The Value of Reference Genomes in the Conservation of Threatened Species

Development of a Novel Mule Deer Genomic Assembly and Species-Diagnostic SNP Panel for Assessing Introgression in Mule Deer, White-Tailed Deer, and Their Interspecific Hybrids

(2019) Ty Russell et al.   G3-Genes Genomes Genetics

Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data

(2019) Toshihiro Kishikawa et al.   Scientific Reports

Too much of a good thing? Finding the most informative genetic dataset to answer conservation questions

(2019) Elspeth A. McLennan et al.   Molecular Ecology Resources

Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer

(2019) Paul A. Hohenlohe et al.   CONSERVATION GENETICS

Emerging genomic applications in mammalian ecology, evolution, and conservation

(2019) Peter A Larsen et al.   JOURNAL OF MAMMALOGY

MHC-associated mate choice under competitive conditions in captive versus wild Tasmanian devils

(2019) Jenna Day et al.   BEHAVIORAL ECOLOGY

A case for genetic parentage assignment in captive group housing

(2019) Katherine A. Farquharson et al.   CONSERVATION GENETICS

From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

(2019) Belinda Wright et al.   BMC GENOMICS

Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian Devils

(2019) Austin H Patton et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conservation genetics: Linking science with practice

(2019) Rolf Holderegger et al.   MOLECULAR ECOLOGY

Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

(2018) Francisco C. Ceballos et al.   BMC GENOMICS

Genotyping-by-sequencing performance in selected livestock species

(2018) Artur Gurgul et al.   GENOMICS

Density trends and demographic signals uncover the long-term impact of transmissible cancer in Tasmanian devils

(2018) Billie T. Lazenby et al.   JOURNAL OF APPLIED ECOLOGY

Performance of commonly requested destructive museum samples for mammalian genomic studies

(2018) Molly M McDonough et al.   JOURNAL OF MAMMALOGY

Adaptation and conservation insights from the koala genome

(2018) Rebecca N. Johnson et al.   NATURE GENETICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

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

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species

(2018) Emma C. Teeling et al.   Annual Review of Animal Biosciences

Immunization Strategies Producing a Humoral IgG Immune Response against Devil Facial Tumor Disease in the Majority of Tasmanian Devils Destined for Wild Release

(2018) Ruth Pye et al.   Frontiers in Immunology

Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild

(2018) Catherine E. Grueber et al.   Evolutionary Applications

Large-effect loci affect survival in Tasmanian devils (Sarcophilus harrisii ) infected with a transmissible cancer

(2018) Mark J. Margres et al.   MOLECULAR ECOLOGY

Founder relationships and conservation management: empirical kinships reveal the effect on breeding programmes when founders are assumed to be unrelated

(2018) C. J. Hogg et al.   ANIMAL CONSERVATION

SNP panel development for genetic management of wild and domesticated white bass (Morone chrysops )

(2018) H. Zhao et al.   ANIMAL GENETICS

The genomic basis of tumor regression in Tasmanian devils (Sarcophilus harrisii)

(2018) Mark J Margres et al.   Genome Biology and Evolution

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

(2018) Stephanie J. Galla et al.   Genes

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Genetics and the conservation of natural populations: allozymes to genomes

(2017) Fred W. Allendorf   MOLECULAR ECOLOGY

Call for a Paradigm Shift in the Genetic Management of Fragmented Populations

(2017) Katherine Ralls et al.   Conservation Letters

Bridging the conservation genetics gap by identifying barriers to implementation for conservation practitioners

(2017) Helen R. Taylor et al.   Global Ecology and Conservation

Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species

(2017) Janna R. Willoughby et al.   PLoS One

Variants in the host genome may inhibit tumour growth in devil facial tumours: evidence from genome-wide association

(2017) Belinda Wright et al.   Scientific Reports

Significant decline in anticancer immune capacity during puberty in the Tasmanian devil

(2017) Yuanyuan Cheng et al.   Scientific Reports

No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding

(2017) Rebecca Gooley et al.   Scientific Reports

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

(2016) Sean Hoban et al.   AMERICAN NATURALIST

A multiplex microsatellite tool for conservation genetics of the endemic limpet Patella candei in the Macaronesian archipelagos

(2016) João Faria et al.   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

Demonstration of immune responses against devil facial tumour disease in wild Tasmanian devils

(2016) Ruth Pye et al.   Biology Letters

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

“Devil Tools & Tech”: A Synergy of Conservation Research and Management Practice

(2016) Carolyn J. Hogg et al.   Conservation Letters

Rapid evolutionary response to a transmissible cancer in Tasmanian devils

(2016) Brendan Epstein et al.   Nature Communications

A suite of potentially amplifiable microsatellite loci for ten reptiles of conservation concern from Africa and Asia

(2016) Kyle J. Shaney et al.   Conservation Genetics Resources

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species

(2016) Suliman Khan et al.   International Journal of Genomics

Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies

(2016) Davoud Torkamaneh et al.   PLoS One

Cathelicidins in the Tasmanian devil (Sarcophilus harrisii)

(2016) E. Peel et al.   Scientific Reports

Development of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population

(2015) Belinda Wright et al.   BMC GENOMICS

Identification and analysis of divergent immune gene families within the Tasmanian devil genome

(2015) Katrina M. Morris et al.   BMC GENOMICS

Influence of genetic provenance and birth origin on productivity of the Tasmanian devil insurance population

(2015) Carolyn J. Hogg et al.   CONSERVATION GENETICS

Diversity in the Toll-like receptor genes of the Tasmanian devil (Sarcophilus harrisii)

(2015) Jian Cui et al.   IMMUNOGENETICS

Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)

(2015) Katrina M. Morris et al.   MOLECULAR ECOLOGY

Assembly: a resource for assembled genomes at NCBI

(2015) Paul A. Kitts et al.   NUCLEIC ACIDS RESEARCH

A second transmissible cancer in Tasmanian devils

(2015) Ruth J. Pye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Accelerated modern human-induced species losses: Entering the sixth mass extinction

(2015) G. Ceballos et al.   Science Advances

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Comparative genomics for biodiversity conservation

(2015) Catherine E. Grueber   Computational and Structural Biotechnology Journal

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

(2014) Anthony Youzhi Cheng et al.   BIOINFORMATICS

Do it yourself guide to genome assembly

(2014) B. Wajid et al.   Briefings in Functional Genomics

How and why should we implement genomics into conservation?

(2014) Barry J. McMahon et al.   Evolutionary Applications

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Characterisation of non-classical MHC class I genes in the Tasmanian devil (Sarcophilus harrisii)

(2014) Yuanyuan Cheng et al.   IMMUNOGENETICS

Selective constraint, background selection, and mutation accumulation variability within and between human populations

(2013) Alan Hodgkinson et al.   BMC GENOMICS

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

(2013) María E. Fernández et al.   GENETICS AND MOLECULAR BIOLOGY

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

Identification of natural killer cell receptor genes in the genome of the marsupial Tasmanian devil (Sarcophilus harrisii)

(2012) Lauren E. van der Kraan et al.   IMMUNOGENETICS

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

(2011) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation and characterisation of 11 MHC-linked microsatellite loci in the Tasmanian devil (Sarcophilus harrisii)

(2011) Yuanyuan Cheng et al.   Conservation Genetics Resources

MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer

(2010) H. V. Siddle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Body mass and extinction risk in Australian marsupials: The ‘Critical Weight Range’ revisited

(2009) CHRISTOPHER N. JOHNSON et al.   AUSTRAL ECOLOGY

Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing

(2009) Jawad Abdelkrim et al.   BIOTECHNIQUES

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison

(2009) M Tokarska et al.   HEREDITY

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Comparison of information content for microsatellites and SNPs in poultry and cattle

(2008) G. C. B. Schopen et al.   ANIMAL GENETICS

Bat White-Nose Syndrome: An Emerging Fungal Pathogen?

(2008) D. S. Blehert et al.   SCIENCE