Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity

There is a prevailing view that the inclusion of fossil data could remedy identifiability issues related to models of diversification, by drastically reducing the number of congruent models. The fossilized birth-death (FBD) model is an appealing way of directly incorporating fossil information when estimating diversification rates. Here we explore the benefits of including fossils by implementing and then testing two-types of FBD models in more complex likelihood-based models that assume multiple rate classes across the tree. We also assess the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants (i.e., k-type fossils), as well as converting a fossil set to represent stratigraphic ranges. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. We also found that severely undercounting the number of k-type fossils produces highly inflated rates of turnover and extinction fraction. Similarly, we found that converting the fossil set to stratigraphic ranges results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.

A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Hotspots are products of multiple evolutionary forces including mutation rate heterogeneity, but this variable is often hard to identify. In this work, we reveal that a near-deterministic genetic hotspot can be built and broken by a handful of silent mutations. We observe this when studying homologous immotile variants of the bacteria Pseudomonas fluorescens, AR2 and Pf0-2x. AR2 resurrects motility through highly repeatable de novo mutation of the same nucleotide in >95% lines in minimal media (ntrB A289C). Pf0-2x, however, evolves via a number of mutations meaning the two strains diverge significantly during adaptation. We determine that this evolutionary disparity is owed to just 6 synonymous variations within the ntrB locus, which we demonstrate by swapping the sites and observing that we are able to both break (>95% to 0%) and build (0% to 80%) a deterministic mutational hotspot. Our work reveals a key role for silent genetic variation in determining adaptive outcomes.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

With over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here we use a dataset of 68 single-copy nuclear protein coding genes sampling 129 out of the 194 recognized extant families as well as the first comprehensive set of fully-justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov., and Staphyliniformia sensu nov., alongside changes below the superfamily level. The heterogeneous former superfamily Cucujoidea is divided into three monophyletic groups: Erotyloidea stat. nov., Nitiduloidea stat. nov., and Cucujoidea sensu nov. Our divergence time analysis recovered an evolutionary timescale congruent with the fossil record: a late Carboniferous origin of Coleoptera, a late Paleozoic origin of all modern beetle suborders, and a Triassic–Jurassic origin of most extant families. While fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution, many polyphagan superfamilies exhibited increases in richness with Cretaceous flowering plants.

Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10−3 to 4.72 × 10−3 in env and 2.3-fold from 0.95 × 10−3 to 2.18 × 10−3 substitutions site−1 year−1 in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits

Substitution rate variation among branches can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Body mass is often assumed to have a major influence on substitution rate, though other factors such as population size, life history traits, and flight demands are also thought to have an influence. Birds of the order Procellariiformes-which encompasses petrels, storm-petrels and albatrosses-show a striking 900-fold difference in body mass between the smallest and largest members, divergent life history traits, and substantial heterogeneity in mitochondrial substitution rates. Here, we used genome-scale nuclear DNA sequence data from 4365 ultraconserved element loci (UCEs) in 51 procellariiform species to examine whether phylogenetic reconstruction using genome-wide datasets is robust to the presence of rate heterogeneity, and to identify predictors of substitution rate variation. Our results provide a backbone phylogeny for procellariiform seabirds and resolve several controversies about the evolutionary history of the order, demonstrating that albatrosses are basal, storm-petrels are paraphyletic and diving petrels nestled within the Procellariidae. We find evidence of rate variation; however, all phylogenetic analyses using both concatenation and multispecies coalescent approaches recovered the same branching topology, including analyses implementing different clock models, and analyses of the most and least clock-like loci. Overall, we find that rate heterogeneity is little impacted by body mass, population size, age at first breeding, and longevity but moderately correlated with hand-wing index, a proxy for wing shape and flight efficiency. Given our results and the context of the broader literature perhaps it is time that we begin to question the prevailing paradigm that one or a few traits largely explain rate variation and accept instead that substitution rate may be the product of weak interactions among many, potentially taxon-specific, variables.

Heterogeneous substrate binding in a glutamate transporter homologue

Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this family, including kinetic models of transport. Recent studies have revealed transport rate heterogeneity in an archaeal glutamate transporter homologue GltPh, inconsistent with simple kinetic models. The structural and mechanistic determinants of this heterogeneity remain undefined. In a mutant form of GltPh, we demonstrate substrate binding heterogeneity in the outward-facing state, modulated by temperature and salts. We observe similar trends in wild-type GltPh that correlate with changes in the transport rate. Extensive cryo-EM analysis of the fully bound mutant GltPh provides multiple potential explanations of heterogeneous substrate binding. At equilibrium, we show subtle differences in tilts of protomers in the outward-facing state and configurations of the substrate-binding pocket. Within seconds of substrate binding, we observe perturbed helical packing of the extracellular half of the substrate-binding domain. Some or all of these may contribute to the heterogeneity observed in binding and transport.

Punctual ecological changes rather than global factors drive species diversification and the evolution of wing phenotypes in Morpho butterflies

Assessing the relative importance of geographical and ecological drivers of evolution is paramount to understand the diversification of species and traits at the macroevolutionary scale. Here, we use an integrative approach, combining phylogenetics, biogeography, ecology, and quantified phenotypes to investigate the drivers of both species and phenotypic diversification of the iconic Neotropical butterfly genus Morpho. We generated a time-calibrated phylogeny for all known species and inferred historical biogeography. We fitted models of time-dependent (accounting for rate heterogeneity across the phylogeny) and paleoenvironment-dependent diversification (accounting for global effect on the phylogeny). We used geometric morphometrics to assess variation of wing size and shape across the tree, and investigated their dynamics of evolution. We found that the diversification of Morpho is best explained when considering multiple independent diversification dynamics across the tree, possibly associated with lineages occupying different microhabitat conditions. First, a shift from understory to canopy was characterized by an increased speciation rate partially coupled with an increasing rate of wing shape evolution. Second, the occupation of dense bamboo thickets accompanying a major host-plant shift from dicotyledons towards monocotyledons was associated with a simultaneous diversification rate shift and an evolutionary “jump” of wing size. Our study points to a diversification pattern driven by punctual ecological changes instead of a global driver or biogeographic history.

Soil Respiration May Overestimate or Underestimate in Forest Ecosystems

The inappropriate selection of measurement points and measurement times in an ecosystem may easily lead to the underestimation or overestimation of soil respiration due to spatial and temporal heterogeneity. To assess the law of spatial and temporal heterogeneity and more accurately determine the soil respiration rate, we measured the soil respiration rate of a forest in the plant growing season from 2011 to 2013 on Changbai Mountain in 8 directions and 7 distances from each tree trunk. Neglecting the direction of the measuring point may overestimate or underestimate the soil respiration rate by 29.81% and 26.09%, respectively; neglecting the distance may overestimate or underestimate the soil respiration rate by 41.36% and 20.28%, respectively; and ignoring the measurement time may overestimate and underestimate the soil respiration rate by 41.71% and 57.64%, respectively. In addition, choosing a measurement point in the eastern direction at a 1.8 m distance and conducting the measurement in September may relatively accurately reflect the soil respiration rate of the ecosystem. These findings can deepen our understanding of soil respiration rate heterogeneity and may provide new ideas for improving the measurement method of soil respiration.

A Spatially Explicit Model of Stabilizing Selection for Improving Phylogenetic Inference

Ultraconserved elements (UCEs) are stretches of hundreds of nucleotides with highly conserved cores flanked by variable regions. Although the selective forces responsible for the preservation of UCEs are unknown, they are nonetheless believed to contain phylogenetically meaningful information from deep to shallow divergence events. Phylogenetic applications of UCEs assume the same degree of rate heterogeneity applies across the entire locus, including variable flanking regions. We present a Wright–Fisher model of selection on nucleotides (SelON) which includes the effects of mutation, drift, and spatially varying, stabilizing selection for an optimal nucleotide sequence. The SelON model assumes the strength of stabilizing selection follows a position-dependent Gaussian function whose exact shape can vary between UCEs. We evaluate SelON by comparing its performance to a simpler and spatially invariant GTR+Γ model using an empirical data set of 400 vertebrate UCEs used to determine the phylogenetic position of turtles. We observe much improvement in model fit of SelON over the GTR+Γ model, and support for turtles as sister to lepidosaurs. Overall, the UCE-specific parameters SelON estimates provide a compact way of quantifying the strength and variation in selection within and across UCEs. SelON can also be extended to include more realistic mapping functions between sequence and stabilizing selection as well as allow for greater levels of rate heterogeneity. By more explicitly modeling the nature of selection on UCEs, SelON and similar approaches can be used to better understand the biological mechanisms responsible for their preservation across highly divergent taxa and long evolutionary time scales.