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In a recent article, Martin et. al. [1] criticize several methodological aspects of our recent study on the timing of the acquisition of mitochondria [2]. Here we show that our results are independent of the model-based partitioning of the data. In addition, we assess the robustness of our inferences by analyzing data from Martin et. al.
The dichotomy between smooth and striated myocytes is fundamental for bilaterian musculature, but its evolutionary origin remains unsolved. Given their absence in Drosophila and Caenorhabditis, smooth muscles have so far been considered a vertebrate innovation. Here, we characterize expression profile, ultrastructure, contractility and innervation of the musculature in the marine annelid Platynereis dumerilii and identify smooth muscles around the midgut, hindgut and heart that resemble their vertebrate counterparts in molecular fingerprint, contraction speed, and nervous control. Our data suggest that both visceral smooth and somatic striated myocytes were present in the protostome-deuterostome ancestor, and that smooth myocytes later co-opted the striated contractile module repeatedly - for example in vertebrate heart evolution. During these smooth-to-striated myocyte conversions the core regulatory complex of transcription factors conveying myocyte identity remained unchanged, reflecting a general principle in cell type evolution.
The Flavivirus genus encompasses several arboviruses of public health significance such as dengue, yellow fever, and Zika viruses. It also includes insect-specific flaviviruses (ISFs) that are only capable of infecting insect hosts. The vast majority of mosquito-infecting flaviviruses have been associated with mosquito species of the Aedes and Culex genera in the Culicinae subfamily, which also includes most arbovirus vectors. Mosquitoes of the Anophelinae subfamily are not considered significant arbovirus vectors, however flaviviruses have occasionally been detected in field-caught Anopheles specimens. Whether such observations reflect occasional spillover or laboratory contamination or whether Anopheles mosquitoes are natural hosts of flaviviruses is unknown. Here, we provide in silico and in vivo evidence of transcriptionally active, flavivirus-derived endogenous viral elements (EVEs) in the genome of Anopheles minimus and Anopheles sinensis. Such non-retroviral endogenization of RNA viruses is consistent with a shared evolutionary history between flaviviruses and Anopheles mosquitoes. Phylogenetic analyses of the two newly described EVEs support the existence of a distinct clade of Anopheles-associated ISFs.
There is accumulating evidence that some genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that can at some point acquire new functions. Here we show for the first time that such peptides do not only exist but that they are prevalent among the translation products of mouse genes that lack homologues in rat and human. The data suggests that the translation of these peptides is due to the chance occurrence of open reading frames with a favorable codon composition. Our approach combines ribosome profiling experiments, proteomics data and non-synonymous and synonymous nucleotide polymorphism analysis. We propose that effectively neutral processes involving the expression of thousands of transcripts all the way down to proteins provide a basis for de novo gene evolution.
Population genomic datasets collected over the past decade have spurred interest in developing methods that can utilize massive numbers of loci for inference of demographic and selective histories of populations. The allele frequency spectrum (AFS) provides a convenient statistic for such analysis and accordingly much attention has been paid to predicting theoretical expectations of the AFS under a number of different models. However, to date, exact solutions for the joint AFS of two or more populations under models of migration and divergence have not been found. Here we present a novel Markov chain representation of the coalescent on the state space of the joint AFS that allows for rapid, exact calculation of the joint AFS under isolation with migration (IM) models. In turn, we show how our Markov chain method, in the context of composite likelihood estimation, can be used for accurate inference of parameters of the IM model using SNP data. Lastly, we apply our method to recent whole genome datasets from African Drosophila melanogaster.
Host-parasite co-evolution belongs among the major processes governing evolution of biodiversity on the global scale. Numerous studies performed at inter-specific level revealed variety of patterns from strict co-speciation to lack of co-divergence and frequent host-switching, even in species tightly linked to their hosts. To explain these observations and formulate ecological hypotheses, we need to acquire better understanding to parasites population genetics and dynamics, and their main determinants. Here, we analyse the impact of co-evolutionary processes on genetic diversity and structure of parasite populations, using a model composed of the louse Polyplax serrata and its hosts, mice of the genus Apodemus, collected from several dozens of localities across Europe. We use mitochondrial DNA sequences and microsatellite data to describe the level of genealogical congruence between hosts and parasites and to assess genetic diversity of the populations. We also explore links between the genetic assignment of the parasite and its host affiliation, and test the prediction that populations of the parasite possessing narrower host specificity show deeper pattern of population structure and lower level of genetic diversity as a result of limited dispersal and smaller effective population size. We demonstrate an overall complexity of the co-evolutionary processes and their variability even among closely related lineages of the parasites. In the analysis of several sympatric parasite populations, we find strong evidence for the link between the width of host specificity and genetic diversity of parasites.
The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.\n\nAuthor summaryFrom specific examples, it has been assumed by comparative biologists that the same gene in different species has the same function, whereas duplication of a gene inside one species to create several copies allows them to acquire different functions. Yet this model was little tested until recently, and then has proven harder than expected to confirm. One of the problems is defining \"function\" in a way which can be easily studied. We introduce a new way of considering function: how specific is the activity (\"expression\") of a gene? Genes which are specific to certain tissues have functions related to these tissues, whereas genes which are broadly active over many or all tissues have more general functions for the organism. We find that this \"tissue-specificity\" evolves very slowly in the absence of duplication, while immediately after duplication the new gene copy differs. This shows that indeed duplication leads to a strong increase in the evolution of new functions.
Few now dispute that a few percent of the DNA of non-African humans is a legacy of interbreeding with Neanderthals. However, heterozygosity and mutation rate appear to be linked such that the loss of diversity associated with humans migrating out of Africa caused a mutational slowdown, allowing Africans to diverge more from both our common ancestor and Neanderthals. Here I use a range of contrasting tests aimed at distinguishing between mutation slowdown and introgression as explanations for the higher rates of base-sharing between non-Africans and Neanderthals. In every instance the mutation slowdown hypothesis fits better. Thus, while some interbreeding likely occurred, as evidenced by the finding of skeletons of admixed individuals, adaptive genes and the apparently large contribution of Denisovan DNA to Oceanian genomes, my results challenge the idea that non-Africans generally carry an appreciable Neanderthal legacy. My analysis shows that inferences about introgression may be unreliable unless variation in mutation rate linked to demographically induced changes in heterozygosity can be excluded as an alternative hypothesis.
Salamanders (Urodela) have among the largest vertebrate genomes, ranging in size from 10 to 120 pg. Although changes in genome size often occur randomly and in the absence of selection pressure, non-random patterns of genome size variation are evident among specific vertebrate lineages. Several reports suggest a relationship between species richness and genome size, but the exact nature of that relationship remains unclear both within and across different taxonomic groups. Here we report i) a negative relationship between haploid genome size (C-value) and species richness at the family taxonomic level in salamander clades; ii) a correlation of C-value and species richness with clade crown-age but not with diversification rates; iii) strong associations between C-value and either geographical area or climatic niche rate. Finally, we report a relationship between C-value diversity and species diversity at both the family and genus level clades in urodeles.
Once restricted to northern China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution due to the evolution of commensalism with humans. In contrast to black rats and the house mouse, which have tracked the regional and global development of human agricultural settlements, brown rats do not appear in the European historical record until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade and modern sea-faring. We inferred the global phylogeography of brown rats using 32k SNPs to reconstruct invasion routes from estimates of population divergence and admixture. Globally, we detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Rapid westward expansion resulted in the colonization of Europe from which subsequent colonization of Africa, the Americas, and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering found both between and within our sampling sites underscored the extent to which urban heterogeneity can shape the genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants despite continual global transport, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and yields greater capacity to develop targeted rat eradication programs.
Honest communication between potential partners with conflicting interests is generally thought to require costly signals. Costly signalling can explain partner choice when it is possible to link a strategic cost to an individuals quality, like in mate choice. However, in mutualisms, it is usually impossible to link a cost to the likelihood that a potential partner will behave cooperatively in the future. In fact, signals like Nod factors in rhizobial bacteria, which form symbioses with leguminous plants, are evidence of cost-free, honest signals in situations of potential conflict. How can such a signalling system evolve? We use a population-genetics model to show that a cost-free, honest signal can evolve when the receiver is under soft selection, which is when high juvenile mortality does not lead to a corresponding reduction in fitness, a common occurrence in many species. Under soft selection, senders evolve increasingly complex messages of identity, a system akin to a password or a lock and key. Thus, a symbiont can signal that it shares a coevolutionary history with a potential host, and if that history is mutualistic, then the host can believe that the symbiont is mutualistic. Password signalling might also explain the acquisition of some defensive symbionts and the evolution of complex species-recognition signals in mate choice. O_QD\"...Say now Shibboleth: and he said Sibboleth: for he could not frame to pronounce it right. Then they took him, and slew him....\" -- Judges 12:6, King James Version\n\nC_QD
One of the most intriguing questions in evolutionary virology is why multipartite viruses exist. Several hypotheses suggest benefits that outweigh the obvious costs associated with encapsidating each genomic segment into a different viral particle: reduced transmission efficiency and segregation of coadapted genes. These putative advantages range from increasing genome size despite high mutation rates (i.e., escaping from Eigens paradox), faster replication, more efficient selection resulting from segment reassortment during mixed infections, or enhanced virion stability and cell-to-cell movement. However, empirical support for these hypotheses is scarce. A more recent hypothesis is that segmentation represents a simple and robust mechanism to regulate gene copy number and, thereby, gene expression. According to this hypothesis, the ratio at which different segments exist during infection of individual hosts should represent a stable situation and would respond to the varying necessities of viral components during infection. Here we report the results of experiments designed to test whether an evolutionary stable equilibrium exists for the three RNAs that constitute the genome of Alfalfa mosaic virus (AMV). Starting infections with many different combinations of the three segments, we found that, as infection progresses, the abundance of each genome segment always evolves towards a constant ratio. Population genetic analyses show that the segments ratio at this equilibrium is determined by frequency-dependent selection; indeed, it represents an evolutionary stable solution. The replication of RNAs 1 and 2 was coupled and collaborative, whereas the replication of RNA 3 interfered with the replication of the other two. We found that the equilibrium solution is slightly different for the total amounts of RNA produced and encapsidated, suggesting that competition exists between all RNAs during encapsidation. Finally, we found that the observed equilibrium appears to be host-species dependent.\n\nAuthor SummaryThis research focuses on the evolution of genome segmentation, the division of an organisms hereditary material into multiple chromosomes. Why has the genome evolved these partitions? When is it advantageous to divide the genome over multiple segments? In the case of RNA viruses segmentation may provide a robust and yet tunable mechanism to regulate the expression of different genes. To explore this possibility, we used a tri-segmented plant RNA virus and found that, as expected under this hypothesis, during infection the system evolves towards an optimal solution. The solution varies among host plant species, suggesting that genome segmentation allows for the rapid adaptation to different host plant species. Genome partition can therefore be seen as a stable yet readily adaptable manner to regulate expression of virus genes, by means of gene copy-number variation. We proposed a novel, general evolutionary framework to analyze and interpret quantitative data on segments relative abundances.
Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly considered chance events and reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridizations, climate, land-use, and field-validated species distribution models for two deeply divergent and naturally sympatric toad species in Europe (Bufo bufo and Bufotes viridis species groups). We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future.
Studies using multi-locus coalescent methods to infer species trees or historical demographic parameters usually require the assumption that the gene tree for each locus (or SNP) is genealogically independent from the gene trees of other sampled loci. In practice, however, researchers have used two different criteria to delimit independent loci in phylogenomic studies. The first criterion, which directly addresses the condition of genealogical independence of sampled loci, considers the long-term effects of homologous recombination and effective population size on linkage between two loci. In contrast, the second criterion, which only considers the single-generation effects of recombination in the meioses of individuals, identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment. Methods that use these criteria to estimate the number of independent loci per genome as well as intra-chromosomal \"distance thresholds\" that can be used to delimit independent loci in phylogenomic datasets are reviewed. To compare the efficacy of each criterion, they are applied to two species (an invertebrate and vertebrate) for which relevant genetic and genomic data are available. Although the independent assortment criterion is relatively easy to apply, the results of this study show that it is overly conservative and therefore its use would unfairly restrict the sizes of phylogenomic datasets. It is therefore recommended that researchers only refer to genealogically independent loci when discussing the independent loci assumption in phylogenomics and avoid using terms that may conflate this assumption with independent assortment. Moreover, whenever feasible, researchers should use methods for delimiting putatively independent loci that take into account both homologous recombination and effective population size (i.e., long-term effective recombination).
Negative selection against deleterious alleles produced by mutation is the most common form of natural selection, which strongly influences within-population variation and interspecific divergence. However, some fundamental properties of negative selection remain obscure. In particular, it is still not known whether deleterious alleles affect fitness independently, so that cumulative fitness loss depends exponentially on the number of deleterious alleles, or synergistically, so that each additional deleterious allele results in a larger decrease in relative fitness. Negative selection with synergistic epistasis must produce negative linkage disequilibrium between deleterious alleles, and therefore, underdispersed distribution of the number of deleterious alleles in the genome. Indeed, we detected underdispersion of the number of rare loss-of-function (LoF) alleles in eight independent datasets from modern human and Drosophila melanogaster populations. Thus, ongoing selection against deleterious alleles is characterized by synergistic epistasis, which can explain how human and fly populations persist despite very high genomic deleterious mutation rates.
Viruses are under relentless selective pressure from host immune defenses. To study how poxviruses adapt to innate immune detection pathways, we performed serial infections of vaccinia virus in primary human cells. Independent courses of experimental evolution with a recombinant strain lacking E3L revealed several high frequency point mutations in conserved poxvirus genes, suggesting important roles for essential poxvirus proteins in innate immune subversion. Two distinct mutations were identified in the viral RNA polymerase gene A24R, which seem to act through different mechanisms to increase virus replication. Specifically, a Leu18Phe substitution in A24R conferred fitness tradeoffs, including increased activation of the antiviral factor Protein kinase R (PKR). Intriguingly, this A24R variant underwent a drastic selective sweep during passaging, despite enhanced PKR activity. We show that the sweep of this variant can be accelerated by the presence of copy number variation (CNV) at the K3L locus, which with multiple copies strongly reduces PKR activation. Therefore, adaptive cases of CNV can also facilitate the accumulation of point mutations separate from the expanded locus. This study reveals how rapid bouts of gene copy number amplification during accrual of distant point mutations can potently facilitate poxvirus adaptation to host defenses.\n\nImportanceViruses can quickly evolve to defeat host immune functions. For poxviruses, little is known about how multiple adaptive mutations might concurrently emerge in populations. In this study, we uncovered a means of vaccinia virus adaptation involving the accumulation of distinct genetic variants within a single population. We identified adaptive point mutations in the viral RNA polymerase gene A24R, and show that these mutations can affect the activation of host nucleic acid sensing pathways through different mechanisms. We also found that structural variants within viral genomes in the form of gene copy number variation (CNV) provide dual benefits to evolving populations, including evidence that CNV facilitates the accumulation of a point mutation distant from the expanded locus. Our data suggest that transient CNV can accommodate the accumulation of mutations conferring modest benefits, or even fitness tradeoffs, and highlight how structural variation might aid poxvirus adaptation through both direct and indirect action.
As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) instead of absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions in the intercross indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in chicken and confirm recent studies that show that different genetic architectures underlie these traits.
Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.