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Journal articles on the topic 'Animal phylogenetics'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Luchetti, Andrea, and Federico Plazzi. "Molecular Phylogenetics and Mitochondrial Evolution." Life 12, no. 1 (2021): 4. http://dx.doi.org/10.3390/life12010004.

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2

GIRIBET, GONZALO, CASEY W. DUNN, GREGORY D. EDGECOMBE, and GREG W. ROUSE. "A modern look at the Animal Tree of Life*." Zootaxa 1668, no. 1 (2007): 61–79. http://dx.doi.org/10.11646/zootaxa.1668.1.8.

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The phylogenetic interrelationships of animals (Metazoa) have been elucidated by refined systematic methods and by new techniques, notably from molecular biology. In parallel with the strong molecular focus of contemporary metazoan phylogenetics, morphology has advanced with the introduction of new approaches, such as confocal laser scanning microscopy and cell-labelling in the study of embryology. The discovery of new animal diversity (previously unknown groups like Cycliophora and Micrognathozoa) has invigorated the field as well. At present, broad consensus exists for the monophyly of bilat

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3

Ghiselin, Michael T. "Classical and molecular phylogenetics." Bolletino di zoologia 58, no. 4 (1991): 289–94. http://dx.doi.org/10.1080/11250009109355771.

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4

SUKPRASERT, APISAK, SURAPOP SUTTHIWISES, VIRAYUTH LAUHACHINDA, and WUT TAKSINTUM. "Two new species of Hemiphyllodactylus Bleeker (Squamata: Gekkonidae) from Thailand." Zootaxa 4369, no. 3 (2018): 363. http://dx.doi.org/10.11646/zootaxa.4369.3.4.

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We investigate the taxonomy of slender geckos (Hemiphyllodactylus) in Thailand by means of molecular phylogenetics and morphological study using specimens from three provinces; Chiang Mai, Kamphaeng Phet, and Chanthaburi. The results of phylogenetic analyses had shown that the genetic data of populations from 2 provinces were distinctly different from known species. In addition, some morphological characters of these two populations such as lamellar formula on fore- and hindfoot differed from the other species. The integrated taxonomy using molecular phylogenetics and morphological study revea

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5

Epstein, V. M. "The version of the contemporary theory of evolutionary systematics." Species and speciation. Analysis of new views and trends 313, Supplement 1 (2009): 272–93. http://dx.doi.org/10.31610/trudyzin/2009.supl.1.272.

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Integral theory of evolutional systematics is presented in this article for the first time in contemporary science. It became formed as the science about evolution of species’ diversity and methods of investigation of it. Here is defined its object, subject, aim and method. Theoretical evolutional systematics is separated from practical systematics. Three sections are included in its content: idiographical systematics, nomothetical systematics and phylogenetical cybernetics. Idiographical systematics includes theories of descriptions (= meronomy), classifications (= taxonomy) and reconstructio

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6

Mandal, Fatik Baran. "Hurdle in taxonomy: A case of malaria parasites and other Haemosporidia." Open Veterinary Science 2, no. 1 (2021): 40–54. http://dx.doi.org/10.1515/ovs-2020-0110.

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Abstract A crucial progress in taxonomy matches with the growth of various branches of biological sciences. This validates the taxonomic positions of many organisms. Haemoproteus, Leucocytozoon and Plasmodium, the members of the Haemosporidia, are the well recognized parasitic genera. Revisiting the progress in animal taxonomy appears to be important to evaluate our studies. Haemosporidia being microscopic, their taxonomy specially the morphotaxonomy has sometimes created confusion. Therefore, analysis of progression of the taxonomy of the avian Haemosporidia demands special attention. Modern

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7

Oliverio, Marco, Marco A. Bologna, Andrea Monciotti, Flavia Annesi, and Paolo Mariottini. "Molecular phylogenetics of the ItalianPodarcislizards (Reptilia, Lacertidae)." Italian Journal of Zoology 65, no. 3 (1998): 315–24. http://dx.doi.org/10.1080/11250008809386765.

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8

FAITH, DANIEL P., FRANK KÖHLER, LOUISE PUSLEDNIK, and J. W. O. BALLARD. "Phylogenies with Corroboration Assessment." Zootaxa 2946, no. 1 (2011): 52. http://dx.doi.org/10.11646/zootaxa.2946.1.11.

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Mooi & Gill (2010) argued that careful character study and well-understood synapomorphies do not have the strong role that they deserve as the basis for evidence in phylogenetics. We agree, but suggest that the problem is even greater. Not only character synapomorphies, but also other forms of phylogenetic evidence, typically do not receive the critical assessment that would support phylogenetic inference. In this paper, our goal is to not simply to highlight problems but to suggest solutions. We will suggest that a stronger role for corroboration assessment in systematics could overcome t

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9

LANDRY, PIERRE-ALEXANDRE, and FRANCOIS-JOSEPH LAPOINTE. "RAPD problems in phylogenetics." Zoologica Scripta 25, no. 4 (1996): 283–90. http://dx.doi.org/10.1111/j.1463-6409.1996.tb00167.x.

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10

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 (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 a

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11

Rodrigues, By P. Duarte. "Taxonomy and phylogenetics: Some considerations." Journal of Zoological Systematics and Evolutionary Research 24, no. 4 (2009): 241–47. http://dx.doi.org/10.1111/j.1439-0469.1986.tb00633.x.

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12

Reeves, Destiny, and Corrie Moreau. "The evolution of foraging behavior in ants (Hymenoptera: Formicidae)." Arthropod Systematics & Phylogeny 77 (September 17, 2019): 351–63. https://doi.org/10.26049/ASP77-2-2019-10.

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Cooperative foraging behavior is a key characteristic of ants. A variety of foraging behaviors are present across this animal family, but little is known of how these behavioral traits evolved and differentiated. In addition, classification of these foraging behaviors has been inconsistent across the literature. Using four classification methods, we infer the ancestral foraging states across the Formicidae, as well as test the transitions between and resulting speciation due to foraging behavior. Our study reinforces the hypothesis that solitary foraging behaviors are ancestral to cooperative

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13

Oshida, Tatsuo, Can Ngoc Dang, Son Truong Nguyen, et al. "Phylogenetics ofPetauristain Light of Specimens Collected from Northern Vietnam." Mammal Study 35, no. 1 (2010): 85–91. http://dx.doi.org/10.3106/041.035.0107.

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14

Edwards, Scott V., Sally Potter, C. Jonathan Schmitt, Jason G. Bragg, and Craig Moritz. "Reticulation, divergence, and the phylogeography–phylogenetics continuum." Proceedings of the National Academy of Sciences 113, no. 29 (2016): 8025–32. http://dx.doi.org/10.1073/pnas.1601066113.

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Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of retic

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15

Ley, Paul De, Mark Dorris, and Mark Blaxter. "Patterns and processes in the evolution of animal parasitic nematodes." Nematology 2, no. 1 (2000): 43–55. http://dx.doi.org/10.1163/156854100508881.

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AbstractThe parasitic Nematoda have traditionally been classified distinct from free-living species, and animal parasites treated separately from plant parasites. In classical concepts of phylogenetic relationships within the phylum, parasitic groups are usually afforded ordinal status and their origins are often obscure. We have been using molecular phylogenetics to examine the interrelationships of animal parasites with free-living and plant-parasitic groups, and find that a new view of the origins and radiation of animal parasites is warranted. Using sequence from the nuclear small subunit

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16

Whiting, Alison S., Jack W. Sites, and Aaron M. Bauer. "Molecular phylogenetics of Malagasy skinks (Squamata: Scincidae)." African Journal of Herpetology 53, no. 2 (2004): 135–46. http://dx.doi.org/10.1080/21564574.2004.9635506.

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17

Livezey, Bradley C., and Richard L. Zusi. "Higher-Order Phylogenetics of Modern Aves Based On Comparative Anatomy." Netherlands Journal of Zoology 51, no. 2 (2001): 179–205. http://dx.doi.org/10.1163/156854201x00260.

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18

Cummings, Michael P., and Axel Meyer. "Magic bullets and golden rules: Data sampling in molecular phylogenetics." Zoology 108, no. 4 (2005): 329–36. http://dx.doi.org/10.1016/j.zool.2005.09.006.

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19

Thorpe, Roger Stephen, Richard Philip Brown, Anita Malhotra, and Wolfgang Wuster. "Geographic variation and population systematics: Distinguishing between ecogenetics and phylogenetics." Bolletino di zoologia 58, no. 4 (1991): 329–35. http://dx.doi.org/10.1080/11250009109355776.

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20

Camp, Lauren E., Marc R. Radke, Danny M. Shihabi, Christopher Pagan, Guangyou Yang, and Steven A. Nadler. "Molecular phylogenetics and species-level systematics of Baylisascaris." International Journal for Parasitology: Parasites and Wildlife 7, no. 3 (2018): 450–62. http://dx.doi.org/10.1016/j.ijppaw.2018.09.010.

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21

CRANDALL, KEITH A. "APPLICATIONS OF PHYLOGENETICS TO ISSUES IN FRESHWATER CRAYFISH BIOLOGY." Bulletin Français de la Pêche et de la Pisciculture, no. 380-381 (2006): 953–64. http://dx.doi.org/10.1051/kmae:2006034.

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22

Prasasty, Gita Dwi, Miftahurrizqiyah, Dalilah, Dwi Handayani, Tia Sabrina, and Ahmad Ghiffari. "Philogenetic Analysis of S. Scabiei Var. Hominis, Var. Cuniculi, and Var. Marmoota." Bioscientia Medicina : Journal of Biomedicine and Translational Research 5, no. 3 (2021): 838–42. http://dx.doi.org/10.32539/bsm.v5i3.352.

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Introduction: Based on data from the 2017 Global Burden of Disease, it is known that Indonesia is the country with the highest number of scabies incidences out of 195 countries in the world. In addition to humans, scabies is also an infectious disease in mammals with a prevalence of 300 million infestations every year, even in animals the mortality rate from scabies is very high. Until now, it is still unclear whether there is a cross-infestation between human and animal scabies. Morphologically, S. scabiei between variants cannot be distinguished, while research on genetic variation is still

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23

Prasasty, Gita Dwi, Miftahurrizqiyah, Dalilah, et al. "Philogenetic Analysis of S. Scabiei Var. Hominis, Var. Cuniculi, and Var. Marmoota." Bioscientia Medicina : Journal of Biomedicine and Translational Research 5, no. 10 (2021): 911–15. http://dx.doi.org/10.32539/bsm.v5i10.352.

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Introduction: Based on data from the 2017 Global Burden of Disease, it is known that Indonesia is the country with the highest number of scabies incidences out of 195 countries in the world. In addition to humans, scabies is also an infectious disease in mammals with a prevalence of 300 million infestations every year, even in animals the mortality rate from scabies is very high. Until now, it is still unclear whether there is a cross-infestation between human and animal scabies. Morphologically, S. scabiei between variants cannot be distinguished, while research on genetic variation is still

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24

Rovito, Sean M., and Gabriela Parra-Olea. "Neotropical Plethodontid Biogeography: Insights from Molecular Phylogenetics." Copeia 104, no. 1 (2016): 222–32. http://dx.doi.org/10.1643/ch-14-190.

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25

Vilela, Raquel, and Leonel Mendoza. "The taxonomy and phylogenetics of the human and animal pathogen Rhinosporidium seeberi: A critical review." Revista Iberoamericana de Micología 29, no. 4 (2012): 185–99. http://dx.doi.org/10.1016/j.riam.2012.03.012.

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26

Bybee, Seth M., Heather D. Bracken-Grissom, Russell A. Hermansen, Mark J. Clement, Keith A. Crandall, and Darryl L. Felder. "Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea)." Zoologischer Anzeiger - A Journal of Comparative Zoology 250, no. 4 (2011): 497–506. http://dx.doi.org/10.1016/j.jcz.2011.05.010.

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27

Osborn, Karen J., and Greg W. Rouse. "Phylogenetics of Acrocirridae and Flabelligeridae (Cirratuliformia, Annelida)." Zoologica Scripta 40, no. 2 (2010): 204–19. http://dx.doi.org/10.1111/j.1463-6409.2010.00460.x.

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28

Zupanc, G. K. H. "Chordate evolution: not just a molecular phylogenetics problem." Journal of Zoology 276, no. 2 (2008): 115–16. http://dx.doi.org/10.1111/j.1469-7998.2008.00513.x.

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29

SCHMIDT, CHRIS. "Molecular phylogenetics of ponerine ants (Hymenoptera: Formicidae: Ponerinae)." Zootaxa 3647, no. 2 (2013): 201. http://dx.doi.org/10.11646/zootaxa.3647.2.1.

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30

Pip, E., and J. P. C. Franck. "Molecular phylogenetics of central Canadian Physidae (Pulmonata: Basommatophora)." Canadian Journal of Zoology 86, no. 1 (2008): 10–16. http://dx.doi.org/10.1139/z07-112.

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The phylogenetic relationships of four nominal south-central Canadian freshwater physids ( Physa (sensu lato) skinneri Taylor, 1954, Physa integra (Haldeman, 1841), Physa gyrina (Say, 1821), and the endemic Physa winnipegensis Pip, 2004) were studied by analyses of combined partial sequences coding for mitochondrial 16S and cytochrome c oxidase (COI) genes. Maximum parsimony and neighbour joining analyses, as well as comparisons with published sequences, supported four major clades of physids, of which three are represented in central Canada. Physa skinneri and P. integra were placed within th

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31

Jenner, Ronald A. "Carrying metazoan phylogenetics forward in the 21st century." Contributions to Zoology 70, no. 3 (2001): 181–84. http://dx.doi.org/10.1163/18759866-07003006.

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32

Chen, Zhong-Guang, Yu-Ting Dai, Shan Ouyang, Xiao-Chen Huang, and Xiao-Ping Wu. "Unveiling the identity of Diaurora Cockerell, 1903 (Bivalvia, Unionidae): morphology, molecular phylogenetics, and the description of a new species." ZooKeys 1173 (August 3, 2023): 131–44. http://dx.doi.org/10.3897/zookeys.1173.106148.

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The monotypic freshwater mussel genus Diaurora Cockerell, 1903 has long been enigmatic due to its rarity and morphological confusion with Acuticosta. In this study, we comprehensively redescribed Diaurora aurorea (Heude, 1883) through a detailed analysis of shell morphology and molecular phylogenetics of recently collected specimens. Moreover, a new species, Diaurora laevesp. nov., was identified from the Fuyishui River, a tributary of the Zishui River in Shaoyang County, Shaoyang City, Hunan Province, China. Molecular phylogenetic analyses showed that D. aurorea and D. laevesp. nov. were reci

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33

Jenner, R. A. "Unleashing the Force of Cladistics? Metazoan Phylogenetics and Hypothesis Testing." Integrative and Comparative Biology 43, no. 1 (2003): 207–18. http://dx.doi.org/10.1093/icb/43.1.207.

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34

Farias, Izeni P., Guillermo Ort�, and Axel Meyer. "Total evidence: Molecules, morphology, and the phylogenetics of cichlid fishes." Journal of Experimental Zoology 288, no. 1 (2000): 76–92. http://dx.doi.org/10.1002/(sici)1097-010x(20000415)288:1<76::aid-jez8>3.0.co;2-p.

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35

Cuevas, C. C., and J. R. Formas. "Cytogenetics ofBatrachylaspecies (Anura: Neobatrachia: Ceratophryidae) of southern South America, with phylogenetics comments." New Zealand Journal of Zoology 35, no. 3 (2008): 191–99. http://dx.doi.org/10.1080/03014220809510114.

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36

Richter, Stefan, Gregory D. Edgecombe, and George D. F. Wilson. "The lacinia mobilis and Similar Structures – a Valuable Character in Arthropod Phylogenetics?" Zoologischer Anzeiger - A Journal of Comparative Zoology 241, no. 4 (2002): 339–61. http://dx.doi.org/10.1078/0044-5231-00083.

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37

Fitzgerald, Lee A., Joseph A. Cook, and A. Luz Aquino. "Molecular Phylogenetics and Conservation of Tupinambis (Sauria: Teiidae)." Copeia 1999, no. 4 (1999): 894. http://dx.doi.org/10.2307/1447965.

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38

Brito, Patrícia H., and Scott V. Edwards. "Multilocus phylogeography and phylogenetics using sequence-based markers." Genetica 135, no. 3 (2008): 439–55. http://dx.doi.org/10.1007/s10709-008-9293-3.

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39

Almendra, Ana Laura, Duke S. Rogers, and Francisco X. González-Cózatl. "Molecular phylogenetics of theHandleyomys chapmanicomplex in Mesoamerica." Journal of Mammalogy 95, no. 1 (2014): 26–40. http://dx.doi.org/10.1644/13-mamm-a-044.1.

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40

PADIAL, JOSÉ M., and IGNACIO DE LA RIVA. "Taxonomy, the Cinderella of science, hidden by its evolutionary stepsister." Zootaxa 1577, no. 1 (2007): 1–2. http://dx.doi.org/10.11646/zootaxa.1577.1.1.

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While taxonomy is being glorified during the Linnaean 300th anniversary (Anonymous 2007; Hopper 2007), we have observed a dangerous trend in phylogenetics: the placement of taxonomic discoveries in the appendices of science. Studies that aim to address biogeographical or evolutionary hypotheses using phylogenetic analyses have been confronted with the problem of how to proceed with the taxonomic discoveries that emerge during the analysis of the information (e. g. when discovering that a taxon that was thought to be monophyletic is instead paraphyletic). Authors of such studies may be forced b

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41

Jowers, Michael J., Stephane Caut, Juan Luis Garcia-Mudarra, Samer Alasaad, and Ivan Ineich. "Molecular Phylogenetics of the Possibly Extinct Martinique Ground Snake." Herpetologica 69, no. 2 (2013): 227. http://dx.doi.org/10.1655/herpetologica-d-12-00085.

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42

LERNER, HEATHER R. L., MATTHEW C. KLAVER, and DAVID P. MINDELL. "MOLECULAR PHYLOGENETICS OF THE BUTEONINE BIRDS OF PREY (ACCIPITRIDAE)." Auk 125, no. 2 (2008): 304–15. http://dx.doi.org/10.1525/auk.2008.06161.

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43

Arrigoni, Roberto, Jarosław Stolarski, Tullia I. Terraneo, et al. "Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae." Contributions to Zoology 92, no. 2 (2023): 130–71. http://dx.doi.org/10.1163/18759866-bja10041.

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Abstract The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstr

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44

Kunz, Florian, Anita Gamauf, Frank E. Zachos, and Elisabeth Haring. "Mitochondrial phylogenetics of the goshawk Accipiter [ gentilis ] superspecies." Journal of Zoological Systematics and Evolutionary Research 57, no. 4 (2019): 942–58. http://dx.doi.org/10.1111/jzs.12285.

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45

Rieppel, Olivier. "Adolf Naef (1883-1949), systematic morphology and phylogenetics." Journal of Zoological Systematics and Evolutionary Research 50, no. 1 (2011): 2–13. http://dx.doi.org/10.1111/j.1439-0469.2011.00635.x.

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46

Ali, Muzaffar, Tahir Yaqub, Nadia Mukhtar, et al. "Prevalence and Phylogenetics of H9n2 in Backyard and Commercial Poultry in Pakistan." Avian Diseases 62, no. 4 (2018): 416. http://dx.doi.org/10.1637/11690-062117-resnote.1.

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47

Caviedes-Solis, Itzue W., Nassima M. Bouzid, Barbara L. Banbury, and Adam D. Leaché. "Uprooting phylogenetic uncertainty in coalescent species delimitation: A meta-analysis of empirical studies." Current Zoology 61, no. 5 (2015): 866–73. http://dx.doi.org/10.1093/czoolo/61.5.866.

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Abstract Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography (BPP) is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified g

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48

Bonvicino, Cibele R., Fabiano A. Fernandes, Maria C. Viana, R. Teixeira Bernardo, and Paulo S. D'Andrea. "Scapteromys aquaticus (Rodentia: Sigmodontinae) in Brazil with comments on karyotype and phylogenetics relationships." Zoologia (Curitiba) 30, no. 2 (2013): 242–47. http://dx.doi.org/10.1590/s1984-46702013000200016.

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49

PERKINS, S. L., E. S. MARTINSEN, and B. G. FALK. "Do molecules matter more than morphology? Promises and pitfalls in parasites." Parasitology 138, no. 13 (2011): 1664–74. http://dx.doi.org/10.1017/s0031182011000679.

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SUMMARYSystematics involves resolving both the taxonomy and phylogenetic placement of organisms. We review the advantages and disadvantages of the two kinds of information commonly used for such inferences – morphological and molecular data – as applied to the systematics of metazoan parasites generally, with special attention to the malaria parasites. The problems that potentially confound the use of morphology in parasites include challenges to consistent specimen preservation, plasticity of features depending on hosts or other environmental factors, and morphological convergence. Molecular

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50

ARTHOFER, WOLFGANG, ANDREA GOLLNER, KAI HELLER, FLORIAN M. STEINER, BIRGIT C. SCHLICK-STEINER, and JULIA SEEBER. "Contribution to the molecular phylogeny of Sciaridae (Diptera) with special attention to the genera Bradysia and Corynoptera." Zootaxa 4951, no. 2 (2021): 391–400. http://dx.doi.org/10.11646/zootaxa.4951.2.12.

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The systematics of the dipteran family Sciaridae is based mainly on morphological characters and has remained quite controversial. In this study, we used two mitochondrial DNA markers (CO1, 16S) and a nuclear one (28S) to take a glimpse into phylogenetic relationships of part of the North and Central European Sciaridae. A total of 91 species from 19 genera were analysed using Maximum Likelihood based phylogenetics (depending on the availability of valid sequences, 50–70 per gene). We strengthen the suggestion of the Chaetosciara group as an independent subfamily. Within the subfamily Megalosph

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