Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

The Novel Evolution of the Sperm Whale Genome

(2017) Wesley C Warren et al.   Genome Biology and Evolution

The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

(2017) Lounès Chikhi et al.   HEREDITY

Diagnosability of mtDNA with Random Forests: Using sequence data to delimit subspecies

(2017) Frederick I. Archer et al.   MARINE MAMMAL SCIENCE

The Pliocene marine megafauna extinction and its impact on functional diversity

(2017) Catalina Pimiento et al.   Nature Ecology & Evolution

Redrawing the map: mtDNA provides new insight into the distribution and diversity of short-finned pilot whales in the Pacific Ocean

(2016) Amy M. Van Cise et al.   MARINE MAMMAL SCIENCE

Large amounts of marine debris found in sperm whales stranded along the North Sea coast in early 2016

(2016) Bianca Unger et al.   MARINE POLLUTION BULLETIN

Genetic variation in blue whales in the eastern pacific: implication for taxonomy and use of common wintering grounds

(2016) R. G. Leduc et al.   MOLECULAR ECOLOGY

What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

(2016) Alana Alexander et al.   MOLECULAR ECOLOGY

stratag: Anrpackage for manipulating, summarizing and analysing population genetic data

(2016) Frederick I. Archer et al.   Molecular Ecology Resources

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

(2016) James A. Cahill et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Critical Decline of the Eastern Caribbean Sperm Whale Population

(2016) Shane Gero et al.   PLoS One

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

(2016) Andrew D. Foote et al.   Nature Communications

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

(2016) Robert G. Moyle et al.   Nature Communications

Mitogenome analysis reveals a complex phylogeographic relationship within the wild tiger population of Thailand

(2016) W Buddhakosai et al.   Endangered Species Research

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

Geographic and temporal dynamics of a global radiation and diversification in the killer whale

(2015) Phillip A. Morin et al.   MOLECULAR ECOLOGY

Demographic inference using genetic data from a single individual: Separating population size variation from population structure

(2015) Olivier Mazet et al.   THEORETICAL POPULATION BIOLOGY

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes

(2015) Susana Caballero et al.   PLoS One

Global assessment of arsenic pollution using sperm whales (Physeter macrocephalus) as an emerging aquatic model organism

(2014) Laura C. Savery et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Nuclear and Mitochondrial Patterns of Population Structure in North Pacific False Killer Whales (Pseudorca crassidens)

(2014) K. K. Martien et al.   JOURNAL OF HEREDITY

Assessment of genetic structure among eastern North Pacific gray whales on their feeding grounds

(2014) Aimée R. Lang et al.   MARINE MAMMAL SCIENCE

Evidence of Positive Selection in Mitochondrial Complexes I and V of the African Elephant

(2014) Tabitha M. Finch et al.   PLoS One

Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae)

(2014) J. A. Jackson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cultural transmission of tool use combined with habitat specializations leads to fine-scale genetic structure in bottlenose dolphins

(2014) A. M. Kopps et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades

(2014) Nicholas J. Matzke   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

No evidence for recovery in the population of sperm whale bulls off Western Australia, 30 years post-whaling

(2014) G Carroll et al.   Endangered Species Research

Distribution of Soviet catches of sperm whales Physeter macrocephalus in the North Pacific

(2014) YV Ivashchenko et al.   Endangered Species Research

Depredating sperm whales in the Gulf of Alaska: local habitat use and long distance movements across putative population boundaries

(2014) JM Straley et al.   Endangered Species Research

Sperm whales,Physeter macrocephalus, in the Mediterranean Sea: a summary of status, threats, and conservation recommendations

(2013) Giuseppe Notarbartolo-Di-Sciara   AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS

Protter: interactive protein feature visualization and integration with experimental proteomic data

(2013) Ulrich Omasits et al.   BIOINFORMATICS

Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales

(2013) CS Baker et al.   MARINE ECOLOGY PROGRESS SERIES

As main meal for sperm whales: Plastics debris

(2013) Renaud de Stephanis et al.   MARINE POLLUTION BULLETIN

Global assessment of oceanic lead pollution using sperm whales (Physeter macrocephalus) as an indicator species

(2013) Laura C. Savery et al.   MARINE POLLUTION BULLETIN

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

(2013) Brittany L. Hancock-Hanser et al.   Molecular Ecology Resources

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

(2013) Rasmus Heller et al.   PLoS One

Mitogenomic Phylogenetics of Fin Whales (Balaenoptera physalus spp.): Genetic Evidence for Revision of Subspecies

(2013) Frederick I. Archer et al.   PLoS One

Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing

(2012) Alana Alexander et al.   Genome Biology and Evolution

A link between male sperm whales, Physeter macrocephalus, of the Azores and Norway

(2012) Lisa Steiner et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Ocean nomads: Distribution and movements of sperm whales in the North Pacific shown by whaling data and Discovery marks

(2012) Sally A. Mizroch et al.   MARINE MAMMAL SCIENCE

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

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mitogenomic sequences better resolve stock structure of southern Greater Caribbean green turtle rookeries

(2012) BRIAN M. SHAMBLIN et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Genetic diversity and demographic history of Dosidicus gigas (Cephalopoda: Ommastrephidae) in the Humboldt Current System

(2011) CM Ibáñez et al.   MARINE ECOLOGY PROGRESS SERIES

Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

(2011) A. Dornburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA

(2011) SARAH L. MESNICK et al.   Molecular Ecology Resources

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Current and Future Patterns of Global Marine Mammal Biodiversity

(2011) Kristin Kaschner et al.   PLoS One

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Positive selection on the killer whale mitogenome

(2010) A. D. Foote et al.   Biology Letters

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

(2010) P. A. Morin et al.   GENOME RESEARCH

Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

(2010) Simon Y. W. Ho et al.   Mitochondrial DNA

Predicting the distributions of marine organisms at the global scale

(2009) Jonathan Ready et al.   ECOLOGICAL MODELLING

Female philopatry in coastal basins and male dispersion across the North Atlantic in a highly mobile marine species, the sperm whale (Physeter macrocephalus)

(2009) DANIEL ENGELHAUPT et al.   MOLECULAR ECOLOGY

Divergence date estimation and a comprehensive molecular tree of extant cetaceans

(2009) Michael R. McGowen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ice Age Terminations

(2009) H. Cheng et al.   SCIENCE

The adaptive evolution of the mammalian mitochondrial genome

(2008) Rute R da Fonseca et al.   BMC GENOMICS

ARCTIC CLIMATE CHANGE AND ITS IMPACTS ON THE ECOLOGY OF THE NORTH ATLANTIC

(2008) Charles H. Greene et al.   ECOLOGY

Culture, population structure, and low genetic diversity in Pleistocene hominins

(2008) L. S. Premo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA