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Phylogenomic approaches reveal how a climatic inversion and glacial refugia shape patterns of diversity in an African rain forest tree species

https://doi.org/10.1101/807727
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Very high resolution interpolated climate surfaces for global land areas
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ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches
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Rainforest responses to past climatic tropical Africa
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Testing Putative African Tropical Forest Refugia Using Chloroplast and Nuclear DNA Phylogeography
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Comparative phylogeography of African rain forest trees: A review of genetic signatures of vegetation history in the Guineo-Congolian region
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Neotropical forest expansion during the last glacial period challenges refuge hypothesis
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Comparative multi-locus phylogeography confirms multiple vicariance events in co-distributed rainforest frogs
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Prediction of phylogeographic endemism in an environmentally complex biome
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Pleistocene population expansions of shade-tolerant trees indicate fragmentation of the African rainforest during the Ice Ages
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
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ENM eval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models
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Late Pleistocene molecular dating of past population fragmentation and demographic changes in African rain forest tree species supports the forest refuge hypothesis
inferredcites →https://doi.org/10.1111/jbi.12570openalex-snapshot
The phylogeography of the rodent genus Malacomys suggests multiple Afrotropical Pleistocene lowland forest refugia
inferredcites →https://doi.org/10.1111/jbi.12902openalex-snapshot
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inferredcites →https://doi.org/10.1111/jbi.12972openalex-snapshot
Comparative analysis of spatial genetic structure in an ant–plant symbiosis reveals a tension zone and highlights speciation processes in tropical Africa
inferredcites →https://doi.org/10.1111/mec.12724openalex-snapshot
Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover
inferredcites →https://doi.org/10.1111/mec.14266openalex-snapshot
Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection
inferredcites →https://doi.org/10.1126/science.1085510openalex-snapshot
Preserving the Tree of Life
inferredcites →https://doi.org/10.1126/science.1166955openalex-snapshot
Stability Predicts Genetic Diversity in the Brazilian Atlantic Forest Hotspot
inferredcites →https://doi.org/10.1126/science.aav6821openalex-snapshot
A 90,000-year record of Afromontane forest responses to climate change
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INTRASPECIFIC PHYLOGEOGRAPHY: The Mitochondrial DNA Bridge Between Population Genetics and Systematics
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
inferredcites →https://doi.org/10.1186/s12862-016-0779-9openalex-snapshot
Demographical history and palaeodistribution modelling show range shift towards Amazon Basin for a Neotropical tree species in the LGM
inferredcites →https://doi.org/10.1186/s12862-016-0807-9openalex-snapshot
Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries
inferredcites →https://doi.org/10.1371/journal.pcbi.1006650openalex-snapshot
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
inferredcites →https://doi.org/10.1371/journal.pgen.1005421openalex-snapshot
New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation
inferredcites →https://doi.org/10.1371/journal.pone.0084307openalex-snapshot
Comparative Phylogeography in Rainforest Trees from Lower Guinea, Africa
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Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2
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fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
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The Anolis Lizards of Bimini: Resource Partitioning in a Complex Fauna
inferredcites →https://doi.org/10.3389/fpls.2018.01941openalex-snapshot
Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes
inferredcites →https://doi.org/10.3732/apps.1600016openalex-snapshot
HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
inferredcites →https://doi.org/10.5281/zenodo.3268813openalex-snapshot
danlwarren/ENMTools: ENMTools 1.0.1
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SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

What points at this work

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

inferred← citeshttps://doi.org/10.1073/pnas.2001018117openalex-snapshot
Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations
inferred← citeshttps://doi.org/10.24072/pci.evolbiol.100094openalex-snapshot
Remarkable insights into processes shaping African tropical tree diversity
inferred← citeshttps://doi.org/10.3390/plants9040549openalex-snapshot
Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)
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