Explanipedia

Parallel sensory compensation following independent subterranean colonization by groundwater salamanders ( Eurycea ) Open

Ruben U. Tovar, Brittany A. Dobbins, Nicholas R. Hartman, Sheena A. Leelani, Thomas J. Devitt , et al. · 2025

Lineages that have invaded subterranean environments have repeatedly evolved remarkable adaptations to life in darkness. However, observational and experimental studies in additional natural systems are needed to further our understanding …

Distinguishing species boundaries from geographic variation Open

E. Anne Chambers, José Daniel Lara-Tufiño, Gustavo Campillo-García, Antonio Yolocalli Cisneros-Bernal, Daniel J. Dudek , et al. · 2025

In an era of unprecedented biodiversity loss, the need for standardized practices to describe biological variation is becoming increasingly important. As with all scientific endeavors, species delimitation needs to be explicit, testable, a…

PAX6 protein in neuromasts of the lateral line system of salamanders (Eurycea) Open

Brittany A. Dobbins, Ruben U. Tovar, Braden J. Oddo, C Teague, Nisa A. Sindhi , et al. · 2024

PAX6 is well known as a transcription factor that drives eye development in animals as widely divergent as flies and mammals. In addition to its localization in eyes, PAX6 expression has been reported in the central nervous system, the pan…

Specimen collection is essential for modern science Open

Michael W. Nachman, Elizabeth J. Beckman, Rauri C. K. Bowie, Carla Cicero, Chris J. Conroy , et al. · 2023

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying w…

PAX6 protein in neuromasts of the lateral line system of salamanders (Eurycea) Open

Brittany A. Dobbins, Ruben U. Tovar, Braden J. Oddo, Thomas J. Devitt, David M. Hillis , et al. · 2023

PAX6 is well known as a transcription factor that drives eye development in animals as widely divergent as flies and mammals. In addition to its localization in eyes, PAX6 expression has been reported in the central nervous system, the pan…

Coevolution With Host Fishes Shapes Parasitic Life Histories in a Group of Freshwater Mussels (Unionidae: Quadrulini). Open

Sakina Neemuchwala, Nathan A. Johnson, John M. Pfeiffer, Manuel Lopes‐Lima, André Gomes‐dos‐Santos , et al. · 2023

Ecological interactions among species often lead to parasitic lineages coevolving with host resources, which is often suggested as the primary driver of parasite diversification. Freshwater mussels are bivalves that possess a parasitic lif…

2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics Open

E. Anne Chambers, Rebecca D. Tarvin, Juan C. Santos, Santiago R. Ron, Mileidy Betancourth‐Cundar , et al. · 2023

Restriction‐site‐associated DNA sequencing (RADseq) has become an accessible way to obtain genome‐wide data in the form of single‐nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods in…

A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance Open

Chase H. Smith, Brendan J. Pinto, Mark Kirkpatrick, David M. Hillis, John M. Pfeiffer , et al. · 2023

In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male m…

The highest-elevation frog provides insights into mechanisms and evolution of defenses against high UV radiation Open

Tingting Fu, Yan-Bo Sun, Wei Gao, Chengbo Long, Chunhua Yang , et al. · 2022

Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains la…

A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance Open

Chase H. Smith, Brendan J. Pinto, Mark Kirkpatrick, David M. Hillis, John M. Pfeiffer , et al. · 2022

In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to these assumptions is called doubly uniparental inheritance (DUI): a phenomenon involving the independent transmission of female and m…

The highest-elevation frog provides insights into mechanisms and evolution of defenses against high ultraviolet radiation Open

Tingting Fu, Yan-Bo Sun, Wei Gao, Chengbo Long, Chunhua Yang , et al. · 2022

Defense against increasing ultraviolet radiation (UV) exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV-defense mechanisms…

Genomic adaptations for arboreal locomotion in Asian flying treefrogs Open

Wei Wu, Yue‐Dong Gao, Dechun Jiang, Juan Lei, Jin‐Long Ren , et al. · 2022

Significance To adapt to arboreal lifestyles, treefrogs have evolved a suite of complex traits that support vertical movement and gliding, thus presenting a unique case for studying the genetic basis for traits causally linked to vertical …

Contemporary Methods and Evidence for Species Delimitation Open

David M. Hillis, E. Anne Chambers, Thomas J. Devitt · 2021

Over the last two decades, mitochondrial DNA (mtDNA) sequence data, as well as analyses of nuclear DNA based on the multispecies coalescent model, have increasingly been used to delimit species, sometimes based on limited sampling and with…

Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification Open

Wei Xu, Wenjie Dong, Tingting Fu, Wei Gao, Chen-Qi Lu , et al. · 2020

The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. The Himalayan region is a relatively small area but with exceptional divers…

The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa Open

E. Anne Chambers, David M. Hillis · 2019

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic cha…

Asymmetric biotic interchange across the Bering land bridge between Eurasia and North America Open

Dechun Jiang, Sebastian Klaus, Ya‐Ping Zhang, David M. Hillis, Jia‐Tang Li · 2019

The exchange of biotas between Eurasia and North America across the Bering land bridge had a major impact on ecosystems of both continents throughout the Cenozoic. This exchange has received particular attention regarding placental mammals…

Species Delimitation in Herpetology Open

David M. Hillis · 2019

The discovery and delimitation of species has changed dramatically over time. Species delimitation practices became more thorough and formal in the 1900s with the introduction of detailed studies of geographic variation, contact zones, and…

Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity Open

Wei Gao, Yanbo Sun, Weiwei Zhou, Zijun Xiong, Luonan Chen , et al. · 2019

Viviparous (live-bearing) vertebrates have evolved repeatedly within otherwise oviparous (egg-laying) clades. Over two-thirds of these changes in vertebrate reproductive parity mode happened in squamate reptiles, where the transition has h…

Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation Open

Thomas J. Devitt, April Wright, David C. Cannatella, David M. Hillis · 2019

Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards–Trinity aquifer sys…

Genome Open

Jürgen Markl, David Sadava, David M. Hillis, H. Craig Heller, Sally D. Hacker · 2019

Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations Open

Yanbo Sun, Tingting Fu, Jie‐Qiong Jin, Robert W. Murphy, David M. Hillis , et al. · 2018

Although many cases of genetic adaptations to high elevations have been reported, the processes driving these modifications and the pace of their evolution remain unclear. Many high-elevation adaptations (HEAs) are thought to have arisen i…

Comparative genomic investigation of high-elevation adaptation in ectothermic snakes Open

Jia‐Tang Li, Yue‐Dong Gao, Liang Xie, Cao Deng, Peng Shi , et al. · 2018

Significance Snakes of the genus Thermophis are endemic to the Tibetan plateau and occur at elevations over 3,500 m and present an opportunity to study the genetics mechanisms of adaptation to high-elevation conditions in ectotherms. Here,…

Rana Supplementary Tables Open

Zhi-Yong Yuan, Wei-Wei Zhou, Xin Chen, Jr. Nikolay Poyarkov, Hong-Man Chen , et al. · 2016

Rana Yuan Nexus file Open

Zhi-Yong Yuan, Wei-Wei Zhou, Xin Chen, Jr. Nikolay Poyarkov, Hong-Man Chen , et al. · 2016

Rana Supplementary Figures Open

Zhi-Yong Yuan, Wei-Wei Zhou, Xin Chen, Jr. Nikolay Poyarkov, Hong-Man Chen , et al. · 2016

Presentation: How a Salamander Saved a City: The Science and Politics of Endangered Species Open

David M. Hillis · 2016

How are endangered species discovered? How can they save a city? Barton Springs is a resource unique to Austin drawing thousands of visitors every year. Yet, Barton Springs is home to endangered species of salamanders rarely seen by the pu…

Complex Homology and the Evolution of Nervous Systems Open

Benjamin J. Liebeskind, David M. Hillis, Harold H. Zakon, Hans A. Hofmann · 2015

How do SNP ascertainment schemes and population demographics affect inferences about population history? Open

Emily Jane McTavish, David M. Hillis · 2015

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes Open

Yan-Bo Sun, Zijun Xiong, Xueyan Xiang, Shiping Liu, Wei-Wei Zhou , et al. · 2015

Significance We provide a de novo genome of the Tibetan frog, Nanorana parkeri , and conduct a series of comparisons with other vertebrates. Approximately one-half of the genome of Nanorana consists of transposable elements (TEs). The freq…

Convergence of ion channel genome content in early animal evolution Open

Benjamin J. Liebeskind, David M. Hillis, Harold H. Zakon · 2015

Significance The early evolution of animal nervous systems is poorly understood, but comparative genomics provides a new window into the past. One important controversy is about whether nervous systems evolved just once or independently in…

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