Genomics of post-bottleneck recovery in the northern elephant seal.

Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence. Recovery was rapid and now there are over 200,000 individuals. We sequenced 260 modern and 8 historical northern elephant seal nuclear genomes to assess the impact of the population bottleneck on individual northern elephant seals and to better understand their recovery. Here we show that inbreeding, an increase in the frequency of alleles compromised by lost function, and allele frequency distortion, reduced the fitness of breeding males and females, as well as the performance of adult females on foraging migrations. We provide a detailed investigation of the impact of a severe bottleneck on fitness at the genomic level and report on the role of specific gene systems. [Abstract copyright: © 2024. The Author(s).

ASHG/ACMG Report Points to Consider: Ethical, Legal and Psychosocial Implications of Genetic Testing in Children and Adolescents

In 1995, the American Society of Human Genetics (ASHG) and American College of Medical Genetics and Genomics (ACMG) jointly published a statement on genetic testing in children and adolescents. In the past 20 years, much has changed in the field of genetics, including the development of powerful new technologies, new data from genetic research on children and adolescents, and substantial clinical experience. This statement represents current opinion by the ASHG on the ethical, legal, and social issues concerning genetic testing in children. These recommendations are relevant to families, clinicians, and investigators. After a brief review of the 1995 statement and major changes in genetic technologies in recent years, this statement offers points to consider on a broad range of test technologies and their applications in clinical medicine and research. Recommendations are also made for record and communication issues in this domain and for professional education

Translational Selection Is Ubiquitous in Prokaryotes

Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nucleotide substitution patterns represented as sequence composition of intergenic DNA. A cornerstone of our method is a Random Forest classifier that outperformed previous distance measure-based approaches, such as the codon adaptation index, in the task of discerning the (highly expressed) ribosomal protein genes by their codon frequencies. Unlike previous reports, we show evidence that translational selection in prokaryotes is practically universal: in 460 of 461 examined microbial genomes, we find that a subset of genes shows a higher codon usage similarity to the ribosomal proteins than would be expected from the local sequence composition. These genes constitute a substantial part of the genome—between 5% and 33%, depending on genome size—while also exhibiting higher experimentally measured mRNA abundances and tending toward codons that match tRNA anticodons by canonical base pairing. Certain gene functional categories are generally enriched with, or depleted of codon-optimized genes, the trends of enrichment/depletion being conserved between Archaea and Bacteria. Prominent exceptions from these trends might indicate genes with alternative physiological roles; we speculate on specific examples related to detoxication of oxygen radicals and ammonia and to possible misannotations of asparaginyl–tRNA synthetases. Since the presence of codon optimizations on genes is a valid proxy for expression levels in fully sequenced genomes, we provide an example of an “adaptome” by highlighting gene functions with expression levels elevated specifically in thermophilic Bacteria and Archaea

Sea Otter Mitogenomes Alignment

43 California sea otter mitogenomes, mapped and aligned in Geneious 9.0.

Annotations for Sea Otter MitoGenomes

Annotation table for 43 California Sea Otter mitogenome

Conservation Genomics Reveals Low Connectivity Among Populations of Threatened Roseate Terns in the Atlantic Basin [PREPRINT].

While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern ( ) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. Within the Atlantic Basin, past work has shown differentiation among roseate terns breeding on different continents, but these results were generated with a limited number of microsatellite markers. Relationships between breeding populations in the Northwestern Atlantic and the Caribbean have never been analyzed. We evaluated population structuring of roseate tern populations in North America and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not among other populations. Within the Caribbean metapopulation, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results suggest that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations

Importance of eIF2α Phosphorylation and Stress Granule Assembly in Alphavirus Translation Regulation

Alphavirus infection results in the shutoff of host protein synthesis in favor of viral translation. Here, we show that during Semliki Forest virus (SFV) infection, the translation inhibition is largely due to the activation of the cellular stress response via phosphorylation of eukaryotic translation initiation factor 2α subunit (eIF2α). Infection of mouse embryo fibroblasts (MEFs) expressing a nonphosphorylatable mutant of eIF2α does not result in efficient shutoff, despite efficient viral protein production. Furthermore, we show that the SFV translation enhancer element counteracts the translation inhibition imposed by eIF2α phosphorylation. In wild-type MEFs, viral infection induces the transient formation of stress granules (SGs) containing the cellular TIA-1/R proteins. These SGs are disassembled in the vicinity of viral RNA replication, synchronously with the switch from cellular to viral gene expression. We propose that phosphorylation of eIF2α and the consequent SG assembly is important for shutoff to occur and that the localized SG disassembly and the presence of the enhancer aid the SFV mRNAs to elude general translational arrest