James M. Alfieri
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View article: From Micro to Macro: Avian Chromosome Evolution is Dominated by Natural Selection
From Micro to Macro: Avian Chromosome Evolution is Dominated by Natural Selection Open
Birds display striking variation in chromosome number, defying the traditional view of highly conserved avian karyotypes. However, the evolutionary drivers of this variability remain unclear. To address this, we fit probabilistic models of…
View article: Genome assembly of the southern pine beetle ( <i>Dendroctonus frontalis</i> Zimmerman) reveals the origins of gene content reduction in <i>Dendroctonus</i>
Genome assembly of the southern pine beetle ( <i>Dendroctonus frontalis</i> Zimmerman) reveals the origins of gene content reduction in <i>Dendroctonus</i> Open
Dendroctonus frontalis also known as southern pine beetle (SPB), is the most damaging insect forest pest in the southeastern United States. Genomic data are important to provide information on pest biology and to identify molecular targets…
View article: A reference quality genome assembly for the jewel scarab <i>Chrysina gloriosa</i>
A reference quality genome assembly for the jewel scarab <i>Chrysina gloriosa</i> Open
The jewel scarab Chrysina gloriosa is one of the most charismatic beetles in the United States and is found from the mountains of West Texas to the Southeastern Arizona sky islands. This species is highly sought by professional and amateur…
View article: Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera
Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera Open
Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an impor…
View article: A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants Open
Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importanc…
View article: A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants Open
View article: A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants Open
View article: Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes)
Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes) Open
Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolatio…
View article: A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants Open
Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial import…
View article: Tempo and Mode of Genome Structure Evolution in Insects
Tempo and Mode of Genome Structure Evolution in Insects Open
The division of the genome into discrete chromosomes is a fundamental characteristic of eukaryotic life. Insect taxonomists’ early adoption of cytogenetics has led to an incredible amount of data describing genome structure across insects.…
View article: Genomic investigation refutes record of most diverged avian hybrid
Genomic investigation refutes record of most diverged avian hybrid Open
The most diverged avian hybrid that has been documented ( Numida meleagris × Penelope superciliaris ) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identificatio…
View article: Why not Y naught
Why not Y naught Open
View article: A Primer for Single-Cell Sequencing in Non-Model Organisms
A Primer for Single-Cell Sequencing in Non-Model Organisms Open
Single-cell sequencing technologies have led to a revolution in our knowledge of the diversity of cell types, connections between biological levels of organization, and relationships between genotype and phenotype. These advances have main…
View article: Fourth Report on Chicken Genes and Chromosomes 2022
Fourth Report on Chicken Genes and Chromosomes 2022 Open
Introduction: The chicken continues to hold its position as a leading model organism within many areas of research, as well as being a major source of protein for human consumption. The First Report on Chicken Genes and Chromosomes [Schmid…
View article: Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, Fundulus heteroclitus
Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, Fundulus heteroclitus Open
This study examined the relationship between urbanization and parasite community structure in the estuarine fish, Fundulus heteroclitus. We measured landscape and physicochemical factors associated with urbanization at 6 sites from 4 colle…
View article: Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, Fundulus heteroclitus
Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, Fundulus heteroclitus Open
Purpose : This document describes the file contents and variable coding for 6 csv files associated with PONE-D-19-21171.File Name : biological.csvFile Description : This file contains parasite abundances, host information, and collection i…
View article: Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, <i>Fundulus heteroclitus</i>
Life-cycle mediated effects of urbanization on parasite communities in the estuarine fish, <i>Fundulus heteroclitus</i> Open
This study examined the relationship between urbanization and parasite community structure in the estuarine fish, Fundulus heteroclitus . We measured landscape and physicochemical factors associated with urbanization at 6 sites from 4 coll…