A5026090964- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Plant and animal studies
- Evolution and Paleontology Studies
- Insect and Arachnid Ecology and Behavior
- Wildlife Ecology and Conservation
- Species Distribution and Climate Change
- Fire effects on ecosystems
- Forest Insect Ecology and Management
- Wildlife Conservation and Criminology Analyses
- Avian ecology and behavior
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Insect and Pesticide Research
- Amphibian and Reptile Biology
- RNA and protein synthesis mechanisms
- Rangeland and Wildlife Management
- Genetic Mapping and Diversity in Plants and Animals
- Ecology and Vegetation Dynamics Studies
- Coleoptera Taxonomy and Distribution
- Evolution and Genetic Dynamics
- Bat Biology and Ecology Studies
- RNA modifications and cancer
- Ichthyology and Marine Biology
- Pacific and Southeast Asian Studies
Occidental College
2017-2025
University of Kansas
2020-2024
American Museum of Natural History
2020-2024
The Asian giant hornet (AGH, Vespa mandarinia ) is the world’s largest hornet, occurring naturally in Indomalayan region, where it a voracious predator of pollinating insects including honey bees. In September 2019, nest hornets was detected outside Vancouver, British Columbia; multiple individuals were Columbia and Washington state 2020; another found eradicated November 2020, indicating that AGH may have successfully wintered North America. Because tend to spread rapidly become pests,...
Here, I describe the R package snpfiltr and demonstrate its functionality as backbone of a customizable, reproducible single nucleotide polymorphism (SNP) filtering pipeline implemented exclusively via widely adopted programming language. SNPfiltR extends existing SNP functionalities by automating visualization key parameters such sequencing depth, quality, missing data proportion, allowing users to visually optimize implement thresholds within single, cohesive work session. All functions...
Abstract Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships species limits. In North America, cases complex speciation are common, due at least in part to the cyclical Pleistocene glacial history continent. Scrub-Jays genus Aphelocoma provide a useful case study because their range throughout America is structured by phylogeographic barriers with secondary contact between divergent lineages. Here, we show...
The highlands of Mesoamerica harbour some the highest biodiversity in world, especially cloud forests, but landscape drivers this diversification are not well known. Taxonomy region has been challenging owing to a lack consensus about how test species limits. We apply integrative taxonomy an emblematic Mesoamerican unicolored jay (Aphelocoma unicolor). assess divergence along three complementary axes (genetics, phenotype and ecological niche), finding evidence for differentiation among five...
Abstract Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately may have unique even conflicting evolutionary histories. Phylogenetic reconstructions from these can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance discordant histories between the mitochondrial genomes) has been widely documented, but its causes often considered idiosyncratic inscrutable. We...
Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range effective population size. We find rapid evolution architecture, including ~100 Mb variation size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat...
Abstract Hybrid zones are natural experiments for the study of avian evolution. can be dynamic, moving as species adjust to new climates and habitats, with unknown implications speciation. There relatively few studies that have comparable modern historic sampling assess change in hybrid zone location width over time, those generally found mixed results, many showing but others stability. The white‐throated magpie‐jay ( Calocitta formosa ) black‐throated colliei occur along western coast...
Abstract Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid also spatially complex, shift time, and even lead to the formation lineages with right combination dispersal vicariance. We reassessed Sibley’s (1950) gradient between Collared Towhee (Pipilo ocai) Spotted maculatus) in Central Mexico test whether it conformed typical tension-zone cline model. By comparing historical modern data, we found that centers...
Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading faulty assumptions of history. Here, we document parallel evolution the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic inference. We sequenced reduced representation genomic loci measured external characters from...
Abstract Hybrid zones, where genetically distinct groups of organisms meet and interbreed, offer valuable insights into the nature species speciation. Here, we present a new R package bgchm, for population genomic analyses hybrid zones. This extends updates existing bgc software combines Bayesian hierarchical clines with methods estimating indexes, interpopulation ancestry proportions, geographic clines. Compared to software, bgchm offers enhanced efficiency through Hamiltonian Monte Carlo...
The concept of a fundamental ecological niche is central to questions geographic distribution, population demography, species conservation, and evolutionary potential. However, robust inference genomic regions associated with adaptation particular environmental conditions remains difficult due the myriad potential confounding processes that can generate heterogeneous patterns variation across genome. Here, we interrogate role genome environment association (GEA) testing as an initial step in...
Abstract We announce the assembly of first de novo reference genome for California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study has revealed novel insights into evolutionary mechanisms driving diversification in natural systems. Additional history this group will require continued development high-quality, publicly available genomic...
Abstract The Steller’s jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report draft reference assembly for the species generated PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate highly contiguous complete with contig N50 7.8 Mb, scaffold 25.8 BUSCO completeness score 97.2%....
Abstract Aim Introduced species offer insight on whether and how organisms can shift their ecological niches during translocation. The genus Amazona offers a clear test case, where sister Red‐crowned ( A. viridigenalis ) Lilac‐crowned Parrots finschi have established breeding populations in southern California following introduction via the pet trade from Mexico they do not coexist. After establishment 1980s, introduced population sizes increased, with mixed flocks found throughout urban Los...
Abstract The paradox of the great speciators describes a contradictory biogeographic pattern exhibited by numerous avian lineages in Oceania. Specifically, these display broad geographic distributions across region, implying strong over-water dispersal capabilities; yet, they also repeated genetic and phenotypic divergence—even between geographically proximate islands—implying poor inter-island capabilities. One group originally cited as evidence for this is dwarf kingfishers genus Ceyx....
ABSTRACT Hybrid zones, where genetically distinct groups of organisms meet and interbreed, offer valuable insights into the nature species speciation. Here, we present a new R package, bgchm , for population genomic analyses hybrid zones. This package extends updates existing bgc software combines Bayesian hierarchical clines with methods estimating indexes, interpopulation ancestry proportions, geographic clines. Compared to software, offers enhanced efficiency through Hamiltonian Monte...
Here I describe the novel R package SNPfiltR and demonstrate its functionalities as backbone of a customizable, reproducible SNP filtering pipeline implemented exclusively via widely adopted programming language. extends existing by automating visualization key parameters such depth, quality, missing data, then allowing users to set filters based on optimized thresholds, all within single, cohesive working environment. All functions require vcfR object input, which can be easily generated...
The Solomon Islands host a diverse terrestrial vertebrate fauna which has played formative role in the development of speciation theory. Yet, despite over century biological exploration region, there are many islands for we have incomplete knowledge fauna. In 2019, spent 20 days on Tetepare Island Western Province, Islands. long history conservation action by local communities and it is now largest uninhabited tropical island world. We recorded 57 species birds, 13 mammals, 5 amphibians, 21...
The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of Americas. rising Panamanian land bridge ended isolation South America and ushered period dispersal, mass extinction, new community assemblages, which sparked competition, adaptation, speciation. Diversification across many bird groups, elevational zonation others, ties back to events triggered by GABI. But exact timing these is still being revealed, with recent studies suggesting much earlier time...
Abstract Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) comprises 7 subspecies, ranging from the Rocky Mountains to southern Mexico. We quantified phenotype of specimens throughout Mexico and found support for significant phenotypic differences between “Sumichrast’s group” in (A. w. sumichrasti A. remota) 2 subspecies northern Mexico, or “Woodhouse’s grisea cyanotis). Despite differentiation body size mantle color, we no clear geographic boundary groups, suggesting either a cline...
Two species of Erythrura parrotfinches, differing mainly in bill size, are described from the New Guinea highlands: Blue-faced Parrotfinch E. trichroa and Papuan papuana. Morphological measurements museum specimens support two non-overlapping groups, but mitochondrial DNA sequence data show negligible differences between species. These observations suggest that papuana may form a single highlands exhibits resource-based size polymorphism.