Neutral and nonneutral mitochondrial genetic variation in deep-sea clams from the family vesicomyidae. 2000

A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
Center for Theoretical and Applied Genetics, 71 Dudley Road, Rutgers University, New Brunswick, NJ 08901-8521, USA. apeek@uci.edu

Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae) were examined for variation consistent with the neutral model of molecular evolution. One gene, cytochrome oxidase subunit I (COI), deviated from the expectations of neutrality by containing an excess of intraspecific nonsynonymous polymorphism. Additionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second mitochondrial gene, the large-subunit 16S ribosomal RNA gene (16S), showed little deviation from neutrality either between or within species. Together, COI and 16S show no deviation from neutral expectations by the HKA test, produce congruent phylogenetic relationships between species, and show correlated numbers of fixed differences between species and polymorphism within species. These patterns of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific nonsynonymous polymorphism at COI is near neutrality. In addition to examining the forces of molecular evolution, we extend hypotheses about interspecific relationships within this family for geographical locations previously unexamined by molecular methods including habitats near the Middle Atlantic, the Aleutian Trench, and Costa Rica.

UI MeSH Term Description Entries
D008800 Mexico A country in NORTH AMERICA, bordering the Caribbean Sea and the Gulf of Mexico, between BELIZE and the UNITED STATES, and bordering the North Pacific Ocean, between Guatemala and the UNITED STATES.
D008928 Mitochondria Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. They contain distinctive RIBOSOMES, transfer RNAs (RNA, TRANSFER); AMINO ACYL T RNA SYNTHETASES; and elongation and termination factors. Mitochondria depend upon genes within the nucleus of the cells in which they reside for many essential messenger RNAs (RNA, MESSENGER). Mitochondria are believed to have arisen from aerobic bacteria that established a symbiotic relationship with primitive protoeukaryotes. (King & Stansfield, A Dictionary of Genetics, 4th ed) Mitochondrial Contraction,Mitochondrion,Contraction, Mitochondrial,Contractions, Mitochondrial,Mitochondrial Contractions
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D003364 Costa Rica A country in CENTRAL AMERICA, bordering both the Caribbean Sea and the North Pacific Ocean, between NICARAGUA and PANAMA.
D003576 Electron Transport Complex IV A multisubunit enzyme complex containing CYTOCHROME A GROUP; CYTOCHROME A3; two copper atoms; and 13 different protein subunits. It is the terminal oxidase complex of the RESPIRATORY CHAIN and collects electrons that are transferred from the reduced CYTOCHROME C GROUP and donates them to molecular OXYGEN, which is then reduced to water. The redox reaction is simultaneously coupled to the transport of PROTONS across the inner mitochondrial membrane. Cytochrome Oxidase,Cytochrome aa3,Cytochrome-c Oxidase,Cytochrome Oxidase Subunit III,Cytochrome a,a3,Cytochrome c Oxidase Subunit VIa,Cytochrome-c Oxidase (Complex IV),Cytochrome-c Oxidase Subunit III,Cytochrome-c Oxidase Subunit IV,Ferrocytochrome c Oxygen Oxidoreductase,Heme aa3 Cytochrome Oxidase,Pre-CTOX p25,Signal Peptide p25-Subunit IV Cytochrome Oxidase,Subunit III, Cytochrome Oxidase,p25 Presequence Peptide-Cytochrome Oxidase,Cytochrome c Oxidase,Cytochrome c Oxidase Subunit III,Cytochrome c Oxidase Subunit IV,Oxidase, Cytochrome,Oxidase, Cytochrome-c,Signal Peptide p25 Subunit IV Cytochrome Oxidase,p25 Presequence Peptide Cytochrome Oxidase
D004275 DNA, Ribosomal DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA. Ribosomal DNA,rDNA
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D014644 Genetic Variation Genotypic differences observed among individuals in a population. Genetic Diversity,Variation, Genetic,Diversity, Genetic,Diversities, Genetic,Genetic Diversities,Genetic Variations,Variations, Genetic
D049872 Bivalvia A class in the phylum MOLLUSCA comprised of mussels; clams; OYSTERS; COCKLES; and SCALLOPS. They are characterized by a bilaterally symmetrical hinged shell and a muscular foot used for burrowing and anchoring. Mussels,Bivalves,Clams,Bivalve,Bivalvias,Clam,Mussel

Related Publications

A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
December 2018, Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
May 2014, Die Naturwissenschaften,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
March 1996, Genetics,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
July 2004, Molecular phylogenetics and evolution,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
August 2018, Ecology and evolution,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
February 2020, Fish & shellfish immunology,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
January 2019, PloS one,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
August 1998, Proceedings of the National Academy of Sciences of the United States of America,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
October 2008, Trends in ecology & evolution,
A S Peek, and B S Gaut, and R A Feldman, and J P Barry, and R E Kochevar, and R A Lutz, and R C Vrijenhoek
October 2018, Molecular biology reports,
Copied contents to your clipboard!