Late Glacial Demographic Expansion Motivates a Clock Overhaul for Population Genetics

Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

(2014) Shengting Li et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Shifting seas: the impacts of Pleistocene sea-level fluctuations on the evolution of tropical marine taxa

(2014) William B. Ludt et al.   JOURNAL OF BIOGEOGRAPHY

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

(2014) S. Duchene et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The changing face of the molecular evolutionary clock

(2014) Simon Y.W. Ho   TRENDS IN ECOLOGY & EVOLUTION

Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota

(2013) Justin C Bagley et al.   BMC EVOLUTIONARY BIOLOGY

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

(2013) Qiaomei Fu et al.   CURRENT BIOLOGY

Losing ground: past history and future fate of Arctic small mammals in a changing climate

(2013) Stefan Prost et al.   GLOBAL CHANGE BIOLOGY

Divergent evolutionary histories of two sympatric spruce bark beetle species

(2013) Coralie Bertheau et al.   MOLECULAR ECOLOGY

The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History

(2013) Rasmus Heller et al.   PLoS One

Mitogenomes from Two Uncommon Haplogroups Mark Late Glacial/Postglacial Expansions from the Near East and Neolithic Dispersals within Europe

(2013) Anna Olivieri et al.   PLoS One

Early adipogenesis is regulated through USP7-mediated deubiquitination of the histone acetyltransferase TIP60

(2013) Yuan Gao et al.   Nature Communications

Incorporating deep and shallow components of genetic structure into the management of Alaskan red king crab

(2012) William Stewart Grant et al.   Evolutionary Applications

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

(2012) W. Stewart Grant et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Poleward bound: biological impacts of Southern Hemisphere glaciation

(2012) Ceridwen I. Fraser et al.   TRENDS IN ECOLOGY & EVOLUTION

Recent progress in paleontological methods for dating the Tree of Life

(2012) Michel Laurin   Frontiers in Genetics

SUBSTITUTION RATES AT NEUTRAL GENES DEPEND ON POPULATION SIZE UNDER FLUCTUATING DEMOGRAPHY AND OVERLAPPING GENERATIONS

(2011) François Balloux et al.   EVOLUTION

Time Dependency of Molecular Evolutionary Rates? Yes and No

(2011) Sankar Subramanian et al.   Genome Biology and Evolution

Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum

(2011) E. D. Crandall et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Time-dependent rates of molecular evolution

(2011) SIMON Y. W. HO et al.   MOLECULAR ECOLOGY

Skyline-plot methods for estimating demographic history from nucleotide sequences

(2011) SIMON Y. W. HO et al.   Molecular Ecology Resources

Evolutionary history of a widespread Indo-Pacific goby: The role of Pleistocene sea-level changes on demographic contraction/expansion dynamics

(2011) Thierry Bernard Hoareau et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species-specific responses of Late Quaternary megafauna to climate and humans

(2011) Eline D. Lorenzen et al.   NATURE

The genome as a life-history character: why rate of molecular evolution varies between mammal species

(2011) L. Bromham   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Glacial History of the North Atlantic Marine Snail, Littorina saxatilis, Inferred from Distribution of Mitochondrial DNA Lineages

(2011) Marina Panova et al.   PLoS One

Reconciling Deep Calibration and Demographic History: Bayesian Inference of Post Glacial Colonization Patterns in Carcinus aestuarii (Nardo, 1847) and C. maenas (Linnaeus, 1758)

(2011) Ilaria A. M. Marino et al.   PLoS One

Phylogeographic analysis reveals a deep lineage split within North Atlantic Littorina saxatilis

(2011) M. M. Doellman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Post-glacial partitioning of mitochondrial genetic variation in the field vole

(2011) J. S. Herman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content

(2011) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

Mutability of Y-Chromosomal Microsatellites: Rates, Characteristics, Molecular Bases, and Forensic Implications

(2010) Kaye N. Ballantyne et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)

(2010) Jean-Marie Cornuet et al.   BMC BIOINFORMATICS

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

(2010) L. Chikhi et al.   GENETICS

Don't forget the ancestral polymorphisms

(2010) D Charlesworth   HEREDITY

Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses

(2010) C. Firth et al.   MOLECULAR BIOLOGY AND EVOLUTION

Revisiting the Insect Mitochondrial Molecular Clock: The Mid-Aegean Trench Calibration

(2010) A. Papadopoulou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure

(2010) BENJAMIN M. PETER et al.   MOLECULAR ECOLOGY

The phylogeography of an alpine leaf beetle: Divergence within Oreina elongata spans several ice ages

(2010) Matthias Borer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Amphibian phylogeography in the Antipodes: Refugia and postglacial colonization explain mitochondrial haplotype distribution in the Patagonian frog Eupsophus calcaratus (Cycloramphidae)

(2010) José J. Nuñez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Last Glacial Termination

(2010) G. H. Denton et al.   SCIENCE

Watching the clock: Studying variation in rates of molecular evolution between species

(2010) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

(2009) Pedro Soares et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

(2009) Johannes Krause et al.   BMC EVOLUTIONARY BIOLOGY

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

(2009) T. Stadler et al.   GENETICS

Genetic diversity and phylogeographic analysis ofPinus leiophylla: a post-glacial range expansion

(2009) Abril Rodríguez-Banderas et al.   JOURNAL OF BIOGEOGRAPHY

Temporal Trails of Natural Selection in Human Mitogenomes

(2009) S. Subramanian   MOLECULAR BIOLOGY AND EVOLUTION

Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

(2009) G. I. Peterson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

(2009) MARJU KORSTEN et al.   MOLECULAR ECOLOGY

Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

(2009) MIGUEL NAVASCUÉS et al.   MOLECULAR ECOLOGY

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Rapid oceanic and atmospheric changes during the Younger Dryas cold period

(2009) Jostein Bakke et al.   Nature Geoscience

Environmental impact of the 73ka Toba super-eruption in South Asia

(2009) Martin A.J. Williams et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

Time Dependency of Molecular Rates in Ancient DNA Data Sets, A Sampling Artifact?

(2009) Regis Debruyne et al.   SYSTEMATIC BIOLOGY

The Crucial Role of Calibration in Molecular Date Estimates for the Peopling of the Americas

(2008) Simon Y.W. Ho et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Bayesian Evaluation of Human Mitochondrial Substitution Rates

(2008) Phillip Endicott et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Great American Schism: Divergence of Marine Organisms After the Rise of the Central American Isthmus

(2008) H.A. Lessios   Annual Review of Ecology Evolution and Systematics

Bayesian inference of population size history from multiple loci

(2008) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

(2008) A.-L. Raquin et al.   GENETICS

Formal definition and dating of the GSSP (Global Stratotype Section and Point) for the base of the Holocene using the Greenland NGRIP ice core, and selected auxiliary records

(2008) Mike Walker et al.   JOURNAL OF QUATERNARY SCIENCE

Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates

(2008) B. M. Henn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories

(2008) A. Rambaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency

(2008) C. P. Burridge et al.   MOLECULAR BIOLOGY AND EVOLUTION

Climate control on ancestral population dynamics: insight from Patagonian fish phylogeography

(2008) DANIEL E. RUZZANTE et al.   MOLECULAR ECOLOGY

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology

(2008) Simon Y. W. Ho et al.   PLoS One

Phylogeographic insights into cryptic glacial refugia

(2008) J PROVAN et al.   TRENDS IN ECOLOGY & EVOLUTION

Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic

(2008) Craig D. Millar et al.   PLoS Genetics

Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe—Evidence for multiple glacial refugia

(2007) H.S. Mäkinen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION