Publications

2026

1. Rapid expansion overcomes inbreeding in cross-hemisphere colonization of Barn Swallows

   Valentina Gomez-Bahamon^*, Juan I Areta^*, Jeremy Summers, Cristian Torres, Facundo Gandoy, Mingzuyu Pan, Zachary A Szpiech, and David Toews

   bioRxiv, 2026

   Abs DOI Bib HTML

   Switching migratory behavior appears to promote speciation in birds through colonization of their wintering grounds for breeding. However, colonization episodes often fail, especially when they lead to inbreeding depression associated with small population sizes. We studied the dynamics of a new and thriving breeding population of migratory Barn Swallows (Hirundo rustica erythrogaster) that began nesting on their traditional wintering grounds in South America in the 1980’s and evolved an "inverse" migration and breeding cycle. We show that in four decades, behavioral flexibility and standing genetic variation have facilitated the establishment of a breeding population that has grown exponentially in abundance and breeding range size. By breeding under bridges and culverts, Barn Swallows exploited ecological opportunities that outweighed the costs of inbreeding and began an independent evolutionary trajectory from their North American relatives.

   @article{gomez2026rapid,
     title = {Rapid expansion overcomes inbreeding in cross-hemisphere colonization of Barn Swallows},
     author = {Gomez-Bahamon, Valentina and Areta, Juan I and Summers, Jeremy and Torres, Cristian and Gandoy, Facundo and Pan, Mingzuyu and Szpiech, Zachary A and Toews, David},
     journal = {bioRxiv},
     year = {2026},
     doi = {10.64898/2026.07.13.738130},
   }

2025

1. The Influence of Demographic History and Genetic Architecture on Complex Traits via Runs of Homozygosity

   Mingzuyu Pan^* and Zachary A Szpiech^*

   bioRxiv, 2025

   Abs DOI Bib HTML

   Runs of homozygosity (ROH) are contiguous genomic regions where all sites are homozygous, inherited from identical haplotypes due to shared ancestry. The number and length of ROH in individuals varies based on population history and sociocultural behaviors. Although often discussed in the context of inbreeding, ROH are ubiquitous in putatively outbred human populations, and their prevalence are associated with multiple complex traits, including height and measures of lung function. Importantly, ROH have been shown to be enriched for deleterious alleles, suggesting a mechanism by which ROH prevalence can influence traits. Here we employ realistic forward-in-time population genetic simulations and a flexible quantitative model of a generic complex phenotype to explore how population history and genetic architecture influence ROH associations with a generic quantitative phenotype. We show that ROH are important for all simulated demographic histories and genetic architectures but especially when phenotypes have a recessive component. This is even more prominent when the rare-allele contribution to the phenotype is upweighted and in high-diversity populations (e.g. African). For a fully recessive phenotype, ROH can account for 25-55% of an individual’s total genotypic score, depending on demographic history and rare-allele weight. Our results emphasize the utility of ROH in helping to explain phenotype variation across different population histories and genetic architectures.

   @article{pan2025influence,
     title = {The Influence of Demographic History and Genetic Architecture on Complex Traits via Runs of Homozygosity},
     author = {Pan, Mingzuyu and Szpiech, Zachary A},
     journal = {bioRxiv},
     year = {2025},
     doi = {10.64898/2025.12.17.694908},
   }

2023

1. Making waves: Comparative analysis of gene drive spread characteristics in a continuous space model

   Mingzuyu Pan and Jackson Champer^*

   Molecular Ecology, 2023

   Abs DOI Bib HTML

   With their ability to rapidly increase in frequency, gene drives can be used to modify or suppress target populations after an initial release of drive individuals. Recent advances have revealed many possibilities for different types of drives, and several of these have been realized in experiments. These drives have advantages and disadvantages related to their ease of construction, confinement and capacity to be used for modification or suppression. Though characteristics of these drives have been explored in modelling studies, assessment in continuous space environments has been limited, often focusing on outcomes rather than fundamental properties. Here, we conduct a comparative analysis of many different gene drive types that have the capacity to form a wave of advance in continuous space using individual-based simulations in continuous space. We evaluate the drive wave speed as a function of drive performance and ecological parameters, which reveals substantial differences between drive performance in panmictic versus spatial environments. In particular, we find that suppression drive waves are uniquely vulnerable to fitness costs and undesired CRISPR cleavage activity in embryos by maternal deposition. Some drives, however, retain robust performance even with widely varying efficiency parameters. To gain a better understanding of drive waves, we compare their panmictic performance and find that the rate of wild-type allele removal is correlated with drive wave speed, though this is also affected by other factors. Overall, our results provide a useful resource for understanding the performance of drives in spatially continuous environments, which may be most representative of potential drive deployment in many relevant scenarios.

   @article{pan2023making,
     title = {Making waves: Comparative analysis of gene drive spread characteristics in a continuous space model},
     author = {Pan, Mingzuyu and Champer, Jackson},
     journal = {Molecular Ecology},
     volume = {32},
     number = {20},
     pages = {5673--5694},
     year = {2023},
     publisher = {Wiley Online Library},
     doi = {10.1111/mec.17131},
   }