BEAST: Bayesian evolutionary analysis by sampling trees

Equation of State Calculations by Fast Computing Machines

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Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data

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Divergence time and evolutionary rate estimation with multilocus data.

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BEAST 2: a software platform for Bayesian evolutionary analysis

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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

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Bayesian inference of species trees from multilocus data

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Whole-genome analyses resolve early branches in the tree of life of modern birds

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Ancient human genomes suggest three ancestral populations for present-day Europeans

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Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire

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Insights into human genetic variation and population history from 929 diverse genomes

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Estimating the timing of early eukaryotic diversification with multigene molecular clocks

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Resolution of ray-finned fish phylogeny and timing of diversification

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Recalibrating equus evolution using the genome sequence of an early middle pleistocene horse

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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

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A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

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A genomic history of Aboriginal Australia

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Reliability of genetic bottleneck tests for detecting recent population declines

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Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

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Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

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A mitochondrial genome sequence of a hominin from Sima de los Huesos

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Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

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Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis.

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Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Xue, Y., Prado-Martinez, J., Sudmant, P. H., Narasimhan, V., Ayub, Q., Szpak, M., Frandsen, P., Chen, Y., Yngvadottir, B., Cooper, D. N., et al. (2015) · Science · doi:10.1126/science.aaa3952 · Cited by 473

StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates

Ogilvie, H. A., Bouckaert, R. R., & Drummond, A. J. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx126 · Cited by 469

Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses

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Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

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Bayesian random local clocks, or one rate to rule them all

Drummond, A. J., & Suchard, M. A. (2010) · BMC Biology · doi:10.1186/1741-7007-8-114 · Cited by 429

INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION: FOSSILS, PHYLOGENIES, AND MODELS OF TRAIT EVOLUTION

Slater, G. J., Harmon, L. J., & Alfaro, M. E. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01723.x · Cited by 334

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

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Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

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Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates

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Diversity versus disparity and the radiation of modern cetaceans

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The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

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Origins and genetic legacy of prehistoric dogs

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Morphological innovation, diversification and invasion of a new adaptive zone

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Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds

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Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage

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Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

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Ancient pathogen genomics as an emerging tool for infectious disease research

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Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

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Speciation with gene flow on lord howe island

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Rapid, global demographic expansions after the origins of agriculture

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An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology

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Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection

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Livestock Origin for a Human Pandemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus

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Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox ( Ovibos moschatus ) population dynamics

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Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages

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Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

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Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

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Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

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Purifying selection can obscure the ancient age of viral lineages

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Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

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Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in the coral triangle

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Why are there so few fish in the sea?

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Gene tree discordance causes apparent substitution rate variation

Mendes, F. K., & Hahn, M. W. (2016) · Systematic Biology · doi:10.1093/sysbio/syw018 · Cited by 189

Specific Association of Human Parechovirus Type 3 with Sepsis and Fever in Young Infants, as Identified by Direct Typing of Cerebrospinal Fluid Samples

Harvala, H., Robertson, I., Chieochansin, T., McWilliam Leitch, E. C., Templeton, K., & Simmonds, P. (2009) · The Journal of Infectious Diseases · doi:10.1086/599094 · Cited by 182

Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

Carroll, S. A., Towner, J. S., Sealy, T. K., McMullan, L. K., Khristova, M. L., Burt, F. J., Swanepoel, R., Rollin, P. E., & Nichol, S. T. (2013) · Journal of Virology · doi:10.1128/jvi.03118-12 · Cited by 177

Mitochondrial phylogeography of baboons (Papiospp.) – Indication for introgressive hybridization?

Zinner, D., Groeneveld, L. F., Keller, C., & Roos, C. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-83 · Cited by 177

New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences

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Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins

Endicott, P., Ho, S. Y. W., & Stringer, C. (2010) · Journal of Human Evolution · doi:10.1016/j.jhevol.2010.04.005 · Cited by 165

Phylogeographic history of grey wolves in Europe

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The unbearable uncertainty of Bayesian divergence time estimation

DOS REIS, M., & YANG, Z. (2013) · Journal of Systematics and Evolution · doi:10.1111/j.1759-6831.2012.00236.x · Cited by 140

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins

Shih, P. M., & Matzke, N. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305813110 · Cited by 151

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

Kendall, M., & Colijn, C. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw124 · Cited by 134

KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes

Presnell, J. S., Schnitzler, C. E., & Browne, W. E. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv141 · Cited by 119

Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories

Statham, M. J., Murdoch, J., Janecka, J., Aubry, K. B., Edwards, C. J., Soulsbury, C. D., Berry, O., Wang, Z., Harrison, D., Pearch, M., et al. (2014) · Molecular Ecology · doi:10.1111/mec.12898 · Cited by 117

Ecological drivers of song evolution in birds: Disentangling the effects of habitat and morphology

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Colletotrichum species associated with mango in southern China

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Transmission networks and population turnover of echovirus 30

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Reconciling migration models to the Americas with the variation of North American native mitogenomes

Achilli, A., Perego, U. A., Lancioni, H., Olivieri, A., Gandini, F., Hooshiar Kashani, B., Battaglia, V., Grugni, V., Angerhofer, N., Rogers, M. P., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306290110 · Cited by 109

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

Bayha, K. M., Dawson, M. N., Collins, A. G., Barbeitos, M. S., & Haddock, S. H. D. (2010) · Integrative and Comparative Biology · doi:10.1093/icb/icq074 · Cited by 102

Complete mitochondrial DNA diversity in Iranians

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Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers

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Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci

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Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda

Wheat, C. W., & Wahlberg, N. (2013) · Systematic Biology · doi:10.1093/sysbio/sys074 · Cited by 80

Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal

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EVOLUTION OF PAEDOMORPHOSIS IN PLETHODONTID SALAMANDERS: ECOLOGICAL CORRELATES AND RE-EVOLUTION OF METAMORPHOSIS

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Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

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