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

Conservation Resource Allocation, Small Population Resiliency, and the Fallacy of Conservation Triage

(2021) David A. Wiedenfeld et al.   CONSERVATION BIOLOGY

Viability of the vaquita, Phocoena sinus (Cetacea: Phocoenidae) population, threatened by poaching of Totoaba macdonaldi (Perciformes: Sciaenidae)

(2021) Miguel A. Cisneros-Mata et al.   REVISTA DE BIOLOGIA TROPICAL

Mexico's final death blow to the vaquita

(2021) Christian Sonne et al.   SCIENCE

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

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction

(2020) Gerardo Ceballos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo assembly of the cattle reference genome with single-molecule sequencing

(2020) Benjamin D Rosen et al.   GigaScience

Vaquitas (Phocoena sinus) continue to die from bycatch not pollutants

(2020) Frances Gulland et al.   VETERINARY RECORD

Reference genome and demographic history of the most endangered marine mammal, the vaquita

(2020) Phillip A. Morin et al.   Molecular Ecology Resources

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

(2020) Yacine Ben Chehida et al.   Scientific Reports

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions

(2020) Felix L. Wu et al.   PLOS BIOLOGY

Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression

(2020) Christopher C. Kyriazis et al.   Evolution Letters

The first chromosome-level genome for a marine mammal as a resource to study ecology and evolution

(2019) Guangyi Fan et al.   Molecular Ecology Resources

Likely annual calving in the vaquita, Phocoena sinus : A new hope?

(2019) Barbara L. Taylor et al.   MARINE MAMMAL SCIENCE

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

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

Decline towards extinction of Mexico's vaquita porpoise ( Phocoena sinus )

(2019) Armando M. Jaramillo-Legorreta et al.   Royal Society Open Science

Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes

(2019) David Castellano et al.   GENETICS

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

(2019) Michael R McGowen et al.   SYSTEMATIC BIOLOGY

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

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

Genome Sequence of the Freshwater Yangtze Finless Porpoise

(2018) Yuan Yuan et al.   Genes

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

(2018) Úlfur Árnason et al.   Science Advances

High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena )

(2018) Marijke Autenrieth et al.   Molecular Ecology Resources

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

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples

(2017) Bernard Y. Kim et al.   GENETICS

The Novel Evolution of the Sperm Whale Genome

(2017) Wesley C Warren et al.   Genome Biology and Evolution

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Conserved non-coding elements: developmental gene regulation meets genome organization

(2017) Dimitris Polychronopoulos et al.   NUCLEIC ACIDS RESEARCH

Determining the factors driving selective effects of new nonsynonymous mutations

(2017) Christian D. Huber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

(2017) Chungang Feng et al.   eLife

Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples

(2017) Bernard Y. Kim et al.   GENETICS

The Genome of the Beluga Whale (Delphinapterus leucas)

(2017) Steven Jones et al.   Genes

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

(2016) Vagheesh Narasimhan et al.   BIOINFORMATICS

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Understanding Inbreeding Depression, Purging, and Genetic Rescue

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

The Limits of Natural Selection in a Nonequilibrium World

(2016) Yaniv Brandvain et al.   TRENDS IN GENETICS

Extinction is Imminent for Mexico's Endemic Porpoise Unless Fishery Bycatch is Eliminated

(2016) Barbara L. Taylor et al.   Conservation Letters

An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans

(2015) Ziyue Gao et al.   GENETICS

Computationally Efficient Composite Likelihood Statistics for Demographic Inference

(2015) Alec J. Coffman et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Estimating the mutation load in human genomes

(2015) Brenna M. Henn et al.   NATURE REVIEWS GENETICS

An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans

(2015) Ziyue Gao et al.   GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

(2014) Matthew W. Pennell et al.   BIOINFORMATICS

Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum

(2014) Andre E. Moura et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minke whale genome and aquatic adaptation in cetaceans

(2013) Hyung-Soon Yim et al.   NATURE GENETICS

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Estimating the success of protected areas for the vaquita, Phocoena sinus

(2011) Tim Gerrodette et al.   MARINE MAMMAL SCIENCE

Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

(2011) A. Dornburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

A combined visual and acoustic estimate of 2008 abundance, and change in abundance since 1997, for the vaquita, Phocoena sinus

(2010) Tim Gerrodette et al.   MARINE MAMMAL SCIENCE

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A BAYESIAN UNCERTAINTY ANALYSIS OF CETACEAN DEMOGRAPHY AND BYCATCH MORTALITY USING AGE-AT-DEATH DATA

(2009) Jeffrey E. Moore et al.   ECOLOGICAL APPLICATIONS

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Estimation of Pairwise Identity by Descent From Dense Genetic Marker Data in a Population Sample of Haplotypes

(2008) S. R. Browning   GENETICS