Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences

Description of Roseibium sediminicola sp. nov. Isolated from Sediment of a Tidal Flat on the Yellow Sea Coast

A Gram-stain-negative, aerobic, rod-shaped, motile, flagellated bacterial strain, designated as CAU 1639T, was isolated from the tidal flat sediment on the Yellow Sea in the Republic of Korea. Growth of the isolate was observed at 20-37 °C, at pH 5.0-10.5 and with 0-7% (w/v) NaCl. The genomic DNA G + C content was 60.8%. Phylogenetic analysis, grounded on 16S rRNA gene sequencing, revealed that strain CAU 1639T was closely related to species within the genus Roseibium. It shared the highest similarity with Roseibium album CECT 5095T, followed by Roseibium aggregatum IAM 12614T and Roseibium salinum Cs25T, with 16S rRNA gene sequence similarity ranging from 98.0-98.4%. It was observed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values ranged between 72.5-79.5 and 20.0-22.9%, respectively. The polyphasic taxonomic analysis reveals that strain CAU 1639T represents a novel species in the genus Roseibium with the proposed name Roseibium sediminicola sp. nov. The type strain is CAU 1639T (= KCTC 82430T = MCCC 1K06081T).

Halomonas jincaotanensis sp. nov., isolated from the Pamir Plateau degrading polycyclic aromatic hydrocarbon

A Gram-strain-negative, rod-shaped, aerobic bacterium, designated strain TRM 85114^T, was isolated from the Jincaotan wetland in the Pamir Plateau of China. This strain grew optimally at 30 °C and pH 6.0 in the presence of 3% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TRM 85114^T was affiliated with the genus Halomonas, and shared high sequence similarity with Halomonas korlensis XK1^T (97.3%) and Halomonas tibetensis pyc13^T (96.4%). Strain TRM 85114^T contained C_16:0 and C_19:0 cyclo ω8c as primary cellular fatty acids, Q-9 as predominate respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids of unknown structure containing glucosamine, unidentified aminophospholipids, unidentified lipids and three unidentified phospholipids as the major polar lipids. The complete genome of TRM 85114^T comprised 3,902 putative genes with a total of 4,126,476 bp and a G + C content of 61.6%. The average nucleotide identity and digital DNA-DNA hybridization values between strain TRM 85114^T and related type Halomonas strains of H. korlensis XK1^T, H. tibetensis pyc13^T, Chromohalobacter salexigens DSM 6768^T, and Halomonas urumqiensis BZ-SZ-XJ27^T were 75.4-88.9% and 22.9-39.2%, respectively. Based on phenotypic, chemotaxonomic, and molecular features, strain TRM 85114^T represents a novel species of the genus Halomonas, for which the name is proposed as Halomonas jincaotanensis sp. nov.. The type strain is TRM 85114^T (CCTCC AB 2021006^T = LMG 32311^T). The amount of 1-naphthylamine degradation by strain TRM 85114^T reached up to 32.0 mg/L in 14 days.

Devosia marina sp. nov., isolated from deep seawater of the South China Sea, and reclassification of Devosia subaequoris as a later heterotypic synonym of Devosia soli

A Gram-stain-negative, aerobic, rod-shaped and motile bacterial strain, designated L53-10-65^T, was isolated from deep seawater of the South China Sea. Strain L53-10-65^T was found to grow at 4-41 °C (optimum, 28 °C), at pH 5.0-9.0 (pH 7.0-8.0) and in 0-7 % (w/v) NaCl (2 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain L53-10-65^T fell within the genus Devosia, with the highest similarity to Devosia indica IO390501^T (98.4 %), followed by 'Devosia lucknowensis' L15^T (97.7 %) and Devosia riboflavina IFO 13584^T (96.8 %). The digital DNA-DNA hybridization (dDDH) values between strain L53-10-65^T and the three relatives above were 43.7, 21.5 and 20.9 %, respectively; the average nucleotide identity (ANI) values were 91.3, 78.4 and 76.8 %, respectively. These values were below the 70 % dDDH and 95-96 % ANI thresholds for bacterial species delineation. The major cellular fatty acids of strain L53-10-65^T were summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c), C_18 : 1 ω7c 11-methyl and C_16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The respiratory quinone was identified as Q-10. The DNA G+C content of strain L53-10-65^T was 61.3 mol%. Based on the results of phylogenetic analysis and distinctive phenotypic characteristics, strain L53-10-65^T is concluded to represent a novel species of the genus Devosia, for which the name Devosia marina sp. nov. is proposed. The type strain of the species is L53-10-65^T (=MCCC 1A05139^T=KCTC 72888^T). Moreover, we propose that Devosia subaequoris is a later heterotypic synonym of Devosia soli based on the present results.

Big data analysis of human mitochondrial DNA substitution models: a regression approach

BACKGROUND

We study Phylotree, a comprehensive representation of the phylogeny of global human mitochondrial DNA (mtDNA) variations, to better understand the mtDNA substitution mechanism and its most influential factors. We consider a substitution model, where a set of genetic features may predict the rate at which mtDNA substitutions occur. To find an appropriate model, an exhaustive analysis on the effect of multiple factors on the substitution rate is performed through Negative Binomial and Poisson regressions. We examine three different inclusion options for each categorical factor: omission, inclusion as an explanatory variable, and by-value partitioning. The examined factors include genes, codon position, a CpG indicator, directionality, nucleotide, amino acid, codon, and context (neighboring nucleotides), in addition to other site based factors. Partitioning a model by a factor's value results in several sub-models (one for each value), where the likelihoods of the sub-models can be combined to form a score for the entire model. Eventually, the leading models are considered as viable candidates for explaining mtDNA substitution rates.

RESULTS

Initially, we introduce a novel clustering technique on genes, based on three similarity tests between pairs of genes, supporting previous results regarding gene functionalities in the mtDNA. These clusters are then used as a factor in our models. We present leading models for the protein coding genes, rRNA and tRNA genes and the control region, showing it is disadvantageous to separate the models of transitions/transversions, or synonymous/non-synonymous substitutions. We identify a context effect that cannot be attributed solely to protein level constraints or CpG pairs. For protein-coding genes, we show that the substitution model should be partitioned into sub-models according to the codon position and input codon; additionally we confirm that gene identity and cluster have no significant effect once the above factors are accounted for.

CONCLUSIONS

We leverage the large, high-confidence Phylotree mtDNA phylogeny to develop a new statistical approach. We model the substitution rates using regressions, allowing consideration of many factors simultaneously. This admits the use of model selection tools helping to identify the set of factors best explaining the mutational dynamics when considered in tandem.

Identification and analysis of a prepro-chicken gonadotropin releasing hormone II (preprocGnRH-II) precursor in the Asian seabass, Lates calcarifer, based on an EST-based assessment of its brain transcriptome

Using a novel library of 5637 expressed sequence tags (ESTs) from the brain tissue of the Asian seabass (Lates calcarifer), we first characterized the brain transcriptome for this economically important species. The ESTs generated from the brain of L. calcarifer yielded 2410 unique transcripts (UTs) which comprise of 982 consensi and 1428 singletons. Based on database similarity, 1005 UTs (41.7%) can be assigned putative functions and were grouped into 12 functional categories related to the brain function. Amongst others, we have identified genes that are putatively involved in energy metabolism, ion pumps and channels, synapse related genes, neurotransmitter and its receptors, stress induced genes and hormone related genes. Subsequently we selected a putative preprocGnRH-II precursor for further characterization. The complete cDNA sequence of the gene obtained was found to code for an 85-amino acid polypeptide that significantly matched preprocGnRH-II precursor sequences from other vertebrates, and possesses structural characteristics that are similar to that of other species, consisting of a signal peptide (23 residues), a GnRH decapeptide (10 residues), an amidation/proteolytic-processing signal (glycine-lysine-argine) and a GnRH associated peptide (GAP) (49 residues). Phylogenetic analysis showed that this putative L. calcarifer preprocGnRH-II sequence is a member of the subcohort Euteleostei and divergent from the sequences of the subcohort Otocephalan. These findings provide compelling evidence that the putative L. calcarifer preprocGnRH-II precursor obtained in this study is orthologous to that of other vertebrates. The functional prediction of this preprocGnRH-II precursor sequence through in silico analyses emphasizes the effectiveness of the EST approach in gene identification in L. calcarifer.

Identification and characterization of sea squirt telomerase reverse transcriptase

Telomerase is essential for maintaining telomere length and chromosome stability in most eukaryotic organisms. The telomerase ribonucleoprotein complex consists of two essential components, the catalytic telomerase reverse transcriptase protein (TERT) and the intrinsic telomerase RNA. The sea squirts, as urochordates, occupy a key position in the phylogenetic tree of the chordates: they diverged from the other chordates just before the lineage of vertebrates, and thus provide special insight into the origin and evolution of vertebrate genes. Here, we report the cloning and characterization of TERT genes from two sea squirts, Ciona intestinalis and Ciona savignyi. The C. intestinalis TERT (CinTERT) gene encodes 907 amino acids and consists of 17 exons, which are similar to vertebrate TERT genes. The C. savignyi TERT (CsaTERT) gene encodes 843 amino acids, but surprisingly does not contain any introns. Both Ciona TERTs contain all of the reverse transcriptase (RT) motifs (1, 2, A, B, C, D, and E) that are typically present in telomerase and viral RTs. Interestingly, the alignment of Ciona and vertebrate TERT sequences reveals a previously unknown motif, named motif 3, located between motifs 2 and A. The Ciona TERT gene is expressed in all tissues analyzed except the brain and heart. This is the first report of the TERT gene in invertebrate chordates.

Genetic markers on HIV-1 gp120 C2-V3 region associated with the expression or absence of cognitive motor complex in HIV/AIDS

In the CNS, HIV-1 causes cognitive motor complex (CMC) in about 30-40% of patients. To explain CMC physiopathology: disequilibrium of cytokine networks, calcium influx, free radicals and toxic effects by HIV-1 have been evoked. Neurotropic mutants have not been unambiguously proven nor 'variants' of HIV-1 with biological properties that could cause CMC. By computerized analysis of gp120 C2-V3 subtype B sequences from retroviral databases, and applying stringent criteria, we found: (i) mutations specific for CMC; (ii) mutations associated with the absence of CMC (N-CMC); (iii) mutations with specificity for the geographical region of origin, and finally (iv) shared mutations representing 'hot spots.' We suggest that the capability to cause or not to cause CMC may be present in the virus prior to infection. In the future, these markers could be used to guide treatments with novel neuroprotective regimes.

Secondary structure of vertebrate telomerase RNA

Telomerase is a ribonucleoprotein enzyme that maintains telomere length by adding telomeric sequence repeats onto chromosome ends. The essential RNA component of telomerase provides the template for telomeric repeat synthesis. To determine the secondary structure of vertebrate telomerase RNA, 32 new telomerase RNA genes were cloned and sequenced from a variety of vertebrate species including 18 mammals, 2 birds, 1 reptile, 7 amphibians, and 4 fishes. Using phylogenetic comparative analysis, we propose a secondary structure that contains four structural domains conserved in all vertebrates. Ten helical regions of the RNA are universally conserved while other regions vary significantly in length and sequence between different classes of vertebrates. The proposed vertebrate telomerase RNA structure displays a strikingly similar topology to the previously determined ciliate telomerase RNA structure, implying an evolutionary conservation of the global architecture of telomerase RNA.

alpha-Crystallin sequences support a galliform/anseriform clade

An unresolved issue in higher avian systematics is the position of the fowl-like and the duck-like birds, Galliformes and Anseriformes, respectively. Most studies place these orders at the base of the neognath radiation. While DNA hybridization data support a sister-group relationship of Galliformes and Anseriformes, macromolecular sequence analyses have not yet been able to provide a clear-cut answer. In this study, we present nucleotide sequences coding for the eye lens proteins alpha A- and alpha B-crystallin of a palaeognath, a galliform, an anseriform, and two other neognathous birds. Phylogenetic analyses of this data set clearly support a galliform/anseriform clade, to the exclusion of other neognaths.

Mammalian homologues of yeast vacuolar protein sorting (vps) genes implicated in Golgi-to-lysosome trafficking

Sec1p, Vps33p, Vps45p and Sly1p constitute a family of proteins implicated in vesicle trafficking at distinct stages of the yeast secretory pathway. Several mammalian homologues of Sec1p have been described, including n-sec1 which has been implicated in the regulation of synaptic vesicle docking at the nerve terminal. We have characterized cDNA clones encoding three additional mammalian homologues belonging to this family: r-vps33a and r-vps33b from rat, which are 30 and 26% identical to yeast Vps33p, respectively, and h-vps45 from human which is 38% identical to yeast Vps45p at the amino acid (aa) level. Phylogenetic analysis of 16 Sec1p-related proteins from several species is consistent with the hypothesis that the evolution of this gene family parallels the specialization of vesicle trafficking to distinct intracellular compartments. By Northern analysis, each of these genes is expressed in all tissues examined (brain, spleen, lung, liver, skeletal muscle, kidney, testis). While n-sec1 binds syntaxin 1a, 2, and 3, r-vps33a, r-vps33b and h-vps45 do not bind any of the known syntaxins. We propose that the three proteins bind as yet unidentified syntaxin homologues involved in vesicle trafficking between the Golgi apparatus, prelysosomal compartment(s), and the lysosome.

Probabilistic reconstruction of ancestral protein sequences

Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales linearly with the number of homologous proteins used to reconstruct the ancestral sequence.

Reconstruction of ancestral sequences by the inferential method, a tool for protein engineering studies

This paper describes the inferential method, an approach for reconstructing protein and nucleotide sequences of ancestral species, starting from known, homologous, contemporary sequences. The method requires knowledge of the topology of the phylogenetic tree, whose nodes are the species to whom the reconstructed sequences belong. The method has been tested by computer simulation of speciation and nucleotide substitutions, starting from a single ancestral sequence, and by subsequent reconstruction of nodal sequences. Results have shown that reconstructions obtained by the inferential method are affected by limited error frequencies, which (1) are proportional to the squares of nucleotide substitution rates and of internodal distances, and (2) are little influenced by non-uniformity of transformation rates of nucleotides. Furthermore, good agreement of the results has been obtained by comparing protein-sequence reconstructions carried out with the inferential method with those obtained using the maximum parsimony method in two different cases: e.g., a reconstruction of simulated sequences and a reconstruction of mammalian ribonuclease sequences.

Human AT1 receptor is a single copy gene: characterization in a stable cell line

To address conflicting reports concerning the number of angiotensin II (AII) receptor type 1 (AT1) coding loci in vertebrates, Southern blot analysis was used to determine the genomic representation of AT1 receptor genes in animals comprising a divergent evolutionary spectrum. The data demonstrate that the AT1 receptor gene is present as a single genomic copy in a broad spectrum of animals including human, monkey, dog, cow, rabbit, and chicken. In contrast, members of the rodent taxonomic order contain two genes in their genomes. These two genes may have arisen in rodents as a consequence of a gene duplication event that occurred during evolution following the branching of rodents from the mammalian phylogenetic tree. In order to investigate the properties of the human AT1 receptor in a pure cell system, the recombinant human AT1 receptor was stably expressed in mouse L cells. An isolated cell line, designated LhAT1-D6, was found to express abundant levels of recombinant receptor [430 +/- 15 fmol/mg] exhibiting high affinity [KD = 0.15 +/- 0.02 nM] for [125I][SAR1, Ile8] angiotensin II (SIA). The pharmacological profile of ligands competing for [125I] SIA binding to the expressed receptor was in accordance with that of the natural receptor. Radioligand binding of the expressed receptor was decreased in the presence of the non-hydrolyzable analog of GTP, guanosine 5'-(gamma-thio) triphosphate [GTP gamma S]. Angiotensin II evoked a rapid efflux of 45Ca2+ from LhAT1-D6 cells that was blocked by AT1 receptor specific antagonists. In addition, AII inhibited forskolin-stimulated cAMP accumulation in these cells which was blocked by the AT-1 antagonist. Thus, the LhAT1-D6 cell line provides a powerful tool to explore the human AT1 receptor regulation.

Confidence limits on the branching order of phylogenetic trees

We describe a confidence test for branching order that can aid protein phylogeny reconstruction as well as the evaluation of the optimal tree. It is proposed that the process resulting in the observed amino acid residue differences, which is the basis for the identification of the order and relative times of divergence events, is appropriately described by a modification of the negative binomial distribution. The relative total numbers of mutations (accepted and nonaccepted), which result in a given number of amino acid differences, may be obtained as the expectation of this distribution. The associated variances enable significant differences in tree branching order to be established. If the total rates of mutation of the genes encoding the compared proteins are equal, the expected total mutations and their associated variances map identically to their relative times of divergence. In addition, significantly different rates of change (due to differences in total mutation rate and/or acceptance rate) may be identified without the requirement of outlying reference group. The method is equally applicable to phylogenies derived from DNA or RNA sequence information.

Characterization of the genes encoding carbonic anhydrase I of chimpanzee and gorilla: comparative analysis of 5' flanking erythroid-specific promoter sequences

The genes encoding carbonic anhydrase I (CA I) have been characterized for chimpanzee (Pan troglodytes) and gorilla (Gorilla gorilla). In addition, 44 nucleotides (nt) at the 5' end of the noncoding first exon (exon 1a), which is unique to the erythroid CA I mRNA, together with 188 nt of the adjacent 5' flanking regions, were sequenced for the corresponding positions of the CA I of orangutan, pigtail macaque, and squirrel monkey. When these 5' flanking regions are compared, along with those published for human and mouse CA I, they were found to contain several conserved sequences that may bind factors involved in the erythroid-specific expression of CA I. Comparisons of the human, chimpanzee, and gorilla coding and noncoding CA I sequences do not significantly deviate from a pattern of trichotomy for the evolutionary origins of these three hominoid species.

Multiple L1 progenitors in prosimian primates: phylogenetic evidence from ORF1 sequences

One of the uncertainties regarding the evolution of L1 elements is whether there are numerous progenitor genes. We present phylogenetic evidence from ORF1 sequences of slow loris (Nycticebus coucang) and galago (Galago crassicaudatus) that there were at least two distinct progenitors, active at the same time, in the ancestor of this family of prosimian primates. A maximum parsimony analysis that included representative L1s from human, rabbit, and rodents, along with the prosimian sequences, revealed that one of the galago L1s (Gc11) grouped very strongly with the slow loris sequences. The remaining galago elements formed their own unique and strongly supported clade. An analysis of replacement and silent site changes for each link of the most parsimonious tree indicated that during the descent of the Gc11 sequence approximately two times more synonymous than nonsynonymous substitutions had occurred, implying that the Gc11 founder was functional for some time after the split of galago and slow loris. Strong purifying selection was also evident on the galago branch of the tree. These data indicate that there were two distinct and contemporaneous L1 progenitors in the lorisoid ancestor, evolving under purifying selection, that were retained as functional L1s in the galago lineage (and presumably also in the slow loris). The prosimian ORF1 sequences could be further subdivided into subfamilies. ORF1 sequences from both the galago and slow loris have a premature termination codon near the 3' end, not shared by the other mammalian sequences, that shortens the open reading frame by 288 bp. An analysis of synonymous and nonsynonymous substitutions for the 5' and 3' portions, that included intra- and inter-subfamily comparisons, as well as comparisons among the other mammalian sequences, suggested that this premature stop codon is a prosimian acquisition that has rendered the 3' portion of ORF1 in these primates noncoding.

Structure and evolutionary implications of a "cysteine-rich" Campoletis sonorensis polydnavirus gene family

For successful parasitization, the female Campoletis sonorensis endoparasitic wasp injects a polydnavirus into its host, Heliothis virescens, during oviposition. Viral gene expression induces immunosuppression and alters development of the host. We report here that three abundantly expressed genes, VHv1.1, WHv1.0, and WHv1.6, describes a polydnavirus "cysteine-rich" gene family which may be important in inducing these host manifestations. These genes have a similar primary gene structure and their proteins contain cysteine motifs characteristic of snail ion-channel ligands, the omega-conotoxins. Like the omega-conotoxins, the intercysteine amino acid residues are hypervariable with only three identical amino acids in all motifs. The conservation of this domain in the three viral genes may reflect an important functional role for these viral proteins in the parasitization of H. virescens. The three genes also contain introns similar in sequence at comparable positions in their 5' untranslated leaders and coding sequences. VHv1.1 contains two cysteine motifs, and each motif is interrupted by an intron at the same position as in the cysteine motifs of WHv1.0 and WHv1.6. Intron 2 sequences of WHv1.0 and WHv1.6 are 92% identical, while the immediately flanking exon sequences encoding the cysteine motifs are only 76% identical. This provides an example of nuclear pre-mRNA introns which are more conserved than flanking exons among members of a gene family.

Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster

Additional DNA sequence information from a range of primates, including 13.7 kb from pygmy chimpanzee (Pan paniscus), was added to data sets of beta-globin gene cluster sequence alignments that span the gamma 1, gamma 2, and psi eta loci and their flanking and intergenic regions. This enlarged body of data was used to address the issue of whether the ancestral separations of gorilla, chimpanzee, and human lineages resulted from only one trichotomous branching or from two dichotomous branching events. The degree of divergence, corrected for superimposed substitutions, seen in the beta-globin gene cluster between human alleles is about a third to a half that observed between two species of chimpanzee and about a fourth that between human and chimpanzee. The divergence either between chimpanzee and gorilla or between human and gorilla is slightly greater than that between human and chimpanzee, suggesting that the ancestral separations resulted from two closely spaced dichotomous branchings. Maximum parsimony analysis further strengthened the evidence that humans and chimpanzees share the longest common ancestry. Support for this human-chimpanzee clade is statistically significant at P = 0.002 over a human-gorilla clade or a chimpanzee-gorilla clade. An analysis of expected and observed homoplasy revealed that the number of sequence changes uniquely shared by human and chimpanzee lineages is too large to be attributed to homoplasy. Molecular clock calculations that accommodated lineage variations in rates of molecular evolution yielded hominoid branching times that ranged from 17-19 million years ago (MYA) for the separation of gibbon from the other hominoids to 5-7 MYA for the separation of chimpanzees from humans. Based on the relatively late dates and mounting corroborative evidence from unlinked nuclear genes and mitochondrial DNA for the close sister grouping of humans and chimpanzees, a cladistic classification would place all apes and humans in the same family. Within this family, gibbons would be placed in one subfamily and all other extant hominoids in another subfamily. The later subfamily would be divided into a tribe for orangutans and another tribe for gorillas, chimpanzees, and humans. Finally, gorillas would be placed in one subtribe with chimpanzees and humans in another, although this last division is not as strongly supported as the other divisions.

Mammalian phylogeny: shaking the tree

Recent palaeontological discoveries and the correspondence between molecular and morphological results provide fresh insight on the deep structure of mammalian phylogeny. This new wave of research, however, has yet to resolve some important issues.

Evolution of the cytochrome b gene of mammals

With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.