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Fallen Leaves to Their Roots: genomic evidence supporting individual colonization of moles into the Taiwan island

https://doi.org/10.2139/ssrn.5699738
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Outgoing claims: the papers this work cites, builds on, or argues with.

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MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent
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Runs of Homozygosity in European Populations
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How was Taiwan created?
inferredcites →https://doi.org/10.1016/j.tree.2008.05.001openalex-snapshot
Are islands the end of the colonization road?
inferredcites →https://doi.org/10.1016/j.ympev.2013.10.002openalex-snapshot
Multilocus phylogeny of talpine moles (Talpini, Talpidae, Eulipotyphla) and its implications for systematics
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1038/ng.3748openalex-snapshot
Robust and scalable inference of population history from hundreds of unphased whole genomes
inferredcites →https://doi.org/10.1086/519795openalex-snapshot
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.301openalex-snapshot
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
inferredcites →https://doi.org/10.1093/bioinformatics/btab096openalex-snapshot
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
inferredcites →https://doi.org/10.1093/bioinformatics/btab468openalex-snapshot
fastsimcoal2 : demographic inference under complex evolutionary scenarios
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btt310openalex-snapshot
Informed and automated k -mer size selection for genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btv646openalex-snapshot
PHYLUCE is a software package for the analysis of conserved genomic loci
inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot
fastp: an ultra-fast all-in-one FASTQ preprocessor
inferredcites →https://doi.org/10.1093/bioinformatics/bty875openalex-snapshot
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files
inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msw221openalex-snapshot
Talpid Mole Phylogeny Unites Shrew Moles and Illuminates Overlooked Cryptic Species Diversity
inferredcites →https://doi.org/10.1093/molbev/msx248openalex-snapshot
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets
inferredcites →https://doi.org/10.1093/molbev/msy069openalex-snapshot
Estimating Improved Partitioning Schemes for Ultraconserved Elements
inferredcites →https://doi.org/10.1093/nar/gkz173openalex-snapshot
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/syac010openalex-snapshot
StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1111/1755-0998.13265openalex-snapshot
Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files
inferredcites →https://doi.org/10.1111/1755-0998.13326openalex-snapshot
pixy : Unbiased estimation of nucleotide diversity and divergence in the presence of missing data
inferredcites →https://doi.org/10.1111/1755-0998.13877openalex-snapshot
Demogenomic inference from spatially and temporally heterogeneous samples
inferredcites →https://doi.org/10.1111/j.1558-5646.1963.tb03295.xopenalex-snapshot
AN EQUILIBRIUM THEORY OF INSULAR ZOOGEOGRAPHY
inferredcites →https://doi.org/10.1111/jbi.13438openalex-snapshot
Geographical and temporal origins of terrestrial vertebrates endemic to Taiwan
inferredcites →https://doi.org/10.1111/mec.17053openalex-snapshot
Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review
inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
inferredcites →https://doi.org/10.1371/journal.pcbi.1006650openalex-snapshot
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
inferredcites →https://doi.org/10.1371/journal.pgen.1000695openalex-snapshot
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003905openalex-snapshot
Robust Demographic Inference from Genomic and SNP Data
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.3897/zookeys.869.33858openalex-snapshot
A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China
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