Chris C. Nice’s research while affiliated with Texas State University and other places

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst‐obligate salamanders of the Eurycea neotenes species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The E. neotenes species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain. We discovered evidence of extensive admixture among species within the complex and with adjacent lineages. We observed relatively low levels of differentiation among all sampling localities which supports the hypothesis of recent divergence. Nominal taxonomy, aquifer region and geography each accounted for a modest amount of the overall population genomic variation; however, these predictors were largely confounded and difficult to disentangle. Importantly, current taxonomy of the three nominal species does not reflect the admixture apparent in clustering analyses. Inference of migration events revealed a complex pattern of gene exchange, suggesting that Eurycea salamanders have a dynamic history of dispersal through the aquifer system. These results highlight the need for greater understanding of how stygobiont populations are connected via dispersal and gene exchange through karst aquifers. These results also highlight the applicability of population genomics data as a powerful lever for investigating connectivity among populations in systems where direct detection of dispersal paths is difficult, as in underground, aquatic systems.

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst-obligate salamanders of the Eurycea neotenes species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The Eurycea neotenes species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain. We discovered evidence of extensive admixture within the species complex and with adjacent lineages. We observed relatively low levels of differentiation among all sampling localities which supports the hypothesis of recent divergence. Nominal taxonomy, aquifer region and geography accounted for a modest amount of the overall population genomic variation, but these predictors were largely collinear and difficult to disentangle. Importantly, the taxonomy of the three nominal species does not reflect the admixture apparent in clustering analyses. Inference of migration events revealed a complex pattern of gene exchange, suggesting that Eurycea salamanders have a dynamic history of dispersal through the aquifer system. These results highlight the need for greater understanding of how stygobiont populations are connected via dispersal and gene exchange through karst aquifers.

Climate warming is considered to be among the most serious of anthropogenic stresses to the environment, because it not only has direct effects on biodiversity, but it also exacerbates the harmful effects of other human‐mediated threats. The associated consequences are potentially severe, particularly in terms of threats to species preservation, as well as in the preservation of an array of ecosystem services provided by biodiversity. Among the most affected groups of animals are insects—central components of many ecosystems—for which climate change has pervasive effects from individuals to communities. In this contribution to the scientists' warning series, we summarize the effect of the gradual global surface temperature increase on insects, in terms of physiology, behavior, phenology, distribution, and species interactions, as well as the effect of increased frequency and duration of extreme events such as hot and cold spells, fires, droughts, and floods on these parameters. We warn that, if no action is taken to better understand and reduce the action of climate change on insects, we will drastically reduce our ability to build a sustainable future based on healthy, functional ecosystems. We discuss perspectives on relevant ways to conserve insects in the face of climate change, and we offer several key recommendations on management approaches that can be adopted, on policies that should be pursued, and on the involvement of the general public in the protection effort.

Plant–insect interactions are common and important in basic and applied biology. Trait and genetic variation can affect the outcome and evolution of these interactions, but the relative contributions of plant and insect genetic variation and how these interact remain unclear and are rarely subject to assessment in the same experimental context. Here, we address this knowledge gap using a recent host-range expansion onto alfalfa by the Melissa blue butterfly. Common garden rearing experiments and genomic data show that caterpillar performance depends on plant and insect genetic variation, with insect genetics contributing to performance earlier in development and plant genetics later. Our models of performance based on caterpillar genetics retained predictive power when applied to a second common garden. Much of the plant genetic effect could be explained by heritable variation in plant phytochemicals, especially saponins, peptides, and phosphatidyl cholines, providing a possible mechanistic understanding of variation in the species interaction. We find evidence of polygenic, mostly additive effects within and between species, with consistent effects of plant genotype on growth and development across multiple butterfly species. Our results inform theories of plant–insect coevolution and the evolution of diet breadth in herbivorous insects and other host-specific parasites.

Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts, and the historical and geographical dynamics of infections that are critical for identifying the factors governing their spread. We used Genotype-by-Sequencing (GBS) data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia reference genome provided high accuracy in detecting infections in host butterflies as determined by confirmatory PCR tests, and maximum accuracy was achieved with a threshold of only five sequence reads per host individual. Using this threshold, we detected Wolbachia in all but two of the 107 sampling localities spanning the continent, with infection frequencies within populations ranging from 0–100% of individuals, but with most localities having high infection frequencies (mean = 91% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent three separate invasions of Lycaeides butterflies by Wolbachia. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other two strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. Within strain wLycA, the two most frequent haplotypes are confined almost exclusively to separate butterfly taxa with haplotype A1 observed largely in L. melissa and haplotype A2 observed most often in L. idas localities, consistent with either cladogenic mode of infection acquisition from a common ancestor or by hybridization and accompanying mutation. More than one major Wolbachia strain was observed in 15 localities. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and infection frequency and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.

Infections by maternally inherited bacterial endosymbionts, especially Wolbachia , are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts and the factors governing their spread. We used Genotype-by-Sequencing (GBS) data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in over 2,700 North American butterflies of the genus Lycaeides . As few as one sequence read identified by assembly to a Wolbachia pan-reference genome provided high accuracy in detecting infections as determined by confirmatory PCR tests. Using a conservative threshold of five reads, we detected Wolbachia in all but two of the 107 sampling localities spanning the continent, and with most localities having high infection frequencies (mean = 91\% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent three separate invasions of Lycaeides butterflies. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLyc C was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other two strains were detected throughout the rest of the continent, strain wLyc B almost always co-occurred with wLyc A. Our demographic modeling suggests wLyc B is a recent invasion. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.

Infections by maternally inherited bacterial endosymbionts, especially Wolbachia , are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts and the factors governing their spread. We used Genotype-by-Sequencing (GBS) data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in over 2,700 North American butterflies of the genus Lycaeides . As few as one sequence read identified by assembly to a Wolbachia pan-reference genome provided high accuracy in detecting infections as determined by confirmatory PCR tests. Using a conservative threshold of five reads, we detected Wolbachia in all but two of the 107 sampling localities spanning the continent, and with most localities having high infection frequencies (mean = 91\% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent three separate invasions of Lycaeides butterflies. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLyc C was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other two strains were detected throughout the rest of the continent, strain wLyc B almost always co-occurred with wLyc A. Our demographic modeling suggests wLyc B is a recent invasion. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long‐read (Oxford nanopore) whole‐genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome‐wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry‐informative SVs exhibiting genomic clines that deviated from null expectations based on genome‐average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z‐linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.

Infections by maternally inherited bacterial endosymbionts, especially Wolbachia , are common in insects and other invertebrates but infection dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infections in novel hosts and the factors governing their spread. We used Genotype-by-Sequencing (GBS) data from previous population genomics studies for range-wide surveys of Wolbachia presence and genetic diversity in over 2,700 North American butterflies of the genus Lycaeides . As few as one sequence read identified by assembly to a Wolbachia pan-reference genome provided high accuracy in detecting infections as determined by confirmatory PCR tests. Using a conservative threshold of five reads, we detected Wolbachia in all but two of the 107 sampling localities spanning the continent, and with most localities having high infection frequencies (mean = 91\% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent three separate invasions of Lycaeides butterflies. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLyc C was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other two strains were detected throughout the rest of the continent, strain wLyc B almost always co-occurred with wLyc A. Our demographic modeling suggests wLyc B is a recent invasion. These results demonstrate the utility of using resequencing data from hosts to quantify Wolbachia genetic variation and provide evidence of multiple colonizations of novel hosts through hybridization between butterfly lineages and complex dynamics between Wolbachia strains.