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

A novel conservation approach provides insights into the management of rare cetaceans

(2012) Kirsten F. Thompson et al.   BIOLOGICAL CONSERVATION

Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins

(2012) Rebecca M. Hamner et al.   CONSERVATION GENETICS

Common misconceptions in molecular ecology: echoes of the modern synthesis

(2012) STEPHEN A. KARL et al.   MOLECULAR ECOLOGY

Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs

(2012) Mingkun Li et al.   NUCLEIC ACIDS RESEARCH

Circumpolar Diversity and Geographic Differentiation of mtDNA in the Critically Endangered Antarctic Blue Whale (Balaenoptera musculus intermedia)

(2012) Angela L. Sremba et al.   PLoS One

Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency

(2012) Maria Ximena Sosa et al.   PLoS Computational Biology

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

(2011) Julia T Vilstrup et al.   BMC EVOLUTIONARY BIOLOGY

The occurrence of mtDNA heteroplasmy in multiple cetacean species

(2011) Nicole L. Vollmer et al.   CURRENT GENETICS

Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters

(2011) Xiang Li et al.   MARINE BIOLOGY

Population structure and individual movement of southern right whales around New Zealand and Australia

(2011) E Carroll et al.   MARINE ECOLOGY PROGRESS SERIES

Population structure of island-associated dolphins: Evidence from mitochondrial and microsatellite markers for common bottlenose dolphins (Tursiops truncatus) around the main Hawaiian Islands

(2011) Karen K. Martien et al.   MARINE MAMMAL SCIENCE

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

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

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

Kinship of long-term associates in the highly social sperm whale

(2011) JOEL G. ORTEGA-ORTIZ et al.   MOLECULAR ECOLOGY

Multiplexed microsatellite recovery using massively parallel sequencing

(2011) T. N. JENNINGS et al.   Molecular Ecology Resources

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

Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation

(2011) Sebastián Duchêne et al.   PLoS One

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

(2011) Hiroki Goto et al.   GENOME BIOLOGY

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

(2011) Brian J Knaus et al.   BMC ECOLOGY

Detecting Heteroplasmy from High-Throughput Sequencing of Complete Human Mitochondrial DNA Genomes

(2010) Mingkun Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

The influence of glacial epochs and habitat dependence on the diversity and phylogeography of a coastal dolphin species: Lagenorhynchus albirostris

(2010) E. Banguera-Hinestroza et al.   CONSERVATION GENETICS

Mitochondrial DNA variation and population structure of Commerson’s dolphins (Cephalorhynchus commersonii) in their southernmost distribution

(2010) Lida E. Pimper et al.   CONSERVATION GENETICS

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

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

Molecular insight into the population structure of common and spotted dolphins inhabiting the pelagic waters of the Northeast Atlantic

(2010) Sophie Quérouil et al.   MARINE BIOLOGY

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

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

Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny

(2010) Benoit Nabholz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.)

(2009) MARC OREMUS et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

A SNP discovery method to assess variant allele probability from next-generation resequencing data

(2009) Y. Shen et al.   GENOME RESEARCH

Erratum to: Population structure of short-beaked common dolphins (Delphinus delphis) in the North Atlantic Ocean as revealed by mitochondrial and nuclear genetic markers

(2009) Luca Mirimin et al.   MARINE BIOLOGY

Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)

(2009) J. A. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans

(2009) Howard C. Rosenbaum et al.   PLoS One

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

(2009) Mette E. Steeman et al.   SYSTEMATIC BIOLOGY

Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters

(2008) GUANG YANG et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system

(2008) G. Dunshea et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Rapid whole-genome mutational profiling using next-generation sequencing technologies

(2008) D. R. Smith et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

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

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

Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA

(2008) James Bruce Stewart et al.   PLOS BIOLOGY