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At least 307 records · Page 17Linked to original sources

bioRxiv2017

Double Maternal Effect: Duplicated Nucleoplasmin 2 Genes, npm2a And npm2b, Are Shared By Fish And Tetrapods, And Have Distinct And Essential Roles In Early Embryogenesis

Nucleoplasmin 2 (npm2) is an essential maternal-effect gene that mediates early embryonic events through its function as a histone chaperone that remodels chromatin. Here we report the existence of two npm2 (npm2a and npm2b) genes in zebrafish. We examined the evolution of npm2a and npm2b in a variety of vertebrates, their potential phylogenetic relationships, and their biological functions using knockout models via the CRISPR/cas9 system. We demonstrated that the two npm2 duplicates exist in a wide range of vertebrates, including sharks, ray-finned fish, amphibians, and sauropsids, while npm2a was lost in Coelacanth and mammals, as well as some specific teleost lineages. Using phylogeny and synteny analyses, we traced their origins to the early stages of vertebrate evolution. Our findings suggested that npm2a and npm2b resulted from an ancient local gene duplication, and their functions diverged although key protein domains were conserved. We then investigated their functions by examining their tissue distribution in a wide variety of species and found that they shared ovarian-specific expression, a key feature of maternal-effect genes. We also showed that both npm2a and npm2b are maternally-inherited transcripts in vertebrates. Moreover, we used zebrafish knockouts to demonstrate that npm2a and npm2b play essential, but distinct, roles in early embryogenesis. npm2a functions very early during embryogenesis, at or immediately after fertilization, while npm2b is involved in processes leading up to or during zygotic genome activation. These novel findings will broaden our knowledge on the evolutionary diversity of maternal-effect genes and underlying mechanisms that contribute to vertebrate reproductive success.\n\nAuthor SummaryThe protein and transcript of the npm2 gene have been previously demonstrated as maternal contributions to embryos of several vertebrates. Recently, two npm2 genes, denoted here as npm2a and npm2b, were discovered in zebrafish. This study was conducted to explore the evolutionary origin and changes that occurred that culminated in their current functions. We found that an ancient local duplication of the ancestral npm2 gene created the current two forms, and while most vertebrates retained both genes, notably, mammals and certain species of fish lost npm2a and, albeit rarely, both npm2a and npm2b. Our functional analyses showed that npm2a and npm2b have diverse but essential functions during embryogenesis, as npm2a mutants failed to undergo development at the earliest stage while npm2b mutants developed, although abnormally, until the zygotic genome activation stage after which their development was arrested followed subsequently by death. Our study is the first to clearly demonstrate the evolution, diversification, and functional analyses of the npm2 genes, which are essential maternal factors that are required for proper embryonic development and survival.

evolutionary biology↗

bioRxiv2016

Recent Cis-Trans Coevolution Driven by the Emergence of A Novel Gene in Drosophila

Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes1. Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome2. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we find a dynamic pattern in which Zeus binding rapidly co-evolved with a previously unknown DNA motif under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Our results suggest that evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic, genome-wide evolutionary processes associated with new genes.

Evolutionary Biology↗

bioRxiv2018

Gene expression plasticity and frontloading promote thermotolerance in Pocilloporid corals

Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investigated the thermal stress response in Pocillopora coral colonies from two contrasting environments by exposing them to heat stress. We compared the physiological state, bacterial and Symbionaceae communities (using 16S and ITS2 metabarcoding), and gene expression levels (using RNA-Seq) between control conditions and heat stress (the temperature just below the first signs of compromised health). Colonies from both thermal regimes remained apparently normal and presented open and colored polyps during heat stress, with no change in bacterial and Symbionaceae community composition. In contrast, they differed in their transcriptomic responses. The colonies from Oman displayed a more plastic transcriptome, but some genes had a higher basal expression level (frontloading) compared to the less thermotolerant colonies from New Caledonia. In terms of biological functions, we observed an increase in the expression of stress response genes (including induction of tumor necrosis factor receptors, heat shock proteins, and detoxification of reactive oxygen species), together with a decrease in the expression of genes involved in morpho-anatomical functions. Gene regulation (transcription factors, mobile elements, histone modifications and DNA methylation) appeared to be overrepresented in the Oman colonies, indicating possible epigenetic regulation. These results show that transcriptomic plasticity and frontloading can be co-occurring processes in corals confronted to highly variable thermal regimes.

evolutionary biology↗

bioRxiv2017

Coalescent models for populations with time-varying population sizes and arbitrary offspring distributions

The coalescent has been used to infer from gene genealogies the population dynamics of biological systems, such as the prevalence of an infectious disease. The offspring distribution affects the relationship between population dynamics and the genealogy, and for infectious diseases, the offspring distribution is often highly overdispersed. Here, we provide a general formula for the coalescent rate for populations with time-varying sizes and any offspring distribution. The formula is valid in the same large population limit as Kingmans original derivation. By relating our derivation to existing formulations of the coalescent, we show that differences in the coalescent rate derived for many population models may be explained by differences in the offspring distribution. The coalescent derivations presented here could be used to quantify the overdispersion in the offspring distribution of infectious diseases, which is useful for accurate modelling disease outbreaks.

evolutionary biology↗

bioRxiv2016

The Monarch Initiative: Insights across species reveal human disease mechanisms

The principles of genetics apply across the whole tree of life: on a cellular level, we share mechanisms with species from which we diverged millions or even billions of years ago. We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species. Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these multimodal data to inform interpretations by geneticists and to suggest experiments. However, the distribution and heterogeneity of databases is a major impediment: databases tend to focus either on a single data type across species, or on single species across data types. Although each database provides rich, high-quality information, no single one provides unified data that is comprehensive across species, biological scales, and data types. Without a big-picture view of the data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.

evolutionary biology↗

bioRxiv2016

Steep difference between ecotypes and intermediate phenotype depression for shell trait integration in a marine snail hybrid zone.

Multivariate analyses of phenotypic integration for a set of characters provide information about biological systems that cannot be obtained in univariate studies of these characters. We studied phenotypic integration for seven shell measures across the phenotypic gradient in a hybrid zone of the marine snail Littorina saxatilis in Galicia, NW Iberia. We found clear differences in the degree of integration between the two ecotypes involved in the hybrid zone, likely related to differences in the strength of natural selection acting on the snails' shells in each ecotype's habitat. We found also evidence of a decrease in integration in the phenotypically intermediate, hybrid snails, consistent with hybridization resulting in a release of multivariate variation and increased evolvability. Across the phenotypic gradient, decreases in overall integration tended to be accompanied by increases in some measures of modularity, but the latter did nor reflect high correlation structure. The increases occurred only in a proportional sense, correlations among modules tending to decrease faster than within modules for low overall integration tiers. Integration analyses based on non partial and partial correlations tended to produce contrasting results, which suggested hierarchical sources of shell integration. Given that the two ecotypes could have differentiated in situ according to a parapatric model, our results would show that changes in integration can occur in a short evolutionary time and be maintained in the presence of gene flow, and also that this gene flow could result in the hybrid release of multi character variation.

Evolutionary Biology↗

bioRxiv2017

A geography aware reconciliation method to investigate host/parasite cospeciation

Cospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX in order to visualize ancestral character states on the phylogenetic trees and highlight zones that are geographically inconsistent in reconciliations computed without geographic constraints. We suggest that the comparison of reconciliations obtained with and without constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography and the advent of next-generation sequencing that leads to better-resolved trees, a geography aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.

evolutionary biology↗

bioRxiv2015

Diversity of immune strategies explained by adaptation to pathogen statistics

Biological organisms have evolved a wide range of immune mechanisms to defend themselves against pathogens. Beyond molecular details, these mechanisms differ in how protection is acquired, processed and passed on to subsequent generations - differences that may be essential to long-term survival. Here, we introduce a mathematical framework to compare the long-term adaptation of populations as a function of the pathogen dynamics that they experience and of the immune strategy that they adopt. We find that the two key determinants of an optimal immune strategy are the frequency and the characteristic timescale of the pathogens. Depending on these two parameters, our framework identifies distinct modes of immunity, including adaptive, innate, bet-hedging and CRISPR-like immunities, which recapitulate the diversity of natural immune systems.

Evolutionary Biology↗

bioRxiv2016

Uniparental inheritance promotes adaptive evolution in cytoplasmic genomes

1Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes--specifically their organization into host cells and their uniparental (maternal) inheritance--enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Mullers ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes--despite their asexual mode of reproduction--can readily undergo adaptive evolution.

Evolutionary Biology↗

bioRxiv2017

Discovering Complete Quasispecies In Bacterial Genomes

Mobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs within a genome are an evolving populations because they replicate and mutate. We know the exact composition of this population and the sequence of each member of a REPIN population, in contrast to most other biological populations. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to ten different REPIN populations from ten different bacterial strains and estimate duplication rates. We find that our estimated duplication rates range from about 5 x 10-9 to 37 x 10-9 duplications per generation per genome. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size and we also see an example of competition between two REPIN populations.

evolutionary biology↗

bioRxiv2014

Conservation and structural analysis of the Xenopus laevis phospho-proteome

The African clawed frog Xenopus laevis is an important model organism for studies in developmental and cell biology, including cell-signaling. However, our knowledge of X. laevis protein post-translational modifications remains scarce. Here, we used a mass spectrometry-based approach to survey the phosphoproteome of this species, compiling a list of 3225 phosphosites. We used this resource to study the conservation between the phosphoproteomes of X. laevis and 13 other species. We found that the degree of conservation of phosphorylation across species is predictive of sites with known molecular function, kinase interactions and functionally relevant phospho-regulatory interactions. In addition, using comparative protein structure models, we find that phosphosites within structured domains tend to be located at positions with high conformational flexibility. A fraction of sites appear to occur in inaccessible positions and have the potential to regulate protein conformation.

Evolutionary Biology↗

bioRxiv2018

Reproduction costs can drive the evolution of groups

A fascinating wealth of life cycles is observed in biology, from unicellularity to the concerted fragmentation of multi-cellular units. However, the understanding of factors driving the evolution of life cycles is still limited. We investigate how reproduction costs influence this process. We consider a basic model of a group structured population of undifferentiated cells, where groups reproduce by fragmentation. Fragmentation events are associated with a cost expressed by either a fragmentation delay, a fragmentation risk, or a fragmentation loss. The introduction of such fragmentation costs vastly increases the set of potentially optimal life cycles. Based on these findings, we suggest that the evolution of life cycles and the splitting into multiple offspring can be directly associated with the fragmentation cost. Moreover, the impact of this cost alone is strong enough to drive the emergence of multicellular groups, even under scenarios that strongly disfavour groups compared to solitary individuals.

evolutionary biology↗

bioRxiv2018

De novo origin of multicellularity in response to predation

The transition from unicellular to multicellular life was one of a few major events in the history of life that created new opportunities for more complex biological systems to evolve. Predation is hypothesized as one selective pressure that may have driven the evolution of multicellularity. Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations. Considerable variation exists in the evolved multicellular life cycles, with both cell number and propagule size varying among isolates. Survival assays show that evolved multicellular traits provide effective protection against predation. These results support the hypothesis that selection imposed by predators may have played a role in some origins of multicellularity.

evolutionary biology↗

bioRxiv2017

Site and gene-wise likelihoods unmask influential outliers in phylogenomic analyses

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Here, we examined two datasets where supermatrix and coalescent-based species trees conflict. We identified two highly influential \"outlier\" genes in each dataset. When removed from each dataset, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate dataset have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant dataset did not exhibit any obvious systematic error and therefore may be the result of some biological process yet to be determined. While topological comparisons among a small set of alternate topologies can be helpful in discovering outlier genes, they can be limited in several ways, such as assuming all genes share the same topology. Coalescent species tree methods relax this assumption but do not explicitly facilitate the examination of specific edges. Coalescent methods often also assume that conflict is the result of incomplete lineage sorting (ILS). Here we explored a framework that allows for quickly examining alternative edges and support for large phylogenomic datasets that does not assume a single topology for all genes. For both datasets, these analyses provided detailed results confirming the support for coalescent-based topologies. This framework suggests that we can improve our understanding of the underlying signal in phylogenomic datasets by asking more targeted edge-based questions.

evolutionary biology↗

bioRxiv2018

Widespread transcriptional scanning in testes modulates gene evolution rates

A long-standing question in molecular biology relates to why the testes express the largest number of genes relative to all other organs. Here, we report a detailed gene expression map of human spermatogenesis using single-cell RNA-Seq. Surprisingly, we found that spermatogenesis-expressed genes contain significantly fewer germline mutations than unexpressed genes, with the lowest mutation rates on the transcribed DNA strands. These results suggest a model of transcriptional scanning to reduce germline mutations by correcting DNA damage. This model also explains the rapid evolution in sensory- and immune-defense related genes, as well as in male reproduction genes. Collectively, our results indicate that widespread expression in the testes achieves a dual mechanism for maintaining the DNA integrity of most genes, while selectively promoting variation of other genes.

evolutionary biology↗

bioRxiv2017

Inferring Continuous and Discrete Population Genetic Structure Across Space

A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the \"clines versus clusters\" problem in modeling population genetic variation. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.\n\nAuthor summaryOne of the first steps in the analysis of genetic data, and a principal mission of biology, is to describe and categorize natural variation. A continuous pattern of differentiation (isolation by distance), where individuals found closer together in space are, on average, more genetically similar than individuals sampled farther apart, can confound attempts to categorize natural variation into groups. This is because current statistical methods for assigning individuals to discrete clusters cannot accommodate spatial patterns, and so are forced to use clusters to describe what is in fact continuous variation. As isolation by distance is common in nature, this is a substantial shortcoming of existing methods. In this study, we introduce a new statistical method for categorizing natural genetic variation - one that describes variation as a combination of continuous and discrete patterns. We demonstrate that this method works well and can capture patterns in population genomic data without resorting to splitting populations where they can be described by continuous patterns of variation.

evolutionary biology↗

bioRxiv2015

Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Transposable elements (TEs) are major drivers of genomic and phenotypic evolution, yet many questions about their biology remain poorly understood. Here, we compare TE abundance between populations of the two sister species D. mauritiana und D. simulans and relate it to the more distantly related D. melanogaster. The low population frequency of most TE insertions in D. melanogaster and D. simulans has been a key feature of several models of TE evolution. In D. mauritiana, however, the majority of TE insertions are fixed (66%). We attribute this to a lower transposition activity of up to 47 TE families in D. mauritiana, rather than stronger purifying selection. Only three families, including the extensively studied Mariner, may have a higher activity in D. mauritiana. This remarkable difference in TE activity between two recently diverged Drosophila species ({approx} 250,000 years), also supports the hypothesis that TE copy numbers in Drosophila may not reflect a stable equilibrium where the rate of TE gains equals the rate of TE losses by negative selection. We propose that the transposition rate heterogeneity results from the contrasting ecology of the two species: the extent of vertical extinction of TE families and horizontal acquisition of active TE copies may be very different between the colonizing D. simulans and the island endemic D. mauritiana. Our findings provide novel insights in the evolution of TEs in Drosophila and suggest that the ecology of the host species could be a major, yet underappreciated, factor governing the evolutionary dynamics of TEs.

Evolutionary Biology↗

bioRxiv2017

Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

Factors explaining global distribution patterns have been central to biology since the 19th century, yet failure to combine dispersal-based biogeography with shifts in habitat suitability remains a present-day setback in understanding geographic distributions present and past, and time-extended trajectories of lineages. The lack of methods in a suitable integrative framework stands as a conspicuous shortcoming for reconstructing these dynamics. Here we showcase novel methods to overcome these methodological gaps, broadening the prospects for phyloclimatic modeling. We focus on a clade in the angiosperm genus Heuchera endemic to southern California that experienced ancient introgression from circumboreally distributed species of Mitella, testing hypotheses regarding biotic contact in the past between ancestral species lacking a fossil record. We obtain strong support for a past contact zone in northwestern North America, resolving this paradox of hybridization between ancestors of taxa currently separated by [~]1300 km.

evolutionary biology↗