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Journal articles on the topic 'Bayesian phylogenetic analysis'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Nylander, Johan A. A., Fredrik Ronquist, John P. Huelsenbeck, and Joséluis Nieves-Aldrey. "Bayesian Phylogenetic Analysis of Combined Data." Systematic Biology 53, no. 1 (2004): 47–67. http://dx.doi.org/10.1080/10635150490264699.

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2

Lewis, Paul O., Mark T. Holder, and David L. Swofford. "Phycas: Software for Bayesian Phylogenetic Analysis." Systematic Biology 64, no. 3 (2015): 525–31. http://dx.doi.org/10.1093/sysbio/syu132.

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3

Kuhn, Kristen L., and Thomas J. Near. "Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences." Antarctic Science 21, no. 6 (2009): 565–70. http://dx.doi.org/10.1017/s0954102009990253.

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AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using bot

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4

Nascimento, Fabrícia F., Mario dos Reis, and Ziheng Yang. "A biologist’s guide to Bayesian phylogenetic analysis." Nature Ecology & Evolution 1, no. 10 (2017): 1446–54. http://dx.doi.org/10.1038/s41559-017-0280-x.

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5

Wang, Liangliang, Shijia Wang, and Alexandre Bouchard-Côté. "An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics." Systematic Biology 69, no. 1 (2019): 155–83. http://dx.doi.org/10.1093/sysbio/syz028.

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Abstract We describe an “embarrassingly parallel” method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo (SMC), based on recent advances in the SMC literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed SMC by reviewing and comparing wi

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6

Sukumaran, J., and C. W. Linkem. "Choice of Topology Estimators in Bayesian Phylogenetic Analysis." Molecular Biology and Evolution 26, no. 1 (2008): 1–3. http://dx.doi.org/10.1093/molbev/msn250.

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7

Villemereuil, Pierre de, Jessie A. Wells, Robert D. Edwards, and Simon P. Blomberg. "Bayesian models for comparative analysis integrating phylogenetic uncertainty." BMC Evolutionary Biology 12, no. 1 (2012): 102. http://dx.doi.org/10.1186/1471-2148-12-102.

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8

Dembo, Mana, Nicholas J. Matzke, Arne Ø. Mooers, and Mark Collard. "Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships." Proceedings of the Royal Society B: Biological Sciences 282, no. 1812 (2015): 20150943. http://dx.doi.org/10.1098/rspb.2015.0943.

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The phylogenetic relationships of several hominin species remain controversial. Two methodological issues contribute to the uncertainty—use of partial, inconsistent datasets and reliance on phylogenetic methods that are ill-suited to testing competing hypotheses. Here, we report a study designed to overcome these issues. We first compiled a supermatrix of craniodental characters for all widely accepted hominin species. We then took advantage of recently developed Bayesian methods for building trees of serially sampled tips to test among hypotheses that have been put forward in three of the mos

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Sansom, Robert S., Peter G. Choate, Joseph N. Keating, and Emma Randle. "Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees." Biology Letters 14, no. 6 (2018): 20180263. http://dx.doi.org/10.1098/rsbl.2018.0263.

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Reconstructing evolutionary histories requires accurate phylogenetic trees. Recent simulation studies suggest that probabilistic phylogenetic analyses of morphological data are more accurate than traditional parsimony techniques. Here, we use empirical data to compare Bayesian and parsimony phylogenies in terms of their congruence with the distribution of age ranges of the component taxa. Analysis of 167 independent morphological data matrices of fossil tetrapods finds that Bayesian trees exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees. As such, taking

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10

Yunita, Mirna, Rachmat Muwardi, and Zendi Iklima. "Implementation of Bayesian inference MCMC algorithm in phylogenetic analysis of Dipterocarpaceae family." SINERGI 27, no. 1 (2023): 23. http://dx.doi.org/10.22441/sinergi.2023..1.004.

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Dipterocarpaceae is one of the most prominent plant families, with more than 500 members of species. This family mostly used timber plants for housing, making ships, decking, and primary materials for making furniture. In Indonesia, many Dipterocarpaceae species have morphological similarities and are challenging to recognize in the field. As a result, the classification process becomes difficult and even results are inconsistent when viewed only from the morphology. This research will analyze the phylogenetic tree of Dipterocarpaceae based on the chloroplast matK gene. The aim of the research

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11

Irinyi, László, György Kövics, and Erzsébet Sándor. "Phylogenetic studies of soybean pathogen Phoma species by Bayesian analysis." Acta Agraria Debreceniensis, no. 35 (October 20, 2009): 53–61. http://dx.doi.org/10.34101/actaagrar/35/2809.

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We carried out phylogenetic study analyzing sequences of genetic markers in the taxonomy of Phoma and Phoma-like fungi. Different species of Phoma and Phoma-like fungi occurring on soybean (Phoma pinodella, Phoma sojicola, Phyllosticta sojicola, Phoma exigua var. exigua) are difficult to identy because of their high morphological and symptomatic similarities.Twenty-two isolates of nine different Phoma species were obtained from reference culture collections. Seven of them were isolated from soybean, the others were collected from different hosts.The Phoma isolates were firstly characterised by

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12

Michael, Lev, Natalia Chousou-Polydouri, Keith Bartolomei, et al. "A Bayesian Phylogenetic Classification of Tupí-Guaraní." LIAMES: Línguas Indígenas Americanas 15, no. 2 (2015): 193. http://dx.doi.org/10.20396/liames.v15i2.8642301.

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This paper presents an internal classification of Tupí-Guaraní based on lexical data from 30 Tupí-Guaraní languages and 2 non-Tupí-Guaraní Tupian languages, Awetí and Mawé. A Bayesian phylogenetic analysis using a generalized binary cognate gain and loss model was carried out on a character table based on the binary coding of cognate sets, which were formed with attention to semantic shift. The classification shows greater internal structure than previous ones, but is congruent with them in several ways.

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13

Heggarty, Paul. "Prehistory by Bayesian phylogenetics? The state of the art on Indo-European origins." Antiquity 88, no. 340 (2014): 566–77. http://dx.doi.org/10.1017/s0003598x00101188.

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Bayesian analysis has come to be widely used in archaeological chronologies and has been a regular feature of recent articles inAntiquity. Its application to linguistic prehistory, however, has proved controversial, in particular on the issue of Indo-European origins. Dating and mapping language distributions back into prehistory has an inevitable fascination, but has remained fraught with difficulty. This review of recent studies highlights the potential of increasingly sophisticated Bayesian phylogenetic models, while also identifying areas of concern, and ways in which the models might be r

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14

Cau, Andrea. "Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors." PeerJ 5 (March 1, 2017): e3055. http://dx.doi.org/10.7717/peerj.3055.

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Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the

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15

Lemmon, Alan R., Jeremy M. Brown, Kathrin Stanger-Hall, and Emily Moriarty Lemmon. "The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference." Systematic Biology 58, no. 1 (2009): 130–45. http://dx.doi.org/10.1093/sysbio/syp017.

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Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study the effects of ambiguous data (i.e., missing characters or gaps) in maximum likelihood (ML) and Bayesian frameworks. By introducing ambiguous data in a way that removes confounding factors, we provide the first clear understanding of 1 mechanism by which ambiguous data can mislead phylogenetic analyses. We find that in both ML and Bayesian frameworks, among-site rate variation can interact with ambiguo

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16

Michu, E. "A short guide to phylogeny reconstruction." Plant, Soil and Environment 53, No. 10 (2008): 442–46. http://dx.doi.org/10.17221/2194-pse.

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This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequen

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17

Furlong, Rebecca F., and Peter W. H. Holland. "Bayesian Phylogenetic Analysis Supports Monophyly of Ambulacraria and of Cyclostomes." Zoological Science 19, no. 5 (2002): 593–99. http://dx.doi.org/10.2108/zsj.19.593.

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18

Lee, Sean, and Toshikazu Hasegawa. "Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages." Proceedings of the Royal Society B: Biological Sciences 278, no. 1725 (2011): 3662–69. http://dx.doi.org/10.1098/rspb.2011.0518.

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Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory mu

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19

Ringen, Erik J., Pavel Duda, and Adrian V. Jaeggi. "The evolution of daily food sharing: A Bayesian phylogenetic analysis." Evolution and Human Behavior 40, no. 4 (2019): 375–84. http://dx.doi.org/10.1016/j.evolhumbehav.2019.04.003.

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20

Alfonso-Morales, Abdulahi, Orlando Martínez-Pérez, Roser Dolz, et al. "Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region." PLOS ONE 8, no. 6 (2013): e65999. https://doi.org/10.5281/zenodo.13531413.

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(Uploaded by Plazi for the Bat Literature Project) Background Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Methodology/Principal Findings Sequences of the hyper-variable region of the VP2 (HV

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21

Alfonso-Morales, Abdulahi, Orlando Martínez-Pérez, Roser Dolz, et al. "Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region." PLOS ONE 8, no. 6 (2013): e65999. https://doi.org/10.5281/zenodo.13531413.

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(Uploaded by Plazi for the Bat Literature Project) Background Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Methodology/Principal Findings Sequences of the hyper-variable region of the VP2 (HV

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22

Cona, Sebastián, Claudio Cornejo, Sebastián Hernández, and Christian M. Ibáñez. "Combining morphological and molecular information to infer phylogenetic relationships of lamniform sharks." Revista de Biología Marina y Oceanografía 57, Especial (2022): press. http://dx.doi.org/10.22370/rbmo.2022.57.especial.3339.

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Sharks of the order Lamniformes are restricted to 15 extant species grouped into 10 genera and 8 families. These species are characterized by two spine-less dorsal fins and a ring-shaped intestinal valve. Their phylogenetic relationships are not congruent among different methods and approaches, such as the use of morphological or molecular data. The present study evaluates the phylogenetic relationships of species of the order Lamniformes by means of phylogenetic reconstructions through Bayesian inference based on morphological and molecular data and using both datasets combined. The consensus

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23

Puttick, Mark N., Joseph E. O'Reilly, Alastair R. Tanner, et al. "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data." Proceedings of the Royal Society B: Biological Sciences 284, no. 1846 (2017): 20162290. http://dx.doi.org/10.1098/rspb.2016.2290.

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Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods s

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24

Van, Den Bussche Ronald A., Serena A. Reeder, Eric W. Hansen, and Steven R. Hoofer. "Utility of the dentin matrix protein 1 (DMP1) gene for resolving mammalian intraordinal phylogenetic relationships." Molecular Phylogenetics and Evolution 26, no. 1 (2003): 89–101. https://doi.org/10.5281/zenodo.13482417.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced exon 6 of the nuclear dentin matrix protein 1 (DMP1) gene from 19 species of bats (order Chiroptera) to assess the utility of this gene for higher-level phylogenetic studies. Bayesian analysis revealed high support (posterior probabilities P 0:95) for monophyly of Noctilionoidea (Phyllostomidae, Noctilionidae, and Mormoopidae), all genera and most families examined. Comparison of the phylogenetic information present in DMP1 with mitochondrial rDNA and nuclear RAG2 genes indicated no significant heterogeneity. Thus, we concatenated

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25

Van, Den Bussche Ronald A., Serena A. Reeder, Eric W. Hansen, and Steven R. Hoofer. "Utility of the dentin matrix protein 1 (DMP1) gene for resolving mammalian intraordinal phylogenetic relationships." Molecular Phylogenetics and Evolution 26, no. 1 (2003): 89–101. https://doi.org/10.5281/zenodo.13482417.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced exon 6 of the nuclear dentin matrix protein 1 (DMP1) gene from 19 species of bats (order Chiroptera) to assess the utility of this gene for higher-level phylogenetic studies. Bayesian analysis revealed high support (posterior probabilities P 0:95) for monophyly of Noctilionoidea (Phyllostomidae, Noctilionidae, and Mormoopidae), all genera and most families examined. Comparison of the phylogenetic information present in DMP1 with mitochondrial rDNA and nuclear RAG2 genes indicated no significant heterogeneity. Thus, we concatenated

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26

Van, Den Bussche Ronald A., Serena A. Reeder, Eric W. Hansen, and Steven R. Hoofer. "Utility of the dentin matrix protein 1 (DMP1) gene for resolving mammalian intraordinal phylogenetic relationships." Molecular Phylogenetics and Evolution 26, no. 1 (2003): 89–101. https://doi.org/10.5281/zenodo.13482417.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced exon 6 of the nuclear dentin matrix protein 1 (DMP1) gene from 19 species of bats (order Chiroptera) to assess the utility of this gene for higher-level phylogenetic studies. Bayesian analysis revealed high support (posterior probabilities P 0:95) for monophyly of Noctilionoidea (Phyllostomidae, Noctilionidae, and Mormoopidae), all genera and most families examined. Comparison of the phylogenetic information present in DMP1 with mitochondrial rDNA and nuclear RAG2 genes indicated no significant heterogeneity. Thus, we concatenated

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27

Van, Den Bussche Ronald A., Serena A. Reeder, Eric W. Hansen, and Steven R. Hoofer. "Utility of the dentin matrix protein 1 (DMP1) gene for resolving mammalian intraordinal phylogenetic relationships." Molecular Phylogenetics and Evolution 26, no. 1 (2003): 89–101. https://doi.org/10.5281/zenodo.13482417.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced exon 6 of the nuclear dentin matrix protein 1 (DMP1) gene from 19 species of bats (order Chiroptera) to assess the utility of this gene for higher-level phylogenetic studies. Bayesian analysis revealed high support (posterior probabilities P 0:95) for monophyly of Noctilionoidea (Phyllostomidae, Noctilionidae, and Mormoopidae), all genera and most families examined. Comparison of the phylogenetic information present in DMP1 with mitochondrial rDNA and nuclear RAG2 genes indicated no significant heterogeneity. Thus, we concatenated

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28

Van, Den Bussche Ronald A., Serena A. Reeder, Eric W. Hansen, and Steven R. Hoofer. "Utility of the dentin matrix protein 1 (DMP1) gene for resolving mammalian intraordinal phylogenetic relationships." Molecular Phylogenetics and Evolution 26, no. 1 (2003): 89–101. https://doi.org/10.5281/zenodo.13482417.

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(Uploaded by Plazi for the Bat Literature Project) We sequenced exon 6 of the nuclear dentin matrix protein 1 (DMP1) gene from 19 species of bats (order Chiroptera) to assess the utility of this gene for higher-level phylogenetic studies. Bayesian analysis revealed high support (posterior probabilities P 0:95) for monophyly of Noctilionoidea (Phyllostomidae, Noctilionidae, and Mormoopidae), all genera and most families examined. Comparison of the phylogenetic information present in DMP1 with mitochondrial rDNA and nuclear RAG2 genes indicated no significant heterogeneity. Thus, we concatenated

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29

Ristori, Maria Vittoria, Fabio Scarpa, Daria Sanna, et al. "Multidrug-Resistant Klebsiella pneumoniae Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology." Microorganisms 12, no. 12 (2024): 2541. https://doi.org/10.3390/microorganisms12122541.

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Multidrug-resistant Klebsiella pneumoniae is a significant healthcare challenge that particularly affects vulnerable patients through opportunistic nosocomial infections. Surveillance is crucial for monitoring the prevalence of these infections. Eighty-four KPC K. pneumoniae strains (2019–2022) were collected from patients admitted in Fondazione Policlinico Universitario Campus Bio-Medico. Strains were identified by MALDI-TOF and tested for antimicrobial susceptibility, and gene amplification was performed to identify the different blaKPC variants. Phylogenetic reconstructions were carried out

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30

Mulvey, Laura P. A., Mark C. Nikolic, Bethany J. Allen, Tracy A. Heath, and Rachel C. M. Warnock. "From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference." Paleobiology 51, no. 1 (2025): 214–36. https://doi.org/10.1017/pab.2024.47.

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AbstractIncorporating paleontological data into phylogenetic inference can greatly enrich our understanding of evolutionary relationships by providing insights into the diversity and morphological evolution of a clade over geological timescales. Phylogenetic analysis of fossil data has been significantly aided by the introduction of the fossilized birth–death (FBD) process, a model that accounts for fossil sampling through time. A decade on from the first implementation of the FBD model, we explore its use in more than 170 empirical studies, summarizing insights gained through its application.

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31

Stoffberg, Samantha, David S. Jacobs, Iain J. Mackie, and Conrad A. Matthee. "Molecular phylogenetics and historical biogeography of Rhinolophus bats." Molecular Phylogenetics and Evolution 54, no. 1 (2010): 1–9. https://doi.org/10.5281/zenodo.13421327.

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(Uploaded by Plazi for the Bat Literature Project) The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated t

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32

Stoffberg, Samantha, David S. Jacobs, Iain J. Mackie, and Conrad A. Matthee. "Molecular phylogenetics and historical biogeography of Rhinolophus bats." Molecular Phylogenetics and Evolution 54, no. 1 (2010): 1–9. https://doi.org/10.5281/zenodo.13421327.

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(Uploaded by Plazi for the Bat Literature Project) The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated t

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33

Stoffberg, Samantha, David S. Jacobs, Iain J. Mackie, and Conrad A. Matthee. "Molecular phylogenetics and historical biogeography of Rhinolophus bats." Molecular Phylogenetics and Evolution 54, no. 1 (2010): 1–9. https://doi.org/10.5281/zenodo.13421327.

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(Uploaded by Plazi for the Bat Literature Project) The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated t

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34

Stoffberg, Samantha, David S. Jacobs, Iain J. Mackie, and Conrad A. Matthee. "Molecular phylogenetics and historical biogeography of Rhinolophus bats." Molecular Phylogenetics and Evolution 54, no. 1 (2010): 1–9. https://doi.org/10.5281/zenodo.13421327.

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(Uploaded by Plazi for the Bat Literature Project) The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated t

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35

Stoffberg, Samantha, David S. Jacobs, Iain J. Mackie, and Conrad A. Matthee. "Molecular phylogenetics and historical biogeography of Rhinolophus bats." Molecular Phylogenetics and Evolution 54, no. 1 (2010): 1–9. https://doi.org/10.5281/zenodo.13421327.

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(Uploaded by Plazi for the Bat Literature Project) The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated t

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36

Stoffberg, Samantha, David S. Jacobs, Iain J. Mackie, and Conrad A. Matthee. "Molecular phylogenetics and historical biogeography of Rhinolophus bats." Molecular Phylogenetics and Evolution 54, no. 1 (2010): 1–9. https://doi.org/10.5281/zenodo.13421327.

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(Uploaded by Plazi for the Bat Literature Project) The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated t

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37

Rama, Taraka. "Three tree priors and five datasets." Language Dynamics and Change 8, no. 2 (2018): 182–218. http://dx.doi.org/10.1163/22105832-00802005.

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Abstract The age of the root of the Indo-European language family has received much attention since the application of Bayesian phylogenetic methods by Gray and Atkinson (2003). With the application of new models, the root age of the Indo-European family has tended to decrease from an age that supported the Anatolian origin hypothesis to an age that supports the Steppe origin hypothesis (Chang et al., 2015). However, none of the published work in Indo-European phylogenetics has studied the effect of tree priors on phylogenetic analyses of the Indo-European family. In this paper, I intend to fi

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38

Xia, Hongyan, Lihong Liu, Niklas Wahlberg, Claudia Baule, and Sándor Belák. "Molecular phylogenetic analysis of bovine viral diarrhoea virus: A Bayesian approach." Virus Research 130, no. 1-2 (2007): 53–62. http://dx.doi.org/10.1016/j.virusres.2007.05.017.

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39

Munch, Kasper, Wouter Boomsma, Eske Willerslev, and Rasmus Nielsen. "Fast phylogenetic DNA barcoding." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1512 (2008): 3997–4002. http://dx.doi.org/10.1098/rstb.2008.0169.

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We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria for determin

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Muhammad, Abu Bakar Abdul-Latiff, Farhani Ruslin, fui vun vui, et al. "Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences." ZooKeys 407 (May 8, 2014): 121–39. https://doi.org/10.3897/zookeys.407.6982.

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Phylogenetic relationships among Malaysia’s long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of <i>Macaca fascicularis </i>in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of <i>M. fascicularis</i> yielding 383 bp of Cytochrome <i>b </i>(Cyt <i>b) </i>sequences were used in phylogenetic analysis along with one sample each of <i>M. nemestrina</i> and <i>M. arctoides</i> used as outgroups. Sequence character analysi

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Esquivel Gomez, Luis Roger, Cyril Savin, Voahangy Andrianaivoarimanana, et al. "Phylogenetic analysis of the origin and spread of plague in Madagascar." PLOS Neglected Tropical Diseases 17, no. 5 (2023): e0010362. http://dx.doi.org/10.1371/journal.pntd.0010362.

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Background Plague is a zoonotic disease caused by the bacterium Yersinia pestis, highly prevalent in the Central Highlands, a mountainous region in the center of Madagascar. After a plague-free period of over 60 years in the northwestern coast city of Mahajanga, the disease reappeared in 1991 and caused several outbreaks until 1999. Previous research indicates that the disease was reintroduced to the city of Mahajanga from the Central Highlands instead of reemerging from a local reservoir. However, it is not clear how many reintroductions occurred and when they took place. Methodology/Principa

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King, Benedict. "Which morphological characters are influential in a Bayesian phylogenetic analysis? Examples from the earliest osteichthyans." Biology Letters 15, no. 7 (2019): 20190288. http://dx.doi.org/10.1098/rsbl.2019.0288.

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There has been much recent debate about which method is best for reconstructing the tree of life from morphological datasets. However, little attention has been paid to which characters, if any, are responsible for topological differences between trees recovered from competing methods on empirical datasets. Indeed, a simple procedure for finding characters supporting conflicting tree topologies is available in a parsimony framework, but an equivalent procedure in a model-based framework is lacking. Here, I introduce such a procedure and apply it to the problem of the ‘psarolepid’ osteichthyans

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Fontana, Carla, Silvia Angeletti, Walter Mirandola, et al. "Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae: evolutionary analysis for outbreak investigation." Future Microbiology 15, no. 3 (2020): 203–12. http://dx.doi.org/10.2217/fmb-2019-0074.

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Aim: Carbapenemase-resistant Enterobacteriaceae represents a major concern in hospital setting. Materials & methods: The evolutionary history of carbapenem-resistant Klebsiella pneumonia strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. Results: A great increase carbapenem-resistant K. pneumoniae causing blood stream infection was observed in the years 2015–2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spannin

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Shi, Huiyang. "How can statistical models improve the accuracy of phylogenetic tree reconstruction?" Theoretical and Natural Science 66, no. 1 (2024): 68–72. https://doi.org/10.54254/2753-8818/2024.17991.

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When building the phylogenetic tree, current methods for calculating phylogenetic trees often lack the desired level of accuracy. This research paper explores the role of statistical models in enhancing the precision of phylogenetic tree reconstruction. The phylogenetic tree plays an important role in phylogenetic analysis and evolutionary biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism. Recent advancements in statistical modeling have more elaborate improvements than traditional met

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ARYA, C. P., and C. K. PRADEEP. "Agaricus section Minores: New and noteworthy species from India." Phytotaxa 634, no. 3 (2024): 255–73. http://dx.doi.org/10.11646/phytotaxa.634.3.5.

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In this study, four species of Agaricus sect. Minores are presented based on morphological and nrITS based phylogenetic analyses (Maximum Likelihood and Bayesian Inference). The molecular analysis and morphological characteristics supported the placement of these species in A. sect. Minores. Three species, viz., Agaricus indicus, A. palodensis, and A. wayanadensis are new to science, while A. purpureofibrillosus is a new phytogeographical record. Comprehensive descriptions, photographs, phylogenetic analyses results, and comparisons with related species are provided.

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Liu, Jingwen, Yafen Hu, Xingxing Luo, Rafael F. Castañeda-Ruíz, and Jian Ma. "Three novel species of Helminthosporium (Massarinaceae, Pleosporales) from China." MycoKeys 94 (December 21, 2022): 73–89. http://dx.doi.org/10.3897/mycokeys.94.95888.

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Three new species of Helminthosporium, H. nabanhensis, H. sinensis and H. yunnanensis collected on dead branches of unidentified plants in Xishuangbanna, China, were proposed by morphological and molecular phylogenetic analysis. Phylogenetic analysis of the combined data of ITS-SSU-LSU-TEF1-RPB2 sequences was performed using Maximum-Likelihood and Bayesian Inference, although H. nabanhensis and H. sinensis lack the RPB2 sequences. Both molecular analyses and morphological data supported H. nabanhensis, H. sinensis and H. yunnanensis as three independent taxa within the Massarinaceae.

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Liu, Jingwen, Yafen Hu, Xingxing Luo, Rafael F. Castañeda-Ruíz, and Jian Ma. "Three novel species of Helminthosporium (Massarinaceae, Pleosporales) from China." MycoKeys 94 (December 21, 2022): 73–89. https://doi.org/10.3897/mycokeys.94.95888.

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Three new species of Helminthosporium, H. nabanhensis, H. sinensis and H. yunnanensis collected on dead branches of unidentified plants in Xishuangbanna, China, were proposed by morphological and molecular phylogenetic analysis. Phylogenetic analysis of the combined data of ITS-SSU-LSU-TEF1-RPB2 sequences was performed using Maximum-Likelihood and Bayesian Inference, although H. nabanhensis and H. sinensis lack the RPB2 sequences. Both molecular analyses and morphological data supported H. nabanhensis, H. sinensis and H. yunnanensis as three independent taxa within the Massarinaceae.

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Berling, Lars, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin, and Alexei J. Drummond. "Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities." PLOS Computational Biology 21, no. 2 (2025): e1012789. https://doi.org/10.1371/journal.pcbi.1012789.

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Bayesian phylogenetic analysis with MCMC algorithms generates an estimate of the posterior distribution of phylogenetic trees in the form of a sample of phylogenetic trees and related parameters. The high dimensionality and non-Euclidean nature of tree space complicates summarizing the central tendency and variance of the posterior distribution in tree space. Here we introduce a new tractable tree distribution and associated point estimator that can be constructed from a posterior sample of trees. Through simulation studies we show that this point estimator performs at least as well and often

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Wu, Junhao, Danping Xu, Xinju Wei, Wenkai Liao, Xiushan Li, and Zhihang Zhuo. "Characterization of the complete mitochondrial genome of the longhorn beetle, Batocera horsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles." ZooKeys 1168 (July 4, 2023): 387–402. http://dx.doi.org/10.3897/zookeys.1168.105328.

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Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocera horsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B. horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B. horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and com

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Wu, Junhao, Danping Xu, Xinju Wei, Wenkai Liao, Xiushan Li, and Zhihang Zhuo. "Characterization of the complete mitochondrial genome of the longhorn beetle, Batocera horsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles." ZooKeys 1168 (July 4, 2023): 387–402. https://doi.org/10.3897/zookeys.1168.105328.

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Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocera horsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B. horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B. horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and com

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