Relevant bibliographies by topics / Community phylogenetics approach

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  2. Dissertations / Theses
  3. Book chapters

Academic literature on the topic 'Community phylogenetics approach'

Author: Grafiati
Published: 6 September 2023
Last updated: 31 July 2025

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Journal articles on the topic "Community phylogenetics approach"

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Villalobos, Fabricio, Thiago F. Rangel, and José Alexandre F. Diniz-Filho. "Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence." Proceedings of the Royal Society B: Biological Sciences 280, no. 1756 (2013): 20122570. https://doi.org/10.5281/zenodo.14817416.

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(Uploaded by Plazi for the Bat Literature Project) Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary c
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Lopez, Bianca, Kevin Burgio, Marcos Carlucci, et al. "A new framework for inferring community assembly processes using phylogenetic information, relevant traits and environmental gradients." One Ecosystem 1 (June 14, 2016): e9501. https://doi.org/10.3897/oneeco.1.e9501.

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Functional and phylogenetic diversity are increasingly used to infer the important community assembly processes that have structured local communities, which is one of the most fundamental issues in ecology. However, there are critical assumptions and pitfalls associated with these analyses, which can create ambiguity in interpreting results. Here, we present a conceptual framework which integrates three approaches to reduce the likelihood of drawing incorrect conclusions from analyses of functional and phylogenetic diversity (FD and PD, respectively): testing hypotheses for how diversity meas
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Guo, Xue, Huaqun Yin, Jing Cong, Zhimin Dai, Yili Liang, and Xueduan Liu. "RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage." Applied and Environmental Microbiology 79, no. 6 (2013): 2019–26. http://dx.doi.org/10.1128/aem.03400-12.

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ABSTRACTThe enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drain
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Vaidya, Gaurav, Hilmar Lapp, and Nico Cellinese. "Enabling Machines to Integrate Biodiversity Data with Evolutionary Knowledge." Biodiversity Information Science and Standards 4 (October 2, 2020): e59088. https://doi.org/10.3897/biss.4.59088.

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Most biological data and knowledge are directly or indirectly linked to biological taxa via taxon names. Using taxon names is one of the most fundamental and ubiquitous ways in which a wide range of biological data are integrated, aggregated, and indexed, from genomic and microbial diversity to macro-ecological data. To this day, the names used, as well as most methods and resources developed for this purpose, are drawn from Linnaean nomenclature. This leads to numerous problems when applied to data-intensive science that depends on computation to take full advantage of the vast – and rapidly
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Humphreys, John M., Angela M. Pelzel-McCluskey, Lee W. Cohnstaedt, et al. "Integrating Spatiotemporal Epidemiology, Eco-Phylogenetics, and Distributional Ecology to Assess West Nile Disease Risk in Horses." Viruses 13, no. 9 (2021): 1811. http://dx.doi.org/10.3390/v13091811.

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Mosquito-borne West Nile virus (WNV) is the causative agent of West Nile disease in humans, horses, and some bird species. Since the initial introduction of WNV to the United States (US), approximately 30,000 horses have been impacted by West Nile neurologic disease and hundreds of additional horses are infected each year. Research describing the drivers of West Nile disease in horses is greatly needed to better anticipate the spatial and temporal extent of disease risk, improve disease surveillance, and alleviate future economic impacts to the equine industry and private horse owners. To help
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Brennan, Ian G., Alan R. Lemmon, Emily Moriarty Lemmon, et al. "Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity." Systematic Biology 70, no. 1 (2020): 120–32. http://dx.doi.org/10.1093/sysbio/syaa046.

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Abstract Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosm
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Vincent, Helvin, Harisree P. Nair, and Dr Sarita G. Bhat. "Community Genomics Involving Culture Independent Approach for Assessing the Phylogenetic Diversity of Mangrove Sediment." Indian Journal of Applied Research 3, no. 10 (2011): 1–4. http://dx.doi.org/10.15373/2249555x/oct2013/10.

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Ribeiro, Izabela Ferreira, Luis Fernando Tavares de Menezes, and Marcelo Trindade Nascimento. "Facilitation between plants and the use of facilitating species as an ecological restoration strategy." Núcleo do Conhecimento 01, no. 03 (2023): 151–69. https://doi.org/10.32749/nucleodoconhecimento.com.br/biology/ecological-restoration.

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Ecosystems subject to extreme abiotic factors are privileged places for studies of positive interactions between plants, such as facilitation mechanisms, which, from biotic or abiotic modifications, generate benefits to the environment. Due to the increase in the number of articles on facilitation in recent decades and the indication of the use of facilitating species in recovery and ecological restoration projects, the present study presents a literature review on facilitation between plant-plant and its applicability between the years 2011 and 2020. A total of 64 studies were considered that
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Meneses, Camila G., Kier Mitchel E. Pitogo, Christian E. Supsup, and Rafe M. Brown. "Philippine herpetology (Amphibia, Reptilia), 20 years on: two decades of progress towards an increasingly collaborative, equitable, and inclusive approach to the study of the archipelago’s amphibians and reptiles." ZooKeys 1190 (January 30, 2024): 213–57. http://dx.doi.org/10.3897/zookeys.1190.109586.

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A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized the diverse topics studied and highlighted the development and achievements in research up to the year 2000. This study revisits and re-assesses what Philippine herpetology has accomplished, both as a discipline and a community, during the last two decades (2002–2022). A total of 423 herpetological publications was collated, revealing a substantial increase in annual publications, rising from approximately four per year during 2002–2008 to around 28 per year in
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Meneses, Camila G., Kier Mitchel E. Pitogo, Christian E. Supsup, and Rafe M. Brown. "Philippine herpetology (Amphibia, Reptilia), 20 years on: two decades of progress towards an increasingly collaborative, equitable, and inclusive approach to the study of the archipelago's amphibians and reptiles." ZooKeys 1190 (January 30, 2024): 213–57. https://doi.org/10.3897/zookeys.1190.109586.

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A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized the diverse topics studied and highlighted the development and achievements in research up to the year 2000. This study revisits and re-assesses what Philippine herpetology has accomplished, both as a discipline and a community, during the last two decades (2002–2022). A total of 423 herpetological publications was collated, revealing a substantial increase in annual publications, rising from approximately four per year during 2002–2008 to around 28 per year in
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Dissertations / Theses on the topic "Community phylogenetics approach"

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Bernard-Verdier, Maud. "Structure et assemblage des communautés végétales de parcours des Grands Causses : approche fonctionnelle, phénologique et phylogénétique." Thesis, Montpellier 2, 2012. http://www.theses.fr/2012MON20047/document.

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Comprendre l'influence de l'environnement sur la distribution des espèces végétales est une préoccupation à la base même de l'écologie végétale. L'objectif de cette thèse est de comprendre comment les communautés végétales de parcours des Grands Causses s'assemblent en fonction de la disponibilité en ressources édaphiques. Pour cela, la structure de niche des communautés a été caractérisée en termes de gestion des ressources, de stratégie de régénération, de niche temporelle et d'histoire évolutive des espèces le long d'un gradient édaphique. Par une approche basée sur les traits fonctionnels,
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Divya, B. "A Phylogenetic Perspective on The Phytogeography of Western Ghats." Thesis, 2019. https://etd.iisc.ac.in/handle/2005/5135.

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I used a finer scale data of 156 published plots across the entire latitudinal range of WG, covering most of the protected forests. The pruned phylogeny for this study consisted of 367 species, of which ~ 50% are taxa endemic to WG. I first tested the southern refuge hypothesis by analysing the PE of all 367 species. my results show that plots significant for PE were more in the southern latitudes, indicating the presence of range restricted clades predominantly in the southern WG. I then partitioned the data to explore the contribution of endemics and non-endemics to the overall PE patt
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Chen, Ting-Wen. "Assembly processes in soil animal communities: Integrating phylogeny and trait-based approaches." Doctoral thesis, 2018. http://hdl.handle.net/11858/00-1735-0000-002E-E372-9.

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Boyle, Elizabeth. "Community phylogenetics: methodological approaches and patterns in subarctic freshwater insect systems." Thesis, 2012. http://hdl.handle.net/10214/4046.

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I aimed to expand our understanding of community assembly and species co-existence by examining the implications of phylogenetic robustness on metrics describing phylogenetic community structure, as well as the phylogenetic patterns of co-occurring insect species in Churchill, MB. Using a variety of tree reconstruction methods, I found that cytochrome c oxidase subunit I (COI) was able to accurately estimate phylogenetic community structure metrics calculated from a multi-gene phylogeny when using more biologically realistic approaches. This included incorporating known phylogenetic relationsh
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Book chapters on the topic "Community phylogenetics approach"

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Lundén, Daniel, Lars Hummelgren, Jan Kudlicka, Oscar Eriksson, and David Broman. "Suspension Analysis and Selective Continuation-Passing Style for Universal Probabilistic Programming Languages." In Programming Languages and Systems. Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-57267-8_12.

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AbstractUniversal probabilistic programming languages (PPLs) make it relatively easy to encode and automatically solve statistical inference problems. To solve inference problems, PPL implementations often apply Monte Carlo inference algorithms that rely on execution suspension. State-of-the-art solutions enable execution suspension either through (i) continuation-passing style (CPS) transformations or (ii) efficient, but comparatively complex, low-level solutions that are often not available in high-level languages. CPS transformations introduce overhead due to unnecessary closure allocations
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Taggart, Dora M., and Trent A. Key. "Molecular Biological Tools Used in Assessment and Remediation of Petroleum Hydrocarbons in Soil and Groundwater." In Advances in the Characterisation and Remediation of Sites Contaminated with Petroleum Hydrocarbons. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-34447-3_10.

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AbstractMolecular biological tools (MBTs) are used to assess and characterize the microbiology and associated biological processes at contaminated sites, including ecological roles, phylogenetic diversity, and metabolic and co-metabolic capabilities related to contaminant biodegradation and biotransformation. MBTs have changed our approach to the assessment and remediation of petroleum hydrocarbons in the environment. In contaminated-site management, several MBTs and stable isotope analysis methods can be used to measure the presence, abundance, and activity of petroleum hydrocarbon-degrading
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le Roux, Johannes J. "Molecular ecology of plant-microbial interactions during invasions: progress and challenges." In Plant invasions: the role of biotic interactions. CABI, 2020. http://dx.doi.org/10.1079/9781789242171.0340.

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Abstract Microbes are omnipresent, yet their interactions with invasive plants remain understudied. This is surprising, given the importance of microbes in plant community ecology and their influence on plant performance in new environments. Recent advances in molecular genetic approaches have opened the door to studying this unseen majority in great detail and to understand how they fit into ecological interaction networks. Molecular approaches allow rapid assessments of microbial diversity at reasonable cost while providing both taxonomic and evolutionary information. Here I discuss how thes
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Cadotte, Marc W., and T. Jonathan Davies. "Phylogenetic Patterns within Communities." In Phylogenies in Ecology. Princeton University Press, 2016. http://dx.doi.org/10.23943/princeton/9780691157689.003.0003.

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This chapter discusses the use of phylogenetic distances to infer mechanisms of ecological assembly. Mechanisms influencing patterns of community assembly act on the ecological similarities and differences of organisms, and not on the number of species. Phylogenetic patterns of relatedness have provided an especially useful and popular approach to quantifying expected species ecological differences for examining community assembly. Over the past decade, phylogenetic information has been widely used in community assembly studies to test a basic set of hypotheses about the relatedness of co-occu
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Cadotte, Marc W., and T. Jonathan Davies. "Randomizations, Null Distributions, and Hypothesis Testing." In Phylogenies in Ecology. Princeton University Press, 2016. http://dx.doi.org/10.23943/princeton/9780691157689.003.0004.

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This chapter examines the logic of null modeling for phylogenetic tests. Developing null expectations for community phylogenetic patterns from randomization procedures is the cornerstone for many ecophylogenetic analysis. The chapter advocates an approach that explicitly considers multiple randomizations to better understand what aspects of community and phylogenetic structure determine observed patterns. It first provides a brief historical overview of randomization tests in ecology, focusing on two important academic conflicts that highlight the need for using randomizations in ecological an
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Losos, Jonathan B. "Community evolution in Greater Antillean Anolis lizards: phylogenetic patterns and experimental tests." In New Uses for New Phylogenies. Oxford University PressOxford, 1996. http://dx.doi.org/10.1093/oso/9780198549857.003.0019.

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Abstract The use of phylogenies in all manner of comparative studies has increased remarkably in recent years. Five years ago, few would have predicted the integral role that phylogenetic approaches play today in fields as disparate as epidemiology. population genetics, and macroevolution, as this volume attests. The goal of this chapter is two-fold: first. to illustrate the importance of a phylogenetic approach to another field. community ecology, and, second, to discuss an important new use to which phylogenies have been put recently: rather than being used to test previously derived hypothe
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Cadotte, Marc W., and T. Jonathan Davies. "The Geography of Speciation and Character Displacement." In Phylogenies in Ecology. Princeton University Press, 2016. http://dx.doi.org/10.23943/princeton/9780691157689.003.0006.

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This chapter examines how phylogenetic approaches can address both ecological character displacement and community-wide character displacement. In ecological character displacement, selection might drive the divergence of ecological phenotypes by negative antagonistic interactions that reduce competition between sympatric populations utilizing the same resource base. In community-wide character displacement, ecological divergence occurs in allopatry, and competition filters species into communities based upon their trait values. The geographic distribution of a species reflects multiple factor
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"Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques." In Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques, edited by Peter B. McIntyre and Alexander S. Flecker. American Fisheries Society, 2010. http://dx.doi.org/10.47886/9781934874141.ch27.

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<em>Abstract</em>.—Ecological stoichiometry refers to the relative availability of elements in ecosystems as both an influence upon and result of ecological interactions. Nutrient ratios have long been analyzed in primary producers, but their application to animals is more recent. Here, we summarize the ecological stoichiometry framework and highlight three key contexts in stream fish ecology: body stoichiometry, dietary stoichiometry, and roles in ecosystem nutrient cycling. Elemental demands for growth depend directly upon the stoichiometry of carbon and nutrients in body tissues
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KEDDY, PAUL A. "The Use of Functional as Opposed to Phylogenetic Systematics: A First Step in Predictive Community Ecology." In Biological Approaches and Evolutionary Trends in Plants. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-402960-6.50027-5.

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"Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques." In Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques, edited by Julian D. Olden and Mark J. Kennard. American Fisheries Society, 2010. http://dx.doi.org/10.47886/9781934874141.ch5.

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<em>Abstract</em>.—The flow regime is considered the primary driver of physical processes in riverine ecosystems; thus we expect that the trait composition of fish assemblages might respond similarly to hydrologic variability, even at broad spatial scales. Here, we test the hypothesis that freshwater fish life history strategies on two continents (southern United States and eastern Australia) converge along gradients of hydrologic variability and primary productivity at the drainage scale. Our results show that the fishes of the United States and Australia conform to the three-dime
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