diversify and acquire new individual genes evolve and diversify. For functions? How do pathogens evolve, and instance, when Hillis and his colleagues how can that information be used to un- studied the evolution of the ZFY gene, derstand diseases? And ultimately, can we then thought to trigger male development reconstruct the complete Tree of Life and in mammals, they found that the gene was use that information to help make pre- unrelated to sex determination in reptiles dictions about biology? (5).
W.H. Freeman & Co (C) 2018

Principles of Life THIRD EDITION 2018 (c) SAMPLE CHAPTERS INSIDE 5: Cell Metabolism: Synthesis and Degra dation of Biological Molecules Co 14: Reconstructing and Using Phylogenies& Freeman David M. Hillis Mary V. Price RichardW.H. W. Hill David W. Hall Marta J. Laskowski Principles of Life—The New Edition Because success as a biologist means more than just succeeding in the first biology course. For instructors concerned that the practical skills of biology are lost when the student moves on to the next course or takes their first step into the “real world,” Principles of Life, Third Edition lays the foundation for later courses and for students’ careers. Expanding on its pioneering concept-driven approach, experimental data-driven exercises, and active learning focus, the new edition introduces features designed to involve students in mastering concepts and becoming skillful at solving biological problems. Research shows that when students engage with a course, it leads to better outcomes. Principles of Life, Third Edition is a holistic solution that has been designed from the ground up to actively engage students in mastering concepts and becoming skilled at solving biological problems. Within LaunchPad, our digital teaching and learning solution, we provide thoughtfully curated assignments and activities to support pre-lecture preparation, classroom activities, and post-lecture assessment. 2018 With its focus on key competencies foundational to biology education and careers, self-guided adaptive learning, and unparalleled instructor resources for active classrooms, Principles of Life is the resource students need to succeed. A FOCUS ON (c) SKILLS AND CORE COMPETENCIES New to this edition, the AAAS Vision and Change report’s six “core competencies” related to quantitative reasoning, simulation, and communication, are integrated both implicitly throughout the text and explicitly in a new Cokey feature, Think Like a Scientist.
REDISCOVERING BIOLOGY Evolution and Molecular to Global Phylogenetics Perspectives

REDISCOVERING BIOLOGY Evolution and Molecular to Global Phylogenetics Perspectives “Systems of classification are not hat racks, objectively presented to us by nature. They are dynamic theories developed by us to express particular views about the history of organisms. Evolution has provided a set of unique species ordered by differing degrees of genealogical relationship. Taxonomy, the search for this natural order, is the fundamental science of history.” STEPHEN J GOULD 1 Perhaps the most striking feature of life is its enormous diversity. There are more than one million described species of animals and plants, with many millions still left undescribed. (See the Biodiversity unit.) Aside from its sheer numerical diversity, organisms differ widely and along numerous dimensions — including morphological appearance, feeding habits, mating behaviors, and physiologies. In recent decades, scientists have also added molecular genetic differences to this list. Some groups of organisms are clearly more similar to some groups than to others. For instance, mallard ducks are more similar to black ducks than either is to herons. At the same time, some groups are very similar along one dimension, yet strikingly different in other respects. Based solely on flying ability, one would group bats and birds together; however, in most other respects, bats and birds are very dissimilar. How do biologists organize and classify biodiversity? In recent decades, methodological and technological advances have radically altered how biologists classify organisms
Biogeography, Phylogeny, and Morphological Evolution of Central Texas Cave and Spring Salamanders

Biogeography, phylogeny, and morphological evolution of central Texas cave and spring salamanders Bendik et al. Bendik et al. BMC Evolutionary Biology 2013, 13:201 http://www.biomedcentral.com/1471-2148/13/201 Bendik et al. BMC Evolutionary Biology 2013, 13:201 http://www.biomedcentral.com/1471-2148/13/201 RESEARCH ARTICLE Open Access Biogeography, phylogeny, and morphological evolution of central Texas cave and spring salamanders Nathan F Bendik1,2*, Jesse M Meik3, Andrew G Gluesenkamp4, Corey E Roelke1 and Paul T Chippindale1 Abstract Background: Subterranean faunal radiations can result in complex patterns of morphological divergence involving both convergent or parallel phenotypic evolution and cryptic species diversity. Salamanders of the genus Eurycea in central Texas provide a particularly challenging example with respect to phylogeny reconstruction, biogeography and taxonomy. These predominantly aquatic species inhabit karst limestone aquifers and spring outflows, and exhibit a wide range of morphological and genetic variation. We extensively sampled spring and cave populations of six Eurycea species within this group (eastern Blepsimolge clade), to reconstruct their phylogenetic and biogeographic history using mtDNA and examine patterns and origins of cave- and surface-associated morphological variation. Results: Genetic divergence is generally low, and many populations share ancestral haplotypes and/or show evidence of introgression. This pattern likely indicates a recent radiation coupled with a complex history of intermittent connections within the aquatic karst system. Cave populations that exhibit the most extreme troglobitic morphologies show no or very low divergence from surface populations and are geographically interspersed among them, suggesting multiple instances of rapid, parallel phenotypic evolution. Morphological variation is diffuse among cave populations; this is in contrast to surface populations, which form a tight cluster in morphospace.
Biogenesis Providing an Evolutionary

Providing an evolutionary framework for biodiversity science GENESIS bio bioGENESIS Science Plan and Implementation Strategy ICSU IUBS SCOPE UNESCO DIVERSITAS Report N°6, bioGENESIS Science Plan and Implementation Strategy © DIVERSITAS 2009 – ISSN: 1813-7105 ISBN: 2-9522982-7-0 Suggested citation: Michael J. Donoghue, Tetsukazu Yahara, Elena Conti, Joel Cracraft, Keith A. Crandall, Daniel P. Faith, Christoph Häuser, Andrew P. Hendry, Carlos Joly, Kazuhiro Kogure, Lúcia G. Lohmann, Susana A. Magallón, Craig Moritz, Simon Tillier, Rafael Zardoya, Anne-Hélène Prieur-Richard, Anne Larigauderie, and Bruno A. Walther. 2009. bioGENESIS: Providing an Evolutionary Framework for Biodiversity Science. DIVERSITAS Report N°6. 52 pp. © A Hendry Cover images credits: J Cracraft, C Körner, B A Walther, D M Hillis, D Zwickl, and R Gutell Contact address Michael J. Donoghue, PhD Department of Ecology and Evolutionary Biology Yale University 21 Sachem Street P.O. Box 208105 New Haven, CT 06520-8105, USA Tel: +1-203-432-2074 Fax: +1-203-432-5176 Email: [email protected] Tetsukazu Yahara, PhD Department of Biology Faculty of Sciences Kyushu University Hakozaki 6-10-1 812-8581 Fukuoka, Japan Tel: +81-92-642-2622 Fax: +81-92-642-2645 Email: [email protected] www.diversitas-international.org © J Cracraft Providing an evolutionary framework for biodiversity science bioGENESIS bioGENESIS Science Plan and Implementation Strategy Authors: Michael J. Donoghue, Tetsukazu Yahara, Elena Conti, Joel Cracraft, Keith A. Crandall, Daniel P. Faith, Christoph Häuser, Andrew P. Hendry, Carlos Joly, Kazuhiro Kogure, Lúcia G. Lohmann, Susana A. Magallón, Craig Moritz, Simon Tillier, Rafael Zardoya, Anne-Hélène Prieur-Richard, Anne Larigauderie, and Bruno A.
David Cannatella

CURRICULUM VITAE 1 JAN 2017 David Cannatella Department of Integrative Biology 1 University Station C0990 University of Texas Austin, TX 78712 [email protected] orcid ID: 0000-0001-8675-0520 EDUCATION 1972-76 University of Southwestern Louisiana BS, Zoology, magna cum laude, 1976. 1976-85 University of Kansas MA, Systematics and Ecology, 1979. MPh, Systematics and Ecology, 1981. PhD, Systematics and Ecology, 1985 with honors. Linda Trueb, advisor. 1986-88 University of California, Berkeley Postdoctoral Fellow, David Wake and Marvalee Wake, advisors. PROFESSIONAL EXPERIENCE 2014- Associate Chairman for Biodiversity Collections, Department of Integrative Biology. 2007- Professor, Department of Integrative Biology, University of Texas. 2005-2007 Associate Professor, Section of Integrative Biology, University of Texas. 2001-2004 Assistant Professor, Section of Integrative Biology, University of Texas. 1995-2000 Senior Lecturer, Department of Zoology (now Department of Integrative Biology), University of Texas. 1990- Curator, Texas Memorial Museum, University of Texas. 1988-90 Assistant Professor and Curator, Museum of Natural Science and Dept. Zoology and Physiology, Louisiana State University, Baton Rouge. 1986-88 NSF Postdoctoral Fellow, University of California, Berkeley. 1986 Visiting Lecturer, Department of Zoology, University of California, Berkeley. Lecturer for Zoology 106: Evolutionary and Functional Vertebrate Morphology. Assistant Research Zoologist, Museum of Vertebrate Zoology, University of California, Berkeley. Curation of herpetological collections. 1984-85 Dissertation Fellow, University of Kansas (KU). 1983 Part-time Faculty, Penn Valley Community College, Kansas City, Missouri. MAJOR AWARDS Big XII Faculty Fellow, 2015. Chair's Fellow, Department of Integrative Biology, 2014. Fulbright Scholar to Brasil, 2011-2012. Curriculum Vitae Cannatella President, Society of Systematic Biologists, 2004-2005.
Response to the Point of View of Gregory B. Pauly, David M

Herpetologica, 65(2), 2009, 136–153 E 2009 by The Herpetologists’ League, Inc. RESPONSE TO THE POINT OF VIEW OF GREGORY B. PAULY, DAVID M. HILLIS, AND DAVID C. CANNATELLA, BY THE ANURAN SUBCOMMITTEE OF THE SSAR/HL/ASIH SCIENTIFIC AND STANDARD ENGLISH NAMES LIST 1,4 2 3 DARREL R. FROST ,ROY W. MCDIARMID , AND JOSEPH R. MENDELSON, III 1Division of Vertebrate Zoology (Herpetology), American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA 2US Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, MRC 111, P.O. Box 37012, Washington, DC 20013-7012, USA 3Zoo Atlanta, 800 Cherokee Avenue Southeast, Atlanta, GA 30315, USA ‘‘Stultum facit Fortuna quem vult perdere’’—Publilius Syrus, Maxim 911 ABSTRACT: The Point of View by Gregory Pauly, David Hillis, and David Cannatella misrepresents the motives and activities of the anuran subcommittee of the Scientific and Standard English Names Committee, contains a number of misleading statements, omits evidence and references to critical literature that have already rejected or superseded their positions, and cloaks the limitations of their nomenclatural approach in ambiguous language. Their Point of View is not about promoting transparency in the process of constructing the English Names list, assuring that its taxonomy is adequately reviewed, or promoting nomenclatural stability in any global sense. Rather, their Point of View focuses in large part on a single publication, The Amphibian Tree of Life, which is formally unrelated to the Standard English Names List, and promotes an approach to nomenclature mistakenly asserted by them to be compatible with both the International Code of Zoological Nomenclature and one of its competitors, the PhyloCode.
Profile of David M. Hillis

PROFILE Proﬁle of David M. Hillis hilippe Padieu was called a mod- down through the maternal line. However, ern-day Casanova. Women said both types of analyses had their short- Pthey were drawn to him for his comings: chloroplast DNA analysis was sweet personality and charm. restricted to plants, and mtDNA evolves However, Padieu harbored a secret. In so quickly that it was best suited for 2009, he was found guilty of aggravated reconstructing relatively recent di- assault for purposefully infecting six vergence events. So Hillis looked to nu- women with HIV and sentenced to 45 clear ribosomal DNA, as well as nuclear- years in prison. Credit for Padieu’s guilty encoded proteins, to reconstruct the verdict goes partly to David Hillis, an evolutionary history of amphibians. The evolutionary biologist at the University results revealed enormous hidden di- of Texas at Austin. versity among morphologically similar Hillis, elected to the National Academy amphibians (2, 3). Rather than throwing of Sciences in 2008, has devoted his re- out centuries of morphological work, search career to phylogeny, the study of however, Hillis worked to integrate mo- evolutionary relationships. His work tack- lecular and morphological studies of les some of the greatest questions of evo- phylogeny (4). lutionary biology: How do species arise? Soon Hillis turned his attention to how How do genes diversify and acquire new individual genes evolve and diversify. For functions? How do pathogens evolve, and instance, when Hillis and his colleagues how can that information be used to un- studied the evolution of the ZFY gene, derstand diseases? And ultimately, can we then thought to trigger male development reconstruct the complete Tree of Life and in mammals, they found that the gene was use that information to help make pre- unrelated to sex determination in reptiles dictions about biology? (5).
Phylogenetic Systematics, Historical Biogeography, and the Evolution of Vocalizations in Nearctic Toads (Bufo)

The Dissertation Committee for Gregory Blair Pauly Certifies that this is the approved version of the following dissertation: Phylogenetic Systematics, Historical Biogeography, and the Evolution of Vocalizations in Nearctic Toads (Bufo) Committee: David C. Cannatella, Co-Supervisor David M. Hillis, Co-Supervisor James J. Bull Michael J. Ryan Robin R. Gutell Phylogenetic Systematics, Historical Biogeography, and the Evolution of Vocalizations in Nearctic Toads (Bufo) by Gregory Blair Pauly, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2008 Dedication To my parents, Matthew and Georgia, for many years of support and encouragement. Acknowledgements Many people have contributed to my dissertation research and to the earlier path that brought me to this point. First, I thank my parents, Matthew and Georgia, for their lifelong support and constant encouragement of my interests in science, the outdoors, and all things herpetological. I also thank my sister, Sara, and extended family for their encouragement. My family's appreciation of education, hard work, and the natural world has strongly influenced my career choices and contributed to my love of biology. I am truly grateful to the research opportunities provided to me by Brad Shaffer and Arthur Shapiro during my undergraduate career. Their mentorship was critical to my development as an academic biologist. In particular, in my first month as an undergraduate researcher in Brad Shaffer's lab, I went from a stressed out senior with no idea of what I would do after graduating to knowing what I would do for the rest of my life.
DNA in Hollywood: Fact, Fiction And

Hot Science - Cool Talk # 49 DNA in Hollywood: Fact, Fiction, and Future Dr. David Hillis September 14, 2007 Produced by and for Hot Science - Cool Talks by the Environmental Science Institute. We request that the use of these materials include an acknowledgement of the presenter and Hot Science - Cool Talks by the Environmental Science Institute at UT Austin. We hope you find these materials educational and enjoyable. DNA in Hollywood Fact, Fiction, and Future David M. Hillis Section of Integrative Biology & Center for Computational Biology The University of Texas at Austin CSI clip Phylogenetic analysis can be used to trace viral infections through a human population • Origins of HIV, SARSand other viruses transmitted between animals and humans • Global virus diversity for vaccine trials • Epidemiological studies • Identification of new diseases • Forensic uses Phylogeny Papers, 1981-2006 (with “phylogeny” or “phylogenetic” in title or abstract) 9000 8000 7000 6000 5000 4000 3000 2000 Number of papers per year 1000 0 1980 1985 1990 1995 2000 2005 Year of publication Phylogeny Evolutionary relationships among lineages, such as genes, individuals, populations, species, etc. Time Consider an ancestral lineage (e.g., descendants from one HIV virus) Phylogeny Evolutionary relationships among lineages, such as genes, individuals, populations, species, etc. Time One lineage splits into two by mutation Phylogeny Evolutionary relationships among lineages, such as genes, individuals, populations, species, etc. Time There are now two HIV lineages Phylogeny Evolutionary relationships among lineages, such as genes, individuals, populations, species, etc. Some lineages become extinct x Time Lineages continue to diversify through time Phylogeny Evolutionary relationships among lineages, such as genes, individuals, populations, species, etc.
No Slide Title

Hot Science - Cool Talk # 9 Hotspot of Biodiversity: Unique and Endangered Animals of Central Texas Dr. David Hillis November 17, 2000 Produced by and for Hot Science - Cool Talks by the Environmental Science Institute. We request that the use of these materials include an acknowledgement of the presenter and Hot Science - Cool Talks by the Environmental Science Institute at UT Austin. We hope you find these materials educational and enjoyable. HotspotHotspotTitle slide ofof Biodiversity:Biodiversity Unique and Endangered Animals of Central Texas Dr. David M. Hillis 1 Lost Biodiversity Jaguar: “Lost Biodiversity” 2 Texas Blind Salamander: “Endangered Species” EndangeredEndangered SpeciesSpecies 3 New Discoveries New Gambusia: “New Discoveries” 4 Rolling Blackland Plains Texas map Tallgrass Cross Timbers Prairies and Prairies High Plains Post Oak Savannah East Texas Pineywoods Trans-Pecos Mountains and Basins Edwards Plateau Gulf Coast Prairies and Marshes South Texas Tamaulipan Thorn Scrub 5 CentralCentral TexasTexas Central Texas, zoom-in Austin 6 LandLand DevelopmentDevelopment // HabitatHabitat DestructionDestruction Comp: frog, ant, salamander, clam, vireo IntroducedIntroduced SpeciesSpecies WaterWater Use:Use: LossLoss ofof AquifersAquifers andand SpringsSprings WaterWater Pollution:Pollution: DegradationDegradation ofof RiversRivers EffectsEffects ofof AgricultureAgriculture 7 HabitatHabitat DestructionDestruction Houston Toad: “Habitat destruction” 8 Breeding Pond 9 Habitat: Lost Pines 10 Habitat loss 11 New: development 12 B. houstonensis x B. woodhousii (amplexus) 13 B. houstonensis x B. valliceps 14 Sound for Mac Click once, with cursor on image, to activate sound. Houston Toad (Bufo houstonensis) Sound for PC: Double click here A warning may come up about viruses. Just click OK. The sound called: 15.b. houst.sing.47.11k.aiffhoust.sing.47.11k.aiff,, does not play in Adobe Acrobat.
Longhorn Legacy: Surprising Origins of Columbus' Cattle Found

3/26/13 Origins of Columbus' Cattle Revealed | Evolution | LiveScience Follow Us: Like 301k Follow @livescience Search Home Space Animals Health Environment Technology Culture History Strange News Quizzes Video Images Topics Shop Album: Animals' Dazzling Headgear Dry and Dying: Images of Drought Image Gallery: 25 Amazing Ancient Beasts Article: Longhorn Legacy: Surprising Origins of Columbus' Cattle Found Tia Ghose, LiveScience Staff Writer Date: 25 March 2013 Time: 03:00 PM ET Recommend 163 www.livescience.com/28154-new-world-cattle-origins.html 1/6 3/26/13 Origins of Columbus' Cattle Revealed | Evolution | LiveScience Tweet 9 0 Sharre 1 The first cows brought to the Americas by explorer Christopher Columbus originated from two extinct wild beasts from India and Europe, a new genetic analysis shows. Because the breeds analyzed, including the longhorn, have been closely connected to humans, the results could shed light on human migration over the past 10,000 years, said study co-author Emily Jane McTavish, an evolutionary biology doctoral candidate at the University of Texas at Austin, whose mascot is the longhorn cow. The findings were published today (March 25) in the New world breeds, such as the Texas journal Proceedings of the National Academy of longhorn, derived from two separate Sciences. lineages originating in Europe and India, new research suggests Wild beasts CREDIT: David Hillis View full size image About 10,000 years ago, ancient people domesticated cows from wild aurochs (bovines that are 1.5 to two times as big as domestic cattle) in two separate events, one in the Indian subcontinent and one in Europe.