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Global phylogeography of the ridley sea turtles (Lepidochelys spp.) as inferred from mitochondrial DNA sequences.

The Kemp's ridley sea turtle (Lepidochelys kempi) is restricted to the warm temperate zone of the North Atlantic Ocean, whereas the olive ridley turtle (L. olivacea) is globally distributed in warm-temperate and tropical seas, including nesting colonies in the North Atlantic that nearly overlap the range of L. kempi. To explain this lopsided distribution, Pritchard (1969) proposed a scenario in which an ancestral taxon was divided into Atlantic and Pacific forms (L. kempi and L. olivacea, respectively) by the Central American land bridge. According to this model, the olive ridley subsequently occupied the Pacific and Indian Oceans and recently colonized the Atlantic Ocean via southern Africa. To assess this biogeographic model, a 470 bp sequence of the mtDNA control region was compared among 89 ridley turtles, including the sole L. kempi nesting population and 7 nesting locations across the range of L. olivacea. These data confirm a fundamental partition between L. olivacea and L. kempi (p = 0.052-0.069), shallow separations within L. olivacea (p = 0.002-0.031), and strong geographic partitioning of mtDNA lineages. The most divergent L. olivacea haplotype is observed in the Indo-West Pacific region, as are the central haplotypes in a parsimony network, implicating this region as the source of the most recent radiation of olive ridley lineage. The most common olive ridley haplotype in Atlantic samples is distinguished from an Indo-West Pacific haplotype by a single nucleotide substitution, and East Pacific samples are distinguished from the same haplotype by two nucleotide substitutions. These shallow separations are consistent with the recent invasion of the Atlantic postulated by Pritchard (1969), and indicate that the East Pacific nesting colonies were also recently colonized from the Indo-West Pacific region. Molecular clock estimates place these invasions within the last 300,000 years.

Animals↗

The amygdala theory of autism.

Brothers (Brothers L. Concepts in Neuroscience 1990;1:27-51) proposed a network of neural regions that comprise the "social brain", which includes the amygdala. Since the childhood psychiatric condition of autism involves deficits in "social intelligence", it is plausible that autism may be caused by an amygdala abnormality. In this paper we review the evidence for a social function of the amygdala. This includes reference to the Kluver-Bucy syndrome (which Hetzler and Griffin suggested may serve as an animal model of autism). We then review evidence for an amygdala deficit in people with autism, who are well known to have deficits in social behaviour. This includes a detailed summary of our recent functional magnetic resonance imaging (fMRI) study involving judging from the expressions of another person's eyes what that other person might be thinking or feeling. In this study, patients with autism or AS did not activate the amygdala when making mentalistic inferences from the eyes, whilst people without autism did show amygdala activity. The amygdala is therefore proposed to be one of several neural regions that are abnormal in autism. We conclude that the amygdala theory of autism contains promise and suggest some new lines of research.

Amygdala↗

Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.

Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20 specificities from completely sequenced bacterial, archaeal, and eukaryotic genomes reveals a complex evolutionary picture. Detailed examination of the domain architecture of aaRSs using sequence profile searches delineated a network of partially conserved domains that is even more elaborate than previously suspected. Several unexpected evolutionary connections were identified, including the apparent origin of the beta-subunit of bacterial GlyRS from the HD superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit of archaeal glutamyl-tRNA amidotransferases, and another previously undetected domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases and synthetases, and a family of GTPases. Comparison of domain architectures and multiple alignments resulted in the delineation of synapomorphies-shared derived characters, such as extra domains or inserts-for most of the aaRSs specificities. These synapomorphies partition sets of aaRSs with the same specificity into two or more distinct and apparently monophyletic groups. In conjunction with cluster analysis and a modification of the midpoint-rooting procedure, this partitioning was used to infer the likely root position in phylogenetic trees. The topologies of the resulting rooted trees for most of the aaRSs specificities are compatible with the evolutionary "standard model" whereby the earliest radiation event separated bacteria from the common ancestor of archaea and eukaryotes as opposed to the two other possible evolutionary scenarios for the three major divisions of life. For almost all aaRSs specificities, however, this simple scheme is confounded by displacement of some of the bacterial aaRSs by their eukaryotic or, less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS genes by bacterial ones, presumably of mitochondrial origin, was observed for three aaRSs. In contrast, there was no convincing evidence of displacement of archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic counterparts is most common among parasitic and symbiotic bacteria, particularly the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the respective eukaryotic genes and two by the archaeal counterpart. Unlike the primary radiation events between the three main divisions of life, that were readily traceable through the phylogenetic analysis of aaRSs, no consistent large-scale bacterial phylogeny could be established. In part, this may be due to additional gene displacement events among bacterial lineages. Argument is presented that, although lineage-specific gene loss might have contributed to the evolution of some of the aaRSs, this is not a viable alternative to horizontal gene transfer as the principal evolutionary phenomenon in this gene class.

Amino Acid Sequence↗

Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system.

Bacteriophage capsid assembly pathways provide excellent model systems to study large-scale conformational changes and other mechanisms that regulate the formation of macromolecular complexes. These capsids are formed from proheads: relatively fragile precursor particles which mature by undergoing extensive remodeling. Phage HK97 employs novel features in its strategy for building capsids, including assembly without a scaffolding protein, and the formation of a network of covalent cross-links between neighboring subunits in the mature virion. In addition, proteolytic cleavage of the capsid protein from 42 kDa to 31 kDa is essential for maturation. To investigate the structural bases for proteolysis and cross-linking, we have used cryo-electron micrographs to reconstruct the three-dimensional structures of purified particles from four discrete stages in the assembly pathway: Prohead I, Prohead II, Head I and Head II. Prohead I has icosahedral T = 7 packing of blister-shaped pentamers and hexamers. The pentamers are 5-fold symmetric, but the hexamers exhibit an unusual departure from 6-fold symmetry, as if two trimers had undergone a shear dislocation of about 25 A. Proteolytic conversion to Prohead II leaves the outer surface largely unchanged, but a major loss of density from the inner surface is observed, which we infer to represent the excision of the amino-terminal domains of the capsid protein. Upon expansion to the Head I state, the capsid becomes markedly larger, thinner walled, and more polyhedral: moreover, the capsomer shapes change radically; especially notable is the disappearance of the large hexon dislocation. No differences between Head I and the covalently cross-linked Head II could be observed at the current resolution of about 25 A, from which we infer that it is the conformational rearrangements effected by expansion that create the micro-environments needed for the autocatalytic formation of the isodipeptide bonds found in the mature virions ("pseudo-active sites").

Amino Acid Sequence↗

Automated decision making: the role of expert computer systems in the future of optometry.

BACKGROUND: Artificial intelligence (AI) refers to the ability of a machine, or system, or computer program to make intelligent decisions using the same methods that humans would use. By definition, and expert system (ES) is a computer program that uses knowledge and inference procedures to solve problems which would otherwise require the application of human expertise. METHODS: The role of expert systems in current and future applications in a number of fields were reviewed. RESULTS: Expert systems have and will be making an impact in many fields, including optometry in the future. CONCLUSIONS: Expert systems present an opportunity for the profession of optometry to become more efficient or accurate, provided that their development cost could be justified.

Artificial Intelligence↗

The striatum in a putative cerebral network activated by verbal awareness in normals and in ADHD children.

The aim of the present study was to evaluate the striatum's involvement in verbal awareness (semantic processing and supra-modal attention) in normals and children with attention deficit hyperactivity disorder (ADHD). Our previous finding of striatal hypoperfusion in ADHD at rest, supports our prediction that the striatum will also show reduced activation in response to tasks requiring verbal awareness. Regional cerebral blood flow (rCBF) was studied with the Xenon133 SPECT method in 12 boys with ADHD and six normal controls. The experimental controls included: (1) White Noise, (2) Passive Listening to a series of animal names, and (3) Detection of Targets ("dangerous animals") from the same series of animal names. The conditions were selected to isolate the semantic processing (Passive Listening - White Noise) and supra-modal attention components (Detection of Targets - Passive Listening of verbal awareness). ADHD children had decreased rCBF in the right striatum when compared to normals (mean difference from grand mean of each subject 8.06 ml/100 g/min vs 14.16 ml/100 g/min, p < 0.05). Factor analysis of the rCBF data revealed high factor I loadings for the frontal and striatal regions, which, in conjunction with the nature of the experimental conditions supported the inference that factor I mediated verbal awareness. Factor scores, which summarized the activity of all of the regions of interest (ROI's) on factor I, were differentially affected by the language component of the experimental tasks. Function scores were derived from factor I for the anterior cingulum and infero-frontal regions to evaluate their respective involvement in supra-modal attention and semantic processing. Function scores were also developed for the striatum, because of its central location and potential role in ADHD. The anterior cingulum was activated by supra-modal attention. The infero-frontal and the striatal regions were both activated by the language demands of the tasks. However, the striatum demonstrated reduced function scores (p < 0.05) in ADHD for all tasks. Our finding that the anterior gyrus cinguli were activated by supramodal attention and that the infero-frontal and striatal regions were activated by semantic processing supports the involvement of these ROI's in verbal awareness. Furthermore, the depressed functional contribution of the striatum to verbal awareness in ADHD children is consistent with and helps to explain their reduced cognitive control over behaviour and mental function.

Journal Article↗

Linear response algorithms for approximate inference in graphical models.

Belief propagation (BP) on cyclic graphs is an efficient algorithm for computing approximate marginal probability distributions over single nodes and neighboring nodes in the graph. However, it does not prescribe a way to compute joint distributions over pairs of distant nodes in the graph. In this article, we propose two new algorithms for approximating these pairwise probabilities, based on the linear response theorem. The first is a propagation algorithm that is shown to converge if BP converges to a stable fixed point. The second algorithm is based on matrix inversion. Applying these ideas to gaussian random fields, we derive a propagation algorithm for computing the inverse of a matrix.

Algorithms↗

Mechanical signalling and angiogenesis. The integration of cell-extracellular matrix couplings.

In vitro angiogenesis assays have shown that the couplings between fibrin gel and cell traction forces trigger biogel pre-patterning, consisting, in the formation of lacunae which evolve toward capillary-like structures (CLS) networks. Depending on the experimental conditions (number of seeded cells, gel elasticity,...), this pre-patterning can be enhanced or inhibited. A theoretical model based on a description of the cell-biogel biochemical and mechanical interactions is proposed as a basis for understanding how integrating these interactions can lead to the pre-patterning of the biogel. We showed that the critical parameter values corresponding to the bifurcation of the model solutions correspond to threshold values of the experimental variables. Furthermore, simulations of the mechanocellular model give rise to dynamic remodelling patterns of the biogel which are in good agreement both with the lacunae morphologies and with the time and space scales derived from the in vitro angiogenesis assays. Special attention has been paid in the simulations to cell proteolytic activity and to the amplitude of cell traction forces. We finally discussed how modelling guided experiments can be inferred from these results.

Biomechanical Phenomena↗

Updated ENIGMA recommendations for reporting germline variants in cancer susceptibility genes and their translation into twenty languages.

Genetic testing for cancer susceptibility underpins precision cancer prevention and care. Gaps in the healthcare providers' genetic literacy and an ambiguous lexicon for variant description may hinder proper delivery and clinical application of consistently trustworthy test results. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) international consortium supports controlled terminology and recommends a framework for reporting germline variants in cancer susceptibility genes, using breast cancer as an exemplar. Moving forward towards terminological coherence across disciplines and borders, the ENIGMA Clinical Working Group launched a multinational effort to release consortium-approved translations of the published recommendations. The herein reported Vocabulary Translation Project offered an opportunity to reappraise and align the reference text to the recent BRCA1 and BRCA2 specifications to the American College of Medical Genetics and Genomics/Association for Molecular Pathology rules by the ENIGMA Variant Curation Expert Panel and to highlight country-specific differences in breast cancer risk assessment and management. The updated recommendations and their 20 translations are now provided as easy to handle documents, covering 11 of the most widely spoken languages in the world. They will contribute to minimised erroneous inferences, more informed decision-making, improved health outcomes and equity in the use of genetic testing for cancer predisposition and in translational oncology.

Humans↗

Shallow groundwater quality on dairy farms with irrigated forage crops.

California's dairies are the largest confined animal industry in the state. A major portion of these dairies, which have an average herd size of nearly 1000 animal units, are located in low-relief valleys and basins. Large amounts of liquid manure are generated and stored in these dairies. In the semi-arid climate, liquid manure is frequently applied via flood or furrow irrigation to forage crops that are grown almost year-round. Little is known about the impact of manure management practices on water quality of the extensive alluvial aquifers underlying these basins. The objective of this work is to assess nitrate and salt leaching to shallow groundwater in a relatively vulnerable hydrogeologic region and to quantify the impact from individual sources on dairies. The complex array of potential point and nonpoint sources was divided into three major source areas representing farm management units: (1) manure water lagoons (ponds); (2) feedlot or exercise yard, dry manure, and feed storage areas (corrals); and (3) manure irrigated forage fields (fields). An extensive shallow groundwater-monitoring network (44 wells) was installed in five representative dairy operations in the northeastern San Joaquin Valley, CA. Water quality (electrical conductivity, nitrate-nitrogen, total Kjehldahl nitrogen) was observed over a 4-year period. Nitrate-N, reduced nitrogen and electrical conductivity (EC, salinity) were subject to large spatial and temporal variability. The range of observed nitrate-N and salinity levels was similar on all five dairies. Average shallow groundwater nitrate-N concentrations within the dairies were 64 mg/l compared to 24 mg/l in shallow wells immediately upgradient of these dairies. Average EC levels were 1.9 mS/cm within the dairies and 0.8 mS/cm immediately upgradient. Within the dairies, nitrate-N levels did not significantly vary across dairy management units. However, EC levels were significantly higher in corral and pond areas (2.3 mS/cm) than in field areas (1.6 mS/cm) indicating leaching from those management units. Pond leaching was further inferred from the presence of reduced nitrogen in three of four wells located immediately downgradient of pond berms. The estimated minimum average annual groundwater nitrate-N and salt loading from manure-treated forage fields were 280 and 4300 kg/ha, respectively. Leaching rates for ponds are estimated to be on the order of 0.8 m/year, at least locally. Since manure-treated fields represent by far the largest land area of the dairy, proper nutrient management will be a key to protecting groundwater quality in dairy regions overlying alluvial aquifers.

Animals↗

IsoSVM--distinguishing isoforms and paralogs on the protein level.

BACKGROUND: Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to the underlying genomic data. Analysis of this information (e.g. for EST clustering or phylogenetic reconstruction from proteome data) is hampered because it is not known if two protein sequences are isoforms (splice variants) or not (i.e. paralogs/orthologs). However, even without knowing the intron/exon structure, visual analysis of the pattern of similarity across the alignment of the two protein sequences is usually helpful since paralogs and orthologs feature substitutions with respect to each other, as opposed to isoforms, which do not. RESULTS: The IsoSVM tool introduces an automated approach to identifying isoforms on the protein level using a support vector machine (SVM) classifier. Based on three specific features used as input of the SVM classifier, it is possible to automatically identify isoforms with little effort and with an accuracy of more than 97%. We show that the SVM is superior to a radial basis function network and to a linear classifier. As an example application we use IsoSVM to estimate that a set of Xenopus laevis EST clusters consists of approximately 81% cases where sequences are each other's paralogs and 19% cases where sequences are each other's isoforms. The number of isoforms and paralogs in this allotetraploid species is of interest in the study of evolution. CONCLUSION: We developed an SVM classifier that can be used to distinguish isoforms from paralogs with high accuracy and without access to the genomic data. It can be used to analyze, for example, EST data and database search results. Our software is freely available on the Web, under the name IsoSVM.

Algorithms↗

Neuronal activity of somatosensory cortex in a cross-modal (visuo-haptic) memory task.

Studies have shown that in the monkey's associative cerebral cortex, cells undergo sustained activation of discharge while the animal retains information for a subsequent action. Recent work has revealed the presence of such "memory cells" in the anterior parietal cortex (Brodmann's areas 3a, 3b, 1, and 2)--the early stage of the cortical somatosensory system. Here we inferred that, in a cross-modal visuo-haptic short-term memory task, somatosensory cells would react to visual stimuli associated with tactile features. Single-unit discharge was recorded from the anterior parietal cortex--including areas of hand representation--of monkeys performing a visuo-haptic delayed matching-to-sample task. Units changed firing frequency during the presentation of a visual cue that the animal had to remember for making a correct tactile choice between two objects at the end of a delay (retention period). Some units showed sustained activation during the delay. In some of them that activation differed depending on the cue. These findings suggest that units in somatosensory cortex react to visual stimuli behaviorally associated with tactile information. Further, the results suggest that some of these neurons are involved in short-term active memory and may, therefore, be part of cross-modal memory networks.

Animals↗

mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America?

On the basis of comprehensive RFLP analysis, it has been inferred that approximately 97% of Native American mtDNAs belong to one of four major founding mtDNA lineages, designated haplogroups "A"-"D." It has been proposed that a fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage in Native Americans. Unlike haplogroups A-D, haplogroup X is also found at low frequencies in modern European populations. To investigate the origins, diversity, and continental relationships of this haplogroup, we performed mtDNA high-resolution RFLP and complete control region (CR) sequence analysis on 22 putative Native American haplogroup X and 14 putative European haplogroup X mtDNAs. The results identified a consensus haplogroup X motif that characterizes our European and Native American samples. Among Native Americans, haplogroup X appears to be essentially restricted to northern Amerindian groups, including the Ojibwa, the Nuu-Chah-Nulth, the Sioux, and the Yakima, although we also observed this haplogroup in the Na-Dene-speaking Navajo. Median network analysis indicated that European and Native American haplogroup X mtDNAs, although distinct, nevertheless are distantly related to each other. Time estimates for the arrival of X in North America are 12,000-36,000 years ago, depending on the number of assumed founders, thus supporting the conclusion that the peoples harboring haplogroup X were among the original founders of Native American populations. To date, haplogroup X has not been unambiguously identified in Asia, raising the possibility that some Native American founders were of Caucasian ancestry.

Asia, Western↗

Mapping of microbial pathways through constrained mapping of orthologous genes.

We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a target genome that is most consistent with (a) predicted orthologous gene relationship, (b) predicted operon structures, and (c) predicted co-regulation relationship of operons. Mathematically, we have formulated this problem as a constrained minimum spanning tree problem (called a Steiner network problem), and demonstrated that this formulation has the desired property through applications. We have solved this mapping problem using a combinatorial optimization algorithm, with guaranteed global optimality. We have implemented this algorithm as a computer program, called PMAP. Our test results on pathway mapping are highly encouraging -- we have mapped a number of pathways of H. influenzae, B. subtilis, H. pylori, and M. tuberculosis to E. coli using P-MAP, whose homologous pathways in E coli. are known and hence the mapping accuracy could be checked. We have then mapped known E. coli pathways in the EcoCyc database to the newly sequenced organism Synechococcus sp WH8102, and predicted 158 Synechococcus pathways. Detailed analyses on the predicted pathways indicate that P-MAP's mapping results are consistent with our general knowledge about (local) pathways. We believe that P-MAP will be a useful tool for microbial genome annotation projects and inference of individual microbial pathways.

Algorithms↗

5-Lipoxygenase inhibitors reduce PC-3 cell proliferation and initiate nonnecrotic cell death.

BACKGROUND: Products of the arachidonic acid-metabolizing enzyme, 5-lipoxygenase, stimulate the growth of several cell types. Selective inhibitors of the enzyme, including SC41661A and MK886, reduce PC-3 prostate cell proliferation. With continued culture, cells die, but the mode of death, necrotic or nonnecrotic, has not been established. METHODS: Flow cytometry, laddering after agarose electrophoresis of DNA from inhibitor-treated cells, and light and electron microscopy were employed to examine the type of death in PC-3 prostate cells cultured with either 5-lipoxygenase inhibitor. RESULTS: The inhibitors induced nonnecrotic, programmed cell death. SC41661A-treated cells exhibited "foamy," vacuolated cytoplasm and mitochondria with disrupted cristae and limiting membranes, while some cells contained numerous polysomes and extended hypertrophic Golgi and secretory cisternal networks. A proportion of the treated cells detached and the nuclei of these cells were characteristic of type 1 "apoptotic" programmed cell death. MK886, a 5-lipoxygenase-inhibitor with a different mechanism of action, induced nonnecrotic changes largely confined to the cytoplasm, most consistent with type 2 "autophagic" programmed cell death. In preliminary studies of mechanism, we demonstrated that PC-3 cells express mRNA for 5-lipoxygenase and for 5-lipoxygenase-activating protein. The less active inhibitor, SC45662 neither reduced proliferation nor induced DNA laddering. The antioxidant, N-acetyl-l-cysteine but not butylated hydroxy toluene or alpha tocopherol, partially reduced the inhibition of proliferation from SC41661A. CONCLUSIONS: SC41661A and MK886 inhibit PC-3 cell proliferation and induce a form of type 1 or type 2 programmed cell death, respectively. PC-3 cells contain messenger RNA for 5-lipoxygenase and 5-lipoxygenase-activating proteins. Drug-induced changes included altered redox potential, inferred from the increased survival due to the antioxidant and glutathione precursor, N-acetyl-l-cysteine. PC-3 cells are an appropriate model for studying the mechanism responsible for 5-lipoxygenase inhibitor-induced cellular suicide.

Amides↗

Necessity of aromatic carboxylate anions to be planar to induce growth of cationic micelles.

It is well-known that some aromatic anions have the ability to induce viscoelastic transformation in aqueous solutions of cationic surfactants even at added salt concentrations as low as 10-20 mM. This behavior is associated with the formation of an entangled network of elongated micelles. However, the effect of aromatic ring substituents on the anion's ability to promote rapid micelle growth is not well-understood. We have performed ab initio calculations of the carbonyl group rotation barriers in a series of substituted benzoate and naphthoate anions at the MP2/STO-3G level of theory. It was found that aromatic carboxylates, known to be particularly effective in causing sphere-rod transition in cationic micelles, preferably adopt conformations with the COO(-) group in the same plane as the ring(s). This structural preference can be attributed to either intramolecular hydrogen bonding (o-hydroxyl derivatives) or pi-conjugation effects (m- and p-halogenated derivatives). In the former case the barrier to rotation is 40-50 kcal/mol, whereas in the latter case the threshold value is around 3.0 kcal/mol. Propensity for the planar conformation correlates with a greater depth of counterion penetration into the micelle surface, as inferred from NMR experiments, compared to the anions with less hindered carbonyl rotation. This points to favorable hydrophobic interactions between the surfactant methylene groups and the aromatic ring(s) of the anion as a possible explanation for the rapid growth of cationic micelles observed upon addition of certain aromatic carboxylates.

Journal Article↗

From annotated genomes to metabolic flux models and kinetic parameter fitting.

Significant advances in system-level modeling of cellular behavior can be achieved based on constraints derived from genomic information and on optimality hypotheses. For steady-state models of metabolic networks, mass conservation and reaction stoichiometry impose linear constraints on metabolic fluxes. Different objectives, such as maximization of growth rate or minimization of flux distance from a reference state, can be tested in different organisms and conditions. In particular, we have suggested that the metabolic properties of mutant bacterial strains are best described by an algorithm that performs a minimization of metabolic adjustment (MOMA) upon gene deletion. The increasing availability of many annotated genomes paves the way for a systematic application of these flux balance methods to a large variety of organisms. However, such a high throughput goal crucially depends on our capacity to build metabolic flux models in a fully automated fashion. Here we describe a pipeline for generating models from annotated genomes and discuss the current obstacles to full automation. In addition, we propose a framework for the integration of flux modeling results and high throughput proteomic data, which can potentially help in the inference of whole-cell kinetic parameters.

Algorithms↗

[Problems of molecular systematics of the genus Salvelinus based on nucleotide sequence variability of the major noncoding region of mitochondrial DNA].

Variability of the major noncoding mitochondrial DNA region of char (Salvelinus alpinus complex) was analyzed by the median network method on the basis of the literature data on nucleotide sequences of this region. A significant portion (21%) of the polymorphic sites of char mtDNA was shown to be evolutionarily unstable, which results in mutation homoplasia at these sites. Using median-joining analysis the chars were divided into three phylogeographical groups: Arctic, Beringian, and chars occurring in the vast region from Lake Baikal and Taimyr Peninsula to the Atlantic Ocean. The latter group includes three subgroups (Siberian, Atlantic, and Acadian), which diverged from a common ancestor. In the Arctic group, the branch of Taranetz char S. taranetzi is clearly separated. It diverged from the common ancestor earlier than S. boganidae and S. elgyticus occurring on the Chukotka Peninsula species and S. a. erythrinus occurring in Alaska. The Beringian group, which includes dolly varden char from various regions of Asia and America, is an intermediate between the two char groups. The main problems of char systematics inferred from the major noncoding mtDNA region variability arise from the high level of mutation homoplasia.

3' Untranslated Regions↗