Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

Limited historical admixture between European wildcats and domestic cats

(2023) Alexandra Jamieson et al.   CURRENT BIOLOGY

The Genic View of Hybridization in the Anthropocene

(2021) Jente Ottenburghs   Evolutionary Applications

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

On the use of genome‐wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat

(2021) Jo Howard‐McCombe et al.   MOLECULAR ECOLOGY

Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats

(2021) He Yu et al.   Science Advances

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

(2021) Yang Luo et al.   NATURE GENETICS

Projecting introgression from domestic cats into European wildcats in the Swiss Jura

(2020) Claudio S. Quilodrán et al.   Evolutionary Applications

Recent demographic history inferred by high-resolution analysis of linkage disequilibrium

(2020) Enrique Santiago et al.   MOLECULAR BIOLOGY AND EVOLUTION

Harmonizing hybridization dissonance in conservation

(2020) Claudio S. Quilodrán et al.   Communications Biology

Recent and rapid anthropogenic habitat fragmentation increases extinction risk for freshwater biodiversity

(2020) Chris J. Brauer et al.   Evolutionary Applications

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

(2020) Reuben M. Buckley et al.   PLoS Genetics

Genetic rescue and the maintenance of native ancestry

(2019) Kelley Harris et al.   CONSERVATION GENETICS

Fine-Scale Inference of Ancestry Segments Without Prior Knowledge of Admixing Groups

(2019) Michael Salter-Townshend et al.   GENETICS

Hybridization as a conservation management tool

(2019) Wing Yan Chan et al.   Conservation Letters

Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones

(2019) Katarzyna Dudek et al.   MOLECULAR ECOLOGY

Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations

(2019) Federica Mattucci et al.   Scientific Reports

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Range expansion as an explanation for introgression in European wildcats

(2018) B. Nussberger et al.   BIOLOGICAL CONSERVATION

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Domestic cat neutering to preserve the Scottish wildcat

(2018) Anna Meredith et al.   VETERINARY RECORD

Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration

(2018) Helen V. Senn et al.   Evolutionary Applications

Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population

(2017) Marco Galaverni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomewide analysis of admixture and adaptation in the Africanized honeybee

(2017) Ronald M. Nelson et al.   MOLECULAR ECOLOGY

HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes

(2017) Idan Alter et al.   PLoS Computational Biology

Hybridization and extinction

(2016) Marco Todesco et al.   Evolutionary Applications

Hybridization and endangered species protection in the molecular era

(2016) Robert K. Wayne et al.   MOLECULAR ECOLOGY

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination

(2016) Gang Li et al.   G3-Genes Genomes Genetics

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

(2015) Gang Li et al.   GENOME RESEARCH

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Strong spatial segregation between wildcats and domestic cats may explain low hybridization rates on the Iberian Peninsula

(2015) J.M. Gil-Sánchez et al.   ZOOLOGY

Improving access to endogenous DNA in ancient bones and teeth

(2015) Peter B. Damgaard et al.   Scientific Reports

Mapping the spatial configuration of hybridization risk for an endangered population of the European wildcat (Felis silvestris silvestris) in Scotland

(2015) Kerry Kilshaw et al.   Mammal Research

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Selective enrichment of damaged DNA molecules for ancient genome sequencing

(2014) Marie-Theres Gansauge et al.   GENOME RESEARCH

A Genetic Atlas of Human Admixture History

(2014) G. Hellenthal et al.   SCIENCE

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

(2014) Christine Grossen et al.   PLoS Genetics

Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds

(2013) Carmen Amador et al.   Evolutionary Applications

The genetic legacy of the 19th-century decline of the British polecat: evidence for extensive introgression from feral ferrets

(2013) M. Costa et al.   MOLECULAR ECOLOGY

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Estimating Contemporary Effective Population Size on the Basis of Linkage Disequilibrium in the Face of Migration

(2011) Robin S. Waples et al.   GENETICS

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The genetic legacy of extirpation and re-colonization in Vancouver Island wolves

(2009) Violeta Muñoz-Fuentes et al.   CONSERVATION GENETICS