Devon A. DeRaad
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View article: Strong selection maintains a narrow, stable tension zone between grosbeak species in the Great Plains
Strong selection maintains a narrow, stable tension zone between grosbeak species in the Great Plains Open
When genetically divergent and geographically isolated lineages come back into contact, their interactions allow us to observe reproductive isolating barriers in action. The avian contact zone between Pheucticus melanocephalus and P. ludov…
View article: Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants
Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants Open
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…
View article: A Next Generation of Hierarchical Bayesian Analyses of Hybrid Zones Enables Model‐Based Quantification of Variation in Introgression in R
A Next Generation of Hierarchical Bayesian Analyses of Hybrid Zones Enables Model‐Based Quantification of Variation in Introgression in R Open
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.…
View article: Phylogeography of the Island Leaf Warbler (Aves: Phylloscopus Poliocephalus) in Northern Melanesia Reveals Rapid Secondary Sympatry or Ecological Speciation on Kolombangara Island, Solomon Islands
Phylogeography of the Island Leaf Warbler (Aves: Phylloscopus Poliocephalus) in Northern Melanesia Reveals Rapid Secondary Sympatry or Ecological Speciation on Kolombangara Island, Solomon Islands Open
Island archipelagos are well known for promoting geographic and adaptive radiations in terrestrial animals. Sympatry of closely related species in island systems has been thought to occur primarily through double-invasions from the same co…
View article: Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators
Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators Open
The paradox of the great speciators describes a contradictory biogeographic pattern exhibited by numerous avian lineages in Oceania. Specifically, these lineages display broad geographic distributions across the region, implying strong ove…
View article: A shallow‐scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)
A shallow‐scale phylogenomics approach reveals repeated patterns of diversification among sympatric lineages of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae) Open
The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this grou…
View article: A next generation of hierarchical Bayesian analyses of hybrid zones enables direct quantification of variation in introgression in R
A next generation of hierarchical Bayesian analyses of hybrid zones enables direct quantification of variation in introgression in R Open
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. T…
View article: Parallel evolution in an island archipelago revealed by genomic sequencing of <i>Hipposideros</i> leaf-nosed bats
Parallel evolution in an island archipelago revealed by genomic sequencing of <i>Hipposideros</i> leaf-nosed bats Open
Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, l…
View article: Convergent niche shifts of endangered parrots (genus <i>Amazona</i> ) during successful establishment in urban southern California
Convergent niche shifts of endangered parrots (genus <i>Amazona</i> ) during successful establishment in urban southern California Open
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 species Red‐crowned ( A. viridigenalis ) and Lilac‐crowned P…
View article: A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)
A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae) Open
The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this grou…
View article: De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, <i>Aphelocoma californica</i>
De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, <i>Aphelocoma californica</i> Open
We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoam…
View article: An elevational shift facilitated the Mesoamerican diversification of Azure‐hooded Jays (<i>Cyanolyca cucullata</i>) during the Great American Biotic Interchange
An elevational shift facilitated the Mesoamerican diversification of Azure‐hooded Jays (<i>Cyanolyca cucullata</i>) during the Great American Biotic Interchange Open
The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction,…
View article: A highly contiguous reference genome for the Steller’s jay (<i>Cyanocitta stelleri</i>)
A highly contiguous reference genome for the Steller’s jay (<i>Cyanocitta stelleri</i>) Open
The Steller’s jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part …
View article: Temporal stability of the hybrid zone between <i>Calocitta</i> magpie‐jays revealed through comparison of museum specimens and <scp>iNaturalist</scp> photos
Temporal stability of the hybrid zone between <i>Calocitta</i> magpie‐jays revealed through comparison of museum specimens and <span>iNaturalist</span> photos Open
Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studi…
View article: Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in<i>Pipilo</i>towhees
Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in<i>Pipilo</i>towhees Open
Hybrid zones can be studied by modeling clines of trait variation (e.g., morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid linea…
View article: SNPfiltR: an R package for interactive and reproducible SNP filtering
SNPfiltR: an R package for interactive and reproducible SNP filtering Open
Here I describe the novel R package SNPfiltR and demonstrate its functionalities as the backbone of a customizable, reproducible SNP filtering pipeline implemented exclusively via the widely adopted R programming language. SNPfiltR extends…
View article: Niche shifts lead to hybridization between two<i>Amazona</i>parrot sister-species introduced to Southern California
Niche shifts lead to hybridization between two<i>Amazona</i>parrot sister-species introduced to Southern California Open
This paper has been withdrawn by the authors while evaluating reviewer concerns about interpretation of the genomic data and due to errors found by the authors in the scoring of photos. Therefore, the authors do not wish this work to be ci…
View article: Geographic potential of the world’s largest hornet, <i>Vespa mandarinia</i> Smith (Hymenoptera: Vespidae), worldwide and particularly in North America
Geographic potential of the world’s largest hornet, <i>Vespa mandarinia</i> Smith (Hymenoptera: Vespidae), worldwide and particularly in North America Open
The Asian giant hornet (AGH, Vespa mandarinia ) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian …
View article: New Guinea Erythrura parrotfinches: one species or two?
New Guinea Erythrura parrotfinches: one species or two? Open
Two species of Erythrura parrotfinches, differing mainly in bill size, are described from the New Guinea highlands: Blue-faced Parrotfinch E. trichroa and Papuan Parrotfinch E. papuana. Morphological measurements from museum specimens supp…
View article: Geographic potential of the world’s largest hornet,<i>Vespa mandarinia</i>Smith (Hymenoptera: Vespidae), worldwide and particularly in North America
Geographic potential of the world’s largest hornet,<i>Vespa mandarinia</i>Smith (Hymenoptera: Vespidae), worldwide and particularly in North America Open
The Asian giant hornet (AGH, Vespa mandarinia ) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian …
View article: Evidence of Intergradation within the Golden-cheeked Woodpecker
Evidence of Intergradation within the Golden-cheeked Woodpecker Open
The Golden-cheeked Woodpecker (Melanerpes chrysogenys), restricted to the Pacific slope of Mexico from Sinaloa to Oaxaca, comprises two subspecies.Nominate M. c. chrysogenys, identified by its extensively red crown, ranges from Sinaloa sou…
View article: Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird
Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird Open
Venkatraman, Madhvi X., Deraad, Devon A., Tsai, Whitney L. E., Zarza, Eugenia, Zellmer, Amanda J., Maley, James M., Mccormack, John E. (2019): Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within…
View article: Geographic Variation and Intergradation in the Elegant Quail
Geographic Variation and Intergradation in the Elegant Quail Open
The Elegant Quail (Callipepla douglasii) is restricted to western mainland Mexico from Sonora south to Jalisco.It comprises five subspecies, described primarily on the basis of differences in plumage color and patterns.To assess patterns o…