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Delimiting Continuity: Comparison of Target Enrichment and ddRAD for Delineating Admixing Parapatric Melitaea Butterflies

https://doi.org/10.1101/2022.02.05.479083

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What this work says

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

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STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

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Hybrid zones-natural laboratories for evolutionary studies

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Genetic variability in a hybrid zone between carrion and hooded crows (Corvus corone corone and C. c. cornix, Passeriformes, Aves) in North-Western Italy

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A Comprehensive and Dated Phylogenomic Analysis of Butterflies

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Species as the basic units in evolution and biodiversity: Recognition of species in the Recent and geological past as exemplified by larger foraminifera

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Hybridization as an invasion of the genome

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A Plea for Standardized Nuclear Markers in Metazoan DNA Taxonomy

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RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

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Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation

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Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study

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An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone

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Use of RAD sequencing for delimiting species

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Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

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DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, ‘living fossils’ from the Triassic

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Ernst Mayr and the modern concept of species

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Species Concepts and Species Delimitation

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CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

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The Sequence Alignment/Map format and SAMtools

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PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

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Natural History's Place in Science and Society

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Inference of Population Structure Using Multilocus Genotype Data

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Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment

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Asymmetric Introgression in a Spotted Salamander Hybrid Zone

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

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New Methods to Calculate Concordance Factors for Phylogenomic Datasets

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Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

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BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design

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UFBoot2: Improving the Ultrafast Bootstrap Approximation

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Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

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Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

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Species Delimitation using Genome-Wide SNP Data

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A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets

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Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

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Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

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Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus

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Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex

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Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris)

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Standardized nuclear markers advance metazoan taxonomy

inferredcites →https://doi.org/10.1111/1755-0998.13059openalex-snapshot

Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies

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Assigning occurrence data to cryptic taxa improves climatic niche assessments: Biodecrypt, a new tool tested on European butterflies

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PATTERNS OF PARAPATRIC SPECIATION

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Varying rates of diversification in the genus Melitaea (Lepidoptera: Nymphalidae) during the past 20 million years

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Along the speciation continuum in sticklebacks

inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04687.xopenalex-snapshot

Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta

inferredcites →https://doi.org/10.1111/mec.12276openalex-snapshot

RAD seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

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Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long‐standing systematic enigma in Central European bees

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The Pleistocene species pump past its prime: Evidence from European butterfly sister species

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Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

inferredcites →https://doi.org/10.1146/annurev.ecolsys.22.1.19openalex-snapshot

Ecology Of Parapatric Distributions

inferredcites →https://doi.org/10.1186/1471-2148-14-82openalex-snapshot

Selecting optimal partitioning schemes for phylogenomic datasets

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/10.1186/s12862-016-0769-yopenalex-snapshot

Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

inferredcites →https://doi.org/10.1186/s12983-014-0081-xopenalex-snapshot

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

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How Many Species Are There on Earth and in the Ocean?

inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pone.0047214openalex-snapshot

Allopatry as a Gordian Knot for Taxonomists: Patterns of DNA Barcode Divergence in Arctic-Alpine Lepidoptera

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treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

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Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies

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An updated checklist of the European Butterflies (Lepidoptera, Papilionoidea)

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An updated checklist of the European Butterflies (Lepidoptera, Papilionoidea)

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The General Lineage Concept of Species and the Defining Properties of the Species Category

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Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

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

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Single-Copy Orthologs (SCOs) improve species discrimination: A case study in subgus Jensoa ( Cymbidium )

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