Felipe Zapata

Synchronizing speciation, extinction, and dispersal to island paleodynamics through Bayesian phylogenetics in a Hawaiian plant radiation

The paper introduces a Bayesian phylogenetic framework to infer divergence times, ancestral ranges, and diversification rates in Hawaiian plants without fossil calibration.

Phylogenomics of the North American Desert Radiation Linanthus (Polemoniaceae) Reveals Mixed Trait Lability and No Single Geographic Mode of Speciation

This study uses genomic data to reconstruct the evolutionary history of Linanthus species, revealing complex speciation patterns and trait evolution in arid environments.

Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation

The paper compares elevational and thermal ranges of sister plant species in tropical and temperate mountains, finding tropical species have narrower thermal ranges and greater similarity between sister species, supporting speciation via thermal specialization.

Pairwise comparisons across species are problematic when analyzing functional genomic data

The paper reanalyzes two studies comparing gene expression across species, showing that pairwise comparisons can mislead conclusions about evolutionary processes by ignoring species relationships.

Revising transcriptome assemblies with phylogenetic information in Agalma1.0

The paper introduces treeinform, a module in Agalma1.0 that improves transcriptome assemblies by using phylogenetic analysis to correct gene misassignment errors.

Phylogenomic analyses support traditional relationships within Cnidaria

The paper uses transcriptome and genome data to analyze phylogenetic relationships within Cnidaria, supporting traditional groupings and resolving deep evolutionary relationships.

Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones

This study identifies stem cell distribution and proliferation patterns in Nanomia bijuga, showing their localization in growth zones and their role in colony development.

Analysis of geographic patterns of molecular, morphological, and bioclimatic variation to evaluate hypotheses of species boundaries in the South American montane genus Escallonia (Escalloniaceae)

The paper evaluates species boundaries in Escallonia using molecular, morphological, and bioclimatic data, finding that most species represent distinct evolutionary trajectories.

Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

The paper re-evaluates gastropod phylogenetic relationships using transcriptome and genome data, rejecting the Orthogastropoda hypothesis and proposing three alternative rooting hypotheses.