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1. Cloacal microbiomes of sympatric and allopatric Sceloporus lizards vary with environment and host relatedness

   https://doi.org/10.1371/journal.pone.0279288  

   Bunker, Marie E.; Weiss, Stacey L. (December 2022, PLOS ONE)

   Ruiz-Rodriguez, Magdalena (Ed.)

   Animals and their microbiomes exert reciprocal influence; the host’s environment, physiology, and phylogeny can impact the composition of the microbiome, while the microbes present can affect host behavior, health, and fitness. While some microbiomes are highly malleable, specialized microbiomes that provide important functions can be more robust to environmental perturbations. Recent evidence suggests Sceloporus virgatus has one such specialized microbiome, which functions to protect eggs from fungal pathogens during incubation. Here, we examine the cloacal microbiome of three different Sceloporus species (spiny lizards; Family Phrynosomatidae)– Sceloporus virgatus , Sceloporus jarrovii , and Sceloporus occidentalis . We compare two species with different reproductive modes (oviparous vs. viviparous) living in sympatry: S . virgatus and S . jarrovii . We compare sister species living in similar habitats (riparian oak-pine woodlands) but different latitudes: S . virgatus and S . occidentalis . And, we compare three populations of one species ( S . occidentalis ) living in different habitat types: beach, low elevation forest, and the riparian woodland. We found differences in beta diversity metrics between all three comparisons, although those differences were more extreme between animals in different environments, even though those populations were more closely related. Similarly, alpha diversity varied among the S . occidentalis populations and between S . occidentalis and S . virgatus , but not between sympatric S . virgatus and S . jarrovii . Despite these differences, all three species and all three populations of S . occcidentalis had the same dominant taxon, Enterobacteriaceae . The majority of the variation between groups was in low abundance taxa and at the ASV level; these taxa are responsive to habitat differences, geographic distance, and host relatedness. Uncovering what factors influence the composition of wild microbiomes is important to understanding the ecology and evolution of the host animals, and can lead to more detailed exploration of the function of particular microbes and the community as a whole. 

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2. Cycling temperature treatments affect estimates of digestive performance in prairie lizards (Sceloporus consobrinus)

   https://doi.org/10.1242/jeb.247006  

   Litmer, Allison R; Beaupre, Steven J (January 2024, Journal of Experimental Biology)

   In nature, many organisms experience a daily range of body temperatures. Thermal performance at stable temperatures is often extrapolated to predict function in cyclical environments. However, temperature order and cyclicity may influence physiological processes. The current study compared energy intake, digestive passage time and energy budgets at a stable temperature (33°C) and two temperature cycles in lizards (Sceloporus consobrinus), to determine (1) whether stable treatments adequately project performance in a cycling environment and (2) whether temperature order influences performance. Cycles had a mean temperature of 33°C, and rotated through 30°C, 33°C and 36°C daily, with equal durations of time at each temperature but differing temperature order, with warm days and cool nights in cycle 1 and cool days and warm nights in cycle 2. For analyses, performance in the stable treatment was compared with that during cycles. If temperature is the primary factor regulating performance, then performance from the stable treatment and cycles should compare favorably. However, physiological performance varied based on temperature treatment. Energy intake and budgets were similar between the stable trial and cycle 1 but not cycle 2. However, passage time did not differ. Notably, the two cycling regimes consistently varied in performance, indicating that temperature order plays a primary role in regulating performance. Physiological data collection requires careful consideration of effects of cycling versus stable temperature treatments. Stable temperatures do not consistently represent performance in cycling regimes and consideration should be paid not only to which temperatures animals experience but also to how temperature is experienced in nature. 

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3. Characterization of a pericentric inversion in plateau fence lizards ( Sceloporus tristichus ): evidence from chromosome-scale genomes

   https://doi.org/10.1093/g3journal/jkab036  

   Bedoya, Ana M; Leaché, Adam D (February 2021, G3 Genes|Genomes|Genetics)

   Sethuraman, A (Ed.)

   Abstract Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n =  22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n =  22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84–1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone. 

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4. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

   https://doi.org/10.1093/jhered/esad037  

   Bishop, Anusha P.; Westeen, Erin P.; Yuan, Michael L.; Escalona, Merly; Beraut, Eric; Fairbairn, Colin; Marimuthu, Mohan P. A.; Nguyen, Oanh; Chumchim, Noravit; Toffelmier, Erin; et al (June 2023, Journal of Heredity)

   Abstract Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards. 

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5. Population‐level variation of digestive physiology costs of mounting an immune response in damselflies

   https://doi.org/10.1111/een.12837  

   Tye, Simon_P; Blaske, Benjamin_K; Siepielski, Adam_M (January 2020, Ecological Entomology)

   1. Trade‐offs are often predicted to occur between energetically costly activities, such as somatic growth and eliciting immune responses to parasites. Although parasitism frequently reduces growth via lowered consumption, it remains unclear if the energetic demands of generating immune responses also affect the digestive physiological processes necessary for growth. Moreover, as local environmental conditions affect energetic investment towards growth and immune responses, the extent of any digestive–immune response trade‐offs may vary among populations and not be fixed at the species‐level. 2. To test these ideas, melanisation – a general innate immune response – was first induced in damselfly larvae (Enallagma vesperum) from two populations. The study then quantified growth and consumption rates, assimilation and production efficiencies, and daily metabolic rates to determine if digestive–immune response trade‐offs were present and, if so, whether they differed between populations. 3. There was no evidence of any trade‐offs between immune responses and digestive physiology components in either population. However, the results did show that populations differentially allocated energy towards different digestive physiology components after an immune response was elicited: one population increased their relative consumption and daily metabolic rates, while the other population had lower assimilation efficiencies and consumption rates. 4. Although researchers lack a mechanistic understanding of the observed population‐level differences, these results suggest that accounting for population‐level variation in digestive physiology and immune responses is critical to inferences about how immunological defences to parasitism may affect the ability for organisms to both acquire and utilise resources. 

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