Staff Publications

Staff Publications

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    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

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    We will mail you new results for this query: keywords==Evolution
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Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs 06 Biological Sciences 0604 Genetics
Auxier, Benjamin ; Dee, Jaclyn ; Berbee, Mary L. ; Momany, Michelle - \ 2019
BMC Evolutionary Biology 19 (2019)1. - ISSN 1471-2148
Ancestral state reconstruction - Evolution - Gene tree-species tree reconciliation - Modelling - Opisthokont - Protein-protein interaction - Septin - Subunit

Background: Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. The heteropolymers can create physical barriers to diffusion or serve as scaffolds organizing other morphogenetic proteins. How the paralogous septin modules interact to form heteropolymers is still unclear. Through comparative analyses, we hoped to clarify the evolutionary origin of septin diversity and to suggest which amino acid residues were responsible for subunit binding specificity. Results: Here we take advantage of newly sequenced genomes to reconcile septin gene trees with a species phylogeny from 22 animals, fungi and protists. Our phylogenetic analysis divided 120 septins representing the 22 taxa into seven clades (Groups) of paralogs. Suggesting that septin genes duplicated early in opisthokont evolution, animal and fungal lineages share septin Groups 1A, 4 and possibly also 1B and 2. Group 5 septins were present in fungi but not in animals and whether they were present in the opisthokont ancestor was unclear. Protein homology folding showed that previously identified conserved septin motifs were all located near interface regions between the adjacent septin monomers. We found specific interface residues associated with each septin Group that are candidates for providing subunit binding specificity. Conclusions: This work reveals that duplication of septin genes began in an ancestral opisthokont more than a billion years ago and continued through the diversification of animals and fungi. Evidence for evolutionary conservation of ~ 49 interface residues will inform mutagenesis experiments and lead to improved understanding of the rules guiding septin heteropolymer formation and from there, to improved understanding of development of form in animals and fungi.

Spontaneously induced prophages are abundant in a naturally evolved bacterial starter culture and deliver competitive advantage to the host
Alexeeva, Svetlana ; Guerra Martínez, Jesús Adrián ; Spus, Maciej ; Smid, Eddy J. - \ 2018
BMC Microbiology 18 (2018)1. - ISSN 1471-2180
Bacteriophage - Evolution - Lactococcus lactis - Lysogeny - Mixed culture - Prophage

Background: In complex microbial ecosystems such as the marine environment, the gastrointestinal tract, but also in mixed culture fermentations, bacteriophages are frequently found to be a part of the microbial community. Moreover, prophages or prophage-like elements are frequently identified in sequenced bacterial genomes. The mixed undefined starter cultures represent an ecosystem which is shaped by long term evolution under relatively defined environmental conditions and provides an interesting model to study co-evolution of phages and their hosts as well as the impact of diversity on microbial community stability. Results: In the present study we investigated the presence, identity and behaviour of prophages in lactococci being part of a complex cheese starter culture. Genome analysis of representative strains of the 7 genetic lineages of Lactococcus lactis constituting the culture indicated the presence of prophages in all strains. Exposure of potential lysogens to mitomycin C confirmed the release of ~ 1010·ml- 1 phage particles from all tested strains. Furthermore, phages were also released in substantial amounts due to spontaneous induction: more than 108·ml- 1 phage particles were present in cultures under non-inducing conditions. This observation suggests continuous release of phage particles by the lactococci. The released bacteriophages exhibited an unusual morphology. For most strains tested, tailless icosahedral phage heads were found. The competitive advantage of lysogens compared to their cured derivatives and their high abundance in the culture suggests that the released tailless bacteriophages play an important role in the ecosystem. Conclusions: The results of this study indicate that chromosomal genetic elements are active participants in the stable complex microbial community of the starter culture. We show that prophages are abundant in such a community, are produced continuously in large amounts and, despite the huge metabolic burden imposed on the cells by phage particle production, provide a selective advantage to the host.

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Pais, Marina ; Yoshida, Kentaro ; Giannakopoulou, Artemis ; Pel, Mathieu A. ; Cano, Liliana M. ; Oliva, Ricardo F. ; Witek, Kamil ; Lindqvist-Kreuze, Hannele ; Vleeshouwers, Vivianne G.A.A. ; Kamoun, Sophien - \ 2018
BMC Evolutionary Biology 18 (2018)1. - ISSN 1471-2148
Asexual reproduction - Clonal lineage - Copy number variation - Emergent pathogen - Evolution - Expression polymorphism - Immunity - Loss of heterozygosity - Phenotypic plasticity - Phytophthora infestans - Structural variation

Background: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. Results: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. Conclusions: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes.

Polyploidy in deep and shallow evolutionary times : from ancient cotton, middle aged tobacco to recently formed monkey-flowers
Kovarik, Ales ; Besendorfer, Višnja ; Plohl, Miroslav ; Schranz, Eric - \ 2017
Plant Systematics and Evolution (2017). - ISSN 0378-2697 - 3 p.
Biodiversity - Biological databases - Ecology - Evolution - Genetic variation - Hybridization - Plant - Polyploidy
Mutation supply and the repeatability of selection for antibiotic resistance
Dijk, Thijs van; Hwang, Sungmin ; Krug, Joachim ; Visser, Arjan de; Zwart, Mark P. - \ 2017
Physical Biology 14 (2017)5. - ISSN 1478-3967
antibiotic resistance - bacteria - Evolution - predictability and repeatability of evolution - TEM-1 Beta-lactamase

Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. We show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.

NLR network mediates immunity to diverse plant pathogens
Wu, Chih Hang ; Abd-El-Haliem, Ahmed ; Bozkurt, Tolga O. ; Belhaj, Khaoula ; Terauchi, Ryohei ; Vossen, Jack H. ; Kamoun, Sophien - \ 2017
Proceedings of the National Academy of Sciences of the United States of America 114 (2017)30. - ISSN 0027-8424 - p. 8113 - 8118.
Evolution - Host–microbe interactions - Immunity
Both plants and animals rely on nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins to respond to invading pathogens and activate immune responses. An emerging concept of NLR function is that “sensor” NLR proteins are paired with “helper” NLRs to mediate immune signaling. However, our fundamental knowledge of sensor/helper NLRs in plants remains limited. In this study, we discovered a complex NLR immune network in which helper NLRs in the NRC (NLR required for cell death) family are functionally redundant but display distinct specificities toward different sensor NLRs that confer immunity to oomycetes, bacteria, viruses, nematodes, and insects. The helper NLR NRC4 is required for the function of several sensor NLRs, including Rpi-blb2, Mi-1.2, and R1, whereas NRC2 and NRC3 are required for the function of the sensor NLR Prf. Interestingly, NRC2, NRC3, and NRC4 redundantly contribute to the immunity mediated by other sensor NLRs, including Rx, Bs2, R8, and Sw5. NRC family and NRC-dependent NLRs are phylogenetically related and cluster into a well-supported superclade. Using extensive phylogenetic analysis, we discovered that the NRC superclade probably emerged over 100 Mya from an NLR pair that diversified to constitute up to one-half of the NLRs of asterids. These findings reveal a complex genetic network of NLRs and point to a link between evolutionary history and the mechanism of immune signaling. We propose that this NLR network increases the robustness of immune signaling to counteract rapidly evolving plant pathogens.
Mining prokaryotes for antimicrobial compounds : From diversity to function
Tracanna, Vittorio ; Jong, Anne de; Medema, Marnix H. ; Kuipers, Oscar P. - \ 2017
FEMS Microbiology Reviews 41 (2017)3. - ISSN 0168-6445 - p. 417 - 429.
Antimicrobial - Bacteria - Biosynthetic - Evolution - Gene clusters - Genome - Mining - NRPS - PKS - RiPP

The bacterial kingdom provides a major source of antimicrobials that can either be directly applied or used as scaffolds to further improve their functionality in the host. The rapidly increasing amount of bacterial genomic, metabolomic and transcriptomic data offers unique opportunities to apply a variety of approaches to mine for existing and novel antimicrobials. Here, we discuss several powerful mining approaches to identify novel molecules with antimicrobial activity across structurally diverse natural products, including ribosomally synthesized and posttranslationally modified peptides, nonribosomal peptides and polyketides. We not only discuss the direct mining of genomes based on identification of biosynthetic gene clusters, but also describe more advanced and integrative approaches in ecology-based mining, functionality-based mining and mode-of-action-based mining. These efforts are likely to accelerate the discovery and development of novel antimicrobial drugs.

The immunomodulatory role of the hypothalamus-pituitary-gonad axis : Proximate mechanism for reproduction-immune trade offs?
Segner, Helmut ; Kemenade, Lidy van; Chadzinska, Magdalena - \ 2017
Developmental and Comparative Immunology 66 (2017). - ISSN 0145-305X - p. 43 - 60.
Evolution - Hypothalamus-pituitary-gonad axis - Immunity - Life history - Neuroendocrine - Reproduction - Trade-off - Vertebrate

The present review discusses the communication between the hypothalamic-pituitary-gonad (HPG) axis and the immune system of vertebrates, attempting to situate the HPG-immune interaction into the context of life history trade-offs between reproductive and immune functions. More specifically, (i) we review molecular and cellular interactions between hormones of the HPG axis, and, as far as known, the involved mechanisms on immune functions, (ii) we evaluate whether the HPG-immune crosstalk serves as proximate mechanism mediating reproductive-immune trade-offs, and (iii) we ask whether the nature of the HPG-immune interaction is conserved throughout vertebrate evolution, despite the changes in immune functions, reproductive modes, and life histories. In all vertebrate classes studied so far, HPG hormones have immunomodulatory functions, and indications exist that they contribute to reproduction-immunity resource trade-offs, although the very limited information available for most non-mammalian vertebrates makes it difficult to judge how comparable or different the interactions are. There is good evidence that the HPG-immune crosstalk is part of the proximate mechanisms underlying the reproductive-immune trade-offs of vertebrates, but it is only one factor in a complex network of factors and processes. The fact that the HPG-immune interaction is flexible and can adapt to the functional and physiological requirements of specific life histories. Moreover, the assumption of a relatively fixed pattern of HPG influence on immune functions, with, for example, androgens always leading to immunosuppression and estrogens always being immunoprotective, is probably oversimplified, but the HPG-immune interaction can vary depending on the physiological and envoironmental context. Finally, the HPG-immune interaction is not only driven by resource trade-offs, but additional factors such as, for instance, the evolution of viviparity shape this neuroendocrine-immune relationship.

Comparative genomics of campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Kik, Marja ; Zomer, Aldert L. ; Wagenaar, Jaap A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)9. - ISSN 1759-6653 - p. 3022 - 3029.
Campylobacter Iguaniorum - Comparative Genomics - Evolution - Phylogeny - Recombination - Reptile

Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, andC. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorumstrain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated froma green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-Associated C. fetus subsp.Testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regionswere identified inC. iguaniorum.One of these regions is>50 kb withdeviantG+Ccontent, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-Associated C. fetus subsp.Testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.

To sing or not to sing : seasonal changes in singing vary with personality in wild great tits
Naguib, Marc ; Rooij, Erica P. van; Snijders, Lysanne ; Oers, Kees Van - \ 2016
Behavioral Ecology 27 (2016)3. - ISSN 1045-2249 - p. 932 - 938.
Aposematism - Color patterns - Evolution - Imperfect Batesian mimicry - Predator - Selection - Visual signals

Many putative Batesian mimics only approximately resemble their supposed models, and such "imperfect" mimics are readily distinguished from defended species by humans and other vertebrates. One explanation for the existence of imperfect mimics is that the most important predators of many mimics have very different sensory and cognitive abilities from those of a typical vertebrate. In such circumstances, selection for more accurate mimicry, as perceived by humans, may be reduced. Little is known, however, about how invertebrate predators perceive and respond to mimicry in insect prey. Here, we investigate the foraging behavior of the crab spider Synema globosum, an important predator of flower-visiting insects at our field site, which frequently encounters both Batesian mimics (hoverflies-Diptera: Syrphidae) and their models (bees and wasps-Hymenoptera). In the field, we found that spiders can distinguish among dipteran and hymenopteran prey taxa, frequently attacking some models and mimics, but avoiding others. Laboratory experiments suggest that some apparently accurate mimic taxa are more likely to be avoided when spiders have prior experience of an aversive wasp model. Avoidance by spiders of black and yellow striped artificial prey suggests visual cues play a role in prey selection, but there was no evidence that olfactory cues are used to identify dangerous or noxious species. Overall, our results provide some support for the hypothesis that invertebrate predator behavior can generate selection on visual signals in putative Batesian mimics.

Private Versus Communal Tenure Systems in Gum Arabic Collection
Mujawamariya, G. ; Burger, C.P.J. - \ 2016
In: Dryland Forests / Bose, P., van Dijk, H., Springer International Publishing Switzerland - ISBN 9783319194042 - p. 53 - 69.
Resource governance - Evolution - Transition - Gum arabic
Communal management systems for acacia stands are still prominent in semi-arid gum producing areas. Competition over plots leads to lower quantities per household and, compared with private access systems, the gum collected is of lower quality. These communal systems also decrease the collectors’ incentives for tree management, may lead to overexploitation and even be sources of conflict over resources. Private systems are emerging either at individual level or through companies; in a gradual transition, mixed systems are found in which privately owned properties and communal forests coexist in villages where gum is collected in the Sylvopastoral Zone and Eastern Region of Senegal. This study investigates factors that influence the currently observed transition from communal to private collection systems at village level, briefly focusing on gender relations. With data from 53 villages in Senegal, a probit model is used to analyse the choice of organizing collection in communal systems. Mixed systems are preferred if markets are developing, labour for collection is available, competition for the resource is high, forests where gum is collected are located near the village or market prices are high enough to attract occasional collectors who reinforce the effect of competition.
Whole-genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms
Hammoudi, Valentin ; Vlachakis, Georgios ; Schranz, Eric ; Burg, Harrold A. van den - \ 2016
New Phytologist 211 (2016)1. - ISSN 0028-646X - p. 172 - 185.
SUMO - Evolution - Immunity - Neofunctionalization - Palaeoploidy - Paralogue - Protein modification - Ubiquitin-like modifier

The ubiquitin-like modifier (UBL) SUMO (Small Ubiquitin-Like Modifier) regulates protein function. Structural rather than sequence homology typifies UBL families. However, individual UBL types, such as SUMO, show remarkable sequence conservation. Selection pressure also operates at the SUMO gene copy number, as increased SUMO levels activate immunity and alter flowering time in Arabidopsis. We show how, despite this selection pressure, the SUMO family has diversified into eight paralogues in Arabidopsis. Relationships between the paralogues were investigated using genome collinearity and gene tree analysis. We show that palaeopolyploidy followed by tandem duplications allowed expansion and then diversification of the SUMO genes. For example, Arabidopsis SUMO5 evolved from the pan-eudicot palaeohexaploidy event (gamma), which yielded three SUMO copies. Two gamma copies were preserved as archetype SUMOs, suggesting subfunctionalization, whereas the third copy served as a hotspot for SUMO diversification. The Brassicaceae-specific alpha duplication then caused the duplication of one archetype gamma copy, which, by subfunctionalization, allowed the retention of both SUMO1 and SUMO2. The other archetype gamma copy was simultaneously pseudogenized (SUMO4/6). A tandem duplication of SUMO2 subsequently yielded SUMO3 in the Brassicaceae crown group. SUMO3 potentially neofunctionalized in Arabidopsis, but it is lost in many Brassicaceae. Our advanced methodology allows the study of the birth and fixation of other paralogues in plants.

What Does It Take to Evolve A Nitrogen-Fixing Endosymbiosis?
Geurts, Rene ; Xiao, Ting Ting ; Reinhold-Hurek, Barbara - \ 2016
Trends in Plant Science 21 (2016)3. - ISSN 1360-1385 - p. 199 - 208.
Common symbiosis signalling pathway - Evolution - Lipochitooligosaccharides - Nitrogen-fixing endosymbiosis

Plant rhizo- and phyllospheres are exposed to a plethora of nitrogen-fixing bacteria, providing opportunities for the establishment of symbiotic associations. Nitrogen-fixing endosymbioses are most profitable and have evolved more than ten times in the angiosperms. This suggests that the evolutionary trajectory towards endosymbiosis is not complex. Here, we argue that microbe-induced cell divisions are a prerequisite for the entrance of diazotrophic prokaryotes into living plant cells. For rhizobia and Frankia bacteria, this is achieved by adapting the readout of the common symbiosis signalling pathway, such that cell divisions are induced. The common symbiosis signalling pathway is conserved in the plant kingdom and is required to establish an endosymbiosis with mycorrhizal fungi. We also discuss the adaptations that may have occurred that allowed nitrogen-fixing root nodule endosymbiosis. Studies in legumes, Parasponia, and actinorhizal plants provided insights into the genetic constraints that guided the evolution of nitrogen-fixing root nodules with rhizobium or Frankia bacteria.Oscillation of the nuclear calcium concentration is a hallmark of symbiotic signaling in legumes and nonlegumes.Calcium oscillations can be triggered not only by lipochitooligosaccharides (LCOs), but, in several root nodule-forming plant species, also by nonLCO signal molecules.Ectopic expression of either wild-type or dominant active alleles of seven genes of the common symbiosis signalling pathway trigger spontaneous nodule formation in legumes.

Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae
Darfour-Oduro, K.A. ; Megens, Hendrik Jan ; Roca, A.L. ; Groenen, M.A.M. ; Schook, L.B. - \ 2016
BMC Evolutionary Biology 16 (2016)1. - ISSN 1471-2148 - 11 p.
Evolution - Selective constraints - Signaling - Suidae - Upstream and downstream genes

Background: The Toll-like receptor (TLR) signaling pathway constitutes an essential component of the innate immune system. Highly conserved proteins, indicative of their critical roles in host survival, characterize this pathway. Selective constraints could vary depending on the gene's position within the pathway as TLR signaling is a sequential process and that genes downstream of the TLRs may be more selectively constrained to ensure efficient immune responses given the important role of downstream genes in the signaling process. Thus, we investigated whether gene position influenced protein evolution in the TLR signaling pathway of the Suidae. The members of the Suidae examined included the European Sus scrofa (wild boar), Asian Sus scrofa (wild boar), Sus verrucosus, Sus celebensis, Sus scebifrons, Sus barbatus, Babyrousa babyrussa, Potamochoerus larvatus, Potamochoerus porcus and Phacochoerus africanus. Results: A total of 33 TLR signaling pathway genes in the Suidae were retrieved from resequencing data. The evolutionary parameter ω (dn/ds) had an overall mean of 0.1668 across genes, indicating high functional conservation within the TLR signaling pathway. A significant relationship was inferred for the network parameters gene position, number of protein-protein interactions, protein length and the evolutionary parameter dn (nonsynonymous substitutions) such that downstream genes had lower nonsynonymous substitution rates, more interactors and shorter protein length than upstream genes. Gene position was significantly correlated with the number of protein-protein interactions and protein length. Thus, the polarity in the selective constraint along the TLR signaling pathway was due to the number of molecules a protein interacted with and the protein's length. Conclusion: Results indicate that the level of selective constraints on genes within the TLR signaling pathway of the Suidae is dependent on the gene's position and network parameters. In particular, downstream genes evolve more slowly as a result of being highly connected and having shorter protein lengths. These findings highlight the critical role of gene network parameters in gene evolution.

Breaking evolutionary constraint with a tradeoff ratchet
Vos, Marjon G.J. De; Dawid, Alexandre ; Sunderlikova, Vanda ; Tans, Sander J. - \ 2015
Proceedings of the National Academy of Sciences of the United States of America 112 (2015)48. - ISSN 0027-8424 - p. 14906 - 14911.
Constraint - Environment - Epistasis - Evolution - Fitness landscape

Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance.

Members of a recently discovered subfamily of cytokinin receptors display differences and similarities to their classical counterparts
Gruhn, Nijuscha ; Seidl, M.F. ; Halawa, Mhyeddeen ; Heyl, Alexander - \ 2015
Plant Signaling & Behavior 10 (2015)2. - ISSN 1559-2316
Cytokinin - Cytokinin receptor - Evolution - Signal transduction - Two-component signaling

Cytokinins represent a group of plant hormones that have been shown to be essential for plant growth and development. A recent large-scale phylogenetic analysis of components of the cytokinin signal transduction pathway revealed, among other findings, the existence of a second, previously unknown subfamily of cytokinin receptors. Here we report that the cytokinin binding domains of the members of the 2 subfamilies contain residues that are highly conserved in either or in both subfamilies. Experiments using fluorescence microscopy hint at an ER and a plasma membrane localization for 2 members of the newly identified subfamily. These data provide new insights in the conservation of sequence and localization properties among the 2 subfamilies.

Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)
Gerhold, Pille ; Cahill, J.F. ; Winter, Marten ; Bartish, I.V. ; Prinzing, Andreas - \ 2015
Functional Ecology 29 (2015)5. - ISSN 0269-8463 - p. 600 - 614.
Coexistence - Competition - Evolution - Functional traits - Habitat filtering - Inter-actions - Lineage-pool - Macroevolutionary diversification - Phylogeny

The subdiscipline of 'community phylogenetics' is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co-occurring species within a community is commonly used as a proxy to identify which community assembly processes may have structured a particular community: phylogenetic clustering as a proxy for abiotic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition. We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii) trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) communities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylogenetic dispersion is driven predominantly by local and present-day processes. Moreover, technical sophistication of the phylogenetic-patterns-as-proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes. Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macroevolutionary diversification of habitat lineage-pools (i.e. phylogenetic-patterns-as-result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage-pools and how it affects present-day species coexistence in local communities (i.e. phylogenetic-patterns-as-cause approach). We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage-pool, for example through competition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage-pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition. 2015 British Ecological Society.

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