jModelTest 2: more models, new heuristics and parallel computing

A new look at the statistical model identification

Akaike, H. (1974) · IEEE Transactions on Automatic Control · doi:10.1109/tac.1974.1100705 · Cited by 51,879

Model Selection in Phylogenetics

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ModelFinder: fast model selection for accurate phylogenetic estimates

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449

ConSurf 2016: An improved methodology to estimate and visualize evolutionary conservation in macromolecules

Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw408 · Cited by 3,163

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

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Emergence of Zaire Ebola Virus Disease in Guinea

Baize, S., Pannetier, D., Oestereich, L., Rieger, T., Koivogui, L., Magassouba, N., Soropogui, B., Sow, M. S., Keïta, S., De Clerck, H., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1404505 · Cited by 1,366

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · Nature · doi:10.1038/nature22401 · Cited by 616

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Karmin, M., Saag, L., Vicente, M., Sayres, M. A. W., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A.-M., Mägi, R., Mitt, M., et al. (2015) · Genome Research · doi:10.1101/gr.186684.114 · Cited by 485

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411

Big data: From beginning to future

Yaqoob, I., Hashem, I. A. T., Gani, A., Mokhtar, S., Ahmed, E., Anuar, N. B., & Vasilakos, A. V. (2016) · International Journal of Information Management · doi:10.1016/j.ijinfomgt.2016.07.009 · Cited by 410

Genomic signatures of evolutionary transitions from solitary to group living

Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., et al. (2015) · Science · doi:10.1126/science.aaa4788 · Cited by 409

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., et al. (2017) · Nature · doi:10.1038/nature22400 · Cited by 353

Million-year-old DNA sheds light on the genomic history of mammoths

van der Valk, T., Pečnerová, P., Díez-del-Molino, D., Bergström, A., Oppenheimer, J., Hartmann, S., Xenikoudakis, G., Thomas, J. A., Dehasque, M., Sağlıcan, E., et al. (2021) · Nature · doi:10.1038/s41586-021-03224-9 · Cited by 345

Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene

Vlad, D., Kierzkowski, D., Rast, M. I., Vuolo, F., Dello Ioio, R., Galinha, C., Gan, X., Hajheidari, M., Hay, A., Smith, R. S., et al. (2014) · Science · doi:10.1126/science.1248384 · Cited by 323

Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria

Hublin, J.-J., Sirakov, N., Aldeias, V., Bailey, S., Bard, E., Delvigne, V., Endarova, E., Fagault, Y., Fewlass, H., Hajdinjak, M., et al. (2020) · Nature · doi:10.1038/s41586-020-2259-z · Cited by 287

Early Holocene chicken domestication in northern China

Xiang, H., Gao, J., Yu, B., Zhou, H., Cai, D., Zhang, Y., Chen, X., Wang, X., Hofreiter, M., & Zhao, X. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1411882111 · Cited by 214

A biologist’s guide to Bayesian phylogenetic analysis

Nascimento, F. F., Reis, M. D., & Yang, Z. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0280-x · Cited by 212

Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

Schuenemann, V. J., Peltzer, A., Welte, B., van Pelt, W. P., Molak, M., Wang, C.-C., Furtwängler, A., Urban, C., Reiter, E., Nieselt, K., et al. (2017) · Nature Communications · doi:10.1038/ncomms15694 · Cited by 201

Detailed characterization of the Arthrospira type species separating commercially grown taxa into the new genus Limnospira (Cyanobacteria)

Nowicka-Krawczyk, P., Mühlsteinová, R., & Hauer, T. (2019) · Scientific Reports · doi:10.1038/s41598-018-36831-0 · Cited by 185

The origin of domestication genes in goats

Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz5216 · Cited by 184

Haplosporidium pinnae sp. nov., a haplosporidan parasite associated with mass mortalities of the fan mussel, Pinna nobilis, in the Western Mediterranean Sea

Catanese, G., Grau, A., Valencia, J. M., Garcia-March, J. R., Vázquez-Luis, M., Alvarez, E., Deudero, S., Darriba, S., Carballal, M. J., & Villalba, A. (2018) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2018.07.006 · Cited by 159

Recombination between heterologous human acrocentric chromosomes

Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Human Pangenome Reference Consortium, Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05976-y · Cited by 134

Dual host–virus arms races shape an essential housekeeping protein

Demogines, A., Abraham, J., Choe, H., Farzan, M., & Sawyer, S. L. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001571 · Cited by 133

Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal

Engelthaler, D. M., Hicks, N. D., Gillece, J. D., Roe, C. C., Schupp, J. M., Driebe, E. M., Gilgado, F., Carriconde, F., Trilles, L., Firacative, C., et al. (2014) · mBio · doi:10.1128/mbio.01464-14 · Cited by 133

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

Jayawardena, R. S., Hyde, K. D., Chen, Y. J., Papp, V., Palla, B., Papp, D., Bhunjun, C. S., Hurdeal, V. G., Senwanna, C., Manawasinghe, I. S., et al. (2020) · Fungal Diversity · doi:10.1007/s13225-020-00460-8 · Cited by 122

Colletotrichum species associated with mango in southern China

Li, Q., Bu, J., Shu, J., Yu, Z., Tang, L., Huang, S., Guo, T., Mo, J., Luo, S., Solangi, G. S., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-54809-4 · Cited by 109

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico

Thézé, J., Li, T., du Plessis, L., Bouquet, J., Kraemer, M. U. G., Somasekar, S., Yu, G., de Cesare, M., Balmaseda, A., Kuan, G., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.04.017 · Cited by 106

Species richness of jellyfishes (Scyphozoa: Discomedusae) in the Tropical Eastern Pacific: missed taxa, molecules, and morphology match in a biodiversity hotspot

Gómez Daglio, L., & Dawson, M. N. (2017) · Invertebrate Systematics · doi:10.1071/is16055 · Cited by 98

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia

Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., et al. (2018) · Science · doi:10.1126/science.aar8486 · Cited by 97

Unmasking Aurelia species in the Mediterranean Sea: an integrative morphometric and molecular approach

Scorrano, S., Aglieri, G., Boero, F., Dawson, M. N., & Piraino, S. (2016) · Zoological Journal of the Linnean Society · doi:10.1111/zoj.12494 · Cited by 95

What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention

Carter, C. (2015) · Life · doi:10.3390/life5010294 · Cited by 95

Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”

McCluskey, B. M., & Postlethwait, J. H. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu325 · Cited by 90

How Really Ancient Is Paulinella Chromatophora?

Delaye, L., Valadez-Cano, C., & Pérez-Zamorano, B. (2016) · PLoS Currents · doi:10.1371/currents.tol.e68a099364bb1a1e129a17b4e06b0c6b · Cited by 72

Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil

Veloso, J. S., Câmara, M. P. S., Lima, W. G., Michereff, S. J., & Doyle, V. P. (2018) · Fungal Biology · doi:10.1016/j.funbio.2018.03.005 · Cited by 65

A comparative approach for species delimitation based on multiple methods of multi-locus DNA sequence analysis: A case study of the genus Giraffa (Mammalia, Cetartiodactyla)

Petzold, A., & Hassanin, A. (2020) · PLOS ONE · doi:10.1371/journal.pone.0217956 · Cited by 60

Howling from the past: historical phylogeography and diversity losses in European grey wolves

Dufresnes, C., Miquel, C., Remollino, N., Biollaz, F., Salamin, N., Taberlet, P., & Fumagalli, L. (2018) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.1148 · Cited by 52

Ancient DNA Reveals Evidence of Abundant Aurochs (Bos Primigenius) in Neolithic Northeast China

Cai, D., Zhang, N., Zhu, S., Chen, Q., Wang, L., Zhao, X., Ma, X., Royle, T. C. A., Zhou, H., & Yang, D. Y. (2018) · Journal of Archaeological Science · doi:10.1016/j.jas.2018.08.003 · Cited by 55

Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data

Pan, T., Miao, J.-S., Zhang, H.-B., Yan, P., Lee, P.-S., Jiang, X.-Y., Ouyang, J.-H., Deng, Y.-P., Zhang, B.-W., & Wu, X.-B. (2021) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlaa074 · Cited by 53

Analysis of biodiversity data suggests that mammal species are hidden in predictable places

Parsons, D. J., Pelletier, T. A., Wieringa, J. G., Duckett, D. J., & Carstens, B. C. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2103400119 · Cited by 52

Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora

Simion, P., Bekkouche, N., Jager, M., Quéinnec, E., & Manuel, M. (2015) · Zoology · doi:10.1016/j.zool.2014.06.004 · Cited by 46

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

Lipid accumulation by Coelastrella multistriata (Scenedesmaceae, Sphaeropleales) during nitrogen and phosphorus starvation

Maltsev, Y., Krivova, Z., Maltseva, S., Maltseva, K., Gorshkova, E., & Kulikovskiy, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-99376-9 · Cited by 40

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

de Santana, C. D., Parenti, L. R., Dillman, C. B., Coddington, J. A., Bastos, D. A., Baldwin, C. C., Zuanon, J., Torrente-Vilara, G., Covain, R., Menezes, N. A., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-97128-3 · Cited by 38

Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns

López-Córdova, D. A., Avaria-Llautureo, J., Ulloa, P. M., Braid, H. E., Revell, L. J., Fuchs, D., & Ibáñez, C. M. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107331 · Cited by 34

Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa

Knapp, M., Thomas, J. E., Haile, J., Prost, S., Ho, S. Y. W., Dussex, N., Cameron-Christie, S., Kardailsky, O., Barnett, R., Bunce, M., et al. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.01.026 · Cited by 33

A New Species of Freshwater Algae Nephrochlamys yushanlensis sp. nov. (Selenastraceae, Sphaeropleales) and Its Lipid Accumulation during Nitrogen and Phosphorus Starvation

Maltsev, Y., Maltseva, I., Maltseva, S., Kociolek, J. P., & Kulikovskiy, M. (2021) · Journal of Phycology · doi:10.1111/jpy.13116 · Cited by 31

Genetic Diversity, Compartmentalization, and Age of HIV Proviruses Persisting in CD4 + T Cell Subsets during Long-Term Combination Antiretroviral Therapy

Jones, B. R., Miller, R. L., Kinloch, N. N., Tsai, O., Rigsby, H., Sudderuddin, H., Shahid, A., Ganase, B., Brumme, C. J., Harris, M., et al. (2020) · Journal of Virology · doi:10.1128/jvi.01786-19 · Cited by 29

Colletotrichum species complexes associated with crops in northern South America: a review

Guevara-Suarez, M., Cárdenas, M., Jiménez, P., Afanador-Kafuri, L., & Restrepo, S. (2022) · Agronomy · doi:10.3390/agronomy12030548 · Cited by 29

The earliest farmers of northwest China exploited grain-fed pheasants not chickens

Barton, L., Bingham, B., Sankaranarayanan, K., Monroe, C., Thomas, A., & Kemp, B. M. (2020) · Scientific Reports · doi:10.1038/s41598-020-59316-5 · Cited by 28

Investigating the role of body size, ecology, and behavior in anuran eye size evolution

Huang, C. H., Zhong, M. J., Liao, W. B., & Kotrschal, A. (2019) · Evolutionary Ecology · doi:10.1007/s10682-019-09993-0 · Cited by 27

Attachment of potential cultivable primo-colonizing bacteria and its implications on the fate of low-density polyethylene (LDPE) plastics in the marine environment

Bitalac, J. M. S., Lantican, N. B., Gomez, N. C. F., & Onda, D. F. L. (2023) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2023.131124 · Cited by 25

Paleolithic divergence and multiple Neolithic expansions of ancestral nomadic emperor-related paternal lineages

Wang, M., Sun, Q., Feng, Y., Wei, L.-H., Liu, K., Luo, L., Huang, Y., Zhou, K., Yuan, H., Lv, H., et al. (2025) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.11.012 · Cited by 19

Oxytocin receptor gene sequences in owl monkeys and other primates show remarkable interspecific regulatory and protein coding variation

Babb, P. L., Fernandez-Duque, E., & Schurr, T. G. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.05.006 · Cited by 16

Old and cosmopolite: molecular phylogeny of tropical–subtropical kites (Aves: Elaninae) with taxonomic implications

Starikov, I. J., & Wink, M. (2020) · Diversity · doi:10.3390/d12090327 · Cited by 9

Draft Genome Assembly of an Iconic Arctic Species: Muskox (Ovibos moschatus)

Prewer, E., Kutz, S., Leclerc, L.-M., & Kyle, C. J. (2022) · Genes · doi:10.3390/genes13050809 · Cited by 3

Revisiting Aurochs Haplogroup C: Paleogenomic Perspectives from Northeastern China

Zhu, Y., Hou, X., Zhao, J., Xiao, B., Song, S., Zou, X., Liu, S., Hofreiter, M., & Lai, X. (2025) · Genes · doi:10.3390/genes16060639 · Cited by 2

This Little Piggy: Pig-Human Entanglement in the Philippines

Lingao, J. Q., Rofes, J., Eusebio, M., Barretto-Tesoro, G., & Herrera, M. (2025) · International Journal of Historical Archaeology · doi:10.1007/s10761-024-00754-6 · Cited by 2