Vivak Soni

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.

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.

Can ancient DNA and other forms of time-sampled data aid in the inference of negative frequency dependent selection?

This paper uses simulation studies to show how time-sampled data can improve inference of negative frequency-dependent selection by distinguishing it from other selection types and population history effects.

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.

Interpreting patterns of X chromosomal relative to autosomal diversity in aye-ayes(Daubentonia madagascariensis)

The paper analyzes X chromosomal diversity in aye-ayes, finding no sex-specific demographic patterns and no evidence for recent selective sweeps.

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.

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 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.

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.