Jeffrey D. Jensen

Inferring the landscapes of mutation and recombination in the common marmoset (Callithrix jacchus) in the presence of twinning and hematopoietic chimerism

This study infers mutation and recombination rates in common marmosets, accounting for twinning and chimerism, and identifies PRDM9-mediated recombination hotspots.

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data

This study infers the demographic history of Chinese and Indian rhesus macaque populations using PacBio HiFi long-read sequencing data, revealing a split time and population size changes.

Inferring the relative contributions of evolutionary processes shaping X chromosome dynamics in the common marmoset (Callithrix jacchus) in the presence of twinning and hematopoietic chimerism

The paper estimates mutation and recombination rates on the X chromosome of common marmosets, accounting for twinning and hematopoietic chimerism, and finds reduced X-linked rates and evidence of recent selective sweeps.

Sex-specific landscapes of crossover and non-crossover recombination in coppery titi monkeys (Plecturocebus cupreus)

This study estimates crossover and non-crossover recombination rates and patterns in coppery titi monkeys, finding sex-neutral rates but sex-specific genomic distributions of non-crossover events.

Inferring fine-scale rates of mutation and recombination in the coppery titi monkey (Plecturocebus cupreus)

The paper infers fine-scale mutation and recombination rates in the coppery titi monkey using divergence and polymorphism data and a high-quality genome, aligning with rates in other primates.

Evolutionary genomics based on PacBio HiFi long-read sequencing data reveals the importance of structural variants in shaping population-specific differences between Chinese and Indian rhesus macaques (Macaca mulatta)

This study uses PacBio HiFi long-read sequencing to analyze structural variants in Chinese and Indian rhesus macaques, revealing population-specific differences in genes related to neural communication and disease susceptibility.

Comparing fine-scale mutation and recombination landscapes in rhesus macaque (Macaca mulatta) populations of Chinese and Indian descent inferred from both short- and long-read sequencing data

This study compares mutation and recombination landscapes in rhesus macaques from Chinese and Indian populations using short- and long-read sequencing data, revealing population-specific recombination hotspots.

Inferring the demographic history of coppery titi monkeys (Plecturocebus cupreus) from high-quality, whole-genome, population-level data

This study uses whole-genome sequencing of coppery titi monkeys to infer their demographic history, finding population size changes align with speciation times and climatic events.

Inferring patterns of purifying, positive and balancing selection in the coppery titi monkey (Plecturocebus cupreus) utilizing a well-fit evolutionary baseline model

This study identifies patterns of purifying, positive, and balancing selection in the coppery titi monkey using a demographic model and genome-wide scans.

Characterizing the rates and patterns of de novo germline mutations in coppery titi monkeys (Plecturocebus cupreus)

This study characterizes de novo mutation rates and patterns in coppery titi monkeys, finding a sex-averaged mutation rate and a strong paternal age effect in males.

The landscape of structural variation in coppery titi monkeys (Plecturocebus cupreus)

This study maps structural variation in coppery titi monkeys using whole-genome sequencing, identifying over 13,000 variants, including disease-associated genes and a high de novo mutation rate.

Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis)

This study infers fine-scale mutation and recombination rate maps in aye-ayes using genomic data, finding lower rates compared to other primates.

Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (Callithrix jacchus)

This study quantifies selection pressures in common marmosets, finding increased purifying selection and balancing selection in immune-related genes.

The landscape of structural variation in aye-ayes (Daubentonia madagascariensis)

This study identifies over 1,000 structural variants in aye-ayes using whole-genome sequencing, revealing their impact on gene function and regulatory elements.

Estimating the distribution of fitness effects in aye-ayes (Daubentonia madagascariensis),accounting for population history as well as mutation and recombination rate heterogeneity

The paper infers the distribution of fitness effects in aye-ayes, considering population history and mutation/recombination rate variation, finding more deleterious mutations and rapid evolution in immune and sensory genes.

Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (Callithrix jacchus) from high-quality, whole-genome, population-level data

The paper develops a Bayesian inference method to account for twin births and chimerism in marmoset population genetics, revealing a population size reduction 7,000 years ago.

A pedigree-based map of crossovers and non-crossovers in aye-ayes (Daubentonia madagascariensis)

The paper maps crossover and non-crossover recombination patterns in aye-ayes using whole-genome sequencing data from pedigrees, providing insights into genomic diversity in an endangered species.

A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model

This study identifies genes under balancing selection in aye-ayes using whole-genome data and an evolutionary baseline model, highlighting olfactory-related genes.

Characterizing the rates and patterns of de novo germline mutations in the aye-aye (Daubentonia madagascariensis)

This study analyzes de novo mutations in aye-ayes using whole-genome sequencing and a novel pipeline to estimate mutation rates and explore parental age and sex effects.

Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data

The paper infers demographic and selective histories from population genomic data using a two-step approach, applied to human data to account for background selection effects.

Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data

This study infers the demographic history of aye-ayes using genomic data, finding two population size reductions linked to human arrival and habitat loss.

The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects

This study shows that ignoring mutation and recombination rate heterogeneity can increase uncertainty and lead to misleading inferences in population genetic analyses.

Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models

The paper evaluates the power to detect recurrent selective sweeps under realistic evolutionary models and finds low detection power despite reduced false positives.

Within-host Mycobacterium tuberculosis evolution: a population genetics perspective

This study develops a population genetics model for Mycobacterium tuberculosis to infer evolutionary parameters within hosts, revealing faster mutation rates and skewed progeny distribution compared to standard models.

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions

The paper introduces MMC-ABC, a method for inferring demography and selection under multiple-merger coalescent models, and applies it to influenza virus data to identify drug-resistance mutations.

The fitness consequences of genetic variation in wild populations of mice

The paper investigates how genetic variation in wild mice affects fitness by linking genotype to phenotype and allele frequency changes through field and lab experiments.