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PubMed1999

Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages.

In prokaryotes, lateral gene transfer across chromosomal lineages may be mediated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary forces that may restrict gene exchange remain largely unexplored in native settings. In this study, tests of phylogenetic congruence are employed to explore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of legumes. Rhizobial strains isolated from nodules of several host plant genera were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a portion of the 16S rRNA gene. Molecular phylogenetic analysis shows that each locus generally subdivides strains into the same major groups, which correspond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broad phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricultural populations showing broad transfer of sym loci across divergent chromosomal lineages. A general correspondence of the three rhizobial genera with major legume groups suggests that host plant associations may be important in the differentiation of rhizobial nod and chromosomal loci and may restrict lateral transfer among strains. The second major result is a significant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics. This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproductively isolated" and diverge independently. Differences across rhizobial genera in the specificity of host associations imply that the evolutionary dynamics of the symbiosis vary considerably across lineages in native settings.

Base Sequence↗
PubMed1994

Mitochondrial phylogeny of the Lamprologini, the major substrate spawning lineage of cichild fishes from Lake Tanganyika in eastern Africa.

Lake Tanganyika harbors the oldest, morphologically and behaviorally most diverse flock of cichlid species. While the cichlids in Lakes Malawi and Victoria breed their eggs exclusively by buccal incubation (termed "mouthbrooding"), the Tanganyikan cichlid fauna comprise mouthbrooding and substrate-spawning lineages (fish spawn on rocks, and never orally incubate eggs or wrigglers). The substrate-spawning tribe Lamprologini appears to occupy a key position that might allow one to elucidate the origin of the Tanganyika flock, because five riverine (therefore nonendemic) species from the Zaire River system have been assigned to this tribe, in addition to the lake's endemic species, which make up almost 50% of all 171 species known from this lake (Poll 1986). From 16 species (18 individuals) of the tribe Lamprologini, a 402-bp segment of the mitochondrial cytochrome b gene was sequenced, and, from 25 lamprologine species (35 individuals), sequences from the mitochondrial control region were obtained. To place the Lamprologini into a larger phylogenetic framework, orthologous sequences were obtained from eight nonlamprologine Tanganyikan cichlid species (13 individuals). The Lamprologini are monophyletic, and a clade of six Tanganyikan lineages of mouthbrooders, representing five tribes (Poll 1986), appears to be their sister group. Comparisons of sequence divergences of the control region indicate that the Lamprologini may be older than the endemic Tanganyikan tribe Ectodini, and short basal branches might suggest a rapid formation of lineages at an early stage of the Tanganyika radiation. It is interesting that three analyzed riverine members of the tribe form a monophyletic group; however, they are not the most ancestral branch of the Lamprologini. This might indicate that they are derived from an endemic lamprologine ancestor that left Lake Tanganyika by entering the Zaire River system. These riverine species may not have seeded the Tanganyikan radiation, as currently thought, but may have recently recolonized the river after a long period of isolation, as soon as the lake was connected to the Zaire River again about 2 Mya. Neolamprologus moorii, endemic to Lake Tanganyika, appears to represent the most basal clade of the Lamprologini. Complex breeding behavior, involving the usage of gastropod shells and associated with dwarfism, is likely to have evolved in parallel in several lineages among the Lamprologini. The tribe Lamprologini may be in need of revision, since several genera appear to be polyphyletic.

Animals↗
PubMed1995

Evolutionary relationships among the male and female mitochondrial DNA lineages in the Mytilus edulis species complex.

A novel form of mitochondrial DNA (mtDNA) inheritance has previously been documented for the blue mussel (Mytilus edulis). Female mussels inherit their mtDNA solely from their mother while males inherit mtDNA from both their mother and their father. In males, the paternal mtDNA is preferentially amplified so that the male gonad is highly enriched for the paternal mtDNA that is then transmitted from fathers to sons. We demonstrate that this mode of mtDNA inheritance also operates in the closely related species M. galloprovincialis and M. trossulus. The evolutionary relationship between the male and female mtDNA lineages is estimated by phylogenetic analysis of 455 nucleotides from the large subunit ribosomal RNA gene. We have found that the male and female lineages are highly divergent; the divergence of these lineages began prior to the speciation of the three species of blue mussels. Further, the separation between the male and female lineages is estimated to have occurred between 5.3 and 5.7 MYA.

Animals↗
PubMed1989

Lineage effects and the index of dispersion of molecular evolution.

Recent efforts to estimate the index of dispersion [R(t)] of molecular evolution-i.e., the ratio of the variance in the number of substitutions on a lineage to the mean number-have suffered from an inability to adjust the data for lineage effects. These effects may include the generation-time dependency of the rate of evolution or improper assumptions about the branching pattern of a phylogenetic tree. In the present paper a method for correcting for lineage effects in the estimation of R(t) is presented for trees made up of three species. The recent data published by Li et al. for 20 loci in three orders of mammals is examined, and the average R(t), corrected for lineage effects, is shown to be 7.75 for replacement substitutions and 3.3 for silent substitutions. Thus the high values reported earlier may not be dismissed as due to generation-time effects or improper assumptions about phylogenies. Computer simulations are presented to give confidence in the estimate for replacement substitutions but also to demonstrate that the estimate for silent substitutions is sensitive to corrections for multiple substitutions and is not as reliable. This work's implications for our understanding of the mechanism of molecular evolution are discussed, and the arguments in favor of the hypothesis that replacement substitutions are mostly selected while silent substitutions are mostly neutral is presented.

Algorithms↗
PubMed2001

Retroviral transduction model of mixed lineage leukemia fused to CREB binding protein.

The in-frame fusion of mixed lineage leukemia to CREB binding protein has been cloned from several patients with t-acute myeloid leukemia and a t(11;16)(q23;p13). A murine retroviral transduction model of mixed lineage leukemia fused to CREB binding protein successfully recapitulates the disease. Interestingly, the mice also develop a preleukemic phase reminiscent of what is often seen in patients with t(11;16). From this work, it was determined that minimally, the amino terminus of mixed lineage leukemia fused to the bromodomain and histone acetyltransferase domain of CREB binding protein are necessary for developing acute myeloid leukemia. This model provides a useful tool for understanding the biologic basis of mixed lineage leukemia leukemogenesis and for developing and testing potential therapeutic agents.

Animals↗
PubMed2005

Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events.

The variability of mtDNA was analysed in local sheep breeds reared throughout Turkey, for which a fragment of the D-loop region and the complete cytochrome b were sequenced. Phylogenetic analyses performed independently for the D-loop and the Cyt b gene revealed three clearly separated clusters indicating three major maternal lineages, two of which had been previously described as types B and A. The new type, C, was present in all the breeds analysed and showed considerable mtDNA variability. Divergence time was obtained on the basis of Cyt b gene and was estimated to be around 160,000-170,000 years ago for lineages B and A, whereas the divergence of lineage C proved to have occurred earlier (between 450,000 and 750,000 years ago). These times greatly predate domestication and suggest that the origin of modern sheep breeds was more complex than previously thought and that at least three independent sheep domestication events occurred. Our results, together with archaeological information and the current wild sheep populations in the Near East region support the high importance of this area in the sheep domestication process. Finally, the evidence of a third maternal lineage has important implications regarding the history of modern sheep.

Animals↗
PubMed2005

An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups.

Fish abundance surveys in the Rhine system have shown in the past two decades that there is a rapid upriver invasion of a freshwater sculpin of the genus Cottus. These fish are found in habitats that are atypical for the known species Cottus gobio, which is confined to small cold streams within the Rhine drainage. Phylogeographic analysis based on mitochondrial haplotypes and diagnostic single nucleotide polymorphisms indicates that the invasive sculpins are hybrids between two old lineages from the River Scheldt drainage and the River Rhine drainage, although it is morphologically more similar to the Scheldt sculpins. Most importantly, however, the invasive population possesses a unique ecological potential that does not occur in either of the source populations from the Rhine or the Scheldt, which allows the colonization of new habitats that have previously been free of sculpins. Microsatellite analysis shows that the new lineage is genetically intermediate between the old lineages and that it forms a distinct genetic group across its whole expansion range. We conclude that hybridization between long separated groups has lead to the fast emergence of a new, adaptationally distinct sculpin lineage.

Adaptation, Physiological↗
PubMed1985

Interspecific cell markers and lineage in mammals.

Study of cell lineage in the mammalian embryo has relied heavily on the use of chimeras to follow the fate of genetically marked cells in later development. Such studies have often been limited by the types of genetic markers available; there are very few markers that allow analysis of the spatial distribution of individual cells at all stages of development. We have developed a marker system that is based on the identification of cells of Mus musculus origin in M. musculus-M. caroli chimeras by in situ DNA-DNA hybridization using a cloned probe to M. musculus satellite DNA. This provides the first ubiquitous in situ cell marker system for mammalian chimeras. We have recently refined the system by the use of biotin-labelled probes and detection of hybridization by streptavidin-peroxidase binding. This increases both the speed and the resolution of the assay. We have used the marker for cell lineage analysis in both embryonic and adult chimeras and results from analysis of the derivatives of early cell lineages in later development and study of coherent growth versus cell mixing in the postimplantation embryo are presented. The importance of understanding embryonic cell lineages as a prelude to molecular studies is emphasized.

Animal Population Groups↗
PubMed1998

Short sequences define genetic lineages: phylogenetic analysis of group A rotaviruses based on partial sequences of genome segments 4 and 9.

Genetic diversity in strains of human group A rotaviruses was analysed by phylogenetic methods. The study material comprised 109 serotype G1 or G4 rotavirus samples isolated in Finland during 1986-1990. Parts of the coding regions of rotaviral genome segments 4 and 9, which encode proteins with serotype specificity, the spike protein VP4 (P serotype) and the outer capsid protein VP7 (G serotype), respectively, were sequenced. As determined by analysis of segment 4 sequences all G1 strains and all except one G4 strain showed P[8] specificity, the one being of P[6] specificity. The G1P[8] strains could be further differentiated into four groups based on segment 9 sequences, while G4P[8] strains formed only one group. Type P[8] (G1P[8] and G4P[8]) strains formed two main groups based on segment 4 sequences, suggesting free segregation of segment 4 between these G strains. Most global G1, G4 and P[8] strains in GenBank/EMBL originating from the 1970s to the present co-clustered with these groups, suggesting that the groups exist as relatively stable lineages. No linear accumulation of nucleotide substitutions was detected in strains of one serotype during the study period. Also, the deduced amino acids of the antigenic regions A, B and C of VP7 were nearly conserved within the phylogenetic lineages. Interestingly, only short amino acid sequences were necessary to divide the e-types correctly into phylogenetic lineages. These amino acid signature motifs were located in aa 29-68 of VP7 and aa 121-135 of VP4 of the G1 and P[8] lineages, respectively.

Amino Acid Sequence↗
PubMed2023

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.

Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called "MitoTracer", which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performance over the existing methods measured by high sensitivity and specificity. MitoTracer is compatible with multiple single cell sequencing platforms. Its application to a cancer evolution dataset revealed the genes related to primary BRAF-inhibitor resistance from scRNA-seq data of BRAF-mutated cancer cells. Overall, our work provided a valuable tool for capturing real informative MT mutations and tracing the lineages among cells.

Journal Article↗
PubMed2019

Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains.

How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)-encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are limited, and the emerging process of STEC and EPEC is largely unknown. Here, we performed a large-scale genomic comparison of bovine commensal E. coli with human commensal and clinical strains, including EPEC and STEC, at a global level. The analyses identified two distinct lineages, in which bovine and human commensal strains are enriched, respectively, and revealed that STEC and EPEC strains have emerged in multiple sublineages of the bovine-associated lineage. In addition to the bovine-associated lineage-specific genes, including fimbriae, capsule, and nutrition utilization genes, specific virulence gene communities have been accumulated in stx- and LEE-positive strains, respectively, with notable overlaps of community members. Functional associations of these genes probably confer benefits to these E. coli strains in inhabiting and/or adapting to the bovine intestinal environment and drive their evolution to highly virulent human pathogens under the bovine-adapted genetic background. Our data highlight the importance of large-scale genome sequencing of animal strains in the studies of zoonotic pathogens.

Animals↗
PubMed1988

T-cell receptor beta-chain gene expression in B-lineage acute lymphoblastic leukemia.

The T-cell receptor beta-chain (T beta) gene expression was examined in 16 children with B-lineage acute lymphoblastic leukemia (ALL), including eight patients with rearrangement of the T beta gene as well as immunoglobulin (Ig) heavy chain gene rearrangement. In contrast to the 1.3 kb full-length transcripts of the T beta observed in T-lineage leukemia and lymphoma cells, no transcript of the T beta gene was detected in 10 patients, including four with T beta gene rearrangement. Low levels of T beta transcripts were found in three patients with T beta gene rearrangement and two patients without T beta gene rearrangement, but those transcripts were truncated. In contrast to those findings, a single patient with T beta gene rearrangement showed abundant 1.3 kb T beta transcripts. These data indicate that T beta gene expression is not restricted to T-lineage cells and demonstrate the heterogeneity of B-lineage ALL at the expression level of the T beta gene. Our findings also suggest that T beta gene expression is not always accompanied with T beta gene rearrangement.

B-Lymphocytes↗
PubMed1993

Sequence variation in D-loop mtDNA of cow lineages selected for high and low maternal effects on milk production.

The four highest and four lowest cow lineages for milk production were selected from 324 maternal lineages of the Israeli Holstein population. For a single cow from each lineage, the mitochondrial D-loop region was amplified using the polymerase chain reaction and directly sequenced for 719bp. Eighteen polymorphic sites were found of which 17 were substitutions and one was an insertion. Only two alleles were found for each polymorphic site, one of which corresponded to the sequence of Anderson et al. (1982), which was the more frequent allele, in all but two sites. None of the polymorphic sites had an apparent effect on milk production, even though an effect > or = 0.33 phenotypic standard deviations, equivalent to 470 kg milk, could be detected by this experimental design. Furthermore, there was no indication that moderately increasing the sample size would have altered the result, since all rare alleles found in more than a single lineage were found in both the high and low subgroups.

Animals↗
PubMed1995

Induction of differentiation into monocyte/macrophage cell lineage of a human eosinophilic leukaemia cell line EoL-1 by simultaneous stimulation with tumour necrosis factor-alpha and interferon-gamma.

Human myeloid leukaemia cell lines have been shown to differentiate into distinct cell lineages in vitro in response to several differentiation-inducing agents. A human eosinophilic leukaemia cell line, EoL-1, has been shown to differentiate into mature eosinophilic granulocytes by treatment with the culture supernatant of a human T-cell line, HIL-3. In this study we have studied whether the EoL-1 cell line has potential to differentiate into cell lineage other than eosinophils. We found that EoL-1 cells cultured in the presence of tumour necrosis factor (TNF)-alpha (10 u/ml) and interferon (IFN)-gamma (1000 u/ml) for 2-4 d differentiated into macrophage-like cells in morphology, and expressed CD14 antigen on their cell surface. It is possible that the small subpopulation of EoL-1 cells which contains non-specific esterase (NSE) activity may be preferentially differentiated by TNF-alpha and IFN-gamma. To clarify this issue, we have cloned the EoL-1 cell line and obtained NSE negative and positive sublines. Both EoL-1 sublines differentiated into monocyte/macrophage-like cells, because: (a) EoL-1 sublines were induced to express CD14 antigen, and (b) they attached firmly to the plastic wells; (c) after differentiation they became strongly positive for NSE staining, and secreted TNF-alpha in response to the stimulation with lipopolysaccharide; and (d) they exhibited potent phagocytic activity. Therefore, we found that the EoL-1 cell line has the ability to differentiate not only into mature eosinophilic cells but also into monocyte/macrophage cell lineage, suggesting that EoL-1 cells represent immature cells with ability to differentiate into multiple cell lineages.

CD11 Antigens↗
PubMed2006

Hybridization between mtDNA-defined phylogeographic lineages of black ratsnakes (Pantherophis sp.).

Phylogeographic analyses using mitochondrial DNA (mtDNA) have revealed many examples of apparently deep historical subdivisions ('phylogroups') within many vertebrates. It remains unclear whether these phylogroups represent independently evolving, adaptively differentiated lineages or groups that show little functional differentiation and, hence, will merge on contact. Here, we use mtDNA sequence data to evaluate the phylogeographic relationships between two of the northernmost populations of black ratsnakes (Pantherophis obsoletus complex) in Ontario, Canada and previously analysed populations in the United States. We then use population-level analyses to evaluate the level of adaptive divergence between previously established mtDNA phylogroups. Phylogenetic analyses show that southern Ontario snakes have mtDNA haplotypes that fall within the Central mtDNA phylogroup, as designated by Burbrink et al. (2000). In contrast, snakes in eastern Ontario carry either Central or Eastern-specific haplotypes. Within the hybrid region, we found highly variable frequencies of mtDNA haplotypes among isolated sub-populations, no association between variation in cytonuclear (mtDNA) and nuclear (microsatellite DNA) markers, no difference in survival or reproductive success among snakes with different mtDNA haplotypes, and no effect of mate similarity in mtDNA on female clutch size. These results argue that the Eastern and Central phylogroups have merged in this region, likely due to a lack of adaptive differentiation between individuals in each lineage. Hence, in these snakes, phylogeographic structure in mtDNA is more a reflection of historical isolation rather than adaptive divergence. The observed reticulation between lineages and lack of evidence for hybrid disgenesis also bears on the classification of these lineages as distinct species.

Adaptation, Physiological↗
PubMed2006

Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islands.

Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Réunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region's white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity.

Animal Migration↗
PubMed2006

A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan.

The genetic structure of populations of Turnip mosaic virus (TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected from Brassica plants in China infected only Brassica plants, whereas those from Japan infected both Brassica and Raphanus (BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal-BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal-BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.

Base Sequence↗
PubMed2006

Simultaneous five cell-lineage flow cytometric analysis system for detection of leucocyte antibodies.

Although flow cytometric (FCM) analysis is one of the most widely used approaches to screen the presence of leucocyte antibodies, it has several drawbacks. First, neutrophils and, especially, monocytes exhibit high background reactivity. Second, to determine antibody specificity, it is often necessary to examine not only neutrophils and monocytes but also other lineage cells including T cells, B cells and platelets. Therefore, we attempted to establish an FCM analysis system in which four lineages of leucocytes and platelets are simultaneously tested with low background. FCM analysis was performed using ethylene diamine tetraacetic acid-anticoagulated whole blood as cell sample without any cell preparation. Discrimination of five cell lineages was carried out based on the differences in forward vs. side scatter distribution and in the expression of CD4, CD20 and CD14. When anti-HNA (human neutrophil antigen) 1b antiserum was applied to HNA 1b-positive blood samples, only neutrophils were unambiguously positive. When anti-Naka (anti-CD36) antiserum was applied, only platelets and monocytes were positive. The background reactivity of neutrophils and monocytes was low enough. When anti-human leucocyte antigen (HLA) class II antiserum was tested, only B-lymphocytes and monocytes were positive. When anti-HLA class I antiserum was tested, all the five-lineage cells were positive.

Antibodies↗