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Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)

https://doi.org/10.1016/j.ympev.2015.12.015

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What this work says

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

inferredcites →https://doi.org/10.1002/j.1537-2197.1978.tb06057.xopenalex-snapshot

THE STRUCTURE OF THE ACERVULUS, THE FLOWER CLUSTER OF CHAMAEDOREOID PALMS

inferredcites →https://doi.org/10.1002/jez.b.21026openalex-snapshot

Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

inferredcites →https://doi.org/10.1007/bf00161167openalex-snapshot

Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants

inferredcites →https://doi.org/10.1007/bf00985578openalex-snapshot

Morphological evolution and ecological diversification of the forest-dwelling poppies (Papaveraceae: Chelidonioideae) as deduced from a molecular phylogeny of the ITS region

inferredcites →https://doi.org/10.1007/s11265-007-0067-4openalex-snapshot

Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell

inferredcites →https://doi.org/10.1016/0304-4149(82)90011-4openalex-snapshot

The coalescent

inferredcites →https://doi.org/10.1016/j.actao.2008.10.001openalex-snapshot

Effects of frugivore impoverishment and seed predators on the recruitment of a keystone palm

inferredcites →https://doi.org/10.1016/j.dib.2016.02.063openalex-snapshot

Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)

inferredcites →https://doi.org/10.1016/j.tplants.2014.02.012openalex-snapshot

Land plant origins and coalescence confusion

inferredcites →https://doi.org/10.1016/j.ympev.2005.12.006openalex-snapshot

Low-copy nuclear DNA, phylogeny and the evolution of dichogamy in the betel nut palms and their relatives (Arecinae; Arecaceae)

inferredcites →https://doi.org/10.1016/j.ympev.2009.05.033openalex-snapshot

Coalescent methods for estimating phylogenetic trees

inferredcites →https://doi.org/10.1016/j.ympev.2009.07.023openalex-snapshot

Working through polytomies: Auklets revisited

inferredcites →https://doi.org/10.1016/j.ympev.2009.08.012openalex-snapshot

Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations

inferredcites →https://doi.org/10.1016/j.ympev.2010.08.024openalex-snapshot

Between a rock and a hard polytomy: Rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae)

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1038/nature12309openalex-snapshot

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

inferredcites →https://doi.org/10.1038/nbt.1860openalex-snapshot

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot

Full-length transcriptome assembly from RNA-Seq data without a reference genome

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nrg2626openalex-snapshot

Sequencing technologies — the next generation

inferredcites →https://doi.org/10.1038/nrg795openalex-snapshot

Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

inferredcites →https://doi.org/10.1073/pnas.0409137102openalex-snapshot

An algorithm for progressive multiple alignment of sequences with insertions

inferredcites →https://doi.org/10.1073/pnas.0709121104openalex-snapshot

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.91.15.6795openalex-snapshot

Rates and patterns of chloroplast DNA evolution.

inferredcites →https://doi.org/10.1073/pnas.93.19.10274openalex-snapshot

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.

inferredcites →https://doi.org/10.1078/1433-8319-00039openalex-snapshot

Interplate dispersal paths for megathermal angiosperms

inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot

Inferring Phylogeny Despite Incomplete Lineage Sorting

inferredcites →https://doi.org/10.1080/10635150590924208openalex-snapshot

Polytomies and Bayesian Phylogenetic Inference

inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot

Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence

inferredcites →https://doi.org/10.1093/aob/mcr020openalex-snapshot

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)

inferredcites →https://doi.org/10.1093/aob/mcr149openalex-snapshot

Ontogeny and structure of the acervulate partial inflorescence in Hyophorbe lagenicaulis (Arecaceae; Arecoideae)

inferredcites →https://doi.org/10.1093/aob/mct264openalex-snapshot

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

inferredcites →https://doi.org/10.1093/aob/mcu133openalex-snapshot

Floral structure and development in the monoecious palm Gaussia attenuata (Arecaceae; Arecoideae)

inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot

MRBAYES: Bayesian inference of phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

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/btt394openalex-snapshot

Naive binning improves phylogenomic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot

ASTRAL: genome-scale coalescent-based species tree estimation

inferredcites →https://doi.org/10.1093/molbev/msi121openalex-snapshot

More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

inferredcites →https://doi.org/10.1093/molbev/msp250openalex-snapshot

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

inferredcites →https://doi.org/10.1093/molbev/mst160openalex-snapshot

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

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/sys029openalex-snapshot

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

inferredcites →https://doi.org/10.1093/sysbio/sys049openalex-snapshot

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

inferredcites →https://doi.org/10.1098/rsbl.2004.0197openalex-snapshot

Falling palm fronds structure Amazonian rainforest sapling communities

inferredcites →https://doi.org/10.1101/gr.9.9.868openalex-snapshot

CAP3: A DNA Sequence Assembly Program

inferredcites →https://doi.org/10.1109/gce.2010.5676129openalex-snapshot

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

inferredcites →https://doi.org/10.1111/bij.12551openalex-snapshot

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

inferredcites →https://doi.org/10.1111/cla.12100openalex-snapshot

Phylogeny and historical biogeography of the cocosoid palms ( A recaceae, A recoideae, C ocoseae) inferred from sequences of six WRKY gene family loci

inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb00119.xopenalex-snapshot

EARLY TERTIARY OUT-OF-INDIA DISPERSAL OF CRYPTERONIACEAE: EVIDENCE FROM PHYLOGENY AND MOLECULAR DATING

inferredcites →https://doi.org/10.1111/j.1095-8339.2004.00307.xopenalex-snapshot

Comparative floral structure and systematics of Pelagodoxa and Sommieria (Arecaceae)

inferredcites →https://doi.org/10.1111/j.1095-8339.2006.00521.xopenalex-snapshot

A new subfamily classification of the palm family (Arecaceae): evidence from plastid DNA phylogeny

inferredcites →https://doi.org/10.1111/j.1096-0031.1989.tb00569.xopenalex-snapshot

RECONSTRUCTING CHARACTER EVOLUTION ON POLYTOMOUS CLADOGRAMS

inferredcites →https://doi.org/10.1111/j.1096-0031.1999.tb00278.xopenalex-snapshot

Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima

inferredcites →https://doi.org/10.1111/j.1096-0031.2008.00217.xopenalex-snapshot

TNT, a free program for phylogenetic analysis

inferredcites →https://doi.org/10.1111/j.1096-0031.2012.00418.xopenalex-snapshot

Plastid genomes and deep relationships among the commelinid monocot angiosperms

inferredcites →https://doi.org/10.1111/j.1365-2699.2012.02794.xopenalex-snapshot

Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. II. Diversification history and origin of regional assemblages

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/nph.13617openalex-snapshot

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

inferredcites →https://doi.org/10.1126/science.1243092openalex-snapshot

Hyperdominance in the Amazonian Tree Flora

inferredcites →https://doi.org/10.1146/annurev-ecolsys-110512-135822openalex-snapshot

High-Throughput Genomic Data in Systematics and Phylogenetics

inferredcites →https://doi.org/10.1186/1741-7007-11-48openalex-snapshot

Tropical rain forest evolution: palms as a model group

inferredcites →https://doi.org/10.1186/1741-7007-9-44openalex-snapshot

Origin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms

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/10.12705/643.9openalex-snapshot

A genus‐level phylogenetic linear sequence of monocots

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.pone.0007353openalex-snapshot

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

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/10.2307/1222111openalex-snapshot

Genera palmarum: A Classification of Palms Based on the Work of Harold E. Moore, Jr.

inferredcites →https://doi.org/10.2307/2399464openalex-snapshot

Changes in Plant Community Diversity and Floristic Composition on Environmental and Geographical Gradients

inferredcites →https://doi.org/10.2307/2657094openalex-snapshot

Coding and noncoding plastid DNA in palm systematics

inferredcites →https://doi.org/10.2307/2807789openalex-snapshot

Monocotyledons: Systematics and Evolution.

inferredcites →https://doi.org/10.2478/acpa-2014-0003openalex-snapshot

Fossil fruit of Cocos L. (Arecaceae) from Maastrichtian-Danian sediments of central India and its phytogeographical significance

inferredcites →https://doi.org/10.3417/2010023openalex-snapshot

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales 1

inferredcites →https://doi.org/10.34885/92openalex-snapshot

Genera Palmarum - The Evolution and Classification of the Palms

inferredcites →https://doi.org/10.3732/ajb.1100491openalex-snapshot

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

inferredcites →https://doi.org/10.3732/ajb.1500057openalex-snapshot

Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next‐generation sequencing

What points at this work

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

inferred← citeshttps://doi.org/10.1002/tax.12421zenodo-depositor-declared

Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

inferred← citeshttps://doi.org/10.1002/ajb2.1019openalex-snapshot

Constructing a broadly inclusive seed plant phylogeny

inferred← citeshttps://doi.org/10.1002/tax.12797openalex-snapshot

Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar

inferred← citeshttps://doi.org/10.1007/978-3-030-76649-8_7openalex-snapshot

Palms in an ‘Omics’ Era

inferred← citeshttps://doi.org/10.1007/978-3-319-95101-0_6openalex-snapshot

The Gene Pool Concept Applied to Crop Wild Relatives: An Evolutionary Perspective

inferred← citeshttps://doi.org/10.1007/s00606-025-01975-wopenalex-snapshot

Evaluation of evolutionary patterns limiting the utility of the rbcLa DNA barcoding locus in palms

inferred← citeshttps://doi.org/10.1007/s10722-024-01960-1openalex-snapshot

In silico study of phosphatidylethanolamine-binding proteins in oil palm, coconut, and date palm: evolutionary insights into genetic relations, sequence conservation, and functional implications

inferred← citeshttps://doi.org/10.1007/s40415-018-0462-zopenalex-snapshot

The first complete chloroplast genome sequence of Syagrus coronata: comparative analysis in Arecoideae (Arecaceae)

inferred← citeshttps://doi.org/10.1016/j.dib.2016.02.063openalex-snapshot

Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.12.030openalex-snapshot

Phylogeny, historical biogeography and diversification rates in an economically important group of Neotropical palms: Tribe Euterpeae

inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107067openalex-snapshot

A robust phylogenomic framework for the calamoid palms

inferred← citeshttps://doi.org/10.1080/00275514.2021.1889276openalex-snapshot

Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes

inferred← citeshttps://doi.org/10.1080/23818107.2024.2426151openalex-snapshot

Fruit characters in early divergent Arecaceae-Arecoideae: comparative carpology of Hyophorbe Gaertn. (Chamaedoreeae)

inferred← citeshttps://doi.org/10.1093/aob/mcaf191openalex-snapshot

Convergent evolution of sex chromosomes in two palm species, Phoenix dactylifera and Kerriodoxa elegans

inferred← citeshttps://doi.org/10.1093/botlinnean/boae060openalex-snapshot

A review of the genus Euterpe: botanical and genetic aspects of açai, the purple gold of the Amazon

inferred← citeshttps://doi.org/10.1093/botlinnean/boaf005openalex-snapshot

Fruit structure and development in representatives of Iriarteeae (Arecaceae–Arecoideae)

inferred← citeshttps://doi.org/10.1093/botlinnean/boz015openalex-snapshot

Phylogenomics, biogeography and evolution in the American genus Brahea (Arecaceae)

inferred← citeshttps://doi.org/10.1093/sysbio/syag022openalex-snapshot

Phylogenomics and a New Fossil Synthesis Illuminate the Early Evolution of Palms (Arecaceae)

inferred← citeshttps://doi.org/10.1093/sysbio/syx050openalex-snapshot

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

inferred← citeshttps://doi.org/10.1101/110296openalex-snapshot

Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

inferred← citeshttps://doi.org/10.1101/2024.06.23.600266openalex-snapshot

Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence

inferred← citeshttps://doi.org/10.1101/467779openalex-snapshot

Phylogenomics, biogeography, and evolution in the American palm genus Brahea

inferred← citeshttps://doi.org/10.1101/511949openalex-snapshot

Phylogenomics within the Anthonotha clade (Detarioideae, Leguminosae) reveals a high diversity in floral trait shifts and a general trend towards organ number reduction

inferred← citeshttps://doi.org/10.1111/boj.12401openalex-snapshot

Beyond Genera Palmarum : progress and prospects in palm systematics

inferred← citeshttps://doi.org/10.1111/geb.13521openalex-snapshot

Recent and local diversification of Central American understorey palms

inferred← citeshttps://doi.org/10.1111/jipb.13609openalex-snapshot

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

inferred← citeshttps://doi.org/10.1186/s12915-023-01544-yopenalex-snapshot

A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.3329/bjpt.v30i2.70498openalex-snapshot

Molecular Phylogenetics and Molecular Dating of Arecaceae In Bangladesh Inferred from Matk and Rbcl Genes

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.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/biology12020233openalex-snapshot

Cytogenetics, Typification, Molecular Phylogeny and Biogeography of Bentinckia (Arecoideae, Arecaceae), an Unplaced Indian Endemic Palm from Areceae

inferred← citeshttps://doi.org/10.6084/m9.figshare.22618343openalex-snapshot

Additional file 1 of A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.6084/m9.figshare.22618346openalex-snapshot

Additional file 2 of A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.6084/m9.figshare.22618349openalex-snapshot

Additional file 3 of A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.6084/m9.figshare.22618352openalex-snapshot

Additional file 4 of A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.6084/m9.figshare.22618355openalex-snapshot

Additional file 5 of A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.6084/m9.figshare.22618358openalex-snapshot

Additional file 6 of A plastid phylogenomic framework for the palm family (Arecaceae)

inferred← citeshttps://doi.org/10.7287/peerj.3569v0.1/reviews/1openalex-snapshot

Peer Review #1 of "Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”? (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.3569v0.1/reviews/2openalex-snapshot

Peer Review #2 of "Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”? (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.3569v0.2/reviews/1openalex-snapshot

Peer Review #1 of "Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”? (v0.2)"

inferred← citeshttps://doi.org/10.7717/peerj.3569openalex-snapshot

Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?

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