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PubMed2006

Adaptive evolution of multicolored fluorescent proteins in reef-building corals.

Here we investigate the evolutionary scenarios that led to the appearance of fluorescent color diversity in reef-building corals. We show that the mutations that have been responsible for the generation of new cyan and red phenotypes from the ancestral green were fixed with the help of positive natural selection. This fact strongly suggests that the color diversity is a product of adaptive evolution. An unexpected finding was a set of residues arranged as an intermolecular binding interface, which was also identified as a target of positive selection but is nevertheless not related to color diversification. We hypothesize that multicolored fluorescent proteins evolved as part of a mechanism regulating the relationships between the coral and its algal endosymbionts (zooxanthellae). We envision that the effect of the proteins' fluorescence on algal physiology may be achieved not only through photosynthesis modulation, but also through regulatory photosensors analogous to phytochromes and cryptochromes of higher plants. Such a regulation would require relatively subtle, but spectrally precise, modifications of the light field. Evolution of such a mechanism would explain both the adaptive diversification of colors and the coevolutionary chase at the putative algae-protein binding interface in coral fluorescent proteins.

Adaptation, Biological↗
PubMed2006

Domain-specific positive selection contributes to the evolution of Arabidopsis leucine-rich repeat receptor-like kinase (LRR RLK) genes.

Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and development, the evolutionary mechanism for this functional diversification is currently unclear. In this study, we focused on the LRRII RLK subfamily to investigate the molecular mechanisms that might have led to the functional differentiation of Arabidopsis LRR RLK genes. Phylogenetic analysis of 14 genes in this subfamily revealed three well-supported groups (I, II, and III). RT-PCR analysis did not find many qualitative differences in expression among these 14 genes in various Arabidopsis tissues, suggesting that evolution of regulatory sequences did not play a major role in their functional divergence. We analyzed substitution patterns in the predicted ligand-binding regions of these genes to examine if positive selection has acted to produce novel ligand-binding specificities, using the nonsynonymous/synonymous rate ratio (d (N)/d (S)) as an indicator of selective pressure. Estimates of d (N)/d (S) ratios from multiple methods indicate that nonsynonymous substitutions accumulated during divergence of the three lineages. Positive selection is likely to have occurred along the lineages ancestral to groups II and III. We suggest that positive selection on the ligand-binding sites of LRRII RLKs promoted diversification of ligand-binding specificities and thus contributed to the functional differentiation of Arabidopsis LRRII RLK genes during evolution.

Amino Acid Sequence↗
PubMed2000

Are RNA viruses adapting or merely changing?

RNA viruses and retroviruses fix substitutions approximately 1 million-fold faster than their hosts. This diversification could represent an inevitable drift under purifying selection, the majority of substitutions being phenotypically neutral. The alternative is to suppose that most fixed mutations are beneficial to the virus, allowing it to keep ahead of the host and/or host population. Here, relative sequence diversification of different proteins encoded by viral genomes is found to be linear. The examples encompass a wide variety of retroviruses and RNA viruses. The smoothness of relative divergence spans quasispeciation following clonal infection, to variation among different isolates of the same virus, to viruses from different species or those associated with different diseases, indicating that the majority of fixed mutations likely reflects drift. This held for both mammalian and plant viruses, indicating that adaptive immunity doesn't necessarily shape the relative accumulation of amino acid substitutions. When compared to their hosts RNA viruses evolution appears conservative.

Adaptation, Physiological↗
PubMedDate not supplied

Evolutionary discontinuity of the Carabine ground beetles.

The Carabine ground beetles are mostly hind wing-less and cannot fly, so that there is more chance of diversification by geographic isolation compared with winged insects. The relationships between morphological diversification and phylogeny of the ground beetles of the world have been inferred mainly by comparisons of mitochondrial ND5 gene sequences. Based on dating by a mitochondrial DNA "clock," it has been deduced that an explosive radiation of the major carabine groups took place 50-40 MYA. This was followed by occasional radiations on various scales, sometimes accompanied by parallel morphological changes. There are also a good number of examples showing that the fundamental morphology has remained unchanged for a long time among geographically isolated populations within the same species. Thus, carabid evolution would have proceeded discontinuously, with phases of rapid morphological change alternating with silent phases.

Animals↗
PubMed2002

Phylogenetic analysis of bacterial communities associated with ectoparasitic chewing lice of pocket gophers: a culture-independent approach.

This study identifies the bacteria associated with ectoparasitic chewing lice that live in the fur of pocket gophers. Samples of chewing lice were collected from pocket gopher hosts in Florida, Missouri, New Mexico, and Costa Rica. We used a molecular sampling method whereby total community DNA was extracted from samples of chewing lice, and PCR was used to selectively amplify small-subunit rRNA genes from bacteria. This culture-independent method yielded ca. 35 distinct lineages representing eight widely divergent groups within the domain Bacteria. Phylogenetic analysis of two lineages (Acinetobacter and Staphylococcus) provides evidence that multiple species of each group are found in chewing lice. Phylogenetic analysis also demonstrated that diversification within chewing lice may be evident in both Acinetobacter and Staphylococcus. Some clones amplified from chewing louse hosts appeared to be distinct from known species of Acinetobacter and Staphylococcus. This diversification may be the result of the extreme isolation of populations of both chewing lice and their pocket gopher hosts.

Animals↗
PubMed2002

The nature of introns 4-7 largely reflects the lineage specificity of HLA-A alleles.

For most HLA-A alleles the phylogeny of the 3' non-coding regions has not yet been studied systematically. In this study, we have determined the sequences of introns 4-7 in 50 HLA-A variants, and have computed nucleotide substitution rates and phylogenetic relationships. The A2/A28, A9, and A10 groups were characterized by clear lineage specificity. For the A19 group, lineage specificity was weaker. A*3001 clustered together with the alleles of the A1/A3/A11/A36 serological family, but not with the A19 group alleles. Reduced lineage specificity was also observed for the alleles of the A1/A3/A11/A36groups. The 3' intron sequences of A*8001 were clearly distinct from all other alleles studied. In several cases two allelic groups shared identical intron sequences, whereby the patterns varied with the introns. A similar situation has been previously described for the 5' introns. Since recombination is the major mechanism of HLA diversification, the intronic lineage specificity corresponds to the comparatively lower recombination rate of the HLA-A 3' exons. The low level of recombination within the 3' region of HLA-A is supported by the low CpG content with a maximum of 3.0% in this region compared with up to 10.7% in the 5' region. Apart from phylogenetic studies of HLA diversity and diversification, the sequence data obtained in our study may prove valuable for the development of a haplotype-specific sequencing strategy for the HLA-A3' exons and for the explanation of recombination events in newly described HLA class I alleles.

Base Sequence↗
PubMed2001

Patterns of evolution in Discula fungi and the origin of dogwood anthracnose in North America, studied using arbitrarily amplified and ribosomal DNA.

The anthracnose epidemic caused by exotic filamentous fungi of the genus Discula threatens the future of the prized flowering (Cornus florida L.) and Pacific (C. nuttalli Aud.) dogwoods in North America. A cross-section of fungi that cause anthracnose in broadleaf temperate trees was characterized using DNA amplification fingerprinting, sequence and secondary structure analysis of the internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA), and compatibility of hyphal anastomosis. ITS-inferred phylogenies rejected the null hypothesis of only one fungal lineage, by defining four monophyletic and well differentiated groups, corresponding to Discula sp., D. quercina, D. umbrinella and D. destructiva, with the last two species sharing a common and recent ancestor. In turn, they showed that the dogwood pathogen, D. destructiva, did not evolve directly from an indigenous population related to Discula sp. In this study, rDNA spacers that are generally considered important for protein synthesis but are selectively neutral, appeared functionally constrained and subject to selective sequence diversification. Results confirmed the high variability of D. umbrinella and the remarkable homogeneity and exotic nature of D. destructiva at the genetic level, clarified the taxonomy and phylogeny of Discula, and provided clues as to the origin and diversification of dogwood anthracnose-causing fungi.

Base Sequence↗
PubMed2005

[Self-responsibility as a component of quality-oriented care-reflections on further development of nursing care insurance].

Further development of nursing care insurance must consider both ethical aspects and scarcity of resources. An economy that serves human life has two principal targets: safeguarding the basis of existence and extension of the fulfillment of life. From an ethical perspective welfare and personal responsibility have to be equilibrated by promoting individuality and self-responsibility and maintaining relatives' willingness to become a caregiver. Discussing the role of prevention and rehabilitation in nursing care it is argued that the legally committed primacy of prevention and rehabilitation over care has still not been put into practise due to unresolved problems at the interface of health insurance and nursing care insurance as well as at the interface of inpatient and outpatient providers. Moreover, it seems necessary to strengthen prevention and rehabilitation in the context of care. A comprehensive understanding of individual demands for help, support, and care requires a revision of the common definition of need for care in terms of activities of daily living which neglects particularly psycho-social needs. Case management is a suitable approach to provide adequate and coordinated support as a prerequisite for quality of life in people in need for care. Overcoming compartmentalization of inpatient and outpatient sectors and crosslinking of services are described as essential challenges for future provision of nursing care insurance. Intensification of counseling and advice for patients and relatives, extension and diversification of local providers, upgrading of ambulant services, daily care and short-term care, diversification of nursing homes and other housing arrangements, further development of hospices and palliative care, and acceptance of institutions for the elderly as indispensable components of the future care system are discussed as specific tasks in the further development of nursing care insurance.

Aged↗
PubMed2005

Transport of magnesium and other divalent cations: evolution of the 2-TM-GxN proteins in the MIT superfamily.

In bacteria, magnesium uptake is mainly mediated by the well-characterized CorA type of membrane proteins. In recent years, functional homologues have been characterized in the inner mitochondrial membrane of yeast and mammals (the MRS2/LPE10 type), in the plasma membrane of yeast (the ALR/MNR type) and, as an extended family of proteins, in the model plant Arabidopsis thaliana. Despite generally low sequence similarity, individual proteins can functionally complement each other over large phylogenetic distances. All these proteins are characterized by a universally conserved Gly-Met-Asn (GMN) motif at the end of the first of two conserved transmembrane domains near the C-terminus. Mutations of the GMN motif are known to abolish Mg(2+) transport, but the naturally occurring variants GVN and GIN may be associated with the transport of other divalent cations, such as zinc and cadmium, respectively. We refer to this whole class of proteins as the 2-TM-GxN type. The functional membrane channel is thought to be formed by oligomers containing four or five subunits. The wealth of sequence data now available allows us to explore the evolutionary diversification of the basic 2-TM-GxN model within the so-called metal ion transporter (MIT) superfamily. Here we report phylogenetic analyses on more than 360 homologous protein sequences derived from genomic sequences from representatives of all three domains of life. Independent gene duplications have occurred in fungi, plants and proteobacteria at different phylogenetic depths. Moreover, there is ample evidence for several instances of horizontal gene transfer of members of the 2-TM-GxN superfamily in Eubacteria and Archaea. Only single genes of the MRS2 type have been identified in vertebrate genomes. In contrast, 15 members are found in the model plant Arabidopsis thaliana, which appear to have arisen by at least four independent founder events before the diversification of flowering plants. Phylogenetic clade assignment seems to correlate with alterations in the highly conserved sequence around the GMN motif. This presumably forms an integral part of the pore surface, and changes in its structure may result in altered transport capacities for different divalent cations.

Amino Acid Motifs↗
PubMed2026

Genome-wide cyclin gene evolution in Arabidopsis and Brassica reveals polyploidization-driven duplication and flowering-time associations.

Cyclin genes are plant cell cycle regulators that play essential roles in growth, development, and reproduction. However, the evolutionary dynamics and genomic organization of cyclin genes across the Brassicaceae family remain poorly understood, particularly in the context of allotetraploid genome evolution. Here, we investigated the diversity, expansion mechanisms, and potential functional diversification of cyclin genes across ten Brassicaceae genomes, including four Arabidopsis and six Brassica species. A total of 1087 cyclin genes representing 23 cyclin types were identified. Comparative genomic analyses revealed that cyclin gene expansion was strongly influenced by polyploidization in Brassica species, with 1845 duplication events involving 1063 genes. Whole-genome duplication was the predominant mechanism driving expansion, while both inter- and intra-genomic duplications contributed to gene retention in tetraploid Brassica species, with the highest duplication frequency observed in Brassica juncea. Across genomes, 120 physical gene clusters were identified, including homogeneous and heterogeneous types. Ortholog analysis between progenitor and allotetraploid species identified 852 orthologous pairs involving 366 genes, indicating extensive conservation following allotetraploid formation. Phylogenetic analysis resolved cyclins into three major clades, while expression-based clustering in Brassica napus grouped genes into four major clusters, suggesting functional diversification. Integration of pan-genomic and flowering-time QTL analyses further identified two cyclin genes, Bna21cycA2 and Bna113cycD4, which contain amino acid polymorphisms and represent putative candidate variations potentially associated with flowering-time variation across multiple genomes. These findings provide new insights into the evolutionary expansion, retention, and potential functional divergence of cyclin genes in Brassicaceae and highlight candidate loci for future functional studies and crop improvement.

Evolution, Molecular↗
PubMed2004

Energy gradients and the geographic distribution of local ant diversity.

Geographical diversity gradients, even among local communities, can ultimately arise from geographical differences in speciation and extinction rates. We evaluated three models--energy-speciation, energy-abundance, and area--that predict how geographic trends in net diversification rates generate trends in diversity. We sampled 96 litter ant communities from four provinces: Australia, Madagascar, North America, and South America. The energy-speciation hypothesis best predicted ant species richness by accurately predicting the slope of the temperature diversity curve, and accounting for most of the variation in diversity. The communities showed a strong latitudinal gradient in species richness as well as inter-province differences in diversity. The former vanished in the temperature-diversity residuals, suggesting that the latitudinal gradient arises primarily from higher diversification rates in the tropics. However, inter-province differences in diversity persisted in those residuals--South American communities remained more diverse than those in North America and Australia even after the effects of temperature were removed.

Animals↗
PubMed2006

Phylogenetic distribution and evolution of mycorrhizas in land plants.

A survey of 659 papers mostly published since 1987 was conducted to compile a checklist of mycorrhizal occurrence among 3,617 species (263 families) of land plants. A plant phylogeny was then used to map the mycorrhizal information to examine evolutionary patterns. Several findings from this survey enhance our understanding of the roles of mycorrhizas in the origin and subsequent diversification of land plants. First, 80 and 92% of surveyed land plant species and families are mycorrhizal. Second, arbuscular mycorrhiza (AM) is the predominant and ancestral type of mycorrhiza in land plants. Its occurrence in a vast majority of land plants and early-diverging lineages of liverworts suggests that the origin of AM probably coincided with the origin of land plants. Third, ectomycorrhiza (ECM) and its derived types independently evolved from AM many times through parallel evolution. Coevolution between plant and fungal partners in ECM and its derived types has probably contributed to diversification of both plant hosts and fungal symbionts. Fourth, mycoheterotrophy and loss of the mycorrhizal condition also evolved many times independently in land plants through parallel evolution.

Biological Evolution↗
PubMed2006

Nucleotide and amino acid mutations in human immunodeficiency virus corresponding to CD4+ decline.

In a meta-analysis, gene sequences of the HIV-1 V3 and surrounding envelope region from studies examining longitudinally derived blood and plasma human immunodeficiency virus forms were analyzed for changes over disease course. CD4+ counts were used as a marker of disease progression; 58 subjects, followed an average of 56 months, were included. Genetic diversification was found early in disease progression. In mid-progression (CD4+ counts dropping from 488 to 329/mm3) diversification did not increase while loop charge dramatically increased. This is consistent with a charged form that dominates and induces disease progression at this critical time. Although the overall mean increase in loop charge was significant, this increase and the transition to amino acids known to change tropism occurred in only half of the subjects who progressed. Those with rapidly progressing disease (within 2 years post-infection) began with a loop charge similar to the end stage of normal progressors. DNA from blood-cell-derived sequences differed from concurrently obtained plasma counterparts by one nucleotide out of 238, but this difference was not reflected in differences in glycosylation patterns, loop charge, or tropism-conferring amino acids. Plasma-derived forms were poorer predictors of future viral forms than were cell-derived sequences.

CD4 Lymphocyte Count↗
PubMed2007

Molecular organization of terminal repetitive DNA in Beta species.

We have isolated families of subtelomeric satellite DNA sequences from species of four sections of the genus Beta and from spinach, a related Chenopodiaceae. Twenty-five clones were sequenced and representative repeats of each family were characterized by Southern blotting and FISH. The families of ApaI restriction satellite repeats were designated pAv34, pAc34, the families of RsaI repeats pRp34, pRn34 and pRs34. The repeating units are 344-362 bp long and 45.7-98.8% homologous with a clear species-specific divergence. Each satellite monomer consists of two subrepeats SR1 and SR2 of 165-184 bp, respectively. The repeats of each subrepeat group are highly identical across species, but share only a homology of 40.8-54.8% with members of the other subrepeat group. Two evolutionary steps could be supposed in the phylogeny of the subtelomeric satellite family: the diversification of an ancestor satellite into groups representing SR1 and SR2 in the progenitor of Beta and Spinacea species, followed by the dimerization and diversification of the resulting 360 bp repeats into section-specific satellite DNA families during species radiation. The chromosomal localization of telomeric, subtelomeric and rDNA tandem repeats was investigated by multi-colour FISH. High-resolution analysis by fibre FISH revealed a unique physical organization of B. vulgaris chromosome ends with telomeric DNA and subtelomeric satellites extending over a maximum of 63 kb and 125 kb, respectively.

Base Sequence↗
PubMed2026

Satellite DNA evolution in Tytonidae (Aves: Strigiformes): dynamic repeat landscapes despite conserved karyotypes.

The elevated chromosome numbers observed in Tytonidae relative to the putative ancestral avian karyotype suggest that lineage-specific chromosomal fissions may have played an important role in the evolutionary history of this family. Here, we provide the first cytogenetic characterization of the American barn owl (Tyto furcata) and performs a comparative repeatome analysis across members of the Tytonidae, including other two species, the Western barn owl (Tyto alba), and the Oriental bay owl (Phodilus badius). The karyotype of T. furcata showed a 2n = 92, closely resembling that previously described for T. alba, indicating a high degree of chromosomal conservation within Tytonidae. Although T. furcata and T. alba exhibit similar karyotypic organization, comparative repeatomic analyses revealed differences in their composition, including variation in satellite DNA (satDNA) repertoires and abundance. Eight satDNA families were identified in T. furcata, nine in T. alba, and 28 in P. badius, highlighting the dynamic evolution of repetitive sequences. Several satDNA families were shared between T. furcata and T. alba, whereas some appeared species-specific, supporting the library hypothesis of satDNA evolution. In P. badius, multiple satDNAs exhibited similarity to transposable elements, suggesting that mobile elements contributed to their diversification. Cytogenetic analyses demonstrated centromeric heterochromatin distribution in T. furcata, as well as a large heterochromatic W chromosome enriched in DNA repeats. The localization of satDNAs in centromeric regions and the apparent accumulation of repeats on the W chromosome reinforce the role of repetitive sequences in chromosome organization and sex chromosome differentiation. Together, these findings reveal repeatome diversification despite conserved macrochromosomal structure and provide new insights into genome evolution and chromosomal dynamics in birds.

Animals↗
PubMed2004

Mapping of the 18S and 5S ribosomal RNA genes in the fish Prochilodus argenteus Agassiz, 1829 (Characiformes, Prochilodontidae).

A single NOR-bearing chromosome pair was identified by silver nitrate staining in a previous study of the fish Prochilodus argenteus from the São Francisco River (MG, Brazil), with a third metacentric chromosome sporadically bearing active NOR. The present study focused on an analysis of the chromosomal localization of both the major (45S) and the minor (5S) rRNA genes using FISH. The use of the 18S rDNA probe confirmed the previous Ag-NOR sites interstitially located in a large metacentric pair and also identified up to three other sites located in the telomeric regions of distinct chromosomes, characterizing an interindividual variation of these sites. In addition, the 5S rDNA site was revealed adjacent to the major NOR site, identified at the end of the large Ag-NOR bearing metacentric chromosome. In a few metaphases, an additional weak hybridization signal was observed in a third chromosome, possibly indicating the presence of another 5S rDNA cluster. Despite a lower karyotype diversification (2n = 54 and FN = 108) often observed among species of Prochilodontidae, variations involving both 45S and 5S rRNA genes could play an important role in their chromosome diversification.

Animals↗
PubMed2005

Rate of chromosome changes and speciation in reptiles.

The chromosome changing rate (i.e. the number of chromosome rearrangements per million years) was studied in 1,329 reptile species in order to evaluate the karyological evolutionary trend and the existence of possible correlations between chromosome mutations and some aspects of the evolution of this class. The results obtained highlight the existence of a general direct correlation between chromosome changing rate and number of living species, although different trends can be observed in the different orders and suborders. In turtles, the separation of pleurodires from cryptodires was accompanied by a considerable karyological diversification. Among pleurodires, the evolution of the Chelidae and Pelomedusidae was also characterised by chromosome variation, while in cryptodires a marked karyological homogeneity is observed between and within infra-orders. Similarly there is no correlation between changing rate and species number in crocodiles, where the evolution of the families and genera has entailed few chromosome mutations. Chromosome variability was greater in lizards and snakes. In the formers variations in chromosome changing rate accompanied the separation of the infra-orders and the evolution of most of the families and of some genera. The origin of snakes has also been accompanied by a marked karyological diversification, while the subsequent evolution of the infra-orders and families has entailed a high level of chromosome variability only in colubroids. The karyological evolution in reptiles generally entailed a progressive reduction in chromosome changing rate, albeit with differences in the diverse orders and suborders. This trend seems to be consistent with the "canalization model" as originally proposed by Bickham and Baker in [Bickham, J.W. & R J. Baker, 1979. Bull. Carnegie Mus. Nat. Hist. 13: 70-84.] However, several inconsistencies have been found excluding that in this class the ultimate goal of chromosome variations was the achievement of a so-called "optimum karyotype'' as suggested by the above-mentioned theory. Other mechanisms could underpin chromosome variability in Reptiles. Among them a genomic composition more or less favourable to promoting chromosome rearrangements and factors favouring the fixation of a mutant karyotype in condition of homozygosis. Turtles and crocodiles would have a genome characterised by large chromosomes and a low level of chromosome compartmentalisation limiting the recombination and the frequency of rearrangements. A low rate of chromosome variability modifying little if at all the gene linkage groups would have favoured a conservative evolutionary strategy. In the course of evolution, lizards and snakes could have achieved a genome characterised by smaller chromosomes and a higher level of compartmentalisation. This would have raised the frequency of recombination and consequently an evolutionary strategy promoting a higher degree of variability and a greater level of speciation.

Animals↗
PubMed2005

Molecular phylogeny and systematics of anoplocephaline cestodes in rodents and lagomorphs.

A molecular phylogenetic hypothesis is presented for the anoplocephaline cestodes of placental mammals based on sequence data from the mitochondrial cytochrome c oxidase I (COI) gene, the nuclear-encoded 28S rRNA gene and the internal transcribed spacer region I of rRNA (ITS1). The material consists of 35 species representing nine genera of cestodes, with emphasis on taxa parasitising rodents and lagomorphs in the Holarctic region. The resulting phylogenies show considerable disagreement with earlier systematic and phylogenetic hypotheses derived from morphology. Specifically, the results contradict the view of uterine morphology being the primary determinant of deeper phylogenetic splits within Anoplocephalinae. Also, the role of genital duplication as a means of generic divergence was not found to follow consistently the pattern suggested by earlier hypotheses. Colonisation of novel host lineages has evidently been the predominant mode of diversification in anoplocephaline cestodes of placental mammals; evidence for phyletic co-evolution was obscure. The phylogenies consistently distinguished a large monophyletic group including all species from arvicoline rodents (voles and lemmings), primarily representing the genera Anoplocephaloides Baer, 1923 and Paranoplocephala Lühe, 1910. Phylogenetic relationships within the "arvicoline clade" of cestodes were generally poorly resolved. Consistent support for nodes above and below the unresolved polytomy indicates a rapid radiation involving a nearly simultaneous diversification of many lineages, a scenario also proposed for the arvicoline hosts.

Animals↗