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Evolutionary Biology
Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction.
Feb 16, 2019   Scientific Reports
Ríos L, Kivell TL, Lalueza-Fox C, Estalrrich A, García-Tabernero A, Huguet R, Quintino Y, de la Rasilla M, Rosas A
Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction.
Feb 16, 2019
Scientific Reports
Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.
Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes.
Feb 12, 2019   Archives Of Virology
Zhang L, Shang J, Jia Q, Li K, Yang H, Liu H, Tang Z, Chang X, Zhang M, Wang W, Yang W
Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes.
Feb 12, 2019
Archives Of Virology
Soybean mosaic virus (SMV) is one of the major pathogens causing serious soybean losses. Little is known about the genetic structure and evolutionary biology of the SMV population in southwestern China. In this study, 29 SMV isolates were obtained from Sichuan Province, and the genomic regions encoding the first protein (P1) and coat protein (CP) were sequenced. Combined with SMV isolates from the southeastern and northeastern regions of China, the genetic and molecular evolution of SMV was studied. Recombination analysis revealed that intraspecific and interspecific recombination had occurred in the SMV population. A phylogenetic tree based on the P1 gene reflected the geographic origin of the non-interspecific recombinant SMV (SMV-NI), while a tree based on the CP gene did not. Though frequent gene flow of the SMV-NI populations was found between the southeastern and northeastern populations, the southwestern population was relatively independent. Genetic differentiation was significant between the SMV interspecific recombinant (SMV-RI) and the non-interspecific recombinant (SMV-NI) populations. It was interesting to note that there was an almost identical recombination breakpoint in SMV-RI and Watermelon mosaic virus (WMV). Population dynamics showed that SMV-RI might be in an expanding state, while the SMV-NI population is relatively stable.
Quorums enable optimal pooling of independent judgements in biological systems.
Feb 16, 2019   ELife
Marshall JA, Kurvers RH, Krause J, Wolf M
Quorums enable optimal pooling of independent judgements in biological systems.
Feb 16, 2019
ELife
Collective decision-making is ubiquitous, and majority-voting and the Condorcet Jury Theorem pervade thinking about collective decision-making. Thus, it is typically assumed that majority-voting is the best possible decision mechanism, and that scenarios exist where individually-weak decision-makers should not pool information. Condorcet and its applications implicitly assume that only one kind of error can be made, yet signal detection theory shows two kinds of errors exist, 'false positives' and 'false negatives'. We apply signal detection theory to collective decision-making to show that majority voting is frequently sub-optimal, and can be optimally replaced by quorum decision-making. While quorums have been proposed to resolve within-group conflicts, or manage speed-accuracy trade-offs, our analysis applies to groups with aligned interests undertaking single-shot decisions. Our results help explain the ubiquity of quorum decision-making in nature, relate the use of sub- and super-majority quorums to decision ecology, and may inform the design of artificial decision-making systems.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Distinguishing three distinct biogeographic regions with an in-house developed 39-AIM-InDel panel and further admixture proportion estimation for Uyghurs.
Feb 13, 2019   Electrophoresis
Lan Q, Shen C, Jin X, Guo Y, Xie T, Chen C, Cui W, Fang Y, Yang G, Zhu B
Distinguishing three distinct biogeographic regions with an in-house developed 39-AIM-InDel panel and further admixture proportion estimation for Uyghurs.
Feb 13, 2019
Electrophoresis
In the forensic field, ancestry-informative markers showing remarkable allele frequency discrepancies can be useful in deducing the likely ancestral origin of a person or estimating the ancestry component proportions of admixed populations or individuals. Diallelic SNPs are genetic markers commonly used for ancestry inference, but the genotyping methods of SNPs fail to fulfil the demands of cost-effectiveness and simplicity of experimental manipulation. To overcome the limitations, a 39 ancestry-informative InDels multiplex panel was developed in the present study to perform ancestry assignment of individuals from three distinct biogeographic regions (African, European, East Asian). And in the panel design, we also attempted to incorporate AIM-InDels exhibiting frequency differences in Han, Uyghur and Tibetan populations into the multiplex assay, further expecting to provide valuable information for refining ancestry inference within Chinese populations. Statistical analyses were performed to estimate efficiency of this panel in clustering individuals from three continents mentioned above into their corresponding populations, which indicated potential of the panel in ancestry inference. Besides, we also estimated the ancestral component proportions of Uyghur group and STRUCTURE analysis revealed that Uyghurs from Urumchi city of northern Xinjiang exhibited a distinctly admixed pattern of East Asian and European ancestry components with a ratio of 49:44, reflecting the relatively higher East Asian ancestry components contribution in the gene pool of the Uyghur group. This article is protected by copyright. All rights reserved.
kuenm: an R package for detailed development of ecological niche models using Maxent.
Feb 16, 2019   PeerJ
Cobos ME, Peterson AT, Barve N, Osorio-Olvera L
kuenm: an R package for detailed development of ecological niche models using Maxent.
Feb 16, 2019
PeerJ
Background: Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way. Results: This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric. Discussion: Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.
Integrating experimental and distribution data to predict future species patterns.
Feb 16, 2019   Scientific Reports
Kotta J, Vanhatalo J, Jänes H, Orav-Kotta H, Rugiu L, Jormalainen V, Bobsien I, Viitasalo M, Virtanen E, Sandman AN, Isaeus M, Leidenberger S, Jonsson PR, Johannesson K
Integrating experimental and distribution data to predict future species patterns.
Feb 16, 2019
Scientific Reports
Predictive species distribution models are mostly based on statistical dependence between environmental and distributional data and therefore may fail to account for physiological limits and biological interactions that are fundamental when modelling species distributions under future climate conditions. Here, we developed a state-of-the-art method integrating biological theory with survey and experimental data in a way that allows us to explicitly model both physical tolerance limits of species and inherent natural variability in regional conditions and thereby improve the reliability of species distribution predictions under future climate conditions. By using a macroalga-herbivore association (Fucus vesiculosus - Idotea balthica) as a case study, we illustrated how salinity reduction and temperature increase under future climate conditions may significantly reduce the occurrence and biomass of these important coastal species. Moreover, we showed that the reduction of herbivore occurrence is linked to reduction of their host macroalgae. Spatial predictive modelling and experimental biology have been traditionally seen as separate fields but stronger interlinkages between these disciplines can improve species distribution projections under climate change. Experiments enable qualitative prior knowledge to be defined and identify cause-effect relationships, and thereby better foresee alterations in ecosystem structure and functioning under future climate conditions that are not necessarily seen in projections based on non-causal statistical relationships alone.
A galling insect activates plant reproductive programs during gall development.
Feb 16, 2019   Scientific Reports
Schultz JC, Edger PP, Body MJA, Appel HM
A galling insect activates plant reproductive programs during gall development.
Feb 16, 2019
Scientific Reports
Many insect species have acquired the ability to redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We tested this hypothesis using RNA sequencing to quantify the transcriptional responses of wild grapevine (Vitis riparia) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology categories were significantly enriched in developing galls, and that expression of many candidate genes involved in floral development were significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall appears to be phenotypically and transcriptionally similar to the carpel, due to the parasite hijacking underlying genetic machinery in the host plant.
Vitamin E Function in Stress Sensing and Signaling in Plants.
Feb 12, 2019   Developmental Cell
Munné-Bosch S
Vitamin E Function in Stress Sensing and Signaling in Plants.
Feb 12, 2019
Developmental Cell
Vitamin E is involved in heat stress acclimation. In this issue of Developmental Cell, Fang et al. (2018) uncover a new link between Vitamin E and plant retrograde signaling and show that vitamin E is required for the accumulation of 3'-phosphoadenosine 5'-phosphate, an inhibitor of exoribonucleases, to protect microRNAs from degradation.
Signals of variation in human mutation rate at multiple levels of sequence context.
Feb 12, 2019   Molecular Biology And Evolution
Aikens RC, Johnson KE, Voight BF
Signals of variation in human mutation rate at multiple levels of sequence context.
Feb 12, 2019
Molecular Biology And Evolution
Our understanding of the human mutation rate helps us build evolutionary models and interpret patterns of genetic variation observed in human populations. Recent work indicates that the frequencies of specific polymorphism types have been elevated in Europe, and that many more, subtler signatures of global polymorphism variation may yet remain unidentified. Here, we present an analysis of the 1,000 Genomes Project supported by analysis in the Simons Genome Diversity Panel, suggesting additional putative signatures of mutation rate variation across populations and the extent to which they are shaped by local sequence context. First, we compiled a list of the most significantly variable polymorphism types in a cross-continental statistical test. Clustering polymorphisms together, we observe three sets that showed distinct shared patterns of relative enrichment among ancestral populations, and we characterize each one of these putative 'signatures' of polymorphism variation. For three of these signatures, we found that a single flanking base pair of sequence context was sufficient to determine the majority of enrichment or depletion of a polymorphism type. However, local genetic context up to 2-3 base pairs away contributes additional variability and may help to interpret a previously noted enrichment of certain polymorphism types in some East Asian groups. Moreover, considering broader local genetic context highlights patterns of polymorphism variation which were not captured by previous approaches. Building our understanding of mutation rate in this way can help us to construct more accurate evolutionary models and better understand the mechanisms that underlie genetic change.
Age of both parents influences reproduction and egg dumping behavior in Drosophila melanogaster.
Feb 12, 2019   The Journal Of Heredity
Mossman JA, Mabeza RMS, Blake E, Mehta N, Rand DM
Age of both parents influences reproduction and egg dumping behavior in Drosophila melanogaster.
Feb 12, 2019
The Journal Of Heredity
Trans-generational maternal effects have been shown to influence a broad range of offspring phenotypes. However, very little is known about paternal trans-generational effects. Here, we tested the trans-generational effects of maternal and paternal age, and their interaction, on daughter and son reproductive fitness in Drosophila melanogaster. We found significant effects of parent ages on offspring reproductive fitness over 10 days post-fertilization. In daughters, older (45 days old) mothers conferred lower reproductive fitness compared to younger mothers (3 days old). In sons, father's age significantly affected reproductive fitness. The effects of two old parents were additive in both sexes and reproductive fitness was lowest when the focal individual had two old parents. Interestingly, daughter fertility was sensitive to father's age but son fertility was insensitive to mother's age, suggesting a sexual asymmetry in trans-generational effects. We found the egg-laying dynamics in daughters dramatically shaped this relationship. Daughters with two old parents demonstrated an extreme egg dumping behavior on day one and laid >2.35 X the number of eggs than the other three age class treatments. Our study reveals significant trans-generational maternal and paternal age effects on fertility and an association with a novel egg laying behavioral phenotype in Drosophila.
Extracellular peptide Kratos restricts cell death during vascular development and stress in Arabidopsis.
Feb 12, 2019   Journal Of Experimental Botany
Escamez S, Stael S, Vainonen J, Willems P, Jin H, Kimura S, Van Breusegem F, Gevaert K, Wrzaczek M, Tuominen H
Extracellular peptide Kratos restricts cell death during vascular development and stress in Arabidopsis.
Feb 12, 2019
Journal Of Experimental Botany
During plant vascular development, xylem tracheary elements (TEs) form water-conducting, empty pipes through genetically regulated cell death. Cell death is prevented from spreading to non-TEs by unidentified intercellular mechanisms, downstream of METACASPASE9 (MC9)-mediated regulation of autophagy in TEs. Here, we identified differentially abundant extracellular peptides in vascular-differentiating wild type and MC9-downregulated Arabidopsis cell suspensions. The peptide Kratos rescued the abnormally high ectopic non-TE death resulting from either MC9 knockout or TE-specific overexpression of the ATG5 autophagy protein during experimentally induced vascular differentiation in Arabidopsis cotyledons. Kratos also reduced cell death following mechanical damage and extracellular ROS production in Arabidopsis leaves. Stress-induced but not vascular non-TE cell death was enhanced by another identified peptide, Bia. Bia is therefore reminiscent of several known plant cell death-inducing peptides acting as damage-associated molecular patterns. In contrast, Kratos plays a novel extracellular cell survival role in the context of development and during stress response.
Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.
Feb 12, 2019   PLoS Genetics
Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J
Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.
Feb 12, 2019
PLoS Genetics
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
Country activities of Global Alliance against Chronic Respiratory Diseases (GARD): focus presentations at the 11th GARD General Meeting, Brussels.
Feb 14, 2019   Journal Of Thoracic Disease
Bousquet J, Mohammad Y, Bedbrook A, To T, McGihon R,   . . . . . .   , Shaaban R, Arrais M, do Céu Teixeira M, Conceição C, Ferrinho P
Globally consistent influences of seasonal precipitation limit grassland biomass response to elevated CO2.
Feb 09, 2019   Nature Plants Add nature.com free-link Cancel
Hovenden MJ, Leuzinger S, Newton PCD, Fletcher A, Fatichi S,   . . . . . .   , Niklaus PA, Song J, Wan S, Classen AT, Langley JA
Globally consistent influences of seasonal precipitation limit grassland biomass response to elevated CO2.
Feb 09, 2019
Nature Plants
Rising atmospheric carbon dioxide concentration should stimulate biomass production directly via biochemical stimulation of carbon assimilation, and indirectly via water savings caused by increased plant water-use efficiency. Because of these water savings, the CO2 fertilization effect (CFE) should be stronger at drier sites, yet large differences among experiments in grassland biomass response to elevated CO2 appear to be unrelated to annual precipitation, preventing useful generalizations. Here, we show that, as predicted, the impact of elevated CO2 on biomass production in 19 globally distributed temperate grassland experiments reduces as mean precipitation in seasons other than spring increases, but that it rises unexpectedly as mean spring precipitation increases. Moreover, because sites with high spring precipitation also tend to have high precipitation at other times, these effects of spring and non-spring precipitation on the CO2 response offset each other, constraining the response of ecosystem productivity to rising CO2. This explains why previous analyses were unable to discern a reliable trend between site dryness and the CFE. Thus, the CFE in temperate grasslands worldwide will be constrained by their natural rainfall seasonality such that the stimulation of biomass by rising CO2 could be substantially less than anticipated.
The Long and Short of Hearing in the Mosquito Aedes aegypti.
Feb 12, 2019   Current Biology : CB
Menda G, Nitzany EI, Shamble PS, Wells A, Harrington LC, Miles RN, Hoy RR
The Long and Short of Hearing in the Mosquito Aedes aegypti.
Feb 12, 2019
Current Biology : CB
Mating behavior in Aedes aegypti mosquitoes occurs mid-air and involves the exchange of auditory signals at close range (millimeters to centimeters) [1-6]. It is widely assumed that this intimate signaling distance reflects short-range auditory sensitivity of their antennal hearing organs to faint flight tones [7, 8]. To the contrary, we show here that male mosquitoes can hear the female's flight tone at surprisingly long distances-from several meters to up to 10 m-and that unrestrained, resting Ae. aegypti males leap off their perches and take flight when they hear female flight tones. Moreover, auditory sensitivity tests of Ae. aegypti's hearing organ, made from neurophysiological recordings of the auditory nerve in response to pure-tone stimuli played from a loudspeaker, support the behavioral experiments. This demonstration of long-range hearing in mosquitoes overturns the common assumption that the thread-like antennal hearing organs of tiny insects are strictly close-range ears. The effective range of a hearing organ depends ultimately on its sensitivity [9-13]. Here, a mosquito's antennal ear is shown to be sensitive to sound levels down to 31 dB sound pressure level (SPL), translating to air particle velocity at nanometer dimensions. We note that the peak of energy of the first formant of the vowels of the human speech spectrum range from about 200-1,000 Hz and is typically spoken at 45-70 dB SPL; together, they lie in the sweet spot of mosquito hearing. VIDEO ABSTRACT.
Contrasting patterns of molecular evolution in metazoan germ line genes.
Feb 12, 2019   BMC Evolutionary Biology
Whittle CA, Extavour CG
Contrasting patterns of molecular evolution in metazoan germ line genes.
Feb 12, 2019
BMC Evolutionary Biology
BACKGROUND: Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm (inheritance) or from an ancestral mechanism of inductive cell-cell signalling (induction). Numerous genes involved in germ line specification and development have been identified and functionally studied. However, little is known about the molecular evolutionary dynamics of germ line genes in metazoan model systems. RESULTS: Here, we studied the molecular evolution of germ line genes within three metazoan model systems. These include the genus Drosophila (N=34 genes, inheritance), the fellow insect Apis (N=30, induction), and their more distant relative Caenorhabditis (N=23, inheritance). Using multiple species and established phylogenies in each genus, we report that germ line genes exhibited marked variation in the constraint on protein sequence divergence (dN/dS) and codon usage bias (CUB) within each genus. Importantly, we found that de novo lineage-specific inheritance (LSI) genes in Drosophila (osk, pgc) and in Caenorhabditis (pie-1, pgl-1), which are essential to germ plasm functions under the derived inheritance mode, displayed rapid protein sequence divergence relative to the other germ line genes within each respective genus. We show this may reflect the evolution of specialized germ plasm functions and/or low pleiotropy of LSI genes, features not shared with other germ line genes. In addition, we observed that the relative ranking of dN/dS and of CUB between genera were each more strongly correlated between Drosophila and Caenorhabditis, from different phyla, than between Drosophila and its insect relative Apis, suggesting taxonomic differences in how germ line genes have evolved. CONCLUSIONS: Taken together, the present results advance our understanding of the evolution of animal germ line genes within three well-known metazoan models. Further, the findings provide insights to the molecular evolution of germ line genes with respect to LSI status, pleiotropy, adaptive evolution as well as PGC-specification mode.
Detection of RNA-Dependent RNA Polymerase of Hubei Reo-Like Virus 7 by Next-Generation Sequencing in Aedes aegypti and Culex quinquefasciatus Mosquitoes from Brazil.
Feb 12, 2019   Viruses
Ribeiro GO, Monteiro FJC, Rego MODS, Ribeiro ESD, Castro DF, Caseiro MM, Souza Marinho RDS, Komninakis SV, Witkin SS, Deng X, Delwart E, Sabino EC, da Costa AC, Leal É
Detection of RNA-Dependent RNA Polymerase of Hubei Reo-Like Virus 7 by Next-Generation Sequencing in Aedes aegypti and Culex quinquefasciatus Mosquitoes from Brazil.
Feb 12, 2019
Viruses
Advancements in next-generation sequencing and bioinformatics have expanded our knowledge of the diversity of viruses (pathogens and non-pathogens) harbored by mosquitoes. Hubei reo-like virus 7 (HRLV 7) was recently detected by the virome analysis of fecal samples from migratory birds in Australia. We now report the detection of RNA-dependent RNA polymerase sequences of HRLV 7 in pools of Aedes aegypti and Culex quinquefasciatus mosquitoes species from the Brazilian Amazon forest. Phylogenetic inferences indicated that all HRLV 7 strains fall within the same independent clade. In addition, HRLV 7 shared a close ancestral lineage with the Dinovernavirus genus of the Reoviridae family. Our findings indicate that HRLV 7 is present in two species of mosquitoes.
Characterization, evolution, and expression analysis of TLR7 gene subfamily members in Mastacembelus armatus (Synbranchiformes: Mastacembelidae).
Feb 11, 2019   Developmental And Comparative Immunology
Han C, Li Q, Liu J, Hao Z, Huang J, Zhang Y
Characterization, evolution, and expression analysis of TLR7 gene subfamily members in Mastacembelus armatus (Synbranchiformes: Mastacembelidae).
Feb 11, 2019
Developmental And Comparative Immunology
TLR7 subfamily members are important pattern recognition receptors participating in the recognition of pathogen-associated molecular patterns. In this study, we successfully identified 3 members of TLR7 subfamily from the spiny eel Mastacembelus armatus (MaTLR7, MaTLR8 and MaTLR9). The amino acid sequence identities of MaTLR7 and MaTLR8 with Monopterus albus TLR7 were 87.2% and 76.5%, respectively and the identity of MaTLR9 with Seriola lalandi TLR9 was 74.7%. The phylogenetic analysis revealed MaTLRs showed close relationship to other species in Synbranchiformes or Perciformes. Quantitative real-time PCR analysis revealed that they were expressed in all tested tissues and higher expression was found in spleen or gill. After infection with Aeromonas veronii, expression of MaTLR7, MaTLR8 and MaTLR9 were all significantly downregulated in spleen and kidney. Evolutionary analysis suggested that the ancestral lineages of teleost TLR8 and TLR9 had been subject to positive selection pressures and multiple Maximum likelihood methods recovered 3 positively selected sites in teleost TLR7, 4 in TLR8 and 8 in TLR9. Domain distribution revealed most positively selected sites were located in leucine-rich repeat domain. Our results will contribute to better understanding the antibacterial mechanism of TLRs and their co-evolution with pathogens.
PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis.
Feb 11, 2019   PLoS Pathogens
Ramos Y, Rocha J, Hael AL, van Gestel J, Vlamakis H, Cywes-Bentley C, Cubillos-Ruiz JR, Pier GB, Gilmore MS, Kolter R, Morales DK
PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis.
Feb 11, 2019
PLoS Pathogens
Bacterial pathogens have evolved strategies that enable them to invade tissues and spread within the host. Enterococcus faecalis is a leading cause of local and disseminated multidrug-resistant hospital infections, but the molecular mechanisms used by this non-motile bacterium to penetrate surfaces and translocate through tissues remain largely unexplored. Here we present experimental evidence indicating that E. faecalis generates exopolysaccharides containing β-1,6-linked poly-N-acetylglucosamine (polyGlcNAc) as a mechanism to successfully penetrate semisolid surfaces and translocate through human epithelial cell monolayers. Genetic screening and molecular analyses of mutant strains identified glnA, rpiA and epaX as genes critically required for optimal E. faecalis penetration and translocation. Mechanistically, GlnA and RpiA cooperated to generate uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that was utilized by EpaX to synthesize polyGlcNAc-containing polymers. Notably, exogenous supplementation with polymeric N-acetylglucosamine (PNAG) restored surface penetration by E. faecalis mutants devoid of EpaX. Our study uncovers an unexpected mechanism whereby the RpiA-GlnA-EpaX metabolic axis enables production of polyGlcNAc-containing polysaccharides that endow E. faecalis with the ability to penetrate surfaces. Hence, targeting carbohydrate metabolism or inhibiting biosynthesis of polyGlcNAc-containing exopolymers may represent a new strategy to more effectively confront enterococcal infections in the clinic.
Plant-soil feedbacks promote coexistence and resilience in multi-species communities.
Feb 11, 2019   PloS One
Mack KML, Eppinga MB, Bever JD
Plant-soil feedbacks promote coexistence and resilience in multi-species communities.
Feb 11, 2019
PloS One
Both ecological theory and empirical evidence suggest that negative frequency dependent feedbacks structure plant communities, but integration of these findings has been limited. Here we develop a generic model of frequency dependent feedback to analyze coexistence and invasibility in random theoretical and real communities for which frequency dependence through plant-soil feedbacks (PSFs) was determined empirically. We investigated community stability and invasibility by means of mechanistic analysis of invasion conditions and numerical simulations. We found that communities fall along a spectrum of coexistence types ranging from strict pair-wise negative feedback to strict intransitive networks. Intermediate community structures characterized by partial intransitivity may feature "keystone competitors" which disproportionately influence community stability. Real communities were characterized by stronger negative feedback and higher robustness to species loss than randomly assembled communities. Partial intransitivity became increasingly likely in more diverse communities. The results presented here theoretically explain why more diverse communities are characterized by stronger negative frequency dependent feedbacks, a pattern previously encountered in observational studies. Natural communities are more likely to be maintained by strict negative plant-soil feedback than expected by chance, but our results also show that community stability often depends on partial intransitivity. These results suggest that plant-soil feedbacks can facilitate coexistence in multi-species communities, but that these feedbacks may also initiate cascading effects on community diversity following from single-species loss.
Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila.
Feb 11, 2019   PLoS Biology
Ellison C, Bachtrog D
Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila.
Feb 11, 2019
PLoS Biology
The repeatability or predictability of evolution is a central question in evolutionary biology and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage-compensation male-specific lethal (MSL) complex to study the mutational paths that have led to the acquisition of hundreds of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the D. melanica and D. robusta species groups by genome sequencing and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve hundreds of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element (TE) insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes and appears to be contingent on genomic properties of that species, such as simple repeat or TE density. This establishes the "genomic environment" as an important determinant in predicting the outcome of evolutionary adaptations.
Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast.
Feb 10, 2019   Molecular Ecology
Baetscher DS, Anderson EC, Gilbert-Horvath EA, Malone DP, Saarman ET, Carr MH, Garza JC
Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast.
Feb 10, 2019
Molecular Ecology
Marine species with pelagic larvae typically exhibit little population structure, suggesting long distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current-dominated ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, since the distance between sedentary parents and their settled offspring is the lifetime dispersal distance. Large sample sizes and intensive sampling are critical for increasing the likelihood of detecting parent-offspring matches in such systems and we sampled more than 6,000 kelp rockfish and analyzed them with a powerful set of 96 microhaplotype markers. We identified eight parent-offspring pairs with high confidence, and they included two juvenile fish that were born inside MPAs and dispersed to areas outside MPAs, and four fish born in MPAs that dispersed to nearby MPAs. Additionally, we identified 25 full-sibling pairs, which occurred throughout the sampling area and included all possible combinations of inferred dispersal trajectories. Intriguingly, these included two pairs of young-of-the-year siblings with one member each sampled in consecutive years. These sibling pairs suggest monogamy, either intentional or accidental, which has not been previously demonstrated in rockfishes. This study provides the first direct observation of larval dispersal events in a current-dominated ecosystem and direct evidence that larvae produced within MPAs are exported both to neighboring MPAs and proximate areas where harvest is allowed. This article is protected by copyright. All rights reserved.
Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards.
Feb 10, 2019   Molecular Ecology
Grundler MR, Singhal S, Cowan MA, Rabosky DL
Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards.
Feb 10, 2019
Molecular Ecology
Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long-term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome-wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long-term estimates of abundance, occupancy, and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to ask whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional-scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size. This article is protected by copyright. All rights reserved.
Phenotypic and Genetic Introgression Across a Moving Woodpecker Hybrid Zone.
Feb 10, 2019   Molecular Ecology
Billerman SM, Cicero C, Bowie RCK, Carling MD
Phenotypic and Genetic Introgression Across a Moving Woodpecker Hybrid Zone.
Feb 10, 2019
Molecular Ecology
In hybrid zones in which two divergent taxa come into secondary contact and interbreed, selection can maintain phenotypic diversity despite widespread genetic introgression. Red-breasted (Sphyrapicus ruber) and Red-naped (S. nuchalis) sapsuckers meet and hybridize along a narrow contact zone that stretches from northern California to southern British Columbia. We found strong evidence for changes in the structure of this hybrid zone across time, with significant temporal shifts in allele frequencies and in the proportions of parental phenotypes across the landscape. In addition to these shifts, we found that differences in plumage predict genetic differences (R2 = 0.80), suggesting that plumage is a useful proxy for assessing ancestry. We also found a significant bimodal distribution of hybrids across the contact zone, suggesting that premating barriers may be driving reproductive isolation, perhaps as a result of assortative mating based on plumage differences. However, despite evidence of selection and strong patterns of population structure between parental samples, we found only weak patterns of genetic divergence. Using museum specimens and genomic data, this study of sapsuckers provides insight into the ways in which phenotypic and genetic structure have changed over a 40-year period, as well as insight into the mechanisms that may contribute to the maintenance of the hybrid zone over time. This article is protected by copyright. All rights reserved.
Experimental evolution reveals divergence in female genital teeth morphology in response to sexual conflict intensity in a moth.
Feb 13, 2019   Journal Of Evolutionary Biology
McNamara KB, Dougherty LR, Wedell N, Simmons LW
Experimental evolution reveals divergence in female genital teeth morphology in response to sexual conflict intensity in a moth.
Feb 13, 2019
Journal Of Evolutionary Biology
The rapid evolutionary divergence of male genital structures under sexual selection is well documented. However, variation in female genital traits and the potential for sexual conflict to drive the coevolution between male and female traits has only recently received attention. In many lepidopterans females possess genital teeth (collectively, signa). Comparative studies suggest these teeth, involved in the deflation of spermatophores, may have coevolved with male spermatophore thickness via sexually antagonistic coevolution in a contest over the rate of deflation of spermatophores within the reproductive tract. We tested the hypothesis that sexual conflict should generate coevolution between genital teeth and spermatophore morphology by examining these traits under experimental manipulation of sexual conflict intensity. Using micro-CT scanning, we examined spermatophore and teeth morphology in populations of the Indian moth, Plodia interpunctella, which had been evolving for 110 generations under different adult sex-ratio biases. We found divergence in female signa morphology in response to sexual conflict: females from female-biased populations (reduced sexual conflict) developed wider signa. However, we found no evidence of coevolution between signa traits and spermatophore thickness as reported from comparative studies. This article is protected by copyright. All rights reserved.

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