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Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

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inferredcites →https://doi.org/10.1002/0471250953.bi1105s31openalex-snapshot
Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies
inferredcites →https://doi.org/10.1002/ece3.3799openalex-snapshot
Hidden endemism, deep polyphyly, and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)
inferredcites →https://doi.org/10.1002/ece3.768openalex-snapshot
Coalescent analyses show isolation without migration in two closely related tropical orioles: the case of Icterus graduacauda and I cterus chrysater
inferredcites →https://doi.org/10.1007/s10336-016-1350-6openalex-snapshot
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inferredcites →https://doi.org/10.1007/s10709-008-9293-3openalex-snapshot
Multilocus phylogeography and phylogenetics using sequence-based markers
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inferredcites →https://doi.org/10.1016/j.cub.2016.06.034openalex-snapshot
Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers
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Hypothesis testing in biogeography
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Coalescent-based species delimitation in an integrative taxonomy
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Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico
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Molecular phylogenetics and diversification of the genus Sporophila (Aves: Passeriformes)
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Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity
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inferredcites →https://doi.org/10.1016/j.ympev.2011.04.007openalex-snapshot
Evolutionary patterns of diversification in the Andean hummingbird genus Adelomyia
inferredcites →https://doi.org/10.1016/j.ympev.2011.07.011openalex-snapshot
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Applications of next-generation sequencing to phylogeography and phylogenetics
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inferredcites →https://doi.org/10.1016/j.ympev.2013.05.001openalex-snapshot
Broad polyphyly and historical biogeography of the neotropical wasp genus Notiospathius (Braconidae: Doryctinae)
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Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds
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Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow
inferredcites →https://doi.org/10.1016/j.ympev.2015.04.018openalex-snapshot
Continental-scale analysis reveals deep diversification within the polytypic Red-crowned Ant Tanager (Habia rubica, Cardinalidae)
inferredcites →https://doi.org/10.1016/j.ympev.2015.08.017openalex-snapshot
Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush ( Catharus frantzii ; Aves: Turdidae)
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Cryptic speciation and gene flow in a migratory songbird Species Complex: Insights from the Red-Eyed Vireo (Vireo olivaceus)
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Neotectonic evolution of the Isthmus of Tehuantepec (southeastern Mexico)
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Applications of next generation sequencing in molecular ecology of non-model organisms
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The drivers of tropical speciation
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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The Great American Biotic Interchange in birds
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Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification
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Bayes Factors
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Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis
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inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr521openalex-snapshot
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
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/genetics/155.2.945openalex-snapshot
Inference of Population Structure Using Multilocus Genotype Data
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
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Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
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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
inferredcites →https://doi.org/10.1093/sysbio/syu056openalex-snapshot
Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades
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The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
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Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics
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More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
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Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
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Comparative Phylogeography of Two Bird Species, Tachyphonus phoenicius (Thraupidae) and Polytmus theresiae (Trochilidae), Specialized in Amazonian White‐sand Vegetation
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Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)
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The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru
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Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds
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HISTORICAL DIVERSIFICATION OF A TERRA-FIRME FOREST BIRD SUPERSPECIES: A PHYLOGEOGRAPHIC PERSPECTIVE ON THE ROLE OF DIFFERENT HYPOTHESES OF AMAZONIAN DIVERSIFICATION
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DIVERGENT TIMING AND PATTERNS OF SPECIES ACCUMULATION IN LOWLAND AND HIGHLAND NEOTROPICAL BIRDS
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Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae)
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Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography
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Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere
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Diversification in Adelomyia hummingbirds follows Andean uplift
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Phylogeographical patterns shed light on evolutionary process in S outh A merica
inferredcites →https://doi.org/10.1111/mec.13140openalex-snapshot
Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a H olarctic songbird
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inferredcites →https://doi.org/10.1126/sciadv.1602404openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.1253226openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.173.3999.771openalex-snapshot
Pleistocene Changes in the Fauna and Flora of South America
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inferredcites →https://doi.org/10.11646/zootaxa.4088.3.2openalex-snapshot
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inferredcites →https://doi.org/10.1177/194008291500800416openalex-snapshot
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inferredcites →https://doi.org/10.1177/194008291600900119openalex-snapshot
Wild Vertebrates Kept as Pets in the Semiarid Region of Brazil
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inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
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IOC World Bird List 7.2
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inferredcites →https://doi.org/10.1525/cond.2012.120012openalex-snapshot
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Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics
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An alternative species taxonomy of the birds of Mexico
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Terrestrial Ecoregions of the World: A New Map of Life on Earth
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Genomic approaches to understanding population divergence and speciation in birds
inferredcites →https://doi.org/10.1890/070075openalex-snapshot
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Patrones biogeográficos de la riqueza de especies y el endemismo de la avifauna en el oeste de México
inferredcites →https://doi.org/10.2307/40168278openalex-snapshot
Historical Biogeography and Patterns of Differentiation within the South American Avifauna: Areas of Endemism
inferredcites →https://doi.org/10.5860/choice.45-2947openalex-snapshot
The Clements checklist of birds of the world
inferredcites →https://doi.org/10.7717/peerj.1660openalex-snapshot
AMAS: a fast tool for alignment manipulation and computing of summary statistics

What points at this work

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

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RELICT HUMID TROPICAL FOREST IN MEXICO PROMOTES DIFFERENTIATION IN BARRED WOODCREEPERS Dendrocolaptes (AVES: FURNARIIDAE)
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Absence of genetic structure among ecologically diverse populations indicate high plasticity in a pantropical seabird
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Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)
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Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow
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Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae)
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Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance
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Highland islands: assessing gene flow among populations of an aquatic highland endemic
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Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters
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Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics
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Integrative taxonomy and geographic sampling underlie successful species delimitation
inferred← citeshttps://doi.org/10.1093/ornithology/ukab016openalex-snapshot
Performance of a points-based scoring system for assessing species limits in birds
inferred← citeshttps://doi.org/10.1111/jzs.12571openalex-snapshot
Diversification and secondary contact in the magpie‐jays (Calocitta) throughout the pacific lowlands of Mesoamerica
inferred← citeshttps://doi.org/10.1111/mec.15626openalex-snapshot
Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient
inferred← citeshttps://doi.org/10.1111/mec.16938openalex-snapshot
Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the variable seedeater (Sporophila corvina)
inferred← citeshttps://doi.org/10.1186/s12862-019-1564-3openalex-snapshot
The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico
inferred← citeshttps://doi.org/10.1186/s13104-019-4481-zopenalex-snapshot
Comparison of ultraconserved elements (UCEs) to microsatellite markers for the study of avian hybrid zones: a test in Aphelocoma jays
inferred← citeshttps://doi.org/10.1642/auk-17-72.1openalex-snapshot
Fifty-eighth supplement to the American Ornithological Society'sCheck-list of North American Birds
inferred← citeshttps://doi.org/10.1642/auk-18-62.1openalex-snapshot
Fifty-ninth Supplement to the American Ornithological Society'sCheck-list of North American Birds
inferred← citeshttps://doi.org/10.18061/bssb.v2i1.9423openalex-snapshot
Species Delimitation of Eastern Pinesnake Complex (Pituophis melanoleucus)
inferred← citeshttps://doi.org/10.22201/ib.20078706e.2023.94.5114openalex-snapshot
Sixty years of Halffter’s Mexican Transition Zone: a systematic review using bibliometric tools
inferred← citeshttps://doi.org/10.22541/au.158757034.48320167openalex-snapshot
High gene flow across heterogeneous tropical montane environments in a Bornean endemic small mammal
inferred← citeshttps://doi.org/10.22541/au.166313526.67537861/v1openalex-snapshot
Replicate hybrid zones suggest a limited role of plumage in reproductive isolation among subspecies of the Variable Seedeater (Sporophila corvina)
inferred← citeshttps://doi.org/10.3390/d13040140openalex-snapshot
Genetic Consequences of Forest Fragmentation in a Widespread Forest Bat (Natalus mexicanus, Chiroptera: Natalidae)
inferred← citeshttps://doi.org/10.7717/peerj.5735openalex-snapshot
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
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