Genome Biology and Evolution

BackgroundNotothenioids are a well characterised species flock endemic to the Antarctic and an important model group for the study of genome adaptation to extreme cold. We used a new reference assembly and clade-wide comparative genomic analysis to investigate cryonotothenioid evolution and the appearance of novel functionalities linked to cold adaptation. ResultsA new phased assembly of a model notothenioid, Harpagifer antarcticus, demonstrated low levels of haplotypic variability across the genome. Nevertheless, numerous insertions from multiple LINE-L2 clades were found, suggesting ongoing transposition with potential contribution to speciation. Contrary to expectations the afgp locus was highly similar between haplotypes, except for large length allelic variants of afgp genes. Analysis suggests a model for the afgp locus expansion in H. antarcticus through segmental tandem duplications involving two pairs of afgp genes at time. Syntenic reconstruction of genomes from across the clade demonstrates conserved macrosyntenic relationships and group specific chromosomal fusions of notothenioids. Quantification of genome gain and transposition rates during cryonotothenioid diversification showed a first ancestral slow genome expansion concurrent with historic temperature drops. This was followed by lineage-specific massive peaks of genomic gain and transposition activity. Finally, we identified a set of genes that underwent ancestral diversifying selection and acquired novel conserved non-coding elements during the cryonotothenioid emergence. These were related to antioxidants and proteostasis, which may have facilitated the notothenioid Antarctic radiation. ConclusionDiversifying selection and genomic gain linked to transposon activity are primary contributors to lineage-specific evolutionary dynamics through the clade which facilitated adaptation to life in the cold.

BackgroundTransposable elements (TEs) are repetitive genetic elements that can jump to new loci causing genome expansions, structural rearrangements, and can, ultimately, propel the evolution of genomes. Despite their significance, the role of TEs in the evolution of genomes and phylogenetic groups remains largely understudied in early diverging lineages. Further, the extent to which TE content varies across species is still an open question. Medusozoa, a group within Cnidaria encompassing jellyfish and hydroids, exhibits an exceptional diversity of life history strategies, body plans, and physiological capabilities. These characteristics, along with its early-diverging phylogenetic position, establish Medusozoa as an ideal system for investigating the composition and evolutionary history of TEs within the group. ResultsWe generated a custom repeat library built from annotations of 25 Medusozoan genomes and used it to characterize TEs, aiming to identify lineage-specific TE content and activity that may correlate with the diversity observed within the group. We found that repetitive element percentage and genome size varied considerably, with Hydrozoa exhibiting the most variation among classes in both respects. DNA transposons were the most prevalent TE classification in all but two genomes, averaging 28% of all genomes. Intra-genus comparisons revealed a surprising degree of differences in TE content. In the genus Aurelia, the expansion of a single DNA transposon superfamily accounted for much of the difference in repetitive element percentage between two species, whereas in the genus Turritopsis, a similar divergence resulted from the proliferation of multiple superfamilies. Interestingly, most genomes showed evidence of recent TE expansions, suggesting ongoing activity in many medusozoan species. ConclusionWe present the first comparative analysis of TEs across all medusozoan classes. Our results reveal class-specific TE dynamics and highlight cases of TE proliferations as lineages diverge. This research provides data on TE activity and diversity that can be used as a resource for future study and fills important gaps in our understanding of TEs in early diverging animal lineages.

BackgroundAlthough strict maternal transmission of mitochondria is a general feature of animals and humans for ensuring homogeneity in mitochondrial DNA (mtDNA) across generations, exceptions were reported in the recent past. For example, some extremely rare but spectacular cases of heteroplasmy and paternal transmission in humans have questioned the universal evolutionary principle. Hence, as an alternative, the Mega-NUMT concept was coined to explain this discovery and was thereafter partly proven to exist. This concept expands on the quite common transfer of mtDNA fragments to the nucleus (NUMTs) by considering the existence of multicopy mitochondrial nuclear insertions. Mega-NUMT reports are currently restricted to a few cases in animals, including humans. However, even in humans, their detailed genomic organization, natural prevalence, and potential biological functions remain unclear. Methodology/Principal FindingsHere, we discovered that up to 60 full-sized mitochondrial genomes are integrated into the nuclear genome of the neotropical fruit fly Drosophila paulistorum using long-read sequencing and confirmed their presence by in situ hybridization. The copies are organized in one cluster on chromosome 3, which we, due to its similarity with the Mega-NUMT concept, designated the "Dpau Mega-NUMT". Contrary to the rarity in humans, this Mega-NUMT is found at high prevalence (40%) in both long-term laboratory lines and natural D. paulistorum populations of different semispecies. Additionally, the mitochondrial copies in the Mega-NUMT cluster are phylogenetically separated from the current mitotypes of D. paulistorum. Together, these observations suggest long-term maintenance of the Mega-NUMT in nature. Hence, we propose that the Dpau Mega-NUMT may have been transferred to the nuclear genome before D. paulistorum semispecies radiation and maintained at relatively high prevalence in nature by balancing selection due to yet undetermined functions. Conclusions/SignificanceTo our knowledge, this is the first verified existence and detailed dissection of a Mega-NUMT outside cats and humans. We show that Mega-NUMTs can be persistent in nature, even at high prevalence, potentially due to balancing selection. Our findings strengthen the importance of high-quality long-read sequencing technologies for deciphering complex repeat-rich genomic regions to deepen our understanding of the dynamics of genome evolution within genomic "dark matter".

Transcription initiation is regulated by proteins called transcription factors (TFs). Though TFs help determine phenotype across the tree of life, they are nonessential for minimal cellular life and are often absent in endosymbiotic and parasitic organisms. Given this and the idea that it is a certain level of organism complexity that calls for specific transcription regulation, we traced the evolutionary history of TF repertoire on a bacterio-archaeal tree of life using a dataset of [~]500,000 TFs, grouped into [~]1,700 orthologous groups (OGs) across [~]3,000 species. The most ancestral prokaryotes encoded multiple TFs. Going by known extant functions of these TFs, they possibly regulated sugar-fermentation metabolism, sensed overall metabolic state and redox, responded to DNA damage or bound metals; many of which are consistent with some reconstructions of ancestral gene pools and physiologies. The number of TFs as well as their superfamily-level diversity, through evolutionary history, matches expectations against genome size derived from extant bacteria, suggesting pre-LUCA diversification of TF sequence families. Emergence of new TFs along the phylogeny largely followed a smooth cumulative distribution curve, suggesting steady innovation, early in prokaryote evolution, in contrast to eukaryotes, in which a majority of TF families emerged in a burst manner at the ancestors of multicellular lineages. Gains of TFs late in prokaryotic evolution predominantly featured recycling of protein families discovered elsewhere in the prokaryotic tree, consistent with the dominance of horizontal gene transfer in these organisms. We speculate on the difference between the evolutionary trajectory of prokaryotic TF repertoire and compare it with the eukaryotic TF repertoire trajectory. This helps us in understanding the manner in which their TF repertoires have evolved in two different super-kingdoms. The difference between the evolutionary dynamics of TF-repertoires might be due to how complexity is envisioned in these two different kingdoms.

The process of evolutionary change remains poorly understood. By analyzing genomic data from 12 populations in Lenskis long-term evolution experiment (LTEE) over 60,000 generations, we identified a clear sequence in gene adaptation: growth-related genes evolved early, while survival-related genes evolved later. Early-evolving genes exhibited higher rates of both nonsynonymous and synonymous substitutions. We also observed a general decline in gene evolutionary rates across LTEE populations, with additional data highlighting the role of fitness gains in determining evolutionary rates. These findings suggest that, in a relatively stable environment, the fitness gains from beneficial mutations decrease as adaptation progresses. This diminishing return on fitness gains may represent a key evolutionary rule, potentially contributing to evolutionary stasis and the prevalence of neutral evolution.

Successful establishment of long-term, obligate endosymbiotic relationships requires integration of hosts and endosymbionts across multiple levels. For example, highly integrated, host-beneficial endosymbionts typically have extremely reduced genomes and metabolisms. However, we do not yet fully understand the specific mechanisms that drive this integration or if there is a specific order in which these changes must occur. To investigate the early stages of endosymbiont genome reduction, we greatly expanded available whole genome data for the nitrogen-fixing endosymbionts (spheroid bodies, SBs) of diatoms in the family Rhopalodiaceae. We used these data to reconstruct SB evolutionary history and to characterize SB core metabolic capacity. We found two key genes missing from all SB genomes, mltA and dnaA, which could provide points of host control over SB cell division. Although most of the SB core genome is experiencing moderately strong purifying selection, we identified 54 genes under positive selection. Eighteen of these are peripheral proteins or involved in cell wall and cell membrane metabolism and could be involved in direct interactions with the host. Unexpectedly, we also found three nif genes under positive selection that are core to the central nitrogen-fixing enzyme. Overall, our results provide early insights into how SBs and their hosts interact, showing that SBs are still in the early stages of endosymbiont genome reduction, but they differ in key ways from current models, including the early loss of all mobile elements.

Population genetic theory predicts that natural selection will be more efficient in large than small populations because genetic drift reduces the efficiency of selection in small populations. Small populations adapting to new environments can also be expected to evolve higher recombination rates to facilitate adaptation as well as to dissociate and purge harmful mutations. We tested these hypotheses (1) by investigating differences in the strength of association between nucleotide diversity ({pi}) and recombination rate across the genomes of nine-spined sticklebacks (Pungitius pungitius) from four small freshwater (mean Ne {approx} 2 578) and four large marine (mean Ne = 86 742) populations, as well as (2) by comparing recombination rates between small and large populations using population specific linkage maps. We found the predicted positive correlation of{pi} with recombination rate from all but the smallest freshwater populations, suggesting prevalent linked selection even after accounting for variation in GC/CpG content, and gene density. Mean recombination rates did not differ between freshwater and marine populations, except that the smallest Ne freshwater population exhibited significantly elevated recombination rate. GWAS analyses suggested a polygenic basis for recombination rates. These results suggest an important role for linked selection in reducing{pi} in low recombination regions especially in large populations. Moreover, as predicted by theory, at least one of the small freshwater populations appears to have evolved a higher recombination rate than its marine ancestors.

Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TE) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that [~]66% of the genome are repeats, in contrast to previous estimates of 43-50%. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This much refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, and also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.

Genomic rearrangements are fundamental drivers of biodiversity, yet dynamics of structural evolution following polyploidization remain poorly understood. Genus Xenopus provides a valuable tool to study these phenomena. Utilizing the diploid X. tropicalis as a reference, we employed cytogenetic and genomic mapping to track the structural evolution of the allotetraploids X. borealis and X. laevis across a 50-million-year timeline. Based on chromosome morphometrics and C-banding patterns, we characterized the X. borealis pseudotetraploid karyotype (2n = 4x = 36), localizing the nucleolus organizer region (NOR) to chromosome 5L, U1 and U2 small nuclear DNAs to 1S and 8L, and 5S rDNA to nearly all chromosomes. Our analysis revealed 17 genomic rearrangements distributed within three temporal strata: ancestral (50-35 Mya), intermediate (35-15 Mya), and recent (< 15 Mya). Although we categorized chromosome 9/10 fusion as an ancestral rearrangement, the 2/9 translocation previously identified in X. mellotropicalis was absent in both studied allotetraploids. Furthermore, we tested for sex-specific structural polymorphism on the X. borealis W chromosome. Despite a large region of recombination suppression between the W and Z, no inversions were detected, indicating persistent sex chromosome homomorphism. Results are consistent with the expectation that tandem repeats such as NORs follow an asymmetric trajectory driven by a jumping mechanism and biased deletion, whereas small nuclear DNA loci are governed by copy number reduction-expansion dynamics. These findings indicate that structural rearrangements in Xenopus were not limited to punctuated bursts immediately following whole-genome duplication; rather, they accumulated over a prolonged evolutionary history, affecting the entire polyploid complement.

Transposable elements are a highly diverse group of selfish genomic elements, prevalent across the tree of life, whose uncontrolled propagation poses a threat to genome stability. Recent studies have explored the evolution of Drosophila melanogaster transposable elements, their co-evolution with the host genome, and mechanisms that regulate their activity. However, little is known about their cross-species evolutionary patterns. Long terminal repeat (LTR) retrotransposons are the most active group of transposable elements in Drosophila. They are broadly separated into retroelements, which are active in the germline, and insect endogenous retroviruses that are active in the soma. Somatic elements are hypothesised to infect the germline through their acquisition of virus-derived proteins such as Envelope and sORF2, thus multiplying through successive generations. In this study, we curated the sequences of LTR retrotransposons in 249 drosophilid genomes, allowing us to study their evolution across these species and highlight their varying degrees of conservation. Furthermore, we reveal multiple instances of Envelope protein loss or inactivation that suggest shifts in the expression pattern of these transposons, likely accompanied by adopting different transcriptional control mechanisms. We contrast this with the evolutionary history of sORF2, which we found to be much more stable. Lastly, we examined variations in transposon LTR regions responsible for transcriptional regulation and use predictive modelling to suggest six transcription factors likely involved in their tissue-specific expression. Altogether, we reveal complex, interspecies evolutionary patterns of Gypsy-family LTR retrotransposons and highlight examples of their co-evolution with their host genome.

Accurate estimation of population demographic history is central to population genetics yet remains challenging due to the sensitivity of inference methods to the number of individuals and the demographic scenario assumed in inference. The site-frequency spectrum (SFS) of neutral variants, a widely used summary statistic of genetic variation, is particularly sensitive to demographic processes, but studies have shown that qualitative results from demographic inference, i.e., population expansion vs. contraction, can depend strongly on the number of individuals in the dataset. Here, we analyzed two simulated datasets and one empirical dataset characterized by an ancient population bottleneck followed by a recent population expansion. Fitting a two-epoch demographic model across a range of sample sizes, we found that inference shifted from signals of ancient population contraction at small sample sizes to signals of recent population expansion at large sample sizes. Other summary statistics, including Tajimas D and the proportion of singletons, also changed with sample size. We found that these changes of inferred evolutionary signals under a two-epoch model can be explained by the epoch which contributes the highest mean proportion of coalescent branch lengths. Our results highlight that demographic inference depends critically on the number of individuals analyzed and suggest that analyzing datasets at multiple sample sizes can reveal complementary aspects of population history.

Organisms cope with environmental changes by modifying gene expression. To understand how regulatory networks controlling expression plasticity evolve, we analyzed RNAseq data from Saccharomyces cerevisiae, Saccharomyces paradoxus, and their F1 hybrids at multiple timepoints after transferring cells from standard laboratory conditions to five environments (low phosphorus, low nitrogen, hydroxyurea shock, heat stress, and cold stress) and during the diauxic shift. In each of the six datasets, we identified genes that changed expression following the transition to the new environment and used hierarchical clustering to identify genes that increased or decreased in expression. We then compared these classifications between orthologs to identify genes with divergent plasticity. For some genes, plasticity was more extreme in one species than the other, and for others, expression of orthologs changed in opposite directions when acclimating to the same environment. Most cases of plasticity divergence were seen only in one environment and were attributable primarily to trans-regulatory divergence. Using environment-specific regulatory networks inferred from data in Yeastract, we found that divergent plasticity of environment-specific transcription factors generally did not predict divergent plasticity of their target genes. We also found that, as a group, genes with conserved plasticity tended to have more regulatory interactions than genes with divergent plasticity. Interesting patterns of expression divergence were also observed for five transcription factors in the pleiotropic drug resistance network and their target genes that might contribute to phenotypic divergence. Together, these findings show how environment-specific trans-regulatory divergence and combinatorial gene regulation shape the evolution of expression plasticity.

Population size is a key factor underlying the mode and tempo of evolution, particularly as it relates to the strength of selection and drift. While the mechanisms underlying the interactions between population size and selection have been studied in population genetics for over a century, empirical knowledge of these dynamics has been limited to species with small-to-moderate historical population sizes. This gap in knowledge highlights the need for empirical studies in systems with historically large population sizes and elevated diversity. The Pacific acorn barnacle (Balanus glandula) presents an exceptional model to study evolution in extremely large populations, exhibiting census sizes often exceeding the tens of thousands of individuals per meter squared. We present one of the first large-scale genomic analyses in this system, generating a new chromosome-level genome assembly for this species. This assembly reveals a highly polymorphic genome with over 3% heterozygosity. At a population level, B. glandula exhibits extreme levels of polymorphism, with nucleotide diversity surpassing 5% genome-wide in just a small collection of individuals. Across the genome, nucleotide diversity predictably decreases at functional elements, including both coding and non-coding sequences, likely reflecting strong purifying selection along the genome. At the same time, McDonald-Kreitman tests reveal that the majority of non-synonymous substitutions between barnacle species were driven by positive selection, consistent with the expected increase in the efficacy of selection in large populations. These remarkable levels of diversity set B. glandula as a unique model for the study of evolution at extreme demographic scales and highlights the importance of testing evolutionary theory across a wide variety of empirical systems.

The origin of eukaryotes is a key event in the evolution of cellular life hypothesized to involve a symbiotic integration between a member of the Asgard archaea and the Alphaproteobacteria. Recent work has provided evidence for additional genetic input from other prokaryotes to the eukaryotic proteome yet the extent and sources of these contributions remain debated. Here we aimed to further resolve the prokaryotic origins of eukaryotic genes to inform our understanding of eukaryogenesis. Specifically, we developed a phylogenetic framework to investigate the origins of eukaryotic gene families associated with metabolism and informational processing for comparison. We found that informational processing genes were predominantly derived by archaea whereas eukaryotic metabolism is highly chimeric in its origin. In contrast to previous studies, we report a substantial number of archaeal origins of diverse metabolic enzymes including key metabolic regulators. This highlights an overlooked participation of archaeal metabolism and pinpoints potential metabolic integrations during eukaryogenesis. Apart from the alphaproteobacterial contributions to the eukaryotic metabolism, we found an additional dominant phylogenetic signal of genes potentially derived from Myxococcota, especially for gene families associated with lipid metabolism. By systematically analysing the origins of eukaryotic metabolism, this research offers novel insights into the origin of eukaryotic membranes and refine our current models for the origin of the eukaryotic cell.

BackgroundAlpha satellites, a superfamily of AT-rich tandem repeats, are the primary DNA component of centromeres in Platyrrhini and Catarrhini. Analyses of the human genome suggest that centromeres behave like biological ridges, with new alpha satellite families expanding at the centromere core, splitting and displacing older ones towards the pericentromeres. The Cercopithecini tribe, which displays an unusual chromosomal evolution involving multiple chromosomal fissions and centromere formations, represents a promising model to enhance our understanding of alpha satellite DNA evolutionary history. We previously applied targeted sequencing to centromere DNA from two distant species drawn from the Cercopithecini terrestrial and arboreal lineages, and characterized six alpha satellite families exhibiting varying mean sequence identities. MethodsCombining classical and molecular cytogenetics, we mapped the chromosomal distribution of these alpha satellite families across 13 Cercopithecini, one Papionini, and one Colobinae species. A nuclear marker-based phylogeny provided an evolutionary framework for interpretation. ResultsOur phylogeny identifies the terrestrial and arboreal lineages, and a newly designated swamp clade. We observed significant interspecies variations in alpha satellite patterns, including differences in presence/absence and distinct chromosomal distribution patterns (centromeric, pericentromeric, or subtelomeric). Families previously described as heterogeneous (83-87% mean sequence identity) exhibit a centromeric position in the swamp lineage, which is characterized by conserved karyotypes. In contrast, these families show a pericentromeric distribution in the terrestrial and arboreal lineages, replaced at the centromere core by more homogeneous families (95-98% mean sequence identity). In the arboreal clade, which is characterized by highly fissioned karyotypes, putative evolutionary new centromeres show a unique co-occurrence of highly homogeneous and heterogeneous families. Conclusion & ImplicationsWe propose a comprehensive evolutionary scenario for alpha satellite DNA in Cercopithecini, where younger families arise at the centromere core, shift toward the pericentromeres as they age, and eventually face extinction. Our study suggests that alpha satellite DNA and chromosomes evolve in an interdependent manner, with satellite diversification and displacement occurring in parallel with chromosome fissions and centromere repositioning. This comparative cytogenomic approach provides both support for the human-based evolutionary model for alpha satellite DNA and novel temporal insights into its diversification dynamics. Beyond evolutionary genomics, our findings highlight the potential of alpha satellite DNA to complement systematic studies in deciphering complex primate evolutionary histories.

Small marsupials in the family Dasyuridae are a key component of Australias arid and semi-arid fauna, whose high species richness is proposed to reflect an opportunity-driven adaptive radiation. Despite growing interest in this group from both ecological and evolutionary perspectives, genomic data for most species is non-existent, or limited to a few marker loci. Here, we generated a chromosome-level reference genome and a de novo mitochondrial genome for the desert-dwelling Wongai ningaui (Ningaui ridei). The nuclear genome assembly is highly contiguous, with a scaffold N50 of 594.484 MB and high BUSCO gene recovery (93.84%). Additionally, we produced a draft assembly for the related, semi-arid slender-tailed dunnart (Sminthopsis murina). We then used these assemblies to explore the demographic histories of these species. We find evidence for contrasting patterns of population growth during the late Pleistocene and early Holocene, corresponding with differences in local climate, potentially consistent with differences in optimal habitat. The new genomic resources and demographic findings presented here provide a foundation for future studies on adaptive specialisation in this group of Australian marsupials. Significance StatementDasyurid marsupials are the primary carnivorous and insectivorous mammals in Australia. This diverse family includes species such as the endangered Tasmanian devil (Sarcophilus harrisii) and quolls (Genus Dasyurus), as well as an emerging laboratory model species, the fat-tailed dunnart (Sminthopsis crassicaudata). Despite the species richness within dasyurids, most species remain under-studied. This is particularly true of arid and semi-arid zone species, who are often small in size, live in remote habitats and are cryptic by nature. By creating genome assemblies for two dasyurid species, this study provides resources to support a variety of phylogenetic, population genetic and evolutionary developmental lines of research. Importantly, the studys finding that arid and semi-arid dasyurids show distinct trajectories of demographic change in response to historical climatic shifts may point to local adaptations with implications for the resilience of these species to ongoing and future climate change.

Tigriopus copepods are found in splash pools on all seven continents from the equator to Arctic and Antarctic regions. Given their geographic distribution, frequent exposure to extreme environmental conditions in the high intertidal zone, and strong signatures of local adaptation, these copepods have become models for exploring patterns of adaptation to stressful environments. However, most studies focus on a relatively small subset of Tigriopus species, and there are few genome resources representing the diversity of Tigriopus species and populations. Here, we combine long-read, Pacific Biosciences HiFi data with short-read, Illumina HiC and RNA-seq data to assemble and annotate a genome sequence representing a Tigriopus population from the coast of central Chile. Based on the level of divergence that we observed in mitochondrial genes, we also performed a comparison of morphological characteristics between individuals of this population and members of the T. angulatus complex. The haplotypes that we assembled (qhTigAngs1.1.hap1 & qhTigAngs1.1.hap2) are placed into 12 major scaffolds (N50 18-19 Mbp, L50 6-7), equivalent to the number of chromosomes in other Tigriopus species. BUSCO and k-mer analyses of each haplotype and BUSCO analyses of gene models are relatively complete (95-99%) with respect to gene and k-mer content. Analyses of mitochondrial data also suggest that the Chilean population of Tigriopus we sampled may represent a novel species that we call Tigriopus aff. angulatus. These genomic resources will help us understand the diversity and structure of Tigriopus species and populations as well as facilitate future comparisons of adaptation across parallel environmental gradients.

Gene amplification is a potent driver of evolution and is thought to contribute to genetic diseases, including cancer. The yeast Saccharomyces cerevisiae is a powerful organism for understanding amplification mechanisms. When yeast is grown long term in sulfate-limiting chemostats, amplification of the gene that encodes the primary sulfate transporter, SUL1, is a common outcome. Here we describe a form of SUL1 amplification in which multiple copies of the right terminal region of chromosome II are appended in tandem to a native telomere. We find this form of amplicon when we delete the origin of replication next to SUL1 or delete a variety of genes involved in DNA metabolism. It is the only form of amplification found in a yku70{Delta} mutant suggesting that unprotected telomeres are involved. We propose that these terminal addition events occur when the unprotected 3 G1-3T telomeric sequence invades a short ([~]7 bp) internal telomere sequence (ITS) to begin a form of microhomology-mediated break-induced replication (mmBIR) that has been documented in type-I survivors of telomerase mutants. In addition to amplification of the right end of chromosome II we also find that telomeres containing the sub-telomeric repeat Y experience similar tandem amplification events and show that their formation is reduced in a pol32{Delta} mutant, a gene required for mmBIR. Within individual amplicons the ITSs and Ys are nearly identical, suggesting that the multiple copies of the amplified region are generated in a single mmBIR event that we describe as pseudo-rolling circle mmBIR. A similar amplification event at the P-telomere of human chromosome 18 has four copies of a [~]54 kb region separated by ITSs of nearly identical size. This finding suggests that these additional copies of the terminal fragment of human chromosome 18 arose by the same pseudo-rolling circle mechanism, perhaps during a period of telomeric stress. AUTHOR SUMMARYThe human genome is peppered with duplicates (or higher numbers) of segments that are located at sites both nearby and distant from the original, ancestral segments. These Copy Number Variants, or CNVs, appear to be highly variable among different individuals and are being examined with great interest as potential loci associated with genetic disease. Experimentally determining how these CNVs arise and become distributed across the genome is nearly impossible using humans. We are using budding yeast as the model organism to explore mechanisms of gene amplification. In this work we show that by destabilizing the ends of yeast chromosomes (telomeres) or by interfering with genes involved in the replication, repair, or recombination of DNA results in a specific form of segmental copy number increase that is initiated at telomeres. We propose that a telomere invades an internal chromosome site and sets up a pseudo-circular template for conservative DNA replication. The outcome is a chromosome with multiple, identical copies of a chromosome end arranged in tandem. We believe that it is also a major mechanism used by cells to repair telomeres that have become eroded during aging.

Antimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.

Global populations are ageing at an unprecedented rate. For many diseases, age is a strong indicator of susceptibility, morbidity, or mortality. Principles of evolutionary biology can be leveraged to understand how pathogens may optimally exploit new populations, and the impact of this on the global burden of infectious-disease-induced mortality. We parameterised an age-specific R0 model with 2017 epidemiological data on Measles, Tuberculosis, Meningitis, and Ebola, and age-specific demographic estimates for 2017 and 2050, for the seven Global Burden of Disease super-regions. We explored the theoretical trade-offs between pathogen virulence & transmission, and virulence & host recovery, parameterising trade-off parameters using Latin Hypercube Sampling. Population ageing between 2017-2050 saw an increase in virulence induced mortality in four settings: 1) Ebola in sub-Saharan Africa, 2) Measles in central/eastern Europe & central Asia region, 3) Measles in North Africa & the Middle East and 4) Tuberculosis in the central/eastern Europe & central Asia region. The decrease in infection duration due to an increase of elderly people drives pathogen virulence down for diseases in the remaining settings. Understanding the mechanisms that shape pathogen dynamics and leveraging this to predict future challenges is key to endemic disease management in a rapidly changing world. Author SummaryKey aspects of disease transmission including susceptibility to infection, the severity of infection, and the probability of dying from that infection, are affected by host age. Global populations are rapidly ageing, so that the mean age of most populations is generally higher than it used to be and is set to continue on this trajectory. This suggests that the dynamics of infectious diseases are also likely to change, although infectious disease dynamics tend to be non-linear as these key parameters interact. We have developed a dynamic modelling framework to explore how changes in population age structure might impact the optimal level of pathogen virulence in a population. We have chosen four infectious diseases as case studies, that differentially impact certain age classes to illustrate these dynamics. We have parameterised this framework with open access data for each of the seven Global Burden of Disease super-regions and show that population ageing can increase virulence for several diseases in differing global regions, whilst increased background rates of mortality can drive virulence down in others.