Transcription factors interact with RNA to regulate genes.

Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.

The Expected Behaviors of Posterior Predictive Tests and Their Unexpected Interpretation.

Poor fit between models of sequence or trait evolution and empirical data is known to cause biases and lead to spurious conclusions about evolutionary patterns and processes. Bayesian posterior prediction is a flexible and intuitive approach for detecting such cases of poor fit. However, the expected behavior of posterior predictive tests has never been characterized for evolutionary models, which is critical for their proper interpretation. Here, we show that the expected distribution of posterior predictive P-values is generally not uniform, in contrast to frequentist P-values used for hypothesis testing, and extreme posterior predictive P-values often provide more evidence of poor fit than typically appreciated. Posterior prediction assesses model adequacy under highly favorable circumstances, because the model is fitted to the data, which leads to expected distributions that are often concentrated around intermediate values. Nonuniform expected distributions of P-values do not pose a problem for the application of these tests, however, and posterior predictive P-values can be interpreted as the posterior probability that the fitted model would predict a dataset with a test statistic value as extreme as the value calculated from the observed data.

Complex Models of Sequence Evolution Improve Fit, but not Gene Tree Discordance, for Tetrapod Mitogenomes.

Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models, and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each includes a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate site-specific rate variation across lineages (heterotachy), and a partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could, in fact, be biological in nature after all.

Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards.

Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.

Axi-Stack: a method for manufacturing freeform air-silica optical fibre.

We present a method with potential for fabricating freeform air-silica optical fibre preforms which is free from the stacking constraints associated with conventional stack-and-draw. The method, termed Axi-Stack, is enabled by the precision machining of short cross-sectional preform discs by ultrafast laser assisted etching; a laser-based microfabrication technique which facilitates near arbitrary shaping of the preform structure. Several preform discs are stacked axially and fused together via ultrafast laser welding to construct the preform, which can be drawn to fibre using conventional methods. To illustrate the Axi-Stack process, we detail the fabrication of a 30 cm long solid-core photonic crystal fibre preform with a square lattice of cladding holes and characterise fibre drawn from it.

Enhancements to quantum communication performance utilizing a prototype photonic lantern and multiplexed single-photon detection.

The optical interfacing between a free-space channel and single-photon detectors (SPDs) can greatly impact the inherent performance of a free-space quantum key distribution receiver. Direct coupling to detectors creates engineering challenges, and a single-mode fiber requires adaptive optics. Using a multimode fiber (MMF) is common; however, larger core diameters limit the achievable bandwidth. We demonstrate a prototype multimode fiber-based photonic lantern that allows us to retain the benefits of the large multimode coupling while transitioning to multiple, less multimodal fibers, reducing bandwidth limitation.

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells.

Interactions between noncoding RNAs and chromatin proteins play important roles in gene regulation, but the molecular details of most of these interactions are unknown. Using protein-RNA photocrosslinking and mass spectrometry on embryonic stem cell nuclei, we identified and mapped, at peptide resolution, the RNA-binding regions in ∼800 known and previously unknown RNA-binding proteins, many of which are transcriptional regulators and chromatin modifiers. In addition to known RNA-binding motifs, we detected several protein domains previously unknown to function in RNA recognition, as well as non-annotated and/or disordered regions, suggesting that many functional protein-RNA contacts remain unexplored. We identified RNA-binding regions in several chromatin regulators, including TET2, and validated their ability to bind RNA. Thus, proteomic identification of RNA-binding regions (RBR-ID) is a powerful tool to map protein-RNA interactions and will allow rational design of mutants to dissect their function at a mechanistic level.

Fiber-connectorized ultrafast-laser-inscribed K-band integrated optics beam combiner for the CHARA telescope array.

A fiber-connectorized K-band integrated-optics two-telescope beam combiner was developed for long-baseline interferometry at the CHARA telescope array utilizing the ultrafast laser inscription (ULI) technique. Single-mode waveguide insertion losses were measured to be ∼1.1d B over the 2-2.3 µm window. The development of asymmetric directional couplers enabled the construction of a beam combiner that includes a 50:50 coupler for interferometric combination and two ∼75:25 couplers for photometric calibration. The visibility of the bare beam combiner was measured at 87% and then at 82% after fiber-connectorization by optimizing the input polarization. These results indicate that ULI technique can fabricate efficient fiber-connectorized K-band beam combiners for astronomical purposes.

A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins.

Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.

Temperate Zone Isolation by Climate: An Extension of Janzen's 1967 Hypothesis.

AbstractOne of the most stunning patterns of the distribution of life on Earth is the latitudinal biodiversity gradient. In an influential article, Janzen (1967) predicted that tropical mountains are more effective migration barriers than temperate mountains of the same elevation, because annual temperature variation in the tropics is lower. A great deal of research has demonstrated that the mechanism envisioned by Janzen operates at broad latitudinal scales. However, the extent that the mechanism mediates biodiversity generally, and at smaller scales, is far less understood. We investigated whether climate overlap is associated with genetic similarity between populations within temperate regions using lizards in the Sierra Nevada mountain range of California as a study system. By comparing genetic differentiation between high- and low-elevation populations, we found that in addition to the expected strong pattern of isolation by distance, high climate overlap was negatively associated with genetic differentiation, indicating that population pairs that inhabit climatically similar environments are less genetically differentiated. Moreover, while climate overlap between high- and low-elevation sites is predicted to increase from the equator to temperate regions, we find that in adjacent mountain ranges at the same latitude in temperate regions, climate overlap values can vary widely. This study suggests that in addition to the well-studied main effect of latitude on climate overlap and population differentiation, local climate factors within bioclimatic regions can also influence genetic differentiation between populations and do so by the same general mechanism that operates at larger geographic scales.

Biogeographic inferences across spatial and evolutionary scales.

The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad-scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.

Testing concordance and conflict in spatial replication of landscape genetics inferences.

The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses with a total of 119 individuals in five areas within the Sierra Nevada mountain range. Genetic distances calculated from thousands of ddRAD markers were used to optimize landscape resistance surfaces and infer the effects of landscape and topographic features on genetic connectivity. Across study areas, we found a great deal of consistency in the primary environmental gradients impacting genetic connectivity, along with some site-specific differences, and a range in the proportion of genetic variance explained by environmental factors across study sites. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Across study areas, canyon valleys were always implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity, though the relative importance varied in different areas. We emphasize that spatial data layers are complex and multidimensional, and careful consideration of spatial data correlation structure and robust analytic frameworks will be critical to our continued understanding of spatial genetics processes.

On the Need for New Measures of Phylogenomic Support.

The scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount of information with which to draw inferences about evolutionary history. However, standard approaches to assessing confidence in those inferences (e.g., nonparametric bootstrap proportions [BP] and Bayesian posterior probabilities [PPs]) are still deeply influenced by statistical procedures and frameworks that were developed when information was much more limited. These approaches largely quantify uncertainty caused by limited amounts of data, which is often vanishingly small with modern, genome-scale sequence data sets. As a consequence, today's phylogenomic studies routinely report near-complete confidence in their inferences, even when different studies reach strongly conflicting conclusions and the sites and loci in a single data set contain much more heterogeneity than our methods assume or can accommodate. Therefore, we argue that BPs and marginal PPs of bipartitions have outlived their utility as the primary means of measuring phylogenetic support for modern phylogenomic data sets with large numbers of sites relative to the number of taxa. Continuing to rely on these measures will hinder progress towards understanding remaining sources of uncertainty in the most challenging portions of the Tree of Life. Instead, we encourage researchers to examine the ideas and methods presented in this special issue of Systematic Biology and to explore the area further in their own work. The papers in this special issue outline strategies for assessing confidence and uncertainty in phylogenomic data sets that move beyond stochastic error due to limited data and offer promise for more productive dialogue about the challenges that we face in reaching our shared goal of understanding the history of life on Earth.[Big data; gene tree variation; genomic era; statistical bias.].

Properties of Markov Chain Monte Carlo Performance across Many Empirical Alignments.

Nearly all current Bayesian phylogenetic applications rely on Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution for trees and other parameters of the model. These approximations are only reliable if Markov chains adequately converge and sample from the joint posterior distribution. Although several studies of phylogenetic MCMC convergence exist, these have focused on simulated data sets or select empirical examples. Therefore, much that is considered common knowledge about MCMC in empirical systems derives from a relatively small family of analyses under ideal conditions. To address this, we present an overview of commonly applied phylogenetic MCMC diagnostics and an assessment of patterns of these diagnostics across more than 18,000 empirical analyses. Many analyses appeared to perform well and failures in convergence were most likely to be detected using the average standard deviation of split frequencies, a diagnostic that compares topologies among independent chains. Different diagnostics yielded different information about failed convergence, demonstrating that multiple diagnostics must be employed to reliably detect problems. The number of taxa and average branch lengths in analyses have clear impacts on MCMC performance, with more taxa and shorter branches leading to more difficult convergence. We show that the usage of models that include both Γ-distributed among-site rate variation and a proportion of invariable sites is not broadly problematic for MCMC convergence but is also unnecessary. Changes to heating and the usage of model-averaged substitution models can both offer improved convergence in some cases, but neither are a panacea.

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis.

Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events versus post formational mutation to patterns of genetic diversity in nature. Here we use restriction site associated DNA genotyping to evaluate genetic diversity and demographic history in Aspidoscelis laredoensis, a diploid unisexual lizard species from the vicinity of the Rio Grande River in southern Texas and northern Mexico. The sexual progenitor species from which one or more lineages are derived also occur in the Rio Grande Valley region, although patterns of distribution across individual sites are quite variable. Results from population genetic and phylogenetic analyses resolved the major axes of genetic variation in this species and highlight how these match predictions based on historical patterns of hybridization. We also found discordance between results of demographic modelling using different statistical approaches with the genomic data. We discuss these insights within the context of the ecological and evolutionary mechanisms that generate and maintain lineage diversity in unisexual species. As one of the most dynamic, intriguing, and geographically well investigated groups of whiptail lizards, these species hold substantial promise for future studies on the constraints of diversification in unisexual vertebrates.

Population differences in the length and early-life dynamics of telomeres among European pied flycatchers.

Telomere length and shortening rate are increasingly being used as biomarkers for long-term costs in ecological and evolutionary studies because of their relationships with survival and fitness. Both early-life conditions and growth, and later-life stressors can create variation in telomere shortening rate. Studies on between-population telomere length and dynamics are scarce, despite the expectation that populations exposed to varying environmental constraints would present divergent telomere length patterns. The pied flycatcher (Ficedula hypoleuca) is a passerine bird breeding across Eurasia (from Spain to western Siberia) and migrating through the Iberian Peninsula to spend the nonbreeding period in sub-Saharan Africa. Thus, different populations show marked differences in migration distance. We studied the large-scale variation of telomere length and early-life dynamics in the pied flycatcher by comparing six European populations across a north-south gradient (Finland, Estonia, England and Spain) predicting a negative effect of migration distance on adult telomere length, and of nestling growth on nestling telomere dynamics. There were clear population differences in telomere length, with English birds from midlatitudes having the longest telomeres. Telomere length did not thus show consistent latitudinal variation and was not linearly linked to differences in migration distance. Early-life telomere shortening rate tended to vary between populations. Fast growth was associated with shorter telomeres in the early life, but faster nestling growth affected telomeres more negatively in northern than southern populations. While the sources of between-population differences in telomere-related biology remain to be more intensively studied, our study illustrates the need to expand telomere studies at the between-population level.

Investigating focus elongation using a spatial light modulator for high-throughput ultrafast-laser-induced selective etching in fused silica.

Ultrafast-laser-induced selective chemical etching is an enabling microfabrication technology compatible with optical materials such as fused silica. The technique offers unparalleled three-dimensional manufacturing freedom and feature resolution but can be limited by long laser inscription times and widely varying etching selectivity depending on the laser irradiation parameters used. In this paper, we aim to overcome these limitations by employing beam shaping via a spatial light modulator to generate a vortex laser focus with controllable depth-of-focus (DOF), from diffraction limited to several hundreds of microns. We present the results of a thorough parameter-space investigation of laser irradiation parameters, documenting the observed influence on etching selectivity and focus elongation in the polarization-insensitive writing regime, and show that etching selectivity greater than 800 is maintained irrespective of the DOF. To demonstrate high-throughput laser writing with an elongated DOF, geometric shapes are fabricated with a 12-fold reduction in writing time compared to writing with a phase-unmodulated Gaussian focus.

Miniaturised gap sensor using fibre optic Fabry-Pérot interferometry for structural health monitoring.

A miniaturised structural health monitoring device has been developed capable of measuring the absolute distance between close parallel surfaces using Fabry-Pérot interferometry with nm-scale sensitivity. This is achieved by fabricating turning mirrors on two opposite cores of a multi-core fibre to produce a probe with dimensions limited only be the fibre diameter. Two fabrication processes have been investigated: Focused ion beam milling, which has resulted in a sensor measurement accuracy, sensitivity and range of ±0.056 µm, ±0.006 µm and ∼16000  µm respectively; and ultrafast laser assisted etching of the cleaved fibre end, where a sensor measurement accuracy, sensitivity and range of ±0.065 µm, ±0.006 µm and ∼7500 µm have been demonstrated.

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].

Ecological engineering across a spatial gradient: Sociable weaver colonies facilitate animal associations with increasing environmental harshness.

The spatial distribution of animals in a landscape depends mainly on the distribution of resources. Resource availability is often facilitated by other species and can positively influence local species diversity and affect community structure. Species that significantly change resource availability are often termed ecosystem engineers. Identifying these species is important, but predicting where they have large or small impacts is a key challenge that will enhance the usefulness of the ecosystem engineering concept. In harsh and stressful environments, the stress gradient hypothesis predicts that community structure and function will be increasingly influenced by facilitative interactions. To test this hypothesis, we investigate how the ecosystem engineering role and importance of sociable weavers Philetairus socius varies across a spatial gradient of harshness, for which aridity served as a proxy. These birds build large colonies that are home to hundreds of weavers and host a wide range of avian and non-avian heterospecifics. We investigated the use of weaver colonies on multiple taxa (invertebrates, reptiles, birds and mammals) at multiple sites across a >1,000 km aridity gradient. We show that sociable weaver colonies create localized biodiversity hotspots across their range. Furthermore, trees containing sociable weaver colonies maintained localized animal diversity at sites with lower rainfall, an effect not as pronounced at sites with higher rainfall. Our results were consistent with predictions of the stress gradient hypothesis, and we provide one of the first tests of this hypothesis in terrestrial animal communities. Facilitation and amelioration by ecosystem engineers may mitigate some of the extreme impacts of environmental harshness.