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in category evolutionary biology
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1,730 downloads evolutionary biology
It has been shown that optimal controller synthesis for positive systems can be formulated as a linear program. Leveraging these results, we propose a scalable iterative algorithm for the systematic design of sparse, small gain feedback strategies that stabilize the evolutionary dynamics of a generic disease model. We achieve the desired feedback structure by augmenting the optimization problems with l1 and l2 regularization terms, and illustrate our method on an example inspired by an experimental study aimed at finding appropriate HIV neutralizing antibody therapy combinations in the presence of escape mutants.
1,730 downloads evolutionary biology
The Bogota Sunangel (Heliangelus zusii) was described based on a historical specimen lacking locality data as a striking - and potentially extinct - new species of hummingbird more than two decades ago. However, it was considered a dubious taxon by some researchers until a molecular study with strong species-level taxon sampling revealed its phylogenetic affinities and validated its status as a distinct species. We reanalysed existing mitochondrial DNA data together with a new data set sampling multiple populations of the Long-tailed Sylph (Aglaiocercus kingii), a species broadly distributed in the Andes of South America. In contrast to previous work, we found that H. zusii shares a haplotype with specimens of A. kingii from the Eastern Cordillera of Colombia, which is phylogenetically nested within a clade formed by populations of A. kingii from the Colombian Andes. These results suggest that H. zusii is not a distinct species, but is most likely the result of hybridization between a female A. kingii and a male of another hummingbird species. These findings highlight the importance of thorough taxonomic and geographic sampling when assessing the likelihood of hybrid origin of an organism, particularly in cases potentially involving wide-ranging species in areas where deep phylogeographic structure is likely.
1,722 downloads evolutionary biology
Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic ‘landscape’ of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a recent radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation ( FST ) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Thus, combined with existing evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the genomic basis of adaptation and speciation in this system. Author summary What can patterns of genome-wide variation tell us about the speciation process? The answer to this question depends upon our ability to infer the evolutionary processes underlying these patterns. This, however, is difficult, because many processes can leave similar footprints, but some have nothing to do with speciation per se . For example, many studies have found highly heterogeneous levels of genetic differentiation when comparing the genomes of emerging species. These patterns are often referred to as differentiation ‘landscapes’ because they appear as a rugged topography of ‘peaks’ and ‘valleys’ as one scans across the genome. It has often been argued that selection against deleterious mutations, a process referred to as background selection, is primarily responsible for shaping differentiation landscapes early in speciation. If this hypothesis is correct, then it is unlikely that patterns of differentiation will reveal much about the genomic basis of speciation. However, using genome sequences from nine emerging species of monkeyflower coupled with simulations of genomic divergence, we show that it is unlikely that background selection is the primary architect of these landscapes. Rather, differentiation landscapes have probably been shaped by adaptation and gene flow, which are processes that are central to our understanding of speciation. Therefore, our work has important implications for our understanding of what patterns of differentiation can tell us about the genetic basis of adaptation and speciation.
1,720 downloads evolutionary biology
Hyphae represent a hallmark structure of multicellular fungi with immense importance in their life cycle, including foraging for nutrients, reproduction, or virulence. Hypha morphogenesis has been the subject to intense interest, yet, the origins and genetic underpinning of the evolution of hyphae are hardly known. Using comparative genomics, we here show that the emergence of hyphae correlates with multiple types of genetic changes, including alterations of gene structure, gene family diversification as well as co-option and exaptation of ancient eukaryotic genes (e.g. phagocytosis-related genes). Half of the gene families involved in hypha morphogenesis have homologs in unicellular fungi and non-fungal eukaryotes and show little or no duplications coincident with the origin of multicellular hyphae. Considerable gene family diversification was observed only in transcriptional regulators and genes related to cell wall synthesis and modification. Despite losing 35-46% of their genes, yeasts retained significantly more multicellularity-related genes than expected by chance. We identified 414 gene families that evolved in a correlated fashion with hyphal multicellularity and may have contributed to its evolution. Contrary to most multicellular lineages, the origin of hyphae did not correlate with the expansion of gene families encoding kinases, receptors or adhesive proteins. Our analyses suggest that fungi took a unique route to multicellularity that involved limited gene family diversification and extensive co-option of ancient eukaryotic genes.
1,709 downloads evolutionary biology
In the late 1980s, Smith, Bruhn, and Anderson discovered a genetic individual of the fungus Armillaria gallica that extended over 37 hectares of forest floor and encompassed hundreds of tree root systems in Northern Michigan. Based on observed growth rates, the individual was estimated to be at least 1500 years old with a mass of 100,000 kg. The conclusion was that the Michigan individual of A. gallica was among the largest and oldest organisms on earth, a remarkable claim given that Armillaria is essentially a microorganism existing largely as microscopic hyphae embedded in their substrate. Nearly three decades on, we returned to the site of the large Michigan individual with the tools of whole-genome sequencing. Here, we show (a) that the large individual is still alive on its original site and (b) that mutation has occurred within the somatic cells of the large individual, reflecting its historical pattern of growth from a single point. The overall rate of mutation, however, was extremely low. On the spectrum of mutability in somatic cells, Armillaria occupies the extreme of stability, opposite the extreme of instability as typified by cancer.
1,703 downloads evolutionary biology
Left-handedness is a costly, sexually dimorphic trait found at low frequencies in all human populations. How the handedness polymorphism is maintained is unclear. The fighting hypothesis argues that left-handed men have a negative frequency-dependent advantage in violent intrasexual competition giving them a selective advantage. In support of this, many studies have found that left-handed men are overrepresented among modern professional fighters, but studies typically find no difference in fighting success between left and right-handed fighters. We studied over 13,800 professional boxers and mixed martial artists of varying abilities in three of the largest samples to test this hypothesis to date, finding robust evidence that left-handed fighters have greater fighting success. This held for both male and female fighters, and for both percentage of fights won and an objective measure of fighting ability. We replicated previous results showing that left-handed fighters are strongly overrepresented in professional combat sports, but left-handed fighters did not show greater variance in fighting ability, a hypothesis suggested in previous studies. Overall we find strong evidence consistent with the fighting hypothesis.
1,692 downloads evolutionary biology
Mammalian females pay high energetic costs for reproduction, the greatest of which is imposed by lactation. The synthesis of milk requires, in part, the mobilization of bodily reserves to nourish developing young. Numerous hypotheses have been advanced to predict how mothers will differentially invest in sons and daughters, however few studies have addressed sex-biased milk synthesis. Here we leverage the dairy cow model to investigate such phenomena. Using 2.39 million lactation records from 1.49 million dairy cows, we demonstrate that the sex of the fetus influences the capacity of the mammary gland to synthesize milk during lactation. Cows favor daughters, producing significantly more milk for daughters than for sons across lactation. Using a sub-sample of this dataset (N=113,750 subjects) we further demonstrate that the effects of fetal sex interact dynamically across parities, whereby the sex of the fetus being gestated can enhance or diminish the production of milk during an established lactation. Moreover the sex of the fetus gestated on the first parity has persistent consequences for milk synthesis on the subsequent parity. Specifically, gestation of a daughter on the first parity increases milk production by ~445 kg over the first two lactations. Our results identify a dramatic and sustained programming of mammary function by offspring in utero. Nutritional and endocrine conditions in utero are known to have pronounced and long-term effects on progeny, but the ways in which the progeny has sustained physiological effects on the dam have received little attention to date.
1,690 downloads evolutionary biology
Danièle Filiault, Evangeline S. Ballerini, Terezie Mandáková, Gökçe Aköz, Nathan Derieg, Jeremy Schmutz, Jerry Jenkins, Jane Grimwood, Shengqiang Shu, Richard D. Hayes, Uffe Hellsten, Kerrie Barry, Juying Yan, Sirma Mihaltcheva, Miroslava Karafiátová, Viktoria Nizhynska, Martin A. Lysak, Scott A. Hodges, Magnus Nordborg
The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea "Goldsmith", complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analysis reveals extensive allele sharing among species, and sheds light on the complex process of radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differed from that of the rest of the genome --- a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
1,671 downloads evolutionary biology
Gigantism is the result of one lineage within a clade evolving extremely large body size relative to its small-bodied ancestors, a phenomenon observed numerous times in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to a genome-wide elevation of the ratio of non-synonymous to synonymous substitution rates (dN/dS) or mutation load. Second, gigantism is achieved through higher number of cells and higher rates of cell proliferation, thus increasing the likelihood of cancer. However, the incidence of cancer in gigantic animals is lower than the theoretical expectation, a phenomenon referred to as Peto's Paradox. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we sequenced the genome of the capybara, the world's largest living rodent. We found that dN/dS is elevated genome wide in the capybara, relative to other rodents, implying a higher mutation load. Conversely, a genome-wide scan for adaptive protein evolution in the capybara highlighted several genes involved in growth regulation by the insulin/insulin-like growth factor signaling (IIS) pathway. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T cell-mediated tumor suppression, offering a potential resolution to Peto's Paradox in this lineage. Gene interaction network analyses also revealed that size regulators function simultaneously as growth factors and oncogenes, creating an evolutionary conflict. Based on our findings, we hypothesize that gigantism in the capybara likely involved three evolutionary steps: 1) Increase in body size by cell proliferation through the ISS pathway, 2) coupled evolution of growth-regulatory and cancer-suppression mechanisms, possibly driven by intragenomic conflict, and 3) establishment of the T cell-mediated tumor suppression pathway as an anticancer adaptation. Interestingly, increased mutation load appears to be an inevitable outcome of an increase in body size.
1,666 downloads evolutionary biology
Throughout the past decade, studying ancient genomes provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.
1,664 downloads evolutionary biology
Human and octopus lineages are separated by over 500 million years of evolution, and show divergent anatomical patterns of brain organization. Moreover, while humans exhibit highly complex social behaviors, octopuses are thought to be largely asocial and solitary. Despite these differences, growing evidence suggests that ancient neurotransmitter systems are shared across vertebrate and invertebrate species, and in many cases enable overlapping functions. Here we provide evidence that, as in humans, the atypical amphetamine derivative (+/-)-3,4-methylendioxymethamphetamine (MDMA) enhances acute prosocial behaviors in Octopus bimaculoides. This finding is paralleled by the evolutionary conservation of the serotonin transporter (SERT, encoded by the Slc6A4 gene) binding site of MDMA in the O. bimaculoides genome. Taken together, these data provide evidence that the neural mechanisms subserving social behaviors exist in O. bimaculoides, and indicate that the role of serotonergic neurotransmission in regulating social behaviors is evolutionarily conserved.
1,649 downloads evolutionary biology
Background and Objectives: Whole genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to iden- tify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterised infectious periods, epidemiological and clinical meta-data which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. Methodology: We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks. Results: We show that different transmission patterns result in quantitatively different phyloge- netic tree shapes. We describe topological features that summarize a phylogenys structure and find that computational classifiers based on these are capable of predicting an outbreaks transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. Conclusions: and implications There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission, and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.
1,641 downloads evolutionary biology
Karina Gutiérrez-García, Edder D. Bustos-Díaz, José Antonio Corona-Gómez, Hilda E. Ramos-Aboites, Nelly Sélem-Mojica, Pablo Cruz-Morales, Miguel A. Pérez-Farrera, Francisco Barona-Gómez, Angélica Cibrián-Jaramillo
Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Nostoc, and Rhizobium species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities and used for whole-genome inferences that suggest two Dioon-specific monophyletic groups and a level of specialization characteristic of co-evolved symbiotic relationships. In agreement with this, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with metabolite profiling using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.
1,638 downloads evolutionary biology
There is an overwhelming archeological and genetic evidence that modern speech apparatus was acquired by hominins by 600,000 years ago 1. On the other hand, artifacts signifying modern imagination, such as (1) composite figurative arts, (2) bone needles with an eye, (3) construction of dwellings, and (4) elaborate burials arose not earlier than 70,000 years ago 2. It remains unclear (1) why there was a long gap between acquisition of modern speech apparatus and modern imagination, (2) what triggered the acquisition of modern imagination 70,000 years ago, and (3) what role language might have played in this process. Our research into evolutionary origin of modern imagination has been driven by the observation of a temporal limit for the development of a particular component of imagination. Modern children not exposed to recursive language in early childhood never acquire the type of active constructive imagination called Prefrontal Synthesis (PFS). Unlike vocabulary and grammar acquisition, which can be learned throughout one's lifetime, there is a strong critical period for the development of PFS and individuals not exposed to recursive language in early childhood can never acquire PFS as adults. Their language will always lack understanding of spatial prepositions and recursion that depend on the PFS ability. In a similar manner, early hominins would not have been able to learn recursive language as adults and, therefore, would not be able to teach recursive language to their children. Thus, the existence of a strong critical period for PFS acquisition creates an evolutionary barrier for behavioral modernity. An evolutionary mathematical model suggests that a synergistic confluence of three events (1) a genetic mutation that extended the critical period by slowing down the prefrontal cortex development simultaneously in two or more children, (2) invention of recursive elements of language, such as spatial prepositions, by these children and (3) their dialogic communications using these recursive elements, resulted in concurrent conversion of a non-recursive communication system of their parents to recursive language and acquisition of PFS around 70,000 years ago.
1,636 downloads evolutionary biology
The palmaris longus muscle is widely recognized for its notable variability in living humans. These variations include not only muscle belly reversal, distinct double muscle bellies, duplication and triplication, but also total uni- or bilateral agenesis (absence). A review of the literature and data novel to this study illustrate that different populations of humans exhibit remarkable variation in the frequency of palmaris longus agenesis, from less than 5% of Chinese to nearly 65% of Indians. Comparative dissection-derived data reveal substantial variation in palmaris longus agenesis (PLA) in populations of extant humans (H. sapiens), chimpanzees (Pan spp.), and gorillas (Gorilla spp.) - but not orangutans (Pongo spp.), which apparently always develop this muscle. From this pattern, we infer that palmaris longus is undergoing non-adaptive, stochastic evolution in the extant African Homininae, while it continues to have adaptive purpose in Pongo, likely due to the orangutans' greater degree of arboreality than the African apes and humans. Clinical evidence supports this conclusion, at least as it applies to humans. This study highlights the utility of comparative soft tissue data collection and interpretation in elucidating the evolution of anatomical structures that do not fossilize.
1,633 downloads evolutionary biology
We consider a model of multilevel selection and the evolution of institutions that distribute power in the form of influence in a group's collective interactions with other groups. In the absence of direct group-level interactions, groups with the most cooperative members will outcompete less cooperative groups, while within any group the least cooperative members will be the most successful. Introducing group-level interactions, however, such as raiding or warfare, changes the selective landscape for groups. Our model suggests that as the global population becomes more integrated and the rate of intergroup conflict increases, selection increasingly favors unequally distributed power structures, where individual influence is weighted by acquired resources. The advantage to less democratic groups rests in their ability to facilitate selection for cooperative strategies – involving cooperation both among themselves and with outsiders – in order to produce the resources necessary to fuel their success in inter-group conflicts, while simultaneously selecting for leaders (and corresponding collective behavior) who are unburdened with those same prosocial norms. The coevolution of cooperative social norms and institutions of power facilitates the emergence of a leadership class of the selfish and has implications for theories of inequality, structures of governance, non-cooperative personality traits, and hierarchy. Our findings suggest an amendment to the well-known doctrine of multilevel selection that "Selfishness beats altruism within groups. Altruistic groups beat selfish groups." In an interconnected world, altruistic groups led by selfish individuals can beat them both.
1,626 downloads evolutionary biology
The plant immune system is innate, encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. We showed that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncovered a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events revealed that homologous receptors can be fused to diverse domains. Furthermore, we discovered a 43 amino acids long motif that was associated with this dominant integration clade and was located immediately upstream of the fusion site. Sequence analysis revealed that DNA transposition and/or ectopic recombination are the most likely mechanisms of NLR-ID formation. The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen baits.
1,620 downloads evolutionary biology
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and, moreover, can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this admixture event contributed to genome-wide patterns of parallel clinal variation. The pervasive effects of admixture meant that only a handful of loci could be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation in D. melanogaster and provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as some temperate endemics.
1,618 downloads evolutionary biology
How animals evolved from their single-celled ancestors over 600 million years ago is poorly understood. Comparisons of genomes from animals and their closest relatives, choanoflagellates, filastereans and ichthyosporeans, have recently revealed the genomic landscape of animal origins. However, the cell and developmental biology of the first animals have been less well examined. Using principles from evolutionary cell biology, we reason that the last common ancestor of animals and choanoflagellates (the "Urchoanozoan") used a collar complex, a flagellum surrounded by a microvillar collar, to capture bacterial prey. The origin of animal multicellularity likely occurred through the modification of pre-existing mechanisms for extracellular matrix synthesis and regulation of cytokinesis. The progenitors of animals likely developed clonally through serial division of flagellated cells, giving rise to sheets of cells that folded into spheres by a morphogenetic process comparable to that seen in modern choanoflagellate rosettes and calcareous sponge embryos. Finally, we infer that cell differentiation evolved in the animal stem-lineage by a combination of three mechanisms: division of labor from ancient plurifunctional cell types, conversion of temporally segregated phenotypes into spatially segregated cell types, and functional innovation.
1,615 downloads evolutionary biology
For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and describe a hidden generality amongst these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law where both depend on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time-dependency is unlikely to be a result of simple statistical artifacts. As such, this time-scaling is likely a genuine feature of the Tree of Life -- hinting that the dynamics of biodiversity over deep time may be driven, in part, by surprisingly simple and general principles.
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