Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone.

Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here, we investigate introgression in a hybrid zone between two rattlesnake species (Crotalus viridis and Crotalus oreganus concolor) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.

Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination.

The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.

Culture-enriched community profiling improves resolution of the vertebrate gut microbiota.

Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.

Body size impacts critical thermal maximum measurements in lizards.

Understanding the mechanisms behind critical thermal maxima (CTmax; the high body temperature at which neuromuscular coordination is lost) of organisms is central to understanding ectotherm thermal tolerance. Body size is an often overlooked variable that may affect interpretation of CTmax, and consequently, how CTmax is used to evaluate mechanistic hypotheses of thermal tolerance. We tested the hypothesis that body size affects CTmax and its interpretation in two experimental contexts. First, in four Sceloporus species, we examined how inter- and intraspecific variation in body size affected CTmax at normoxic and experimentally induced hypoxic conditions, and cloacal heating rate under normoxic conditions. Negative relationships between body size and CTmax were exaggerated in larger species, and hypoxia-related reductions in CTmax were unaffected by body size. Smaller individuals had faster cloacal heating rates and higher CTmax, and variation in cloacal heating rate affected CTmax in the largest species. Second, we examined how body size interacted with the location of body temperature measurements (i.e., cloaca vs. brain) in Sceloporus occidentalis, then compared this in living and deceased lizards. Brain temperatures were consistently lower than cloacal temperatures. Smaller lizards had larger brain-cloacal temperature differences than larger lizards, due to a slower cloacal heating rate in large lizards. Both live and dead lizards had lower brain than cloacal temperatures, suggesting living lizards do not actively maintain lower brain temperatures when they cannot pant. Thermal inertia influences CTmax data in complex ways, and body size should therefore be considered in studies involving CTmax data on species with variable sizes.

Thermal ecology of the federally endangered blunt-nosed leopard lizard (Gambelia sila).

Recognizing how climate change will impact populations can aid in making decisions about approaches for conservation of endangered species. The blunt-nosed leopard lizard (Gambelia sila) is a federally endangered species that, despite protection, remains in extremely arid, hot areas and may be at risk of extirpation due to climate change. We collected data on the field-active body temperatures, preferred body temperatures and upper thermal tolerance of G. sila. We then described available thermal habitat using biophysical models, which allowed us to (i) describe patterns in lizard body temperatures, microhabitat temperatures and lizard microhabitat use; (ii) quantify the lizards' thermoregulatory accuracy; (iii) calculate the number of hours they are currently thermally restricted in microhabitat use; (iv) project how the number of restricted hours will change in the future as ambient temperatures rise; and (v) assess the importance of giant kangaroo rat burrows and shade-providing shrubs in the current and projected future thermal ecology of G. sila. Lizards maintained fairly consistent daytime body temperatures over the course of the active season, and use of burrows and shrubs increased as the season progressed and ambient temperatures rose. During the hottest part of the year, lizards shuttled among kangaroo rat burrows, shrubs, and open habitat to maintain body temperatures below their upper thermal tolerance, but, occasionally, higher than their preferred body temperature range. Lizards are restricted from staying in the open habitat for 75% of daylight hours and are forced to seek refuge under shrubs or burrows to avoid surpassing their upper thermal threshold. After applying climatic projections of 1 and 2°C increases to 2018 ambient temperatures, G. sila will lose additional hours of activity time that could compound stressors faced by this population, potentially leading to extirpation.

Effects of Experimental Anthropogenic Noise Exposure on the Reproductive Success of Secondary Cavity Nesting Birds.

Artificial nest boxes are critical nesting sites for secondary cavity-nesting birds; however, they are often placed near roadways and in urban areas that experience noise pollution and other human-caused stressors. Recent correlative studies document both negative and positive influences of noise pollution on reproductive success. Additionally, observational studies have not determined which stage of the breeding process is most vulnerable to noise pollution-settlement, incubation, and/or provisioning. Here, we controlled for possible effects from non-random settlement and eliminated potential effects of roadways, such as collisions and chemical and light pollution, by experimentally introducing traffic noise into nest boxes after clutch initiation in two secondary-cavity nesting bird species. We found no evidence for an influence of noise on clutch size, brood size, number of fledglings, or overall nest success in western bluebirds (Sialia mexicana). In contrast, we found that ash-throated flycatcher (Myiarchus cinerascens) nests exposed to noise had lower reproductive success than quiet nests due to higher rates of abandonment at the incubation stage. Our results match recent research demonstrating that ash-throated flycatchers avoid energy-sector noise in their nest placement and, when they do nest in noise, experience stress hormone dysregulation and fitness costs. The lack of a response among western bluebirds differs from reported declines in reproductive success due to exposure to energy-sector noise; however, the absence of a response matches the response seen in other species using an in-box noise playback experiment. These results suggest that in-box noise exposure experiments may be appropriate for assessing noise impacts at the nest, and through some pathways (e.g., direct effects of noise on nestlings), but do not capture other ways in which noise can negatively affect birds during the breeding season that may ultimately cause declines in fitness. Additionally, although manipulative experiments that examine the influence of a single anthropogenic stressor on a single life stage can help reveal causal pathways, urban and other human-dominated environments are characterized by many stressors and future studies should seek to understand how noise interacts with other stressors to impact birds and other wildlife. Finally, in light of mounting evidence demonstrating declines in reproductive success due to noise, our results suggest that nest box placement near roads may be counterproductive to efforts to bolster population densities of some species.