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Journal articles on the topic 'Phylogenetic analyses'

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Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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1

Sanderson, Michael J., and H. Bradley Shaffer. "Troubleshooting Molecular Phylogenetic Analyses." Annual Review of Ecology and Systematics 33, no. 1 (November 2002): 49–72. http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150509.

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2

Kuhn, Kristen L., and Thomas J. Near. "Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences." Antarctic Science 21, no. 6 (December 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 both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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3

LI, JIA-XIN, MAO-QIANG HE, and RUI-LIN ZHAO. "Three new species of Micropsalliota (Agaricaceae, Agaricales) from China." Phytotaxa 491, no. 2 (March 19, 2021): 167–76. http://dx.doi.org/10.11646/phytotaxa.491.2.6.

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Species diversity of Micropsalliota in China remains poorly known, especially in southwestern China, a hotspot of biodiversity. Based on morphological characteristics and molecular phylogenetic analyses using ITS and nrLSU sequences, three new species named Micropsalliota delicatula, M. dentatomarginata and M. digitatocystis are introduced from China. Phylogenetc analyses results indicated the unique phylogenetic positions of three new species in Micropsalliota. Full descriptions, photo plates, illustrations and a phylogenetic tree to show the placement of three new species are presented.

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4

Moore, Jenna M., Eijiroh Nishi, and Greg W. Rouse. "Phylogenetic analyses of Chaetopteridae (Annelida)." Zoologica Scripta 46, no. 5 (March 14, 2017): 596–610. http://dx.doi.org/10.1111/zsc.12238.

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5

Michu, E. "A short guide to phylogeny reconstruction." Plant, Soil and Environment 53, No. 10 (January 7, 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 sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

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6

Farmer, Susan. "Phylogenetic Analyses and Biogeography of Trilliaceae." Aliso 22, no. 1 (2006): 579–92. http://dx.doi.org/10.5642/aliso.20062201.45.

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7

Sullivan, Patrick S., and Alexandra M. Oster. "Phylogenetic analyses of local HIV transmission." Lancet HIV 5, no. 6 (June 2018): e270-e271. http://dx.doi.org/10.1016/s2352-3018(18)30101-2.

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8

STUDLEY, WILLIAM KEITH, MUTSUO YAMAGUCHI, YOUSSEF HATEFI, and MILTON H. SAIER. "Phylogenetic Analyses of Proton-Translocating Transhydrogenases." Microbial & Comparative Genomics 4, no. 3 (January 1999): 173–86. http://dx.doi.org/10.1089/omi.1.1999.4.173.

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9

Irinyi, László, György Kövics, and Erzsébet Sándor. "Phylogenetic analysis of Phoma species." Acta Agraria Debreceniensis, no. 26 (July 16, 2007): 100–107. http://dx.doi.org/10.34101/actaagrar/26/3062.

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The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasites, and saprophyte fungal species. Up to now, the characterization of Phoma species and other taxa of Phoma has been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive complement.In this study, we tried to find molecular markers which can be used as phylogenetics markers in the molecular based classification in the Phoma genus.We employed a part of the translation elongation factor 1 subunit alpha (EF-1α=tef1) containing both introns and exons and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA, as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twelve different Phoma species sequences were analysed together with the closely related Ascochyta ones. The constructed phylogenetic trees, based on tef1 and ITS sequences, do not support the traditional Phoma sections based on morphological characterization. However, we managed to distinguish between the Phoma strains and Ascochyta species by comparing their tef1 sequences through parsimony analysis. We proved that a tef1 can be a useful phylogenetic marker to resolve phylogenetic relationships at species level in Phoma genus.Both parsimony sequence analyses confirmed that the Phyllosticta sojicola species is identical to the Phoma exigua var. exigua species as Kövics et al. (1999) claimed. However, the evolutionary distance by ITS sequences within Phoma species is too small to get well based consequences for the phylogenetic relationships of Phoma genus.Further investigations would be necessary to clarify whether the tef1 and ITS sequences as phylogenetic molecular markers are well suited for the classification of Phoma species.

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10

Mortimer, Sebastian M. E., James Boyko, Jeremy M. Beaulieu, and David C. Tank. "Synthesizing Existing Phylogenetic Data to Advance Phylogenetic Research in Orobanchaceae." Systematic Botany 47, no. 2 (June 15, 2022): 533–44. http://dx.doi.org/10.1600/036364422x16512564801560.

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Abstract— To date, no comprehensive phylogenetic analyses have been conducted in Orobanchaceae that include both a wide sampling of genera and a large sampling of species. In addition, a lack of fossil evidence in the clade precludes the use of primary fossil calibrations for divergence time estimation, preventing the establishment of a comprehensive temporal framework for use in macroevolutionary studies. Here, we use a recently developed set of tools for synthesizing publicly available data, apply these to reconstruct a comprehensive timetree for Orobanchaceae, and then investigate diversification dynamics in this clade of mostly parasitic plants using two model based methods. The assembled supermatrix included more than 900 species, representing approximately 40% of the known species diversity of the family, and the resulting phylogeny largely confirmed relationships revealed in earlier studies; however, we identified ten non-monophyletic genera that will require focused systematic attention to resolve. Diversification rate analyses found substantial support for character-dependent diversification, with elevated rates in hemiparasitic clades, and evidence for a number of speciation rate changes throughout the tree that are likely linked to other traits. Importantly, our multi-state HiSSE (Hidden State Speciation and Extinction) analysis revealed that transitions to a parasitic lifestyle only occur when there is a prior transition in an unobserved precursor state. For Orobanchaceae, our study provides a new comprehensive framework for the clade that can serve as a stepping-stone for future macroevolutionary studies.

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11

Ahmed, Mohammed, and Oleksandr Holovachov. "Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?" Animals 11, no. 12 (December 7, 2021): 3479. http://dx.doi.org/10.3390/ani11123479.

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Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.

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12

PÉREZ-EMÁN, JORGE L., JHONIEL PERDIGÓN FERREIRA, NATALIA GUTIÉRREZ-PINTO, ANDRÉS M. CUERVO, LAURA N. CÉSPEDES, CHRISTOPHER C. WITT, and CARLOS DANIEL CADENA. "An extinct hummingbird species that never was: a cautionary tale about sampling issues in molecular phylogenetics." Zootaxa 4442, no. 3 (July 2, 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 the validity of a potentially extinct species of Neotropical bird were likely compromised because within-species variation was not accounted for in phylogenetic analyses evaluating the alternative hypothesis that the only known specimen may represent a hybrid.

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13

Ryberg, Martin. "Phylommand - a command line software package for phylogenetics." F1000Research 5 (December 22, 2016): 2903. http://dx.doi.org/10.12688/f1000research.10446.1.

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Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.

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14

Vinh, Lê Sỹ. "Phylogenetic and Phylogenomic Analyses for Large Datasets." Journal of Research and Development on Information and Communication Technology 2019, no. 2 (December 31, 2019): 84–92. http://dx.doi.org/10.32913/mic-ict-research.v2019.n2.898.

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The phylogenetic tree is a main tool to study the evolutionary relationships among species. Computational methods for building phylogenetic trees from gene/protein sequences have been developed for decades and come of age. Efficient approaches, including distance-based methods, maximum likelihood methods, or classical maximum parsimony methods, are now able to analyze datasets with thousands of sequences. The advanced sequencing technologies have resulted in a huge amount of data including whole genomes. A number of methods have been proposed to analyze the wholegenome datasets, however, numerous challenges need to be addressed and solved to translate phylogenomic inferences into practices. In this paper, we will analyze widely-used methods to construct large phylogenetic trees, and available methods to build phylogenomic trees from whole-genome datasets. We will also give recommendations for best practices when performing phylogenetic and phylogenomic analyses. The paper will enable researchers to comprehend the state-ofthe-art methods and available software to efficiently study the evolutionary relationships among species from large datasets.

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15

Dittmar, Katharina, Sheila Mendonça de Souza, and Adauto Araújo. "Challenges of phylogenetic analyses of aDNA sequences." Memórias do Instituto Oswaldo Cruz 101, suppl 2 (December 2006): 9–13. http://dx.doi.org/10.1590/s0074-02762006001000003.

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16

Koziak, Alexandra T. E., Kei Chin Cheng, and R. Greg Thorn. "Phylogenetic analyses of Nematoctonus and Hohenbuehelia (Pleurotaceae)." Canadian Journal of Botany 85, no. 8 (August 2007): 762–73. http://dx.doi.org/10.1139/b07-083.

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Hohenbuehelia (Agaricales, Pleurotaceae) and Nematoctonus (Hyphomycetes) are the names for the sexual and asexual stages of a genus of nematode-destroying fungi (Basidiomycota). We obtained partial sequences of nuclear ribosomal DNA, including the internal transcribed spacer region and the 5′ end of the large subunit, of 37 isolates of Hohenbuehelia and Nematoctonus representing 13 of the 16 described species in Nematoctonus. Phylogenetic analyses support Hohenbuehelia–Nematoctonus as a monophyletic clade of the Pleurotaceae, within which the species were placed in five main subclades. Exclusively predatory species ( Nematoctonus brevisporus Thorn & G.L. Barron, Nematoctonus campylosporus Drechsler, Nematoctonus robustus F.R. Jones, and Nematoctonus sp. UAMH 5317) appear to be basal. In these species, adhesive knobs to capture prey are produced on their hyphae but not on their conidia. A single mycelial individual may feed on many nematodes. From these have arisen both exclusively parasitoid species ( Nematoctonus cylindrosporus Thorn & G.L. Barron, Nematoctonus leiosporus Drechsler, Nematoctonus leptosporus Drechsler, Nematoctonus pachysporus Drechsler, Nematoctonus tylosporus Drechsler), and species that we call intermediate predators ( Nematoctonus angustatus Thorn & G.L. Barron, Nematoctonus concurrens Drechsler, Nematoctonus geogenius Thorn & GL. Barron, Nematoctonus hamatus Thorn & G.L. Barron, and Nematoctonus subreniformis Thorn & G.L. Barron). Exclusively parasitoid species have conidia that germinate to form sticky knobs that attach to passing nematodes but lack adhesive knobs on the hyphae. Each mycelial individual feeds on only one nematode. Intermediate predators have adhesive knobs both on hyphae and on germinated conidia and can act in both predatory and parasitoid modes. Most morphospecies are resolved as monophyletic, but sequences of additional gene regions are required to clarify species limits within the N. angustatus – N. geogenius group.

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17

Frank, Daniel N., and Norman R. Pace. "Molecular-phylogenetic analyses of human gastrointestinal microbiota." Current Opinion in Gastroenterology 17, no. 1 (January 2001): 52–57. http://dx.doi.org/10.1097/00001574-200101000-00010.

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18

Rangel, Thiago F., Robert K. Colwell, Gary R. Graves, Karolina Fučíková, Carsten Rahbek, and José Alexandre F. Diniz-Filho. "Phylogenetic uncertainty revisited: Implications for ecological analyses." Evolution 69, no. 5 (April 29, 2015): 1301–12. http://dx.doi.org/10.1111/evo.12644.

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19

Hoef-Emden, K. "Molecular Phylogenetic Analyses and Real-Life Data." Computing in Science and Engineering 7, no. 3 (May 2005): 86–91. http://dx.doi.org/10.1109/mcse.2005.55.

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20

Mangubat, Erwin Z., Tsai-Tien Tseng, and Eric Jakobsson. "Phylogenetic Analyses of Potassium Channel Auxiliary Subunits." Journal of Molecular Microbiology and Biotechnology 5, no. 4 (2003): 216–24. http://dx.doi.org/10.1159/000071073.

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21

RICHTER, S. "Homologies in phylogenetic analyses – concept and tests." Theory in Biosciences 124, no. 2 (November 10, 2005): 105–20. http://dx.doi.org/10.1016/j.thbio.2005.09.004.

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22

O'Brien, S. J. "Genetic and Phylogenetic Analyses of Endangered Species." Annual Review of Genetics 28, no. 1 (December 1994): 467–89. http://dx.doi.org/10.1146/annurev.ge.28.120194.002343.

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23

Bogdanowicz, W., and R. D. Owen. "Phylogenetic analyses of the bat family Rhinolophidae." Journal of Zoological Systematics and Evolutionary Research 30, no. 2 (June 1992): 142–60. http://dx.doi.org/10.1111/j.1439-0469.1992.tb00164.x.

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24

Rafferty, Nicole E., and Anthony R. Ives. "Phylogenetic trait-based analyses of ecological networks." Ecology 94, no. 10 (October 2013): 2321–33. http://dx.doi.org/10.1890/12-1948.1.

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25

Kron, Kathleen A., Walter S. Judd, and Darren M. Crayn. "Phylogenetic analyses of Andromedeae (Ericaceae subfam. Vaccinioideae)." American Journal of Botany 86, no. 9 (September 1999): 1290–300. http://dx.doi.org/10.2307/2656777.

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26

Creevey, C. J., and J. O. McInerney. "Clann: investigating phylogenetic information through supertree analyses." Bioinformatics 21, no. 3 (September 16, 2004): 390–92. http://dx.doi.org/10.1093/bioinformatics/bti020.

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27

Hart, Michael. "Phylogenetic analyses of mode of larval development." Seminars in Cell & Developmental Biology 11, no. 6 (December 2000): 411–18. http://dx.doi.org/10.1006/scdb.2000.0194.

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28

Parczewski, Miłosz. "Subtype variability and phylogenetic analyses in HIV." HIV & AIDS Review 12, no. 4 (2013): 93–96. http://dx.doi.org/10.1016/j.hivar.2013.09.002.

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29

Richter, Stefan. "Homologies in phylogenetic analyses—concept and tests." Theory in Biosciences 124, no. 2 (November 2005): 105–20. http://dx.doi.org/10.1007/bf02814479.

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30

Molina‐Venegas, Rafael, Markus Fischer, and Andreas Hemp. "Disentangling the fundamental branching patterns of phylogenetic divergence to refine eco‐phylogenetic analyses." Journal of Biogeography 46, no. 12 (August 22, 2019): 2722–34. http://dx.doi.org/10.1111/jbi.13692.

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31

Xia, Xuhua. "Phylogenetic Relationship Among Horseshoe Crab Species: Effect of Substitution Models on Phylogenetic Analyses." Systematic Biology 49, no. 1 (January 1, 2000): 87–100. http://dx.doi.org/10.1080/10635150050207401.

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32

Thakur, Rabindra, Takashi Shiratori, and Ken-ichiro Ishida. "Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles." Protist 170, no. 5 (November 2019): 125682. http://dx.doi.org/10.1016/j.protis.2019.125682.

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33

Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (September 21, 2022): 782. http://dx.doi.org/10.3390/d14100782.

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Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.

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34

Martínez-Aquino, Andrés, Victor M. Vidal-Martínez, and M. Leopoldina Aguirre-Macedo. "A molecular phylogenetic appraisal of the acanthostominesAcanthostomumandTimoniellaand their position within Cryptogonimidae (Trematoda: Opisthorchioidea)." PeerJ 5 (December 11, 2017): e4158. http://dx.doi.org/10.7717/peerj.4158.

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The phylogenetic position of three taxa from two trematode genera, belonging to the subfamily Acanthostominae (Opisthorchioidea: Cryptogonimidae), were analysed using partial 28S ribosomal DNA (Domains 1–2) and internal transcribed spacers (ITS1–5.8S–ITS2). Bayesian inference and Maximum likelihood analyses of combined 28S rDNA and ITS1 + 5.8S + ITS2 sequences indicated the monophyly of the genusAcanthostomum(A.cf.americanumandA. burminis) and paraphyly of the Acanthostominae.These phylogenetic relationships were consistent in analyses of 28S alone and concatenated 28S + ITS1 + 5.8S + ITS2 sequences analyses. Based on molecular phylogenetic analyses, the subfamily Acanthostominae is therefore a paraphyletic taxon, in contrast with previous classifications based on morphological data. Phylogenetic patterns of host specificity inferred from adult stages of other cryptogonimid taxa are also well supported. However, analyses using additional genera and species are necessary to support the phylogenetic inferences from this study. Our molecular phylogenetic reconstruction linked two larval stages ofA.cf.americanumcercariae and metacercariae. Here, we present the evolutionary and ecological implications of parasitic infections in freshwater and brackish environments.

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35

Berčič, Rebeka Lucijana, Krisztián Bányai, Daniel Růžek, Enikő Fehér, Marianna Domán, Vlasta Danielová, Tamás Bakonyi, and Norbert Nowotny. "Phylogenetic Analysis of Lednice Orthobunyavirus." Microorganisms 7, no. 10 (October 13, 2019): 447. http://dx.doi.org/10.3390/microorganisms7100447.

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Lednice virus (LEDV) has been detected in Culex modestus mosquitoes in several European countries within the last six decades. In this study, phylogenetic analyses of the complete genome segments confirm that LEDV belongs to the Turlock orthobunyavirus (Orthobunyavirus, Peribunyaviridae) species and is closely related to Umbre, Turlock, and Kedah viruses.

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36

DE MATTOS, LETICIA, ANDRÉ LUIZ GAGLIOTI, PAULO ROBERTO DA-SILVA, LEANDRO CARDOSO PEDERNEIRAS, and SERGIO ROMANIUC-NETO. "Molecular phylogenetics of Sorocea (Moraceae)." Phytotaxa 549, no. 2 (June 8, 2022): 185–98. http://dx.doi.org/10.11646/phytotaxa.549.2.4.

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Sorocea (Moraceae) includes approximately 25 species with a Neotropical distribution and can be recognized by being shrubs to dioecious trees with paired or solitary racemose inflorescences in the leaf axils. The number of species and the phylogenetic position of this genus are divergent according to different studies. In this work, we performed a comprehensive phylogenetic analysis of Sorocea including species after Berg’s study of the genus for the Flora Neotropica. We analysed 42 accessions of Moraceae (34 taxa), including all tribes, being 21 accessions of Sorocea (13 taxa). The phylogenetic analyses were based on plastid (trnL-F) and nuclear (ITS 4-5 and FA16180b) markers using maximum parsimony, maximum likelihood and Bayesian inference. The analyses of the combined data strongly supported the monophyly of Sorocea and its position in the Moreae tribe. The genus can be divided into three major well-supported clades, for which we described novel morphological characteristics. Morphological and phylogenetic analyses suggest the ressurection of S. jureiana, S. klotzschiana, S. racemosa and S. uaupensis as species.

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37

Bastide, Paul, Claudia Solís-Lemus, Ricardo Kriebel, K. William Sparks, and Cécile Ané. "Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations." Systematic Biology 67, no. 5 (June 15, 2018): 800–820. http://dx.doi.org/10.1093/sysbio/syy033.

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Abstract The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species’ traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel’s $\lambda$ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a data set of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

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38

Pedersen, Vest. "European bumblebees (Hymenoptera: Bombini)- phylogenetic relationships inferred from DNA sequences." Insect Systematics & Evolution 33, no. 4 (2002): 361–86. http://dx.doi.org/10.1163/187631202x00208.

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AbstractThe phylogenetics of 40 taxa of European bumblebees were analysed based on PCR amplified and direct sequenced DNA from one region of the mitochondrial gene Cytochrome Oxidase I (1046 bp) and for 26 taxa from two regions in the nuclear gene Elongation Factor 1α (1056 bp). The sequences were aligned to the corresponding sequences in the honey bee. Phylogenetic analyses based on parsimony, as well as maximum likelihood, indicate that the bumblebees can be separated into several well-supported clades. Most of the terminal clades correspond very well with the clades known from former phylogenetic analyses based on morphology and recognized as the subgenera: Mendacibombus, Confusibombus, Psithyrus, Thoracobombus, Megabombus, Rhodobombus, Kallobombus, Alpinobombus, Subterraneobombus, Alpigenobombus, Pyrobombus, Bombus and Melanobombus. All the cuckoo bumblebees form a well-supported clade, the subgenus Psithyrus, within the true bumblebees. All the analyses place Kallobombus as the most basal taxon in contradiction to former analyses. The other deeper nodes of the phylogenetic trees, which are weakly supported, deviate significantly from former published trees - especially the trees based on mtCO-I. Presumably, the reasons are that multiple hits and the strong bias of the bases A and T blur the relationships in the deepest part of the trees. Analyses of the region in mtCO-I show a very strong A+T bias (A+T= 75%), which also indicate preferences in the use of codons with A or T in third positions. In closely related entities, there is only a weak transversion bias (A+T). In the studied regions in EF 1-α, no nucleotide bias is observed. The observed differences in bases between the investigated taxa are relatively small and the gene is too conserved to solve all the questions that the analyses of the deeper nodes using mtCO-I raise.

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Sanchis, Daniel, Carlos Padilla, Francisca F. Del Campo, Antonio Quesada, and Soledad Sanz-Alférez. "Phylogenetic and morphological analyses of Microcystis strains (Cyanophyta/Cyanobacteria) from a Spanish water reservoir." Nova Hedwigia 81, no. 3-4 (November 1, 2005): 431–48. http://dx.doi.org/10.1127/0029-5035/2005/0081-0431.

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Andrés-Hernández, Agustina Rosa, Teresa Terrazas, Gerardo Salazar, and Helga Ochoterena. "Phylogenetic analysis based on structural and combined analyses ofRhus s.s. (Anacardiaceae)." Botanical Journal of the Linnean Society 176, no. 4 (October 27, 2014): 452–68. http://dx.doi.org/10.1111/boj.12222.

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Zanis, Michael J., Pamela S. Soltis, Yin Long Qiu, Elizabeth Zimmer, and Douglas E. Soltis. "Phylogenetic Analyses and Perianth Evolution in Basal Angiosperms." Annals of the Missouri Botanical Garden 90, no. 2 (2003): 129. http://dx.doi.org/10.2307/3298579.

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Wu, Sheng-Hua, David S. Hibbett, and Manfred Binder. "Phylogenetic Analyses of Aleurodiscus s.l. and Allied Genera." Mycologia 93, no. 4 (July 2001): 720. http://dx.doi.org/10.2307/3761826.

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Pires, J. Chris, Michael F. Fay, Warren S. Davis, Larry Hufford, Johan Rova, Mark W. Chase, and Kenneth J. Sytsma. "Molecular and Morphological Phylogenetic Analyses of Themidaceae (Asparagales)." Kew Bulletin 56, no. 3 (2001): 601. http://dx.doi.org/10.2307/4117686.

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Chen, Cheng-Wei, Michael Sundue, Li-Yaung Kuo, Wei-Chih Teng, and Yao-Moan Huang. "Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae." PhytoKeys 78 (April 7, 2017): 83–107. http://dx.doi.org/10.3897/phytokeys.78.12040.

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Clennett, John C. B., Mark W. Chase, Félix Forest, Olivier Maurin, and Paul Wilkin. "Phylogenetic systematics ofErythronium(Liliaceae): morphological and molecular analyses." Botanical Journal of the Linnean Society 170, no. 4 (October 24, 2012): 504–28. http://dx.doi.org/10.1111/j.1095-8339.2012.01302.x.

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Shiojiri, Nobuyoshi, Harunobu Kametani, Noriaki Ota, Yusuke Akai, Tomokazu Fukuchi, Tomoka Abo, Sho Tanaka, Junri Sekiguchi, Sachie Matsubara, and Hayato Kawakami. "Phylogenetic analyses of the hepatic architecture in vertebrates." Journal of Anatomy 232, no. 2 (December 4, 2017): 200–213. http://dx.doi.org/10.1111/joa.12749.

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Ochoterena, Mark P. Simmons, Helga. "Gaps as Characters in Sequence-Based Phylogenetic Analyses." Systematic Biology 49, no. 2 (April 1, 2000): 369–81. http://dx.doi.org/10.1080/10635159950173889.

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Hillis, D. M., and J. P. Huelsenbeck. "Signal, Noise, and Reliability in Molecular Phylogenetic Analyses." Journal of Heredity 83, no. 3 (June 1992): 189–95. http://dx.doi.org/10.1093/oxfordjournals.jhered.a111190.

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Qin, Qing-Ming, Gary E. Vallad, Bo Ming Wu, and Krishna V. Subbarao. "Phylogenetic Analyses of Phytopathogenic Isolates of Verticillium spp." Phytopathology® 96, no. 6 (June 2006): 582–92. http://dx.doi.org/10.1094/phyto-96-0582.

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To better understand the genetic relationships between Verticillium dahliae isolates from lettuce and other phytopathogenic Verticillium spp. isolates from various hosts and geographic locations, the complete intergenic spacer (IGS) region of the nuclear ribosomal RNA gene (rDNA) and the β-tubulin gene were amplified and sequenced. The sequences of the complete IGS region and the β-tubulin gene were used alone and in combination to infer genetic relationships among different isolates of Verticillium with the maximum-likelihood distance method. Phylogenetic analyses set sequences into four distinct groups comprising isolates of V. albo-atrum, V. tricorpus, and V. dahliae from cruciferous and noncruciferous hosts. Within the four Verticillium groups, isolates of V. dahliae from cruciferous hosts displayed the closest affinity to V. dahliae from noncruciferous hosts. Isolates of V. dahliae from noncruciferous hosts could be further divided into four subgroups based on sequence similarities within the IGS region. Cross-pathogenicity tests demonstrated that most Verticillium isolates were as virulent on other hosts as on their hosts of origin. A phenogram based on the cross pathogenicity of individual isolates resembled those derived from the IGS and β-tubulin sequence comparisons. On the basis of the data presented, the potential origin of some isolates of V. dahliae pathogenic on lettuce is proposed.

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Ramírez-Valencia, Valentina, and David Sanín. "Spores of Serpocaulon (Polypodiaceae): morphometric and phylogenetic analyses." Grana 56, no. 3 (July 7, 2016): 187–203. http://dx.doi.org/10.1080/00173134.2016.1184307.

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