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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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High‐throughput DNA sequencing – concepts and limitations

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Social Organization in Sperm Whales, Physeter macrocephalus

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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

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Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA

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Population differentiation of the Atlantic spotted dolphin (Stenella frontalis) in the western North Atlantic, including the Gulf of Mexico

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

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

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

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The Mitochondrial Genome of the Sperm Whale and a New Molecular Reference for Estimating Eutherian Divergence Dates

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The Power of Relative Rates Tests Depends on the Data

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The occurrence of mtDNA heteroplasmy in multiple cetacean species

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Can Genetic Differences Explain Vocal Dialect Variation in Sperm Whales, Physeter macrocephalus?

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Genetic differentiation and intraspecific structure of Eastern Tropical Pacific spotted dolphins, Stenella attenuata, revealed by DNA analyses

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Population genetic structure of Bryde’s whales (Balaenoptera brydei) at the inter-oceanic and trans-equatorial levels

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

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

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

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Molecular cloning: A laboratory manual

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Nuclear integrations: challenges for mitochondrial DNA markers

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Pantropical Spotted Dolphin

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

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

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Mitogenomic analyses provide new insights into cetacean origin and evolution

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

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The mitochondrial genome: mutation, selection and recombination

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Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep?

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Non‐geographically based population structure of South Pacific sperm whales: dialects, fluke‐markings and genetics

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Phylogeography, population structure and dispersal patterns of the beluga whale Delphinapterus leucas in the western Nearctic revealed by mitochondrial DNA

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Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): analysis of mitochondrial and nuclear loci

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Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific

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Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers

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Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes

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Past and Distant Whaling and the Rapid Decline of Sperm Whales off the Galápagos Islands

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Geographic Isolation of Hector's Dolphin Populations Described by Mitochondrial DNA Sequences

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DNA evidence for historic population size and past ecosystem impacts of gray whales

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Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

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Body size, metabolic rate, generation time, and the molecular clock.

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Patterns of kinship in groups of free-living sperm whales (Physeter macrocephalus) revealed by multiple molecular genetic analyses.

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Fast and accurate short read alignment with Burrows–Wheeler transform

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The Sequence Alignment/Map format and SAMtools

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NUMTs in Sequenced Eukaryotic Genomes

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Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences

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Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis

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

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

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

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

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

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025578openalex-snapshot

Low diversity and biased substitution patterns in the mitochondrial DNA control region of sperm whales: implications for estimates of time since common ancestry

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Evolution of the cetacean mitochondrial D-loop region.

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Quantitative Phyletics and the Evolution of Anurans

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Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

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Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences

inferredcites →https://doi.org/10.1098/rspb.2002.2033openalex-snapshot

Low worldwide genetic diversity in the killer whale (Orcinus orca): implications for demographic history

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Habitat structure and the dispersal of male and female bottlenose dolphins ( Tursiops truncatus )

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

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

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

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

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HISTORICAL POPULATION SIZE CHANGE OF BOWHEAD WHALES INFERRED FROM DNA SEQUENCE POLYMORPHISM DATA

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

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

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TESTING SIGNIFICANCE OF INCONGRUENCE

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TNT, a free program for phylogenetic analysis

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Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world‐wide

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Evidence for male dispersal along the coasts but no migration in pelagic waters in dusky dolphins (Lagenorhynchus obscurus)

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Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata

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

inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05274.xopenalex-snapshot

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

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Common misconceptions in molecular ecology: echoes of the modern synthesis

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SPERM WHALES TAGGED WITH TRANSPONDERS AND TRACKED UNDERWATER BY SONAR

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POPULATION STRUCTURE IN AN INSHORE CETACEAN REVEALED BY MICROSATELLITE AND mtDNA ANALYSIS: BOTTLENOSE DOLPHINS (TURSIOPS SP.) IN SHARK BAY, WESTERN AUSTRALIA

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GENETIC DIVERSITY IN THE MATRILINEAL WHALES: MODELS OF CULTURAL HITCHHIKING AND GROUP-SPECIFIC NON-HERITABLE DEMOGRAPHIC VARIATION

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GENETIC VARIATION OF KOGIA SPP. WITH PRELIMINARY EVIDENCE FOR TWO SPECIES OF KOGIA SIMA

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

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

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Multiplexed microsatellite recovery using massively parallel sequencing

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Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals

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Comment on "Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals"

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Cultural Selection and Genetic Diversity in Matrilineal Whales

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Culture and Genetic Evolution in Whales

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Genetic variation and evidence for population structure in eastern North Pacific false killer whales (Pseudorca crassidens)

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The Effects of Genetic and Geographic Structure on Neutral Variation

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THE PHYSIOLOGICAL BASIS OF DIVING TO DEPTH: Birds and Mammals

inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

inferredcites →https://doi.org/10.1186/1471-2148-11-65openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot

BEAST: Bayesian evolutionary analysis by sampling trees

inferredcites →https://doi.org/10.1186/1472-6785-11-10openalex-snapshot

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

inferredcites →https://doi.org/10.1186/gb-2001-2-11-research0049openalex-snapshot

Optimality of the genetic code with respect to protein stability and amino-acid frequencies

inferredcites →https://doi.org/10.1186/gb-2011-12-6-r59openalex-snapshot

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

inferredcites →https://doi.org/10.1266/ggs.78.81openalex-snapshot

Phylogeography and population structure of the Dall's porpoise, Phocoenoides dalli, in Japanese waters revealed by mitochondrial DNA.

inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot

Relaxed Phylogenetics and Dating with Confidence

inferredcites →https://doi.org/10.1371/journal.pbio.0060010openalex-snapshot

Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA

inferredcites →https://doi.org/10.1371/journal.pcbi.1002737openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pone.0001615openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pone.0007318openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pone.0027138openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pone.0032579openalex-snapshot

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

inferredcites →https://doi.org/10.2307/2992406openalex-snapshot

The Retention Index and Homoplasy Excess

inferredcites →https://doi.org/10.2307/4089130openalex-snapshot

Numts: A Challenge for Avian Systematics and Population Biology

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

inferredcites →https://doi.org/10.3354/meps09145openalex-snapshot

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

inferredcites →https://doi.org/10.3354/meps116001openalex-snapshot

Distribution of mtDNA haplotypes in North Atlantic humpback whales: the influence of behaviour on population structure

inferredcites →https://doi.org/10.3354/meps242295openalex-snapshot

Estimates of the current global population size and historical trajectory for sperm whales

inferredcites →https://doi.org/10.47536/jcrm.v4i2.847openalex-snapshot

Small-scale population structure of eastern North Pacific harbour porpoises (Phocoena phocoena) indicated by molecular genetic analyses

inferredcites →https://doi.org/10.5860/choice.41-3452openalex-snapshot

Sperm whales: social evolution in the ocean

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Abundance estimate of Eastern Caribbean sperm whales using large scale regional surveys

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Common dolphin (Delphinus delphis) mitochondrial genomes from Senegal reveal geographic structure across the North Atlantic but provide no support for global long‐beaked clade

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Range‐wide phylogeographic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) using expanded sampling from contemporary and historical specimens

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Australian sperm whales from different whaling stocks belong to the same population

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What factors shape genetic diversity in cetaceans?

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Sperm Whale Physeter macrocephalus Linnaeus, 1758

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Sperm Whale Physeter macrocephalus Linnaeus, 1758

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Cultural Hitchhiking in the Matrilineal Whales

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Sperm Whale

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Sperm whale Physeter macrocephalus Linnaeus, 1758

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Comparative analysis of the genetic structures of Kogia spp. populations in the western North Pacific

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Kinship and association do not explain vocal repertoire variation among individual sperm whales or social units

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Low genetic diversity, limited gene flow and widespread genetic bottleneck effects in a threatened dolphin species, the Australian humpback dolphin

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Mitogenome of a monotypic genus, Oliotius Kottelat, 2013 (Cypriniformes: Cyprinidae): Genomic characterization and phylogenetic position

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Putative origin and maternal relatedness of male sperm whales (Physeter macrocephalus) recently stranded in the North Sea

inferred← citeshttps://doi.org/10.1016/j.ympev.2017.09.022openalex-snapshot

More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2017.12.027openalex-snapshot

Cryptic lineage differentiation among Indo-Pacific bottlenose dolphins (Tursiops aduncus) in the northwest Indian Ocean

inferred← citeshttps://doi.org/10.1038/s41437-026-00824-xopenalex-snapshot

Mitochondrial structure despite nuclear panmixia: sex-specific dispersal dictates population structure in sperm whales

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The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes

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Multidisciplinary studies on a sick-leader syndrome-associated mass stranding of sperm whales (Physeter macrocephalus) along the Adriatic coast of Italy

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Marine mammal strandings recorded in New Caledonia, South West Pacific Ocean, 1877 to 2022

inferred← citeshttps://doi.org/10.1073/pnas.1620736114openalex-snapshot

Gene–culture coevolution in whales and dolphins

inferred← citeshttps://doi.org/10.1093/bib/bbz060openalex-snapshot

Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses

inferred← citeshttps://doi.org/10.1093/jhered/esac042openalex-snapshot

mtDNA heteroplasmy gives rise to a new maternal lineage in North Pacific humpback whales (Megaptera novaeangliae)

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Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes

inferred← citeshttps://doi.org/10.1093/jhered/esy050openalex-snapshot

The Influence of Selection on MHC DQA and DQB Haplotypes in the Endemic New Zealand Hector’s and Māui Dolphins

inferred← citeshttps://doi.org/10.1098/rsbl.2025.0666openalex-snapshot

Trans-oceanic kinship in the sperm whale ( Physeter macrocephalus )

inferred← citeshttps://doi.org/10.1098/rsos.180914openalex-snapshot

Kinship influences sperm whale social organization within, but generally not among, social units

inferred← citeshttps://doi.org/10.1098/rsos.201794openalex-snapshot

Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean

inferred← citeshttps://doi.org/10.1098/rstb.2015.0332openalex-snapshot

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

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Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs

inferred← citeshttps://doi.org/10.1111/mec.13638openalex-snapshot

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

inferred← citeshttps://doi.org/10.1111/mec.14698openalex-snapshot

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

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Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea

inferred← citeshttps://doi.org/10.1111/mms.12893openalex-snapshot

New haplotypes found in stranded long‐finned pilot whales (Globicephala melas) in the eastern North Atlantic and adjacent waters

inferred← citeshttps://doi.org/10.1111/mms.12933openalex-snapshot

Worldwide phylogeography of rough‐toothed dolphins ( Steno bredanensis ) provides evidence for subspecies delimitation

inferred← citeshttps://doi.org/10.1126/science.ady9280openalex-snapshot

Cooperation by non-kin during birth underpins sperm whale social complexity

inferred← citeshttps://doi.org/10.1186/s12864-021-08030-1openalex-snapshot

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

inferred← citeshttps://doi.org/10.1371/journal.pone.0123543openalex-snapshot

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

inferred← citeshttps://doi.org/10.1371/journal.pone.0158129openalex-snapshot

Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

inferred← citeshttps://doi.org/10.21203/rs.3.rs-54147/v1openalex-snapshot

Breed-specific Reference Sequence Optimizes Mapping Accuracy of NGS Analyses for Pigs

inferred← citeshttps://doi.org/10.29244/haj.2.1.21openalex-snapshot

Identifikasi Karakterstik Molekuler Gen 16S rRNA Parsial pada Paus Sperma (Physeter macrocephalus Linnaeus, 1758)

inferred← citeshttps://doi.org/10.3354/meps14819openalex-snapshot

Change in matrilineal structure over time in an isolated population of sperm whales

inferred← citeshttps://doi.org/10.3389/fevo.2020.505233openalex-snapshot

Using Ancient DNA Analysis and Radiocarbon Dating to Determine the Provenance of an Unusual Whaling Artifact

inferred← citeshttps://doi.org/10.3390/oceans1020006openalex-snapshot

Cetaceans as Exemplars of Evolution and Evolutionary Ecology: A Glossary

inferred← citeshttps://doi.org/10.3732/apps.1300063openalex-snapshot

A long PCR–based approach for DNA enrichment prior to next‐generation sequencing for systematic studies

inferred← citeshttps://doi.org/10.6084/m9.figshare.16800178openalex-snapshot

Additional file 1 of Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

inferred← citeshttps://doi.org/10.6084/m9.figshare.16800181openalex-snapshot

Additional file 2 of Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

inferred← citeshttps://doi.org/10.6084/m9.figshare.16800184openalex-snapshot

Additional file 3 of Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

inferred← citeshttps://doi.org/10.6084/m9.figshare.16800187openalex-snapshot

Additional file 4 of Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

inferred← citeshttps://doi.org/10.6084/m9.figshare.16800190openalex-snapshot

Additional file 5 of Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

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