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Journal articles on the topic 'Phylogenetic variation'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Pereira, Islandia Silva, and Pedro Vasconcellos Eisenlohr. "It Is Neither the Environment Nor the Space, But Phylogeny, That Best Explains The Variation in Tree Species Composition in Brazil." Revista de Gestão Social e Ambiental 19, no. 2 (2025): e011087. https://doi.org/10.24857/rgsa.v19n2-041.

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Objective: This study aims to evaluate the relative importance of phylogenetic, environmental, and spatial components in explaining the floristic variation of tree communities, with the goal of understanding the different processes shaping tree assemblages in Brazil. Methodology: The methodology adopted for this research includes the construction of eigenvectors to operationalize the predictor variables (phylogeny, environment, and space) in our models. We employed variation partitioning using canonical models, predicting that the phylogenetic component would play a stronger role in explaining

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2

Freckleton, Robert P., and Walter Jetz. "Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data." Proceedings of the Royal Society B: Biological Sciences 276, no. 1654 (2008): 21–30. http://dx.doi.org/10.1098/rspb.2008.0905.

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Variation in traits across species or populations is the outcome of both environmental and historical factors. Trait variation is therefore a function of both the phylogenetic and spatial context of species. Here we introduce a method that, within a single framework, estimates the relative roles of spatial and phylogenetic variations in comparative data. The approach requires traits measured across phylogenetic units, e.g. species, the spatial occurrences of those units and a phylogeny connecting them. The method modifies the expected variance of phylogenetically independent contrasts to inclu

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Peres-Neto, Pedro R., and Steven W. Kembel. "Phylogenetic gradient analysis: environmental drivers of phylogenetic variation across ecological communities." Plant Ecology 216, no. 5 (2015): 709–24. http://dx.doi.org/10.1007/s11258-014-0405-0.

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Shapoval, Nazar A., and Vladimir A. Lukhtanov. "Intragenomic variations of multicopy ITS2 marker in Agrodiaetus blue butterflies (Lepidoptera, Lycaenidae)." Comparative Cytogenetics 9, no. (4) (2015): 483–97. https://doi.org/10.3897/CompCytogen.v9i4.5429.

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The eukaryotic ribosomal DNA cluster consists of multiple copies of three genes, 18S, 5. 8S and 28S rRNAs, separated by multiple copies of two internal transcribed spacers, ITS1 and ITS2. It is an important, frequently used marker in both molecular cytogenetic and molecular phylogenetic studies. Despite this, little is known about intragenomic variations within the copies of eukaryotic ribosomal DNA genes and spacers. Here we present data on intraindividual variations of ITS2 spacer in three species of Agrodiaetus Hübner, 1822 blue butterflies revealed by cloning technique. We demonstrate that

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Suchard, Marc A., Robert E. Weiss, Karin S. Dorman, and Janet S. Sinsheimer. "Inferring Spatial Phylogenetic Variation Along Nucleotide Sequences." Journal of the American Statistical Association 98, no. 462 (2003): 427–37. http://dx.doi.org/10.1198/016214503000215.

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6

Cros, J., M. C. Combes, P. Trouslot, et al. "Phylogenetic Analysis of Chloroplast DNA Variation inCoffeaL." Molecular Phylogenetics and Evolution 9, no. 1 (1998): 109–17. http://dx.doi.org/10.1006/mpev.1997.0453.

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7

Powell, Jeffrey R., and Adalgisa Caccone. "Intraspecific and interspecific genetic variation in Drosophila." Genome 31, no. 1 (1989): 233–38. http://dx.doi.org/10.1139/g89-040.

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Utilizing the technique of DNA – DNA hybridization, we have characterized the degree of genetic variability in single-copy DNA both within and between several species of Drosophila. The results of intraspecific variation studies indicate considerable variation both for levels of nucleotide heterozygosity (estimated to be over 2%) as well as for insertions–deletions. Interspecific studies confirm this great deal of variability and further establish an extreme heterogeneity within Drosophila genomes for rates of divergence. This heterogeneity is much more extreme than that seen between exons and

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KRASNOV, BORIS R., SHAI PILOSOF, GEORGY I. SHENBROT, IRINA S. KHOKHLOVA, and A. ALLAN DEGEN. "Phylogenetic structure of host spectra in Palaearctic fleas: stability versus spatial variation in widespread, generalist species." Parasitology 141, no. 2 (2013): 181–91. http://dx.doi.org/10.1017/s0031182013001376.

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SUMMARYWe investigated spatial variation in the phylogenetic structure of host spectra in fleas parasitic on small mammals. Measures of phylogenetic host specificity ((phylogenetic species clustering (PSC) and phylogenetic species variability (PSV)) varied significantly more between than within flea species, but the proportion of variation which accounted for among-species differences was low. In 13 of 18 common flea species, at least one of the indices of the phylogenetic structure of regional host spectra revealed a significantly positive association with the phylogenetic structure of region

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Cisneros, Laura M., Matthew E. Fagan, and Michael R. Willig. "Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes." PeerJ 4 (October 13, 2016): e2551. http://dx.doi.org/10.7717/peerj.2551.

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BackgroundAssembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively

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Xu, Huiying, Han Wang, Iain Colin Prentice, and Sandy P. Harrison. "Leaf carbon and nitrogen stoichiometric variation along environmental gradients." Biogeosciences 20, no. 22 (2023): 4511–25. http://dx.doi.org/10.5194/bg-20-4511-2023.

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Abstract. Leaf stoichiometric traits are central to ecosystem function and biogeochemical cycling, yet no accepted theory predicts their variation along environmental gradients. Using data in the China Plant Trait Database version 2, we aimed to characterize variation in leaf carbon and nitrogen per unit mass (Cmass, Nmass) and their ratio and to test an eco-evolutionary optimality model for Nmass. Community-mean trait values were related to climate variables by multiple linear regression. Climatic optima and tolerances of major genera were estimated; Pagel's λ was used to quantify phylogeneti

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11

Phung, Chee-Chean, Pooi-San Heng, and Thor-Seng Liew. "Land snails ofLeptopomaPfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form." PeerJ 5 (October 31, 2017): e3981. http://dx.doi.org/10.7717/peerj.3981.

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Leptopomais a species rich genus with approximately 100 species documented. Species-level identification in this group has been based on shell morphology and colouration, as well as some anatomical features based on small sample sizes. However, the implications of the inter- and intra-species variations in shell form to the taxonomy ofLeptopomaspecies and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. There are fourLeptopomaspecies found in Sabah, Borneo, and their taxonomy status remains uncertain due to substantial variation in shell forms.

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Barbadillo, Luis J., and Iñigo Martínez-Solano. "Vertebral Intercentra in Lacertidae: Variation and Phylogenetic Implications." Copeia 2002, no. 1 (2002): 208–12. http://dx.doi.org/10.1643/0045-8511(2002)002[0208:viilva]2.0.co;2.

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13

Woods, H. A., W. F. Fagan, J. J. Elser, and J. F. Harrison. "Allometric and phylogenetic variation in insect phosphorus content." Functional Ecology 18, no. 1 (2004): 103–9. http://dx.doi.org/10.1111/j.1365-2435.2004.00823.x.

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14

BERTOLANI, ROBERTO, LORENA REBECCHI, and SANDRA K. CLAXTON. "Phylogenetic significance of egg shell variation in tardigrades." Zoological Journal of the Linnean Society 116, no. 1-2 (1996): 139–48. http://dx.doi.org/10.1111/j.1096-3642.1996.tb02339.x.

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15

Broadley, Martin R., Neil J. Willey, Janine C. Wilkins, Alan J. M. Baker, Andrew Mead, and Philip J. White. "Phylogenetic variation in heavy metal accumulation in angiosperms." New Phytologist 152, no. 1 (2001): 9–27. http://dx.doi.org/10.1046/j.0028-646x.2001.00238.x.

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HODSON, M. J., P. J. WHITE, A. MEAD, and M. R. BROADLEY. "Phylogenetic Variation in the Silicon Composition of Plants." Annals of Botany 96, no. 6 (2005): 1027–46. http://dx.doi.org/10.1093/aob/mci255.

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17

Santorelli, Sergio, William Magnusson, Efrem Ferreira, Erica Caramaschi, Jansen Zuanon, and Sidnéia Amadio. "Phylogenetic community structure: temporal variation in fish assemblage." Ecology and Evolution 4, no. 11 (2014): 2146–53. http://dx.doi.org/10.1002/ece3.1026.

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18

Northcutt, R. Glenn. "Brain variation and phylogenetic trends in elasmobranch fishes." Journal of Experimental Zoology 252, S2 (1989): 83–100. http://dx.doi.org/10.1002/jez.1402520410.

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19

Wang, Mao, Jinshi Xu, Yongfu Chai, Yaoxin Guo, Xiao Liu, and Ming Yue. "Differentiation of Environmental Conditions Promotes Variation of Two Quercus wutaishanica Community Assembly Patterns." Forests 11, no. 1 (2019): 43. http://dx.doi.org/10.3390/f11010043.

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Two contradictory niche-based processes, environmental filtering and competitive exclusion, are important ecological processes in community assembly. Quercus wutaishanica forests are the climax communities in the Qinling Mountains and the Loess Plateau, China. Since these areas are characterized by different climate and evolutionary histories, these forests could be a suitable study system to test the phylogenetic niche conservatism hypothesis. We compared variation in community assembly of two distinct Q. wutaishanica forest communities and analyzed how the variations are formed. Quercus wuta

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20

Sweeney, Robert J., Irby J. Lovette, and Erica L. Harvey. "Evolutionary Variation in Feather Waxes of Passerine Birds." Auk 121, no. 2 (2004): 435–45. http://dx.doi.org/10.1093/auk/121.2.435.

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Abstract Feather waxes are ubiquitous in passerine birds, but their composition, phylogenetic distribution, and function are poorly characterized. We used gas chromatography–mass spectrometry to survey the diversity of saturated fatty acids in feather waxes of 91 taxa representing most major passerine groups, and used an independent phylogenetic hypothesis to explore evolutionary variation in the expression of those compounds. Saturated fatty acids are highly stable, and we obtained congruent results in comparisons of extracts from fresh material and from museum skins as much as a century old.

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21

Baele, Guy, Mandev S. Gill, Paul Bastide, Philippe Lemey, and Marc A. Suchard. "Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST." Systematic Biology 70, no. 1 (2020): 181–89. http://dx.doi.org/10.1093/sysbio/syaa037.

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Abstract Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting differen

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22

Cortés-Ramírez, Gala, César A. Ríos-Muñoz, and Adolfo G. Navarro-Sigüenza. "Influence of phylogenetic structure and climate gradients on geographical variation in the morphology of Mexican flycatcher forests assemblages (Aves: Tyrannidae)." PeerJ 7 (October 15, 2019): e6754. http://dx.doi.org/10.7717/peerj.6754.

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Morphological variation is strongly related to variation in the ecological characteristics and evolutionary history of each taxon. To explore how geographical variation in morphology is related to different climatic gradients and phylogenetic structure, we analyzed the variation of morphological traits (body size, bill, and wing) of 64 species of tyrant flycatchers (Tyrannidae) distributed in Mexico. We measured these morphological traits in specimens from biological collections and related them to the climatic and topographic data of each collection locality. We performed the analyses separat

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23

Dayananda, P. D., Harendra de Silva, LakKumar Fernando, and B. G. D. N. K. de Silva. "Genetic Variation in the Domain II, 3′ Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka." Viruses 13, no. 3 (2021): 421. http://dx.doi.org/10.3390/v13030421.

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Genetic variations in dengue virus (DENV) play a distinct role in epidemic emergence. The DENV 3′ UTR has become a recent interest in research. The objective of the study was to examine the genetic variation in the domain II, 3′ UTR region of human and mosquito-derived DENV. DENV-infected human sera were orally infected to laboratory reared Aedes aegypti mosquitoes. The domain II, 3′ UTR of each human- and mosquito-derived sample was amplified. The nucleotide sequence variation, phylogenetic and secondary structure analysis was carried out incorporating respective regions of so far recorded Sr

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24

Castanet, Jacques, Jorge Cubo, and Laëtitia Montes. "Relationship between bone growth rate and bone tissue organization in amniotes: first test of Amprino's rule in a phylogenetic context." Animal Biology 60, no. 1 (2010): 25–41. http://dx.doi.org/10.1163/157075610x12610595764093.

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AbstractA debate on the determinism (phylogenetic versus functional) of the diversity of bone histological features has centred the interest of bone comparative biologists. While some authors have noticed the presence of a phylogenetic signal in bone tissue variation, many others have argued that these characters may not include much phylogenetic information, but rather reflect functional factors. Here we quantify both components in a sample of amniotes. We hypothesize that: 1/ the observed variation is partly the outcome of shared ancestry (phylogenetic factor) and 2/ for a given quantity of

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25

Bell, Michael A. "Intraspecific Systematics of Gasterosteus Aculeatus Populations: Implications for Behavioral Ecology." Behaviour 132, no. 15-16 (1995): 1131–52. http://dx.doi.org/10.1163/156853995x00496.

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AbstractThe threespine stickleback is widespread in diverse coastal marine and freshwater habitats of the Holarctic. Extensive information on its behavior and evolution provide an exceptional background for behavioral ecology. The behavioral phenotype links studies of proximate and ultimate (evolutionary) causes of behavior. Analyses of the ultimate causes of behavior should be placed in a phylogenetic context. There have been four phases of interpretation of phenotypic variation in threespine stickleback: (1) taxonomic, (2) dispersalist-neutralist, (3) adaptationist, and (4) adaptationist-phy

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Haq, Faiz Ul, Sidrah Saleem, Muhammad Imran, et al. "Phylogenetic analyses and genomic variation of the 2019-nCoV." Journal of Pharmaceutical and Biopharmaceutical Research 2, no. 1 (2020): 126–30. http://dx.doi.org/10.25082/jpbr.2020.01.004.

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There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenet

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Arnan, Xavier, Xim Cerdá, and Javier Retana. "Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants." PeerJ 3 (September 29, 2015): e1241. http://dx.doi.org/10.7717/peerj.1241.

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We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how m

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Moody, Eric K., Fernando Alda, Krista A. Capps, Oscar Puebla, and Benjamin L. Turner. "Trophic Trait Evolution Explains Variation in Nutrient Excretion Stoichiometry among Panamanian Armored Catfishes (Loricariidae)." Diversity 11, no. 6 (2019): 88. http://dx.doi.org/10.3390/d11060088.

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Variation in nutrient excretion rates and stoichiometric ratios (e.g., nitrogen to phosphorus) by consumers can have substantial effects on aquatic ecosystem function. While phylogenetic signals within an assemblage often explain variation in nutrient recycling rates and stoichiometry, the phylogenetically conserved traits that underlie this phenomenon remain unclear. In particular, variation in nutrient excretion stoichiometry across a phylogeny might be driven by phylogenetic patterns in either diet or body stoichiometry. We examined the relative importance of these traits in explaining vari

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PÉREZ-EMÁN, JORGE L., JHONIEL PERDIGÓN FERREIRA, NATALIA GUTIÉRREZ-PINTO, et al. "An extinct hummingbird species that never was: a cautionary tale about sampling issues in molecular phylogenetics." Zootaxa 4442, no. 3 (2018): 491. http://dx.doi.org/10.11646/zootaxa.4442.3.11.

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The selection of species and individuals for molecular analyses critically affects inferences in various fields of systematic biology including phylogenetics, phylogeography, and species delimitation. Especially in areas like the Neotropical region where molecular analyses have recovered substantial within-species divergence and unexpected affinities of populations (Turchetto-Zolet et al. 2013), biases resulting from incomplete taxonomic or geographic sampling may compromise the understanding of phylogenetic relationships (Avendaño et al. 2017). Here we describe a case in which assessments of

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Fišer, Cene, and Ester Premate. "Phenotype Variation in Niphargus (Amphipoda: Niphargidae): Possible Explanations and Open Challenges." Diversity 16, no. 7 (2024): 375. http://dx.doi.org/10.3390/d16070375.

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Understanding phenotype variation is among the central topics in biology. We revise and reanalyze studies of the amphipod genus Niphargus to confront two potential mechanisms driving its phenotype variation, namely, cladogenesis and adaptive evolution. We found evidence for both mechanisms. Reanalysis of a subset of traits using molecular phylogeny showed moderate phylogenetic signal, consistent with the hypothesis that overall phylogenetic variation increases with phylogeny. The phylogenetic signal in Niphargus traits seems to be stronger at the tips of the phylogeny than at basal splits. Ind

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Milner, Melita L., Emma J. McIntosh, Michael D. Crisp, Peter H. Weston, and Maurizio Rossetto. "Microsatellite variation for phylogenetic, phylogeographic and population-genetic studies in Lomatia (Proteaceae)." Australian Systematic Botany 26, no. 3 (2013): 186. http://dx.doi.org/10.1071/sb13002.

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Lomatia R.Br. is a genus of 12 species in South America and eastern Australia. Hybridisation is extensive in the Australian species and molecular work is required to understand phylogenetic relationships and examine potential gene flow among species. We developed a library of microsatellite markers for Lomatia silaifolia (Sm.) R.Br. These markers were tested across population samples of L. silaifolia and L. myricoides (C.F.Gaertn.) Domin, assessed for cross amplification across all 12 species of Lomatia, sequenced and inspected for variation in the microsatellite flanking region (MFR), and uti

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Chen, Shufen, Wataru Ishizuka, Toshihiko Hara, and Susumu Goto. "Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population." Forests 11, no. 8 (2020): 884. http://dx.doi.org/10.3390/f11080884.

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Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit popu

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Davis, Jerrold I., and Kevin C. Nixon. "Populations, Genetic Variation, and the Delimitation of Phylogenetic Species." Systematic Biology 41, no. 4 (1992): 421. http://dx.doi.org/10.2307/2992584.

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Stevens, P. F. "Character States, Morphological Variation, and Phylogenetic Analysis: A Review." Systematic Botany 16, no. 3 (1991): 553. http://dx.doi.org/10.2307/2419343.

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INDA, LUIS A., MANUEL PIMENTEL, and MARK W. CHASE. "Chalcone synthase variation and phylogenetic relationships in Dactylorhiza (Orchidaceae)." Botanical Journal of the Linnean Society 163, no. 2 (2010): 155–65. http://dx.doi.org/10.1111/j.1095-8339.2010.01055.x.

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36

Brasher, D. J., J. R. Ovenden, and R. W. G. White. "Mitochondrial DNA variation and phylogenetic relationships ofJasusspp. (Decapoda: Palinuridae)." Journal of Zoology 227, no. 1 (1992): 1–16. http://dx.doi.org/10.1111/j.1469-7998.1992.tb04340.x.

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37

Alberts, Allison C. "Phylogenetic and Adaptive Variation in Lizard Femoral Gland Secretions." Copeia 1991, no. 1 (1991): 69. http://dx.doi.org/10.2307/1446249.

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Kim, Ki-Joong, Robert K. Jansen, Robert S. Wallace, Helen J. Michaels, and Jeffrey D. Palmer. "Phylogenetic Implications of rbcL Sequence Variation in the Asteraceae." Annals of the Missouri Botanical Garden 79, no. 2 (1992): 428. http://dx.doi.org/10.2307/2399779.

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Orti, G., D. E. Pearse, and J. C. Avise. "Phylogenetic assessment of length variation at a microsatellite locus." Proceedings of the National Academy of Sciences 94, no. 20 (1997): 10745–49. http://dx.doi.org/10.1073/pnas.94.20.10745.

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Broadley, M. R., H. C. Bowen, H. L. Cotterill, et al. "Phylogenetic variation in the shoot mineral concentration of angiosperms." Journal of Experimental Botany 55, no. 396 (2004): 321–36. http://dx.doi.org/10.1093/jxb/erh002.

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Yoder, Jeremy B., Roman Briskine, Joann Mudge, et al. "Phylogenetic Signal Variation in the Genomes of Medicago (Fabaceae)." Systematic Biology 62, no. 3 (2013): 424–38. http://dx.doi.org/10.1093/sysbio/syt009.

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Sakurai, Akira, and Paul S. Katz. "Phylogenetic and individual variation in gastropod central pattern generators." Journal of Comparative Physiology A 201, no. 9 (2015): 829–39. http://dx.doi.org/10.1007/s00359-015-1007-6.

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Maekawa, S., N. Enomoto, M. Kurosaki, F. Marumo, and C. Sato. "Host dependent variation of hepatitis C virus: phylogenetic analyses." Archives of Virology 140, no. 12 (1995): 2123–33. http://dx.doi.org/10.1007/bf01323235.

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Davis, J. I., and K. C. Nixon. "Populations, Genetic Variation, and the Delimitation of Phylogenetic Species." Systematic Biology 41, no. 4 (1992): 421–35. http://dx.doi.org/10.1093/sysbio/41.4.421.

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Ito, Tsuyoshi, Takeshi Nishimura, and Masanaru Takai. "Ecogeographical and phylogenetic effects on craniofacial variation in macaques." American Journal of Physical Anthropology 154, no. 1 (2014): 27–41. http://dx.doi.org/10.1002/ajpa.22469.

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Sun, Kuo, Qingxiong Wang, Kun Bian, et al. "Complete Mitochondrial Genomes of Pluvialis fulva and Charadrius dubius with Phylogenetic Analysis of Charadriiformes." Genes 15, no. 12 (2024): 1642. https://doi.org/10.3390/genes15121642.

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Background: Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of Charadrius and the phylogenetic placement of Pluvialis remain contentious. Nevertheless, recent studies utilizing complete mitogenomes from available databases to construct phylogenetic trees for Charadriidae and Charadriiformes remain scarce. Metho

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KRASNOV, BORIS R., DAVID MOUILLOT, IRINA S. KHOKHLOVA, GEORGY I. SHENBROT, and ROBERT POULIN. "Compositional and phylogenetic dissimilarity of host communities drives dissimilarity of ectoparasite assemblages: geographical variation and scale-dependence." Parasitology 139, no. 3 (2012): 338–47. http://dx.doi.org/10.1017/s0031182011002058.

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SUMMARYWe tested the hypothesis that compositional and/or phylogenetic dissimilarity of host assemblages affect compositional and/or phylogenetic dissimilarity of parasite assemblages, to different extents depending on scale, using regional surveys of fleas parasitic on small mammals from 4 biogeographical realms. Using phylogenetic community dissimilarity metric, we calculated the compositional and phylogenetic dissimilarity components between all pairs of host and parasite communities within realms and hemispheres. We then quantified the effect of compositional or phylogenetic dissimilarity

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Titus, G. O., G. N. Ani, M. Animashaun, Z. O. Abdulrahman-Giwa, and A. O. Giwa. "Stop Codon Usage of Three Gene Families in Selected Medical Insects, and their Phylogenetic Relationships." Nigerian Journal of Entomology 40, no. 2 (2024): 196–209. http://dx.doi.org/10.36108/nje/4202/04.0251.

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Medical insects pose significant health risks, transmitting disease causing agents with significant morbidity and mortality globally. Understanding their genetic composition and evolutionary relationship is crucial to developing control techniques to combat them. This study aims to compare the stop codon usage of gustatory, odorant and kinase genes, and assess their use as markers for evaluating the phylogenetic relationship between selected medical insects. Fifteen genes from three gene families including gustatory receptors, odorant receptors, and kinases were studied in thirty-four insect s

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Liu, G. H., B. Li, J. Y. Li, et al. "Genetic variation among Clonorchis sinensis isolates from different geographic regions in China revealed by sequence analyses of four mitochondrial genes." Journal of Helminthology 86, no. 4 (2011): 479–84. http://dx.doi.org/10.1017/s0022149x11000757.

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AbstractThe present study examined sequence variation in four mitochondrial (mt) genes, namely cytochrome c oxidase subunits 1 (cox1) and 2 (cox2), and NADH dehydrogenase subunits 1 and 2 (nad1 and nad2) among Clonorchis sinensis isolates from different endemic regions in China, and their phylogenetic relationships with other zoonotic trematodes were reconstructed. A portion of the cox1 and cox2 genes (pcox1 and pcox2), and nad1 and nad2 genes (pnad1 and pnad2) were amplified separately from individual liver flukes by polymerase chain reaction (PCR) and the amplicons were subjected to sequenci

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Levin, David B., and Beatrixe Whittome. "Codon usage in nucleopolyhedroviruses." Journal of General Virology 81, no. 9 (2000): 2313–25. http://dx.doi.org/10.1099/0022-1317-81-9-2313.

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Phylogenetic analyses based on baculovirus polyhedrin nucleotide and amino acid sequences revealed two major nucleopolyhedrovirus (NPV) clades, designated Group I and Group II. Subsequent phylogenetic analyses have revealed three Group II subclades, designated A, B and C. Variations in amino acid frequencies determine the extent of dissimilarity for divergent but structurally and functionally conserved genes and therefore significantly influence the analysis of phylogenetic relationships. Hence, it is important to consider variations in amino acid codon usage. The Genome Hypothesis postulates

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