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  1. Free, publicly-accessible full text available December 10, 2024
  2. Abstract

    Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari,C. esox,Chaenocephalus aceratus, andPseudochaenichthys georgianus) and the cold-specializedTrematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding geneND6, two transfer RNAs,and the control region with different copy number variants present within the same individuals and with someND6duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model inC. esoxandC. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy inC. aceratusandC. esox. We also observed a large inversion in the mitogenome ofT. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.

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    Free, publicly-accessible full text available December 1, 2024
  3. Abstract Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes. 
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    Free, publicly-accessible full text available December 1, 2024
  4. Abstract

    Conditional instability and the buoyancy of plumes drive moist convection but have a variety of representations in model convective schemes. Vertical thermodynamic structure information from Atmospheric Radiation Measurement (ARM) sites and reanalysis (ERA5), satellite-derived precipitation (TRMM3b42), and diagnostics relevant for plume buoyancy are used to assess climate models. Previous work has shown that CMIP6 models represent moist convective processes more accurately than their CMIP5 counterparts. However, certain biases in convective onset remain pervasive among generations of CMIP modeling efforts. We diagnose these biases in a cohort of nine CMIP6 models with subdaily output, assessing conditional instability in profiles of equivalent potential temperature,θe, and saturation equivalent potential temperature,θes, in comparison to a plume model with different mixing assumptions. Most models capture qualitative aspects of theθesvertical structure, including a substantial decrease with height in the lower free troposphere associated with the entrainment of subsaturated air. We define a “pseudo-entrainment” diagnostic that combines subsaturation and aθesmeasure of conditional instability similar to what entrainment would produce under the small-buoyancy approximation. This captures the trade-off between largerθeslapse rates (entrainment of dry air) and small subsaturation (permits positive buoyancy despite high entrainment). This pseudo-entrainment diagnostic is also a reasonable indicator of the critical value of integrated buoyancy for precipitation onset. Models with poorθe/θesstructure (those using variants of the Tiedtke scheme) or low entrainment runs of CAM5, and models with low subsaturation, such as NASA-GISS, lie outside the observational range in this diagnostic.

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  5. Kelley, Joanna (Ed.)

    White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.

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  6. Lewandowski, H. (Ed.)
    Covariance mapping is widely used to study correlations of different variables in the dataset. The power of the method has been demonstrated in multi-particle imaging, including two- and three-body covariance on molecules of biological relevance and Coulomb explosion imaging (CEI) of molecular dissociation dynamics. While covariance for two particles is rather straightforward, for four-body correlations, one needs to extend covariance mapping to cumulant mapping, which has been tested in recent measurements of strong field ionization of formaldehyde. Here, I will discuss the details of how to compute cumulant mapping for the momentum sum of all four fragments of the formaldehyde molecule, and how one can perform the calculation with a faster and better algorithm. 
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