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bioRxiv2016

Phenotypic switching can speed up biological evolution of microbes

Stochastic phenotype switching has been suggested to play a beneficial role in microbial populations by leading to the division of labour among cells, or ensuring that at least some of the population survives an unexpected change in environmental conditions. Here we use a computational model to investigate an alternative possible function of stochastic phenotype switching - as a way to adapt more quickly even in a static environment. We show that when a genetic mutation causes a population to become less fit, switching to an alternative phenotype with higher fitness (growth rate) may give the population enough time to develop compensatory mutations that increase the fitness again. The possibility of switching phenotypes can reduce the time to adaptation by orders of magnitude if the \"fitness valley\" caused by the deleterious mutation is deep enough. Our work has important implications for the emergence of antibiotic-resistant bacteria. In line with recent experimental findings we hypothesise that switching to a slower growing but less sensitive phenotype helps bacteria to develop resistance by exploring a larger set of beneficial mutations while avoiding deleterious ones.

Evolutionary Biology↗

bioRxiv2016

The adaptive significance of phasic colony cycles in army ants

Army ants are top arthropod predators in tropical forests around the world. The colonies of many army ant species undergo stereotypical behavioral and reproductive cycles, alternating between brood care and reproductive phases. In the brood care phase, colonies contain a cohort of larvae that are synchronized in their development and have to be fed. In the reproductive phase larvae are absent and oviposition takes place. Despite these colony cycles being a striking feature of army ant biology, their adaptive significance is unclear. Here we use a modelling approach to show that cyclic reproduction is favored under conditions where per capita foraging costs decrease with the number of larvae in a colony (\"High Cost of Entry\" scenario), while continuous reproduction is favored under conditions where per capita foraging costs increase with the number of larvae (\"Resource Exhaustion\" scenario). We argue that the former scenario specifically applies to army ants, because large raiding parties are required to overpower prey colonies. However, once raiding is successful it provides abundant food for a large cohort of larvae. The latter scenario, on the other hand, will apply to non-army ants, because in those species local resource depletion will force workers to forage over larger distances to feed large larval cohorts. Our model provides the first quantitative framework for understanding the adaptive value of phasic colony cycles in ants.

evolutionary biology↗

bioRxiv2015

Systematic Review of the Research on Morphological Modularity

The modular organization of the phenotype is an emergent property that derives from a semi-independent relation of body parts in their inheritance, development, function, and evolution. Understanding the modular organization of living beings is essential to understand the evolvability and plasticity of organismal form, and how morphological variation is structured during evolution and development. For this reason, delimiting morphological modules and establishing the factors originating them is a lively field of inquiry in biology today. However, unifying the results of the available body of knowledge is a challenge because of the large number of species studied and the disparity of morphological system, from the flower of angiosperms to the wing of insects and the head of primates (to name a few). The specific factors behind each pattern of modularity and the methods used to identify vary widely as well. This review summarizes more than 190 original research articles since 1958, in order to get a quantitative appraisal on what is studied, how is studied, and how results are explained. The results reveal an heterogeneous picture, where some taxa, systems, and approaches are over-studied, while others receive minor attention; other major trends and gaps in the study of morphological modularity through time are also discussed. In sum, this systematic review seeks to offer an objective view of this research field and highlight future research niches.

Evolutionary Biology↗

bioRxiv2015

The design and analysis of binary variable traits in common garden genetic experiments of highly fecund species to assess heritability

Many biologically important traits are binomially distributed, with their key phenotypes being presence or absence. Despite their prevalence, estimating the heritability of binomial traits presents both experimental and statistical challenges. Here we develop both an empirical and computational methodology for estimating the narrow-sense heritability of binary traits for highly fecund species. Our experimental approach controls for undesirable culturing effects, while minimizing culture numbers, increasing feasibility in the field. Our statistical approach accounts for known issues with model-selection by using a permutation test to calculate significance values and includes both fitting and power calculation methods. We illustrate our methodology by estimating the narrow-sense heritability for larval settlement, a key life-history trait, in the reef-building coral Orbicella faveolata. The experimental, statistical and computational methods, along with all of the data from this study, were deployed in the R package multiDimBio.

Evolutionary Biology↗

bioRxiv2016

Speciation by Symbiosis: The Microbiome and Behavior

Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms is now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction, and the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species.

Evolutionary Biology↗

bioRxiv2016

Phylogenetic scale in ecology and evolution

AimMany important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Yet, phylogenetic scale has never been formally conceptualized and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields, and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.\n\nMethodsWe summarize how phylogenetic scale has been treated in macroevolution, community ecology, biogeography, and macroecology, illustrating how it can inform, and possibly resolve, some of the longstanding controversies in these fields. To promote the concept empirically, we define phylogenetic grain and extent, scale-dependence, scaling, and the domains of phylogenetic scale. We illustrate how existing phylogenetic data and statistical tools can be employed to investigate the effects of scale on a variety of well-known patterns and processes, including diversification rates, community structure, niche conservatism, or species-abundance distributions.\n\nMain conclusionsExplicit consideration of phylogenetic scale can provide new and more complete insight into many longstanding questions across multiple fields (macroevolution, community ecology, biogeography, macroevolution). Building on the existing resources and isolated efforts across fields, future research centered on phylogenetic scale might enrich our understanding of the processes that together, but over different scales, shape the diversity of life.

Evolutionary Biology↗

bioRxiv2017

A novel unbiased test for molecular convergent evolution and discoveries in echolocating, aquatic and high-altitude mammals

Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. The extent to which genomic molecular convergence, and the extent to which coding mutations underlie this convergent phenotypic evolution remain unknown. Using a novel test, we ask which group of functionally coherent genes is most affected by convergent amino acid substitutions between phenotypically convergent lineages. This most affected sets reveals 75 novel coding convergences in important genes that pattern a highly adapted organ: the cochlea, skin and lung in echolocating, aquatic and high-altitude mammals, respectively. Our test explicitly requires the enriched converged term to not be simultaneously enriched for divergent mutations, and correctly dismisses relaxation-based signals, such as those produced by vision genes in subterranean mammals. This novel test can be readily applied to birds, fish, flies, worms etc., to discover more of the fascinating contribution of protein coding convergence to phenotype convergence.

evolutionary biology↗

bioRxiv2018

How the Central American Seaway and an ancient northern passage affected Flatfish diversification

While the natural history of flatfish has been debated for decades, the mode of diversification of this biologically and economically important group has never been elucidated. To address this question, we assembled the largest molecular data set to date, covering > 300 species (out of ca. 800 extant), from 13 of the 14 known families over nine genes, and employed relaxed molecular clocks to uncover their patterns of diversification. As the fossil record of flatfish is contentious, we used sister species distributed on both sides of the American continent to calibrate clock models based on the closure of the Central American Seaway (CAS), and on their current species range. We show that flatfish diversified in two bouts, as species that are today distributed around the Equator diverged during the closure of CAS, while those with a northern range diverged after this, hereby suggesting the existence of a post-CAS closure dispersal for these northern species, most likely along a trans-Arctic northern route, a hypothesis fully compatible with paleogeographic reconstructions.

evolutionary biology↗

bioRxiv2018

Soft song: help thine enemy!

The proximity risk model offers one possible explanation of honest signalling of aggressive intent in biology. This model assumes that the probability of successful attack is a function of the distance between the contestants and that this distance can be correctly estimated. This later assumption may not hold in nature where contestants have to estimate this distance under noisy conditions. Here I investigate with the help of a game theoretical model whether short-range ranging signals can be evolutionarily stable under such conditions. These signals can help the opponent to estimate the correct distance, thus they can promote honest signalling of intentions. Here I show that ranging signals that help the estimation of distance between opponents can be evolutionarily stable. However, such help only benefits those individuals who are able and willing to attack. As a result, ranging signals in themselves are an honest cue of proximity and in turn they are honest cues of aggressive intent. I give an example: \"soft-song\" in birds, and I discuss the predictions of the model.

evolutionary biology↗

bioRxiv2017

Allee dynamics: growth, extinction and range expansion

In population biology, the Allee dynamics refer to negative growth rates below a critical population density. In this Letter, we study a reaction-diffusion (RD) model of population growth and dispersion in one dimension, which incorporates the Allee effect in both the growth and mortality rates. In the absence of diffusion, the bifurcation diagram displays regions of both finite population density and zero population density, i.e., extinction. The early signatures of the transition to extinction at a bifurcation point are computed in the presence of additive noise. For the full RD model, the existence of travelling wave solutions of the population density is demonstrated. The parameter regimes in which the travelling wave advances (range expansion) and retreats are identified. In the weak Allee regime, the transition from the pushed to the pulled wave is shown as a function of the mortality rate constant. The results obtained are in agreement with the recent experimental observations on budding yeast populations.

evolutionary biology↗

bioRxiv2018

Honesty needs no cost: beneficial signals can be honest and evolutionarily stable

How and why animals communicate honestly is a key issue in biology. The role of signal cost is strongly entrenched in the maintenance in honest signalling. The handicap principle claims that honest signals have to be costly at the equilibrium and this cost is a theoretical necessity. The handicap principle further claims that signalling is fundamentally different from any other adaptation because honest signalling would collapse in the absence of cost. Here I investigate this claim in simple action-response game where signals do not have any cost, instead they have benefits. I show that such beneficial signals can be honest and evolutionarily stable. These signals can be beneficial to both high and low-quality signallers independently of the receivers response, yet they can maintain honest signalling just as much as costly signals. Signal cost-at or out of equilibrium-is not a necessary condition of honesty. Benefit functions can maintain honest signalling as long as the marginal cost-loss of benefit-is high enough for potential cheaters.

evolutionary biology↗

bioRxiv2018

Estimating the timing of multiple admixture pulses during local ancestry inference.

Admixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can only detect the most recent admixture event, here we present coalescent theory and associated software that can be used to estimate the timing of multiple admixture events in an admixed population. We extensively validate this approach and evaluate the conditions under which it can succesfully distinguish one from two-pulse admixture models. We apply our approach to real and simulated data of Drosophila melanogaster. We find evidence of a single very recent pulse of cosmopolitan ancestry contributing to African populations as well as evidence for more ancient admixture among genetically differentiated populations in sub-Saharan Africa. These results suggest our method can quantify complex admixture histories involving genetic material introduced by multiple discrete admixture pulses. The new method facilitates the exploration of admixture and its contribution to adaptation, ecological divergence, and speciation.

evolutionary biology↗

bioRxiv2017

Interdependence, Reflexivity, Fidelity, Impedance Matching, And The Evolution Of Genetic Coding

Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide*RNA partnership, eliminating the epistemological need for a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. Inversion symmetries in aaRS structural biology arising from genetic complementarity would have stabilized the initial and subsequent differentiation of coding specificities and hence rapidly promoted diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexivity in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: (i) any set of aaRS must be interdependent; (ii) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; (iii) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; (iv) the Central Dogmas emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene-replicase-translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today.

evolutionary biology↗

bioRxiv2017

Likelihood analysis of population genetic data under coalescent models: computational and inferential aspects

Likelihood methods are being developed for inference of migration rates and past demographic changes from population genetic data. We survey an approach for such inference using sequential importance sampling techniques derived from coalescent and diffusion theory. The consistent application and assessment of this approach has required the re-implementation of methods often considered in the context of computer experiments methods, in particular of Kriging which is used as a smoothing technique to infer a likelihood surface from likelihoods estimated in various parameter points, as well as reconsideration of methods for sampling the parameter space appropriately for such inference. We illustrate the performance and application of the whole tool chain on simulated and actual data, and highlight desirable developments in terms of data types and biological scenarios.\n\nResumeDiverses approches ont ete developpees pour linference des taux de migration et des changements demo-graphiques passes a partir de la variation genetique des populations. Nous decrivons une de ces approches utilisant des techniques dechantillonnage pondere sequentiel, fondees sur la modelisation par approches de coalescence et de diffusion de levolution de ces polymorphismes. Lapplication et levaluation systematique de cette approche ont requis la re-implementation de methodes souvent considerees pour lanalyse de fonctions simulees, en particulier le krigeage, ici utilise pour inferer une surface de vraisemblance a partir de vraisemblances estimees en differents points de lespace des parametres, ainsi que des techniques dechantillonage de ces points. Nous illustrons la performance et lapplication de cette serie de methodes sur donnees simulees et reelles, et indiquons les ameliorations souhaitables en termes de types de donnees et de scenarios biologiques.\n\nMots-cleshistoire demographique, processus de coalescence, importance sampling, genetic polymorphism\n\nAMS 2000 subject classifications92D10, 62M05, 65C05

evolutionary biology↗

bioRxiv2017

Subsurface Zircons With Presumptive "Biogenic" Inclusions As Potentially Useful Proxies For Studying Precambrian Bygone Biospheres In Goa

This work was inspired by recent report by Bell et al., 2015 who studied potentially biogenic carbon preserved in a 4.1 billion-year-old Zircon and need to assess the potential of Zircons found in Goa. Zircons (ZrSiO4) are naturally occurring silicate minerals which show radioactivity and high ductility and contain traces of Thorium and Uranium useful in Uranium-Thorium /Thorium -230 dating techniques. Zircons can be found in igneous, metamorphic rocks, sedimentary deposits and occurs as a detrital minerals in river and beach sands. Previous reports show that the Zircons can occur in different shapes such as round, elongated and with surface characteristics (Gartner et al.,2013). U-Pb Zircon dating methods had been used to study the continental growth in the western Dharwar craton of southern India (Jayananda et al., 2015). The present study was aimed at detection of subsurface Zircons with biogenic inclusions and assess their use as proxies for studying bygone Precambrium biospheres in Goa. Deep tubewell drilled Cores (60 and 65 m deep from surface) in island of Tiswadi at Taleigao were analyzed by light microscopy, Phase contrast microscopy and SEM to detect and classify the Zircons. In rapid preliminary sampling, total 50 Zircons were identified and 98% indicated the presence of interesting inclusions. These could be bubbles or kerogens or unidentified biological material. Zircons were classified as elongated, slightly rounded with sharp edges and showed widespread variety of surface characteristics like fracturing, cracks, scratches, striations and impact pits which may occur during transport processes. It is suggested that Zircons with presumptive biogenic inclusions can be further studied using techniques such as Raman Spectroscopy, Carbon Isotopic Measurements, X-Ray Microscopy, Trace Element Measurement consistent with Bell et al., 2015. More exhaustive studies have been undertaken to create a detail image database of Zircons from various other local samples to pinpoint those specifically useful for advanced work based on image analysis of the presumptive bioinclusions. Further attempts would be made to develop specific harvesting techniques to select potentially useful Zircons. International collaborations would be sought for applications of advanced techniques to local Zircons. Such studies would shed light on nature of bygone Precambrian biospheres in Goa and help in understanding evolution of life and the impact of plate tectonics and cataclysmic events shaping life on this planet.

evolutionary biology↗

bioRxiv2018

Fitness effects of altering gene expression noise in Saccharomyces cerevisiae

Gene expression noise is an evolvable property of biological systems that describes differences in gene expression among genetically identical cells in the same environment. Prior work has shown that expression noise is heritable and can be shaped by natural selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for the TDH3 gene in Saccharomyces cerevisiae. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns that are consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise.

evolutionary biology↗

bioRxiv2014

Genetic dissection of courtship song variation using the Drosophila Synthetic Population Resource

Connecting genetic variation to trait variation is a grand challenge in biology. Natural populations contain a vast reservoir of fascinating and potentially useful variation, but it is unclear if the causal alleles will generally have large enough effects for us to detect. Without knowing the effect sizes or allele frequency of typical variants, it is also unclear what methods will be most successful. Here, we use a multi-parent advanced intercross population (the Drosophila Synthetic Population Resource) to map natural variation in Drosophila courtship song traits. Most additive genetic variation in this population can be explained by a modest number of highly resolved QTL. Mapped QTL are universally multiallelic, suggesting that individual genes are \"hotspots\" of natural variation due to a small target size for major mutations and/or filtering of variation by positive or negative selection. Using quantitative complementation in randomized genetic backgrounds, we provide evidence that one causal allele is harbored in the gene Fhos, making this one of the few genes associated with behavioral variation in any taxon.

Evolutionary Biology↗

bioRxiv2016

Comment on Smaers et al. (2016): A nonviable phylogenetic comparative method hampered by circularity, inaccuracy, and bias

Smaers, Mongle & Kandler (2016) (Biological Journal of the Linnean Society, 118: 78-94) introduced a new phylogenetic comparative method, multiple variance Brownian motion (mvBM), for reconstructing ancestral states given a phylogenetic tree and continuous trait data. The authors conducted a simulation study and argued that mvBM outperforms constant variance Brownian motion (BM) when rates of evolution vary across the phylogeny. In this comment, we argue that mvBM is not a viable statistical method because it is fundamentally a circular analysis that overfits phylogenetic branch lengths to the data. We further argue that the comparison of mvBM to BM under conditions where the assumptions of BM are clearly violated is not an informative performance analysis, and that the simulation study of Smaers et al. (2016) exaggerates the performance of mvBM by focusing on a narrow range of simulation conditions and reporting aggregated accuracy metrics that obscure severe inaccuracy and bias in its ancestral state estimates. Our arguments are supported by simulation results. We conclude that mvBM is not a viable phylogenetic comparative method.

Evolutionary Biology↗