Within-host genomic evolution of methicillin-resistant Staphylococcus aureus in long-term carriers.

Assessing the genomic evolution of Staphylococcus aureus can help us understand how the bacteria adapt to its environment. In this study, we aimed to assess the mutation rate within 144 methicillin-resistant Staphylococcus aureus (MRSA) carriers with a carriage time from 4 to 11 years, including some carriers who belonged to the same households. We found that 23 of the 144 individuals had completely different MRSA types over time and were therefore not long-term carriers of the same MRSA. From the remaining 121 individuals, we performed whole-genome sequencing (WGS) on 424 isolates and then compared these pairwise using core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses. We found a median within-host mutation rate in long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year and 2.7 (1.8-4.2) allelic differences/genome/year, when excluding presumed recombination. Furthermore, we stratified the cohort into subgroups and found no significant difference between the median mutation rate of members of households, individuals with presumed continued exposure, e.g., from travel and persons without known continued exposure. Finally, we found that SNPs occurred at random within the genes in our cohort. KEY POINTS: • Median mutation rate within long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year • Similar median mutation rates in subgroups (households, travelers) • No hotspots for SNPs within the genome.

Long-term carriage and evolution of VREfmLong-term carriage and evolution of vancomycin-resistant Enterococcus faecium: a genomic study on consecutive isolates.

Objectives: To determine if vancomycin-resistant Enterococcus faecium (VREfm) carriers carry the same VREfm clone after a minimum follow-up of 365 days. For those carrying the same clone, we investigated the genomic evolution per year per genome. Methods: We used WGS results to assign VREfm clones to each isolate and determine clone shifts. Finally, we calculated distance in core-genome MLST alleles, and the number of SNPs between consecutive VREfm isolates from patients carrying the same VREfm clone. Results: In total, 44.2% of patients carried the same VREfm clone, and the genomic evolution was 1.8 alleles and 2.6 SNPs per genome per year. Conclusions: In our population of long-term carriers, we calculated a molecular clock of 2.6 SNPs.

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator.

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.

Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.

Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role.

BACKGROUND: Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array of novel traits suited to its Arctic lifestyle. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage. Here, we survey a comprehensive dataset of 109 polar bear and 33 brown bear genomes to investigate the genomic variants within these top genes present in each species. Specifically, we investigate whether fixed homozygous variants in polar bears derived from selection on standing variation in the ancestral gene pool or on de novo mutation in the polar bear lineage. RESULTS: We find that a large number of sites fixed in polar bears are biallelic in brown bears, suggesting selection on standing variation. Moreover, we uncover sites in which polar bears are fixed for a derived allele while brown bears are fixed for the ancestral allele, which we suggest may be a signal of de novo mutation in the polar bear lineage. CONCLUSIONS: Our findings suggest that, among other mechanisms, natural selection acting on changes in genes derived from a combination of variation already in the ancestral gene pool, and from de novo missense mutations in the polar bear lineage, may have enabled the rapid adaptation of polar bears to their new Arctic environment.

Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros.

The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine mammals to past climatic shifts, but narwhals (Monodon monoceros) are considered one of the endemic Arctic species most vulnerable to environmental change. Here, we analyse 121 complete mitochondrial genomes from narwhals sampled across their range and use them in combination with species distribution models to elucidate the influence of past and ongoing climatic shifts on their population structure and demographic history. We find low levels of genetic diversity and limited geographic structuring of genetic clades. We show that narwhals experienced a long-term low effective population size, which increased after the Last Glacial Maximum, when the amount of suitable habitat expanded. Similar post-glacial habitat release has been a key driver of population size expansion of other polar marine predators. Our analyses indicate that habitat availability has been critical to the success of narwhals, raising concerns for their fate in an increasingly warming Arctic.

Palaeogenomic insights into the origins of French grapevine diversity.

The Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent-offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 CE was a genetic match to 'Savagnin Blanc', providing evidence for 900 years of uninterrupted vegetative propagation.

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.

Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk.

The beluga whale is one of three endemic Arctic whales. The species is philopatric, and its migration patterns are passed from mother to calf. Management of the species is informed by the levels of genetic structuring among summer aggregation sites based on mitochondrial D-Loop data. To assess the levels of differentiation across the entire mitochondrial genome within belugas, we present a comparison between the first two complete mitochondrial genomes from opposite sides of their distribution range: Baffin Bay and the Russian Far East. Our analyses reveal that additional phylogenetic insights can be gained from expanding the genetic region analyzed. Further, we estimate the divergence time between the two mitochondrial genomes to be 0.469 MYA.

Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing.

BACKGROUND: Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent of the occurrence of these organellar-derived inserted sequences (odins) is still unknown, but if not accounted for in genomic and phylogenetic studies, they can be a source of error. However, if correctly identified, these inserted sequences can be used for evolutionary and comparative genomic studies. Although such insertions can be detected using various laboratory and bioinformatic strategies, there is currently no straightforward way to apply them as a standard organellar genome assembly on next-generation sequencing data. Furthermore, most current methods for identification of such insertions are unsuitable for use on non-model organisms or ancient DNA datasets. RESULTS: We present a bioinformatic method that uses phasing algorithms to reconstruct both source and inserted organelle sequences. The method was tested in different shotgun and organellar-enriched DNA high-throughput sequencing (HTS) datasets from ancient and modern samples. Specifically, we used datasets from lions (Panthera leo ssp. and Panthera leo leo) to characterize insertions from mitochondrial origin, and from common grapevine (Vitis vinifera) and bugle (Ajuga reptans) to characterize insertions derived from plastid genomes. Comparison of the results against other available organelle genome assembly methods demonstrated that our new method provides an improvement in the sequence assembly. CONCLUSION: Using datasets from a wide range of species and different levels of complexity we showed that our novel bioinformatic method based on phasing algorithms can be used to achieve the next two goals: i) reference-guided assembly of chloroplast/mitochondrial genomes from HTS data and ii) identification and simultaneous assembly of odins. This method represents the first application of haplotype phasing for automatic detection of odins and reference-based organellar genome assembly.