Susanne P. Pfeifer
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View article: Interpreting Patterns of X Chromosomal Relative to Autosomal Diversity in Aye‐Ayes ( <i>Daubentonia madagascariensis</i> )
Interpreting Patterns of X Chromosomal Relative to Autosomal Diversity in Aye‐Ayes ( <i>Daubentonia madagascariensis</i> ) Open
We here present high‐quality, population‐level sequencing data from the X chromosome of the highly‐endangered aye‐aye, Daubentonia madagascariensis . Using both polymorphism‐ and divergence‐based inference approaches, we quantify fine‐scal…
View article: Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye‐Aye ( <i>Daubentonia madagascariensis</i> )
Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye‐Aye ( <i>Daubentonia madagascariensis</i> ) Open
Endemic to the island of Madagascar, the enigmatic aye‐aye is amongst the most endangered primates on the planet. Due to their nocturnal and arboreal lifestyle and large geographic ranges, much remains unknown about these lemurs. The publi…
View article: Inferring Fine‐Scale Mutation and Recombination Rate Maps in Aye‐Ayes ( <i>Daubentonia madagascariensis</i> )
Inferring Fine‐Scale Mutation and Recombination Rate Maps in Aye‐Ayes ( <i>Daubentonia madagascariensis</i> ) Open
The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species but also across…
View article: Re‐Evaluating the Demographic History of, and Inferring the Fine‐Scale Recombination Landscape For, Wild Chinese Rhesus Macaques ( <i>Macaca mulatta</i> )
Re‐Evaluating the Demographic History of, and Inferring the Fine‐Scale Recombination Landscape For, Wild Chinese Rhesus Macaques ( <i>Macaca mulatta</i> ) Open
As a major model for biomedical research, the rhesus macaque ( Macaca mulatta ) is one of the most important and heavily studied nonhuman primates. Despite this importance, the level of population structure and subspecific division in this…
View article: Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (Callithrix jacchus)
Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (Callithrix jacchus) Open
The common marmoset ( Callithrix jacchus ) is of considerable biomedical importance, yet there remains a need to characterize the evolutionary forces shaping empirically observed patterns of genomic variation in the species. However, two u…
View article: The Landscape of Structural Variation in Aye-Ayes (<i>Daubentonia madagascariensis</i>)
The Landscape of Structural Variation in Aye-Ayes (<i>Daubentonia madagascariensis</i>) Open
Aye-ayes (Daubentonia madagascariensis) are one of the 25 most critically endangered primate species in the world. Endemic to Madagascar, their small and highly fragmented populations make them particularly vulnerable to both genetic disea…
View article: Inferring the landscapes of mutation and recombination in the common marmoset (<i>Callithrix jacchus</i>) in the presence of twinning and hematopoietic chimerism
Inferring the landscapes of mutation and recombination in the common marmoset (<i>Callithrix jacchus</i>) in the presence of twinning and hematopoietic chimerism Open
The common marmoset is an important model in biomedical and clinical research, particularly for the study of age-related, neurodegenerative, and neurodevelopmental disorders (due to their biological similarities with humans), infectious di…
View article: Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (<i>Callithrix jacchus</i>)
Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (<i>Callithrix jacchus</i>) Open
The common marmoset ( Callithrix jacchus ) is of considerable biomedical importance, yet there remains a need to characterize the evolutionary forces shaping empirically observed patterns of genomic variation in the species. However, two u…
View article: Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets ( <i>Callithrix jacchus</i> ) from High-Quality, Whole-Genome, Population-Level Data
Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets ( <i>Callithrix jacchus</i> ) from High-Quality, Whole-Genome, Population-Level Data Open
As a species of considerable biomedical importance, characterizing the evolutionary genomics of the common marmoset (Callithrix jacchus) is of significance across multiple fields of research. However, at least 2 peculiarities of this speci…
View article: A Pedigree-Based Map of Crossovers and Noncrossovers in Aye-Ayes ( <i>Daubentonia madagascariensis</i> )
A Pedigree-Based Map of Crossovers and Noncrossovers in Aye-Ayes ( <i>Daubentonia madagascariensis</i> ) Open
Gaining a better understanding of the rates and patterns of meiotic recombination is crucial for improving evolutionary genomic modeling, with applications ranging from demographic to selective inference. Although previous research has pro…
View article: A whole-genome scan for evidence of positive and balancing selection in aye-ayes ( <i>Daubentonia madagascariensis</i> ) utilizing a well-fit evolutionary baseline model
A whole-genome scan for evidence of positive and balancing selection in aye-ayes ( <i>Daubentonia madagascariensis</i> ) utilizing a well-fit evolutionary baseline model Open
The aye-aye (Daubentonia madagascariensis) is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation within…
View article: Characterizing the Rates and Patterns of <i>De Novo</i> Germline Mutations in the Aye-Aye (<i>Daubentonia madagascariensis</i>)
Characterizing the Rates and Patterns of <i>De Novo</i> Germline Mutations in the Aye-Aye (<i>Daubentonia madagascariensis</i>) Open
Given the many levels of biological variation in mutation rates observed to date in primates—spanning from species to individuals to genomic regions—future steps in our understanding of mutation rate evolution will not only be aided by a g…
View article: Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (<i>Callithrix jacchus</i>) from high-quality, whole-genome, population-level data
Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (<i>Callithrix jacchus</i>) from high-quality, whole-genome, population-level data Open
As a species of considerable biomedical importance, characterizing the evolutionary genomics of the common marmoset ( Callithrix jacchus ) is of significance across multiple fields of research. However, at least two peculiarities of this s…
View article: Interpreting patterns of X chromosomal relative to autosomal diversity in aye-ayes (<i>Daubentonia madagascariensis</i>)
Interpreting patterns of X chromosomal relative to autosomal diversity in aye-ayes (<i>Daubentonia madagascariensis</i>) Open
We here present high-quality, population-level sequencing data from the X chromosome of the highly-endangered aye-aye, Daubentonia madagascariensis . Using both polymorphism- and divergence-based inference approaches, we quantify fine-scal…
View article: Estimating the distribution of fitness effects in aye-ayes (<i>Daubentonia madagascariensis</i>), accounting for population history as well as mutation and recombination rate heterogeneity
Estimating the distribution of fitness effects in aye-ayes (<i>Daubentonia madagascariensis</i>), accounting for population history as well as mutation and recombination rate heterogeneity Open
The distribution of fitness effects (DFE) characterizes the range of selection coefficients from which new mutations are sampled, and thus holds a fundamentally important role in evolutionary genomics. To date, DFE inference in primates ha…
View article: Inferring the Demographic History of Aye-Ayes ( <i>Daubentonia madagascariensis</i> ) from High-Quality, Whole-Genome, Population-Level Data
Inferring the Demographic History of Aye-Ayes ( <i>Daubentonia madagascariensis</i> ) from High-Quality, Whole-Genome, Population-Level Data Open
The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of populat…
View article: Inferring fine-scale mutation and recombination rate maps in aye-ayes (<i>Daubentonia madagascariensis</i>)
Inferring fine-scale mutation and recombination rate maps in aye-ayes (<i>Daubentonia madagascariensis</i>) Open
The rate of input of new genetic mutations, and the rate at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations and species, but also acros…
View article: A pedigree-based map of crossovers and non-crossovers in aye-ayes (<i>Daubentonia madagascariensis</i>)
A pedigree-based map of crossovers and non-crossovers in aye-ayes (<i>Daubentonia madagascariensis</i>) Open
Gaining a better understanding of rates and patterns of meiotic recombination is crucial for improving evolutionary genomic modelling, with applications ranging from demographic to selective inference. Although previous research has provid…
View article: Inferring the demographic history of aye-ayes (<i>Daubentonia madagascariensis</i>) from high-quality, whole-genome, population-level data
Inferring the demographic history of aye-ayes (<i>Daubentonia madagascariensis</i>) from high-quality, whole-genome, population-level data Open
The nocturnal aye-aye, Daubentonia madagascariensis , is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of popula…
View article: A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (<i>Daubentonia madagascariensis</i>) utilizing a well-fit evolutionary baseline model
A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (<i>Daubentonia madagascariensis</i>) utilizing a well-fit evolutionary baseline model Open
The aye-aye ( Daubentonia madagascariensis ) is one of the 25 most endangered primate species in the world, maintaining amongst the lowest genetic diversity of any primate measured to date. Characterizing patterns of genetic variation with…
View article: The landscape of structural variation in aye-ayes (<i>Daubentonia madagascariensis</i>)
The landscape of structural variation in aye-ayes (<i>Daubentonia madagascariensis</i>) Open
Aye-ayes ( Daubentonia madagascariensis ) are one of the 25 most critically endangered primate species in the world. Endemic to Madagascar, their small and highly fragmented populations make them particularly vulnerable to both genetic dis…
View article: Characterizing the rates and patterns of<i>de novo</i>germline mutations in the aye-aye (<i>Daubentonia madagascariensis</i>)
Characterizing the rates and patterns of<i>de novo</i>germline mutations in the aye-aye (<i>Daubentonia madagascariensis</i>) Open
Given the many levels of biological variation in mutation rates observed to date in primates – spanning from species to individuals to genomic regions – future steps in our understanding of mutation rate evolution will be aided by both a g…
View article: The professional identity of STEM faculty as instructors of course-based research experiences
The professional identity of STEM faculty as instructors of course-based research experiences Open
The professional identity of scientists has historically been cultivated to value research over teaching, which can undermine initiatives that aim to reform science education. Course-Based Research Experiences (CRE) and the inclusive Resea…
View article: A hybrid genome assembly of the endangered aye-aye (<i>Daubentonia madagascariensis</i>)
A hybrid genome assembly of the endangered aye-aye (<i>Daubentonia madagascariensis</i>) Open
The aye-aye (Daubentonia madagascariensis) is the only extant member of the Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, the predominant usage of short-read sequencing h…
View article: De Novo Genome Assembly for the Coppery Titi Monkey (<i>Plecturocebus cupreus</i>): An Emerging Nonhuman Primate Model for Behavioral Research
De Novo Genome Assembly for the Coppery Titi Monkey (<i>Plecturocebus cupreus</i>): An Emerging Nonhuman Primate Model for Behavioral Research Open
The coppery titi monkey (Plecturocebus cupreus) is an emerging nonhuman primate model system for behavioral and neurobiological research. At the same time, the almost entire absence of genomic resources for the species has hampered insight…
View article: Complete genome sequence of the <i>Streptomyces</i> bacteriophage Amabiko
Complete genome sequence of the <i>Streptomyces</i> bacteriophage Amabiko Open
Amabiko is a lytic subcluster BE2 bacteriophage that infects Streptomyces scabiei —a bacterium causing common scab in potatoes. Its 131,414 bp genome has a GC content of 49.5% and contains 245 putative protein-coding genes, 45 tRNAs, and o…
View article: The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects
The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects Open
Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavor; however, despite clear evidence that both mutation a…
View article: Computational host range prediction—The good, the bad, and the ugly
Computational host range prediction—The good, the bad, and the ugly Open
The rapid emergence and spread of antimicrobial resistance across the globe have prompted the usage of bacteriophages (i.e. viruses that infect bacteria) in a variety of applications ranging from agriculture to biotechnology and medicine. …
View article: Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (<i>Macaca mulatta</i>)
Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (<i>Macaca mulatta</i>) Open
Meiotic recombination landscapes differ greatly between distantly and closely related taxa, populations, individuals, sexes, and even within genomes; however, the factors driving this variation are yet to be well elucidated. Here, we direc…
View article: The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects
The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects Open
Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavour; however, despite clear evidence that both mutation …