Ellie E. Armstrong

CBS-tools identifies, phases, and annotates sex chromosomes using k-mer analysis from whole-genome sequencing data across multiple species.

This study shows that higher recombination rates modestly speed up adaptation in populations, primarily by reducing Hill-Robertson interference, with effects varying by demographic history.

The paper analyzes deleterious mutations in cheetah populations, finding higher inbreeding and sperm-related mutation enrichment in certain populations.

This study sequenced whole genomes of black-footed cats to analyze their population structure and genetic diversity, finding low diversity but no long runs of homozygosity and evidence of recent population contraction.

This study uses whole-genome sequencing of 41 snow leopards to show they have the lowest genetic diversity of any big cat species due to long-term small population size, not recent inbreeding.

This study shows that using a conspecific reference genome improves variant detection and genetic diversity estimates compared to heterospecific references in gray foxes.

The paper estimates de novo mutation rates in Panthera and Neofelis species using pedigrees, finding rates between 0.5 and 1.4e-08 per generation per base pair.

The paper uses whole-genome sequencing of historical and recent lion populations to show population fragmentation and genetic diversity loss in East Africa over the past century.

The paper develops a SNP panel for identifying snow leopard individuals from fecal samples, validated with zoo and field samples, showing high accuracy and utility for population assessment.

This paper develops a SNP selection pipeline, mPCRselect, to design cost-effective SNP panels for population assignment and individual identification in non-model species.

The paper presents a chromosome-level genome assembly for the gray fox, confirming the loss of PRDM9 functionality in the basal canid lineage.

The paper provides genomic resources for Asian and African savannah elephants to aid conservation and health research through genome sequencing, mutation rate estimation, demographic reconstruction, and a capture assay for genotyping.

RatesTools detects de novo germline mutations in pedigree sequence data by analyzing parent-offspring trio data and calculating mutation rates.

The paper presents chromosome-level genome assemblies for the snow leopard, African leopard, and tiger to support evolutionary and conservation research.

This paper presents a high-quality, chromosome-level genome assembly of the brown bear, improving upon previous assemblies and enabling better analysis of evolutionary and medical traits.

This study analyzes tiger genomes to understand their evolutionary history, finding genetic differentiation, recent divergence, and selection pressures in different subspecies.

The paper presents a chromosome-level genome assembly for the African lion using linked-read, Hi-C, and long-read data, revealing population history insights.

The paper sequenced genomes of birds-of-paradise to identify genomic changes linked to their phenotypic diversity, finding strong selection on coloration, morphology, and sensory systems.

This paper presents a cost-effective method to assemble high-quality genomes for the African wild dog using linked-read sequencing, highlighting its high heterozygosity and potential applications in conservation genetics.