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Identifying how natural (i.e., unaltered by human activity) and anthropogenic landscape variables influence contemporary functional connectivity in terrestrial organisms can elucidate the genetic consequences of environmental change. We examine population genetic structure and functional connectivity among populations of a declining species, the Blainville's horned lizard (Phrynosoma blainvillii), in the urbanized landscape of the Greater Los Angeles Area in Southern California, USA. Using single nucleotide polymorphism data, we assessed genetic structure among populations occurring at the interface of two abutting evolutionary lineages, and at a fine scale among habitat fragments within the heavily urbanized area. Based on the ecology of P. blainvillii, we predicted which environmental variables influence population structure and gene flow and used gravity models to distinguish among hypotheses to best explain population connectivity. Our results show evidence of admixture between two evolutionary lineages and strong population genetic structure across small habitat fragments. We also show that topography, microclimate, and soil and vegetation types are important predictors of functional connectivity, and that anthropogenic disturbance, including recent fire history and urban development, are key factors impacting contemporary population dynamics. Examining how natural and anthropogenic sources of landscape variation affect contemporary population genetics is critical to understanding how to best manage sensitive species in a rapidly changing landscape. [ABSTRACT FROM AUTHOR]

Abstract 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 suggest 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 with 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.

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.

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 suggest 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 with 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. [ABSTRACT FROM AUTHOR]

Global climate change involves both prolonged periods of higher‐than‐normal temperatures and short but extreme heat waves. Both types of temperature increases are likely to be detrimental to ectotherms, and even if such temperature increases do not cause mortality directly, compensating for such temperature increases will likely entail costs to organisms. We tested the effects of prolonged periods of higher‐than‐average temperatures and short‐term, acute heat stress in wild populations of greater short‐horned lizards (Phrynosoma hernandesi), a temperate, montane lizard of the Colorado Plateau, UT, USA. We transplanted one group of lizards from a high‐ to a low‐elevation site, exposing them to a prolonged period of warmer temperatures. These lizards, exposed to prolonged periods of higher‐than‐average temperatures, experienced no change in sprint speed, endurance, or heat shock protein (HSP) production after treatment compared to baseline levels; however, they had lower water content after the transplant to a warmer climate compared to before the transplant. We exposed a second group of lizards to acute heat stress by exposing them to thermally stressful temperatures for 4 h. These lizards, exposed to a short period of acute heat stress, had no change in endurance, water content, or HSP production following acute heat stress; however, lizards exposed to acute heat stress had slower sprint speeds than control lizards. Our results demonstrate that both prolonged temperature increases and acute heat stress, each of which are predicted to occur with climate change, had different cellular and/or whole organismal‐level effects on lizards. Highlights: Lizards exposed to a prolonged period of higher‐than‐normal temperature showed decreased tissue water content compared to control animals. In contrast, lizards exposed to brief, acute heat stress had slower sprint speeds than control lizards. [ABSTRACT FROM AUTHOR]

Wildlife translocation is an often-used technique to augment populations or remove animals from harm’s way. Unfortunately, many translocation efforts fail to meet their goals for myriad reasons, particularly because translocated animals make large, erratic movements after release, which can result in high mortality rates. Soft release, holding animals in acclimation pens for some period of time at the recipient site before release, has been proposed as a technique to reduce these large movements and increase the survival of translocated animals. Here, we compared the survival and movement patterns of soft-released Texas horned lizards (Phrynosoma cornutum) with resident lizards, as well as hard-released lizards from a prior study. Juvenile lizards that were soft-released had high survival rates similar to resident lizards, despite still moving more frequently and occupying larger home ranges than residents. Conversely, soft-released adult lizards had survival rates similar to those that were hard-released, and much lower rates than resident adults. Curiously, soft-released adults did not have significantly higher movement rates or home range sizes than residents. Our results suggest that caution should be used before adult Texas horned lizards are translocated. However, juveniles responded well to soft release, and future research should explore whether they are more resilient to translocation in general, or if soft release provided a specific survival advantage. Contrary to our predictions, the survival of translocated animals was not related to their post-release movement patterns, and the mechanism underlying the observed survival patterns is unclear.

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. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites.We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two newacquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis.Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support formany of the accepted relationships among phrynosomatid lizards, suggesting thatRAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths. [ABSTRACT FROM AUTHOR]

Thermoregulatory studies of ectothermic organisms are an important tool for ecological physiology, evolutionary ecology and behavior, and recently have become central for evaluating and predicting global climate change impacts. Here, we present a novel combination of field, laboratory, and modeling approaches to examine body temperature regulation, habitat thermal quality, and hours of thermal restriction on the activity of two sympatric, aridlands horned lizards ( Phrynosoma cornutum and Phrynosoma modestum ) at three contrasting Chihuahuan Desert sites in Mexico. Using these physiological data, we estimate local extinction risk under predicted climate change within their current geographical distribution. We followed the Hertz et al. (1993, Am. Nat. , 142, 796–818) protocol for evaluating thermoregulation and the Sinervo et al. (2010, Science , 328, 894–899) eco-physiological model of extinction under climatic warming. Thermoregulatory indices suggest that both species thermoregulate effectively despite living in habitats of low thermal quality, although high environmental temperatures restrict the activity period of both species. Based on our measurements, if air temperature rises as predicted by climate models, the extinction model projects that P. cornutum will become locally extinct at 6% of sites by 2050 and 18% by 2080 and P. modestum will become extinct at 32% of sites by 2050 and 60% by 2080. The method we apply, using widely available or readily acquired thermal data, along with the modeling, appeared to identify several unique ecological traits that seemingly exacerbate climate sensitivity of P. modestum . [ABSTRACT FROM AUTHOR]

Viviparity, the bearing of live young, has evolved well over 100 times among squamate reptiles. This reproductive strategy is hypothesized to allow maternal control of the foetus' thermal environment and thereby to increase the fitness of the parents and offspring. Two hypotheses have been posited to explain this phenomenon: (i) the cold-climate hypothesis ( CCH), which advocates low temperatures as the primary selective force; and (ii) the maternal manipulation hypothesis ( MMH), which advocates temperature variability as the primary selective force. Here, we investigate whether climatic and geographic variables associated with the CCH vs. the MMH best explain the current geographical distributions of viviparity in lizards while incorporating recent advances in comparative methods, squamate phylogenetics and geospatial analysis. To do this, we compared nonphylogenetic and phylogenetic models predicting viviparity based on point-of-capture data from 20 994 museum specimens representing 215 lizard species in conjunction with spatially explicit bioclimatic and geographic (elevation and latitude) data layers. The database we analysed emphasized Nearctic lizards from three species-rich genera ( Phrynosoma, Plestiodon and Sceloporus); however, we additionally analysed a less substantial, but worldwide sample of species to verify the universality of our Nearctic results. We found that maximum temperature of the warmest month (and, less commonly, elevation and maximum temperature of the driest quarter) was frequently the best predictor of viviparity and showed an association consistent with the CCH. Our results strongly favour the CCH over the MMH in explaining lizard reproductive mode evolution. [ABSTRACT FROM AUTHOR]

Abstract: The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5–3million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands. [Copyright &y& Elsevier]

Abstract: It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1kb of mtDNA (12S rRNA, 16S rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2.2kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira–Hasegawa tests, with the (P. platyrhinos + P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcallii × P. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: (1) Tapaja, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; (2) Anota, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); (3) Doliosaurus, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and (4) Brevicauda, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus). [Copyright &y& Elsevier]

Desert horned lizards Phrynosoma platyrhinos consumed the solitary-foraging seed-harvester ant, Pogonomyrmex califonicus, 10 to 100 times more often than expected based upon its relative abundance in the environment. The group-foraging seed-harvester ants, Pogonomyrmex rugosus and Veromessor pergandei, were correspondingly underrepresented in the horned lizard's natural diet. In a series of laboratory prey choice tests, where prey availabilities were held constant and equal, these preferences were confirmed: P.californicus was eaten more often than P. rugosus which was eaten more often than V. pergandei. These preferences correspond to differences in ant aggressive behavior which, in turn, correspond to differences in ant foraging-group size and foraging method. Colonies of solitary-foraging ants have small foraging groups and are generally incapable of mobbing a lizard, but they are also difficult to find. Colonies of group-foraging ants have large to massive foraging groups and vigorously mob lizards. Such aggressiveness is probably effective by increasing the risk of exposure of a lizard to predators of its own; the indirect costs of preying upon these ant species, normally assumed constant over all prey types for most predators, are variable here. Differences in experience with ant aggressive behavior probably account for differences in prey preferences found among adult lizards captured from the same area. Ant-species-specific predation by Phrynosoma may be an important ecological force structuring the Mohave Desert seed-harvesting ant community. [ABSTRACT FROM AUTHOR]

Simple Summary: Wildlife are moved (translocated) for numerous reasons, whether it is to establish a new population for conservation purposes or to move animals out of harm's way. Unfortunately, animals that are moved often fail to survive in their new homes. Soft release is a technique of penning animals at the release site before letting them free, which allows them to become acclimated to their new surroundings and prevents them from immediately trying to return to their capture location. We soft-released Texas horned lizards at an urban military installation in Oklahoma, United States. While soft-released adults did have reduced post-release movements, they also had low survival, suggesting that they do not respond well to translocation. However, post-release survival of juveniles was high and equivalent to resident juveniles. Translocation efforts of Texas horned lizards may be most successful if they focus on relocation of juveniles rather than adults. Wildlife translocation is an often-used technique to augment populations or remove animals from harm's way. Unfortunately, many translocation efforts fail to meet their goals for myriad reasons, particularly because translocated animals make large, erratic movements after release, which can result in high mortality rates. Soft release, holding animals in acclimation pens for some period of time at the recipient site before release, has been proposed as a technique to reduce these large movements and increase the survival of translocated animals. Here, we compared the survival and movement patterns of soft-released Texas horned lizards (Phrynosoma cornutum) with resident lizards, as well as hard-released lizards from a prior study. Juvenile lizards that were soft-released had high survival rates similar to resident lizards, despite still moving more frequently and occupying larger home ranges than residents. Conversely, soft-released adult lizards had survival rates similar to those that were hard-released, and much lower rates than resident adults. Curiously, soft-released adults did not have significantly higher movement rates or home range sizes than residents. Our results suggest that caution should be used before adult Texas horned lizards are translocated. However, juveniles responded well to soft release, and future research should explore whether they are more resilient to translocation in general, or if soft release provided a specific survival advantage. Contrary to our predictions, the survival of translocated animals was not related to their post-release movement patterns, and the mechanism underlying the observed survival patterns is unclear. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths., (© The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.)

Female-biased sexual size dimorphism is uncommon among vertebrates and traditionally has been attributed to asymmetric selective pressures favoring large fecund females (the fecundity-advantage hypothesis) and/or small mobile males (the small-male advantage hypothesis). I use a phylogenetically based comparative method to address these hypotheses for the evolution and maintenance of sexual size dimorphism among populations of three closely related lizard species (Phrynosoma douglasi, P. ditmarsi, and P. hernandezi). With independent contrasts I estimate evolutionary correlations among female body size, male body size, and sexual size dimorphism (SSD) to determine whether males have become small, females have become large, or both sexes have diverged concurrently in body size during the evolutionary Xhistory of this group. Population differences in degree of SSD are inversely correlated with average male body size, but are not correlated with average female body size. Thus, variation in SSD among populations has occurred predominantly through changes in male size, suggesting that selective pressures on small males may affect degree of SSD in this group. I explore three possible evolutionary mechanisms by which the mean male body size in a population could evolve: changes in size at maturity, changes in the variance of male body sizes, and changes in skewness of male body size distributions. Comparative analyses indicate that population differentiation in male body size is achieved by changes in male size at maturity, without changes in the variance or skewness of male and female size distributions. This study demonstrates the potential of comparative methods at lower taxonomic levels (among populations and closely related species) for studying microevolutionary processes that underlie population differentiation., (© 1998 The Society for the Study of Evolution.)