Published in Syst Biol on October 05, 2009
Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One (2014) 2.51
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc Biol Sci (2011) 2.06
A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evol Biol (2012) 2.00
A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evol Biol (2011) 1.74
Reconciling molecular phylogenies with the fossil record. Proc Natl Acad Sci U S A (2011) 1.72
Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum. Mol Biol Evol (2014) 1.60
Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity. R Soc Open Sci (2015) 1.56
Diversity versus disparity and the radiation of modern cetaceans. Proc Biol Sci (2010) 1.53
The comparative osteology of the petrotympanic complex (ear region) of extant baleen whales (Cetacea: Mysticeti). PLoS One (2011) 1.39
Host shifts and evolutionary radiations of butterflies. Proc Biol Sci (2010) 1.36
Phylogenomics of the killer whale indicates ecotype divergence in sympatry. Heredity (Edinb) (2014) 1.29
The pygmy right whale Caperea marginata: the last of the cetotheres. Proc Biol Sci (2012) 1.29
Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One (2011) 1.17
Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome B and cytochrome oxidase subunit I mitochondrial genes. PLoS One (2010) 1.14
Biogeography and ecology: towards the integration of two disciplines. Philos Trans R Soc Lond B Biol Sci (2011) 1.09
Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol Biol (2011) 1.07
Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proc Biol Sci (2010) 1.07
Rod monochromacy and the coevolution of cetacean retinal opsins. PLoS Genet (2013) 0.98
Fossil dolphin Otekaikea marplesi (latest Oligocene, New Zealand) expands the morphological and taxonomic diversity of Oligocene cetaceans. PLoS One (2014) 0.98
Asynchronous origins of ectomycorrhizal clades of Agaricales. Proc Biol Sci (2011) 0.94
A new dolphin species, the Burrunan Dolphin Tursiops australis sp. nov., endemic to southern Australian coastal waters. PLoS One (2011) 0.94
Elevated Extinction Rates as a Trigger for Diversification Rate Shifts: Early Amniotes as a Case Study. Sci Rep (2015) 0.92
The molecular phylogenetic signature of clades in decline. PLoS One (2011) 0.86
Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of 'river dolphins' in the Americas. PeerJ (2015) 0.86
Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing. Genome Biol Evol (2013) 0.84
Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans. BMC Evol Biol (2012) 0.84
A Link No Longer Missing: New Evidence for the Cetotheriid Affinities of Caperea. PLoS One (2016) 0.83
Is evolutionary history repeatedly rewritten in light of new fossil discoveries? Proc Biol Sci (2010) 0.83
Dietary innovations spurred the diversification of ruminants during the Caenozoic. Proc Biol Sci (2013) 0.83
No deep diving: evidence of predation on epipelagic fish for a stem beaked whale from the Late Miocene of Peru. Proc Biol Sci (2015) 0.81
A new Miocene baleen whale from the Peruvian desert. R Soc Open Sci (2016) 0.81
A comparative study of mammalian diversification pattern. Int J Biol Sci (2012) 0.80
Environmental changes define ecological limits to species richness and reveal the mode of macroevolutionary competition. Ecol Lett (2016) 0.79
Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences. BMC Evol Biol (2011) 0.79
Ultrasonic hearing and echolocation in the earliest toothed whales. Biol Lett (2016) 0.78
Physicochemical evolution and molecular adaptation of the cetacean osmoregulation-related gene UT-A2 and implications for functional studies. Sci Rep (2015) 0.76
Echolocation by the harbour porpoise: life in coastal waters. Front Physiol (2013) 0.75
Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins. PLoS One (2011) 0.75
Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time. Syst Biol (2016) 0.75
Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change. Proc Biol Sci (2016) 0.75
The remarkable convergence of skull shape in crocodilians and toothed whales. Proc Biol Sci (2017) 0.75
Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora. Ecol Evol (2017) 0.75
Frequency of decompression illness among recent and extinct mammals and "reptiles": a review. Naturwissenschaften (2017) 0.75
MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (2003) 130.85
Trends, rhythms, and aberrations in global climate 65 Ma to present. Science (2001) 27.08
The delayed rise of present-day mammals. Nature (2007) 15.98
Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol (2002) 15.22
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics (2007) 8.63
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol (2005) 8.42
The Phanerozoic record of global sea-level change. Science (2005) 7.11
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol (2006) 5.74
Testing macro-evolutionary models using incomplete molecular phylogenies. Proc Biol Sci (2000) 4.63
Tempo and mode of evolution revealed from molecular phylogenies. Proc Natl Acad Sci U S A (1992) 4.40
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol (2009) 4.01
Resolution of a supertree/supermatrix paradox. Syst Biol (2002) 3.71
LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol Bioinform Online (2007) 3.40
Density-dependent cladogenesis in birds. PLoS Biol (2008) 3.14
Likelihood methods for detecting temporal shifts in diversification rates. Evolution (2006) 2.95
Density-dependent diversification in North American wood warblers. Proc Biol Sci (2008) 2.78
Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Syst Biol (2008) 2.76
Revised phylogeny of whales suggested by mitochondrial ribosomal DNA sequences. Nature (1993) 2.70
Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution (2008) 2.55
Timing and climatic consequences of the opening of Drake Passage. Science (2006) 2.52
Rapid stepwise onset of Antarctic glaciation and deeper calcite compensation in the Pacific Ocean. Nature (2005) 2.49
SYMMETREE: whole-tree analysis of differential diversification rates. Bioinformatics (2004) 2.39
Divergent timing and patterns of species accumulation in lowland and highland neotropical birds. Evolution (2006) 2.18
Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc Natl Acad Sci U S A (2001) 2.11
Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature (2007) 2.01
A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biol Rev Camb Philos Soc (2005) 1.79
Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree. Mol Biol Evol (2002) 1.70
Morphology, molecules, and the phylogenetics of cetaceans. Syst Biol (1998) 1.60
The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies. Mol Phylogenet Evol (2008) 1.59
Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc Natl Acad Sci U S A (2000) 1.56
Phylogeny of mysticete whales based on mitochondrial and nuclear data. Mol Phylogenet Evol (2004) 1.52
Habitat preference and the marine-speciation paradox. Proc Biol Sci (2003) 1.51
Mitochondrial phylogenetics and evolution of mysticete whales. Syst Biol (2005) 1.44
Evolution of river dolphins. Proc Biol Sci (2001) 1.36
Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene (2004) 1.34
Evolution of the eastern tropical Pacific through Plio-Pleistocene glaciation. Science (2006) 1.28
Cytochrome b and Bayesian inference of whale phylogeny. Mol Phylogenet Evol (2005) 1.22
Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol Ecol (2007) 1.16
Relationship of baleen whales established by cytochrome b gene sequence comparison. Nature (1994) 1.00
New protocetid whale from the middle eocene of pakistan: birth on land, precocial development, and sexual dimorphism. PLoS One (2009) 0.99
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Mol Biol Evol (2005) 0.95
The marine indo-west pacific break: contrasting the resolving power of mitochondrial and nuclear genes. Integr Comp Biol (2002) 0.87
Phylogenetic position of Platanista gangetica: insights from the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences. Mol Phylogenet Evol (2004) 0.81
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol (2012) 11.97
Broad phylogenomic sampling improves resolution of the animal tree of life. Nature (2008) 11.84
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science (2011) 8.23
Rise and fall of the Beringian steppe bison. Science (2004) 7.91
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science (2005) 6.92
Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63
Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 6.61
Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A (2005) 5.94
Geographic range size and determinants of avian species richness. Science (2002) 5.65
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A (2007) 5.64
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci U S A (2009) 5.57
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res (2006) 5.31
Localizing recent adaptive evolution in the human genome. PLoS Genet (2007) 5.11
An update of Wallace's zoogeographic regions of the world. Science (2012) 5.09
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res (2006) 4.70
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
DNA from pre-Clovis human coprolites in Oregon, North America. Science (2008) 3.92
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet (2007) 3.83
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science (2012) 3.82
The cost of inbreeding in Arabidopsis. Nature (2002) 3.80
Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science (2007) 3.79
Ecology. How does climate change affect biodiversity? Science (2006) 3.70
Linkage disequilibrium as a signature of selective sweeps. Genetics (2004) 3.52
The mid-domain effect and species richness patterns:what have we learned so far? Am Nat (2004) 3.51
Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol (2011) 3.45
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol (2009) 3.42
Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol (2003) 3.42
Stochastic mapping of morphological characters. Syst Biol (2003) 3.08
Accommodating the effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol (2008) 3.07
The distribution of cultural and biological diversity in Africa. Proc Biol Sci (2002) 2.98
Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science (2007) 2.85
Additive threats from pathogens, climate and land-use change for global amphibian diversity. Nature (2011) 2.77
Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One (2012) 2.75
A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol (2010) 2.73
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science (2007) 2.62
Characterization of genetic miscoding lesions caused by postmortem damage. Am J Hum Genet (2002) 2.61
Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc Biol Sci (2007) 2.61
Species-specific responses of Late Quaternary megafauna to climate and humans. Nature (2011) 2.60
Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A (2007) 2.56
Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol (2010) 2.56
Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics (2008) 2.53
Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res (2010) 2.50
Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol Biol Evol (2006) 2.48
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46
Distribution patterns of postmortem damage in human mitochondrial DNA. Am J Hum Genet (2002) 2.46
Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet (2011) 2.44
Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol (2012) 2.43
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol (2011) 2.37
Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol (2011) 2.33
Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29
A global evaluation of metabolic theory as an explanation for terrestrial species richness gradients. Ecology (2007) 2.29
Glacial survival of boreal trees in northern Scandinavia. Science (2012) 2.28
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol (2008) 2.25
Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics (2005) 2.21
Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science (2008) 2.19
Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children. Proc Natl Acad Sci U S A (2012) 2.17
Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet (2010) 2.14
Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol (2008) 2.13
Estimation of 2Nes from temporal allele frequency data. Genetics (2008) 2.12
Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington. Science (2011) 2.11
Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci U S A (2009) 2.10
The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci (2012) 2.07
Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol (2010) 2.06