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Description: Raw sequence reads Summary: We used pooled whole-genome sequence data from more than 20 populations representing three nominal species and multiple admixed or taxonomically ambiguous populations, we show that widespread admixture in Lycaeides butterflies has resulted in distinct evolutionary histories within and among chromosomes, with the most notable differences between the autosomes and the Z sex chromosome. This is part of a larger project analyzing evolution in this butterfly group across space and over time. 

Research-based learning is among the highest impact experiences college students can have. For the last four years, undergraduate students from the Honors Program enrolled in the introductory-level biology lab course at Utah State University have been filling gaps in the scientific community’s knowledge about the abiotic and biotic factors that affect a mutualistic relationship between caterpillars and ants. Sugar-consuming-ants protect caterpillars from predators and parasitoids, and the caterpillars feed the ants honeydew from a dorsal organ and communicate with them through skin chemicals (cuticular hydrocarbons or CHCs). Students begin by learning about the scientific method, as well as developing collaboration and communication skills, through instructional videos and standalone experiments, which they then apply to this 7-week research experience. They work in small groups to make general observations about the study system, search and read the published literature, build off of what previous students have learned, and write a short research proposal. One of the proposed experiments is chosen for the class. Students use caterpillars hatched from hibernating eggs collected from multiple Lycaeides populations the previous summer by scientists. A small support team rears the caterpillars until they have developed their ant-tending organs. This ensures students have adequate sample sizes for data analysis. Through these experiments, the students have shown that Lycaeides population affects the amount of attention received by ants, and that different ant species interact with the caterpillars to different extents. The project concludes when students individually produce and record a 5-minute “lightning talk”. This classroom research filters into a larger project about the long-term effects of natural selection in wild Lycaeides populations, funded by an NSF CAREER grant. The student discoveries have indicated that Lycaeides ant-tending traits are good candidates for studying rapid evolution. Students have felt this experience prepares them for their future STEM careers. 

Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence in cryptic color pattern in a stick insect is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We found that color pattern in populations of stick insects on two mountains is associated with translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and involve some of the same gene regions. Moreover, this structural variation is subject to divergent selection and arose without introgression between species. Our results show how the origin of structural variation provides a mechanism for repeated bouts of adaptation. 

ABSTRACT Hybrid zones, where genetically distinct groups of organisms meet and interbreed, offer valuable insights into the nature of species and speciation. Here, we present a new R package,bgchm, for population genomic analyses of hybrid zones. This R package extends and updates the existingbgcsoftware and combines Bayesian analyses of hierarchical genomic clines with Bayesian methods for estimating hybrid indexes, interpopulation ancestry proportions, and geographic clines. Compared to existing software,bgchmoffers enhanced efficiency through Hamiltonian Monte Carlo sampling and the ability to work with genotype likelihoods combined with a hierarchical Bayesian approach, enabling inference for diverse types of genetic data sets. The package also facilitates the quantification of introgression patterns across genomes, which is crucial for understanding reproductive isolation and speciation genetics. We first describe the models underlyingbgchmand then provide an overview of the R package and illustrate its use through the analysis of simulated and empirical data sets. We show thatbgchmgenerates accurate estimates of model parameters under a variety of conditions, especially when the genetic loci analyzed are highly ancestry informative. This includes relatively robust estimates of genome‐wide variability in clines, which has not been the focus of previous models and methods. We also illustrate how both selection and genetic drift contribute to variability in introgression among loci and how additional information can be used to help distinguish these contributions. We conclude by describing the promises and limitations ofbgchm, comparingbgchmto other software for genomic cline analyses, and identifying areas for fruitful future development. 

ABSTRACT Hybridisation and admixture are common in nature and can serve as important sources of adaptive potential by generating novel genotype combinations and phenotypes. However, hybrid incompatibilities can also reduce hybrid fitness. Given the pervasiveness of admixture and its potential role in facilitating adaptation, understanding how admixture influences the rate and repeatability of evolution is critical for advancing our understanding of evolutionary dynamics. Yet, few studies have examined how patterns of evolutionary repeatability in admixed lineages are shaped by strong ecological pressures. In this experiment, we evaluated patterns of evolution and repeatability in admixed and non‐admixed cowpea seed beetles (Callosobruchus maculatus) adapting to a novel, stressful host: lentil. Specifically, we asked (1) whether admixture facilitates adaptation to lentil, (2) whether repeatability is greater in admixed or non‐admixed lineages, and (3) to what extent repeatability in admixed lineages is driven by selection on globally adaptive alleles versus epistatic effects and hybrid incompatibilities. We found that admixture facilitated adaptation to lentil, and evolutionary rescue–defined as adaptation that prevents population extinction–occurred in all lineages. Evolutionary repeatability was highest in two admixed lineages, though evident across all lineages. Adaptation to lentil appeared largely driven by selection on globally adaptive alleles. Nevertheless, even under conditions of evolutionary rescue in a marginal environment, the purging of hybrid incompatibilities contributed substantially to repeated evolution in admixed lineages. 

Abstract Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping‐by‐sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species. 

Understanding how mutations arise and spread through individuals and populations is fundamental to evolutionary biology. Most organisms have a life cycle with unicellular bottlenecks during reproduction. However, some organisms like plants, fungi, or colonial animals can grow indefinitely, changing the manner in which mutations spread throughout both the individual and the population. Furthermore, clonally reproducing organisms may also achieve exceedingly long lifespans, making somatic mutation an important mechanism of creating heritable variation for Darwinian evolution by natural selection. Yet, little is known about intra-organism mutation rates and evolutionary trajectories in long-lived species. Here, we study the Pando aspen clone, the largest known quaking aspen (Populus tremuloides) clone founded by a single seedling and thought to be one of the oldest studied organisms. Aspen reproduce vegetatively via new root-borne stems forming clonal patches, sometimes spanning several hectares. To study the evolutionary history of the Pando clone, we collected and sequenced over 500 samples from Pando and neighboring clones, as well as from various tissue types within Pando, including leaves, roots, and bark. We applied a series of filters to distinguish somatic mutations from the pool of both somatic and germline mutations, incorporating a technical replicate sequencing approach to account for uncertainty in somatic mutation detection. Despite root spreading being spatially constrained, we observed only a modest positive correlation between genetic and spatial distance, suggesting the presence of a mechanism preventing the accumulation and spread of mutations across units. Phylogenetic models estimate the age of the clone to between ~16,000-80,000 years. This age is generally corroborated by the near-continuous presence of aspen pollen in a lake sediment record collected from Fish Lake near Pando. Overall, this work enhances understanding of mutation accumulation and dispersal within and between ramets of long-lived, clonally-reproducing organisms. Significance StatementThis study enhances our understanding of evolutionary processes in long-lived clonal organisms by investigating somatic mutation accumulation and dispersal patterns within the iconic Pando aspen clone. The authors estimated the clone to be between 10,000 and 80,000 years old and uncovered a modest spatial genetic structure in the 42.6-hectare clone, suggesting localized mutation build-up rather than dispersal along tissue lineages. This work sheds light on an ancient organism and how plants may evolve to preserve genetic integrity in meristems fueling indefinite growth, with implications for our comprehension of adaptive strategies in long-lived perennials.