David Peede
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View article: Highly contiguous assemblies of 101 drosophilid genomes
Highly contiguous assemblies of 101 drosophilid genomes Open
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for severa…
View article: The genomics of the domestication syndrome in a songbird model species
The genomics of the domestication syndrome in a songbird model species Open
Many domesticated animals share a syndromic phenotype marked by a suite of traits that include more variable patterns of coloration, reduced stress, aggression, and altered risk-taking and exploratory behaviors relative to their wild count…
View article: Not Just $N_e$ $N_e$-more: New Applications for SMC from Ecology to Phylogenies
Not Just $N_e$ $N_e$-more: New Applications for SMC from Ecology to Phylogenies Open
Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Markovian coalescent (SMC) is a versatile…
View article: Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis
Sex differentiation, divergence, and introgression in the leishmaniasis vector Lutzomyia longipalpis Open
An estimated one billion people are at risk of acquiring the disease leishmaniasis annually. This disease, among others, is transmitted to humans via sandfly vectors of the family Psychodidae. In the Neotropics, Lutzomyia longipalpis is on…
View article: To Tame a Songbird: The Genomics of the Domestication Syndrome in a Songbird Model Species
To Tame a Songbird: The Genomics of the Domestication Syndrome in a Songbird Model Species Open
Many domesticated animals share a syndromic phenotype marked by a suite of traits that include more variable patterns of coloration, reduced stress, aggression, and altered risk-taking and exploratory behaviors relative to their wild count…
View article: Toward the integration of speciation research
Toward the integration of speciation research Open
Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly div…
View article: Leveraging shared ancestral variation to detect local introgression
Leveraging shared ancestral variation to detect local introgression Open
Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson’s D statistic can detect introgression by measuring an excess of shared derive…
View article: Toward the integration of speciation research
Toward the integration of speciation research Open
Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly div…
View article: Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications
Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications Open
Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes—…
View article: The <i>MUC19</i> Gene: An Evolutionary History of Recurrent Introgression and Natural Selection
The <i>MUC19</i> Gene: An Evolutionary History of Recurrent Introgression and Natural Selection Open
We study the gene MUC19 , for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype…
View article: Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia
Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia Open
Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancie…
View article: Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Full text Figures and data Side by side Abstract eLife assessment Introduction Data availability References Peer review Author response Article and author information Metrics Abstract Simulation is a key tool in population genetics for bot…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulati…
View article: Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Author Response: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulati…
View article: The Utility of Ancestral and Derived Allele Sharing for Genome-Wide Inferences of Introgression
The Utility of Ancestral and Derived Allele Sharing for Genome-Wide Inferences of Introgression Open
The past decade has ushered in a resurgence of studies highlighting the importance of introgression throughout the Tree of Life. Several methods exist for detecting and quantifying introgression on a genomic scale, yet the majority of thes…
View article: Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations Open
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulat…
View article: Patterns of Population Structure and Introgression Among Recently Differentiated <i>Drosophila melanogaster</i> Populations
Patterns of Population Structure and Introgression Among Recently Differentiated <i>Drosophila melanogaster</i> Populations Open
Despite a century of genetic analysis, the evolutionary processes that have generated the patterns of exceptional genetic and phenotypic variation in the model organism Drosophila melanogaster remains poorly understood. In particular, how …
View article: A need for standardized reporting of introgression: Insights from studies across eukaryotes
A need for standardized reporting of introgression: Insights from studies across eukaryotes Open
With the rise of affordable next-generation sequencing technology, introgression—or the exchange of genetic materials between taxa—has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by sev…
View article: Correction: Highly contiguous assemblies of 101 drosophilid genomes
Correction: Highly contiguous assemblies of 101 drosophilid genomes Open
View article: Widespread introgression across a phylogeny of 155 Drosophila genomes
Widespread introgression across a phylogeny of 155 Drosophila genomes Open
View article: <i>P</i> ‐elements strengthen reproductive isolation within the <i>Drosophila simulans</i> species complex
<i>P</i> ‐elements strengthen reproductive isolation within the <i>Drosophila simulans</i> species complex Open
Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in mod…
View article: Highly contiguous assemblies of 101 drosophilid genomes
Highly contiguous assemblies of 101 drosophilid genomes Open
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this …
View article: Author response: Highly contiguous assemblies of 101 drosophilid genomes
Author response: Highly contiguous assemblies of 101 drosophilid genomes Open
Article Figures and data Abstract Introduction Results and discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Over 100 years of studies in Drosophil…
View article: 15 years of introgression studies: quantifying gene flow across Eukaryotes
15 years of introgression studies: quantifying gene flow across Eukaryotes Open
With the rise of affordable next generation sequencing technology, introgression — or the exchange of genetic materials between taxa — is widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several…
View article: Highly contiguous assemblies of 101 drosophilid genomes
Highly contiguous assemblies of 101 drosophilid genomes Open
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this …
View article: Widespread introgression across a phylogeny of 155<i>Drosophila</i>genomes
Widespread introgression across a phylogeny of 155<i>Drosophila</i>genomes Open
Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across en…