Deren A. R. Eaton
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View article: Estimating waiting distances between genealogy changes under a Multi-Species Extension of the Sequentially Markov Coalescent
Estimating waiting distances between genealogy changes under a Multi-Species Extension of the Sequentially Markov Coalescent Open
Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genealogical relationships among multiple genomes vary spatially across different genomic regions. …
View article: Pollination niche shifts in sympatric globular cacti Eriosyce: Consequences on reproductive isolation and species formation
Pollination niche shifts in sympatric globular cacti Eriosyce: Consequences on reproductive isolation and species formation Open
Pollination niches, which encompass the factors influencing pollen exchange among angiosperms, are fundamental to understanding reproductive success and the intricate eco-evolutionary dynamics of plants. In this study, we investigated poll…
View article: Phylogeny does not predict the outcome of heterospecific pollen–pistil interactions in a species‐rich alpine plant community
Phylogeny does not predict the outcome of heterospecific pollen–pistil interactions in a species‐rich alpine plant community Open
Premise Co‐occurring plant species that share generalist pollinators often exchange pollen. This heterospecific pollen transfer (HPT) impacts male and female reproductive success through pollen loss and reductions in seed set, respectively…
View article: A historical stepping-stone path for an island-colonizing cactus across a submerged “bridge” archipelago
A historical stepping-stone path for an island-colonizing cactus across a submerged “bridge” archipelago Open
View article: Caught in the Act: Incipient Speciation at the Southern limit of Viburnum in the Central Andes
Caught in the Act: Incipient Speciation at the Southern limit of Viburnum in the Central Andes Open
<p>Repository for:</p>\n\n<p><strong>Caught in the Act: Incipient Speciation at the Southern limit of Viburnum in the Central Andes </strong></p>\n\n<p> </p>\n\n<p>In this reposito…
View article: Estimating Waiting Distances Between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent
Estimating Waiting Distances Between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent Open
Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genealogical relationships among multiple genomes vary spatially across different genomic regions. …
View article: Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps
Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps Open
Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species-specificity. However, cases in which two or more pollinator species share a single host spe…
View article: Publisher Correction: Replicated radiation of a plant clade along a cloud forest archipelago
Publisher Correction: Replicated radiation of a plant clade along a cloud forest archipelago Open
View article: Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism
Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism Open
Orobanchaceae is the largest family of parasitic plants, containing autotrophic and parasitic plants with all degrees of parasitism. This makes it by far the best family for studying the origin and evolution of plant parasitism. Here we pr…
View article: Selection on the gametophyte: Modeling alternation of generations in plants
Selection on the gametophyte: Modeling alternation of generations in plants Open
Premise The degree of gametophyte dependence on the sporophyte life stage is a major feature that differentiates the life cycles of land plants, yet the evolutionary consequences of this difference remain poorly understood. Most evolutiona…
View article: Replicated radiation of a plant clade along a cloud forest archipelago dataset
Replicated radiation of a plant clade along a cloud forest archipelago dataset Open
Raw data complementary of https://github.com/eaton-lab/Orienotinus-phylogeny repository Assembly output of Oreinotinus species (Viburnum, Adoxaceae) using ipyrad pipeline and morphological matrix: List of files: full_data…
View article: Replicated radiation of a plant clade along a cloud forest archipelago dataset
Replicated radiation of a plant clade along a cloud forest archipelago dataset Open
Raw data complementary of https://github.com/eaton-lab/Orienotinus-phylogeny repository Assembly output of Oreinotinus species (Viburnum, Adoxaceae) using ipyrad pipeline and morphological matrix: List of files: full_data…
View article: Resolved phylogenetic relationships in the <i>Ocotea</i> complex (<i>Supraocotea</i>) facilitate phylogenetic classification and studies of character evolution
Resolved phylogenetic relationships in the <i>Ocotea</i> complex (<i>Supraocotea</i>) facilitate phylogenetic classification and studies of character evolution Open
Premise The Ocotea complex contains the greatest diversity of Lauraceae in the Neotropics. However, the traditional taxonomy of the group has relied on only three main floral characters, and previous molecular analyses have used only a few…
View article: Genetic incompatibilities do not snowball in a demographic model of speciation
Genetic incompatibilities do not snowball in a demographic model of speciation Open
Two populations evolving in isolation can accumulate genetic differences over time that cause incompatibilities in their hybrid offspring. These “Dobzhansky-Muller incompatibilities” (DMIs) are predicted to accumulate at a rate faster than…
View article: Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos
Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos Open
Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tri…
View article: The Multispecies Coalescent in Space and Time
The Multispecies Coalescent in Space and Time Open
A key distinction between species tree inference under the multi-species coalescent model (MSC), and the inference of gene trees in sliding windows along a genome, is in the effect of genetic linkage. Whereas the MSC explicitly assumes gen…
View article: ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network Open
Summary ipcoal is a free and open source Python package for simulating and analyzing genealogies and sequences. It automates the task of describing complex demographic models (e.g., with divergence times, effective population sizes, migrat…
View article: Dataset: Using genome-wide RAD sequences to resolve rapid radiations: A case study from the Cactaceae
Dataset: Using genome-wide RAD sequences to resolve rapid radiations: A case study from the Cactaceae Open
The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, …
View article: Resolved phylogenetic relationships in the Ocotea complex (Supraocotea) facilitate a phylogenetic classification and character ancestral reconstruction
Resolved phylogenetic relationships in the Ocotea complex (Supraocotea) facilitate a phylogenetic classification and character ancestral reconstruction Open
All ipyrad outfiles for species of Supraocotea + outgroups with all loci shared across at least 10, 20, 40, and 50 individuals.
View article: Dataset: The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae
Dataset: The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae Open
The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, …
View article: Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of<i>Viburnum</i>
Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of<i>Viburnum</i> Open
Phylogeny, fossils, biogeography, and biome occupancy provide evidence that reflects the singular evolutionary history of a clade. Despite the connections that bind them together, these lines of evidence are most often studied separately, …
View article: eaton-lab/toytree: v1.0 publication release
eaton-lab/toytree: v1.0 publication release Open
This version corresponds to the final submission of the toytree manuscript to Methods in Ecology and Evolution.
View article: Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression
Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression Open
Hawaiian Melicope are one of the major adaptive radiations of the Hawaiian Islands comprising 54 endemic species. The lineage is monophyletic with an estimated crown age predating the rise of the current high islands. Phylogenetic i…
View article: Inferring Processes of Coevolutionary Diversification in a Community of Panamanian Strangler Figs and Associated Pollinating Wasps
Inferring Processes of Coevolutionary Diversification in a Community of Panamanian Strangler Figs and Associated Pollinating Wasps Open
1 Abstract The fig and pollinator wasp obligate mutualism is diverse (~750 described species), ecologically important, and ancient (~80-90 Ma), providing model systems for generating and testing many questions in evolution and ecology. Onc…
View article: Genome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species
Genome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species Open
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared with those based on "traditional" …
View article: Sterile marginal flowers increase visitation and fruit set in the hobblebush (<i>Viburnum lantanoides</i>, Adoxaceae) at multiple spatial scales
Sterile marginal flowers increase visitation and fruit set in the hobblebush (<i>Viburnum lantanoides</i>, Adoxaceae) at multiple spatial scales Open
The presence of SMFs significantly increased pollinator attraction and female reproductive success both in contemporary and simulated ancestral contexts, indicating that stabilizing selection is responsible for their maintenance, and direc…
View article: Practical considerations for plant phylogenomics
Practical considerations for plant phylogenomics Open
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of p…
View article: Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants
Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants Open
Restriction-site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with the consequence that mutations disrupting these sites lead t…
View article: Supplement 2. Genbank accession numbers of DNA sequences used in phylogeny reconstruction. Voucher information is provided for new sequences generated for this study.
Supplement 2. Genbank accession numbers of DNA sequences used in phylogeny reconstruction. Voucher information is provided for new sequences generated for this study. Open
File List Supplement_2.txt (md5: 91ebfca65bd6cfc123b253d0d8683b9d) Description Supplement_2.txt is a tab-separated file. Row names contain a species or sample name. The column names indicate accession and voucher labels for each of three g…
View article: Appendix B. Representation of six floral traits distributed across samples within the two-dimensional morphospace created by the first two PC axes.
Appendix B. Representation of six floral traits distributed across samples within the two-dimensional morphospace created by the first two PC axes. Open
Representation of six floral traits distributed across samples within the two-dimensional morphospace created by the first two PC axes.