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Journal articles on the topic 'Community phylogenetics approach'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

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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2

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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6

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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8

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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10

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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11

Grant, Heather E., Rachel Alcraft, Pablo Bousquets-Muñoz, et al. "Abstract B004: PISCA-box: A user-friendly interface for Phylogenetic Inference using Somatic Chromosomal Alterations (PISCA)." Cancer Research 84, no. 3_Supplement_2 (2024): B004. http://dx.doi.org/10.1158/1538-7445.canevol23-b004.

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Abstract PISCA, originally introduced by Martinez et al. in 2018, represents a pivotal Bayesian phylogenetics tool for the modeling of tumor evolution using multi-region somatic chromosomal alteration (SCA) data. PISCA takes allele-specific copy number data, typically obtained from deep genome sequencing or SNP arrays, or absolute copy number data from low-pass genome sequencing methodologies. It extends the classic BEAST1 framework and inherits a rich repertoire of evolutionary models. Importantly, PISCA leverages longitudinal sampling to estimate SCA mutational clock rates, either employing

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Garner, Beulah, Alfried Vogler, Terry Erwin, and Laura Zamorano. "The carabids in the trees: rapid biodiversity assessment of an Ecuadorian rainforest." ARPHA Conference Abstracts 2 (August 20, 2019): e39251. https://doi.org/10.3897/aca.2.e39251.

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Accessing extreme environments historically unexplored by entomologists poses logistical financial and scientific challenges. Today, much of the world's natural habitats are under threat, particularly in the Neotropics. Threats from human development, exploration and indeed climate change pose the necessity for rapid arthropod biodiversity discovery and documentation. This study forms part of a long-term ecological assessment of the effects of an oil company road on primary forest within the Yasuni National Park, Ecuador. In the past 40 years this study has generated thousands of carabid speci

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13

Tofts, Richard, and Jonathan Silvertown. "A phylogenetic approach to community assembly from a local species pool." Proceedings of the Royal Society of London. Series B: Biological Sciences 267, no. 1441 (2000): 363–69. http://dx.doi.org/10.1098/rspb.2000.1010.

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14

Mohd, Hanafi Idris, Hena Mustafa Kamal Abu, Hamli Hadi, Rajaee Amy, and Al-Asif Abdulla-. "The molecular approach reveals the relationship among Venus clams (Meretrix spp.) community in Malaysia." Biotropia 29, no. 3 (2022): 213–24. https://doi.org/10.11598/btb.2022.29.3.1583.

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Molecular study is important to detect variations and similarities among species from the same genus, in case if they do not encompass any morphological or physiological differences. The study was conducted to differentiate among species of Meretrix spp. (Meretrix lyrata, M. meretrix, and M. lusoria) obtained from two locations in Malaysia through the phylogenetic tree. The adductor muscle tissues were used to extract DNA and to perform other procedures; the samples were subjected to analyses using PCR and gel electrophoresis. The multiple sequence comparison was conducted by MUSCLE and the ph

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15

Hausberger, Barbara, and Judith Korb. "A phylogenetic community approach for studying termite communities in a West African savannah." Biology Letters 11, no. 10 (2015): 20150625. http://dx.doi.org/10.1098/rsbl.2015.0625.

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Termites play fundamental roles in tropical ecosystems, and mound-building species in particular are crucial in enhancing species diversity, from plants to mammals. However, it is still unclear which factors govern the occurrence and assembly of termite communities. A phylogenetic community approach and null models of species assembly were used to examine structuring processes associated with termite community assembly in a pristine savannah. Overall, we did not find evidence for a strong influence of interspecific competition or environmental filtering in structuring these communities. Howeve

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16

Smeti, Evangelia, Konstantinos Ar Kormas, and Sofie Spatharis. "A non-phylogenetic alpha diversity approach on prokaryotic community structure in aquatic systems." Ecological Indicators 29 (June 2013): 361–66. http://dx.doi.org/10.1016/j.ecolind.2013.01.027.

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17

Quattrini, Andrea M., Peter J. Etnoyer, Cheryl Doughty, et al. "A phylogenetic approach to octocoral community structure in the deep Gulf of Mexico." Deep Sea Research Part II: Topical Studies in Oceanography 99 (January 2014): 92–102. http://dx.doi.org/10.1016/j.dsr2.2013.05.027.

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18

von Wintzingerode, Friedrich, Burkhard Selent, Werner Hegemann, and Ulf B. Göbel. "Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium." Applied and Environmental Microbiology 65, no. 1 (1999): 283–86. http://dx.doi.org/10.1128/aem.65.1.283-286.1999.

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ABSTRACT A culture-independent phylogenetic survey for an anaerobic trichlorobenzene-transforming microbial community was carried out. Small-subunit rRNA genes were PCR amplified from community DNA by using primers specific for Bacteria or Euryarchaeotaand were subsequently cloned. Application of a new hybridization-based screening approach revealed 51 bacterial clone families, one of which was closely related to dechlorinating Dehalobacter species. Several clone sequences clustered to rDNA sequences obtained from a molecular study of an anaerobic aquifer contaminated with hydrocarbons and chl

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19

Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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21

Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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22

Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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23

Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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24

Delhaye, Guillaume, Olivier J. Hardy, Maxime Séleck, Edouard Ilunga wa Ilunga, Grégory Mahy, and Pierre Meerts. "Plant community assembly along a natural metal gradient in central Africa: Functional and phylogenetic approach." Journal of Vegetation Science 31, no. 1 (2019): 151–61. http://dx.doi.org/10.1111/jvs.12829.

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25

VAN DER MESCHT, LUTHER, IRINA S. KHOKHLOVA, ELIZABETH M. WARBURTON, and BORIS R. KRASNOV. "Revisiting the role of dissimilarity of host communities in driving dissimilarity of ectoparasite assemblages: non-linear vs linear approach." Parasitology 144, no. 10 (2017): 1365–74. http://dx.doi.org/10.1017/s003118201700066x.

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SUMMARYWe revisited the role of dissimilarity of host assemblages in shaping dissimilarity of flea assemblages using a non-linear approach. Generalized dissimilarity models (GDMs) were applied using data from regional surveys of fleas parasitic on small mammals in four biogeographical realms. We compared (1) model fit, (2) the relative effects of host compositional and phylogenetic turnover and geographic distance on flea compositional and phylogenetic turnover, and (3) the rate of flea turnover along gradients of host turnover and geographic distance with those from earlier application of a l

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Santos, Alisson Borges Miranda, Vinicius Andrade Maia, Cléber Rodrigo de Souza, et al. "Disentangling spatial, environmental and historical effects on tropical forest tree species turnover." Journal of Plant Ecology 14, no. 4 (2021): 717–29. http://dx.doi.org/10.1093/jpe/rtab027.

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Abstract Aims We aimed at disentangling the effects of spatial distance, current and past environmental dissimilarity, and their combinations on tree community taxonomic and phylogenetic turnover by addressing the following questions: (i) Is tree community taxonomic and phylogenetic turnover related to the indirect effects of spatial distance via environmental dissimilarity? (ii) Does tree community taxonomic and phylogenetic turnover respond to paleoclimate (Last Glacial Maximum and Mid-Holocene)? Methods The study was carried out in 14 Atlantic rainforest sites in Brazil (20.4 ha sampled) co

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Popov, Nikolay, Ignat Sonets, Anastasia Evdokimova, et al. "AliMarko: A Pipeline for Virus Identification Using an Expert-Guided Approach." Viruses 17, no. 3 (2025): 355. https://doi.org/10.3390/v17030355.

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Viruses are ubiquitous across all kingdoms of cellular life, posing a significant threat to human health, and analyzing viral communities is challenging due to their genetic diversity and lack of a single, universally conserved marker gene. To address this challenge, we developed the AliMarko pipeline, a tool designed to streamline virus identification in metagenomic data. Our pipeline uses a dual approach, combining mapping reads with reference genomes and a de novo assembly-based approach involving an HMM-based homology search and phylogenetic analysis, to enable comprehensive detection of v

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Li, Binqiang, Jian Lu, Xin Zhong, et al. "Silent changes in taxonomic, functional and phylogenetic diversity of birds in Qiyunshan National Nature Reserve, south China." Biodiversity Data Journal 13 (March 25, 2025): e145093. https://doi.org/10.3897/BDJ.13.e145093.

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Temporal taxonomic shifts have been documented in bird communities within protected areas. However, the potential impact of these changes on functional diversity and phylogenetic diversity remains poorly understood. In this study, we monitored bird communities in Qiyunshan National Nature Reserve in southern China for nine years (2014-2022). We examined temporal trends in taxonomic, functional and phylogenetic diversity metrics and compared observed phylogenetic diversity values with expected values to determine the mechanisms driving community assembly. Additionally, we evaluated the temporal

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Presti, Alessandra Lo, Federica Del Chierico, Annamaria Altomare, et al. "Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS." Future Microbiology 14, no. 17 (2019): 1497–509. http://dx.doi.org/10.2217/fmb-2019-0175.

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Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials & methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which w

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Veldkornet, D. A., J. B. Adams, J. S. Boatwright, and A. Rajkaran. "Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline." Genome 62, no. 9 (2019): 585–95. http://dx.doi.org/10.1139/gen-2018-0067.

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Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 6

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31

Podani, János, Sandrine Pavoine, and Carlo Ricotta. "A Generalized Framework for Analyzing Taxonomic, Phylogenetic, and Functional Community Structure Based on Presence–Absence Data." Mathematics 6, no. 11 (2018): 250. http://dx.doi.org/10.3390/math6110250.

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Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based repre

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Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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35

Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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36

Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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37

Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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38

Carnicer, Jofre, Pedro Jordano, and Carlos J. Melián. "The temporal dynamics of resource use by frugivorous birds: a network approach." Ecology 90, no. 7 (2009): 1958–70. https://doi.org/10.5281/zenodo.13409528.

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(Uploaded by Plazi for the Bat Literature Project) Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant–frugivore interaction networks spanning

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39

Emerson, Brent C., Francesco Cicconardi, Pietro P. Fanciulli, and Peter J. A. Shaw. "Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1576 (2011): 2391–402. http://dx.doi.org/10.1098/rstb.2011.0057.

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There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have litt

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Casalla Daza, Robin, and Judith Korb. "Phylogenetic Community Structure and Niche Differentiation in Termites of the Tropical Dry Forests of Colombia." Insects 10, no. 4 (2019): 103. http://dx.doi.org/10.3390/insects10040103.

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The mechanisms that structure species communities are still debated. We addressed this question for termite assemblages from tropical dry forests in Colombia. These forests are endangered and poorly understood ecosystems and termites are important ecosystem engineers in the tropics. Using biodiversity and environmental data, combined with phylogenetic community analyses, trait mapping, and stable isotopes studies, we investigated the termite community composition of three protected dry forests in Colombia. Our data suggest that the structuring mechanisms differed between sites. Phylogenetic ov

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WIJAYANTI, MARINI, ARIS TRI WAHYUDI, MUNTI YUHANA, MARTIN ENGELHAUPT, and ANJA MERYANDINI. "Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia." Biodiversitas Journal of Biological Diversity 20, no. 3 (2019): 811–18. http://dx.doi.org/10.13057/biodiv/d200326.

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Abstract. Wijayanti M, Wahyudi AT, Yuhana M, Engelhaupt M, Meryandini A. 2019. Impact of Bukit Dua Belas rainforest transformation to oil palm plantation on phylogenetic of soil bacterial communities in Sarolangun, Jambi, Sumatra, Indonesia. Biodiversitas 20: 811-818. Land use change from forest to oil palm plantation at Sumatra could decrease biodiversity, including bacterial diversity. The case of Bukit Dua Belas transformation from forest to oil palm plantation was gotten for measuring shift community of soil bacterial in both areas. The diversity of bacterial communities from rainforest an

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Lin, Bin, Carlos M. Monreal, James T. Tambong, Carlos B. Miguez, and Lorna Carrasco-Medina. "Phylogenetic analysis of methanotrophic communities in cover soils of a landfill in Ontario." Canadian Journal of Microbiology 55, no. 9 (2009): 1103–12. http://dx.doi.org/10.1139/w09-069.

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We examined the methanotrophs in the Trail Road Landfill soils, Ottawa, Ontario, through cultivation-independent molecular assay and the culturing approach. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified methanotroph-specific 16S rDNA gene fragments revealed a more diverse type I (RuMP pathway) methanotrophic community than type II (serine pathway) in 17 soil samples taken along a 50 m transect. The type II methanotrophic community was less diverse, with the dominance of Methylocystis in almost all samples, and clustering with high similarity (85%–88%). Also, the results

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Rey-Suárez, Paola, Lina Preciado Rojo, Jeisson Gómez-Robles, et al. "Micrurus nigrocinctus in Colombia: Integrating Venomics Research, Citizen Science, and Community Empowerment." Toxins 17, no. 6 (2025): 268. https://doi.org/10.3390/toxins17060268.

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Snakebite is a high-priority neglected tropical disease, and a strategic goal based on four pillars has been recommended to reduce mortality and morbidity. One is empowering rural communities through citizen science, education, and engagement. In this study, an integrative approach was used to expand our knowledge of Micrurus nigrocinctus status and characterize its venom. Using citizen science data and field visits to local communities, 99 records of M. nigrocinctus distributed in Antioquia, Chocó, and Córdoba were obtained. Children, young people, and adults recognized M. nigrocinctus as the

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Lam, Tony J., Moses Stamboulian, Wontack Han, and Yuzhen Ye. "Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species." PLOS Computational Biology 16, no. 10 (2020): e1007951. http://dx.doi.org/10.1371/journal.pcbi.1007951.

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Microbial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of cooperative and competitive metabolic interactions between bacterial species. By nature, phylogenetically similar microbial species are more likely to share common functional profiles or biological pathways due

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Wijayanti, Marini, Aris Tri Wahyudi, Munti Yuhana, Martin Engelhaupt, and Anja Meryandini. "Bacterial Communities in Aquatic Sediment from Bukit Duabelas Raintforest and Oil Palm Plantation at Sumatra Indonesia." HAYATI Journal of Biosciences 25, no. 2 (2018): 85. http://dx.doi.org/10.4308/hjb.25.2.85.

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The diversity of bacterial communities in aquatic sediment of rainforest and oil palm plantation at Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices. Phylogenetic approach was used for revealing the community shift of bacterial phyla and genera in both areas. Ecological approach used soil pH, total Carbon (TC), total Nitrogen (TN), available Phosphorus (AP) measurement and bacterial diversity with Shanon and Simpson indices, and bacterial richness with Chao1-ACE indices and OTUs. Bacterial diversity and richness in aquatic sediment of forest area was hi

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Gómez, Juan Pablo, Gustavo A. Bravo, Robb T. Brumfield, José G. Tello, and Carlos Daniel Cadena. "A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds." Journal of Animal Ecology 79, no. 6 (2010): 1181–92. http://dx.doi.org/10.1111/j.1365-2656.2010.01725.x.

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Li, Yongmin, Xiaoyu Wang, Xu Yong, Yatao Wu, Chuansheng Wu, and Wenfeng Hu. "Assembly Processes of Waterbird Communities Across Different Types of Wetlands in the Middle Reaches of the Huaihe River Basin." Water 17, no. 8 (2025): 1118. https://doi.org/10.3390/w17081118.

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Understanding the processes and potential mechanisms of species coexistence within biological communities is a key issue in biodiversity conservation. The Huaihe River Basin, situated in the transitional zone between northern and southern China, encompasses diverse wetland types in its middle reaches, including lakes, ponds, rivers, and subsidence areas. This unique combination of habitats provides an ideal natural laboratory for investigating the mechanisms governing bird community dynamics. Here, we quantified the species, taxonomic, functional, and phylogenetic diversity of waterbird commun

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Youssef, Noha, Brandi L. Steidley, and Mostafa S. Elshahed. "Novel High-Rank Phylogenetic Lineages within a Sulfur Spring (Zodletone Spring, Oklahoma), Revealed Using a Combined Pyrosequencing-Sanger Approach." Applied and Environmental Microbiology 78, no. 8 (2012): 2677–88. http://dx.doi.org/10.1128/aem.00002-12.

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ABSTRACTThe utilization of high-throughput sequencing technologies in 16S rRNA gene-based diversity surveys has indicated that within most ecosystems, a significant fraction of the community could not be assigned to known microbial phyla. Accurate determination of the phylogenetic affiliation of such sequences is difficult due to the short-read-length output of currently available high-throughput technologies. This fraction could harbor multiple novel phylogenetic lineages that have so far escaped detection. Here we describe our efforts in accurate assessment of the novelty and phylogenetic af

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Mukti, Roushney Fatima, and Sanjida Sakhawat Sinthee. "Metagenomic Approach: Transforming In-Silico Research for Improved Biogas Production." International Journal of Applied Sciences and Biotechnology 7, no. 1 (2019): 6–11. http://dx.doi.org/10.3126/ijasbt.v7i1.23315.

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The complexity of the microbial communities and metabolic pathways involved in the microbiological process of biogas production is poorly understood and numerous microorganisms in the fermentation sample of the biogas plant are still unclassified or unknown. The structure and function of microbial communities and the effects of the addition of trace elements are needed to be known, to control and channel the energy sources microbes produce and to capture and store the useful by-products or for targeted screening of novel enzymes. In this review, we discussed an emerging idea that Metagenome se

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GUTIÉRREZ, P. A. "Monogenean community structure on the gills of Pimelodus albicans from Río de la Plata (Argentina): a comparative approach." Parasitology 122, no. 4 (2001): 465–70. http://dx.doi.org/10.1017/s003118200100748x.

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The community structure of monogeneans on the gills of a catfish Pimelodus albicans, in the Río de la Plata, was studied and compared with previous findings on P. maculatus. Six Monogenea species belonging to 3 genera were found: Demidospermus majusculus Kritsky & Gutiérrez, 1998; Demidospermus armostus Kritsky & Gutiérrez, 1998; Demidospermus idolus Kritsky & Gutiérrez, 1998; Demidospermus bidiverticulatum (Suriano & Incorvaia, 1995) Kritsky & Gutiérrez, 1998; Scleroductus yuncensi Jara & Cone, 1989; and Unibarra paranoplatensis Suriano & Incorvaia, 1995. The relat

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