ResearchPad - convergent-evolution https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Modeling competitive evolution of multiple languages]]> https://www.researchpad.co/article/elastic_article_7854 Increasing evidence demonstrates that in many places language coexistence has become ubiquitous and essential for supporting language and cultural diversity and associated with its financial and economic benefits. The competitive evolution among multiple languages determines the evolution outcome, either coexistence, or decline, or extinction. Here, we extend the Abrams-Strogatz model of language competition to multiple languages and then validate it by analyzing the behavioral transitions of language usage over the recent several decades in Singapore and Hong Kong. In each case, we estimate from data the model parameters that measure each language utility for its speakers and the strength of two biases, the majority preference for their language, and the minority aversion to it. The values of these two biases decide which language is the fastest growing in the competition and what would be the stable state of the system. We also study the system convergence time to stable states and discover the existence of tipping points with multiple attractors. Moreover, the critical slowdown of convergence to the stable fractions of language users appears near and peaks at the tipping points, signaling when the system approaches them. Our analysis furthers our understanding of evolution of various languages and the role of tipping points in behavioral transitions. These insights may help to protect languages from extinction and retain the language and cultural diversity.

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<![CDATA[Adaptation to unstable coordination patterns in individual and joint actions]]> https://www.researchpad.co/article/elastic_article_7665 Previous research on interlimb coordination has shown that some coordination patterns are more stable than others, and function as attractors in the space of possible phase relations between different rhythmic movements. The canonical coordination patterns, i.e. the two most stable phase relations, are in-phase (0 degree) and anti-phase (180 degrees). Yet, musicians are able to perform other coordination patterns in intrapersonal as well as in interpersonal coordination with remarkable precision. This raises the question of how music experts manage to produce these unstable patterns of movement coordination. In the current study, we invited participants with at least five years of training on a musical instrument. We used an adaptation paradigm to address two factors that may facilitate producing unstable coordination patterns. First, we investigated adaptation in different coordination settings, to test the hypothesis that the lower coupling strength between individuals during joint performance makes it easier to achieve stability outside of the canonical patterns than the stronger coupling during individual bimanual performance. Second, we investigated whether adding to the structure of action effects may support achieving unstable coordination patterns, both intra- and inter-individually. The structure of action effects was strengthened by adding a melodic contour to the action effects, a measure that has been shown to improve the acquisition of bimanual coordination skills. Adaptation performance was measured both in terms of asynchrony and variability thereof. As predicted, we found that producing unstable patterns benefitted from the weaker coupling during joint performance. Surprisingly, the structure of action effects did not help with achieving unstable coordination patterns.

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<![CDATA[Algorithmic bias amplifies opinion fragmentation and polarization: A bounded confidence model]]> https://www.researchpad.co/article/5c8823d7d5eed0c484639133

The flow of information reaching us via the online media platforms is optimized not by the information content or relevance but by popularity and proximity to the target. This is typically performed in order to maximise platform usage. As a side effect, this introduces an algorithmic bias that is believed to enhance fragmentation and polarization of the societal debate. To study this phenomenon, we modify the well-known continuous opinion dynamics model of bounded confidence in order to account for the algorithmic bias and investigate its consequences. In the simplest version of the original model the pairs of discussion participants are chosen at random and their opinions get closer to each other if they are within a fixed tolerance level. We modify the selection rule of the discussion partners: there is an enhanced probability to choose individuals whose opinions are already close to each other, thus mimicking the behavior of online media which suggest interaction with similar peers. As a result we observe: a) an increased tendency towards opinion fragmentation, which emerges also in conditions where the original model would predict consensus, b) increased polarisation of opinions and c) a dramatic slowing down of the speed at which the convergence at the asymptotic state is reached, which makes the system highly unstable. Fragmentation and polarization are augmented by a fragmented initial population.

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<![CDATA[Copy-the-majority of instances or individuals? Two approaches to the majority and their consequences for conformist decision-making]]> https://www.researchpad.co/article/5c57e654d5eed0c484ef2bca

Cultural evolution is the product of the psychological mechanisms that underlie individual decision making. One commonly studied learning mechanism is a disproportionate preference for majority opinions, known as conformist transmission. While most theoretical and experimental work approaches the majority in terms of the number of individuals that perform a behaviour or hold a belief, some recent experimental studies approach the majority in terms of the number of instances a behaviour is performed. Here, we use a mathematical model to show that disagreement between these two notions of the majority can arise when behavioural variants are performed at different rates, with different salience or in different contexts (variant overrepresentation) and when a subset of the population act as demonstrators to the whole population (model biases). We also show that because conformist transmission changes the distribution of behaviours in a population, how observers approach the majority can cause populations to diverge, and that this can happen even when the two approaches to the majority agree with regards to which behaviour is in the majority. We discuss these results in light of existing findings, ranging from political extremism on twitter to studies of animal foraging behaviour. We conclude that the factors we considered (variant overrepresentation and model biases) are plausibly widespread. As such, it is important to understand how individuals approach the majority in order to understand the effects of majority influence in cultural evolution.

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<![CDATA[Opinion limits study for the multi-selection bounded confidence model]]> https://www.researchpad.co/article/5c5217aad5eed0c484794327

In this work, we study the opinion limit states for a generalized bounded confidence agent-based opinion model. Agents can select multiple opinions in the network, and the confidence bound is considered on the distance between the average of the selected opinions and agent opinion itself. The number of selection agents for a certain agent, which is also called the selection number, means the agent opinion interaction degree. It is known that when the confidence bound is large sufficiently, opinions reach consensus almost surely. We mainly study the opinion consensus and the opinion polarization when the confidence bound is small sufficiently. Firstly, we provide and prove the upper and lower bounds for the opinion consensus probability of this bound confidence model. It shows that the opinion consensus probability almost always decreases as the confidence bound decreases. Secondly, the opinion consensus probability is larger than the one for the opinion evolution of the Deffuant-Weisbuch model. Finally, we demonstrate the ultimate probability distribution of one agent opinion and compare it with the gossip form and the general bounded confidence form, and demonstrate how the opinion polarization probabilities evolve as the selection number changes. Specially, different from other studies, we find that the opinion polarization would happen more easily if the opinion interaction degree is strengthened. In a sum, the multiple selection mechanism will increase the opinion consensus probability and the opinion polarization probability, respectively, comparing to the single selection mechanism.

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<![CDATA[Nonstrabismic binocular dysfunctions and cervical complaints: The possibility of a cross-dysfunction]]> https://www.researchpad.co/article/5c478c66d5eed0c484bd2192

The aim of this study is to establish a relationship between non-strabismic binocular dysfunction and neck pain. One hundred twelve participants underwent binocular vision assessment by evaluating horizontal heterophoria, horizontal and vertical fusional vergence ranges and vergence facility. The subjects were classified into two groups: binocular anomalies and normal binocular function. Neck complaints were measured with the Neck Disability Index, visual analogue scale, cervical range of motion, deep-flexor muscle activation score (AS) and performance index (PI). Our results showed that participants with low AS had significantly altered values of lateral phoria (near) (mean = -6.99 SD ± 6.96 PD) and PFV (near) blur (mean = 9.49 SD ± 5.45 PD) against those who presented normal AS (lateral phoria (near) mean = -3.64 SD ± 6.37 PD; PFV (near) blur mean = 12.84 SD ± 6.20 PD). In addition, participants with NFV (near) recovery outside the norm had a significantly lower right side-bending (mean = 35.63 SD ± 8.35 PD) than those within the standard (mean = 39.64 SD ± 9 PD). The subjects with binocular vision impairment showed a diminished response to the deep cervical musculature, with low AS and PI, as well as a tendency to suffer from cervicalgia of more than three months’ evolution and a lower range of motion.

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<![CDATA[An evolutionary game perspective on quantised consensus in opinion dynamics]]> https://www.researchpad.co/article/5c390ba9d5eed0c48491dbf3

Quantised consensus has been used in the context of opinion dynamics. In this context agents interact with their neighbours and they change their opinion according to their interests and the opinions of their neighbours. We consider various quantised consensus models, where agents have different levels of susceptibility to the inputs received from their neighbours. The provided models share similarities with collective decision making models inspired by honeybees and evolutionary games. As first contribution, we develop an evolutionary game-theoretic model that accommodates the different consensus dynamics in a unified framework. As second contribution, we study equilibrium points and extend such study to the symmetric case where the transition probabilities of the evolutionary game dynamics are symmetric. Symmetry is associated with the case of equally favourable options. As third contribution, we study stability of the equilibrium points for the different cases. We corroborate the theoretical results with some simulations to study the outcomes of the various models.

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<![CDATA[A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images]]> https://www.researchpad.co/article/5989da1bab0ee8fa60b7cfb0

Modern fluorescence microscopy modalities, such as light-sheet microscopy, are capable of acquiring large three-dimensional images at high data rate. This creates a bottleneck in computational processing and analysis of the acquired images, as the rate of acquisition outpaces the speed of processing. Moreover, images can be so large that they do not fit the main memory of a single computer. We address both issues by developing a distributed parallel algorithm for segmentation of large fluorescence microscopy images. The method is based on the versatile Discrete Region Competition algorithm, which has previously proven useful in microscopy image segmentation. The present distributed implementation decomposes the input image into smaller sub-images that are distributed across multiple computers. Using network communication, the computers orchestrate the collectively solving of the global segmentation problem. This not only enables segmentation of large images (we test images of up to 1010 pixels), but also accelerates segmentation to match the time scale of image acquisition. Such acquisition-rate image segmentation is a prerequisite for the smart microscopes of the future and enables online data compression and interactive experiments.

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<![CDATA[Comparable Ages for the Independent Origins of Electrogenesis in African and South American Weakly Electric Fishes]]> https://www.researchpad.co/article/5989d9f3ab0ee8fa60b6f101

One of the most remarkable examples of convergent evolution among vertebrates is illustrated by the independent origins of an active electric sense in South American and African weakly electric fishes, the Gymnotiformes and Mormyroidea, respectively. These groups independently evolved similar complex systems for object localization and communication via the generation and reception of weak electric fields. While good estimates of divergence times are critical to understanding the temporal context for the evolution and diversification of these two groups, their respective ages have been difficult to estimate due to the absence of an informative fossil record, use of strict molecular clock models in previous studies, and/or incomplete taxonomic sampling. Here, we examine the timing of the origins of the Gymnotiformes and the Mormyroidea using complete mitogenome sequences and a parametric Bayesian method for divergence time reconstruction. Under two different fossil-based calibration methods, we estimated similar ages for the independent origins of the Mormyroidea and Gymnotiformes. Our absolute estimates for the origins of these groups either slightly postdate, or just predate, the final separation of Africa and South America by continental drift. The most recent common ancestor of the Mormyroidea and Gymnotiformes was found to be a non-electrogenic basal teleost living more than 85 millions years earlier. For both electric fish lineages, we also estimated similar intervals (16–19 or 22–26 million years, depending on calibration method) between the appearance of electroreception and the origin of myogenic electric organs, providing rough upper estimates for the time periods during which these complex electric organs evolved de novo from skeletal muscle precursors. The fact that the Gymnotiformes and Mormyroidea are of similar age enhances the comparative value of the weakly electric fish system for investigating pathways to evolutionary novelty, as well as the influences of key innovations in communication on the process of species radiation.

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<![CDATA[Lagrange Interpolation Learning Particle Swarm Optimization]]> https://www.researchpad.co/article/5989da33ab0ee8fa60b85697

In recent years, comprehensive learning particle swarm optimization (CLPSO) has attracted the attention of many scholars for using in solving multimodal problems, as it is excellent in preserving the particles’ diversity and thus preventing premature convergence. However, CLPSO exhibits low solution accuracy. Aiming to address this issue, we proposed a novel algorithm called LILPSO. First, this algorithm introduced a Lagrange interpolation method to perform a local search for the global best point (gbest). Second, to gain a better exemplar, one gbest, another two particle’s historical best points (pbest) are chosen to perform Lagrange interpolation, then to gain a new exemplar, which replaces the CLPSO’s comparison method. The numerical experiments conducted on various functions demonstrate the superiority of this algorithm, and the two methods are proven to be efficient for accelerating the convergence without leading the particle to premature convergence.

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<![CDATA[Entangling Credit and Funding Shocks in Interbank Markets]]> https://www.researchpad.co/article/5989d9d8ab0ee8fa60b66741

Credit and liquidity shocks represent main channels of financial contagion for interbank lending markets. On one hand, banks face potential losses whenever their counterparties are under distress and thus unable to fulfill their obligations. On the other hand, solvency constraints may force banks to recover lost fundings by selling their illiquid assets, resulting in effective losses in the presence of fire sales—that is, when funding shortcomings are widespread over the market. Because of the complex structure of the network of interbank exposures, these losses reverberate among banks and eventually get amplified, with potentially catastrophic consequences for the whole financial system. Inspired by the recently proposed Debt Rank, in this work we define a systemic risk metric that estimates the potential amplification of losses in interbank markets accounting for both credit and liquidity contagion channels: the Debt-Solvency Rank. We implement this framework on a dataset of 183 European banks that were publicly traded between 2004 and 2013, showing indeed that liquidity spillovers substantially increase systemic risk, and thus cannot be neglected in stress-test scenarios. We also provide additional evidence that the interbank market was extremely fragile up to the global financial crisis, becoming slightly more robust only afterwards.

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<![CDATA[Molecular Inferences Suggest Multiple Host Shifts of Rabies Viruses from Bats to Mesocarnivores in Arizona during 2001–2009]]> https://www.researchpad.co/article/5989dad6ab0ee8fa60bb7e06

In nature, rabies virus (RABV; genus Lyssavirus, family Rhabdoviridae) represents an assemblage of phylogenetic lineages, associated with specific mammalian host species. Although it is generally accepted that RABV evolved originally in bats and further shifted to carnivores, mechanisms of such host shifts are poorly understood, and examples are rarely present in surveillance data. Outbreaks in carnivores caused by a RABV variant, associated with big brown bats, occurred repeatedly during 2001–2009 in the Flagstaff area of Arizona. After each outbreak, extensive control campaigns were undertaken, with no reports of further rabies cases in carnivores for the next several years. However, questions remained whether all outbreaks were caused by a single introduction and further perpetuation of bat RABV in carnivore populations, or each outbreak was caused by an independent introduction of a bat virus. Another question of concern was related to adaptive changes in the RABV genome associated with host shifts. To address these questions, we sequenced and analyzed 66 complete and 20 nearly complete RABV genomes, including those from the Flagstaff area and other similar outbreaks in carnivores, caused by bat RABVs, and representatives of the major RABV lineages circulating in North America and worldwide. Phylogenetic analysis demonstrated that each Flagstaff outbreak was caused by an independent introduction of bat RABV into populations of carnivores. Positive selection analysis confirmed the absence of post-shift changes in RABV genes. In contrast, convergent evolution analysis demonstrated several amino acids in the N, P, G and L proteins, which might be significant for pre-adaptation of bat viruses to cause effective infection in carnivores. The substitution S/T242 in the viral glycoprotein is of particular merit, as a similar substitution was suggested for pathogenicity of Nishigahara RABV strain. Roles of the amino acid changes, detected in our study, require additional investigations, using reverse genetics and other approaches.

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<![CDATA[Understanding and coping with extremism in an online collaborative environment: A data-driven modeling]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbf4c

The Internet has provided us with great opportunities for large scale collaborative public good projects. Wikipedia is a predominant example of such projects where conflicts emerge and get resolved through bottom-up mechanisms leading to the emergence of the largest encyclopedia in human history. Disaccord arises whenever editors with different opinions try to produce an article reflecting a consensual view. The debates are mainly heated by editors with extreme views. Using a model of common value production, we show that the consensus can only be reached if groups with extreme views can actively take part in the discussion and if their views are also represented in the common outcome, at least temporarily. We show that banning problematic editors mostly hinders the consensus as it delays discussion and thus the whole consensus building process. To validate the model, relevant quantities are measured both in simulations and Wikipedia, which show satisfactory agreement. We also consider the role of direct communication between editors both in the model and in Wikipedia data (by analyzing the Wikipedia talk pages). While the model suggests that in certain conditions there is an optimal rate of “talking” vs “editing”, it correctly predicts that in the current settings of Wikipedia, more activity in talk pages is associated with more controversy.

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<![CDATA[HSTLBO: A hybrid algorithm based on Harmony Search and Teaching-Learning-Based Optimization for complex high-dimensional optimization problems]]> https://www.researchpad.co/article/5989db52ab0ee8fa60bdc785

Harmony Search (HS) and Teaching-Learning-Based Optimization (TLBO) as new swarm intelligent optimization algorithms have received much attention in recent years. Both of them have shown outstanding performance for solving NP-Hard optimization problems. However, they also suffer dramatic performance degradation for some complex high-dimensional optimization problems. Through a lot of experiments, we find that the HS and TLBO have strong complementarity each other. The HS has strong global exploration power but low convergence speed. Reversely, the TLBO has much fast convergence speed but it is easily trapped into local search. In this work, we propose a hybrid search algorithm named HSTLBO that merges the two algorithms together for synergistically solving complex optimization problems using a self-adaptive selection strategy. In the HSTLBO, both HS and TLBO are modified with the aim of balancing the global exploration and exploitation abilities, where the HS aims mainly to explore the unknown regions and the TLBO aims to rapidly exploit high-precision solutions in the known regions. Our experimental results demonstrate better performance and faster speed than five state-of-the-art HS variants and show better exploration power than five good TLBO variants with similar run time, which illustrates that our method is promising in solving complex high-dimensional optimization problems. The experiment on portfolio optimization problems also demonstrate that the HSTLBO is effective in solving complex read-world application.

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<![CDATA[Host-Pathogen O-Methyltransferase Similarity and Its Specific Presence in Highly Virulent Strains of Francisella tularensis Suggests Molecular Mimicry]]> https://www.researchpad.co/article/5989db35ab0ee8fa60bd2e0c

Whole genome comparative studies of many bacterial pathogens have shown an overall high similarity of gene content (>95%) between phylogenetically distinct subspecies. In highly clonal species that share the bulk of their genomes subtle changes in gene content and small-scale polymorphisms, especially those that may alter gene expression and protein-protein interactions, are more likely to have a significant effect on the pathogen's biology. In order to better understand molecular attributes that may mediate the adaptation of virulence in infectious bacteria, a comparative study was done to further analyze the evolution of a gene encoding an o-methyltransferase that was previously identified as a candidate virulence factor due to its conservation specifically in highly pathogenic Francisella tularensis subsp. tularensis strains. The o-methyltransferase gene is located in the genomic neighborhood of a known pathogenicity island and predicted site of rearrangement. Distinct o-methyltransferase subtypes are present in different Francisella tularensis subspecies. Related protein families were identified in several host species as well as species of pathogenic bacteria that are otherwise very distant phylogenetically from Francisella, including species of Mycobacterium. A conserved sequence motif profile is present in the mammalian host and pathogen protein sequences, and sites of non-synonymous variation conserved in Francisella subspecies specific o-methyltransferases map proximally to the predicted active site of the orthologous human protein structure. Altogether, evidence suggests a role of the F. t. subsp. tularensis protein in a mechanism of molecular mimicry, similar perhaps to Legionella and Coxiella. These findings therefore provide insights into the evolution of niche-restriction and virulence in Francisella, and have broader implications regarding the molecular mechanisms that mediate host-pathogen relationships.

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<![CDATA[The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion]]> https://www.researchpad.co/article/5989d9dbab0ee8fa60b677fd

Background

Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult. This is especially true in its most interesting cases, where rapid and multiple duplications are likely to reflect adaptation to rapidly changing environments and life styles. This may be so for Class I of alcohol dehydrogenases (ADH1s), where multiple duplications occurred in primate lineages in Old and New World monkeys (OWMs and NWMs) and hominoids.

Methodology/Principal Findings

To build a preferred model for the natural history of ADH1s, we determined the sequences of nine new ADH1 genes, finding for the first time multiple paralogs in various prosimians (lemurs, strepsirhines). Database mining then identified novel ADH1 paralogs in both macaque (an OWM) and marmoset (a NWM). These were used with the previously identified human paralogs to resolve controversies relating to dates of duplication and gene conversion in the ADH1 family. Central to these controversies are differences in the topologies of trees generated from exonic (coding) sequences and intronic sequences.

Conclusions/Significance

We provide evidence that gene conversions are the primary source of difference, using molecular clock dating of duplications and analyses of microinsertions and deletions (micro-indels). The tree topology inferred from intron sequences appear to more correctly represent the natural history of ADH1s, with the ADH1 paralogs in platyrrhines (NWMs) and catarrhines (OWMs and hominoids) having arisen by duplications shortly predating the divergence of OWMs and NWMs. We also conclude that paralogs in lemurs arose independently. Finally, we identify errors in database interpretation as the source of controversies concerning gene conversion. These analyses provide a model for the natural history of ADH1s that posits four ADH1 paralogs in the ancestor of Catarrhine and Platyrrhine primates, followed by the loss of an ADH1 paralog in the human lineage.

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<![CDATA[Positive Selection Shaped the Convergent Evolution of Independently Expanded Kallikrein Subfamilies Expressed in Mouse and Rat Saliva Proteomes]]> https://www.researchpad.co/article/5989da02ab0ee8fa60b74543

We performed proteomics studies of salivas from the genome mouse (C57BL/6 strain) and the genome rat (BN/SsNHsd/Mcwi strain). Our goal was to identify salivary proteins with one or more of three characteristics that may indicate that they have been involved in adaptation: 1) rapid expansion of their gene families; 2) footprints of positive selection; and/or 3) sex-limited expression. The results of our proteomics studies allow direct comparison of the proteins expressed and their levels between the sexes of the two rodent species. Twelve members of the Mus musculus species-specific kallikrein subfamily Klk1b showed sex-limited expression in the mouse saliva proteomes. By contrast, we did not find any of the Rattus norvegicus species-specific kallikrein subfamily Klk1c proteins in male or female genome rat, nor transcripts in their submandibular glands. On the other hand, we detected expression of this family as transcripts in the submandibular glands of both sexes of Sprague-Dawley rats. Using the CODEML program in the PAML package, we demonstrate that the two rodent kallikrein subfamilies have apparently evolved rapidly under the influence of positive selection that continually remodeled the amino acid sites on the same face in the members of the subfamilies. Thus, although their kallikrein subfamily expansions were independent, this evolutionary pattern has occurred in parallel in the two rodent species, suggesting a form of convergent evolution at the molecular level. On the basis of this new data, we suggest that the previous speculative function of the species-specific rodent kallikreins as important solely in wound healing in males be investigated further. In addition to or instead of that function, we propose that their sex-limited expression, coupled with their rapid evolution may be clues to an as-yet-undetermined interaction between the sexes.

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<![CDATA[Vocal Communications and the Maintenance of Population Specific Songs in a Contact Zone]]> https://www.researchpad.co/article/5989d9fcab0ee8fa60b72373

Bird song has been hypothesized to play a role in several important aspects of the biology of songbirds, including the generation of taxonomic diversity by speciation; however, the role that song plays in speciation within this group may be dependent upon the ability of populations to maintain population specific songs or calls in the face of gene flow and external cultural influences. Here, in an exploratory study, we construct a spatially explicit model of population movement to examine the consequences of secondary contact of populations singing distinct songs. We concentrate on two broad questions: 1) will population specific songs be maintained in a contact zone or will they be replaced by shared song, and 2) what spatial patterns in the distribution of songs may result from contact? We examine the effects of multiple factors including song-based mating preferences and movement probabilities, oblique versus paternal learning of song, and both cultural and genetic mutations. We find a variety of conditions under which population specific songs can be maintained, particularly when females have preferences for their population specific songs, and we document many distinct patterns of song distribution within the contact zone, including clines, banding, and mosaics.

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<![CDATA[Pre-Existing Isoniazid Resistance, but Not the Genotype of Mycobacterium Tuberculosis Drives Rifampicin Resistance Codon Preference in Vitro]]> https://www.researchpad.co/article/5989da72ab0ee8fa60b95575

Both the probability of a mutation occurring and the ability of the mutant to persist will influence the distribution of mutants that arise in a population. We studied the interaction of these factors for the in vitro selection of rifampicin (RIF)-resistant mutants of Mycobacterium tuberculosis. We characterised two series of spontaneous RIF-resistant in vitro mutants from isoniazid (INH)-sensitive and -resistant laboratory strains and clinical isolates, representing various M. tuberculosis genotypes. The first series were selected from multiple parallel 1 ml cultures and the second from single 10 ml cultures. RIF-resistant mutants were screened by Multiplex Ligation-dependent Probe Amplification (MLPA) or by sequencing the rpoB gene. For all strains the mutation rate for RIF resistance was determined with a fluctuation assay. The most striking observation was a shift towards rpoB-S531L (TCG→TTG) mutations in a panel of laboratory-generated INH-resistant mutants selected from the 10-ml cultures (p<0.001). All tested strains showed similar mutation rates (1.33×10−8 to 2.49×10−7) except one of the laboratory-generated INH mutants with a mutation rate measured at 5.71×10−7, more than 10 times higher than that of the INH susceptible parental strain (5.46–7.44×10−8). No significant, systematic difference in the spectrum of rpoB-mutations between strains of different genotypes was observed. The dramatic shift towards rpoB-S531L in our INH-resistant laboratory mutants suggests that the relative fitness of resistant mutants can dramatically impact the distribution of (subsequent) mutations that accumulate in a M. tuberculosis population, at least in vitro. We conclude that, against specific genetic backgrounds, certain resistance mutations are particularly likely to spread. Molecular screening for these (combinations of) mutations in clinical isolates could rapidly identify these particular pathogenic strains. We therefore recommend that isolates are screened for the distribution of resistance mutations, especially in regions that are highly endemic for (multi)drug resistant tuberculosis.

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<![CDATA[The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes]]> https://www.researchpad.co/article/5989dabfab0ee8fa60baff1d

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.

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