Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales.

Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription-factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.

Hunting behavior and feeding ecology of Mojave rattlesnakes (Crotalus scutulatus), prairie rattlesnakes (Crotalus viridis), and their hybrids in southwestern New Mexico.

Predators must contend with numerous challenges to successfully find and subjugate prey. Complex traits related to hunting are partially controlled by a large number of co-evolved genes, which may be disrupted in hybrids. Accordingly, research on the feeding ecology of animals in hybrid zones has shown that hybrids sometimes exhibit transgressive or novel behaviors, yet for many taxa, empirical studies of predation and diet across hybrid zones are lacking. We undertook the first such field study for a hybrid zone between two snake species, the Mojave rattlesnake (Crotalus scutulatus) and the prairie rattlesnake (Crotalus viridis). Specifically, we leveraged established field methods to quantify the hunting behaviors of animals, their prey communities, and the diet of individuals across the hybrid zone in southwestern New Mexico, USA. We found that, even though hybrids had significantly lower body condition indices than snakes from either parental group, hybrids were generally similar to non-hybrids in hunting behavior, prey encounter rates, and predatory attack and success. We also found that, compared to C. scutulatus, C. viridis was significantly more active while hunting at night and abandoned ambush sites earlier in the morning, and hybrids tended to be more viridis-like in this respect. Prey availability was similar across the study sites, including within the hybrid zone, with kangaroo rats (Dipodomys spp.) as the most common small mammal, both in habitat surveys and the frequency of encounters with hunting rattlesnakes. Analysis of prey remains in stomachs and feces also showed broad similarity in diets, with all snakes preying primarily on small mammals and secondarily on lizards. Taken together, our results suggest that the significantly lower body condition of hybrids does not appear to be driven by differences in their hunting behavior or diet and may instead relate to metabolic efficiency or other physiological traits we have not yet identified.

Century-long butterfly range expansions in northern Europe depend on climate, land use and species traits.

Climate change is an important driver of range shifts and community composition changes. Still, little is known about how the responses are influenced by the combination of land use, species interactions and species traits. We integrate climate and distributional data for 131 butterfly species in Sweden and Finland and show that cumulative species richness has increased with increasing temperature over the past 120 years. Average provincial species richness increased by 64% (range 15-229%), from 46 to 70. The rate and direction of range expansions have not matched the temperature changes, in part because colonisations have been modified by other climatic variables, land use and vary according to species characteristics representing ecological generalisation and species interactions. Results emphasise the role of a broad ecological filtering, whereby a mismatch between environmental conditions and species preferences limit the ability to disperse and establish populations in emerging climates and novel areas, with potentially widespread implications for ecosystem functioning.

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions.

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annotations being limited to a set of already known reactions. Here, we introduce Network Integrated Computational Explorer for Gap Annotation of Metabolism (NICEgame), a workflow to identify and curate nonannotated metabolic functions in genomes using the ATLAS of Biochemistry and genome-scale metabolic models (GEMs). To resolve gaps in GEMs, NICEgame provides alternative sets of known and hypothetical reactions, assesses their thermodynamic feasibility, and suggests candidate genes to catalyze these reactions. We identified metabolic gaps and applied NICEgame in the latest GEM of Escherichia coli, iML1515, and enhanced the E. coli genome annotation by resolving 47% of these gaps. NICEgame, applicable to any GEM and functioning from open-source software, should thus enhance all GEM-based predictions and subsequent biotechnological and biomedical applications.

Differences in phenology, daily timing of activity, and associations of temperature utilization with survival in three threatened butterflies.

We used observational data collected during a mark-recapture study that generated a total of 7503 captures of 6108 unique individuals representing three endangered butterfly species to quantify inter-and intraindividual variation in temperature utilization and examine how activity patterns vary according to season, time of day, and ambient temperature. The Marsh Fritillary, the Apollo, and the Large Blue differed in utilized temperatures and phenology. Their daily activity patterns responded differently to temperature, in part depending on whether they were active in the beginning, middle or end of the season, in part reflecting interindividual variation and intraindividual flexibility, and in part owing to differences in ecology, morphology, and colouration. Activity temperatures varied over the season, and the Apollo and the Large Blue were primarily active at the highest available ambient temperatures (on the warmest days and during the warmest part of the day). The Marsh Fritillary was active early in the season and decreased activity during the highest temperatures. The relationship between individual lifespan and the average temperature was qualitatively different in the three species pointing to species-specific selection. Lifespan increased with an increasing range of utilized temperatures in all species, possibly reflecting that intra-individual flexibility comes with a general survival benefit.

Breeders are less active foragers than non-breeders in wild Damaraland mole-rats.

Eusocial societies are characterized by a clear division of labour between non-breeding workers and breeding queens, and queens often do not contribute to foraging, defence and other maintenance tasks. It has been suggested that the structure and organization of social mole-rat groups resembles that of eusocial insect societies. However, the division of labour has rarely been investigated in wild mole-rats, and it is unknown whether breeders show decreased foraging activity compared with non-breeding helpers in natural groups. Here, we show that, in wild Damaraland mole-rats (Fukomys damarensis), breeders show lower activity in foraging areas than non-breeding group members. Both breeders and non-breeders displayed variation in activity across the different seasons. Our results suggest that group living allows social mole-rat breeders to reduce their investment in energetically costly behaviour, or alternatively, that the high cost of reproduction in this species forces a behavioural trade-off against foraging investment.