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evolutionary ecology

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https://www.readbyqxmd.com/read/28335474/coccolithoviruses-a-review-of-cross-kingdom-genomic-thievery-and-metabolic-thuggery
#1
Jozef I Nissimov, António Pagarete, Fangrui Ma, Sean Cody, David D Dunigan, Susan A Kimmance, Michael J Allen
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis...
March 18, 2017: Viruses
https://www.readbyqxmd.com/read/28334227/a-phylogenetic-biogeographic-and-taxonomic-study-of-all-extant-species-of-anolis-squamata-iguanidae
#2
Steven Poe, Adrián Nieto-Montes de Oca, Omar Torres-Carvajal, Kevin de Queiroz, Julián A Velasco, Brad Truett, Levi N Gray, Mason J Ryan, Gunther Köhler, Fernando Ayala-Varela, Ian Latella
Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles...
February 27, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28334218/reconciliation-between-operational-taxonomic-units-and-species-boundaries
#3
Mohamed Mysara, Peter Vandamme, Ruben Props, Frederiek-Maarten Kerckhof, Natalie Leys, Nico Boon, Jeroen Raes, Pieter Monsieurs
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into Operational Taxonomic Units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for a bacterial species. Our results show that the robustness of such a generalized cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene...
March 10, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334085/environmental-niche-divergence-among-three-dune-shrub-sister-species-with-parapatric-distributions
#4
Sergio Chozas, Rosa M Chefaoui, Otília Correia, Raúl Bonal, Joaquín Hortal
Background and Aims: The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus , which have a parapatric distribution in the Iberian Peninsula. Methods: Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula...
February 20, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28333307/formation-physiology-ecology-evolution-and-clinical-importance-of-bacterial-persisters
#5
Bram Van den Bergh, Maarten Fauvart, Jan Michiels
Persisters are transiently tolerant variants that allow populations to avoid eradication by antibiotic treatment. Their antibiotic tolerance is non-genetic, not inheritable and results from a phenotypic switch from the normal, sensitive cell type to the tolerant, persister state. Here we give a comprehensive overview on bacterial persistence. We first define persistence, summarize the various aspects of persister physiology and show their heterogeneous nature. We then focus on the role of key cellular processes and mechanisms controlling the formation of a subpopulation of tolerant cells...
February 15, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28330250/deciphering-the-evolutionary-affiliations-among-bacterial-strains-pseudomonas-and-frankia-sp-inhabiting-same-ecological-niche-using-virtual-rflp-and-simulation-based-approaches
#6
Meenakshi Srivastava, Manish Singh Kaushik, Amrita Srivastava, Anumeha Singh, Ekta Verma, Arun Kumar Mishra
To decipher an evolutionary lineage between two different but important bacterial groups, i.e., Pseudomonas strain (γ-Proteobacteria) and Frankia strain (actinobacteria) growing in the same ecological niche in and around of an actinorhizal plant Hippophae salicifolia D. Don, genetic diversity and comparative molecular phylogeny have been investigated using 16S rRNA gene sequences and computer-simulated and virtually directed restriction fragment length polymorphism (RFLP) through 10 restriction enzymes. Bayesian and coalescent analyses on the basis of 16S rRNA gene sequences suggested three major groups with close proximity between Pseudomonas and Frankia isolates...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328079/intraspecific-chemical-communication-in-microalgae
#7
REVIEW
Marianna Venuleo, John A Raven, Mario Giordano
Contents I. II. III. IV. V. VI. VII. References SUMMARY: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs...
March 22, 2017: New Phytologist
https://www.readbyqxmd.com/read/28326540/a-life-history-approach-to-delineating-how-harsh-environments-and-hawk-temperament-traits-differentially-shape-children-s-problem-solving-skills
#8
Jennifer H Suor, Melissa L Sturge-Apple, Patrick T Davies, Dante Cicchetti
BACKGROUND: Harsh environments are known to predict deficits in children's cognitive abilities. Life history theory approaches challenge this interpretation, proposing stressed children's cognition becomes specialized to solve problems in fitness-enhancing ways. The goal of this study was to examine associations between early environmental harshness and children's problem-solving outcomes across tasks varying in ecological relevance. In addition, we utilize an evolutionary model of temperament toward further specifying whether hawk temperament traits moderate these associations...
March 22, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28325881/probabilistic-models-of-species-discovery-and-biodiversity-comparisons
#9
Stewart M Edie, Peter D Smits, David Jablonski
Inferring large-scale processes that drive biodiversity hinges on understanding the phylogenetic and spatial pattern of species richness. However, clades and geographic regions are accumulating newly described species at an uneven rate, potentially affecting the stability of currently observed diversity patterns. Here, we present a probabilistic model of species discovery to assess the uncertainty in diversity levels among clades and regions. We use a Bayesian time series regression to estimate the long-term trend in the rate of species description for marine bivalves and find a distinct spatial bias in the accumulation of new species...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28323336/digest-trait-variation-in-mimulus-provides-new-evidence-for-the-joint-action-of-ecological-sorting-and-character-displacement
#10
Katherine E Eisen
Understanding how closely related species coexist in communities is one of the oldest goals of ecology and evolutionary biology. One long-standing hypothesis is that the evolution of key differences in species' niches or ecological requirements (a process known as niche differentiation) can minimize competition and promote coexistence. This article is protected by copyright. All rights reserved.
March 21, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28323330/insights-on-the-evolutionary-origin-of-detarioideae-a-clade-of-ecologically-dominant-tropical-african-trees
#11
Manuel de la Estrella, Félix Forest, Jan J Wieringa, Marie Fougère-Danezan, Anne Bruneau
African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae...
March 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28322874/reconstructing-the-genotype-to-fitness-map-for-the-bacterial-chemotaxis-network-and-its-emergent-behavioural-phenotypes
#12
Alberto Nakauma, G Sander van Doorn
The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes...
March 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28322334/the-evolutionary-origin-of-jaw-yaw-in-mammals
#13
David M Grossnickle
Theria comprises all but three living mammalian genera and is one of the most ecologically pervasive clades on Earth. Yet, the origin and early history of therians and their close relatives (i.e., cladotherians) remains surprisingly enigmatic. A critical biological function that can be compared among early mammal groups is mastication. Morphometrics and modeling analyses of the jaws of Mesozoic mammals indicate that cladotherians evolved musculoskeletal anatomies that increase mechanical advantage during jaw rotation around a dorsoventrally-oriented axis (i...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28319183/an-integrated-analysis-of-micro-and-macro-habitat-features-as-a-tool-to-detect-weather-driven-constraints-a-case-study-with-cavity-nesters
#14
D Campobello, J Lindström, R Di Maggio, M Sarà
The effects of climate change on animal populations may be shaped by habitat characteristics at both micro- and macro-habitat level, however, empirical studies integrating these two scales of observation are lacking. As analyses of the effects of climate change commonly rely on data from a much larger scale than the microhabitat level organisms are affected at, this mismatch risks hampering progress in developing understanding of the details of the ecological and evolutionary responses of organisms and, ultimately, effective actions to preserve their populations...
2017: PloS One
https://www.readbyqxmd.com/read/28316610/integrative-approaches-for-studying-mitochondrial-and-nuclear-genome-co-evolution-in-oxidative-phosphorylation
#15
Paul Sunnucks, Hernán E Morales, Annika M Lamb, Alexandra Pavlova, Chris Greening
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28316142/evolutionary-ecology-of-beta-lactam-gene-clusters-in-animals
#16
Wouter Suring, Karen Meusemann, Alexander Blanke, Janine Mariën, Tim Schol, Valeria Agamennone, Anna Faddeeva-Vakhrusheva, Matty P Berg, Bram Brouwer, Nico M van Straalen, Dick Roelofs
Beta-lactam biosynthesis was thought to occur only in fungi and bacteria, but we recently reported the presence of isopenicillin N synthase in a soil-dwelling animal, Folsomia candida. However, it has remained unclear whether this gene is part of a larger beta-lactam biosynthesis pathway and how widespread the occurrence of penicillin biosynthesis is among animals. Here, we analyzed the distribution of beta-lactam biosynthesis genes throughout the animal kingdom and identified a beta-lactam gene cluster in the genome of F...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28316119/animal-tracking-meets-migration-genomics-transcriptomic-analysis-of-a-partially-migratory-bird-species
#17
Paolo Franchini, Iker Irisarri, Adam Fudickar, Andreas Schmidt, Axel Meyer, Martin Wikelski, Jesko Partecke
Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown...
March 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28316112/molecular-ecology-studies-of-species-radiations-current-research-gaps-opportunities-and-challenges
#18
Marylaure de la Harpe, Margot Paris, Dirk N Karger, Jonathan Rolland, Michael Kessler, Nicolas Salamin, Christian Lexer
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and re-visit recent high-profile examples of evolutionary genomic research on radiations...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28306137/empirical-phylogenies-and-species-abundance-distributions-are-consistent-with-pre-equilibrium-dynamics-of-neutral-community-models-with-gene-flow
#19
Anne-Sophie Bonnet-Lebrun, Andrea Manica, Anders Eriksson, Ana S L Rodrigues
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow...
March 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28303527/chemical-ecology-of-cave-dwelling-millipedes-defensive-secretions-of-the-typhloiulini-diplopoda-julida-julidae
#20
Slobodan E Makarov, Michaela Bodner, Doris Reineke, Ljubodrag V Vujisić, Marina M Todosijević, Dragan Ž Antić, Boyan Vagalinski, Luka R Lučić, Bojan M Mitić, Plamen Mitov, Boban D Anđelković, Sofija Pavković Lucić, Vlatka Vajs, Vladimir T Tomić, Günther Raspotnig
Cave animals live under highly constant ecological conditions and in permanent darkness, and many evolutionary adaptations of cave-dwellers have been triggered by their specific environment. A similar "cave effect" leading to pronounced chemical interactions under such conditions may be assumed, but the chemoecology of troglobionts is mostly unknown. We investigated the defensive chemistry of a largely cave-dwelling julid group, the controversial tribe "Typhloiulini", and we included some cave-dwelling and some endogean representatives...
March 16, 2017: Journal of Chemical Ecology
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