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 1,153 records · Page 64Linked to original sources
PubMed2005

Substitution patterns in alleles of immunoglobulin V genes in humans and mice.

Immunoglobulins (Igs) constitute a subfamily of rapidly evolving proteins. It is postulated that this characteristic is due mainly to the participation of these proteins in highly diverse functions of recognition and defense. Although this vision of rapid evolution in Igs is widely accepted, various studies have demonstrated that diverse and contradictory forces not yet completely understood converge in the evolution of these receptors. In a recent study of the substitution patterns in the alleles that form the human IGHV locus, we found that the variation in genetic and structural information does not occur homogeneously among the different genes, nor among the regions and positions conforming said locus. In view of these results and of the importance of a better understanding of the basic evolutionary process in specific receptors (such as Igs) for both immunology and molecular evolution, it is important to explore the nature of the diversification process in these proteins in detail. In this work, therefore, we analyzed the substitution patterns in all the alleles reported for loci IGKV and IGLV in humans and mice, and we compared the results with those previously observed in the human IGHV locus. We found that the process of evolutionary variation of the Igs reflect the diversity of selective pressures operating on the different loci, genes, sub-regions and positions; for example, diversification through substitution is generally centered on CDRs, but only few positions inside the CDRs were frequently substituted. In spite of this general tendency, it is possible to observe differences in the degree of diversification among loci, families and genes. These tendencies to modify only certain attributes of IGV genes seem to be in agreement with differential strategies associated with the restrictions of the molecular immune recognition mechanism. The complexity of the evolutionary patterns observed in this study leads us to think that the predispositions observed herein may also be due in part to processes of DNA dynamics.

Alleles↗
PubMed2004

Glacial cycles and the tempo of avian speciation.

How old are most species of North American birds? A longstanding debate centers on whether Pleistocene events caused substantial avian diversification. Two new syntheses of speciation times by Johnson and Cicero, and Weir and Schluter provide compelling evidence of recent Pleistocene speciation, whereas diversification rate analyses by Zink et al. suggest that most speciation events occurred earlier. Although these results are seemingly contradictory, when considered together they provide a robust and complementary perspective on the tempo of avian diversification in North America.

Journal Article↗
PubMed2004

Molecular phylogenetics and biogeography of transisthmian and amphi-Atlantic needlefishes (Belonidae: Strongylura and Tylosurus): perspectives on New World marine speciation.

Phylogenetic relationships among New World and eastern Atlantic species in the belonid genera Strongylura and Tylosurus were hypothesized using 3689bp of nucleotide sequence; including the entire mitochondrial (mtDNA) ATP synthase 6 and 8 genes; partial cytochrome b; 12S and 16S ribosomal genes; and introns and exons, 2 and 3 of the nuclear-encoded creatine kinase B gene. Concordant mtDNA and nuclear genealogies permitted well-supported inference of species relationships within Strongylura and Tylosurus, and of the chronology of diversification in the two genera. Our phylogenetic hypothesis permitted an assessment of Rosen's [Syst. Zool. 24 (1975) 431] model of species diversification across the eastern Atlantic to eastern Pacific marine biogeographic track. The spatial predictions of the Rosen model were generally supported, but not the temporal predictions. Furthermore, long branches leading to terminal Belonidae indicated that many species have persisted for millions of years or that nucleotide substitution rates were elevated for some clades. Though heterogeneity of nucleotide substitution rate was indicated across some belonid lineages, molecular clock estimates were used to hypothesize biogeographic scenarios for Strongylura across the eastern Pacific and Atlantic region. Furthermore, use of a molecular clock indicated; that early diversification among contemporary Strongylura may have been initiated by changes in Atlantic Ocean circulation precipitated by closure of the Tethys Sea; and provided approximate dates for the isolation of the freshwater species on the American continents.

ATP Synthetase Complexes↗
PubMed2004

Plate tectonics and biogeographical patterns of the Pseudophoxinus (Pisces: Cypriniformes) species complex of central Anatolia, Turkey.

We investigated the phylogenetic relationships of Pseudophoxinus (Cyprinidae: Leuciscinae) species from central Anatolia, Turkey to test the hypothesis of geographic speciation driven by early Pliocene orogenic events. We analyzed 1141 aligned base pairs of the complete cytochrome b mitochondrial gene. Phylogenetic relationships reconstructed by maximum likelihood, Bayesian likelihood, and maximum parsimony methods are identical, and generally well supported. Species and clades are restricted to geologically well-defined units, and are deeply divergent from each other. The basal diversification of central Anatolian Pseudophoxinus is estimated to have occurred approximately 15 million years ago. Our results are in agreement with a previous study of the Anatolian fish genus Aphanius that also shows a diversification pattern driven by the Pliocene orogenic events. The distribution of clades of Aphanius and Pseudophoxinus overlap, and areas of distribution comprise the same geological units. The geological history of Anatolia is likely to have had a major impact on the diversification history of many taxa occupying central Anatolia; many of these taxa are likely to be still unrecognized as distinct.

Animals↗
PubMed2004

Discordant temporal and geographic patterns in maternal lineages of eastern North American frogs, Rana catesbeiana (Ranidae) and Pseudacris crucifer (Hylidae).

Whether the Pleistocene has had a disproportionate impact on the recent diversification of temperate species, or played a lesser role in a more protracted process, has been a prominent evolutionary debate for the past decade. We used cytochrome b sequences to reconstruct the evolutionary histories of two widely co-distributed, and ecologically divergent frogs (Rana catesbeiana and Pseudacris crucifer) to examine the role of the Pleistocene in structuring these species. Results for R. catesbeiana reflect a pattern of allopatric fragmentation, likely in Coastal Plain refugia on either side of the Mississippi River dating to the mid to early Pleistocene. In contrast, P. crucifer contains numerous divergent lineages, including one west of the Mississippi River in the Interior Highlands, and in the east, multiple lineages that likely expanded from a number of southern Appalachian refugia with lineage sundering originating in the late Pliocene. Large-scale phylogeographic comparisons between these and other eastern North American species reflect both congruent and independent patterns of diversification, possibly reflecting the relative importance of dispersal ability and habitat associations. Although intra-lineage diversification has been structured by repeated Pleistocene glaciations, lineage sundering likely dates at least to the Pliocene in most (but not all) northern temperate amphibian and reptile species studied to date.

Animals↗
PubMed2005

Interspecific phylogeography of the Stator limbatus species complex: the geographic context of speciation and specialization.

Diversification in phytophagous insects is often attributed to a propensity toward specialization and to a tendency for speciation to be associated with host-shifts. Phylogenetic analysis revealed a sister relationship between the generalist Stator limbatus and the specialist host-shifted Stator beali, providing a system to examine the genealogical and geographic origins of the main processes involved in this diversification: host-shifts, specialization, and reproductive isolation. We examine the interspecific phylogeographic relationships between these species using mitochondrial DNA sequence data. S. beali is derived within S. limbatus, rendering the latter paraphyletic and suggesting a budding process of speciation. The inherent polarity in this genealogical pattern indicates that the specialist habit, clumping oviposition behavior, and distinct genitalia of S. beali are all derived from the ancestral S. limbatus. The phylogeography of S. limbatus also shows strong geographic structure with divergences corresponding to known biogeographic boundaries, indicating that this evolutionary signal has not been erased by the vagaries of history. However, the derivation of S. beali and the evolution of reproductive isolation between the two species does not correspond to these known biogeographic boundaries, as S. beali and its sister clade of S. limbatus are restricted to the same geographic province. The geographic proximity of diversification combined with a divergence time estimated at the beginning of the Pleistocene indicates that speciation likely occurred very rapidly, although further genetic and ecological work is necessary to examine the mode of speciation. This study provides the historical context for ongoing evolutionary, ecological, and quantitative genetic research on the divergence in diet breadth between these species.

Animals↗
PubMed2005

Mitochondrial phylogeny of pine cone beetles (Scolytinae, Conophthorus) and their affiliation with geographic area and host.

Pine cone beetles (Conophthorus spp.) feed and kill immature cones of Pinus species, thereby reducing seed production and seriously impairing reforestation of forest ecosystems. Population variation of Conophthorus reproductive behavior has hampered the development of semiochemical control of these pests. This difficulty is compounded by a lack of taxonomic knowledge and species diagnostic characters. Researchers and managers rely, in part, on host associations and geographic locality for species identifications and these have arguable taxonomic utility. However, host use and/or geographic separation may influence Conophthorus lineage diversification. To improve Conophthorus taxonomy and understand the association of host and geography with lineage diversification, a phylogeny of 43 individuals, including all valid species and a robust sample of C. ponderosae from different hosts, is reconstructed using 785 nucleotides of the 3'-end of the mitochondrial cytochrome oxidase I gene. Thirty trees were recovered in a parsimony analysis and the strict consensus was well resolved and supported by branch support measures. Conophthorus was monophyletic but mitochondrial polyphyly was uncovered for several species. The data also suggested an underestimation of species diversity. Phylogenetically related Conophthorus lineages were significantly associated with geographic proximity but not with host, as indicated by comparisons of character optimized geographic distributions and host associations against randomized distributions of these attributes on the parsimony tree. These results suggest that geographic separation better explains the mode of Conophthorus lineage diversification than does host specialization. Based on these results, researchers and managers of Conophthorus should consider populations as potentially different evolutionary entities until species boundaries are delineated via a robust phylogenetic revision of Conophthorus.

Amino Acids↗
PubMed2006

Molecular evidence for adaptive radiation of Micromeria Benth. (Lamiaceae) on the Canary Islands as inferred from chloroplast and nuclear DNA sequences and ISSR fingerprint data.

The Canary Islands have been a focus for phylogeographic studies on the colonization and diversification of endemic angiosperm taxa. Based on phylogeographic patterns, both inter island colonization and adaptive radiation seem to be the driving forces for speciation in most taxa. Here, we investigated the diversification of Micromeria on the Canary Islands and Madeira at the inter- and infraspecific level using inter simple sequence repeat PCR (ISSR), the trnK-Intron and the trnT-trnL-spacer of the cpDNA and a low copy nuclear gene. The genus Micromeria (Lamiaceae, Mentheae) includes 16 species and 13 subspecies in Macaronesia. Most taxa are restricted endemics, or grow in similar ecological conditions on two islands. An exception is M. varia, a widespread species inhabits the lowland scrub on each island of the archipelago and could represent an ancestral taxon from which radiation started on the different islands. Our analyses support a split between the "eastern" islands Fuerteventura, Lanzarote and Gran Canaria and the "western" islands Tenerife, La Palma and El Hierro. The colonization of Madeira started from the western Islands, probably from Tenerife as indicated by the sequence data. We identified two lineages of Micromeria on Gomera but all other islands appear to be colonized by a single lineage, supporting adaptive radiation as the major evolutionary force for the diversification of Micromeria. We also discuss the possible role of gene flow between lineages of different Micromeria species on one island after multiple colonizations.

Adaptation, Biological↗
PubMed1999

Resource partition history and evolutionary specialization of subunits in complex systems.

Specialization for part of the resources available is a common adaptation leading to diversification in biological systems. In complex ecological communities, the history of diversification of parts of a system correlates with the structure of the system in present times. Abundances and sequences of resource partition of species expected by a sequential broken stick model are compared with observed abundances of species and their sequences of evolutionary divergence. Where resources are abundant, first resource partitions correspond to most ancient speciations, and last to recent speciations. The inverse is true when resources are scarce, agreeing with the occupation of extreme habitats by recent species. Diverging species seem to specialize by dividing the niche of common ancestors. Similar trends exist inside genera as well as between families, suggesting similar patterns in diversification and specialization at other levels of biological organization, such as evolution of functional complexes of macromolecules and organs embryogenesis.

Animals↗
PubMed1997

Generation of antibody diversity in rabbits.

Most rabbit B lymphocytes use the same VH gene in V(D)J gene rearrangements and undergo somatic diversification by gene conversion and hypermutation. Recent experiments have shown that V(D)J genes in essentially all rabbit B cells diversify shortly after birth and that this diversification occurs in the gut-associated lymphoid tissue. Still to be determined is whether this diversification is developmentally programmed or is driven by exogenous microbial antigens.

Animals↗
PubMed2002

Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice.

BACKGROUND: We have previously proposed that deamination of cytosine to uracil at sites within the immunoglobulin loci by activation-induced deaminase (AID) triggers antibody diversification. The pattern of diversification (phase 1 or 2 hypermutation, gene conversion, or switch recombination) is viewed as depending on the mode of resolution of the dU/dG lesion. A major resolution mode involves excising the uracil, an activity that at least four different enzymes can accomplish in the mouse. RESULTS: Deficiency in UNG uracil-DNA glycosylase alone is sufficient to distort the pathway of hypermutation in mice. In ung(-/-) animals, mutations at dC/dG pairs are dramatically shifted toward transitions (95%), indicating that the generation of abasic sites (which can induce transversions) has been inhibited. The pattern of substitutions at dA/dT pairs is unaffected. Class-switch recombination is substantially, but not totally, inhibited. CONCLUSIONS: The results provide strong support for the DNA deamination model for antibody diversification with respect to class-switching as well as hypermutation and, in the context of this model, suggest that (i) UNG is the major mouse DNA glycosylase responsible for processing the programmed dU/dG lesions within the immunoglobulin locus; (ii) the second (dA/dT-biased) phase of mutation is probably triggered by recognition of the initiating dU/dG lesion; and (iii) switch recombination largely proceeds via formation of an abasic site, although (iv) an UNG-independent pathway of switch recombination exists, which could reflect action by another uracil-DNA glycosylase but might alternatively be explained by a distinct pathway of resolution, for example, one involving MSH2/MSH6 recognition of the dU/dG lesion.

Animals↗
PubMed2002

Phylogenetic position of Mediterranean Astereae and character evolution of daisies (Bellis, Asteraceae) inferred from nrDNA ITS sequences.

Phylogenetic analyses of nrITS sequences of Asteraceae revealed that the Bellis group is a natural assemblage comprising all the species of Bellis and Bellium, but not Rhynchospermum. In contrast, we propose to include the genera Bellis, Bellium, and Bellidastrum in the subtribe Bellidinae in the interest of circumscribing natural groups. Our results also suggest an early diversification in the western Mediterranean Basin of two monophyletic lineages, Bellis and Bellium. Three major groups can be distinguished within BELLIS: (1) the B. perennis group, containing five annual and perennial species with three ploidy levels (diploid, octoploid, and decaploid), which are distributed throughout the Mediterranean Basin despite lack of pappus; (2) the Bellis sylvestris group, with five annual and perennial species primarily from the western Mediterranean, in which there are five ploidy levels (diploid, tetraploid, hexaploid, octoploid, and decaploid); and (3) a basal grade consisting of three diploid, perennial species which displays remarkable diversification of morphologies. Striking characteristics, such as an annual life form, polyploidy, and loss of pappus, seem to have occurred in parallel several times and in different geographical areas during the early diversification of Bellis species in the western Mediterranean. Character evolution reconstructions allow us to describe a putative ancestor of the genus Bellis (proto-Bellis).

Asteraceae↗
PubMed2005

Evolutionary relationships between Saccharomyces cerevisiae and other fungal species as determined from genome comparisons.

The increasing number of fungal genomes whose sequence has been completed permits their comparison both at the nucleotide and protein levels. The information thus obtained improves our knowledge on evolutionary relationships between fungi. Comparison of the Saccharomyces cerevisiae genome with other Hemiascomycetes genomes confirms that a whole-genome duplication occurred before the diversification between Candida glabrata and the Saccharomyces sensu stricto species and after separation from the branch leading to the other Hemiascomycetes. Duplication was followed by individual gene losses and rearrangements affecting extensive DNA regions. Although S. cerevisiae and C. glabrata are two closely related yeast species at an evolutionary scale, their different habitats and life styles correlate with specific gene differences and with more extensive gene loses having occurred in the parasitic C. glabrata. At a closer evolutive scale, diversification among the sensu stricto species began with nucleotide changes at the intergenic regions affecting sequences that are not relevant for gene regulation, together with more extensive genome rearrangements involving transposons and telomeric regions. One important characteristic of fungal genomes that is shared with other eukaryotes is the fusion of gene sequences coding for separate protein modules into a single open reading frame. This allows diversification of protein functions while saving gene information.

Evolution, Molecular↗
PubMed1991

A model of onshore-offshore change in faunal diversity.

Onshore-offshore patterns of faunal change occurred at many taxonomic scales during the Paleozoic Era, ranging from replacement of the Cambrian evolutionary fauna by the Paleozoic fauna to the environmental expansion of many orders and classes. A simple mathematical model is constructed to investigate such change. The environmental gradient across the marine shelf-slope is treated as a linear array of discrete habitats, each of which holds a set number of species, as observed in the fossil record. During any interval of time, some portion of the species in each habitat becomes extinct by background processes, with rates of extinction varying among both clades and habitats, as also observed in the record. After extinction, species are replaced from within the habitat and from immediately adjacent habitats, with proportions dependent on surviving species. This model leads to the prediction that extinction-resistant clades will always diversify at the expense of extinction-prone clades. But if extinction intensity is highest in nearshore habitats, extinction-resistant clades will expand preferentially in the onshore direction, build up diversity there, and then diversify outward toward the offshore. Thus, onshore-offshore patterns of diversification may be the expectation for faunal change quite independently of whether or not clades originate onshore. When the model is parameterized for Paleozoic trilobites and brachiopods, numerical solutions exhibit both a pattern of faunal change and a time span for diversification similar to that seen in the fossil record. They also generate structure similar to that seen in global diversification, including logistic patterns of growth, declining origination but constant extinction within clades through time, and declining overall extinction across clades through time.

Algorithms↗
PubMed2005

The Paleogene fossil record of birds in Europe.

The Paleogene (Paleocene-Oligocene) fossil record of birds in Europe is reviewed and recent and fossil taxa are placed into a phylogenetic framework, based on published cladistic analyses. The pre-Oligocene European avifauna is characterized by the complete absence of passeriform birds, which today are the most diverse and abundant avian taxon. Representatives of small non-passeriform perching birds thus probably had similar ecological niches before the Oligocene to those filled by modern passerines. The occurrence of passerines towards the Lower Oligocene appears to have had a major impact on these birds, and the surviving crown-group members of many small arboreal Eocene taxa show highly specialized feeding strategies not found or rare in passeriform birds. It is detailed that no crown-group members of modern 'families' are known from pre-Oligocene deposits of Europe, or anywhere else. The phylogenetic position of Paleogene birds thus indicates that diversification of the crown-groups of modern avian 'families' did not take place before the Oligocene, irrespective of their relative position within Neornithes (crown-group birds). The Paleogene fossil record of birds does not even support crown-group diversification of Galliformes, one of the most basal taxa of neognathous birds, before the Oligocene, and recent molecular studies that dated diversification of galliform crown-group taxa into the Middle Cretaceous are shown to be based on an incorrect interpretation of the fossil taxa used for molecular clock calibrations. Several taxa that occur in the Paleogene of Europe have a very different distribution than their closest extant relatives. The modern survivors of these Paleogene lineages are not evenly distributed over the continents, and especially the great number of taxa that are today restricted to South and Central America is noteworthy. The occurrence of stem-lineage representatives of many taxa that today have a restricted Southern Hemisphere distribution conflicts with recent hypotheses on a Cretaceous vicariant origin of these taxa, which were deduced from the geographical distribution of the basal crown-group members.

Animals↗
PubMed2004

Ferns diversified in the shadow of angiosperms.

The rise of angiosperms during the Cretaceous period is often portrayed as coincident with a dramatic drop in the diversity and abundance of many seed-free vascular plant lineages, including ferns. This has led to the widespread belief that ferns, once a principal component of terrestrial ecosystems, succumbed to the ecological predominance of angiosperms and are mostly evolutionary holdovers from the late Palaeozoic/early Mesozoic era. The first appearance of many modern fern genera in the early Tertiary fossil record implies another evolutionary scenario; that is, that the majority of living ferns resulted from a more recent diversification. But a full understanding of trends in fern diversification and evolution using only palaeobotanical evidence is hindered by the poor taxonomic resolution of the fern fossil record in the Cretaceous. Here we report divergence time estimates for ferns and angiosperms based on molecular data, with constraints from a reassessment of the fossil record. We show that polypod ferns (> 80% of living fern species) diversified in the Cretaceous, after angiosperms, suggesting perhaps an ecological opportunistic response to the diversification of angiosperms, as angiosperms came to dominate terrestrial ecosystems.

Biodiversity↗
PubMed2005

Species diversity can drive speciation.

A fundamental question in evolutionary ecology and conservation biology is: why do some areas contain greater species diversity than others? Island biogeographic theory has identified the roles of immigration and extinction in relation to area size and proximity to source areas, and the role of speciation is also recognized as an important factor. However, one as yet unexplored possibility is that species diversity itself might help to promote speciation, and indeed the central tenets of island biogeographic theory support such a prediction. Here we use data for plants and arthropods of the volcanic archipelagos of the Canary and Hawaiian Islands to address whether there is a positive relationship between species diversity and rate of diversification. Our index of diversification for each island is the proportion of species that are endemic, and we test our prediction that this increases with increasing species number. We show that even after controlling for several important physical features of islands, diversification is strongly related to species number.

Animals↗
PubMed2005

The MRE11-RAD50-NBS1 complex accelerates somatic hypermutation and gene conversion of immunoglobulin variable regions.

Targeted diversification of immunoglobulin variable regions is induced by activation-induced deaminase and may occur by either somatic hypermutation or gene conversion. MRE11-RAD50-NBS1 (MRN) is a ubiquitous and conserved nuclease complex critical for DNA break repair and is essential in class-switch recombination. Here we show that ectopic expression of NBS1, the regulatory subunit of MRN, accelerated hypermutation in the human B cell line Ramos and accelerated gene conversion in the chicken B cell line DT40. In both cases, accelerated diversification depended on MRN complex formation. These data suggest that MRN promotes DNA cleavage and/or mutagenic repair of lesions initiated by activation-induced deaminase, acting in the shared pathway of immunoglobulin gene diversification.

Acid Anhydride Hydrolases↗