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opencc-zeroApr 2024View details →

Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape

Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analyzed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and Salton Sea. We recommend additional lands in the U.S. and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy (RMS). We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change and other long-term impacts.

opencc-zeroJun 2021View details →

Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10+ species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.

opencc-zeroJul 2021View details →

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP dataset, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations, and we found substantial evidence that genetic diversity of lizards differs along the two colonization routes.

opencc-zeroJun 2023View details →

Data for: Thermal refugia and persistence of Texas horned lizards (Phrynosoma cornutum) in small towns

Vegetation loss is a primary cause of habitat degradation and results in a decline in reptile species abundance due to loss of refuge from predators and hot temperatures, and foraging opportunities. Texas horned lizards (Phrynosoma cornutum) have disappeared from many areas in Texas, especially from urbanized areas, probably in large part due to loss of suitable habitat. This species still occurs in some small towns in Texas that still contain suitable habitat. Long-term data from Kenedy and Karnes City, Texas indicate that when study sites experienced significant shrub and vegetation removal horned lizards declined by 79%. We hypothesize the decline was due to the degradation of the thermal landscape for these lizards. We determined the preferred temperature range (Tset25 −Tset75) of lizards at our study sites and took field measurements of body temperature (Tb). Temperature loggers were also placed in three microhabitats across our study sites. Shrubs and vegetation provided the highest quality thermal environment, especially for about 5 hours midday when temperatures in the open and buried under the surface in the open exceeded the lizards' critical maximum temperature (CTmax) or were above their preferred temperature range. Horned lizard density was positively related to the thermal quality of the habitat across our sites. Texas horned lizards in these towns require a heterogeneous mix of closely spaced microhabitats and especially thermal refugia, such as shrubs and vegetation along fence lines and in open fields. Maintaining thermal refugia is one of the most important and practical conservation actions that can be taken to help small ectotherms persist in modified human landscapes and cope with increasing temperatures due to climate change.

publicApr 2024View details →

Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape

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publicFeb 2023View details →

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

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publicJun 2021View details →

Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)

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publicMay 2018View details →

Data from: A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)

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publicJul 2023View details →

Data for: Thermal refugia and persistence of Texas horned lizards (Phrynosoma cornutum) in small towns

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opencc-zeroDec 2014View details →

Data from: Phylogenomics of horned lizards (genus: Phrynosoma) using targeted sequence capture data

New genome sequencing techniques are enabling phylogenetic studies to scale-up from using a handful of loci to hundreds or thousands of loci from throughout the genome. In this study, we use targeted sequence capture (TSC) data from 540 ultraconserved elements and 44 protein-coding genes to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma. Previous molecular phylogenetic analyses of Phrynosoma based on a few nuclear genes, restriction site associated DNA (RAD) sequencing, or mitochondrial DNA (mtDNA) have produced conflicting relationships. Some of these conflicts are likely the result of rapid speciation at the start of Phrynosoma diversification, whereas other examples of gene tree discordance appear to be caused by active and residual traces of hybridization. Concatenation and coalescent-based species tree phylogenetic analyses of these new TSC data support the same topology, and a divergence dating analysis suggests that the Phrynosoma crown group is up to 30 million years old. The new phylogenomic tree supports the recognition of four main clades within Phrynosoma, including Anota (P. mcallii, P. solare, and the P. coronatum complex), Doliosaurus (P. modestum, P. goodei, and P. platyrhinos), Tapaja (P. ditmarsi, P. douglasii, P. hernandesi, and P. orbiculare), and Brevicauda (P. braconnieri, P. sherbrookei, and P. taurus). The phylogeny provides strong support for the relationships among all species of Phrynosoma and provides a robust new framework for conducting comparative analyses.

publicMar 2019View details →

Data from: Is dietary or microhabitat specialization associated with environmental heterogeneity in horned lizards (Phrynosoma)?

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publicJun 2016View details →

Data from: Phylogenomics of horned lizards (genus: Phrynosoma) using targeted sequence capture data

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publicJan 2015View details →

Data from: A new species of horned lizard (genus Phrynosoma) from Guerrero, México, with an updated multilocus phylogeny

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opencc-zeroDec 2016View details →

Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.

opencc-zeroDec 2021View details →

Data from: Thermal physiology responds to interannual temperature shifts in a montane horned lizard, Phrynosoma orbiculare

As climate change marches on, rapidly rising temperatures shatter records every year, presenting ever‐growing physiological challenges to organisms worldwide. Ectotherms rely on behavioral and physiological plasticity to contend with environmental fluctuations. Nonetheless, our understanding of thermal plasticity has been largely limited to laboratory settings. Here, we test whether aspects of thermal physiology respond to interannual shifts in thermal environment in a natural population of Phrynosoma orbiculare, a montane horned lizard, from Hidalgo, Mexico. At our field site, 2019 was markedly warmer than the year that preceded it. We detected population‐level increases in three key thermal physiological traits: preferred temperature, the critical thermal minimum, and the critical thermal maximum. Thus, thermal phenotypes appear to shift in tandem in response to environmental fluctuations. A subset of individuals were resampled across years, allowing insight into plastic shifts within an organism's lifetime. We detected parallel increases in these lizards for the preferred temperature and the critical thermal minimum, but not for the critical thermal maximum. Our results support a growing body of literature indicating that preferred conditions and cold tolerance can be highly labile over the course of an organism's lifetime, whereas hardening over shorter time periods is more common for heat tolerance. Given that heat tolerance increased at the population‐level, but not in resampled individuals, it is possible that rapid evolution occurred due to temperature increases. In short, physiological shifts can be observed in natural populations over relatively short timespans, and these shifts might reflect a combination of evolutionary and acclimatory responses.

opencc-zeroMar 2022View details →

Predation release of Texas horned lizards (Phrynosoma cornutum) living in small towns

Texas horned lizards (Phrynosoma cornutum) have a number of ways to avoid predation, including camouflage, sharp cranial horns, flattening of the body, and the ability to squirt blood from the eyes. These characteristics and their relatively low survival rates in the wild suggests these lizards are under high predation pressure. These lizards have been declining in much of their eastern range due to increased urbanization, agriculture, and loss of prey species. However, they can be still be found in some small south Texas towns where they can reach densities that are much higher (~50 lizards/ha) than in natural areas (~4-10 lizards/ha). We hypothesized that one reason for the high densities observed in these towns may be due to reduced predation pressure. We used model Texas horned lizards to test whether predation levels were lower in two south Texas towns than on a nearby ranch. We constructed models from urethane foam, a material that is ideal for preserving marks left behind by predators. Models (n = 126) and control pieces of foam (n = 21) were left in the field for 9 days in each location in early and late summer and subsequent predation marks were categorized by predator taxa. We observed significantly more predation attempts on the models than on controls and significantly fewer attempts in town (n = 1) compared to the ranch (n = 60). On the ranch, avian predation attempts appear to be common especially when the models did not match the color of the soil. Our results suggest that human modified environments that have suitable habitat and food resources may provide a refuge for some prey species like horned lizards from predators.

publicMar 2022View details →

Predation release of Texas horned lizards (Phrynosoma cornutum) living in small towns

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publicDec 2021View details →

Data from: Thermal physiology responds to interannual temperature shifts in a montane horned lizard, Phrynosoma orbiculare

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