Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Diversification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,441 records · Page 80Linked to original sources
PubMed1993

Ancestry and diversity of the HMG box superfamily.

The HMG box is a novel type of DNA-binding domain found in a diverse group of proteins. The HMG box superfamily comprises a.o. the High Mobility Group proteins HMG1 and HMG2, the nucleolar transcription factor UBF, the lymphoid transcription factors TCF-1 and LEF-1, the fungal mating-type genes mat-Mc and MATA1, and the mammalian sex-determining gene SRY. The superfamily dates back to at least 1,000 million years ago, as its members appear in animals, plants and yeast. Alignment of all known HMG boxes defined an unusually loose consensus sequence. We constructed phylogenetic trees connecting the members of the HMG box superfamily in order to understand their evolution. This analysis led us to distinguish two subfamilies: one comprising proteins with a single sequence-specific HMG box, the other encompassing relatively non sequence-specific DNA-binding proteins with multiple HMG boxes. By studying the extent of diversification of the superfamily, we found that the speed of evolution was very different within the various groups of HMG-box containing factors. Comparison of the evolution of the two boxes of ABF2 and of mtTF1 implied different diversification models for these two proteins. Finally, we provide a tree for the highly complex group of SRY-like ('Sox' genes), clustering at least 40 different loci that rapidly diverged in various animal lineages.

Amino Acid Sequence↗
PubMed2001

Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives.

Endogenous retrovirus-like elements characterizable by a leucine tRNA primer (ERV-Ls) are reiterated genomic sequences known to be widespread in mammals, including humans. They may have arisen from an ancestral foamy virus-like element by successful germ line infection followed by copy number expansion. However, among mammals, only primates and rodents have thus far exhibited high copy number amplification and sequence diversification. Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa having good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing proboscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L sequences, and thus it was expected that uranotheres should as well. Here, we show that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lineages. Selection is the most parsimonious explanation for observed differences in ERV-L distribution and frequency, with relative success being reflected in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant elephantid samples).

Animals↗
PubMed1993

Molecular mechanisms of colicin evolution.

This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the origin and diversification of colicin clusters. Such mechanisms include movement of colicin plasmids between strains of E. coli and subsequent plasmid cointegration, transposition- and recombination-mediated transfer of colicin and related sequences, and rapid diversification of colicin and immunity proteins through the action of positive selection. The wealth of information contained in colicin sequence comparisons makes this an ideal system with which to explore molecular mechanisms of evolutionary change.

Amino Acid Sequence↗
PubMed1986

Temporal scaling of molecular evolution in primates and other mammals.

Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constancy. Temporal scaling provides a test of rates, where scaling coefficients of 1.0 (isochrony) represent stochastic rate constancy. The fossil record of primates and other mammals is now known in sufficient detail to provide several independent divergence times for major taxonomic groups. Molecular difference should scale negatively or isochronically (scaling coefficients less than 1.0) with divergence time: where two or more divergence times are available, molecular difference appears to scale positively (scaling coefficient greater than 1.0). A minimum of four divergence times are required for adequate statistical power in testing the linear model: scaling is significantly nonlinear and positive in six of 11 published investigations meeting this criterion. All groups studied show some slowdown in rates of molecular change over Cenozoic time. The break from constant or increasing rates during the Mesozoic to decreasing rates during the Cenozoic appears to coincide with extraordinary diversification of placental mammals at the beginning of this era. High rates of selectively neutral molecular change may be concentrated in such discrete events of evolutionary diversification.

Amino Acid Sequence↗
PubMed2002

Functional significance of gap junctional coupling in preimplantation development.

Gap junctional intercellular coupling allows cells to share low molecular weight metabolites and second messengers, thus facilitating homeostatic and developmental processes. Gap junctions make their appearance very early in rodent development, during compaction in the eight-cell stage. Surprisingly, preimplantation mouse embryos lacking the gap junction protein connexin 43 develop normally and establish full-term pregnancies despite severely reduced gap junctional coupling. It was suggested that this might be explained by the presence of at least five additional connexins known to be expressed in blastocysts. In the present study, we set out to clarify the number of connexins present in preimplantation rodent embryos and the role of gap junctional coupling, if any, in blastocyst development. We provide evidence from reverse transcription-polymerase chain reaction analysis that the genes encoding 3 additional connexins (connexin 30 or beta6, connexin 36 or alpha9, and connexin 57 or alpha10) are also transcribed in preimplantation mouse embryos. Furthermore, we show that multiple connexins are expressed in rat preimplantation embryos, indicating that multiplicity of connexin expression may be a common feature of early mammalian embryogenesis. We could detect no up-regulation of any of 3 coexpressed connexins examined in mouse embryos lacking connexin 43. Impaired intercellular coupling caused either by the loss of connexin 43 or by treatment of cultured embryos with the gap junctional coupling blocker 18alpha-glycyrrhetinic acid (AGA) had no discernable effect on either apoptosis or glucose utilization, parameters known to be affected by gap junctional coupling in other contexts. These results, taken together with the reported inability of AGA to perturb blastocyst formation, imply that gap junctional coupling is not essential during this developmental period. We propose that connexin expression and the assembly of multiple types of gap junction channels in preimplantation embryos facilitates the diversification of communication pathways that will appear during postimplantation development. New evidence of this diversification is presented using rat blastocyst outgrowths.

Animals↗
PubMed2001

Daily interferon therapy for hepatitis C virus infection in liver transplant recipients.

BACKGROUND: Hepatitis C virus infection persists after liver transplantation and causes recurrent liver injury in the majority of patients. Standard dose interferon therapy has been largely unsuccessful for hepatitis C in transplant recipients. METHODS: Twelve patients, at least 7 months posttransplant, with detectable hepatitis C virus RNA in serum and features of hepatitis C on liver biopsy were randomized to interferon-alpha2a, 3 mU daily for 12 months (n=8) or no treatment (n=4). The tolerability of daily interferon dosing in liver transplant recipients was evaluated and effects on hepatitis C virus RNA level, quasispecies evolution, and liver histology were studied. RESULTS: Treated patients had an improvement in histological activity index at the end of therapy relative to controls (median reduction of 2 versus median increase of 1.5) (P=0.04). Four treated patients had a virological response (all bDNA negative, one qualitative polymerase chain reaction negative) compared with none of the untreated patients. Only two of six treated patients tested had evidence of quasispecies diversification on therapy. Seven of eight patients in the treatment group required dose reduction for fatigue and/or depression. They tolerated 1.5 mU of interferon-alpha2a daily. Two treated patients developed graft dysfunction, one of who had histological evidence of rejection and subsequent graft loss. CONCLUSIONS: Low daily doses of interferon were tolerated by liver transplant recipients and provided histological benefit without associated quasispecies diversification in most cases. These findings provide a rationale to study low dose daily or pegylated interferon maintenance therapy for the management of hepatitis C posttransplant.

Adult↗
PubMed2004

Perinatal transmission and viral evolution of hepatitis C virus quasispecies in infants coinfected with HIV.

OBJECTIVES: Three HIV/hepatitis C virus (HCV)-coinfected children and the mothers of 2 were studied to examine the nature of perinatal HCV infection in HIV-coinfected infants and to assess the evolution of viral quasispecies thereafter. Sequences of the hypervariable region in the N terminus of the E2/NS1 region (HVR-1) of the children and their mothers were compared. HCV quasispecies changes in the infants were tracked over several years. METHODS: Sequence similarity comparisons and phylogenetic trees were derived from cDNA of plasma isolates. Quantitation of plasma HCV and HIV was performed in the children, as well as CD4 T-cell percentage and liver transaminases. RESULTS: Phylogenetic analysis of the mother-child pairs suggested that transmission of multiple dominant and nondominant variants identified in the mother were seen. HCV diversification in the children was seen as early as 2 months of life. The child with the best immune status and HIV control demonstrated the most diversification throughout. CONCLUSION: Multiples HCV variants transmitted from mother to child and their early changes in the child may be related to maternal antibody. Variation after the 1st year of life may reflect immunologic pressure from the child. There was no trend suggesting that the presence or absence of selective immunologic pressure affected HCV load or liver transaminase values.

Amino Acid Sequence↗
PubMed2002

Antibodies to acetylcholine receptor in parous women with myasthenia: evidence for immunization by fetal antigen.

The weakness in myasthenia gravis (MG) is mediated by autoantibodies against adult muscle acetylcholine receptors (AChR) at the neuromuscular junction; most of these antibodies also bind to fetal AChR, which is present in the thymus. In rare cases, babies of mothers with MG, or even of asymptomatic mothers, develop a severe developmental condition, arthrogryposis multiplex congenita, caused by antibodies that inhibit the ion channel function of the fetal AChR while not affecting the adult AChR. Here we show that these fetal AChR inhibitory antibodies are significantly more common in females sampled after pregnancy than in those who present before pregnancy, suggesting that they may be induced by the fetus. Moreover, we were able to clone high-affinity combinatorial Fab antibodies from thymic cells of two mothers with MG who had babies with arthrogryposis multiplex congenita. These Fabs were highly specific for fetal AChR and did not bind the main immunogenic region that is common to fetal and adult AChR. The Fabs show strong biases to VH3 heavy chains and to a single Vkappa1 light chain in one mother. Nevertheless, they each show extensive intraclonal diversification from a highly mutated consensus sequence, consistent with antigen-driven selection in successive steps. Collectively, our results suggest that, in some cases of MG, initial immunization against fetal AChR is followed by diversification and expansion of B cells in the thymus; maternal autoimmunity will result if the immune response spreads to the main immunogenic region and other epitopes common to fetal and adult AChR.

Adult↗
PubMed2000

Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish.

The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining the history of diversification for a species of catfish (Pimelodella chagresi) whose distribution spans multiple, isolated drainage basins across the Isthmian landscape and into north-western South America. Analysis of mitochondrial DNA haplotypes and morphological traits indicated that P. chagresi, as currently recognized, comprises a species complex. In addition, along the Pacific slope of Panama, repeated dispersion, diversification, extinction and possibly hybridization are thought to underlie a complex distribution of haplotypes. Overall, the results underscore the tremendous importance of historical processes on regional biodiversity.

Animals↗
PubMed2004

Evidence for mycorrhizal races in a cheating orchid.

Disruptive selection on habitat or host-specificity has contributed to the diversification of several animal groups, especially plant-feeding insects. Photosynthetic plants typically associate with a broad range of mycorrhizal fungi, while non-photosynthetic plants that capture energy from mycorrhizal fungi ('mycoheterotrophs') are often specialized towards particular taxa. Sister myco-heterotroph species are often specialized towards different fungal taxa, suggesting rapid evolutionary shifts in specificity. Within-species variation in specificity has not been explored. Here, we tested whether genetic variation for mycorrhizal specificity occurs within the myco-heterotrophic orchid Corallorhiza maculata. Variation across three single-nucleotide polymorphisms revealed six multilocus genotypes across 122 orchids from 30 sites. These orchids were associated with 22 different fungal species distributed across the Russulaceae (ectomycorrhizal basidiomycetes) according to internal-transcribed-spacer sequence analysis. The fungi associated with four out of the six orchid genotypes fell predominantly within distinct subclades of the Russulaceae. This result was supported by Monte Carlo simulation and analyses of molecular variance of fungal sequence diversity. Different orchid genotypes were often found growing in close proximity, but maintained their distinct fungal associations. Similar patterns are characteristic of insect populations diversifying onto multiple hosts. We suggest that diversification and specialization of mycorrhizal associations have contributed to the rapid radiation of the Orchidaceae.

Base Sequence↗
PubMed2004

Life-history trade-offs and ecological dynamics in the evolution of longevity.

Longevity is a life-history trait that is shaped by natural selection. An unexplored consequence is how selection on this trait affects diversity and diversification in species assemblages. Motivated by the diverse rockfish (Sebastes) assemblage in the North Pacific, the effects of trade-offs in longevity against competitive ability are explored. A competition model is developed and used to explore the potential for species diversification and coexistence. Invasion analyses highlight that life-history trait trade-offs in longevity can mitigate the effects of competitive ability and favour the coexistence of a finite number of species. Our results have implications for niche differentiation, limiting similarity and assembly dynamics in multispecies interactions.

Animals↗
PubMed2005

Photoreceptor spectral sensitivities in terrestrial animals: adaptations for luminance and colour vision.

This review outlines how eyes of terrestrial vertebrates and insects meet the competing requirements of coding both spatial and spectral information. There is no unique solution to this problem. Thus, mammals and honeybees use their long-wavelength receptors for both achromatic (luminance) and colour vision, whereas flies and birds probably use separate sets of photoreceptors for the two purposes. In particular, we look at spectral tuning and diversification among 'long-wavelength' receptors (sensitivity maxima at greater than 500 nm), which play a primary role in luminance vision. Data on spectral sensitivities and phylogeny of visual photopigments can be incorporated into theoretical models to suggest how eyes are adapted to coding natural stimuli. Models indicate, for example, that animal colour vision--involving five or fewer broadly tuned receptors--is well matched to most natural spectra. We can also predict that the particular objects of interest and signal-to-noise ratios will affect the optimal eye design. Nonetheless, it remains difficult to account for the adaptive significance of features such as co-expression of photopigments in single receptors, variation in spectral sensitivities of mammalian L-cone pigments and the diversification of long-wavelength receptors that has occurred in several terrestrial lineages.

Adaptation, Biological↗
PubMed2005

Strikingly variable divergence times inferred across an Amazonian butterfly 'suture zone'.

'Suture zones' are areas where hybrid and contact zones of multiple taxa are clustered. Such zones have been regarded as strong evidence for allopatric divergence by proponents of the Pleistocene forest refugia theory, a vicariance hypothesis frequently used to explain diversification in the Amazon basin. A central prediction of the refugia and other vicariance theories is that the taxa should have a common history so that divergence times should be coincident among taxa. A suture zone for Ithomiinae butterflies near Tarapoto, NE Peru, was therefore studied to examine divergence times of taxa in contact across the zone. We sequenced 1619bp of the mitochondrial COI/COII region in 172 individuals of 31 species from across the suture zone. Inferred divergence times differed remarkably, with divergence between some pairs of widespread species (each of which may have two or more subspecies interacting in the zone, as in the genus Melinaea) being considerably less than that between hybridizing subspecies in other genera (for instance in Oleria). Our data therefore strongly refute a simple hypothesis of simultaneous vicariance and suggest that ongoing parapatric or other modes of differentiation in continuous forest may be important in driving diversification in Amazonia.

Animals↗
PubMed2006

Possible human impacts on adaptive radiation: beak size bimodality in Darwin's finches.

Adaptive radiation is facilitated by a rugged adaptive landscape, where fitness peaks correspond to trait values that enhance the use of distinct resources. Different species are thought to occupy the different peaks, with hybrids falling into low-fitness valleys between them. We hypothesize that human activities can smooth adaptive landscapes, increase hybrid fitness and hamper evolutionary diversification. We investigated this possibility by analysing beak size data for 1755 Geospiza fortis measured between 1964 and 2005 on the island of Santa Cruz, Galápagos. Some populations of this species can display a resource-based bimodality in beak size, which mirrors the greater beak size differences among species. We first show that an historically bimodal population at one site, Academy Bay, has lost this property in concert with a marked increase in local human population density. We next show that a nearby site with lower human impacts, El Garrapatero, currently manifests strong bimodality. This comparison suggests that bimodality can persist when human densities are low (Academy Bay in the past, El Garrapatero in the present), but not when they are high (Academy Bay in the present). Human activities may negatively impact diversification in 'young' adaptive radiations, perhaps by altering adaptive landscapes.

Adaptation, Physiological↗
PubMed2006

The distribution of species diversity across a flora's component lineages: dating the Cape's 'relicts'.

The Cape Floristic Region is exceptionally species-rich both for its area and latitude, and this diversity is highly unevenly distributed among genera. The modern flora is hypothesized to result largely from recent (post-Oligocene) speciation, and it has long been speculated that particular species-poor lineages pre-date this burst of speciation. Here, we employ molecular phylogenetic data in combination with fossil calibrations to estimate the minimum duration of Cape occupation by 14 unrelated putative relicts. Estimates vary widely between lineages (7-101 Myr ago), and when compared with the estimated timing of onset of the modern flora's radiation, it is clear that many, but possibly not all, of these lineages pre-date its establishment. Statistical comparisons of diversities with lineage age show that low species diversity of many of the putative relicts results from a lower rate of diversification than in dated Cape radiations. In other putative relicts, however, we cannot reject the possibility that they diversify at the same underlying rate as the radiations, but have been present in the Cape for insufficient time to accumulate higher diversity. Although the extremes in diversity of currently dated Cape lineages fall outside expectations under a constant underlying diversification rate, sampling of all Cape lineages would be required to reject this null hypothesis.

Base Sequence↗
PubMed2007

Macroevolutionary dynamics in environmental space and the latitudinal diversity gradient in New World birds.

Correlations between species richness and climate suggest non-random occupation of environmental space and niche evolution through time. However, the evolutionary mechanisms involved remain unresolved. Here, we partition the occupation of environmental space into intra- and inter-clade components to differentiate a model based on pure conservation of ancestral niches with higher diversification rates in the tropics, and an adaptive radiation model based on shifts in adaptive peaks at the family level allowing occupation of temperate regions. We examined these mechanisms using within- and among-family skewness components based on centroids of 3560 New World bird species across four environmental variables. We found that the accumulation of species in the tropics is a result of both processes. The components of adaptive radiation have family level skewness of species' distributions strongly structured in space, but not phylogenetically, according to the integrated analyses of spatial filters and phylogenetic eigenvectors. Moreover, stronger radiation components were found for energy variables, which are often used to argue for direct climatic effects on diversity. Thus, the correspondence between diversity and climate may be due to the conservation of ancestral tropical niches coupled with repeated broad shifts in adaptive peaks during birds' evolutionary history more than by higher diversification rates driven by more energy in the tropics.

Adaptation, Physiological↗
PubMed2026

Phylogenomics of Manticorini tiger beetles supports ancient Gondwanan vicariance and recent American amphitropical disjunction.

Disjunct distributions have long fascinated biologists, particularly those found in the Southern Hemisphere. Gondwanan vicariance has been invoked to explain these patterns, with relatively limited studies having phylogenetically tested this hypothesis. Another intriguing pattern of disjunction involving South America is the American amphitropical distribution, where Western Hemisphere taxa have close relatives either north or south of the tropics. While better known in plants, this pattern is rarely proposed for animals and only phylogenetically tested in a handful of studies on hymenopteran insects. The Manticorini is a tribe of large-bodied, flightless tiger beetles whose members possess a complex distribution pattern attributable to both Gondwanan vicariance and American amphitropical disjunction. Using genomic-scale data we perform phylogenetic analyses to produce a time-calibrated evolutionary history of the Manticorini. With the resultant time tree we perform ancestral range reconstruction in order to recover the historical biogeography of this group. Our results show deep divergence between most manticorine genera, contrasted with young crown ages indicative of recent diversification. Our analyses support Gondwanan vicariance and amphitropical disjunction resulting from recent dispersal as part of the historical biogeography of the tribe. These findings highlight the role of both vicariance and dispersal in shaping diversification and complex modern distributions.

Animals↗
PubMed2000

The relationships of vascular plants.

Recent phylogenetic research indicates that vascular plants evolved from bryophyte-like ancestors and that this involved extensive modifications to the life cycle. These conclusions are supported by a range of systematic data, including gene sequences, as well as evidence from comparative morphology and the fossil record. Within vascular plants, there is compelling evidence for two major clades, which have been termed lycophytes (clubmosses) and euphyllophytes (seed plants, ferns, horsetails). The implications of recent phylogenetic work are discussed with reference to life cycle evolution and the interpretation of stratigraphic inconsistencies in the early fossil record of land plants. Life cycles are shown to have passed through an isomorphic phase in the early stages of vascular plant evolution. Thus, the gametophyte generation of all living vascular plants is the product of massive morphological reduction. Phylogenetic research corroborates earlier suggestions of a major representational bias in the early fossil record. Mega-fossils document a sequence of appearance of groups that is at odds with that predicted by cladogram topology. It is argued here that the pattern of appearance and diversification of plant megafossils owes more to changing geological conditions than to rapid biological diversification.

Biological Evolution↗