SummaryThe 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. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group.An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma.This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.

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. We evaluate the effect of the prior number of expected shifts in the phylogenetic tree. • Key results Major diversification increases took place over 100 Ma, from the Early Cretaceous to the end of the Paleogene, and are distributed across the angiosperm phylogeny. The long-term diversification trajectory of angiosperms shows moderate rate variation, but is underlain by increasing speciation and extinction, and results from temporally overlapping, independent radiations and depletions in component lineages. • Conclusions The identified deep time diversification shifts are clues to the identification of ultimate drivers of angiosperm megadiversity, which probably involve multivariate interactions among intrinsic traits and extrinsic forces. An enhanced understanding of angiosperm diversification will involve a more precise phylogenetic location of diversification shifts, and integration of fossil information.

We conducted a pilot study using Anchored Hybrid Enrichment to resolve relationships among a mostly Neotropical sage lineage that may have undergone a recent evolutionary radiation. Conventional markers (ITS, trnL-trnF and trnH-psbA) have not been able to resolve the relationships among species nor within portions of the backbone of the lineage. We sampled 12 representative species of subgenus Calosphace and included one species of Salvia's s.l. closest relative, Lepechinia, as outgroup. Hybrid enrichment and sequencing were successful, yielding 448 alignments of individual loci with an average length of 704bp. The performance of the phylogenomic data in phylogenetic reconstruction was superior to that of conventional markers, increasing both support and resolution. Because the captured loci vary in the amount of net phylogenetic informativeness at different phylogenetic depths, these data are promising in phylogenetic reconstruction of this group and likely other lineages within Lamiales. However, special attention should be placed on the amount of phylogenetic noise that the data could potentially contain. A prior exploration step using phylogenetic informativeness profiles to detect loci with sites with disproportionately high substitution rates (showing "phantom" spikes) and, if required, the ensuing filtering of the problematic data is recommended. In our dataset, filtering resulted in increased support and resolution for the shallow nodes in maximum likelihood phylogenetic trees resulting from concatenated analyses of all the loci. Additionally, it is expected that an increase in sampling (loci and taxa) will aid in resolving weakly supported, short deep internal branches.

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. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.

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6 1 abstract.-The combination of new analytical techniques, availability of more fossil and molecular data, and 7 better practices in data sharing has resulted in a steady accumulation of chronograms in public and open 8 databases such as TreeBASE, Dryad, and Open Tree of Life for a large quantity and diversity of organisms 9in the last few decades. However, getting a tree with branch lengths proportional to time remains difficult 10 for many biologists and the non-academic community, despite its importance in many areas of research, 11 education, and science communication. datelife is a service implemented via an R package and a web site 12 (http://www.datelife.org/) for efficient reuse, summary and reanalysis of published data on lineage divergence 13 times. The main workflow starts with at least two taxon names as input, either as tip labels on a tree, or 14 as a simple comma separated character string. A name search is then performed across the chronogram 15 database and positively identified source trees are pruned to maintain queried taxa only and stored as a 16 named list of patristic distance matrices. Source chronogram data can be summarised using branch length 17 summary statistics or variance minimizing approaches to generate a single summary chronogram. Source 18 chronogram data can also be used as calibration points to date a tree containing some or all names from the 19 initial query. If there is no information available for any queried taxa, data can be simulated. All source 20 and summary chronograms can be saved in formats that permit easy reuse and reanalysis. Summary and 21 newly generated trees are potentially useful to evaluate evolutionary hypothesis in different areas of research 22 in biology. How well this trees work for this purpose still needs to be tested. datelife will be useful to 23 increase awereness on the existing variation in expert time of divergence data, and might foster exploration of 24 the effect of alternative divergence time hypothesis on the results of analyses, nurturing a culture of more 25 cautious interpretation of evolutionary results. 26 Supertree; Calibrations 28Clade ages represent a fundamental piece of information for evolutionary understanding in many areas 30 of research, from developmental to conservation biology (Felsenstein 1985; Webb 2000), from historical 31 biogeography to species diversification studies (Posadas et al. 2006; Morlon 2014). The primary information 32 needed for these time estimates comes from the fossil record. Coupled with phylogenies with branch lengths 33 based on molecular and/or morphological data, the time of divergence of extant and extinct lineages can be 34 reconstructed with molecular dating methods. The number of studies publishing phylogenies with branch 35 lengths proportional to geological time (hereafter chronograms) have constantly increased in number for the 36 last two decades (Kumar et al. 2017). Still, generating a chronogram is not an easy task unless you have 37 specialized training: it requires inferring a tree, u...

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