The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). The macronuclear genome sequences of P. biaurelia and P. sexaurelia are ...presented and compared to the published sequence of P. tetraurelia. Levels of duplicate-gene retention from the recent WGD differ by > 10% across species, with P. sexaurelia losing significantly more genes than P. biaurelia or P. tetraurelia. In addition, historically high rates of gene conversion have homogenized WGD paralogs, probably extending the paralogs' lifetimes. The probability of duplicate retention is positively correlated with GC content and expression level; ribosomal proteins, transcription factors, and intracellular signaling proteins are overrepresented among maintained duplicates. Finally, multiple sources of evidence indicate that P. sexaurelia diverged from the two other lineages immediately following, or perhaps concurrent with, the recent WGD, with approximately half of gene losses between P. tetraurelia and P. sexaurelia representing divergent gene resolutions (i.e., silencing of alternative paralogs), as expected for random duplicate loss between these species. Additionally, though P. biaurelia and P. tetraurelia diverged from each other much later, there are still more than 100 cases of divergent resolution between these two species. Taken together, these results indicate that divergent resolution of duplicate genes between lineages acts to reinforce reproductive isolation between species in the Paramecium aurelia complex.
Understanding the controls on the amount and persistence of soil organic carbon (C) is essential for predicting its sensitivity to global change. The response may depend on whether C is unprotected, ...isolated within aggregates, or protected from decomposition by mineral associations. Here, we present a global synthesis of the relative influence of environmental factors on soil organic C partitioning among pools, abundance in each pool (mg C g−1 soil), and persistence (as approximated by radiocarbon abundance) in relatively unprotected particulate and protected mineral‐bound pools. We show that C within particulate and mineral‐associated pools consistently differed from one another in degree of persistence and relationship to environmental factors. Soil depth was the best predictor of C abundance and persistence, though it accounted for more variance in persistence. Persistence of all C pools decreased with increasing mean annual temperature (MAT) throughout the soil profile, whereas persistence increased with increasing wetness index (MAP/PET) in subsurface soils (30–176 cm). The relationship of C abundance (mg C g−1 soil) to climate varied among pools and with depth. Mineral‐associated C in surface soils (<30 cm) increased more strongly with increasing wetness index than the free particulate C, but both pools showed attenuated responses to the wetness index at depth. Overall, these relationships suggest a strong influence of climate on soil C properties, and a potential loss of soil C from protected pools in areas with decreasing wetness. Relative persistence and abundance of C pools varied significantly among land cover types and soil parent material lithologies. This variability in each pool's relationship to environmental factors suggests that not all soil organic C is equally vulnerable to global change. Therefore, projections of future soil organic C based on patterns and responses of bulk soil organic C may be misleading.
In the first global meta‐analysis to examine both radiocarbon and C concentrations among different soil C pools, we found that three critical carbon pools (free particulate, occluded particulate, and mineral associated) respond differently to climate. Moisture had an almost equal influence as temperature on C persistence and abundance, highlighting the need for climate change studies focused on moisture manipulations. The strong variation in pool characteristics and their relationship to environmental factors indicates that we need to go beyond bulk soil carbon measurements to understand and model the responses of soil organic carbon to global change; it is critical to evaluate distinct pools as response variables.
Duplicate genes act as a source of genetic material from which new functions arise. They exist in large numbers in every sequenced eukaryotic genome and may be responsible for many differences in ...phenotypes between species. However, recent work searching for the targets of positive selection in humans has largely ignored duplicated genes due to complications in orthology assignment. Here we find that a high proportion of young gene duplicates in the human, macaque, mouse, and rat genomes have experienced adaptive natural selection. Approximately 10% of all lineage-specific duplicates show evidence for positive selection on their protein sequences, larger than any reported amount of selection among single-copy genes in these lineages using similar methods. We also find that newly duplicated genes that have been transposed to new chromosomal locations are significantly more likely to have undergone positive selection than the ancestral copy. Human-specific duplicates evolving under adaptive natural selection include a surprising number of genes involved in neuronal and cognitive functions. Our results imply that genome scans for selection that ignore duplicated loci are missing a large fraction of all adaptive substitutions. The results are also in agreement with the classical model of evolution by gene duplication, supporting a common role for neofunctionalization in the long-term maintenance of gene duplicates.
Abstract
Pulsar timing arrays (PTAs) are Galactic-scale gravitational wave (GW) detectors consisting of precisely timed pulsars distributed across the sky. Within the decade, PTAs are expected to ...detect nanohertz GWs emitted by close-separation supermassive black hole binaries (SMBHBs), thereby opening up the low-frequency end of the GW spectrum for science. Individual SMBHBs which power active galactic nuclei are also promising multi-messenger sources; they may be identified via theoretically predicted electromagnetic (EM) signatures and be followed up by PTAs for GW observations. In this work, we study the detection and parameter estimation prospects of a PTA which targets EM-selected SMBHBs. Adopting a simulated Galactic millisecond pulsar population, we envisage three different pulsar timing campaigns which observe three mock sources at different sky locations. We find that an all-sky PTA which times the best pulsars is an optimal and feasible approach to observe EM-selected SMBHBs and measure their source parameters to high precision (i.e., comparable to or better than conventional EM measurements). We discuss the implications of our findings in the context of future PTA experiments with the planned Deep Synoptic Array-2000 and the multi-messenger studies of SMBHBs such as the well-known binary candidate OJ 287.
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