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Results for “Evolutionary Biology”

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bioRxiv2016

Horizontal transfer in bacterial Methionyl tRNA synthetase is very common shown by Genus and phyla level phylogenetic analysis.

Methionyl tRNA synthetase is single copy informational gene in Salmonella typhimurium. Informational genes are more conserved than operational genes. In this study we had analyzed HGT events within MetG sequences of different bacterial genera. A species tree based on 16srRNA sequences of the same genus was drawn evaluated against the generally accepted species tree of the bacteria. MetG phylogenetic tree was evaluated against the 16srRNAS tree and HGT event identified. Similarly phyla trees were made and HGT event identified. 24 HGT events were identified between genus and 11 within phyla. MetG is a considered as conserved gene finding so many HGT event in this gene indicate that horizontal gene transfer is very common in this gene. Manual tree making for phyla could help to understand phylogenetic relationships between very large trees.

Evolutionary Biology↗

bioRxiv2016

Resolving the conflict between associative overdominance and background selection

In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance), and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical and simulation studies that shed light on the conditions under which retardation versus acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection, with no linkage disequilibrium. With mutation and selection, retardation only occurs when S, the product of twice the effective population size and the selection coefficient, is of order one. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, there is nearly always a retardation of loss of variability. The results shed light on experiments on the loss of variability at marker loci in laboratory populations, and on the results of computer simulations of the effects of multiple selected loci on neutral variability.

Evolutionary Biology↗

bioRxiv2016

Have coral snake mimics diversified more than non-mimics?

Dipsadidae is the most diversified family of snakes, composed of species showing an impressive variety of color patterns. Some species are cryptic whereas others have contrasting patterns comprised by bright colors alternated with darker shades, including particular combinations of vivid colors characteristic of coral snakes (Elapidae). Species with such patterns are thought to be mimics of coral snakes based on their color pattern similarity, predator avoidance of such patterns in field experiments, and the geographical concordance between models and mimics. Here we test whether color patterns associated with coral snake mimicry and contrasting color patterns in general influenced the diversification dynamics of the group. We compile the largest database of color patterns among reptiles to date, with color descriptions for the majority (594 species) of dipsadids. We used trait-dependent diversification models along with extensive simulations to deal with the recently described statistical bias associated with such methods. Despite the apparent survival advantage associated with coral snake mimicry, we show that there is no detectable influence of color types in the dynamics of diversification in Dipsadidae. We discuss insights into the function of color patterns and argue that non-mimic contrasting patterns might serve as pre-adaptations to mimicry of coral snakes.\n\nData archival locationBEAST XML file and BiSSE MCMC results: http://dx.doi.org/10.6084/m9.figshare.831493\n\nR code for analyses and simulations: https://github.com/Caetanods/Dipsadidae_color_evolution

Evolutionary Biology↗

bioRxiv2016

Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid

Long chain polyunsaturated fatty acids (LCPUFA) are bioactive components of membrane phospholipids and serve as substrates for signaling molecules. LCPUFA can be obtained directly from animal foods or synthesized endogenously from 18 carbon precursors via the FADS2 coded enzyme. Vegans rely almost exclusively on endogenous synthesis to generate LCPUFA and we hypothesized that an adaptive genetic polymorphism would confer advantage. The rs66698963 polymorphism, a 22 bp insertion-deletion within FADS2, is associated with basal FADS1 expression, and coordinated induction of FADS1 and FADS2 in vitro. Here we determined rs66698963 genotype frequencies from 234 individuals of a primarily vegetarian Indian population and 311 individuals from the U.S. A much higher I/I genotype frequency was found in Indians (68%) than in the U.S. (18%). Analysis using 1000 Genomes Project data confirmed our observation, revealing a global I/I genotype of 70% in South Asians, 53% in Africans, 29% in East Asians, and 17% in Europeans. Tests based on population divergence, site frequency spectrum and long-range haplotype consistently point to positive selection encompassing rs66698963 in South Asian, African and some East Asian populations. Basal plasma phospholipid arachidonic acid status was 8% greater in I/I compared to D/D individuals. The biochemical pathway product-precursor difference, arachidonic acid minus linoleic acid, was 31% and 13% greater for I/I and I/D compared to D/D, respectively. Our study is consistent with previous in vitro data suggesting that the insertion allele enhances n-6 LCPUFA synthesis and may confer an adaptive advantage in South Asians because of the traditional plant-based diet practice.

Evolutionary Biology↗

bioRxiv2016

Does linked selection explain the narrow range of genetic diversity across species?

The relatively narrow range of genetic polymorphism levels across species has been a major source of debate since the inception of molecular population genetics. Recently Corbett-Detig et al found evidence that linked selection strongly constrains levels of polymorphism in species with large census sizes. Here I reexamine this claim and find weak support for this conclusion. While linked selection is an important determinant of polymorphism levels along the genome in many species, we currently lack compelling evidence that it is a major determinant of polymorphism levels among obligately sexual species.

Evolutionary Biology↗

bioRxiv2016

Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit

Forward Wright-Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the CPU, thus limiting their usefulness. The single-locus Wright-Fisher forward algorithm is, however, exceedingly parallelizable, with many steps which are so-called embarrassingly parallel, consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright-Fisher simulation, or GO Fish for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of well over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data - all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/

Evolutionary Biology↗

bioRxiv2016

Older fathers’ children have lower evolutionary fitness across four centuries and in four populations

Higher paternal age at offspring conception increases de novo genetic mutations (Kong et al., 2012). Based on evolutionary genetic theory we predicted that the offspring of older fathers would be less likely to survive and reproduce, i.e. have lower fitness. In a sibling control study, we find clear support for negative paternal age effects on offspring survival, mating and reproductive success across four large populations with an aggregate N > 1.3 million in main analyses. Compared to a sibling born when the father was 10 years younger, individuals had 4-13% fewer surviving children in the four populations. Three populations were pre-industrial (1670-1850) Western populations and showed a pattern of paternal age effects across the offsprings lifespan. In 20th-century Sweden, we found no negative paternal age effects on child survival or marriage odds. Effects survived tests for competing explanations, including maternal age and parental loss. To the extent that we succeeded in isolating a mutation-driven effect of paternal age, our results can be understood to show that de novo mutations reduce offspring fitness across populations and time. We can use this understanding to predict the effect of increasingly delayed reproduction on offspring genetic load, mortality and fertility.

Evolutionary Biology↗

bioRxiv2016

Epistasis and the dynamics of reversion in molecular evolution

Recent studies of protein evolution contend that the longer an amino acid substitution is present at a site, the less likely it is to revert to the amino acid previously occupying that site. Here we study this phenomenon of decreasing reversion rates rigorously, and in a much more general context. We show that, under weak mutation and for arbitrary fitness landscapes, reversion rates decrease with time for any site that is involved in at least one epistatic interaction. Specifically, we prove that, at stationarity, the hazard function of the distribution of waiting times until reversion is strictly decreasing for any such site. Thus, in the presence of epistasis, the longer a particular character has been absent from a site, the less likely the site will revert to its prior state. We also explore several examples of this general result, which share a common pattern whereby the probability of having reverted increases rapidly at short times to some substantial value before becoming almost flat after a few substitutions at other sites. This pattern indicates a characteristic tendency for reversion to occur either almost immediately after the initial substitution or only after a very long time.

Evolutionary Biology↗

bioRxiv2016

Evolutionary consequences of DNA methylation in a basal metazoan

Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that gbM correlates with breadth and abundance of transcription and with slow sequence evolution. We also show a strong correlation between gbM and codon bias due to systematic replacement of CpG bearing codons. We suggest that the ancestral function of gene body methylation is tied to selective pressure for accurate and stable gene expression, and that mutation caused by gbM may be a previously unrecognized driver of adaptive codon evolution.

Evolutionary Biology↗

bioRxiv2016

Antimicrobial functions of lactoferrin promote genetic conflicts in ancient primates and modern humans

Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with pathogens remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by pathogens. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with pathogenic bacteria causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions.

Evolutionary Biology↗

bioRxiv2016

Genetics of cortico-cerebellar expansion in anthropoid primates: a comparative approach

What adaptive changes in brain structure and function underpin the evolution of increased cognitive performance in humans and our close relatives? Identifying the genetic basis of brain evolution has become a major tool in answering this question. Numerous cases of positive selection, altered gene expression or gene duplication have been identified that may contribute to the evolution of the neocortex, which is widely assumed to play a predominant role in cognitive evolution. However, the neocortex co-evolves with other, functionally inter-dependent, regions of the brain, most notably the cerebellum. The cerebellum is linked to a range of cognitive tasks and expanded rapidly during hominoid evolution, independently of neocortex size. Here we demonstrate that, across primates, genes with known roles in cerebellum development are just as likely to be targeted by selection as genes linked to cortical development. In fact, cerebellum genes are more likely to have evolved adaptively during hominoid evolution, consistent with phenotypic data suggesting an accelerated rate of cerebellar expansion in apes. Finally, we present evidence that selection targeted genes with specific effects on either the neocortex or cerebellum, not both. This suggests cortico-cerebellar co-evolution is maintained by selection acting on independent developmental programs.

Evolutionary Biology↗

bioRxiv2016

Adaptive divergence in brain composition between ecologically distinct incipient species

During ecological speciation diverging populations are exposed to contrasting sensory and spatial information that present new behavioral and perceptive challenges. Here, we investigate how brain composition evolves during the early stages of speciation. The incipient species pair, Heliconius erato cyrbia and H. himera, have parapatric ranges across an environmental and altitudinal gradient. Despite continuing gene-flow, these species have divergent ecological, behavioral and physiological traits. We demonstrate that these incipient species also differ significantly in brain composition, especially in the size of sensory structures. H. erato has larger visual components whilst H. himera invests more heavily in olfaction. These differences are not explained by environmentally-induced plasticity, but reflect non-allometric shifts in brain structure. Our results suggest the adaptive evolution of brain structure and function play an important role in facilitating the emergence of ecologically distinct species, and imply that plasticity alone may be insufficient to meet the demands of novel environments.

Evolutionary Biology↗

bioRxiv2016

Replicator Dynamics with Feedback-Evolving Games: Towards a Co-Evolutionary Game Theory

A tragedy of the commons occurs when individuals take actions to maximize their payoffs even as their combined payoff is less than the global maximum had the players coordinated. The originating example is that of over-grazing of common pasture lands. In game theoretic treatments of this example there is rarely consideration of how individual behavior subsequently modifies the commons and associated payoffs. Here, we generalize evolutionary game theory by proposing a class of replicator dynamics with feedback-evolving games in which environment-dependent payoffs and strategies coevolve. We initially apply our formulation to a system in which the payoffs favor unilateral defection and cooperation, given replete and depleted environments respectively. Using this approach we identify and characterize a new class of dynamics: an oscillatory tragedy of the commons in which the system cycles between deplete and replete environmental states and cooperation and defection behavior states. We generalize the approach to consider outcomes given all possible rational choices of individual behavior in the depleted state when defection is favored in the replete state. In so doing we find that incentivizing cooperation when others defect in the depleted state is necessary to avert the tragedy of the commons. In closing, we propose new directions for the study of control and influence in games in which individual actions exert a substantive effect on the environmental state.

Evolutionary Biology↗

bioRxiv2016

Can secondary contact following range expansion be distinguished from barriers to gene flow?

Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of Linkage Disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index {Psi}, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.

Evolutionary Biology↗

bioRxiv2016

Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

Premise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses have found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.\n\nMethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.\n\nKey resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.\n\nConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from recent linkage maps, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

Evolutionary Biology↗

bioRxiv2016

Royal decree: gene expression in transgenerationally immune primed bumblebee workers mimics a primary immune response

Invertebrates lack the cellular and physiological machinery of the adaptive immune system, but show specificity in their immune response [1, 2] and immune priming [3-11]. Functionally, immune priming is comparable to immune memory in vertebrates. Individuals that have survived exposure to a given parasite are better protected against subsequent exposures. Protection may be cross-reactive (e.g. [12]), but demonstrations of persistent and specific protection in invertebrates are increasing [3, 5]. This immune priming can cross generations (\"trans-generational\" immune priming) [4, 8], preparing offspring for the prevailing parasite environment. While these phenomena gain increasing support, the mechanistic foundations underlying such immune priming, both within and across generations, remain largely unknown. Using a transcriptomic approach, we show a bacterial challenge to bumblebee queens, known to induce trans-generational immune priming, alters daughter (worker) gene expression. Daughters, even when unchallenged themselves, constitutively express a core set of the genes induced upon direct bacterial exposure, including high expression of antimicrobial peptides, a beta-glucan receptor protein implicated in bacterial recognition and the induction of the toll signaling pathway[13], and slit-3 which is important in honeybee immunity[14]. Maternal challenge results in a distinct upregulation of their daughters immune system, with a signature overlapping with the induced individual response to a direct immune challenge. This will mediate mother-offspring protection, but also associated costs related to reconfiguration of constitutive immune expression. Identification of conserved immune pathways in memory-like responses has important implications for our understanding of the innate immune system, including the innate components in vertebrates, which share many of these pathways[15].\n\nAuthor SummaryInvertebrate individuals surviving exposure to an infectious disease can become better at fighting future infection by that same disease. This protection, known as immune priming, can even be transferred to the individuals offspring. The functional outcome is very similar to that of vertebrate immune memory, but the mechanisms of how invertebrates achieve immune priming within an individual or across generations remain enigmatic. We found that bumblebee daughters of mothers exposed to a simulated bacterial infection express strongly many of the genes that they would activate if they were themselves infected. Our results show how immune priming across generations might be produced in bumblebees. Many parts of the invertebrate immune system are shared with us, and thus our study also sheds a light on how diverse immune memory-like effects could be achieved.

Evolutionary Biology↗

bioRxiv2016

Spirals, Scalp Whorls and Skin Biomechanics: Nature’s Own Design For Expansion

This paper began as an exercise in curiosity - logarithmic spiral designs abound in nature -- in galaxies, flowers, pinecones and on human scalps as whorls. Why are humans the only primates to have whorls on the scalp? Is the formation of scalp whorls mechanical or genetic? A mechanical theory has long been postulated- the mechanical theory suggests that hair whorl patterning is determined by the tension on the epidermis during rapid expansion of the cranium while the hair follicle is growing downwards - however, this has never before been experimentally proven conclusively. We found, that under certain conditions, we were able to experimentally recreate spirals on the scalp to demonstrate that the basis of scalp whorls is indeed mechanical - and that logarithmic spirals are indeed natures own design for rapid expansion of organic tissues. Given our experiments only created whorls when certain conditions were satisfied (and not in others), they have given us great insight into the mechanical formation of skin whorls and the physiology of skin stretch. We believe that these findings will lead to many more advances in understanding skin dynamics and indeed the behavior of any living tissue when confronted by stretch. As a corollary, the application of the results of these studies have led us to the discovery of a new surgical technique for closure of scalp defects using the golden spiral pattern, and this will be the subject of a separate paper.

Evolutionary Biology↗

bioRxiv2016

The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

The formation of an allopolyploid species involves the merger of two genomes with separate evolutionary histories. In allopolyploids, genes derived from one progenitor species are often expressed at higher levels than those from the other progenitor. It has been suggested that this could be due to differences in transposable element (TE) content among progenitors, as silencing of TEs can affect expression of nearby genes. Here, we examine the role of TEs for expression biases in the widespread allotetraploid Capsella bursa-pastoris and in diploid F1 hybrids generated by crossing Capsella orientalis and Capsella rubella, two close relatives of the progenitors of C. bursa-pastoris. As C. rubella harbors more TEs than C. orientalis, we expect C. orientalis alleles to be expressed at higher levels if TE content is key for expression biases. To test this hypothesis, we quantified expression biases at approximately 5800 genes in flower buds and leaves, while correcting for read mapping biases using genomic data. While three of four C. bursa-pastoris accessions exhibited a shift toward higher relative expression of C. orientalis alleles, the fourth C. bursa-pastoris accession had the opposite direction of expression bias, as did diploid F1 hybrids. Associations between TE polymorphism and expression bias were weak, and the effect of TEs on expression bias was small. These results suggest that differences in TE content alone cannot fully explain expression biases in these species. Future studies should investigate the role of differences in TE silencing efficacy, as well as a broader set of other factors. Our results are important for a more general understanding of the role of TEs for cis-regulatory evolution in plants.

Evolutionary Biology↗