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The Effects of Inference Method, Population Sampling, and Gene Sampling on Species Tree Inferences: An Empirical Study in Slender Salamanders (Plethodontidae: Batrachoseps)

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

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The incomplete natural history of mitochondria
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APE: Analyses of Phylogenetics and Evolution in R language
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TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
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phangorn: phylogenetic analysis in R
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inferredcites →https://doi.org/10.1093/molbev/mst160openalex-snapshot
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Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
inferredcites →https://doi.org/10.1093/sysbio/syt059openalex-snapshot
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seqphase : a web tool for interconverting phase input/output files and fasta sequence alignments
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Escape to Alcatraz: evolutionary history of slender salamanders (Batrachoseps) on the islands of San Francisco Bay
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Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels
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Discordance of Species Trees with Their Most Likely Gene Trees
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Impact of Deep Coalescence on the Reliability of Species Tree Inference from Different Types of DNA Markers in Mammals
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New Species of Slender Salamander, Genus Batrachoseps, from the Southern Sierra Nevada of California
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Examination of nuclear loci across a zone of mitochondrial introgression between Tamias ruficaudus and T. amoenus
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Molecular Phylogenetic Analysis of Slender Salamanders, Genus Batrachoseps (Amphibia: Plethodontidae), from Central Coastal California with Descriptions of Four New Species
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Ecology and Evolution in Island Populations of Salamanders in the San Francisco Bay Region
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New species of slender salamanders, Batrachoseps (Amphibia: Plethodontidae), from the Sierra Nevada of California
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