MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582

Evolutionary trees from DNA sequences: A maximum likelihood approach.

Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571

Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.

Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687

Molecular identification of Giardia and Cryptosporidium from dogs and cats

Sotiriadou, I., Pantchev, N., Gassmann, D., & Karanis, P. (2013) · Parasite · doi:10.1051/parasite/2013008 · Cited by 61

Modern and ancient red fox (Vulpes vulpes) in Europe show an unusual lack of geographical and temporal structuring, and differing responses within the carnivores to historical climatic change

Teacher, A. G., Thomas, J. A., & Barnes, I. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-214 · Cited by 60

Identification of highly divergent diatom-derived chloroplasts in dinoflagellates, including a description of Durinskia kwazulunatalensis sp. nov. (Peridiniales, Dinophyceae)

Yamada, N., Sym, S. D., & Horiguchi, T. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx054 · Cited by 59

Evolutionary pattern in the OXT-OXTR system in primates: Coevolution and positive selection footprints

Vargas-Pinilla, P., Paixão-Côrtes, V. R., Paré, P., Tovo-Rodrigues, L., Vieira, C. M. D. A. G., Xavier, A., Comas, D., Pissinatti, A., Sinigaglia, M., Rigo, M. M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419399112 · Cited by 59

Colletotrichum incanum sp. nov., a curved-conidial species causing soybean anthracnose in USA

Yang, H.-C., Haudenshield, J. S., & Hartman, G. L. (2014) · Mycologia · doi:10.3852/13-013 · Cited by 60

Organization of lamprey variable lymphocyte receptor C locus and repertoire development

Das, S., Hirano, M., Aghaallaei, N., Bajoghli, B., Boehm, T., & Cooper, M. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1302500110 · Cited by 57

PhotoBiobox: A tablet sized, low-cost, high throughput photobioreactor for microalgal screening and culture optimization for growth, lipid content and CO2 sequestration

Heo, J., Cho, D.-H., Ramanan, R., Oh, H.-M., & Kim, H.-S. (2015) · Biochemical Engineering Journal · doi:10.1016/j.bej.2015.07.013 · Cited by 54

Sun-screening bioactive compounds mycosporine-like amino acids in naturally occurring cyanobacterial biofilms: role in photoprotection

Rastogi, R. P., Madamwar, D., & Incharoensakdi, A. (2015) · Journal of Applied Microbiology · doi:10.1111/jam.12879 · Cited by 55

Variation and signatures of selection on the human face

Guo, J., Tan, J., Yang, Y., Zhou, H., Hu, S., Hashan, A., Bahaxar, N., Xu, S., Weaver, T. D., Jin, L., et al. (2014) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.08.001 · Cited by 54

Morphological and molecular discrimination of two closely related jellyfish species, Cyanea capillata and C. lamarckii (Cnidaria, Scyphozoa), from the northeast Atlantic

Holst, S., & Laakmann, S. (2014) · Journal of Plankton Research · doi:10.1093/plankt/fbt093 · Cited by 54

Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment

Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53

Evolutionary diversification of banded tube-dwelling anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean

Stampar, S. N., Maronna, M. M., Vermeij, M. J. A., Silveira, F. L. D., & Morandini, A. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041091 · Cited by 50

Characterization of the Ca2+-Gated and Voltage-Dependent K+-Channel Slo-1 of Nematodes and Its Interaction with Emodepside

Kulke, D., von Samson-Himmelstjerna, G., Miltsch, S. M., Wolstenholme, A. J., Jex, A. R., Gasser, R. B., Ballesteros, C., Geary, T. G., Keiser, J., Townson, S., et al. (2014) · PLoS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0003401 · Cited by 52

Molecular detection of Setaria tundra (Nematoda: Filarioidea) and an unidentified filarial species in mosquitoes in Germany

Czajka, C., Becker, N., Poppert, S., Jöst, H., Schmidt-Chanasit, J., & Krüger, A. (2012) · Parasites & Vectors · doi:10.1186/1756-3305-5-14 · Cited by 51

Nramp

(2012) · Current Topics in Membranes · doi:10.1016/b978-0-12-394390-3.00010-0 · Cited by 47

Genetic diversity and dispersal potential of the stonefly Dinocras cephalotes in a central European low mountain range

Elbrecht, V., Feld, C. K., Gies, M., Hering, D., Sondermann, M., Tollrian, R., & Leese, F. (2014) · Freshwater Science · doi:10.1086/674536 · Cited by 49

Screening blood-fed mosquitoes for the diagnosis of filarioid helminths and avian malaria

Zittra, C., Kocziha, Z., Pinnyei, S., Harl, J., Kieser, K., Laciny, A., Eigner, B., Silbermayr, K., Duscher, G. G., Fok, É., et al. (2015) · Parasites & Vectors · doi:10.1186/s13071-015-0637-4 · Cited by 49

Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle

Xia, X., Qu, K., Zhang, G., Jia, Y., Ma, Z., Zhao, X., Huang, Y., Chen, H., Huang, B., & Lei, C. (2019) · Animal Genetics · doi:10.1111/age.12749 · Cited by 48

Development of patient-specific AAV vectors after neutralizing antibody selection for enhanced muscle gene transfer

Li, C., Wu, S., Albright, B., Hirsch, M., Li, W., Tseng, Y.-S., Agbandje-McKenna, M., McPhee, S., Asokan, A., & Samulski, R. J. (2016) · Molecular Therapy · doi:10.1038/mt.2015.134 · Cited by 48

Microbial community structures in an integrated two-phase anaerobic bioreactor fed by fruit vegetable wastes and wheat straw

Wang, C., Zuo, J., Chen, X., Xing, W., Xing, L., Li, P., Lu, X., & Li, C. (2014) · Journal of Environmental Sciences · doi:10.1016/j.jes.2014.06.035 · Cited by 47

A genome-wide analysis of annexins from parasitic organisms and their vectors

Cantacessi, C., Seddon, J. M., Miller, T. L., Leow, C. Y., Thomas, L., Mason, L., Willis, C., Walker, G., Loukas, A., Gasser, R. B., et al. (2013) · Scientific Reports · doi:10.1038/srep02893 · Cited by 46

DNA barcode and lipid analysis of new marine algae potential for biofuel

Ahmad, I., Fatma, Z., Yazdani, S. S., & Kumar, S. (2013) · Algal Research · doi:10.1016/j.algal.2012.10.003 · Cited by 42

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

Mohajeri, K., Cantsilieris, S., Huddleston, J., Nelson, B. J., Coe, B. P., Campbell, C. D., Baker, C., Harshman, L., Munson, K. M., Kronenberg, Z. N., et al. (2016) · Genome Research · doi:10.1101/gr.211284.116 · Cited by 42

Early phenylpropanoid biosynthetic steps in Cannabis sativa: link between genes and metabolites.

Docimo, T., Consonni, R., Coraggio, I., & Mattana, M. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms140713626 · Cited by 39

Species diversity of Pseudocercospora from Far East Asia

Nakashima, C., Motohashi, K., Chen, C.-Y., Groenewald, J. Z., & Crous, P. W. (2016) · Mycological Progress · doi:10.1007/s11557-016-1231-7 · Cited by 38

Putative Monofunctional Type I Polyketide Synthase Units: A Dinoflagellate-Specific Feature?

Eichholz, K., Beszteri, B., & John, U. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048624 · Cited by 37

Sterol C-22 desaturase ERG5 mediates the sensitivity to antifungal azoles in Neurospora crassa and Fusarium verticillioides.

Sun, X., Wang, W., Wang, K., Yu, X., Liu, J., Zhou, F., Xie, B., & Li, S. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00127 · Cited by 37

Yeasts found on an ephemeral reproductive caste of the leaf-cutting ant Atta sexdens rubropilosa

Arcuri, S. L., Pagnocca, F. C., da Paixão Melo, W. G., Nagamoto, N. S., Komura, D. L., & Rodrigues, A. (2014) · Antonie van Leeuwenhoek · doi:10.1007/s10482-014-0216-2 · Cited by 35

Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

Dittami, S. M., Barbeyron, T., Boyen, C., Cambefort, J., Collet, G., Delage, L., Gobet, A., Groisillier, A., Leblanc, C., Michel, G., et al. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00241 · Cited by 35

Expanded Functional Diversity of Shaker K+ Channels in Cnidarians Is Driven by Gene Expansion

Jegla, T., Marlow, H. Q., Chen, B., Simmons, D. K., Jacobo, S. M., & Martindale, M. Q. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051366 · Cited by 35

Cutaneous distribution and localization of Cercopithifilaria sp. microfilariae in dogs

Otranto, D., Brianti, E., Abramo, F., Gaglio, G., Napoli, E., Latrofa, M. S., Ramos, R. A., Dantas-Torres, F., & Bain, O. (2012) · Veterinary Parasitology · doi:10.1016/j.vetpar.2012.05.016 · Cited by 35

Identification of the DNA methyltransferases establishing the methylome of the cyanobacterium Synechocystis sp. PCC 6803

Hagemann, M., Gärtner, K., Scharnagl, M., Bolay, P., Lott, S. C., Fuss, J., Huettel, B., Reinhardt, R., Klähn, S., & Hess, W. R. (2018) · DNA Research · doi:10.1093/dnares/dsy006 · Cited by 34

Colletotrichum species associated with jute (Corchorus capsularis L.) anthracnose in southeastern China

Niu, X., Gao, H., Qi, J., Chen, M., Tao, A., Xu, J., Dai, Z., & Su, J. (2016) · Scientific Reports · doi:10.1038/srep25179 · Cited by 34

Isolation and molecular characterization of a second serotype of the encephalomyocarditis virus

Philipps, A., Dauber, M., Groth, M., Schirrmeier, H., Platzer, M., Krumbholz, A., Wutzler, P., & Zell, R. (2012) · Veterinary Microbiology · doi:10.1016/j.vetmic.2012.07.006 · Cited by 33

Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms

Ahmad, K. M., Ishchuk, O. P., Hellborg, L., Jørgensen, G., Skvarc, M., Stenderup, J., Jørck-Ramberg, D., Polakova, S., & Piškur, J. (2013) · Antonie van Leeuwenhoek · doi:10.1007/s10482-013-9931-3 · Cited by 29

Fibrolytic Bacteria Isolated from the Rumen of North American Moose (Alces alces) and Their Use as a Probiotic in Neonatal Lambs

Ishaq, S. L., Kim, C. J., Reis, D., & Wright, A.-D. G. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144804 · Cited by 29

ZnuD, a Potential Candidate for a Simple and Universal Neisseria meningitidis Vaccine

Hubert, K., Devos, N., Mordhorst, I., Tans, C., Baudoux, G., Feron, C., Goraj, K., Tommassen, J., Vogel, U., Poolman, J. T., et al. (2013) · Infection and Immunity · doi:10.1128/iai.01312-12 · Cited by 28

Distribution and diversity of the haemoglobin–haptoglobin iron-acquisition systems in pathogenic and non-pathogenic Neisseria

Harrison, O. B., Bennett, J. S., Derrick, J. P., Maiden, M. C. J., & Bayliss, C. D. (2013) · Microbiology · doi:10.1099/mic.0.068874-0 · Cited by 26

Metagenomic mining of glycoside hydrolases from the hindgut bacterial symbionts of a termite (Trinervitermes trinervoides) and the characterization of a multimodular β‐1,4‐xylanase (GH11)

Rashamuse, K., Sanyika Tendai, W., Mathiba, K., Ngcobo, T., Mtimka, S., & Brady, D. (2017) · Biotechnology and Applied Biochemistry · doi:10.1002/bab.1480 · Cited by 27

Identification of laccase-like multicopper oxidases from the pathogenic fungus Setosphaeria turcica and their expression pattern during growth and infection

Liu, N., Cao, Z., Cao, K., Ma, S., Gong, X., Jia, H., Dai, D., & Dong, J. (2019) · European Journal of Plant Pathology · doi:10.1007/s10658-018-01632-8 · Cited by 27

Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus

Shao, Z.-Q., Zhang, Y.-M., Pan, X.-Z., Wang, B., & Chen, J.-Q. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060116 · Cited by 27

Kinetics of heme transfer by the Shr NEAT domains of Group A Streptococcus

Ouattara, M., Pennati, A., Devlin, D. J., Huang, Y.-S., Gadda, G., & Eichenbaum, Z. (2013) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2013.08.009 · Cited by 26

Isochrysis sp. IOAC724S, a newly isolated, lipid-enriched, marine microalga for lipid production, and optimized cultivation conditions

Liu, Q., Pang, T., Li, L., Liu, J., & Lin, W. (2014) · Biomass and Bioenergy · doi:10.1016/j.biombioe.2013.11.003 · Cited by 25

NHX-5, an endosomal Na+/H+ exchanger, is associated with metformin action

Kim, J., Lee, H.-Y., Ahn, J., Hyun, M., Lee, I., Min, K.-J., & You, Y.-J. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.c116.744037 · Cited by 25

Natural history of SLC11 genes in vertebrates: tales from the fish world

Neves, J. V., Wilson, J. M., Kuhl, H., Reinhardt, R., Castro, L. F. C., & Rodrigues, P. N. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-106 · Cited by 24

Mycobiota of the weed Tradescantia fluminensis in its native range in Brazil with particular reference to classical biological control

Macedo, D. M., Pereira, O. L., Hora Júnior, B. T., Weir, B. S., & Barreto, R. W. (2016) · Australasian Plant Pathology · doi:10.1007/s13313-015-0388-x · Cited by 24

Occurrence and Characterization of Candida nivariensis from a Culture Collection of Candida glabrata Clinical Isolates in Malaysia

Tay, S. T., Lotfalikhani, A., Sabet, N. S., Ponnampalavanar, S., Sulaiman, S., Na, S. L., & Ng, K. P. (2014) · Mycopathologia · doi:10.1007/s11046-014-9778-9 · Cited by 22

Genetic and physiological characterization of denitrifying bacteria from brackishwater shrimp culture ponds of India

Dineshkumar, N., Saravanakumar, C., Vasanth, M., Muralidhar, M., & Alavandi, S. V. (2014) · International Biodeterioration & Biodegradation · doi:10.1016/j.ibiod.2014.04.017 · Cited by 22

Complete Mitochondrial Genome of Wild Aurochs (Bos Primigenius) Reconstructed from Ancient DNA

Zeyland, J., Wolko, Ł., Bocianowski, J., Szalata, M., Słomski, R., Dzieduszycki, A. M., Ryba, M., Przystałowska, H., & Lipiński, D. (2013) · Polish Journal of Veterinary Sciences · doi:10.2478/pjvs-2013-0037 · Cited by 22

A new genus for the Andean mice Akodon latebricola and A. bogotensis(Rodentia: Sigmodontinae)

Alvarado-Serrano, D. F., & D'Elía, G. (2013) · Journal of Mammalogy · doi:10.1644/12-mamm-a-276.1 · Cited by 22

Regional selection of the brain size regulating gene CASC5 provides new insight into human brain evolution

Shi, L., Hu, E., Wang, Z., Liu, J., Li, J., Li, M., Chen, H., Yu, C., Jiang, T., & Su, B. (2017) · Human Genetics · doi:10.1007/s00439-016-1748-5 · Cited by 20

Post‐transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans

Wells, M. L., Washington, O. L., Hicks, S. N., Nobile, C. J., Hartooni, N., Wilson, G. M., Zucconi, B. E., Huang, W., Li, L., Fargo, D. C., et al. (2015) · Molecular Microbiology · doi:10.1111/mmi.12913 · Cited by 20

Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels

Malyarchuk, B., Derenko, M., Denisova, G., Khoyt, S., Woźniak, M., Grzybowski, T., & Zakharov, I. (2013) · Journal of Human Genetics · doi:10.1038/jhg.2013.108 · Cited by 19

Association between Anaplasma phagocytophilum seroprevalence in dogs and distribution of Ixodes ricinus and Ixodes persulcatus ticks in Latvia

Berzina, I., Capligina, V., Bormane, A., Pavulina, A., Baumanis, V., Ranka, R., Granta, R., & Matise, I. (2013) · Ticks and Tick-borne Diseases · doi:10.1016/j.ttbdis.2012.08.003 · Cited by 17

Molecular and phenotypic characterization revealed six Colletotrichum species responsible for anthracnose disease of small cardamom in South India

Chethana, C. S., Chowdappa, P., Biju, C. N., Praveena, R., & Sujatha, A. M. (2016) · European Journal of Plant Pathology · doi:10.1007/s10658-016-0931-9 · Cited by 14

Identification of avian and hemoparasite DNA in blood-engorged abdomens of Culex pipiens (Diptera; Culicidae) from a west nile virus epidemic region in suburban Chicago, Illinois

Boothe, E., Medeiros, M. C. I., Kitron, U. D., Brawn, J. D., Ruiz, M. O., Goldberg, T. L., Walker, E. D., & Hamer, G. L. (2015) · Journal of Medical Entomology · doi:10.1093/jme/tjv029 · Cited by 13

Map-Based Cloning and Functional Analysis of YE1 in Rice, Which Is Involved in Light-Dependent Chlorophyll Biogenesis and Photoperiodic Flowering Pathway

Peng, Y., Zou, T., Li, L., Tang, S., Li, Q., Zhang, J., Chen, Y., Wang, X., Yang, G., & Hu, Y. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20030758 · Cited by 13

Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle

Xia, X., Wang, F., Luo, X., Li, S., Lyu, Y., Zheng, Y., Ma, Z., Qu, K., Song, R., Liu, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202503258 · Cited by 14

Comparative transcriptome analysis of purple-fleshed sweet potato and its yellow-fleshed mutant provides insight into the transcription factors involved in anthocyanin biosynthesis in tuberous root

Dong, W., Tang, L., Peng, Y., Qin, Y., Lin, Y., Xiong, X., & Hu, X. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.924379 · Cited by 12

Blue-light regulation of ZmPHOT1 and ZmPHOT2 gene expression and the possible involvement of Zmphot1 in phototropism in maize coleoptiles

Suzuki, H., Okamoto, A., Kojima, A., Nishimura, T., Takano, M., Kagawa, T., Kadota, A., Kanegae, T., & Koshiba, T. (2014) · Planta · doi:10.1007/s00425-014-2082-6 · Cited by 12

Untitled work

Bromhead, D., Scholey, V., Nicol, S., Margulies, D., Wexler, J., & Stein, M. (2015) · Deep-Sea Research II · doi:10.1016/j.dsr2.2015.04.017 · Cited by 12

Genome-guided Investigation of Antibiotic Substances produced by Allosalinactinospora lopnorensis CA15-2T from Lop Nor region, China

Huang, C., Leung, R. K.-K., Guo, M., Tuo, L., Guo, L., Yew, W. W., Lou, I., Lee, S. M. Y., & Sun, C. (2016) · Scientific Reports · doi:10.1038/srep20667 · Cited by 11

Fabrication, Evolution, and Mutual Conversion of d -Fucose-Activatable and -Repressible Acetyltransferase upon Mutations

Yanai, Y., Tsukada, M., Kimura, Y., & Umeno, D. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00169 · Cited by 1