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1. Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii

   https://doi.org/10.1111/mec.17310  

   Springer, Amy L. ; Gompert, Zachariah ( March 2024 , Molecular Ecology)

   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.

    

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2. Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome

   https://doi.org/10.1111/mec.16087  

   Colicchio, Jack M. ; Hamm, Lauren N. ; Verdonk, Hannah E. ; Kooyers, Nicholas J. ; Blackman, Benjamin K. ( August 2021 , Molecular Ecology)

   Genetic diversity becomes structured among populations over time due to genetic drift and divergent selection. Although population structure is often treated as a uniform underlying factor, recent resequencing studies of wild populations have demonstrated that diversity in many regions of the genome may be structured quite dissimilar to the genome‐wide pattern. Here, we explored the adaptive and nonadaptive causes of such genomic heterogeneity using population‐level, whole genome resequencing data obtained from annualMimulus guttatusindividuals collected across a rugged environment landscape. We found substantial variation in how genetic differentiation is structured both within and between chromosomes, although, in contrast to other studies, known inversion polymorphisms appear to serve only minor roles in this heterogeneity. In addition, much of the genome can be clustered into eight among‐population genetic differentiation patterns, but only two of these clusters are particularly consistent with patterns of isolation by distance. By performing genotype‐environment association analysis, we also identified genomic intervals where local adaptation to specific climate factors has accentuated genetic differentiation among populations, and candidate genes in these windows indicate climate adaptation may proceed through changes affecting specialized metabolism, drought resistance, and development. Finally, by integrating our findings with previous studies, we show that multiple aspects of plant reproductive biology may be common targets of balancing selection and that variants historically involved in climate adaptation among populations have probably also fuelled rapid adaptation to microgeographic environmental variation within sites.

    

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3. Phenotypic and genetic introgression across a moving woodpecker hybrid zone

   https://doi.org/10.1111/mec.15043  

   Billerman, Shawn M. ; Cicero, Carla ; Bowie, Rauri C. K. ; Carling, Matthew D. ( April 2019 , Molecular Ecology)

   In hybrid zones in which two divergent taxa come into secondary contact and interbreed, selection can maintain phenotypic diversity despite widespread genetic introgression. Red‐breasted (Sphyrapicus ruber) and red‐naped (S. nuchalis) sapsuckers meet and hybridize along a narrow contact zone that stretches from northern California to southern British Columbia. We found strong evidence for changes in the structure of this hybrid zone across time, with significant temporal shifts in allele frequencies and in the proportions of parental phenotypes across the landscape. In addition to these shifts, we found that differences in plumage predict genetic differences (R² = 0.80), suggesting that plumage is a useful proxy for assessing ancestry. We also found a significant bimodal distribution of hybrids across the contact zone, suggesting that premating barriers may be driving reproductive isolation, perhaps as a result of assortative mating based on plumage differences. However, despite evidence of selection and strong patterns of population structure between parental samples, we found only weak patterns of genetic divergence. Using museum specimens and genomic data, this study of sapsuckers provides insight into the ways in which phenotypic and genetic structure have changed over a 40‐year period, as well as insight into the mechanisms that may contribute to the maintenance of the hybrid zone over time.

    

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4. How Veeries vary: Whole genome sequencing resolves genetic structure in a long-distance migratory bird

   https://doi.org/10.1093/ornithology/ukad061  

   Kimmitt, Abigail A. ; Pegan, Teresa M. ; Jones, Andrew W. ; Winker, Kevin ; Winger, Benjamin M. ( December 2023 , Ornithology)

   In high-latitude species with high dispersal ability, such as long-distance migratory birds, populations are often assumed to exhibit little genetic structure due to high gene flow or recent postglacial expansion. We sequenced over 120 low-coverage whole genomes from across the breeding range of a long-distance migratory bird, the Veery (Catharus fuscescens), revealing strong evidence for isolation by distance. Additionally, we found distinct genetic structure between boreal, western montane U.S., and southern Appalachian sampling regions. We suggest that population genetic structure in this highly migratory species is detectable with the high resolution afforded by whole-genomic data because, similar to many migratory birds, the Veery exhibits high breeding-site fidelity, which likely limits gene flow. Resolution of isolation by distance across the breeding range was sufficient to assign likely breeding origins of individuals sampled in this species’ poorly understood South American nonbreeding range, demonstrating the potential to assess migratory connectivity in this species using genomic data. As the Veery’s breeding range extends across both historically glaciated and unglaciated regions in North America, we also evaluated whether contemporary patterns of structure and genetic diversity are consistent with historical population isolation in glacial refugia. We found that patterns of genetic diversity did not support southern montane regions (southern Appalachians or western U.S. mountains) as glacial refugia. Overall, our findings suggest that isolation by distance yields subtle associations between genetic structure and geography across the breeding range of this highly vagile species even in the absence of obvious historical vicariance or contemporary barriers to dispersal.

    

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5. Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis )

   https://doi.org/10.1002/ece3.7159  

   Martin, Alynn M. ; Cassirer, E. Frances ; Waits, Lisette P. ; Plowright, Raina K. ; Cross, Paul C. ; Andrews, Kimberly R. ( March 2021 , Ecology and Evolution)

   Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population‐level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused byMycoplasma ovipneumoniaehave been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shedM. ovipneumoniaeand expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage ofM. ovipneumoniaein a well‐studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family‐based genome‐wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome‐wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP‐based heritability) forM. ovipneumoniaecarriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.

    

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