Domain combinations in archaeal, eubacterial and eukaryotic proteomes, Journal of Molecular Biology, vol.310, issue.2, pp.311-325, 2001. ,
DOI : 10.1006/jmbi.2001.4776
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling, Bioinformatics, vol.22, issue.2, pp.195-201, 2006. ,
DOI : 10.1093/bioinformatics/bti770
The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection, Proceedings of the National Academy of Sciences, vol.100, issue.10, pp.5885-5890, 2003. ,
DOI : 10.1073/pnas.1037686100
QMEAN: A comprehensive scoring function for model quality assessment, Proteins: Structure, Function, and Bioinformatics, vol.215, issue.Web Server issu, pp.261-277, 2008. ,
DOI : 10.1002/prot.21715
Stability of domain structures in multi-domain proteins, Scientific Reports, vol.25, issue.1, p.40, 2011. ,
DOI : 10.1093/bioinformatics/btp242
Domain Rearrangements in Protein Evolution, Journal of Molecular Biology, vol.353, issue.4, pp.911-923, 2005. ,
DOI : 10.1016/j.jmb.2005.08.067
Nemoglobins: Divergent nematode globins, Parasitology Today, vol.9, issue.10, pp.353-360, 1993. ,
DOI : 10.1016/0169-4758(93)90082-Q
Structural characterization of an Ascaris myoglobin, J Biol Chem, vol.269, pp.30181-30186, 1994. ,
Repeated Sequences in DNA, Science, vol.161, issue.3841, pp.529-540, 1968. ,
DOI : 10.1126/science.161.3841.529
. Evidence for unsaturated haem-binding sites, Biochemical Journal, vol.242, issue.3, pp.689-694, 1987. ,
DOI : 10.1042/bj2420689
Polar zipper sequence in the high-affinity hemoglobin of Ascaris suum: amino acid sequence and structural interpretation., Proceedings of the National Academy of Sciences, vol.89, issue.10, pp.4638-4642, 1992. ,
DOI : 10.1073/pnas.89.10.4638
Formation of two hydrogen bonds from the globin to the heme-linked oxygen molecule in Ascaris hemoglobin., Proceedings of the National Academy of Sciences, vol.91, issue.4, pp.1594-1597, 1994. ,
DOI : 10.1073/pnas.91.4.1594
Long-term anaerobic metabolism of erythrocytes of the arcid clam Scapharca inaequivalvis, Journal of Experimental Marine Biology and Ecology, vol.187, issue.1, pp.27-37, 1995. ,
DOI : 10.1016/0022-0981(94)00168-D
Daphnia pulex didomain hemoglobin: structure and evolution of polymeric hemoglobins and their coding genes, Molecular Biology and Evolution, vol.16, issue.9, pp.1208-1218, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026211
Isolation and sequencing of a cDNA for an unusual hemoglobin from the parasitic nematode Pseudoterranova decipiens., Proceedings of the National Academy of Sciences, vol.88, issue.13, pp.5655-5659, 1991. ,
DOI : 10.1073/pnas.88.13.5655
A nematode gene con? tains an intron previously thought to be unique to plants, J Mol Evol, vol.35, pp.131-136, 1992. ,
The evolution of `bricolage', Trends in Genetics, vol.14, issue.2, pp.54-59, 1998. ,
DOI : 10.1016/S0168-9525(97)01358-9
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
[20] VERIFY3D: Assessment of protein models with three-dimensional profiles, Methods Enzymol, vol.277, pp.396-404, 1997. ,
DOI : 10.1016/S0076-6879(97)77022-8
Comparative protein structure modeling with MODELLER. Current protocols in bioinformatics, pp.5-6, 2006. ,
The zinc?mediated sulfide?binding mechanism of hydrothermal vent tubeworm 400?kDa hemoglobin, Cah Biol Mar, vol.47, pp.371-377, 2006. ,
Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin, Proceedings of the National Academy of Sciences, vol.102, issue.8, pp.2713-2718, 2005. ,
DOI : 10.1073/pnas.0407455102
Kinet? ics of ligand to Pseudoterranova decipiens and Ascaris suum hemoglobins and to Leu?29??>; Tyr sperm?whale myoglobin mutant, J Biol Chem, vol.268, pp.16993-16998, 1993. ,
A codon?based model of nucleotide substitution for protein?coding DNA sequences, Mol Biol Evol, vol.11, pp.725-736, 1994. ,
Oxygen equilibria and structural characteristics of the tetrameric and polymeric intracellular hemoglobins from the bivalve molluscBarbatia reeveana, Journal of Comparative Physiology B, vol.16, issue.5, pp.675-682, 1986. ,
DOI : 10.1007/BF00692745
The folding and evolution of multidomain proteins, Nature Reviews Molecular Cell Biology, vol.10, issue.4, pp.319-330, 2007. ,
DOI : 10.1038/nrm2144
The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification, BMC Evolutionary Biology, vol.8, issue.1, p.279, 2008. ,
DOI : 10.1186/1471-2148-8-279
Hemoglobins from deep???sea hydrothermal vent scaleworms of the genus Branchipolynoe: A new type of quaternary structure, Proteins: Structure, Function, and Genetics, vol.34, issue.4, pp.427-434, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990301)34:4<427::AID-PROT2>3.3.CO;2-C
Characterization and functional properties of the extracellular coelomic hemoglobins from the deep???sea, hydrothermal vent scaleworm Branchipolynoe symmytilida, Proteins: Structure, Function, and Genetics, vol.34, issue.4, pp.435-442, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990301)34:4<435::AID-PROT3>3.3.CO;2-8
Duplication and divergence: the evolution of nematode globins, J Nematol, vol.41, pp.35-51, 2009. ,
Evolutionary history of introns in a multidomain globin gene, Journal of Molecular Evolution, vol.1171, issue.6, pp.641-647, 1996. ,
DOI : 10.1007/BF02338797
Two-domain hemoglobin gene of the water flea Moina macrocopa: duplication in the ancestral Cladocera, diversification, and loss of a bridge intron, Gene, vol.273, issue.1, pp.41-50, 2001. ,
DOI : 10.1016/S0378-1119(01)00569-8
MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005. ,
DOI : 10.1093/nar/gki198
The SWISS-MODEL Repository and associated resources, Nucleic Acids Research, vol.37, issue.Database, pp.387-392, 1993. ,
DOI : 10.1093/nar/gkn750
Evolution of a polymeric globin in the brine shrimp Artemia, Nature, vol.348, issue.6302, pp.653-656, 1990. ,
DOI : 10.1038/348653a0
Variable Substitution Rates of the 18 Domain Sequences in Artemia Hemoglobin, Journal of Molecular Evolution, vol.46, issue.6, pp.729-733, 1998. ,
DOI : 10.1007/PL00006354
Assessing protein structures with a non-local atomic interaction energy, Journal of Molecular Biology, vol.277, issue.5, pp.1141-1152, 1998. ,
DOI : 10.1006/jmbi.1998.1665
Determinants of Ascaris Hemoglobin Octamer Formation, Journal of Biological Chemistry, vol.273, issue.49, pp.32644-32649, 1998. ,
DOI : 10.1074/jbc.273.49.32644
Detecting Individual Sites Subject to Episodic Diversifying Selection, PLoS Genetics, vol.351, issue.7, p.1002764, 2012. ,
DOI : 10.1371/journal.pgen.1002764.s025
URL : http://doi.org/10.1371/journal.pgen.1002764
Origin of a "bridge" intron in the gene for a two-domain globin., Proceedings of the National Academy of Sciences, vol.88, issue.15, pp.6672-6676, 1991. ,
DOI : 10.1073/pnas.88.15.6672
Molecular evolution and phylogenetics Likelihood models for detecting positively selected amino acid sites and applications to the HIV?1 envelope gene, Genetics, vol.148, pp.929-936, 1998. ,
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods, Proceedings of the National Academy of Sciences, vol.106, issue.16, pp.6700-6705, 2009. ,
DOI : 10.1073/pnas.0901855106
GUIDANCE: a web server for assessing alignment confidence scores, Nucleic Acids Research, vol.38, issue.Web Server, pp.23-28, 2010. ,
DOI : 10.1093/nar/gkq443
Towards a molecular phylogeny of Mollusks: Bivalves??? early evolution as revealed by mitochondrial genes, Molecular Phylogenetics and Evolution, vol.57, issue.2, pp.641-657, 2010. ,
DOI : 10.1016/j.ympev.2010.08.032
jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1256, 2008. ,
DOI : 10.1093/molbev/msn083
URL : http://mbe.oxfordjournals.org/cgi/content/short/25/7/1253
Origin and Evolution of the Unique Tetra-Domain Hemoglobin from the Hydrothermal Vent Scale Worm Branchipolynoe, Molecular Biology and Evolution, vol.27, issue.1, pp.143-152, 2010. ,
DOI : 10.1093/molbev/msp218
URL : https://hal.archives-ouvertes.fr/hal-01250930
Self?association, cooperativity and supercooperativity of oxygen binding by hemoglobins, J Exp Biol, vol.201, pp.1073-1084, 1998. ,
The 2.0 ?? Crystal Structure ofScapharcaTetrameric Hemoglobin: Cooperative Dimers within an Allosteric Tetramer, Journal of Molecular Biology, vol.253, issue.1, pp.168-186, 1995. ,
DOI : 10.1006/jmbi.1995.0543
URL : https://hal.archives-ouvertes.fr/ujm-01378510
Cooperative hemoglobins: conserved fold, diverse quaternary assemblies and allosteric mechanisms, Trends in Biochemical Sciences, vol.26, issue.5, pp.297-304, 2001. ,
DOI : 10.1016/S0968-0004(01)01811-4
Allosteric Hemoglobin Assembly: Diversity and Similarity, Journal of Biological Chemistry, vol.280, issue.30, pp.27477-27480, 2005. ,
DOI : 10.1074/jbc.R500006200
Two-domain hemoglobin from the blood clam,Barbatia lima. The cDNA-derived amino acid sequence, Journal of Protein Chemistry, vol.106, issue.7, pp.499-502, 1995. ,
DOI : 10.1007/BF01886875
Primary struc? ture of chain I of the heterodimeric hemoglobin from the blood clam Barbatia virescens, J Protein Chem, vol.1, pp.629-633, 1992. ,
resulted from the recent gene duplication of the single-domain ?? chain, Biochemical Journal, vol.313, issue.2, pp.561-566, 1996. ,
DOI : 10.1042/bj3130561
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011. ,
DOI : 10.1093/molbev/msr121
The Relationship Between Domain Duplication and Recombination, Journal of Molecular Biology, vol.346, issue.1, pp.355-365, 2005. ,
DOI : 10.1016/j.jmb.2004.11.050
STUDIES ON THE ANAEROBIC METABOLISM AND THE AEROBIC CARBOHYDRATE CONSUMPTION OF SOME FRESH WATER SNAILS, The Biological Bulletin, vol.98, issue.3, pp.266-276, 1950. ,
DOI : 10.2307/1538675
2012) reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplica? tion Nonvertebrate hemoglobins: functions and molecular adaptations, PLoS Biol Physiol Rev, vol.10, issue.81, pp.569-628, 2001. ,
Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites, Genetics, vol.168, issue.2, pp.1041-1051, 2004. ,
DOI : 10.1534/genetics.104.031153
PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-556, 1997. ,
DOI : 10.1093/bioinformatics/13.5.555
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution, Molecular Biology and Evolution, vol.15, issue.5, pp.568-573, 1998. ,
DOI : 10.1093/oxfordjournals.molbev.a025957
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1585-1591, 2007. ,
DOI : 10.1093/molbev/msm088
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.322.1650
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages, Molecular Biology and Evolution, vol.19, issue.6, pp.908-917, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004148
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection, Molecular Biology and Evolution, vol.22, issue.4, pp.1107-1118, 2005. ,
DOI : 10.1093/molbev/msi097
S-Sulfohemoglobin and disulfide exchange: The mechanisms of sulfide binding by Riftia pachyptila hemoglobins, Proceedings of the National Academy of Sciences, vol.95, issue.15, pp.8997-9002, 1998. ,
DOI : 10.1073/pnas.95.15.8997
Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level, Molecular Biology and Evolution, vol.22, issue.12, pp.2472-2479, 2005. ,
DOI : 10.1093/molbev/msi237