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Genomic Data from an Endangered Amphibian Reveal Unforeseen Consequences of Fragmentation by Roads

https://doi.org/10.1101/306340
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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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Colour displays for categorical images
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Effects of tail‐clipping on survivorship and growth of larval salamanders
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Informativeness of Microsatellite Markers
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Delineating fine-scale genetic units in amphibians:Probing the primacy of ponds
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Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense
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Connectivity and gene flow among Eastern Tiger Salamander (Ambystoma tigrinum) populations in highly modified anthropogenic landscapes
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Can road mortality limit populations of pool-breeding amphibians?
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Allele frequencies after a bottleneck
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Genome size and metabolic rate in salamanders
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A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution
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Estimation of effective population size from data on linkage disequilibrium
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Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci
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Comparative population genomics in animals uncovers the determinants of genetic diversity
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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Fast gapped-read alignment with Bowtie 2
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Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog
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Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing
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Microsatellite variation and fine‐scale population structure in the wood frog (Rana sylvatica)
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Fine‐scale genetic pattern and evidence for sex‐biased dispersal in the túngara frog, Physalaemus pustulosus
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Amphibian Declines: Judging Stability, Persistence, and Susceptibility of Populations to Local and Global Extinctions
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A Note on Exact Tests of Hardy-Weinberg Equilibrium
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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The variant call format and VCFtools
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A high-performance computing toolset for relatedness and principal component analysis of SNP data
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ISOLATION BY DISTANCE
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Accuracy of Coalescent Likelihood Estimates: Do We Need More Sites, More Sequences, or More Loci?
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Genetic Management of Fragmented Animal and Plant Populations
inferredcites →https://doi.org/10.1101/014662openalex-snapshot
Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences
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Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.116491.110openalex-snapshot
Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
inferredcites →https://doi.org/10.1101/gr.128124.111openalex-snapshot
Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
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XSEDE: Accelerating Scientific Discovery
inferredcites →https://doi.org/10.1111/1755-0998.12157openalex-snapshot
NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size ( N e ) from genetic data
inferredcites →https://doi.org/10.1111/1755-0998.12538openalex-snapshot
Exon capture optimization in amphibians with large genomes
inferredcites →https://doi.org/10.1111/1755-0998.12541openalex-snapshot
An evaluation of transcriptome‐based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
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Dismantling the Mantel tests
inferredcites →https://doi.org/10.1111/eva.12479openalex-snapshot
Population genetic and field‐ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian
inferredcites →https://doi.org/10.1111/evo.12193openalex-snapshot
DISENTANGLING THE EFFECTS OF GEOGRAPHIC AND ECOLOGICAL ISOLATION ON GENETIC DIFFERENTIATION
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EVIDENCE FOR MULTIPLE PLEISTOCENE REFUGIA IN THE POSTGLACIAL EXPANSION OF THE EASTERN TIGER SALAMANDER, AMBYSTOMA TIGRINUM TIGRINUM
inferredcites →https://doi.org/10.1111/j.1365-294x.2006.03139.xopenalex-snapshot
Fine‐scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations
inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04122.xopenalex-snapshot
Landscape genetics and least‐cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense)
inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04175.xopenalex-snapshot
A new method for estimating effective population sizes from a single sample of multilocus genotypes
inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04338.xopenalex-snapshot
Fine‐scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04554.xopenalex-snapshot
On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04718.xopenalex-snapshot
Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04757.xopenalex-snapshot
Considering spatial and temporal scale in landscape‐genetic studies of gene flow
inferredcites →https://doi.org/10.1111/j.1472-4642.2012.00897.xopenalex-snapshot
Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad
inferredcites →https://doi.org/10.1111/j.1523-1739.2006.00554.xopenalex-snapshot
Demographic and Genetic Estimates of Effective Population and Breeding Size in the Amphibian Rana temporaria
inferredcites →https://doi.org/10.1111/j.1558-5646.1993.tb01215.xopenalex-snapshot
ISOLATION BY DISTANCE IN EQUILIBRIUM AND NON-EQUILIBRIUM POPULATIONS
inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01356.xopenalex-snapshot
COMPARATIVE ANALYSES OF EFFECTIVE POPULATION SIZE WITHIN AND AMONG SPECIES: RANID FROGS AS A CASE STUDY
inferredcites →https://doi.org/10.1111/j.1752-4571.2009.00104.xopenalex-snapshot
Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02847.xopenalex-snapshot
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
inferredcites →https://doi.org/10.1111/jbi.14281openalex-snapshot
The detection of disease clustering and a generalized regression approach.
inferredcites →https://doi.org/10.1111/mec.12049openalex-snapshot
Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the N orth A merican tiger salamander ( A mbystoma tigrinum) species complex
inferredcites →https://doi.org/10.1111/mec.13391openalex-snapshot
Amphibian molecular ecology and how it has informed conservation
inferredcites →https://doi.org/10.1111/mec.13909openalex-snapshot
Sequence capture and next‐generation sequencing of ultraconserved elements in a large‐genome salamander
inferredcites →https://doi.org/10.1146/annurev-animal-022114-110920openalex-snapshot
Conservation Genetics and Genomics of Amphibians and Reptiles
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-15-182openalex-snapshot
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
inferredcites →https://doi.org/10.1214/aos/1013699998openalex-snapshot
The control of the false discovery rate in multiple testing under dependency
inferredcites →https://doi.org/10.1371/journal.pgen.0020190openalex-snapshot
Population Structure and Eigenanalysis
inferredcites →https://doi.org/10.1534/genetics.114.164350openalex-snapshot
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
inferredcites →https://doi.org/10.1534/genetics.114.164822openalex-snapshot
Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size
inferredcites →https://doi.org/10.1643/0045-8511(2000)000[0365:lhadvi]2.0.co;2openalex-snapshot
Life History and Demographic Variation in the California Tiger Salamander (Ambystoma californiense)
inferredcites →https://doi.org/10.2307/1447434openalex-snapshot
Habitat Use during Breeding and Emigration in Radio-Implanted Tiger Salamanders, Ambystoma tigrinum
inferredcites →https://doi.org/10.2307/2410811openalex-snapshot
The Polytypic Species Revisited: Genetic Differentiation and Molecular Phylogenetics of the Tiger Salamander Ambystoma tigrinum (Amphibia: Caudata) Complex
inferredcites →https://doi.org/10.2307/2425164openalex-snapshot
The Albany Pine Bush: A Northern Outpost for Southern Species of Amphibians and Reptiles in New York
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.

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Conservation of biodiversity in the genomics era
inferred← citeshttps://doi.org/10.2172/1779055openalex-snapshot
Acoustic and Genetic Approaches for Informing Population Status and Trends of Migratory Tree Bats
inferred← citeshttps://doi.org/10.2305/iucn.ch.2019.05.enopenalex-snapshot
Genetic frontiers for conservation: an assessment of synthetic biology and biodiversity conservation: technical assessment
inferred← citeshttps://doi.org/10.3389/fevo.2024.1336747openalex-snapshot
Framework for multi-stressor physiological response evaluation in amphibian risk assessment and conservation
inferred← citeshttps://doi.org/10.3390/ani12010081openalex-snapshot
Acoustic and Genetic Data Can Reduce Uncertainty Regarding Populations of Migratory Tree-Roosting Bats Impacted by Wind Energy
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