Journal articles on the topic 'Degree Discipline: Ecology and Evolutionary Biology'
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1
Li, Jia, Zhu Xianglei, and Xu Guoliang. "Research status and development trend of altruism in the biological field - knowledge graph analysis based on CiteSpace." Journal of Biology and Medicine 6, no. 1 (December 1, 2022): 042–47. http://dx.doi.org/10.17352/jbm.000034.
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Based on the visualization analysis of foreign literature on altruistic behavior in recent ten years (2012-2022) by CiteSpace, it is found that the research on altruistic behavior in the field of biology abroad has experienced the initial exploratory stage, the outbreak stage, and now enters the stable and deepening stage. The discipline distribution is mainly behavioral ecology, supplemented by evolutionary biology, biomathematics, and genetics. The author has three main cooperative groups, and a relatively tight cooperative network has been formed locally in related fields. From the perspective of cooperation degree, the cooperation density of major research institutions is high, and relevant research has been relatively mature. Judging from the period calculated in the software, altruism, cooperation, kin Selection, reciprocity, and inclusive fitness emerged earlier. In recent years, constitutive theory, density dependence, and Habitat construction have emerged, which may become a new direction for future research. Therefore, future research can expand the scope of disciplines, strengthen the cooperation between authors and units, and explore other research hotspots.
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Sattler, Rolf, and Rolf Rutishauser. "Fundamentals of Plant Morphology and Plant Evo-Devo (Evolutionary Developmental Morphology)." Plants 12, no. 1 (December 26, 2022): 118. http://dx.doi.org/10.3390/plants12010118.
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Morphological concepts are used in plant evo-devo (evolutionary developmental biology) and other disciplines of plant biology, and therefore plant morphology is relevant to all of these disciplines. Many plant biologists still rely on classical morphology, according to which there are only three mutually exclusive organ categories in vascular plants such as flowering plants: root, stem (caulome), and leaf (phyllome). Continuum morphology recognizes a continuum between these organ categories. Instead of Aristotelian identity and either/or logic, it is based on fuzzy logic, according to which membership in a category is a matter of degree. Hence, an organ in flowering plants may be a root, stem, or leaf to some degree. Homology then also becomes a matter of degree. Process morphology supersedes structure/process dualism. Hence, structures do not have processes, they are processes, which means they are process combinations. These process combinations may change during ontogeny and phylogeny. Although classical morphology on the one hand and continuum and process morphology on the other use different kinds of logic, they can be considered complementary and thus together they present a more inclusive picture of the diversity of plant form than any one of the three alone. However, continuum and process morphology are more comprehensive than classical morphology. Insights gained from continuum and process morphology can inspire research in plant morphology and plant evo-devo, especially MorphoEvoDevo.
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Bianchi, Thomas S., Madhur Anand, Chris T. Bauch, Donald E. Canfield, Luc De Meester, Katja Fennel, Peter M. Groffman, Michael L. Pace, Mak Saito, and Myrna J. Simpson. "Ideas and perspectives: Biogeochemistry – some key foci for the future." Biogeosciences 18, no. 10 (May 19, 2021): 3005–13. http://dx.doi.org/10.5194/bg-18-3005-2021.
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Abstract. Biogeochemistry has an important role to play in many environmental issues of current concern related to global change and air, water, and soil quality. However, reliable predictions and tangible implementation of solutions, offered by biogeochemistry, will need further integration of disciplines. Here, we refocus on how further developing and strengthening ties between biology, geology, chemistry, and social sciences will advance biogeochemistry through (1) better incorporation of mechanisms, including contemporary evolutionary adaptation, to predict changing biogeochemical cycles, and (2) implementing new and developing insights from social sciences to better understand how sustainable and equitable responses by society are achieved. The challenges for biogeochemists in the 21st century are formidable and will require both the capacity to respond fast to pressing issues (e.g., catastrophic weather events and pandemics) and intense collaboration with government officials, the public, and internationally funded programs. Keys to success will be the degree to which biogeochemistry can make biogeochemical knowledge more available to policy makers and educators about predicting future changes in the biosphere, on timescales from seasons to centuries, in response to climate change and other anthropogenic impacts. Biogeochemistry also has a place in facilitating sustainable and equitable responses by society.
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Bateman, PW, and NC Bennett. "The biology of human sexuality: evolution, ecology and physiology." Verbum et Ecclesia 27, no. 1 (November 17, 2006): 245–64. http://dx.doi.org/10.4102/ve.v27i1.133.
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Many evolutionary biologists argue that human sexual behaviour can be studied in exactly the same way as that of other species. Many sociologists argue that social influences effectively obscure, and are more important than, a reductionist biological approach to human sexual behaviour. Here,we authors attempt to provide a broad introduction to human sexual behaviour from a biological standpoint and to indicate where the ambiguous areas are. We outline the evolutionary selective pressures that are likely to have influenced human behaviour and mate choice in the past and in the present; ecological features that influence such things as degree of parental care and polygamy; and the associated physiology of human sexuality. Then they end with a discussion of ‘abnormal’ sexuality.
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Dziubenko, Olena. "Professional training of future teachers of biologists in studying the discipline «Evolutionary Teaching»." HUMANITARIUM 44, no. 2 (December 31, 2019): 56–63. http://dx.doi.org/10.31470/2308-5126-2019-44-2-56-63.
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The article analyzes the curriculum for the discipline «Evolutionary Teaching» for future teachers of biologists at the SHEI «Pereiaslav-Khmelnytskyi Hryhoriy Skovoroda State Pedagogical University». The author points out the main tasks that future teachers of biologists are facing – methodological, cognitive and practical. The main themes of the course «Evolutionary Teaching» are described and the detailed description of the key topics of the lecture material is given. Pay attention to the mechanisms of disclosure of the material. The essence of the evolutionary doctrine, which lies in the interdisciplinary scientific field, combines research on molecular biology, genetics, biology of development, botany, zoology, ecology, anthropology, biogeography and paleontology.The author examines in detail the main professional competencies that are formed during the study of the key topics that manifest themselves in the understanding of the molecular mechanisms of conservation and implementation of genetic information in organisms, analysis of the results of the interaction of living organisms of different levels of organization, their role in biospheric processes and the possibility of use in various fields of the economy, and environmental protection. It has been established that this course is one of the key ones, as in the process of its study students are significantly exposed to creativity in expressing their own thoughts; they independently predict the possible further development and change of living organisms in anthropogenic transformations, successfully make conclusions and formulate appropriate conclusions. It is noted that during the study of this course, the future teachers of biologists are formed by the professional ability to apply the acquired knowledge of the subject field for the formation of students general and substantive competences and a holistic natural science picture of the world through intersubject connections with physics, biology, geography, in accordance with requirements of the state standard in the educational field «Natural Science».
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Konstantinidis, Konstantinos T., Margrethe H. Serres, Margaret F. Romine, Jorge L. M. Rodrigues, Jennifer Auchtung, Lee-Ann McCue, Mary S. Lipton, et al. "Comparative systems biology across an evolutionary gradient within theShewanellagenus." Proceedings of the National Academy of Sciences 106, no. 37 (September 1, 2009): 15909–14. http://dx.doi.org/10.1073/pnas.0902000106.
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To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology including the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of 10 closely relatedShewanellastrains and species to provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended on the degree of ecological specialization of the organisms evaluated. Using the gradient of evolutionary relatedness formed by these genomes, we were able to partly isolate the effect of ecology from that of evolutionary divergence and to rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms, when the organisms were grown under identical conditions, were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for (new) species description. Collectively, our results provide important new information toward beginning a systems-level understanding of bacterial species and genera.
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Slynko, Yu V. "Evolutionary ecology of water animals: concept, subject, experience for application in the analysis of breeding systems." Marine Biological Journal 3, no. 2 (June 29, 2018): 3–32. http://dx.doi.org/10.21072/mbj.2018.03.2.01.
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The basic concepts in the field of evolutionary ecology are presented. A brief historiography of the question is given, the prerequisites for the emergence of this section of biology are given. The definitions of the subject of the study of the discipline in question, as well as brief characteristics of the objects of study, basic concepts and methodological approaches are given. It is pointed out that evolutionary ecology is a section of evolutionary teaching focused on the study of the adaptation and evolution of communities of species, faunas and biogeocenoses. It is emphasized that the subjects of evolutionary ecology studying are species and their populations as well as communities, cenoses and ecosystems. The main idea of the work is reduced to an attempt to implement the epistemological synthesis of two basic methodological approaches: the ecosystem and population approaches. Two preferential methodological approaches in the field of evolutionary ecology are considered: firstly, it is genetic one, namely, population genetic (based on the dynamics of frequencies of polymorphic genes), molecular genetic (dynamics of pairs of nucleotides) and evolutionary genetic (phylogeography and molecular phylogeny); secondly, it is epigenetic one, in particular, the analysis of the developmental trajectories of morphological structures. The principal characteristics of the evolutionary ecology peculiarities of aquatic animals are postulated. An attempt has been made to justify the fact that the evolutionary ecology of aquatic organisms as a whole is of greater interest for studying the processes of adaptation and evolution than terrestrial. In the aquatic environment, all the factors of abiotics, the type of reproduction and the nature of isolation acquire a somewhat greater significance for evolution. The main items of the subject are provided with research materials, which served as the basis for developing their own ideas about evolutionary ecology. The work is significantly concentrated on the problems of evolutionary and ecological importance of interspecific hybridization, in particular on the effective co-adaptation of the genomes of the crossed species. The combination of heterogeneous genomes among remote hybrids can make the evolution of genomes go along to additional and multipolar orientation, which allows to consider hybrids as a living model for studying the problem of coordinating the work of different genomes in ontogenesis, especially during a critical period of early development. It is assumed that the success of hybridization is provided by the forming of a genetic program of a system response to structural transformations of the genome. The main result of our research in this field has not only been the discovery of a fundamentally new system of vertebrates reproduction, but also the evolutionary-ecological consequences of natural remote hybridization.
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Kamilar, Jason M., and Natalie Cooper. "Phylogenetic signal in primate behaviour, ecology and life history." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1618 (May 19, 2013): 20120341. http://dx.doi.org/10.1098/rstb.2012.0341.
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Examining biological diversity in an explicitly evolutionary context has been the subject of research for several decades, yet relatively recent advances in analytical techniques and the increasing availability of species-level phylogenies, have enabled scientists to ask new questions. One such approach is to quantify phylogenetic signal to determine how trait variation is correlated with the phylogenetic relatedness of species. When phylogenetic signal is high, closely related species exhibit similar traits, and this biological similarity decreases as the evolutionary distance between species increases. Here, we first review the concept of phylogenetic signal and suggest how to measure and interpret phylogenetic signal in species traits. Second, we quantified phylogenetic signal in primates for 31 variables, including body mass, brain size, life-history, sexual selection, social organization, diet, activity budget, ranging patterns and climatic variables. We found that phylogenetic signal varies extensively across and even within trait categories. The highest values are exhibited by brain size and body mass, moderate values are found in the degree of territoriality and canine size dimorphism, while low values are displayed by most of the remaining variables. Our results have important implications for the evolution of behaviour and ecology in primates and other vertebrates.
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Lunghi, Enrico, and Raoul Manenti. "Cave Communities: From the Surface Border to the Deep Darkness." Diversity 12, no. 5 (April 25, 2020): 167. http://dx.doi.org/10.3390/d12050167.
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The discipline of subterranean biology has provided us incredible information on the diversity, ecology and evolution of species living in different typologies of subterranean habitats. However, a general lack of information on the relationships between cave species still exists, leaving uncertainty regarding the dynamics that hold together cave communities and the roles of specific organisms (from the least to the most adapted species) for the community, as well as the entire ecosystem. This Special Issue aims to stimulate and gather studies which are focusing on cave communities belonging to all different typologies of subterranean habitats, with the overarching goal to corroborate the key role of the subterranean biology in ecological and evolutionary studies.
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Graves, Joseph L. "The Myth of the Genetically Sick African." Genealogy 6, no. 1 (February 11, 2022): 15. http://dx.doi.org/10.3390/genealogy6010015.
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Western medicine has an unfortunate history where it has been applied to address the health of African Americans. At its origins, it was aligned with the objectives of colonialism and chattel slavery. The degree to which medical “science” concerned itself with persons of African descent was to keep them alive for sale on the auction block, or to keep them healthy as they toiled to generate wealth for their European owners. Medicine in early America relied upon both dead and live African bodies to test its ideas to benefit Europeans. As medicine moved from quackery to a discipline based in science, its understanding of human biological variation was flawed. This was not a problem confined to medicine alone, but to the biological sciences in general. Biology had no solid theoretical basis until after 1859. As medicine further developed in the 20th century, it never doubted the difference between Europeans and Africans, and also asserted the innate inferiority of the latter. The genomic revolution in the latter 20th century produced tools that were deployed in a biomedical culture still mired in “racial” medicine. This lack of theoretical perspective still misdirects research associated with health disparity. In contrast to this is evolutionary medicine, which relies on a sound unification of evolutionary (ultimate) and physiological, cellular, and molecular (proximate) mechanisms. Utilizing the perspectives of evolutionary medicine is a prerequisite for an effective intervention in health disparity and finally dispelling the myth of the genetically sick African.
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Luty, Jerzy. "Sztuka jako adaptacja: uniwersalizm w estetyce ewolucyjnej." Studia Philosophica Wratislaviensia 16, no. 1 (November 8, 2021): 9–30. http://dx.doi.org/10.19195/1895-8001.16.1.1.
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The paper is a synoptic review of my monograph Art as an adaptation. Universalism in evolutionary aesthetics (2018), which is the analysis of the evolutionary theory of art — a theoretical phenomenon that has been developed in recent years, a discipline that explains the origin of human admiration for beauty and human inclination to create and admire art based on Darwinian theories of natural and sexual selection. The main objective of the paper is to determine to what extent the evolutionary perspective enriches our concept of art and whether naturalization and universalization of the analysis of art can be enlivening for aesthetics in the face of its crisis. On a more general level, the aim of the work is to demonstrate that the use of evolutionary hypotheses in the humanities, based on the achievements of, among others, biology and evolutionary psychology, human behavioural ecology and cognitive archaeology, can become a recipe for the conceptual and identity impasse in the humanities in general. In the paper I make a case for the claim that the evolutionary study of art and artistic behaviour indicates art’s inalienability “as a result of the inner human need”. It also formulates justified assumptions in a philosophical debate on the existence of aesthetic universals and the credibility of the universalist position in art theory. According to this, art operates as part of a natural, immutable apparatus of sensations, universal to all humans.
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Rose, Steven. "Précis of Lifelines: Biology, freedom, determinism." Behavioral and Brain Sciences 22, no. 5 (October 1999): 871–85. http://dx.doi.org/10.1017/s0140525x99002204.
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There are many ways of describing and explaining the properties of living systems; causal, functional, and reductive accounts are necessary but no one account has primacy. The history of biology as a discipline has given excessive authority to reductionism, which collapses higher level accounts, such as social or behavioural ones, into molecular ones. Such reductionism becomes crudely ideological when applied to the human condition, with its claims for genes “for” everything from sexual orientation to compulsive shopping. The current enthusiasm for genetics and ultra-Darwinist accounts, with their selfish-gene metaphors for living processes, misunderstand both the phenomena of development and the interactive role that DNA and the fluid genome play in the cellular orchestra. DNA is not a blueprint, and the four dimensions of life (three of space, one of time) cannot be read off from its one-dimensional strand. Both developmental and evolutionary processes are more than merely instructive or selective; the organism constructs itself, a process known as autopoiesis, through a lifeline trajectory. Because organisms are thermodynamically open systems, living processes are homeodynamic, not homeostatic. The self-organising membrane-bound and energy-utilising metabolic web of the cell must have evolved prior to so-called naked replicators. Evolution is constrained by physics, chemistry, and structure; not all change is powered by natural selection, and not all phenotypes are adaptive. Finally, therefore, living processes are radically indeterminate; like all other living organisms, but to an even greater degree, we make our own future, though in circumstances not of our own choosing.
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Membrebe, Jade Vincent, Marc A. Suchard, Andrew Rambaut, Guy Baele, and Philippe Lemey. "Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates." Molecular Biology and Evolution 36, no. 8 (April 19, 2019): 1793–803. http://dx.doi.org/10.1093/molbev/msz094.
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AbstractMany factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.
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Leong, Jason Cheok Kuan, Masahiro Uesaka, and Naoki Irie. "Distinguishing Evolutionary Conservation from Derivedness." Life 12, no. 3 (March 17, 2022): 440. http://dx.doi.org/10.3390/life12030440.
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While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.
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Seymour, Danelle K., and Brandon S. Gaut. "Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation." Molecular Biology and Evolution 37, no. 1 (August 27, 2019): 31–43. http://dx.doi.org/10.1093/molbev/msz195.
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Abstract A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number of associated characteristics. They tend to have longer sequences, to be enriched for intermediate expression levels, and to be associated with slower rates of molecular evolution. Most importantly, gbM genes tend to maintain their level of DNA methylation between species, suggesting that this trait is under evolutionary constraint. Given the degree of conservation in gbM, we still know surprisingly little about its function in plant genomes or whether gbM is itself a target of selection. To address these questions, we surveyed DNA methylation across eight grass (Poaceae) species that span a gradient of genome sizes. We first established that genome size correlates with genome-wide DNA methylation levels, but less so for genic levels. We then leveraged genomic data to identify a set of 2,982 putative orthologs among the eight species and examined shifts of methylation status for each ortholog in a phylogenetic context. A total of 55% of orthologs exhibited a shift in gbM, but these shifts occurred predominantly on terminal branches, indicating that shifts in gbM are rarely conveyed over time. Finally, we found that the degree of conservation of gbM across species is associated with increased gene length, reduced rates of molecular evolution, and increased gene expression level, but reduced gene expression variation across species. Overall, these observations suggest a basis for evolutionary pressure to maintain gbM status over evolutionary time.
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Heraghty, Sam D., John M. Sutton, Meaghan L. Pimsler, Janna L. Fierst, James P. Strange, and Jeffrey D. Lozier. "De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii." G3: Genes|Genomes|Genetics 10, no. 8 (June 25, 2020): 2585–92. http://dx.doi.org/10.1534/g3.120.401437.
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Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.
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Ferrer, Miguel. "The Naked Ape Is Still an Ape: Contradictions in Conservation Biology." Diversity 14, no. 8 (August 9, 2022): 630. http://dx.doi.org/10.3390/d14080630.
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The scientific discipline known as Conservation Biology was established in the early 1980s with the aim of becoming a tool for the management of biodiversity and ecosystems on the planet. The reality today is that there is no consensus among researchers even as to which species and spaces we should protect and how or what are the ecosystem services that we should preserve. I believe that Environmental Thinking is seriously affecting Conservation Biology. The two most influential schools in environmental philosophy thought have been land ethics and deep ecology. In both, especially in deep ecology, we still consider human beings as separate from nature and “bad” from a moral point of view.Intrinsic values beliefs oblige us to avoid any extinction, even if this is a necessary part of the evolutionary process. Both shortcomings are seriously limiting our ability to focus on the real problem. We should overcome the man–nature dichotomy by understanding that we are neither more nor less than a part of it. When we talk about protecting nature, we are actually talking about protecting human–nature habitats, maintaining conditions that make life possible for our species in a world full of opportunities and living beings, including ourselves.
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Sharir-Ivry, Avital, and Yu Xia. "Quantifying evolutionary importance of protein sites: A Tale of two measures." PLOS Genetics 17, no. 4 (April 7, 2021): e1009476. http://dx.doi.org/10.1371/journal.pgen.1009476.
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A key challenge in evolutionary biology is the accurate quantification of selective pressure on proteins and other biological macromolecules at single-site resolution. The evolutionary importance of a protein site under purifying selection is typically measured by the degree of conservation of the protein site itself. A possible alternative measure is the strength of the site-induced conservation gradient in the rest of the protein structure. However, the quantitative relationship between these two measures remains unknown. Here, we show that despite major differences, there is a strong linear relationship between the two measures such that more conserved protein sites also induce stronger conservation gradient in the rest of the protein. This linear relationship is universal as it holds for different types of proteins and functional sites in proteins. Our results show that the strong selective pressure acting on the functional site in general percolates through the rest of the protein via residue-residue contacts. Surprisingly however, catalytic sites in enzymes are the principal exception to this rule. Catalytic sites induce significantly stronger conservation gradients in the rest of the protein than expected from the degree of conservation of the site alone. The unique requirement for the active site to selectively stabilize the transition state of the catalyzed chemical reaction imposes additional selective constraints on the rest of the enzyme.
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Boero, Ferdinando. "Observational articles: a tool to reconstruct ecological history based on chronicling unusual events." F1000Research 2 (August 9, 2013): 168. http://dx.doi.org/10.12688/f1000research.2-168.v1.
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Natural history is based on observations, whereas modern ecology is mostly based on experiments aimed at testing hypotheses, either in the field or in a computer. Furthermore, experiments often reveal generalities that are taken as norms. Ecology, however, is a historical discipline and history is driven by both regularities (deriving from norms) and irregularities, or contingencies, which occur when norms are broken. If only norms occured, there would be no history. The current disregard for the importance of contingencies and anecdotes is preventing us from understanding ecological history. We need rules and norms, but we also need records about apparently irrelevant things that, in non-linear systems like ecological ones, might become the drivers of change and, thus, the determinants of history. The same arguments also hold in the field of evolutionary biology, with natural selection being the ecological driver of evolutionary change. It is important that scientists are able to publish potentially important observations, particularly those that are unrelated to their current projects that have no sufficient grounds to be framed into a classical eco-evolutionary paper, and could feasibly impact on the history of the systems in which they occurred. A report on any deviation from the norm would be welcome, from the disappearance of species to their sudden appearance in great quantities. Any event that an “expert eye” (i.e. the eye of a naturalist) might judge as potentially important is worth being reported.
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Putman, Rory, and Werner T. Flueck. "Intraspecific variation in biology and ecology of deer: magnitude and causation." Animal Production Science 51, no. 4 (2011): 277. http://dx.doi.org/10.1071/an10168.
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It has been noted that the search for patterns in biology to assist our understanding, often leads to over-simplification. That is, we are satisfied with statements that ‘the species as a rule does this’ or, ‘males of this species do that’. But within such generalisations are masked what are often important variations from that supposed norm and in practice there is tremendous variation in morphology, physiology, social organisation and behaviour of any one species. The focus on a supposedly mean optimal phenotype has diverted attention away from variation around that mean, which is regularly regarded as a kind of ‘noise’ stemming merely from stochastic effects, and thus irrelevant to evolution. Yet it is becoming increasingly clear that this variation is by converse extremely significant and of tremendous importance both to evolutionary biologists and to managers. Such intraspecific variation (IV) may be directly due to underlying genetic differences between individuals or populations within a species, but equally may include a degree of phenotypic plasticity whether as ‘non-labile’, traits which are expressed once in an individual’s lifetime, as fixed characteristics inherited from the parents or as more labile traits which are expressed repeatedly and reversibly in a mature individual according to prevailing conditions. Recognition of the extraordinary degree of IV which may be recorded within species has important consequences for management of cervids and conservation of threatened species. We review the extent of IV in diet, in morphology, mature bodyweight, reproductive physiology, in population demography and structure (sex ratio, fecundity, frequency of reproduction) before also reviewing the striking variation to be observed in behaviour: differences between individuals or populations in ranging behaviour, migratory tendency, differences in social and sexual organisation. In each case we explore the factors which may underlie the variation observed, considering the extent to which variation described has a primarily genetic basis or is a more plastic response to more immediate social and ecological cues.
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Marcovich, Irina, Marcelo J. Moglie, Agustín E. Carpaneto Freixas, Anabella P. Trigila, Lucia F. Franchini, Paola V. Plazas, Marcela Lipovsek, and Ana Belén Elgoyhen. "Distinct Evolutionary Trajectories of Neuronal and Hair Cell Nicotinic Acetylcholine Receptors." Molecular Biology and Evolution 37, no. 4 (December 10, 2019): 1070–89. http://dx.doi.org/10.1093/molbev/msz290.
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Abstract The expansion and pruning of ion channel families has played a crucial role in the evolution of nervous systems. Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels with distinct roles in synaptic transmission at the neuromuscular junction, the central and peripheral nervous system, and the inner ear. Remarkably, the complement of nAChR subunits has been highly conserved along vertebrate phylogeny. To ask whether the different subtypes of receptors underwent different evolutionary trajectories, we performed a comprehensive analysis of vertebrate nAChRs coding sequences, mouse single-cell expression patterns, and comparative functional properties of receptors from three representative tetrapod species. We found significant differences between hair cell and neuronal receptors that were most likely shaped by the differences in coexpression patterns and coassembly rules of component subunits. Thus, neuronal nAChRs showed high degree of coding sequence conservation, coupled to greater coexpression variance and conservation of functional properties across tetrapod clades. In contrast, hair cell α9α10 nAChRs exhibited greater sequence divergence, narrow coexpression pattern, and great variability of functional properties across species. These results point to differential substrates for random change within the family of gene paralogs that relate to the segregated roles of nAChRs in synaptic transmission.
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Literman, Robert, and Rachel Schwartz. "Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions of Concordant Data." Molecular Biology and Evolution 38, no. 6 (February 2, 2021): 2306–18. http://dx.doi.org/10.1093/molbev/msab026.
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Abstract Many evolutionary relationships remain controversial despite whole-genome sequencing data. These controversies arise, in part, due to challenges associated with accurately modeling the complex phylogenetic signal coming from genomic regions experiencing distinct evolutionary forces. Here, we examine how different regions of the genome support or contradict well-established relationships among three mammal groups using millions of orthologous parsimony-informative biallelic sites (PIBS) distributed across primate, rodent, and Pecora genomes. We compared PIBS concordance percentages among locus types (e.g. coding sequences (CDS), introns, intergenic regions), and contrasted PIBS utility over evolutionary timescales. Sites derived from noncoding sequences provided more data and proportionally more concordant sites compared with those from CDS in all clades. CDS PIBS were also predominant drivers of tree incongruence in two cases of topological conflict. PIBS derived from most locus types provided surprisingly consistent support for splitting events spread across the timescales we examined, although we find evidence that CDS and intronic PIBS may, respectively and to a limited degree, inform disproportionately about older and younger splits. In this era of accessible wholegenome sequence data, these results:1) suggest benefits to more intentionally focusing on noncoding loci as robust data for tree inference and 2) reinforce the importance of accurate modeling, especially when using CDS data.
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Scheuerl, Thomas, Johannes Cairns, Lutz Becks, and Teppo Hiltunen. "Predator coevolution and prey trait variability determine species coexistence." Proceedings of the Royal Society B: Biological Sciences 286, no. 1902 (May 15, 2019): 20190245. http://dx.doi.org/10.1098/rspb.2019.0245.
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Predation is one of the key ecological mechanisms allowing species coexistence and influencing biological diversity. However, ecological processes are subject to contemporary evolutionary change, and the degree to which predation affects diversity ultimately depends on the interplay between evolution and ecology. Furthermore, ecological interactions that influence species coexistence can be altered by reciprocal coevolution especially in the case of antagonistic interactions such as predation or parasitism. Here we used an experimental evolution approach to test for the role of initial trait variation in the prey population and coevolutionary history of the predator in the ecological dynamics of a two-species bacterial community predated by a ciliate. We found that initial trait variation both at the bacterial and ciliate level enhanced species coexistence, and that subsequent trait evolutionary trajectories depended on the initial genetic diversity present in the population. Our findings provide further support to the notion that the ecology-centric view of diversity maintenance must be reinvestigated in light of recent findings in the field of eco-evolutionary dynamics.
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Spatafora, Aime, Zhang, and Seifert. "A Festschrift in Honor of Meredith Blackwell." Mycologia 110, no. 1 (January 2, 2018): 1–3. http://dx.doi.org/10.1080/00275514.2018.1466586.
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The end of the 20th century and the beginning of the 21st will be remembered as the golden age of molecular systematics of Fungi. The development of the Polymerase Chain Reaction (PCR), automated sequencing, and explicit algorithms for inferring phylogenetic trees transformed fungal systematics into a hypothesis-testing discipline that would go on to serve as the foundation for comparative and evolutionary genomics. Many mycologists participated in this modernization of mycology and perhaps none more than Meredith Blackwell. She has played – and continues to play – a leadership role in transforming mycology into a modern science based on a robust understanding of organismal biology, development, testing and refinement of biologically meaningful hypotheses, and incorporation of emerging technologies to data collection and analysis. In this volume we recognize Meredith and her contributions to mycology with the publication of the first Festschrift issue in the 110 year history of Mycologia.
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Rundle, Simon, and John Spicer. "Out of place and out of time – towards a more integrated approach to heterochrony." Animal Biology 56, no. 4 (2006): 487–502. http://dx.doi.org/10.1163/157075606778967810.
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AbstractHeterochrony (changes in the relative timing of development between species) has been studied almost exclusively using morphological characters, with a focus on changes in size and shape (as a surrogate for time) between ancestral species and their descendents. Such an approach is restrictive in that it precludes the investigation of heterochronies in other, non-morphological traits and, therefore, hampers a more integrated approach to heterochrony. Such an integrated approach, where cellular, molecular and genetic approaches are used within a comparative phylogenetic framework to investigate developmental sequences, has been advocated by workers such as Smith and Raff. Here we suggest that equal emphasis should be given to the importance of physiological and ecological mechanisms that relate to changes in developmental sequence. Reviews of the history and status of physiological and ecological heterochrony reveal several examples for each, although progress has been hampered to some degree by a lack of recognition of physiological heterochrony and a lack of mechanistic understanding (heterochronies in evolutionary ecology). What emerges is that each discipline potentially brings something quite different, and complementary, to the study of heterochrony. The emergence of physiological heterochrony has arguably put the emphasis back on the object of selection and how the developing organism works: studies relating ecology and heterochrony have sought to establish whether or not there is an adaptive basis to altered sequences. We propose that any future studies of heterochrony should seek to exploit these different strengths rather than see them as merely complementary approaches.
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Völkl, Wolfgang, and Manfred Mackauer. "OVIPOSITION BEHAVIOUR OF APHIDIINE WASPS (HYMENOPTERA: BRACONIDAE, APHIDIINAE): MORPHOLOGICAL ADAPTATIONS AND EVOLUTIONARY TRENDS." Canadian Entomologist 132, no. 2 (April 2000): 197–212. http://dx.doi.org/10.4039/ent132197-2.
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AbstractWe examined oviposition behaviour in 49 species representing 19 genera of Aphidiinae. All species are solitary parasitoids of aphids (Hemiptera: Aphidoidea). Six general types are described that differ in oviposition time, behaviour, and morphology. The Ephedrini have the least specialized oviposition behaviour within the subfamily, with Praini and Aphidiini displaying various adaptations for host capture and oviposition. Use of the forelegs to grasp and orient aphids for oviposition has arisen twice, in Praini and, independently, in the genus Monoctonus Haliday (Aphidiini: Monoctonina). Morphological modifications of the terminal abdominal segments for host capture are found in Trioxina and in several species of Pauesia Quilis (Aphidiina). A “quick” sting is characteristic of species in the genus Aphidius Nees and related genera. The greatest degree of behavioural diversification occurred among Pauesia species, including cryptic behaviour, ant mimicry, and “sneak” oviposition. Acquired chemical camouflage and mimicry of the host’s cuticular hydrocarbon pattern to avoid detection by guarding ants is found in Aclitus obscuripennis Foerster, the genus Paralipsis Foerster, and the two closely related genera Adialytus Foerster and Lysiphlebus Foerster. It is suggested that the main driving forces in the evolution of parasitoid oviposition behaviour were aphid defensive behaviour and avoidance of aggression by trophobiotic ants. The results are compared with phylogenetic relationships inferred from morphological and molecular data.
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Poulin, Robert, Boris R. Krasnov, David Mouillot, and David W. Thieltges. "The comparative ecology and biogeography of parasites." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1576 (August 27, 2011): 2379–90. http://dx.doi.org/10.1098/rstb.2011.0048.
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Comparative ecology uses interspecific relationships among traits, while accounting for the phylogenetic non-independence of species, to uncover general evolutionary processes. Applied to biogeographic questions, it can be a powerful tool to explain the spatial distribution of organisms. Here, we review how comparative methods can elucidate biogeographic patterns and processes, using analyses of distributional data on parasites (fleas and helminths) as case studies. Methods exist to detect phylogenetic signals, i.e. the degree of phylogenetic dependence of a given character, and either to control for these signals in statistical analyses of interspecific data, or to measure their contribution to variance. Parasite–host interactions present a special case, as a given trait may be a parasite trait, a host trait or a property of the coevolved association rather than of one participant only. For some analyses, it is therefore necessary to correct simultaneously for both parasite phylogeny and host phylogeny, or to evaluate which has the greatest influence on trait expression. Using comparative approaches, we show that two fundamental properties of parasites, their niche breadth, i.e. host specificity, and the nature of their life cycle, can explain interspecific and latitudinal variation in the sizes of their geographical ranges, or rates of distance decay in the similarity of parasite communities. These findings illustrate the ways in which phylogenetically based comparative methods can contribute to biogeographic research.
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Foley, Robert, and Clive Gamble. "The ecology of social transitions in human evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 364, no. 1533 (November 12, 2009): 3267–79. http://dx.doi.org/10.1098/rstb.2009.0136.
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We know that there are fundamental differences between humans and living apes, and also between living humans and their extinct relatives. It is also probably the case that the most significant and divergent of these differences relate to our social behaviour and its underlying cognition, as much as to fundamental differences in physiology, biochemistry or anatomy. In this paper, we first attempt to demarcate what are the principal differences between human and other societies in terms of social structure, organization and relationships, so that we can identify what derived features require explanation. We then consider the evidence of the archaeological and fossil record, to determine the most probable context in time and taxonomy, of these evolutionary trends. Finally, we attempt to link five major transitional points in hominin evolution to the selective context in which they occurred, and to use the principles of behavioural ecology to understand their ecological basis. Critical changes in human social organization relate to the development of a larger scale of fission and fusion; the development of a greater degree of nested substructures within the human community; and the development of intercommunity networks. The underlying model that we develop is that the evolution of ‘human society’ is underpinned by ecological factors, but these are influenced as much by technological and behavioural innovations as external environmental change.
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Adams, Richard H., Heath Blackmon, and Michael DeGiorgio. "Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data." Systematic Biology 70, no. 4 (February 15, 2021): 660–80. http://dx.doi.org/10.1093/sysbio/syab009.
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Abstract Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing two phylogenies in terms of their induced probability distributions that are functions of many model parameters, these distances can be more informative than traditional approaches that rely strictly on differences in topology or branch lengths alone. Currently, however, these approaches are designed for comparing models of nucleotide substitution and gene tree distributions, and thus, are unable to address other classes of traits and associated models that may be of interest to evolutionary biologists. Here, we expand the principles of probabilistic phylogenetic distances to compute tree distances under models of continuous trait evolution along a phylogeny. By explicitly considering both the degree of relatedness among species and the evolutionary processes that collectively give rise to character traits, these distances provide a foundation for comparing models and their predictions, and for quantifying the impacts of assuming one phylogenetic background over another while studying the evolution of a particular trait. We demonstrate the properties of these approaches using theory, simulations, and several empirical data sets that highlight potential uses of probabilistic distances in many scenarios. We also introduce an open-source R package named PRDATR for easy application by the scientific community for computing phylogenetic distances under models of character trait evolution.[Brownian motion; comparative methods; phylogeny; quantitative traits.]
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Lerch, Brian A., Derek A. Smith, Thomas Koffel, Sarah C. Bagby, and Karen C. Abbott. "How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods." PLOS Computational Biology 18, no. 11 (November 1, 2022): e1010666. http://dx.doi.org/10.1371/journal.pcbi.1010666.
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The production of costly public goods (as distinct from metabolic byproducts) has largely been understood through the realization that spatial structure can minimize losses to non-producing “cheaters” by allowing for the positive assortment of producers. In well-mixed systems, where positive assortment is not possible, the stable production of public goods has been proposed to depend on lineages that become indispensable as the sole producers of those goods while their neighbors lose production capacity through genome streamlining (the Black Queen Hypothesis). Here, we develop consumer-resource models motivated by nitrogen-fixing, siderophore-producing bacteria that consider the role of colimitation in shaping eco-evolutionary dynamics. Our models demonstrate that in well-mixed environments, single “public goods” can only be ecologically and evolutionarily stable if they are partially privatized (i.e., if producers reserve a portion of the product pool for private use). Colimitation introduces the possibility of subsidy: strains producing a fully public good can exclude non-producing strains so long as the producing strain derives sufficient benefit from the production of a second partially private good. We derive a lower bound for the degree of privatization necessary for production to be advantageous, which depends on external resource concentrations. Highly privatized, low-investment goods, in environments where the good is limiting, are especially likely to be stably produced. Coexistence emerges more rarely in our mechanistic model of the external environment than in past phenomenological approaches. Broadly, we show that the viability of production depends critically on the environmental context (i.e., external resource concentrations), with production of shared resources favored in environments where a partially-privatized resource is scarce.
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Pentz, Jennifer T., and Peter A. Lind. "Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens." PLOS Genetics 17, no. 8 (August 5, 2021): e1009722. http://dx.doi.org/10.1371/journal.pgen.1009722.
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Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were changed compared to the SBW25 system to test if forecasts were extendable to a non-identical environment. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the Pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including an uncharacterized polysaccharide synthase operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spot sites were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.
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Gordon, Reyna L., Andrea Ravignani, Julia Hyland Bruno, Cristina M. Robinson, Alyssa Scartozzi, Rebecca Embalabala, Maria Niarchou, Nancy J. Cox, and Nicole Creanza. "Linking the genomic signatures of human beat synchronization and learned song in birds." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1835 (August 23, 2021): 20200329. http://dx.doi.org/10.1098/rstb.2020.0329.
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The development of rhythmicity is foundational to communicative and social behaviours in humans and many other species, and mechanisms of synchrony could be conserved across species. The goal of the current paper is to explore evolutionary hypotheses linking vocal learning and beat synchronization through genomic approaches, testing the prediction that genetic underpinnings of birdsong also contribute to the aetiology of human interactions with musical beat structure. We combined state-of-the-art-genomic datasets that account for underlying polygenicity of these traits: birdsong genome-wide transcriptomics linked to singing in zebra finches, and a human genome-wide association study of beat synchronization. Results of competitive gene set analysis revealed that the genetic architecture of human beat synchronization is significantly enriched for birdsong genes expressed in songbird Area X (a key nucleus for vocal learning, and homologous to human basal ganglia). These findings complement ethological and neural evidence of the relationship between vocal learning and beat synchronization, supporting a framework of some degree of common genomic substrates underlying rhythm-related behaviours in two clades, humans and songbirds (the largest evolutionary radiation of vocal learners). Future cross-species approaches investigating the genetic underpinnings of beat synchronization in a broad evolutionary context are discussed. This article is part of the theme issue ‘Synchrony and rhythm interaction: from the brain to behavioural ecology’.
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Barclay, Hugh J. "ASSESSING NATURAL SELECTION IN WHITE PINE WEEVILS (PISSODES STROBI PECK) (COLEOPTERA: CURCULIONIDAE) FOR OVERCOMING RESISTANCE IN TREES: AN EVOLUTIONARY MODEL." Canadian Entomologist 129, no. 6 (December 1997): 1105–20. http://dx.doi.org/10.4039/ent1291105-6.
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AbstractAn evolutionary model was constructed for the white pine weevil (Pissodes strobi Peck). This weevil attacks Sitka spruce [Picea sitchensis (Bongard) Carriere], and Sitka spruce trees have two forms, one being susceptible to the insect attacks and the other being resistant to attack. There is a fear that insects may develop tolerance to the resistant trees. The strategy of interplanting susceptible and resistant trees to minimize the likelihood of the insects developing tolerance mechanisms to circumvent the resistance is examined. It is found that if only one gene locus is involved, the development of tolerance occurs more quickly than if resistance is governed by two independent loci. The rate of evolution of tolerance to tree resistance is retarded by increased adult survivorship, the degree of recessiveness of the gene, preferential attack of susceptible trees, redistribution of intolerant insects from resistant to susceptible trees, and the immigration of wild-type insects.
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Bertels, Frederic, Christine Leemann, Karin J. Metzner, and Roland R. Regoes. "Parallel Evolution of HIV-1 in a Long-Term Experiment." Molecular Biology and Evolution 36, no. 11 (July 4, 2019): 2400–2414. http://dx.doi.org/10.1093/molbev/msz155.
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AbstractOne of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost 1 year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over 1 year in each evolution line. Many majority mutations appeared in more than one evolution line, that is, our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by phylogenetic methods. We show that one can infer the correct phylogenetic topology by including minority mutations in our analysis. We also find that mutation diversity at the beginning of the experiment is predictive of the frequency of majority mutations at the end of the experiment.
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Tusso, Sergio, Bart P. S. Nieuwenhuis, Fritz J. Sedlazeck, John W. Davey, Daniel C. Jeffares, and Jochen B. W. Wolf. "Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast." Molecular Biology and Evolution 36, no. 9 (May 20, 2019): 1975–89. http://dx.doi.org/10.1093/molbev/msz126.
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Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
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Wang, Jing, Shiyong Dong, Lihua Yang, Aj Harris, Harald Schneider, and Ming Kang. "Allopolyploid Speciation Accompanied by Gene Flow in a Tree Fern." Molecular Biology and Evolution 37, no. 9 (April 17, 2020): 2487–502. http://dx.doi.org/10.1093/molbev/msaa097.
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Abstract Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid speciation as an evolutionary process in fern lineages remains poorly understood. Here, we employ flow cytometry, phylogeny, genomewide single nucleotide polymorphism data sets, and admixture and coalescent modeling to show that the scaly tree fern, Gymnosphaera metteniana is a naturally occurring allotetraploid species derived from hybridization between the diploids, G. denticulata and G. gigantea. Moreover, we detected ongoing gene flow between the hybrid species and its progenitors, and we found that G. gigantea and G. metteniana inhabit distinct niches, whereas climatic niches of G. denticulata and G. metteniana largely overlap. Taken together, these results suggest that either some degree of intrinsic genetic isolation between the hybrid species and its parental progenitors or ecological isolation over short distances may be playing an important role in the evolution of reproductive barriers. Historical climate change may have facilitated the origin of G. metteniana, with the timing of hybridization coinciding with a period of intensification of the East Asian monsoon during the Pliocene and Pleistocene periods in southern China. Our study of allotetraploid G. metteniana represents the first genomic-level documentation of hybrid speciation in scaly tree ferns and, thus, provides a new perspective on evolution in the lineage.
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Vara, Covadonga, Laia Capilla, Luca Ferretti, Alice Ledda, Rosa A. Sánchez-Guillén, Sofia I. Gabriel, Guillermo Albert-Lizandra, et al. "PRDM9 Diversity at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice." Molecular Biology and Evolution 36, no. 8 (April 19, 2019): 1686–700. http://dx.doi.org/10.1093/molbev/msz091.
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Abstract One of the major challenges in evolutionary biology is the identification of the genetic basis of postzygotic reproductive isolation. Given its pivotal role in this process, here we explore the drivers that may account for the evolutionary dynamics of the PRDM9 gene between continental and island systems of chromosomal variation in house mice. Using a data set of nearly 400 wild-caught mice of Robertsonian systems, we identify the extent of PRDM9 diversity in natural house mouse populations, determine the phylogeography of PRDM9 at a local and global scale based on a new measure of pairwise genetic divergence, and analyze selective constraints. We find 57 newly described PRDM9 variants, this diversity being especially high on Madeira Island, a result that is contrary to the expectations of reduced variation for island populations. Our analysis suggest that the PRDM9 allelic variability observed in Madeira mice might be influenced by the presence of distinct chromosomal fusions resulting from a complex pattern of introgression or multiple colonization events onto the island. Importantly, we detect a significant reduction in the proportion of PRDM9 heterozygotes in Robertsonian mice, which showed a high degree of similarity in the amino acids responsible for protein–DNA binding. Our results suggest that despite the rapid evolution of PRDM9 and the variability detected in natural populations, functional constraints could facilitate the accumulation of allelic combinations that maintain recombination hotspot symmetry. We anticipate that our study will provide the basis for examining the role of different PRDM9 genetic backgrounds in reproductive isolation in natural populations.
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Sanaei, Ehsan, Marjan Seiedy, and Farzaneh Momtazi. "A uni- and multivariate analysis approach to reveal sexual size dimorphism in Iranian populations of Hypera postica (Coleoptera: Curculionidae)." Biologia 70, no. 9 (September 1, 2015): 1228–33. http://dx.doi.org/10.1515/biolog-2015-0137.
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Abstract Body size dimorphism between genders is a commonly observed phenomenon in insects, usually manifested in larger female body size. Sexual Size Dimorphism (SSD) varies from species to species, the degree and direction influenced by certain evolutionary pressures. Intraspecific variation in SSD may also occur between populations. The Hypera postica (Gyllenhal, 1813) is a well-known alfalfa plant pest that shows a degree of morphological divergence in its populations. The female alfalfa weevils are very fecund and have a larger body size compared to males. To improve our knowledge on magnitude and direction of SSD in alfalfa weevil, we studied 200 specimens of H. postica from four Iranian populations (Karaj1, Karaj2, Tuyserkan and Jovein). 10 morphological variables from three external anatomic parts (pronotum, elytra and rostrum) and 45 ratio characters were statistically analyzed in order to determine the amount of SSD in Iranian populations. In addition we investigated for morphological divergence pattern in mentioned populations. The results of this study show that a low degree of morphological divergence occurs in Iranian populations. Measured variables indicate that the SSD pattern of H. postica is compatible with the Rensch’s rule, and is related to high fecundity of females and a lack of strong sexual selection. Also it is mentioned that the larger rostrum in females may correspond to its unique role in egg laying.
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Clements, Matthew. "The circle and the maze: Two images of ecosemiotics." Sign Systems Studies 44, no. 1/2 (July 5, 2016): 69–93. http://dx.doi.org/10.12697/sss.2016.44.1-2.05.
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This article compares the work of Jakob von Uexküll and Charles S. Peirce to elucidate two contrasting yet connected images of ecosemiotics. The intent is not simply to oppose their work, but to explore a tension which has implications for the ethical dimension of this emerging discipline. Uexküll’s functional cycle is associated with the image of a circle, which, while emphasizing the integration of organism and environment, is shown to invoke solipsism, and an overly deterministic depiction of ecological relations. Peirce’s drawing of a labyrinth is taken to represent a maze, which, while exemplifying the evolutionary play of ecosystems, may entail a level of unpredictability that is catastrophically chaotic. The root of these diverging depictions is identified with the role of subjectivity in engendering semiotic relations in the work of both Uexküll and Peirce. Where the more regressive aspects of Uexküll’s theoretical biology are mitigated by a teleological interpretation of life’s underlying causality, orientating agency within Peirce’s work depends upon attention to the idea of the self in his philosophy of signs. In conclusion, Eduardo Kohn’s conception of an ‘ecology of selves’ is cited, and the status of the organism as a living symbol of its environment is reaffirmed.
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Graham, Allie M., and Felipe S. Barreto. "Independent Losses of the Hypoxia-Inducible Factor (HIF) Pathway within Crustacea." Molecular Biology and Evolution 37, no. 5 (January 31, 2020): 1342–49. http://dx.doi.org/10.1093/molbev/msaa008.
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Abstract Metazoans respond to hypoxic stress via the hypoxia-inducible factor (HIF) pathway, a mechanism thought to be extremely conserved due to its importance in monitoring cellular oxygen levels and regulating responses to hypoxia. However, recent work revealed that key members of the HIF pathway have been lost in specific lineages (a tardigrade and a copepod), suggesting that this pathway is not as widespread in animals as previously assumed. Using genomic and transcriptomic data from 70 different species across 12 major crustacean groups, we assessed the degree to which the gene HIFα, the master regulator of the HIF pathway, was conserved. Mining of protein domains, followed by phylogenetic analyses of gene families, uncovered group-level losses of HIFα, including one across three orders within Cirripedia, and in three orders within Copepoda. For these groups, additional assessment showed losses of HIF repression machinery (EGLN and VHL). These results suggest the existence of alternative mechanisms for cellular response to low oxygen and highlight these taxa as models useful for probing these evolutionary outcomes.
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Bro-Jørgensen, Jakob, Daniel W. Franks, and Kristine Meise. "Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1781 (July 29, 2019): 20190008. http://dx.doi.org/10.1098/rstb.2019.0008.
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The impact of environmental change on the reproduction and survival of wildlife is often behaviourally mediated, placing behavioural ecology in a central position to quantify population- and community-level consequences of anthropogenic threats to biodiversity. This theme issue demonstrates how recent conceptual and methodological advances in the discipline are applied to inform conservation. The issue highlights how the focus in behavioural ecology on understanding variation in behaviour between individuals, rather than just measuring the population mean, is critical to explaining demographic stochasticity and thereby reducing fuzziness of population models. The contributions also show the importance of knowing the mechanisms by which behaviour is achieved, i.e. the role of learning, reasoning and instincts, in order to understand how behaviours change in human-modified environments, where their function is less likely to be adaptive. More recent work has thus abandoned the ‘adaptationist’ paradigm of early behavioural ecology and increasingly measures evolutionary processes directly by quantifying selection gradients and phenotypic plasticity. To support quantitative predictions at the population and community levels, a rich arsenal of modelling techniques has developed, and interdisciplinary approaches show promising prospects for predicting the effectiveness of alternative management options, with the social sciences, movement ecology and epidemiology particularly pertinent. The theme issue furthermore explores the relevance of behaviour for global threat assessment, and practical advice is given as to how behavioural ecologists can augment their conservation impact by carefully selecting and promoting their study systems, and increasing their engagement with local communities, natural resource managers and policy-makers. Its aim to uncover the nuts and bolts of how natural systems work positions behavioural ecology squarely in the heart of conservation biology, where its perspective offers an all-important complement to more descriptive ‘big-picture’ approaches to priority setting. This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.
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Merlo, J. L., A. P. Cutrera, and R. R. Zenuto. "Inflammation in response to phytohemagglutinin injection in the Talas tuco-tuco (Ctenomys talarum): implications for the estimation of immunocompetence in natural populations of wild rodents." Canadian Journal of Zoology 92, no. 8 (August 2014): 689–97. http://dx.doi.org/10.1139/cjz-2013-0306.
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The immunological variation in wild populations and its relation to life-history traits has recently become a central topic in the field of evolutionary biology, considering the critical contribution of immunity to an individual’s fitness. A common technique used by ecologists to estimate immunocompetence in wild populations is the phytohemagglutinin (PHA) – skin test. In this test, the degree of local swelling triggered by PHA is usually considered an estimate of T-lymphocyte activity, although there is an ongoing debate regarding this interpretation. Here, we coupled the PHA–skin test with a histological analysis to examine the temporal development of the cell-mediated response in the subterranean rodent Talas tuco-tuco (Ctenomys talarum Thomas, 1898). The inflammation response involved lymphocytes, neutrophils, eosinophils, and macrophages at the site of injection, achieving an increase of total leukocytes from 12 to 48 h after injection. However, the abundance of any of the leukocytes observed did not correlate with the degree of swelling at any time studied, suggesting that caution should be taken when interpreting the results of the PHA-induced swelling response. Particularly, the magnitude of macroscopic swelling should not be considered a priori as indicative of T-lymphocyte activity in wild-caught rodents. Our results highlight the importance of avoiding oversimplified approaches to measuring immunocompetence.
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Perissinotto, Renzo. "Systematics and biology of the Ichnestomina, including new genera and species (Coleoptera: Scarabaeidae, Cetoniinae)." Fragmenta Entomologica 52, no. 2 (November 15, 2020): 217–320. http://dx.doi.org/10.4081/fe.2020.473.
Full textAbstract:
The subtribe Ichnestomina, endemic to southern Africa, exhibits a suite of plesiomorphic features that reflects a particularly old evolutionary age among the Goliathini. Sexual dimorphism is extreme and females are generally brachypterous and unable to fly. Also, adult stages do not feed, and therefore remain active for only a few days after emerging from the soil, devoting all their energy reserves to reproduction. Consequently, populations are range-bound to small areas, often completely isolated on high mountain peaks or ridges, leading to rapid speciation. Results of recent investigations and historical data are hereby combined to provide an updated and revised structure of the systematics of this subtribe. As a result, four genera are now recognised in place of the perceived uniformity earlier expressed with much reservation by Holm (1992). This involves the rehabilitation of the original name of Gariep Gory & Percheron, 1833, to accommodate species with fully winged and flying females as well as elongate and incision-free dorsal lobes of parameres (Gariep patera and G. perstriata. It is further proposed that the genus Ichnestoma Gory & Percheron, 1833 be restricted to species with moderate female brachyptery and males with cretaceous markings on their body surface. Consequently, two new genera are erected (Karooida gen. nov., Mzansica gen. nov.) and four species-complexes (Ichnestoma cuspidata, I. albomaculata, Mzansica nasula and M. luridipennis), are added in order to account for key differences among species, including degree of female brachyptery (wing:elytron length ratio), presence/absence of cretaceous markings, aedeagal structure and biogeographic distribution. Eleven new species (Ichnestoma carbonaria sp. nov., I. dealbata sp. nov., I. furcata sp. nov., I. karoominoris sp. nov., I. spatulata sp. nov., Karooida balli sp. nov., K. sagittata sp. nov., Mzansica botswanica sp. nov., M. clarki sp. nov., M. denticulata sp. nov., M. falcipata sp. nov.) are added to the 13 species and three subspecies currently recognised in this subtribe. The three subspecies are elevated to species status (Ichnestoma cochleata stat. nov., I. fuscipennis stat. nov., Karooida kikvorsti comb. et stat. nov.). The diagnostic characters of each taxon are described along with all available knowledge on the habitat characteristics and general biology of each species.
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Solovieva, Vera Valentinovna, Aleksandr Alekseevich Semenov, and Andrey Stepanovich Yaitsky. "Environmental education of students by means of hydrobotany." Samara Journal of Science 8, no. 1 (February 28, 2019): 298–303. http://dx.doi.org/10.17816/snv201981315.
Full textAbstract:
Currently, environmental education is considered as a key principle of sustainable development of society and nature. It represents the uniform continuous educational process directed on development of a system of ecological knowledge, abilities, skills, valuable installations, experience of activity and competence of the careful attitude to environment and rational nature management. Hydrobotany has great opportunities in terms of environmental education of students. We consider hydrobotanics to be the science of aquatic plants, their communities, processes of overgrowing of ponds and streams. It studies the features of external and internal water macrophytes structure, their life processes, the relationship between them and the environment, diversity, distribution, introduction, role in nature and human life (outecology); composition and structure of aquatic phytocenoses, their production and destruction, as well as the processes of formation of aquatic vegetation and its dynamics (synecology). Hydrobotany has its purpose and objectives, object, subject and methods of research, open laws, special conceptual apparatus, history of development. It occupies a certain place in the system of sciences. In Samara State University of Social Sciences and Education Hydrobotany is included in the curriculum of the main professional educational programs of the bachelors degree Pedagogical education (majors Biology and Geography, Biology and Chemistry, Biology) as a discipline for students choice. We have developed a model of environmental education of students in the process of teaching Hydrobotany. It consists of four components: targeted, substantive, procedural, monitoring and evaluation. The target component-includes the purpose and objectives of the discipline Hydrobotany in the field of environmental education of students. Content component-covers the system of environmental knowledge on Hydrobotany; skills and experience of activities on the ecology of aquatic plants; value systems for aquatic plants and their communities; special competence of aquatic plants ecology study, their protection, careful and rational use. Procedural component-contains forms, methods, tools and technologies of environmental education. Control and evaluation component includes educational results; forms, types and methods of control, as well as a system of evaluation of individual achievements of students.
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Luo, Arong, David A. Duchêne, Chi Zhang, Chao-Dong Zhu, and Simon Y. W. Ho. "A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process." Systematic Biology 69, no. 2 (May 27, 2019): 325–44. http://dx.doi.org/10.1093/sysbio/syz038.
Full textAbstract:
Abstract Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth–death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth–death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth–death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth–death model, which will inform further development of the method and its application to key questions in evolutionary biology.
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Talbot, Benoit, Nusha Keyghobadi, and Brock Fenton. "Bed bugs: The move to humans as hosts." FACETS 4, no. 1 (June 1, 2019): 105–10. http://dx.doi.org/10.1139/facets-2018-0038.
Full textAbstract:
Cimicid insects, bed bugs and their allies, include about 100 species of blood-feeding ectoparasites. Among them, a few have become widespread and abundant pests of humans. Cimicids vary in their degree of specialization to hosts. Whereas most species specialize on insectivorous birds or bats, the common bed bug can feed on a range of distantly related host species, such as bats, humans, and chickens. We suggest that association with humans and generalism in bed bugs led to fundamentally different living conditions that fostered rapid growth and expansion of their populations. We propose that the evolutionary and ecological success of common bed bugs reflected exploitation of large homeothermic hosts (humans) that sheltered in buildings. This was a departure from congeners whose hosts are much smaller and often heterothermic. We argue that interesting insights into the biology of pest species may be obtained using an integrated view of their ecology and evolution.
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Gilchrist, J. S. "Aggressive monopolization of mobile carers by young of a cooperative breeder." Proceedings of the Royal Society B: Biological Sciences 275, no. 1650 (July 22, 2008): 2491–98. http://dx.doi.org/10.1098/rspb.2008.0597.
Full textAbstract:
Competition between young of the same brood or litter is of particular interest in the fields of behavioural and evolutionary ecology, because the competing individuals are likely to be closely related, where evolutionary theory predicts a greater degree of cooperation. Studies of cooperative breeding species typically concentrate on who contributes care to rearing young, and assume a passive role of the young. Relatively, little attention has been devoted to considering how intralitter competition between young affects the distribution of care in cooperative breeders. In banded mongoose ( Mungos mungo ) groups, the majority of pups each form a stable exclusive one-to-one association with an adult group member (its ‘escort’) that is its principal care provider. This paper presents experimental evidence that each pup aggressively defends access to its escort, preventing other pups approaching, and therefore monopolizes the care provided by its escort. Each pup travels with the group and follows its escort, around which its exclusion zone is fixed: a form of mobile territoriality. This represents a novel system of care of young in a mammal species, but has general implications for the study of the distribution of care of young, particularly in cooperative breeding species. Parents and helpers may provide biased care to young, not due to preference but due to the competitive actions of the young within the brood or litter.
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Ord, Terry J., and Joan Garcia-Porta. "Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1597 (July 5, 2012): 1811–28. http://dx.doi.org/10.1098/rstb.2011.0215.
Full textAbstract:
Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups.
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Rasko, David A., M. J. Rosovitz, Ole Andreas Økstad, Derrick E. Fouts, Lingxia Jiang, Regina Z. Cer, Anne-Brit Kolstø, Steven R. Gill, and Jacques Ravel. "Complete Sequence Analysis of Novel Plasmids from Emetic and Periodontal Bacillus cereus Isolates Reveals a Common Evolutionary History among the B. cereus-Group Plasmids, Including Bacillus anthracis pXO1." Journal of Bacteriology 189, no. 1 (October 13, 2006): 52–64. http://dx.doi.org/10.1128/jb.01313-06.
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ABSTRACTThe plasmids of the members of theBacillus cereussensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example,Bacillus anthraciscontains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid definesBacillus thuringiensisisolates. In this study the plasmids fromB. cereusisolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical ∼272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one ∼270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of theseB. cereusplasmids revealed a high degree of sequence similarity to theB. anthracispXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identifiedB. cereusplasmids. Screening of a population ofB. cereusgroup isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenicB. cereusisolates in the same way that pXO1 and pXO2 define theB. anthracisspecies.
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Soares, Simone Cardoso, Eduardo Schmidt Eler, Carlos Eduardo Faresin e Silva, Maria Nazareth Ferreira da Silva, Naiara Pereira Araújo, Marta Svartman, and Eliana Feldberg. "LINE-1 and SINE-B1 mapping and genome diversification in Proechimys species (Rodentia: Echimyidae)." Life Science Alliance 5, no. 6 (March 18, 2022): e202101104. http://dx.doi.org/10.26508/lsa.202101104.
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This study aimed to understand the impact of LINE-1 and SINE-B1 retroelements on the architecture and karyotypic diversification of five rodent species of the genus Proechimys from different regions of the Amazon. Karyotype comparisons were performed using fluorescent interspecific in situ hybridization. The L1 and B1 retroelements showed a non-random arrangement and a conserved pattern when the genomes of the five species of Proechimys were compared, including the two cytotypes of Proechimys guyannensis. The signal homeology among the chromosomes and the degree of similarity among the formed clusters indicate rearrangements such as fusion/fission, and demonstrates that these retroelements can behave as derived characters shared in Proechimys. The differentiated distribution and organization of these retroelements in the karyotypes and in the chromosomal fiber, respectively, may represent a strong indication of their role as generating sources of karyotypic diversity in the genus Proechimys and provide insights into the evolutionary relationships between taxa.