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Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

https://doi.org/10.1111/bij.12551
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What this work says

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

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Concordance trees, concordance factors, and the exploration of reticulate genealogy
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Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate
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Gene tree discordance, phylogenetic inference and the multispecies coalescent
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Basic Local Alignment Search Tool
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Inferring ancient divergences requires genes with strong phylogenetic signals
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De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Fast gapped-read alignment with Bowtie 2
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jModelTest 2: more models, new heuristics and parallel computing
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An algorithm for progressive multiple alignment of sequences with insertions
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Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
inferredcites →https://doi.org/10.1073/pnas.1106502108openalex-snapshot
Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning
inferredcites →https://doi.org/10.1073/pnas.1934576100openalex-snapshot
Probable extirpation of a breeding colony of Short-tailed Albatross ( Phoebastria albatrus ) on Bermuda by Pleistocene sea-level rise
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Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
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A Molecular Phylogenetic Study of the Palmae (Arecaceae) Based on atpB, rbcL, and 18S nrDNA Sequences
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Inferring Phylogeny Despite Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
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Automatic annotation of organellar genomes with DOGMA
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btl629openalex-snapshot
Assembling millions of short DNA sequences using SSAKE
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BEST: Bayesian estimation of species trees under the coalescent model
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STEM: species tree estimation using maximum likelihood for gene trees under coalescence
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Fast and accurate short read alignment with Burrows–Wheeler transform
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BEDTools: a flexible suite of utilities for comparing genomic features
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BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
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Naive binning improves phylogenomic analyses
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The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees
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Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle
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PlantTribes: a gene and gene family resource for comparative genomics in plants
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RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
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STRAW: Species TRee Analysis Web server
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Phylogenetic Relationships and Ancient Incomplete Lineage Sorting Among Cichlid Fishes in Lake Tanganyika as Revealed by Analysis of the Insertion of Retroposons
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/oxfordjournals.molbev.a040605openalex-snapshot
Chloroplast DNA evolves slowly in the palm family (Arecaceae).
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syp021openalex-snapshot
Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches
inferredcites →https://doi.org/10.1093/sysbio/syp031openalex-snapshot
Estimating Species Phylogenies Using Coalescence Times among Sequences
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What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?
inferredcites →https://doi.org/10.1093/sysbio/syp054openalex-snapshot
Species Trees from Highly Incongruent Gene Trees in Rice
inferredcites →https://doi.org/10.1093/sysbio/syr123openalex-snapshot
Miocene Dispersal Drives Island Radiations in the Palm Tribe Trachycarpeae (Arecaceae)
inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.9.9.868openalex-snapshot
CAP3: A DNA Sequence Assembly Program
inferredcites →https://doi.org/10.1111/j.0014-3820.2004.tb00416.xopenalex-snapshot
PHYLOGENY AND PHYLOGEOGRAPHY OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE): EVIDENCE FOR INTROGRESSION AND INCOMPLETE LINEAGE SORTING
inferredcites →https://doi.org/10.1111/j.1365-2699.2012.02795.xopenalex-snapshot
Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography
inferredcites →https://doi.org/10.1111/j.1756-1051.1996.tb00212.xopenalex-snapshot
Field guide to the Palms of the Americas
inferredcites →https://doi.org/10.1126/science.1163197openalex-snapshot
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
inferredcites →https://doi.org/10.1130/spe300openalex-snapshot
Terrestrial and shallow marine geology of the Bahamas and Bermuda
inferredcites →https://doi.org/10.1139/e74-118openalex-snapshot
Deep Drill 1972. Potassium–Argon Dating of the Bermuda Drill Core
inferredcites →https://doi.org/10.11646/phytotaxa.27.1.2openalex-snapshot
A preliminary evaluation of the ancestry of a putative Sabal hybrid (Arecaceae: Coryphoideae), and the description of a new nothospecies, Sabal × brazoriensis
inferredcites →https://doi.org/10.1179/174328208x322251openalex-snapshot
Pireella cymbifolia(Pterobryaceae) new to the flora, with comments on sea level and other factors influencing the phytogeography of Bermuda
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2148-10-61openalex-snapshot
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryzaand their phylogenetic utility across various taxonomic levels
inferredcites →https://doi.org/10.1186/1471-2164-15-s6-s11openalex-snapshot
BBCA: Improving the scalability of *BEAST using random binning
inferredcites →https://doi.org/10.1186/1741-7007-7-84openalex-snapshot
Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes
inferredcites →https://doi.org/10.1186/gb-2011-12-1-r1openalex-snapshot
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
inferredcites →https://doi.org/10.1371/journal.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
inferredcites →https://doi.org/10.1371/journal.pgen.0020173openalex-snapshot
Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting
inferredcites →https://doi.org/10.1371/journal.pone.0011375openalex-snapshot
Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards
inferredcites →https://doi.org/10.1371/journal.pone.0050226openalex-snapshot
Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes
inferredcites →https://doi.org/10.1371/journal.pone.0054848openalex-snapshot
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
inferredcites →https://doi.org/10.1670/0022-1511(2006)40[394:gcoeas]2.0.co;2openalex-snapshot
Geological Constraints on Evolution and Survival in Endemic Reptiles on Bermuda
inferredcites →https://doi.org/10.2307/2666644openalex-snapshot
Phylogeny, Character Evolution, and a New Classification of the Calamoid Palms
inferredcites →https://doi.org/10.2307/j.ctvcszzzdopenalex-snapshot
Field Guide to the Palms of the Americas
inferredcites →https://doi.org/10.3417/2010023openalex-snapshot
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales 1
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Targeted sequence capture as a powerful tool for evolutionary analysis1
inferredcites →https://doi.org/10.3732/apps.1300085openalex-snapshot
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae
inferredcites →https://doi.org/10.3732/apps.1400042openalex-snapshot
Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics
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A Monograph of Sabal (Arecaceae: Coryphoideae)

What points at this work

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

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Genomic patterns of native palms from the Leeward Antilles confirm single-island endemism and guide conservation priorities
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Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment
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Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)
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Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae)
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Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment
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Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex
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Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes
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Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations
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Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae)
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Low genetic differentiation among morphologically distinct Cycas species informs the delineation of conservation management units
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Phylogenomic analysis of Ranunculales resolves branching events across the order
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Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence
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A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering
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Capturing Darwin's dream
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A dedicated target capture approach reveals variable genetic markers across micro‐ and macro‐evolutionary time scales in palms
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A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids
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Collections-based research in the genomic era
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An introduction to plant phylogenomics with a focus on palms
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Beyond Genera Palmarum : progress and prospects in palm systematics
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The palm family (Arecaceae): a microcosm of sexual system evolution
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Recent and local diversification of Central American understorey palms
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Pleistocene climatic fluctuations promoted alternative evolutionary histories in Phytelephas aequatorialis, an endemic palm from western Ecuador
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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution
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Island floras as model systems for studies of plant speciation: Prospects and challenges
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Evolution and developmental genetics of floral display—A review of progress
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Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
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Taxonomy as a hypothesis: testing the status of the Bermuda buckeye butterfly Junonia coenia bergi (Lepidoptera: Nymphalidae)
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Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants
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Phylogenomics and barcoding of Panax: toward the identification of ginseng species
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Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives
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A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens
inferred← citeshttps://doi.org/10.1371/journal.pone.0235569openalex-snapshot
The utility of DNA barcodes to confirm the identification of palm collections in botanical gardens
inferred← citeshttps://doi.org/10.1600/036364419x15710776741486openalex-snapshot
Isodon hsiwenii (Lamiaceae: Nepetoideae), A New Species From Yunnan, China
inferred← citeshttps://doi.org/10.1600/036364421x16312067913471openalex-snapshot
Elucidating the Evolutionary History ofOenotheraSect.Pachylophus(Onagraceae): A Phylogenomic Approach
inferred← citeshttps://doi.org/10.1600/036364421x16312067913543openalex-snapshot
Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species ofMauritiella
inferred← citeshttps://doi.org/10.1600/036364424x17267811220461openalex-snapshot
Chilling Out: Cooler Climates Triggered Divergence of Sabal (Arecaceae: Coryphoideae: Sabaleae) at the End of the Mid-Miocene Climatic Optimum
inferred← citeshttps://doi.org/10.17129/botsci.3112openalex-snapshot
Perspectives in plant evolutionary genetics: A field guide in 15 “easy steps” to modern tools in evolutionary genetics and genomics
inferred← citeshttps://doi.org/10.21248/palmengarten.457openalex-snapshot
Attalea speciosa, die Babassupalme
inferred← citeshttps://doi.org/10.3100/hpib.v28iss1.2023.n13openalex-snapshot
Biogeographical History of the Yucatan Peninsula Endemic Flora (Spermatophyta) from a Phylogenetic Perspective1
inferred← citeshttps://doi.org/10.3389/ffgc.2021.711414openalex-snapshot
Global ex situ Conservation of Palms: Living Treasures for Research and Education
inferred← citeshttps://doi.org/10.3389/fgene.2019.01407openalex-snapshot
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
inferred← citeshttps://doi.org/10.3389/fgene.2020.596662openalex-snapshot
Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm
inferred← citeshttps://doi.org/10.3389/fgene.2022.1085692openalex-snapshot
A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae
inferred← citeshttps://doi.org/10.3389/fpls.2015.00710openalex-snapshot
Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)
inferred← citeshttps://doi.org/10.3389/fpls.2018.01941openalex-snapshot
Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes
inferred← citeshttps://doi.org/10.3389/fpls.2019.00864openalex-snapshot
Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae
inferred← citeshttps://doi.org/10.3389/fpls.2019.01761openalex-snapshot
Target Nuclear and Off-Target Plastid Hybrid Enrichment Data Inform a Range of Evolutionary Depths in the Orchid Genus Epidendrum
inferred← citeshttps://doi.org/10.3389/fpls.2021.638650openalex-snapshot
Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing
inferred← citeshttps://doi.org/10.3389/fpls.2022.960588openalex-snapshot
Plastome structure, phylogenomic analyses and molecular dating of Arecaceae
inferred← citeshttps://doi.org/10.3390/plants9040549openalex-snapshot
Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)
inferred← citeshttps://doi.org/10.3732/ajb.1500057openalex-snapshot
Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next‐generation sequencing
inferred← citeshttps://doi.org/10.70675/d804ecc1z7f37z4c03z8b7fz898f3ccb4090openalex-snapshot
Dynamique évolutive des forêts tropicales humides d'Afrique centrale : cas d'étude de la famille des palmiers (Arecaceae)
inferred← citeshttps://doi.org/10.7717/peerj.3569openalex-snapshot
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
inferred← citeshttps://doi.org/10.7717/peerj.5175openalex-snapshot
SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
inferred← citeshttps://doi.org/10.7717/peerj.6142openalex-snapshot
Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
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