Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9.

Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions-a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions-a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.

Resolving tradeoffs among crypsis, escape behavior, and microhabitat use in sexually dichromatic species.

Variation in color pattern between populations of cryptic animals is common and typically attributed to selection pressures from visual predators combined with variation in substrate composition. However, little is known about how cryptic color pattern relates to varied rates of predation, and few studies simultaneously analyze patterns of escape behavior and microhabitat use along with variation in color pattern, even though these traits evolve in tandem. Here, we use a combination of calibrated photographs and spectrometry to examine the influence of spatial heterogeneity in rates of predation on dorsal brightness in the Florida scrub lizard (Sceloporus woodi), a cryptic and sexually dimorphic species. Simultaneously, we analyze patterns of escape behavior and microhabitat use measured in the field. The results of this study indicate that populations inhabiting environments of increased predation have less color variation and more closely match the color of local substrate than populations sampled in environments of relaxed predation. Populations exposed to increased predation also show more pronounced escape behavior and are more selective in their use of microhabitat. Interestingly, geographic variation of dorsal brightness, escape behavior, and microhabitat use were greater for females than for males. Our results not only provide empirical evidence for theories of adaptive coloration, but suggest that sexual dichromatism can be maintained by selection pressures related to predation.

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.

Mite load predicts the quality of sexual color and locomotor performance in a sexually dichromatic lizard.

Since Darwin, the maintenance of bright sexual colors has recurrently been linked to mate preference. However, the mechanisms underpinning such preferences for bright colors would not be resolved for another century. Likely, the idea of selection for colors that could decrease the chances of survival (e.g., flashy colors that can inadvertently attract predators) was perceived as counterintuitive. It is now widely accepted that these extreme colors often communicate to mates the ability to survive despite a "handicap" and act as honest signals of individual quality when they are correlated with the quality of other traits that are directly linked to individual fitness. Sexual colors in males are frequently perceived as indicators of infection resistance, in particular. Still, there remains considerable discord among studies attempting to parse the relationships between the variables associating sexual color and infection resistance, such as habitat type and body size. This discord may arise from complex interactions between these variables. Here, we ask if sexual color in male Florida scrub lizards (Sceloporus woodi) is an honest signal of resistance to chigger mite infection. To this end, we use linear modeling to explore relationships between mite load, different components of sexual color, ecological performance, body size, and habitat type. Our data show that that the brightness of sexual color in scrub lizards is negatively associated with the interaction between mite load and body size, and scrub lizards suffer decreased endurance capacity with increases in mite load. Our data also indicate that mite load, performance, and sexual color in male scrub lizards can vary between habitat types. Collectively, these results suggest that sexual color in scrub lizards is an honest indicator of individual quality and further underscore the importance of considering multiple factors when testing hypotheses related to the maintenance of sexual color.

Conservation and Management Strategies Create Opportunities for Integrative Organismal Research.

Conservation and management activities are geared toward the achievement of particular goals for a specific species, or groups of species, at the population level or higher. Conversely, organismal or functional research is typically organized by hypothesis tests or descriptive work that examines a broader theory studying individual organismal traits. Here, we outline how integrative organismal biologists might conduct mutually beneficial and meaningful research to inform or assist conservation and management biologists. We argue that studies of non-target species are very useful to both groups because non-target species can meet the goals of managers and organismal biologists alike, while also informing the other. We highlight our work on a threatened lizard species' thermal physiology, behavior, and color pattern-all of which are impacted by species management plans for sympatric, threatened, bird species. We show that management practices affect activity time, thermal adaptation, and substrate use, while also altering predation rates, crypsis, ectoparasite load, and sexual coloration in the study species. These case studies exemplify the challenges of conservation and management efforts for threatened or endangered species in that non-target species can be both positively and negatively affected by those efforts. Yet, the collaboration of organismal biologists with conservation and management efforts provides a productive system for mutually informative research.