Mitochondrial OXPHOS genes provides insights into genetics basis of hypoxia adaptation in anchialine cave shrimps

[1]  Xuejia Shi,et al.  Evolution of mitochondrial energy metabolism genes associated with hydrothermal vent adaption of Alvinocaridid shrimps , 2017, Genes & Genomics.

[2]  T. Iliffe,et al.  Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps , 2017, Scientific Reports.

[3]  Wenhua Ren,et al.  Evolution of Digestive Enzymes and RNASE1 Provides Insights into Dietary Switch of Cetaceans , 2016, Molecular biology and evolution.

[4]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[5]  Shixia Xu,et al.  Evolutionary Genetics of Hypoxia Tolerance in Cetaceans during Diving , 2016, Genome biology and evolution.

[6]  Wenhua Ren,et al.  ‘Obesity’ is healthy for cetaceans? Evidence from pervasive positive selection in genes related to triacylglycerol metabolism , 2015, Scientific Reports.

[7]  R. E. Bishop,et al.  'Anchialine' redefined as a subterranean estuary in a crevicular or cavernous geological setting , 2015 .

[8]  Y. Fujita,et al.  Taking their breath away: metabolic responses to low-oxygen levels in anchialine shrimps (Crustacea: Atyidae and Alpheidae). , 2014, Comparative biochemistry and physiology. Part A, Molecular & integrative physiology.

[9]  Shixia Xu,et al.  Adaptive Evolution of Mitochondrial Energy Metabolism Genes Associated with Increased Energy Demand in Flying Insects , 2014, PloS one.

[10]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[11]  Ming Li,et al.  Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations , 2013, Nature Communications.

[12]  R. Jenner,et al.  The First Venomous Crustacean Revealed by Transcriptomics and Functional Morphology: Remipede Venom Glands Express a Unique Toxin Cocktail Dominated by Enzymes and a Neurotoxin , 2013, Molecular biology and evolution.

[13]  Yuan Zhang,et al.  Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau , 2013, Nature Communications.

[14]  G. Scholtz,et al.  Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. , 2013, Molecular phylogenetics and evolution.

[15]  T. Iliffe,et al.  Historical biogeography and phylogeny of Typhlatya cave shrimps (Decapoda: Atyidae) based on mitochondrial and nuclear data , 2013 .

[16]  J. Smeitink,et al.  OXPHOS mutations and neurodegeneration , 2012, The EMBO journal.

[17]  Ya-ping Zhang,et al.  Genome-Wide Scan for Bats and Dolphin to Detect Their Genetic Basis for New Locomotive Styles , 2012, PloS one.

[18]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[19]  C. Hiser,et al.  Gating and regulation of the cytochrome c oxidase proton pump. , 2012, Biochimica et biophysica acta.

[20]  R. E. Bishop,et al.  Ecological physiology of the anchialine shrimp Barbouria cubensis: a comparison of epigean and hypogean populations , 2012, Marine Biodiversity.

[21]  Ramón Doallo,et al.  ProtTest 3: fast selection of best-fit models of protein evolution , 2011, Bioinform..

[22]  Meredith E. Protas,et al.  Genetic basis of eye and pigment loss in the cave crustacean, Asellus aquaticus , 2011, Proceedings of the National Academy of Sciences.

[23]  Ya-ping Zhang,et al.  Adaptive evolution of energy metabolism genes and the origin of flight in bats , 2010, Proceedings of the National Academy of Sciences.

[24]  Qing Wang,et al.  Measurement of the molecular masses of hydrophilic and hydrophobic subunits of ATP synthase and complex I in a single experiment. , 2009, Analytical biochemistry.

[25]  Keshav K. Singh,et al.  Tumorigenic transformation of human breast epithelial cells induced by mitochondrial DNA depletion , 2008, Cancer biology & therapy.

[26]  L. Putignani,et al.  Alteration of expression levels of the oxidative phosphorylation system (OXPHOS) in breast cancer cell mitochondria , 2008, Breast Cancer Research and Treatment.

[27]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[28]  Jayatri Das.  The role of mitochondrial respiration in physiological and evolutionary adaptation , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[29]  Jianzhi Zhang.  Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys , 2006, Nature Genetics.

[30]  Sergei L. Kosakovsky Pond,et al.  Datamonkey: rapid detection of selective pressure on individual sites of codon alignments , 2005, Bioinform..

[31]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[32]  S. Seneca,et al.  Respiratory chain complex V deficiency due to a mutation in the assembly gene ATP12 , 2004, Journal of Medical Genetics.

[33]  Keith A. Crandall,et al.  TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees , 2003, Bioinform..

[34]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[35]  S. Yokoyama,et al.  The "five-sites" rule and the evolution of red and green color vision in mammals. , 1998, Molecular biology and evolution.

[36]  Kathrin Hüppop.  Oxygen consumption of Astyanax fasciatus (Characidae, Pisces): a comparison of epigean and hypogean populations , 1986, Environmental Biology of Fishes.

[37]  J. Childress.  The respiratory rates of midwater crustaceans as a function of depth of occurrence and relation to the oxygen minimum layer off Southern California. , 1975, Comparative biochemistry and physiology. A, Comparative physiology.

[38]  J. Childress,et al.  Circulatory adaptations to the oxygen minimum layer in the bathypelagic mysid Gnathophausia ingens. , 1971, The Biological bulletin.

[39]  A L Lehninger,et al.  Mitochondria and calcium ion transport. , 1970, The Biochemical journal.

[40]  David Posada,et al.  Selection of models of DNA evolution with jModelTest. , 2009, Methods in molecular biology.

[41]  M. Lazarou,et al.  Chapter 18 Analysis of respiratory chain complex assembly with radiolabeled nuclear- and mitochondrial-encoded subunits. , 2009, Methods in enzymology.

[42]  S. Frost,et al.  Detecting signatures of selection from DNA sequences using Datamonkey. , 2009, Methods in molecular biology.

[43]  T. Iliffe,et al.  PLEOMOTHRA FRAGILIS N. SP. (REMIPEDIA) FROM THE BAHAMAS, WITH REMARKS ON MORPHOLOGIC REDUCTIONS AND POSTNAUPLIAR DEVELOPMENT , 2008 .

[44]  T. Iliffe,et al.  BEHAVIOR OF REMIPEDIA IN THE LABORATORY, WITH SUPPORTING FIELD OBSERVATIONS , 2007 .

[45]  L. Mejía-Ortíz,et al.  ARE THERE ADAPTATION LEVELS TO CAVE LIFE IN CRAYFISH? , 2005 .

[46]  R. E. Bishop,et al.  LIFE IN THE HYPOXIC AND ANOXIC ZONES: METABOLISM AND PROXIMATE COMPOSITION OF CARIBBEAN TROGLOBITIC CRUSTACEANS WITH OBSERVATIONS ON THE WATER CHEMISTRY OF TWO ANCHIALINE CAVES , 2004 .

[47]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.

[48]  I. Scheffler.  Molecular genetics of succinate:quinone oxidoreductase in eukaryotes. , 1998, Progress in nucleic acid research and molecular biology.

[49]  D. Platvoet,et al.  First record of a cavernicolous atyid decapod Crustacean in the Iberian Peninsul, new perspectives on the evolution of the genus Typhlatya miravetensis n.sp. , 1995 .

[50]  D. Platvoet,et al.  New perspectives on the evolution of the genus Typhlatya (Crustacea, Decapoda): first record of a cavernicolous atyid in the Iberian Peninsula, Typhlatya miravetensis n. sp. , 1995 .

[51]  T. Ohta.  THE NEARLY NEUTRAL THEORY OF MOLECULAR EVOLUTION , 1992 .

[52]  G. Dickson,et al.  Respiration rates, ATP turnover and adenylate energy charge in excised gills of surface and cave crayfish , 1980 .