| 1. |
- Anderson, Frank E., et al.
(författare)
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Bilaterian phylogeny based on analyses of a region of the sodium-potassium ATPase alpha-subunit gene
- 2004
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 58:3, s. 252-268
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Tidskriftsartikel (refereegranskat)abstract
- Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the subunit of the nuclear-encoded sodium–potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium–potassium ATPase -subunit gene appears to be useful for deep-level studies of metazoan phylogeny.
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| 2. |
- Arvestad, Lars
(författare)
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Efficient methods for estimating amino acid replacement rates
- 2006
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 62:6, s. 663-673
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Tidskriftsartikel (refereegranskat)abstract
- Replacement rate matrices describe the process of evolution at one position in a protein and are used in many applications where proteins are studied with an evolutionary perspective. Several general matrices have been suggested and have proved to be good approximations of the real process. However, there are data for which general matrices are inappropriate, for example, special protein families, certain lineages in the tree of life, or particular parts of proteins. Analysis of such data could benefit from adaption of a data-specific rate matrix. This paper suggests two new methods for estimating replacement rate matrices from independent pairwise protein sequence alignments and also carefully studies Muller-Vingron's resolvent method. Comprehensive tests on synthetic datasets show that both new methods perform better than the resolvent method in a variety of settings. The best method is furthermore demonstrated to be robust on small datasets as well as practical on very large datasets of real data. Neither short nor divergent sequence pairs have to be discarded, making the method economical with data. A generalization to multialignment data is suggested and used in a test on protein-domain family phylogenies, where it is shown that the method offers family-specific rate matrices that often have a significantly better likelihood than a general matrix.
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| 3. |
- Arvestad, Lars, et al.
(författare)
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Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences
- 1997
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Ingår i: Journal of Molecular Evolution. - 0022-2844 .- 1432-1432. ; 45:6, s. 696-703
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Tidskriftsartikel (refereegranskat)abstract
- We present a method for estimating the most general reversible substitution matrix corresponding to a given collection of pairwise aligned DNA sequences. This matrix can then be used to calculate evolutionary distances between pairs of sequences in the collection. If only two sequences are considered, our method is equivalent to that of Lanave et al. (1984). The main novelty of our approach is in combining data from different sequence pairs. We describe a weighting method for pairs of taxa related by a known tree that results in uniform weights for all branches. Our method for estimating the rate matrix results in fast execution times, even on large data sets, and does not require knowledge of the phylogenetic relationships among sequences. In a test case on a primate pseudogene, the matrix we arrived at resembles one obtained using maximum likelihood, and the resulting distance measure is shown to have better linearity than is obtained in a less general model.
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| 4. |
- Baltscheffsky, Herrick, et al.
(författare)
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On an Early Gene for Membrane-Integral Inorganic Pyrophosphatase in the Genome of an Apparently Pre-LUCA Extremophile, the Archaeon Candidatus Korarchaeum cryptofilum
- 2014
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 78:2, s. 140-147
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Tidskriftsartikel (refereegranskat)abstract
- A gene for membrane-integral inorganic pyrophosphatase (miPPase) was found in the composite genome of the extremophile archaeon Candidatus Korarchaeum cryptofilum (CKc). This korarchaeal genome shows unusual partial similarity to both major archaeal phyla Crenarchaeota and Euryarchaeota. Thus this Korarchaeote might have retained features that represent an ancestral archaeal form, existing before the occurrence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota. In addition, CKc lacks five genes that are common to early genomes at the LUCA border. These two properties independently suggest a pre-LUCA evolutionary position of this extremophile. Our finding of the miPPase gene in the CKc genome points to a role for the enzyme in the energy conversion of this very early archaeon. The structural features of its miPPase indicate that it can pump protons through membranes. An miPPase from the extremophile bacterium Caldicellulosiruptor saccharolyticus also has a sequence indicating a proton pump. Recent analysis of the three-dimensional structure of the miPPase from Vigna radiata has resulted in the recognition of a strongly acidic substrate (orthophosphate: Pi, pyrophosphate: PPi) binding pocket, containing 11 Asp and one Glu residues. Asp (aspartic acid) is an evolutionarily very early proteinaceous amino acid as compared to the later appearing Glu (glutamic acid). All the Asp residues are conserved in the miPPase of CKc, V. radiata and other miPPases. The high proportion of Asp, as compared to Glu, seems to strengthen our argument that biological energy conversion with binding and activities of orthophosphate (Pi) and energy-rich pyrophosphate (PPi) in connection with the origin and early evolution of life may have started with similar or even more primitive acidic peptide funnels and/or pockets.
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| 5. |
- Berg, Mikael
(författare)
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Emergence of Avian coronavirus Escape Mutants Under Suboptimal Antibody Titers
- 2022
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 90, s. 176-181
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Tidskriftsartikel (refereegranskat)abstract
- To perform a quasispecies assessment of the effect of vaccine combinations and antibody titers on the emergence of Avian coronavirus (AvCoV) escape mutants, 5-week-old males from a commercial chicken breeder lineage were vaccinated intramuscularly with one dose of a monovalent (genotype GI-1) or a bivalent (genotypes GI-1 and GI-11 (n = 40 birds/group) AvCoV vaccine. Seven birds were kept as controls. Six weeks later, pools of sera of each group were prepared and incubated at virus neutralization doses of 10 and 10(-1) with the Beaudette strain (GI-1) of AvCoV in VERO cells. Rescued viruses were then submitted to genome-wide deep sequencing for subconsensus variant detection. After treatment with serum from birds vaccinated with the bivalent vaccine at a titer of 10(-1), an F307I variant was detected in the spike glycoprotein that mapped to an important neutralizing region, which indicated an escape mutant derived from natural selection. Further variants were detected in nonstructural proteins and non-coding regions that are not targets of neutralizing antibodies and might be indicators of genetic drift. These results indicate that the evolution of AvCoV escape mutants after vaccination depends on the type of vaccine strain and the antibody titer and must be assessed based on quasispecies rather than consensus dominant sequences only because quasispecies may be otherwise undetected.
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| 6. |
- Berggren, Karin T., et al.
(författare)
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Allelic combinations of promoter and exon 2 in DQB1 in dogs and wolves
- 2008
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 67:1, s. 76-84
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Tidskriftsartikel (refereegranskat)abstract
- Polymorphism of PBRs of the major histocompatibility complex (MHC) genes is well recognized, but the polymorphism also extends to proximal promoter regions. Examining DQB1 variability in dogs and wolves, we identified 7 promoter variants and 13 exon 2 alleles among 89 dogs, including a previously unknown DQB1 exon 2 allele, and 8 promoter variants and 9 exon 2 alleles among 85 wolves. As expected from previous studies and from a close chromosomal location, strong linkage disequilibrium was demonstrated in both wolves and dogs by having significantly fewer promoter/exon 2 combinations than expected from simulations of randomized data sets. Interestingly, we noticed weaker haplotypic associations in dogs than in wolves. Dogs had twice as many promoter/exon 2 combinations as wolves and an almost 2-fold difference in the number of exon 2 alleles per promoter variant. This difference was not caused by an admixture of breeds in our group of dogs because the high ratio of observed to expected number of haplotypes persisted within a single dog breed, the German Shepherd. Ewens-Watterson tests indicated that both the promoter and exon 2 are under the balancing selection, and both regions appear to be more recently derived in the dog than in the wolf. Hence, although reasons for the differences are unknown, they may relate to altered selection pressure on patterns of expression. Deviations from normal MHC expression patterns have been associated with autoimmune diseases, which occur frequently in several dog breeds. Further knowledge about these deviations may help us understand the source of such diseases.
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| 7. |
- Berglund-Sonnhammer, Ann-Charlotte, et al.
(författare)
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Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
- 2006
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 63:2, s. 240-250
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Tidskriftsartikel (refereegranskat)abstract
- Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.
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| 8. |
- Berlin, Sofia, et al.
(författare)
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Adaptive Evolution of Gamete-Recognition Proteins in Birds
- 2008
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Ingår i: Journal of Molecular Evolution. - : Springer Science and Business Media LLC. - 0022-2844 .- 1432-1432. ; 67:5, s. 488-496
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Tidskriftsartikel (refereegranskat)abstract
- Gamete-recognition proteins have been shown to evolve by positive selection in diverse organism groups, such as marine invertebrates and mammals, although underlying evolutionary mechanisms driving this rapid divergence are poorly understood. However, several hypotheses have been put forward to explain the observed pattern, including different forms of sexual conflict and sperm competition. Because female gametes require more energy to produce than male gametes, female organisms suffer more when fertilisation goes wrong. One process that results in a failed mammalian fertilisation is polyspermy, when > 1 sperm fertilises the egg. However in birds, there is no such sexual conflict because multiple sperm typically bind and fuse with the egg. If sexual conflict driven by polyspermy avoidance is important for the evolution of gamete-recognition proteins in vertebrates, we expect to find positive selection in the genes to be less pronounced in birds. We therefore sequenced six genes (ZP1, ZP2, ZP4, ZPAX, CD9, and Acrosin) encoding gamete-recognition proteins in several bird species to test for positive selection. For comparison, we also analysed ortologous sequences in a set of mammalian species. We found no major differences in the occurrence of adaptive evolution and the strength of selection between bird and mammal orthologs. From this we conclude that polyspermy avoidance does not act as the main underlying evolutionary force shaping the rate of evolution in these genes. We discuss other possible processes that could explain positive selection of gamete-recognition proteins in birds and mammals, such as hybridisation avoidance, cryptic female choice, and postcopulatory sperm competition.
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| 9. |
- Dalevi, Daniel A., et al.
(författare)
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Measuring genome divergence in bacteria : A case study using Chlamydian data
- 2002
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Ingår i: Journal of Molecular Evolution. - New York, USA : Springer-Verlag New York. - 0022-2844 .- 1432-1432. ; 55, s. 24-36
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estimated to 59 6 events, including 13% inversions, 38% short inversions, and 49% transpositions. In contrast to previous findings, no examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications. A statistical model was used to compare nucleotide frequencies for a set of genes uniquely present in one species to a set of orthologous genes present in both species. The two data sets were not significantly different, which is indicative of a low frequency of horizontal gene transfer events. This is based on the assumption that a foreign gene of different nucleotide content will not have become completely ameliorated, as verified by simulations of the amelioration rate at twofold and fourfold degenerate codon sites. The frequencies of nucleotide substitutions at twofold and fourfold degenerate sites, deletions, inversions, and translocations were estimated to 1.42, 0.62, 0,18, 0.01, and 0.01 per site, respectively.
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| 10. |
- Fedosov, Alexander, 1983-, et al.
(författare)
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Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production
- 2023
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Ingår i: Journal of Molecular Evolution. - 0022-2844 .- 1432-1432. ; 91, s. 837-853
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Tidskriftsartikel (refereegranskat)abstract
- Venomous marine gastropods of the family Conidae are among the most diversifed predators in marine realm—in large due to their complex venoms. Besides being a valuable source of bioactive neuropeptides conotoxins, cone-snails venoms are an excellent model for molecular evolution studies, addressing origin of key innovations. However, these studies are handicapped by scarce current knowledge on the tissues involved in venom production, as it is generally assumed the sole prerogative of the venom gland (VG). The role of other secretory glands that are present in all Conus species (salivary gland, SG) or only in some species (accessory salivary gland, ASG) remains poorly understood. Here, for the frst time, we carry out a detailed analysis of the VG, SG, and ASG transcriptomes in the vermivorous Conus virgo. We detect multiple transcripts clusters in both the SG and ASG, whose annotations imply venom-related functions. Despite the subsets of transcripts highly-expressed in the VG, SG, and ASG being very distinct, SG expresses an L-, and ASG—Cerm08-, and MEFRR- superfamily conotoxins, all previously considered specifc for VG. We corroborate our results with the analysis of published SG and VG transcriptomes from unrelated fsh-hunting C. geographus, and C. striatus, possibly fsh-hunting C. rolani, and worm-hunting Conus quercinus. In spite of low expression levels of conotoxins, some other specifc clusters of putative venom-related peptides are present and may be highly expressed in the SG of these species. Further functional studies are necessary to determine the role that these peptides play in envenomation. In the meantime, our results show importance of routine multi-tissue sampling both for accurate interpretation of tissue-specifc venom composition in cone-snails, and for better understanding origin and evolution of venom peptides genes.
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