Inbreeding depression explains killer whale population dynamics

The critically endangered vaquita is not doomed to extinction by inbreeding depression

(2022) Jacqueline A. Robinson et al.   SCIENCE

Some hope and many concerns on the future of the vaquita

(2022) Aurora Garcia-Dorado et al.   HEREDITY

The genetic architecture of fitness drives population viability during rapid environmental change

(2021) Marty Kardos et al.   AMERICAN NATURALIST

The inflated significance of neutral genetic diversity in conservation genetics

(2021) João C. Teixeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Marine mammal conservation: over the horizon

(2021) SE Nelms et al.   Endangered Species Research

Mutation load decreases with haplotype age in wild Soay sheep

(2021) Martin A. Stoffel et al.   Evolution Letters

Vessels and their sounds reduce prey capture effort by endangered killer whales (Orcinus orca)

(2021) Marla M. Holt et al.   MARINE ENVIRONMENTAL RESEARCH

Runs of homozygosity in killer whale genomes provide a global record of demographic histories

(2021) Andrew D. Foote et al.   MOLECULAR ECOLOGY

Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal

(2021) M. A. Stoffel et al.   Nature Communications

The crucial role of genome-wide genetic variation in conservation

(2021) Marty Kardos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

(2021) Anubhab Khan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Passive acoustic monitoring of killer whales (Orcinus orca) reveals year-round distribution and residency patterns in the Gulf of Alaska

(2021) Hannah J. Myers et al.   Scientific Reports

Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex

(2020) Christine Grossen et al.   Nature Communications

Evaluating the outcomes of genetic rescue attempts

(2020) Zachary Robinson et al.   CONSERVATION BIOLOGY

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

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

Genetics and extinction and the example of Isle Royale wolves

(2019) P. W. Hedrick et al.   ANIMAL CONSERVATION

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction

(2019) Jacqueline A. Robinson et al.   Science Advances

Inbreeding reduces long-term growth of Alpine ibex populations

(2019) Claudio Bozzuto et al.   Nature Ecology & Evolution

Inbreeding in an endangered killer whale population

(2018) M. J. Ford et al.   ANIMAL CONSERVATION

Current global risks to marine mammals: Taking stock of the threats

(2018) Isabel C. Avila et al.   BIOLOGICAL CONSERVATION

Runs of homozygosity: windows into population history and trait architecture

(2018) Francisco C. Ceballos et al.   NATURE REVIEWS GENETICS

Are Lethal Alleles Too Abundant in Humans?

(2018) Mallory A. Ballinger et al.   TRENDS IN GENETICS

Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load

(2018) Pirmin Nietlisbach et al.   Evolutionary Applications

Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes

(2018) Jacqueline A. Robinson et al.   CURRENT BIOLOGY

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

(2017) Marty Kardos et al.   GENETICS

brms: An R Package for Bayesian Multilevel Models Using Stan

(2017) Paul-Christian Bürkner   Journal of Statistical Software

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

Experimental test of genetic rescue in isolated populations of brook trout

(2017) Zachary L. Robinson et al.   MOLECULAR ECOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

(2017) Marty Kardos et al.   GENETICS

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

Genomic consequences of intensive inbreeding in an isolated wolf population

(2017) Marty Kardos et al.   Nature Ecology & Evolution

Population growth is limited by nutritional impacts on pregnancy success in endangered Southern Resident killer whales (Orcinus orca)

(2017) Samuel K. Wasser et al.   PLoS One

Competing tradeoffs between increasing marine mammal predation and fisheries harvest of Chinook salmon

(2017) Brandon E. Chasco et al.   Scientific Reports

Genomic Flatlining in the Endangered Island Fox

(2016) Jacqueline A. Robinson et al.   CURRENT BIOLOGY

Genomics advances the study of inbreeding depression in the wild

(2016) Marty Kardos et al.   Evolutionary Applications

Inbreeding depression across the lifespan in a wild mammal population

(2016) Jisca Huisman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding Inbreeding Depression, Purging, and Genetic Rescue

(2016) Philip W. Hedrick et al.   TRENDS IN ECOLOGY & EVOLUTION

Long-distance migration of prey synchronizes demographic rates of top predators across broad spatial scales

(2016) E. J. Ward et al.   Ecosphere

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

(2015) M Kardos et al.   HEREDITY

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans

(2015) Ron Do et al.   NATURE GENETICS

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Accelerating extinction risk from climate change

(2015) M. C. Urban   SCIENCE

Genetic rescue to the rescue

(2015) Andrew R. Whiteley et al.   TRENDS IN ECOLOGY & EVOLUTION

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Long Runs of Homozygosity Are Enriched for Deleterious Variation

(2013) Zachary A. Szpiech et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

(2013) E. A. Thompson   GENETICS

Geographic Patterns of Genetic Differentiation among Killer Whales in the Northern North Pacific

(2013) Kim M. Parsons et al.   JOURNAL OF HEREDITY

Using opportunistic photo-identifications to detect a population decline of killer whales (Orcinus orca) in British and Irish waters

(2013) Suzanne Beck et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Life history and population dynamics of southern Alaska resident killer whales (Orcinus orca)

(2013) Craig O. Matkin et al.   MARINE MAMMAL SCIENCE

Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium?

(2013) Marty Kardos et al.   Molecular Ecology Resources

NeEstimatorv2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data

(2013) C. Do et al.   Molecular Ecology Resources

Genomic Patterns of Homozygosity in Worldwide Human Populations

(2012) Trevor J. Pemberton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Understanding and Predicting the Fitness Decline of Shrunk Populations: Inbreeding, Purging, Mutation, and Standard Selection

(2012) A. Garcia-Dorado   GENETICS

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

(2012) James W. Kijas et al.   PLOS BIOLOGY

Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) Population

(2011) Michael J. Ford et al.   JOURNAL OF HEREDITY

Shark predation and tooth wear in a population of northeastern Pacific killer whales

(2010) JKB Ford et al.   Aquatic Biology

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genomic Runs of Homozygosity Record Population History and Consanguinity

(2010) Mirna Kirin et al.   PLoS One

Linking killer whale survival and prey abundance: food limitation in the oceans' apex predator?

(2009) J. K. B. Ford et al.   Biology Letters

Quantifying the effects of prey abundance on killer whale reproduction

(2009) Eric J. Ward et al.   JOURNAL OF APPLIED ECOLOGY

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

Eastern temperate North Pacific offshore killer whales (Orcinus orca): Occurrence, movements, and insights into feeding ecology

(2008) Marilyn E. Dahlheim et al.   MARINE MAMMAL SCIENCE