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Journal articles on the topic 'Nuclear phylogeny'

Author: Grafiati

Published: 7 June 2025

Last updated: 2 August 2025

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1

SAARMA, U., I. JÕGISALU, E. MOKS, et al. "A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence." Parasitology 136, no. 3 (2009): 317–28. http://dx.doi.org/10.1017/s0031182008005453.

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SUMMARYThe taxonomic status of Echinococcus, an important zoonotic cestode genus, has remained controversial, despite numerous attempts to revise it. Although mitochondrial DNA (mtDNA) has been the source of markers of choice for reconstructing the phylogeny of the genus, results derived from mtDNA have led to significant inconsistencies with earlier species classifications based on phenotypic analysis. Here, we used nuclear DNA markers to test the phylogenic relationships of members of the genus Echinococcus. The analysis of sequence data for 5 nuclear genes revealed a significantly different

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2

Górniak, Marcin, Dariusz L. Szlachetko, Natalia Olędrzyńska, et al. "Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae)." International Journal of Molecular Sciences 22, no. 21 (2021): 11393. http://dx.doi.org/10.3390/ijms222111393.

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The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused

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3

Holst-Jensen, Arne, Linda M. Kohn, and Trond Schumacher. "Nuclear rDNA Phylogeny of the Sclerotiniaceae." Mycologia 89, no. 6 (1997): 885. http://dx.doi.org/10.2307/3761109.

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4

Holst-Jensen, Arne, Linda M. Kohn, and Trond Schumacher. "Nuclear rDNA phylogeny of the Sclerotiniaceae." Mycologia 89, no. 6 (1997): 885–99. http://dx.doi.org/10.1080/00275514.1997.12026859.

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5

Cameron, Kenneth, and Chengxin Fu. "A Nuclear rDNA Phylogeny of Smilax (Smilacaceae)." Aliso 22, no. 1 (2006): 598–605. http://dx.doi.org/10.5642/aliso.20062201.47.

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6

Cavalier-Smith, T., J. A. Couch, K. E. Thorsteinsen, et al. "Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny." European Journal of Phycology 31, no. 4 (1996): 315–28. http://dx.doi.org/10.1080/09670269600651541.

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7

Spooner, David M., Holly Ruess, Philipp Simon, and Douglas Senalik. "Mitochondrial DNA Sequence Phylogeny of Daucus." Systematic Botany 45, no. 2 (2020): 403–8. http://dx.doi.org/10.1600/036364420x15862837791311.

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Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were commo

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8

Small, Randall L., Richard C. Cronn, and Jonathan F. Wendel. "Use of nuclear genes for phylogeny reconstruction in plants." Australian Systematic Botany 17, no. 2 (2004): 145. http://dx.doi.org/10.1071/sb03015.

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Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic

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Palmé, A. E., T. Pyhäjärvi, W. Wachowiak, and O. Savolainen. "Selection on Nuclear Genes in a Pinus Phylogeny." Molecular Biology and Evolution 26, no. 4 (2009): 893–905. http://dx.doi.org/10.1093/molbev/msp010.

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Fujita, Matthew K., Tag N. Engstrom, David E. Starkey, and H. Bradley Shaffer. "Turtle phylogeny: insights from a novel nuclear intron." Molecular Phylogenetics and Evolution 31, no. 3 (2004): 1031–40. http://dx.doi.org/10.1016/j.ympev.2003.09.016.

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Li, Blaise, Agnès Dettaï, Corinne Cruaud, Arnaud Couloux, Martine Desoutter-Meniger, and Guillaume Lecointre. "RNF213, a new nuclear marker for acanthomorph phylogeny." Molecular Phylogenetics and Evolution 50, no. 2 (2009): 345–63. http://dx.doi.org/10.1016/j.ympev.2008.11.013.

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12

Slowinski, Joseph B., and Robin Lawson. "Snake phylogeny: evidence from nuclear and mitochondrial genes." Molecular Phylogenetics and Evolution 24, no. 2 (2002): 194–202. http://dx.doi.org/10.1016/s1055-7903(02)00239-7.

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13

Callejón, Rocío, Cristina Cutillas, and Steven A. Nadler. "Nuclear and mitochondrial genes for inferring Trichuris phylogeny." Parasitology Research 114, no. 12 (2015): 4591–99. http://dx.doi.org/10.1007/s00436-015-4705-7.

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14

Zhang, Lin, Chien-Hsun Huang, Guojin Zhang, et al. "Nuclear Phylogenomics of Angiosperms and Evolutionary Implications." Diversity 17, no. 2 (2025): 136. https://doi.org/10.3390/d17020136.

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Angiosperms are the largest group of land plants with ~375,000 species, which are classified into ~416 families and ~13,000 genera; they exhibit tremendous morphological and physiological diversities and are important members of diverse terrestrial and aquatic ecosystems. Angiosperms have attracted continuous efforts to describe and understand these diversities in a framework of interrelationships—the phylogeny, which provides strong support for angiosperm classifications and relies on morphological, anatomical, and increasing molecular markers. Today, great advances in sequencing technology h

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15

Guyeux, Christophe, Stéphane Chrétien, Nathalie M. L. Côté, and Jacques M. Bahi. "Systematic investigations of gene effects on both topologies and supports: An Echinococcus illustration." Journal of Bioinformatics and Computational Biology 15, no. 05 (2017): 1750019. http://dx.doi.org/10.1142/s0219720017500196.

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In this paper, we propose a high performance computing toolbox implementing efficient statistical methods for the study of phylogenies. This toolbox, which implements logit models and LASSO-type penalties, gives a way to better understand, measure, and compare the impact of each gene on a global phylogeny. As an application, we study the Echinococcus phylogeny, which is often considered as a particularly difficult example. Mitochondrial and nuclear genomes (19 coding sequences) of nine Echinococcus species are considered in order to investigate the molecular phylogeny of this genus. First, we

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Jabeen, Sana, and Abdul Nasir Khalid. "Pseudosperma flavorimosum sp. nov. from Pakistan." Mycotaxon 135, no. 1 (2020): 183–93. http://dx.doi.org/10.5248/135.183.

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Pseudosperma flavorimosum is a new species described from Khyber Pakhtunkhwa province, Pakistan. It is delimited based on morphological characters combined with a molecular phylogeny inferred from nuclear ribosomal DNA internal transcribed spacer (ITS) sequence analyses. The ITS-based phylogeny supports the independence of the new species, which is also is morphologically distinct from closely related taxa.

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Perktaş, Utku, Jeff G. Groth, and George F. Barrowclough. "Phylogeography, Species Limits, Phylogeny, and Classification of the Turacos (Aves: Musophagidae) Based on Mitochondrial and Nuclear DNA Sequences." American Museum Novitates 2020, no. 3949 (2020): 1–64. https://doi.org/10.1206/3949.1.

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Perktaş, Utku, Groth, Jeff G., Barrowclough, George F. (2020): Phylogeography, Species Limits, Phylogeny, and Classification of the Turacos (Aves: Musophagidae) Based on Mitochondrial and Nuclear DNA Sequences. American Museum Novitates 2020 (3949): 1-64, DOI: 10.1206/3949.1, URL: https://bioone.org/journals/american-museum-novitates/volume-2020/issue-3949/3949.1/Phylogeography-Species-Limits-Phylogeny-and-Classification-of-the-Turacos-Aves/10.1206/3949.1.full

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18

Guillon, Jean-Michel, Loreleï Guéry, Vincent Hulin, and Marc Girondot. "A large phylogeny of turtles (Testudines) using molecular data." Contributions to Zoology 81, no. 3 (2012): 147–58. http://dx.doi.org/10.1163/18759866-08103002.

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Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA sequences from nuclear and mitochondrial genes for more than two thirds of the total number of turtle species to infer a large phylogeny for this taxon. Our results enable us to discuss previous hypotheses on species phylogeny or taxonomy. We are thus able to discriminate between competing hypothese

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19

Wang, Huan, Dongfa Sun, and Genlou Sun. "Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets." Genome 54, no. 12 (2011): 986–92. http://dx.doi.org/10.1139/g11-063.

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The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and

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20

Ricroch, A., R. Yockteng, S. C. Brown, and S. Nadot. "Evolution of genome size across some cultivated Allium species." Genome 48, no. 3 (2005): 511–20. http://dx.doi.org/10.1139/g05-017.

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Allium L. (Alliaceae), a genus of major economic importance, exhibits a great diversity in various morphological characters and particularly in life form, with bulbs and rhizomes. Allium species show variation in several cytogenetic characters such as basic chromosome number, ploidy level, and genome size. The purpose of the present investigation was to study the evolution of nuclear DNA amount, GC content, and life form. A phylogenetic approach was used on a sample of 30 Allium species, including major vegetable crops and their wild allies, belonging to the 3 major subgenera Allium, Ameralliu

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21

Martins, Talline R., and Todd J. Barkman. "Reconstruction of Solanaceae Phylogeny Using the Nuclear Gene SAMT." Systematic Botany 30, no. 2 (2005): 435–47. http://dx.doi.org/10.1600/0363644054223675.

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22

Hochbach, Anne, H. Peter Linder, and Martin Röser. "Nuclear genes, matK and the phylogeny of the Poales." Taxon 67, no. 3 (2018): 521–36. http://dx.doi.org/10.12705/673.5.

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23

Asher, Robert J., and Michael Hofreiter. "Tenrec Phylogeny and the Noninvasive Extraction of Nuclear DNA." Systematic Biology 55, no. 2 (2006): 181–94. http://dx.doi.org/10.1080/10635150500433649.

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24

Cotton, James A., and Roderic D. M. Page. "Going nuclear: gene family evolution and vertebrate phylogeny reconciled." Proceedings of the Royal Society of London. Series B: Biological Sciences 269, no. 1500 (2002): 1555–61. http://dx.doi.org/10.1098/rspb.2002.2074.

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25

Winkworth, Richard C., and Michael J. Donoghue. "Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI." Molecular Phylogenetics and Evolution 33, no. 1 (2004): 109–26. http://dx.doi.org/10.1016/j.ympev.2004.05.006.

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26

Phillips, Matthew J., Dalal Haouchar, Renae C. Pratt, Gillian C. Gibb, and Michael Bunce. "Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes." PLoS ONE 8, no. 2 (2013): e57745. http://dx.doi.org/10.1371/journal.pone.0057745.

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27

Crampton, A., I. McKay, and S. C. Barker. "Phylogeny of ticks (Ixodida) inferred from nuclear ribosomal DNA." International Journal for Parasitology 26, no. 5 (1996): 511–17. http://dx.doi.org/10.1016/0020-7519(96)89379-9.

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28

Yang, Lei, Richard L. Mayden, and Gavin J. P. Naylor. "Phylogeny and Polyploidy Evolution of the Suckers (Teleostei: Catostomidae)." Biology 13, no. 12 (2024): 1072. https://doi.org/10.3390/biology13121072.

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Fishes in the cypriniform family Catostomidae (suckers) are evolutionary tetraploids. The use of nuclear markers in the phylogenetic study of this important group has been greatly hindered by the challenge of identifying paralogous copies of genes. In the present study, we used two different methods to separate the gene copies of five single-copy nuclear genes (i.e., RAG1, EGR2B, EGR3, IRBP2, and RAG2). For each gene, all sequences of Copy I formed a clade that was sister to the clade formed by all sequences of Copy II in the phylogenetic trees. The maternal and paternal progenitor of the tetr

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29

Clary, Karen H., and Beryl B. Simpson. "Sistemática y evolución del género Yucca (Agavaceae): evidencias de análisis nunfológicos y moleculares." Botanical Sciences, no. 56 (April 26, 2017): 77. http://dx.doi.org/10.17129/botsci.1466.

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Yucca L. (the Desert Soaptree, Agavaceae) consists of 45 perennial species distributed primarily in the deserts of Mexico and the United States. Although several taxonomic treatments of yuccas exist; the-phylogeny of the group is poorly known. It is unclear which taxa retain primitive characters and how characters have evolved. In addition, relationships of taxa within the genus are uncertain. We compare our phylogeny based upon reproductive characters with a chloroplast phylogeny (Hanson and Rieseberg, 1991 ; Hanson, 1993) and with data from the ITS region of the nuclear genome (Bogler, this

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30

Meng, Kai-Kai, Su-Fang Chen, Min Lin, Wen-Bo Liao, Jian-Hua Jin, and Qiang Fan. "Eriobotrya crassifolia (Rosaceae), a new species from Yunnan Province, China." PhytoKeys 214 (November 22, 2022): 17–25. http://dx.doi.org/10.3897/phytokeys.214.96425.

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The new species Eriobotrya crassifolia, collected from Yunnan Province, China, is characterised and illustrated. A phylogeny based on chloroplast genomes supported its closest affinity with E. tengyuehensis, while a phylogeny based on 197 single-copy nuclear genes supported its closest affinity with E. fragrans and E. deflexa. Morphologically, however, it resembles E. angustissima. Nevertheless, it can be easily distinguished from E. angustissima by its abaxially retroflexed and sharply serrate leaf margins, densely rusty tomentose inflorescences, and oblong or elliptic leaves.

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Meng, Kai-Kai, Su-Fang Chen, Min Lin, Wen-Bo Liao, Jian-Hua Jin, and Qiang Fan. "Eriobotrya crassifolia (Rosaceae), a new species from Yunnan Province, China." PhytoKeys 214 (November 22, 2022): 17–25. https://doi.org/10.3897/phytokeys.214.96425.

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The new species Eriobotrya crassifolia, collected from Yunnan Province, China, is characterised and illustrated. A phylogeny based on chloroplast genomes supported its closest affinity with E. tengyuehensis, while a phylogeny based on 197 single-copy nuclear genes supported its closest affinity with E. fragrans and E. deflexa. Morphologically, however, it resembles E. angustissima. Nevertheless, it can be easily distinguished from E. angustissima by its abaxially retroflexed and sharply serrate leaf margins, densely rusty tomentose inflorescences, and oblong or elliptic leaves.

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32

Lee, Byoung Yoon, and Chong-Wook Park. "Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences." Journal of Species Research 3, no. 1 (2014): 39–52. https://doi.org/10.12651/JSR.2014.3.1.039.

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Lee, Byoung Yoon, Park, Chong-Wook (2014): Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences. Journal of Species Research 3 (1): 39-52, DOI: 10.12651/JSR.2014.3.1.039, URL: http://dx.doi.org/10.12651/jsr.2014.3.1.039

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Wang, Guang-Yan, Ying Meng, Tao Deng, and Yong-Ping Yang. "Molecular phylogeny of Faberia (Asteraceae: Cichorieae) based on nuclear and chloroplast sequences." Phytotaxa 167, no. 3 (2014): 223–34. https://doi.org/10.11646/phytotaxa.167.3.1.

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Wang, Guang-Yan, Meng, Ying, Deng, Tao, Yang, Yong-Ping (2014): Molecular phylogeny of Faberia (Asteraceae: Cichorieae) based on nuclear and chloroplast sequences. Phytotaxa 167 (3): 223-234, DOI: 10.11646/phytotaxa.167.3.1, URL: http://dx.doi.org/10.11646/phytotaxa.167.3.1

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NABHOLZ, BENOIT, STÉPHANE PUISSANT, and BERNARD DEFAUT. "A cautionary note on synonymization based on mitochondrial data in Orthoptera: a comment of Hochkirch et al. 2023." Zootaxa 5481, no. 1 (2024): 146–50. http://dx.doi.org/10.11646/zootaxa.5481.1.10.

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Hochkirch et al. (2023) recently published a phylogeny of the band-winged grasshopper genus Oedipoda. Using three mitochondrial and one nuclear loci, they estimated the phylogeny of 177 specimens. This phylogeny offers insights into the evolutionary history and biogeography of the group and demonstrates the usefulness of molecular data to estimated populations and species histories. They also provide valid taxonomical changes, raising two former subspecies and one former synonymy to the species level. However, we believe that taxonomic changes regarding synonymization proposed by the authors a

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35

Iacolina, Laura, Elena Buzan, Toni Safner, et al. "A Mother’s Story, Mitogenome Relationships in the Genus Rupicapra." Animals 11, no. 4 (2021): 1065. http://dx.doi.org/10.3390/ani11041065.

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Although the two species of chamois (Rupicapra rupicapra and R. pyrenaica) are currently classified as least-concern by the IUCN (International Union for Conservation of Nature), inconsistencies on the subspecies classification reported in literature make it challenging to assess the conservation status of the single subspecies. Previous studies relying on mitochondrial genes, sometimes in combination with nuclear or Y-chromosome markers, reported the presence of clusters corresponding to the geographic distribution but highlighting ambiguities in the genus phylogeny. Here we report novel de n

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CÁRDENAS, GLENDA G., and SAMULI LEHTONEN. "The third opinion on fern phylogenetics with novel insights into their mitogenome evolution." Phytotaxa 625, no. 3 (2023): 227–47. http://dx.doi.org/10.11646/phytotaxa.625.3.1.

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The current understanding of fern phylogeny is primarily based on plastid and nuclear sequences, but the third genome—the mitogenome—has remained practically unstudied. We inferred the first broad scale fern phylogeny based on mitogenomic data, obtained from the One Thousand Plant Transcriptomes Initiative project, and compared it with the plastid phylogeny. The trees were mostly congruent and corresponded to the current understanding of the fern phylogeny, but we observed different evolutionary patterns between the two genomes. Protein-coding markers located in the plastome had, on average, o

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37

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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38

Wang, Guang-Yan, Ying Meng, Jin-Ling Huang, and Yong-Ping Yang. "Molecular Phylogeny of Ophiopogon (Asparagaceae) Inferred from Nuclear and Plastid DNA Sequences." Systematic Botany 39, no. 3 (2014): 776–84. https://doi.org/10.1600/036364414X682201.

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Wang, Guang-Yan, Meng, Ying, Huang, Jin-Ling, Yang, Yong-Ping (2014): Molecular Phylogeny of Ophiopogon (Asparagaceae) Inferred from Nuclear and Plastid DNA Sequences. Systematic Botany (Basel, Switzerland) 39 (3): 776-784, DOI: 10.1600/036364414X682201, URL: https://doi.org/10.1600/036364414x682201

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Moyle, Robert G. "A Molecular Phylogeny of Kingfishers (Alcedinidae) With Insights Into Early Biogeographic History." Auk 123, no. 2 (2006): 487–99. http://dx.doi.org/10.1093/auk/123.2.487.

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Abstract The phylogeny of kingfishers was reconstructed by comparing mitochondrial and nuclear DNA sequences representing 38 ingroup species. Analysis of the combined data and the nuclear data alone recovered the Alcedininae as the basal lineage in the family. This basal arrangement, and support for many relationships within the three subfamilies, allows discussion of biogeographic issues. The Australian region and Pacific islands display the highest diversity of kingfishers, but this diversity is not a reflection of a long history in the region. Rather, high diversity and endemism in the Aust

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40

Peterson, Kristin R., and Donald H. Pfister. "Phylogeny ofCyttariainferred from nuclear and mitochondrial sequence and morphological data." Mycologia 102, no. 6 (2010): 1398–416. http://dx.doi.org/10.3852/10-046.

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Schoch, C. L., R. A. Shoemaker, K. A. Seifert, S. Hambleton, J. W. Spatafora, and P. W. Crous. "A multigene phylogeny of the Dothideomycetes using four nuclear loci." Mycologia 98, no. 6 (2006): 1041–52. http://dx.doi.org/10.3852/mycologia.98.6.1041.

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42

White, M. M., T. Y. James, K. O'Donnell, M. J. Cafaro, Y. Tanabe, and J. Sugiyama. "Phylogeny of the Zygomycota based on nuclear ribosomal sequence data." Mycologia 98, no. 6 (2006): 872–84. http://dx.doi.org/10.3852/mycologia.98.6.872.

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43

Harshman, John, Christopher J. Huddleston, Jonathan P. Bollback, Thomas J. Parsons, and Michael J. Braun. "True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia." Systematic Biology 52, no. 3 (2003): 386–402. http://dx.doi.org/10.1080/10635150390197028.

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Boršić, Igor, Alfonso Susanna, Svetlana Bancheva, and Núria Garcia-Jacas. "Centaurea Sect. Cyanus: Nuclear Phylogeny, Biogeography, and Life-Form Evolution." International Journal of Plant Sciences 172, no. 2 (2011): 238–49. http://dx.doi.org/10.1086/657645.

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Rychel, Amanda L., Tod W. Reeder, and Annalisa Berta. "Phylogeny of mysticete whales based on mitochondrial and nuclear data." Molecular Phylogenetics and Evolution 32, no. 3 (2004): 892–901. http://dx.doi.org/10.1016/j.ympev.2004.02.020.

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Capelli, Cristian, Ross D. E. MacPhee, Alfred L. Roca, et al. "A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius)." Molecular Phylogenetics and Evolution 40, no. 2 (2006): 620–27. http://dx.doi.org/10.1016/j.ympev.2006.03.015.

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Wang, Zheng, Manfred Binder, Conrad L. Schoch, Peter R. Johnston, Joseph W. Spatafora, and David S. Hibbett. "Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny." Molecular Phylogenetics and Evolution 41, no. 2 (2006): 295–312. http://dx.doi.org/10.1016/j.ympev.2006.05.031.

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Pagès, Marie, Sébastien Calvignac, Catherine Klein, Mathilde Paris, Sandrine Hughes, and Catherine Hänni. "Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny." Molecular Phylogenetics and Evolution 47, no. 1 (2008): 73–83. http://dx.doi.org/10.1016/j.ympev.2007.10.019.

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Kanduma, Esther G., Richard P. Bishop, Naftaly W. Githaka, Robert A. Skilton, Heloise Heyne, and Joram M. Mwacharo. "Mitochondrial and nuclear multilocus phylogeny of Rhipicephalus ticks from Kenya." Molecular Phylogenetics and Evolution 140 (November 2019): 106579. http://dx.doi.org/10.1016/j.ympev.2019.106579.

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White, Merlin M., Timothy Y. James, Kerry O’Donnell, Matías J. Cafaro, Yuuhiko Tanabe, and Junta Sugiyama. "Phylogeny of the Zygomycota based on nuclear ribosomal sequence data." Mycologia 98, no. 6 (2006): 872–84. http://dx.doi.org/10.1080/15572536.2006.11832617.

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