DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.

Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task.

Why don't we share data and code? Perceived barriers and benefits to public archiving practices.

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives.

Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.

Background: Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study.

OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life.

The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses.

Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees.

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy.

Thirty clues to the exceptional diversification of flowering plants.

Background And Aims: As angiosperms became one of the megadiverse groups of macroscopic eukaryotes, they forged modern ecosystems and promoted the evolution of extant terrestrial biota. Unequal distribution of species among lineages suggests that diversification, the process that ultimately determines species richness, acted differentially through angiosperm evolution.

Methods: We investigate how angiosperms became megadiverse by identifying the phylogenetic and temporal placement of exceptional radiations, by combining the most densely fossil-calibrated molecular clock phylogeny with a Bayesian model that identifies diversification shifts among evolutionary lineages and through time.

Recent radiation and dispersal of an ancient lineage: The case of Fouquieria (Fouquiericeae, Ericales) in North American deserts.

Arid biomes are particularly prominent in the Neotropics providing some of its most emblematic landscapes and a substantial part of its species diversity. To understand some of the evolutionary processes underlying the speciation of lineages in the Mexican Deserts, the diversification of Fouquieria is investigated, which includes eleven species, all endemic to the warm deserts and dry subtropical regions of North America. Using a phylogeny from plastid DNA sequences with samples of individuals from populations of all the species recognized in Fouquieria, we estimate divergence times, test for temporal diversification heterogeneity, test for geographical structure, and conduct ancestral area reconstruction.

Uncovering Higher-Taxon Diversification Dynamics from Clade Age and Species-Richness Data.

The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time-dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age), and taxonomic delimitation can affect estimates of the age-richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations.

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity.

The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks.

Hierarchical clustering of genetic diversity associated to different levels of mutation and recombination in Escherichia coli: a study based on Mexican isolates.

Escherichia coli occur as either free-living microorganisms, or within the colons of mammals and birds as pathogenic or commensal bacteria. Although the Mexican population of intestinal E. coli maintains high levels of genetic diversity, the exact mechanisms by which this occurs remain unknown.