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Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

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The Fall and Rise of the Scimitar‐Horned Oryx

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Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

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Chromosomal variation and perinatal mortality in San Diego zoo Soemmerring's gazelles

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Chromosome studies in the superfamily Bovoidea

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Genetic assessment of the Arabian oryx founder population in the Emirate of Abu Dhabi, UAE: an example of evaluating unmanaged captive stocks for reintroduction

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Captive breeding genetics and reintroduction success

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The reduction of genetic diversity in threatened vertebrates and new recommendations regarding IUCN conservation rankings

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Benefits and pitfalls of captive conservation genetic management: Evaluating diversity in scimitar-horned oryx to support reintroduction planning

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes

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Genomic Flatlining in the Endangered Island Fox

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Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis

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Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size

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Orbital scale vegetation change in Africa

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The Third Revolution in Sequencing Technology

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The alluring simplicity and complex reality of genetic rescue

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Genomics and the challenging translation into conservation practice

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Introduction to Conservation Genetics

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Guidelines for reintroductions and other conservation translocations

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A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

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Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

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On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

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Inference of human population history from individual whole-genome sequences

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Draft genome sequence of the Tibetan antelope

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Fast and sensitive protein alignment using DIAMOND

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Determinants of genetic diversity

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Genomics and the future of conservation genetics

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Variation in the mutation rate across mammalian genomes

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The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

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Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history

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The Genetic Basis of Black‐Footed Ferret Reintroduction

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Large numbers of vertebrates began rapid population decline in the late 19th century

inferredcites →https://doi.org/10.1073/pnas.1704949114openalex-snapshot

Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines

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Beware of mis-assembled genomes

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

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The variant call format and VCFtools

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

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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gVolante for standardizing completeness assessment of genome and transcriptome assemblies

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Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations

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Chromosomal Heterozygosity and Fertility in House Mice (Mus musculus domesticus) From Northern Italy

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Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

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The genome sequence of the wisent ( Bison bonasus )

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A near-chromosome-scale genome assembly of the gemsbok ( Oryx gazella ): an iconic antelope of the Kalahari desert

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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter

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AUGUSTUS: ab initio prediction of alternative transcripts

inferredcites →https://doi.org/10.1093/nar/gks1265openalex-snapshot

Dfam: a database of repetitive DNA based on profile hidden Markov models

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eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a111215openalex-snapshot

Chromosome Conservation in the Bovidae

inferredcites →https://doi.org/10.1098/rsbl.2006.0453openalex-snapshot

Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline

inferredcites →https://doi.org/10.1101/254797openalex-snapshot

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

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Fast and flexible simulation of DNA sequence data

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Adaptive seeds tame genomic sequence comparison

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Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony

inferredcites →https://doi.org/10.1111/2041-210x.12410openalex-snapshot

popart : full‐feature software for haplotype network construction

inferredcites →https://doi.org/10.1111/2041-210x.12700openalex-snapshot

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

inferredcites →https://doi.org/10.1111/cobi.13157openalex-snapshot

Genome sequencing and conservation genomics in the Scandinavian wolverine population

inferredcites →https://doi.org/10.1111/eva.12414openalex-snapshot

Genomics advances the study of inbreeding depression in the wild

inferredcites →https://doi.org/10.1111/eva.12600openalex-snapshot

Genetic and genomic monitoring with minimally invasive sampling methods

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Back into the wild: establishing a migratory Northern bald ibis Geronticus eremita population in Europe

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Recent demographic bottlenecks are not accompanied by a genetic signature in banner‐tailed kangaroo rats (Dipodomys spectabilis)

inferredcites →https://doi.org/10.1111/j.1365-294x.2007.03291.xopenalex-snapshot

Remnants of ancient genetic diversity preserved within captive groups of scimitar‐horned oryx (Oryx dammah)

inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03876.xopenalex-snapshot

To what extent do microsatellite markers reflect genome‐wide genetic diversity in natural populations?

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05650.xopenalex-snapshot

Comparative phylogeography of African savannah ungulates 1

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Loss of Genetic Diversity from Managed Populations: Interacting Effects of Drift, Mutation, Immigration, Selection, and Population Subdivision

inferredcites →https://doi.org/10.1111/j.1523-1739.1990.tb00316.xopenalex-snapshot

Endangered Greater One‐horned Rhinoceros Carry High Levels of Genetic Variation

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THE BOTTLENECK EFFECT AND GENETIC VARIABILITY IN POPULATIONS

inferredcites →https://doi.org/10.1111/j.1748-1090.1993.tb03519.xopenalex-snapshot

A brief history of the reintroduction of the Arabian oryx Oryx leucoryx into Oman 1980–1992

inferredcites →https://doi.org/10.1111/j.1752-4571.2011.00192.xopenalex-snapshot

Assessing the benefits and risks of translocations in changing environments: a genetic perspective

inferredcites →https://doi.org/10.1111/mec.14374openalex-snapshot

Demographic inference from whole‐genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age

inferredcites →https://doi.org/10.1126/science.1228899openalex-snapshot

Integrating the Captive and the Wild

inferredcites →https://doi.org/10.1126/science.aal3327openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.aav6202openalex-snapshot

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

inferredcites →https://doi.org/10.1146/annurev-animal-090414-014900openalex-snapshot

The Genome 10K Project: A Way Forward

inferredcites →https://doi.org/10.1159/000015416openalex-snapshot

Centric fusion differences among Oryx dammah, O. gazella, and O. leucoryx (Artiodactyla, Bovidae)

inferredcites →https://doi.org/10.1159/000063054openalex-snapshot

The effect of multiple simple Robertsonian heterozygosity on chromosome pairing and fertility of wild-stock house mice (Mus musculus domesticus)

inferredcites →https://doi.org/10.1186/1471-2105-14-244openalex-snapshot

RCircos: an R package for Circos 2D track plots

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A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

inferredcites →https://doi.org/10.1186/2047-217x-2-1openalex-snapshot

Peering into peer-review at GigaScience

inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

inferredcites →https://doi.org/10.1186/gb-2009-10-4-r42openalex-snapshot

A whole-genome assembly of the domestic cow, Bos taurus

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ANGSD: Analysis of Next Generation Sequencing Data

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Genomic legacy of the African cheetah, Acinonyx jubatus

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Ancient DNA and the rewriting of human history: be sparing with Occam’s razor

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Fitness consequences of polymorphic inversions in the zebra finch genome

inferredcites →https://doi.org/10.1186/s13059-018-1520-3openalex-snapshot

Conservation of biodiversity in the genomics era

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Repbase Update, a database of repetitive elements in eukaryotic genomes

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The Pattern of Polymorphism in Arabidopsis thaliana

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A Catalog of Neutral and Deleterious Polymorphism in Yeast

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Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

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Robust Demographic Inference from Genomic and SNP Data

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

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Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories

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Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity inex Situandin SituPopulations

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Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

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Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

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

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Oryx dammah: IUCN SSC Antelope Specialist Group

inferredcites →https://doi.org/10.4324/9780203439357openalex-snapshot

The Third Revolution

inferredcites →https://doi.org/10.48550/arxiv.1605.04619openalex-snapshot

An end-to-end assembly of the Aedes aegypti genome

inferredcites →https://doi.org/10.5860/choice.40-1529openalex-snapshot

Introduction to conservation genetics

inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot

Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41576-023-00671-0openalex-snapshot

Translating genomic advances into biodiversity conservation

inferred← citeshttps://doi.org/10.1111/eva.13515openalex-snapshot

Genetic diversity in global populations of the critically endangered addax ( Addax nasomaculatus ) and its implications for conservation

inferred← citeshttps://doi.org/10.1111/mec.17729openalex-snapshot

Toward a Global Science of Conservation Genomics: Coldspots in Genomic Resources Highlight a Need for Equitable Collaborations and Capacity Building

inferred← citeshttps://doi.org/10.17816/ecogen65152openalex-snapshot

Whole genome approach in conservation biology and its perspectives

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