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PubMed2005

Rapid generation of specific antibodies by enhanced homologous recombination.

In the chicken immune system, gene conversion, a type of homologous recombination, primarily contributes to diversification of the immunoglobulin gene. Here, we report on the rapid generation of specific monoclonal antibodies using the chicken DT40 B-cell line undergoing gene conversion. We discovered that the gene conversion frequency at the immunoglobulin locus is increased by treating DT40 cells with a histone deacetylase inhibitor, trichostatin A (TSA), thereby generating diversity at the immunoglobulin locus in the majority of treated cells. This indicates that TSA treatment accelerates the autonomous diversification of surface IgMs on DT40 cells. We took advantage of this effect to select DT40 cells producing specific antibodies with antigen-conjugated magnetic beads. This autonomously diversifying library (ADLib) selection system enables the quick establishment (approximately 1 week from a diversifying library) of various clones producing monoclonal IgMs with enough specificity and affinity for immunological assays, and is applicable to various biotechnologies including rational protein design.

Animals↗
PubMed2007

Notch signal organizes the Drosophila olfactory circuitry by diversifying the sensory neuronal lineages.

An essential feature of the organization and function of the vertebrate and insect olfactory systems is the generation of a variety of olfactory receptor neurons (ORNs) that have different specificities in regard to both odorant receptor expression and axonal targeting. Yet the underlying mechanisms that generate this neuronal diversity remain elusive. Here we demonstrate that the Notch signal is involved in the diversification of ORNs in Drosophila melanogaster. A systematic clonal analysis showed that a cluster of ORNs housed in each sensillum were differentiated into two classes, depending on the level of Notch activity in their sibling precursors. Notably, ORNs of different classes segregated their axonal projections into distinct domains in the antennal lobes. In addition, both the odorant receptor expression and the axonal targeting of ORNs were specified according to their Notch-mediated identities. Thus, Notch signaling contributes to the diversification of ORNs, thereby regulating multiple developmental events that establish the olfactory map in Drosophila.

Animals↗
PubMed2003

Phylogenomics of the nucleosome.

Histones are best known as the architectural proteins that package the DNA of eukaryotic organisms, forming octameric nucleosome cores that the double helix wraps tightly around. Although histones have traditionally been viewed as slowly evolving scaffold proteins that lack diversification beyond their abundant tail modifications, recent studies have revealed that variant histones have evolved for diverse functions. H2A and H3 variants have diversified to assume roles in epigenetic silencing, gene expression and centromere function. Such diversification of histone variants and 'deviants' contradicts the perception of histones as monotonous members of multigene families that indiscriminately package and compact the genome. How these diverse functions have evolved from ancestral forms can be addressed by applying phylogenetic tools to increasingly abundant sequence data.

Amino Acid Sequence↗
PubMed2026

Comparative mitogenomics of Ocnus glacialis reveals lineage-specific evolutionary rates and complex gene rearrangements in Dendrochirotida.

The order Dendrochirotida (Class Holothuroidea) is a species-rich echinoderm group, yet its internal evolutionary history remains poorly resolved due to limited mitogenomic resources. In this study, we characterized the first complete mitochondrial genome of Ocnus glacialis and conducted comparative analyses to elucidate its phylogenetic position and molecular evolutionary patterns. The circular mitogenome of O. glacialis is 16,776 bp in length, containing the canonical set of 37 genes. Among the analyzed dendrochirotids, O. glacialis exhibited the highest A + T content (70.88%) and a near-zero AT-skew, a compositional profile often linked to lineage-specific evolution in specialized environments. Selection pressure analyses, including branch-model tests, revealed that these compositional features are associated with relaxed purifying selection and an accelerated rate of sequence evolution. Branch-site analyses further identified specific codon sites in cytb, nad2, nad4l, nad5, and nad6 under positive or relaxed constraints. Structurally, O. glacialis displayed the most complex gene rearrangement pattern among the studied species, characterized by multiple tandem duplication-random loss (TDRL) events and extensive intergenic sequences. Furthermore, divergence time estimation suggests that these structural and compositional shifts occurred in tandem with the lineage's diversification. We propose that these mitogenomic signatures reflect a synergistic outcome of habitat transition toward Arctic cold-water and deep-sea environments, coupled with demographic factors such as reduced effective population sizes inherent to its benthic life history. By resolving taxonomic uncertainties, this study provides a robust temporal and molecular framework for understanding the evolutionary history and ecological diversification of the Ocnus lineage.

Animals↗
PubMed2006

Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice.

To understand the expansion of multicopy microRNA (miRNA) families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miR160 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

Arabidopsis↗
PubMed2005

Rapid recent radiation of S-RNase lineages in Witheringia solanacea (Solanaceae).

Strong frequency-dependent selection as found in the self-incompatibility loci of flowering plants maintains allelic lineages for extremely long time scales, such that allelic genealogies can shed insight into long-term demographic patterns of species. Effective mutation rate, as well as demographic change such as population bottlenecks, can influence genealogical structure. In addition, loss of functionality at the self-incompatibility locus is likely to affect radiation rates. Partial sequences for 21 S-RNase alleles of the mid-elevation tropical species Witheringia solanacea were obtained in order to compare their substitution rates and genealogy with those of Witheringia maculata and two species in the closely related genus Physalis. Sequences for W. solanacea fell into the three clades within the Solanaceae already identified for the genus. Terminal branch lengths for W. solanacea, scaled to the total depth of its phylogeny, were intermediate between the unusually short terminal branches of W. maculata and those of the two Physalis species. In contrast to the Physalis species, where interspecific dN/dS for closely related alleles exceeded 1.0 to the same degree as did intraspecific dN/dS, in Witheringia only intraspecific comparisons showed an excess of nonsynonymous substitutions, suggesting postspeciation radiation of alleles. Alleles associated with lowered S-RNase production and self-compatibility showed extremely short terminal branches. In summary, it appears that rapid recent diversification of alleles characterizes the Witheringia lineages. In some cases, this rapid diversification can be attributed to relaxed constraints due to breakdown of self-incompatibility.

Alleles↗
PubMed2006

Heliconius wing patterns: an evo-devo model for understanding phenotypic diversity.

Evolutionary Developmental Biology aims for a mechanistic understanding of phenotypic diversity, and present knowledge is largely based on gene expression and interaction patterns from a small number of well-known model organisms. However, our understanding of biological diversification depends on our ability to pinpoint the causes of natural variation at a micro-evolutionary level, and therefore requires the isolation of genetic and developmental variation in a controlled genetic background. The colour patterns of Heliconius butterflies (Nymphalidae: Heliconiinae) provide a rich suite of naturally occurring variants with striking phenotypic diversity and multiple taxonomic levels of variation. Diversification in the genus is well known for its dramatic colour-pattern divergence between races or closely related species, and for Müllerian mimicry convergence between distantly related species, providing a unique system to study the development basis of colour-pattern evolution. A long history of genetic studies has showed that pattern variation is based on allelic combinations at a surprisingly small number of loci, and recent developmental evidence suggests that pattern development in Heliconius is different from the eyespot determination of other butterflies. Fine-scale genetic mapping studies have shown that a shared toolkit of genes is used to produce both convergent and divergent phenotypes. These exciting results and the development of new genomic resources make Heliconius a very promising evo-devo model for the study of adaptive change.

Animals↗
PubMed1998

Antigen receptor signaling: integration of protein tyrosine kinase functions.

Antigen receptors on T and B cells function to transduce signals leading to a variety of biologic responses minimally including antigen receptor editing, apoptotic death, developmental progression, cell activation, proliferation and survival. The response to antigen depends upon antigen affinity and valence, involvement of coreceptors in signaling and differentiative stage of the responding cell. The requirement that these receptors integrate signals that drive an array of responses may explain their evolved structural complexity. Antigen receptors are composed of multiple subunits compartmentalized to provide antigen recognition and signal transduction function. In lieu of on-board enzymatic activity these receptors rely on associated Protein Tyrosine Kinases (PTKs) for their signaling function. By aggregating the receptors, and hence their appended PTKs, antigens induce PTK transphosphorylation, activating them to phosphorylate the receptor within conserved motifs termed Immunoreceptor Tyrosine-based Activation Motifs (ITAMs) found in transducer subunits. The tyrosyl phosphorylated ITAMs then interact with Src Homology 2 (SH2) domains within the PTKs leading to their further activation. As receptor phosphorylation is amplified, other effectors, such as Shc, dock by virtue of SH2 binding, and serve, in-turn, as substrates for these PTKs. This sequence of events not only provides a signal amplification mechanism by combining multiple consecutive steps with positive feedback, but also allows for signal diversification by differential recruitment of effectors that provide access to distinct parallel downstream signaling pathways. The subject of antigen receptor signaling has been recently reviewed in depth (DeFranco, 1997; Kurosaki, 1997). Here we discuss the biochemical basis of antigen receptor signal transduction, using the B cell receptor (BCR) as a paradigm, with specific emphasis on the involved PTKs. We review several specific mechanisms by which responses through these receptors are propagated and modified by accessory molecules, and discuss how signal amplification and diversification are achieved.

Agammaglobulinaemia Tyrosine Kinase↗
PubMed1999

Molecular phylogeny of the ETS gene family.

We have constructed a molecular phylogeny of the ETS gene family. By distance and parsimony analysis of the ETS conserved domains we show that the family containing so far 29 different genes in vertebrates can be divided into 13 groups of genes namely ETS, ER71, GABP, PEA3, ERG, ERF, ELK, DETS4, ELF, ESE, TEL, YAN, SPI. Since the three dimensional structure of the ETS domain has revealed a similarity with the winged-helix-turn-helix proteins, we used two of them (CAP and HSF) to root the tree. This allowed us to show that the family can be divided into five subfamilies: ETS, DETS4, ELF, TEL and SPI. The ETS subfamily comprises the ETS, ER71, GABP, PEA3, ERG, ERF and the ELK groups which appear more related to each other than to any other ETS family members. The fact that some members of these subfamilies were identified in early metazoans such as diploblasts and sponges suggests that the diversification of ETS family genes predates the diversification of metazoans. By the combined analysis of both the ETS and the PNT domains, which are conserved in some members of the family, we showed that the GABP group, and not the ERG group, is the one most closely related to the ETS group. We also observed that the speed of accumulation of mutations in the various genes of the family is highly variable. Noticeably, paralogous members of the ELK group exhibit strikingly different evolutionary speed suggesting that the evolutionary pressure they support is very different.

Amino Acid Sequence↗
PubMed2000

Genetics of adaptive radiation in Hawaiian species of Tetramolopium (Asteraceae). III. Evolutionary genetics of sex expression.

Despite numerous studies of speciation on oceanic islands, few insights exist on the genetic changes involved in the origin and diversification of island taxa. Here we report a genetic analysis of the evolutionary change in sex expression in Hawaiian Tetramolopium. The most diverse clade in the genus is characterized by a monoecious breeding system. The breeding system resulted from a change in sex expression in disc florets from the ancestral hermaphroditic condition to the derived male state. Analysis of an F2 population from a cross between the two forms of sex expression indicates two regions of the Tetramolopium linkage map are associated with the loss of female function in disc florets. Quantitative trait locus mapping of the two linkage groups confirms that two loci control 56% of the phenotypic variation of the trait in the F2 population. Additive and dominance effects are apparent but no statistical evidence of epistasis was found. Several related reproductive traits also have few genetic associations on the linkage map, but are generally distinct from the control of sex expression. Although modifier loci are likely to be involved, the apparent simple genetic change underlying sex expression parallels a major evolutionary diversification in Hawaiian Tetramolopium and may have initiated the divergence of this novel clade.

Adaptation, Biological↗
PubMed1998

Speciation and phylogeography of Hawaiian terrestrial arthropods.

The Hawaiian archipelago is arguably the world's finest natural laboratory for the study of evolution and patterns of speciation. Arthropods comprise over 75% of the endemic biota of the Hawaiian Islands and a large proportion belongs to species radiations. We classify patterns of speciation within Hawaiian arthropod lineages into three categories: (i) single representatives of a lineage throughout the islands; (ii) species radiations with either (a) single endemic species on different volcanoes or islands, or (b) multiple species on each volcano or island; and (iii) single widespread species within a radiation of species that exhibits local endemism. A common pattern of phylogeography is that of repeated colonization of new island groups, such that lineages progress down the island chain, with the most ancestral groups (populations or species) on the oldest islands. While great dispersal ability and its subsequent loss are features of many of these taxa, there are a number of mechanisms that underlie diversification. These mechanisms may be genetic, including repeated founder events, hybridization, and sexual selection, or ecological, including shifts in habitat and/or host affiliation. The majority of studies reviewed suggest that natural selection is a primary force of change during the initial diversification of taxa.

Animals↗
PubMed2001

Speciation in rapidly diverging systems: lessons from Lake Malawi.

Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand- and rock-dwellers, each adapted to a major benthic macrohabitat. Among the rock-dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.

Africa, Eastern↗
PubMed2001

Extensive trans-species mitochondrial polymorphisms in the carabid beetles Carabus subgenus Ohomopterus caused by repeated introgressive hybridization.

To study the potential importance of introgressive hybridization to the evolutionary diversification of a carabid beetle lineage, we studied intraspecific and trans-species polymorphisms in the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequence (1083 bp) in four species of the subgenus Ohomopterus (genus Carabus) in central and eastern Honshu, Japan. Of the four species, C. insulicola is parapatric with the other three, and can hybridize naturally with at least two. This species possesses two haplotypes of remote lineages. We classified ND5 haplotypes using polymerase chain reaction-restriction fragment length polymorphism with TaqI endonuclease for 524 specimens, and sequenced 143 samples. Analysis revealed that each species was polyphyletic in its mitochondrial DNA phylogeny, representing a marked case of trans-species polymorphism. Recent one-way introgression of mitochondria from C. arrowianus nakamurai to C. insulicola, and from C. insulicola to C. esakii, was inferred from the frequency of identical sequences between these species and from direct evidence of hybridization in their contact zones. Other intraspecific polymorphisms in the four species may be due to undetected introgressive hybridization (e.g. C. insulicola to C. maiyasanus) or from stochastic lineage sorting of ancestral polymorphisms. This beetle group has a genital lock-and-key system, with species-specific or subspecies-specific genital morphology that may act as a barrier to hybridization. However, our results demonstrate that introgressive hybridization has occurred multiple times, at least for mitochondria, despite differences among, and stability within, morphological characters that distinguish local populations. Thus, hybridization and introgression could have been key processes in the evolutionary diversification of Ohomopterus.

Animals↗
PubMed2003

Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history.

Duplicated genes are important in the evolution and ecology of plant-defences because herbivore and pathogen attack can be countered via functional diversification at two levels: among duplicated loci and within loci. We explore molecular sequence variation for two members of a defence-related gene family, Arabidopsis thaliana trypsin inhibitors (ATTI), in A. thaliana and a closely related species, A. lyrata subspp. petraea. A worldwide sample of the inbreeding annual A. thaliana had less genetic variation at two ATTI loci (piTOTAL <or= 0.0006) than observed previously at other functional loci. A significant excess of high frequency derived alleles in the signal sequence and 5' UTR of ATTI2 was consistent with a model of positive selection. However, demographic processes such as population subdivision and expansion, both likely to have occurred in A. thaliana during the last 10 000 years, can also give rise to similar deviations from neutrality. A single population of A. lyrata subspp. petraea in Germany had up to an order of magnitude more standing genetic variation at ATTI loci than the species-wide sample of A. thaliana. Although the level of variability for ATTI1 and ATTI2 within this single population was similar to, or even greater than, observed species-wide diversity for other loci in A. lyrata, there was little evidence to reject an equilibrium neutral model. A spatially explicit sample of 87 A. lyrata subspp. petraea individuals detected outbreeding (FIS = -0.16; FIT = -0.15) but little population subdivision (FST = 0.006) in this self-incompatible perennial herb. Genetic differences between Arabidopsis species were consistent with, but not fully explained by, divergence in ecology and life history. Diversification appears to have occurred in different functional domains for the tandemly duplicated ATTI1 and ATTI2 genes; the majority of fixed replacements in ATTI1 surround the enzyme binding site of the mature protein, whereas in ATTI2 most functional evolutionary change is located in the signal peptide. This pattern is consistent with a hypothesis of subfunctionalization in trypsin inhibitory function.

Arabidopsis↗
PubMed2003

Comparative phylogeography of short-tailed bats (Carollia: Phyllostomidae).

This is the first study of comparative phylogeography involving closely related species of Neotropical bats of the family Phyllostomidae. We compared patterns of geographical variation within the five species of fruit-eating bats currently recognized in the genus Carollia using the complete mitochondrial cytochrome-b gene. Our results suggest that the combined effect of the uplift of the Andes and the Panamanian land bridge has been as important for bats as for terrestrial mammals in shaping present-day biodiversity in the New World tropics. Species in this genus can be arranged in two highly supported clades, with a deep subdivision within each that corresponds well to differences across the Andes. We found three congruent phylogeographical patterns across species in this genus. First, the closer relationship between samples from western Ecuador and those from Central America, compared with populations east of the Andes in C. brevicauda, C. castanea and C. perspicillata. Second, the likelihood of a similar timing in South America for the arrival and diversification of C. brevicauda and C. perspicillata from their Central America ancestors. Third, the expansion of C. perspicillata and C. sowelli into northwestern Central America in the relatively recent past. Using a molecular clock, with rates ranging from 2.3 to 5% per 10(6) years, diversification within Carollia would have occurred over the last 1-4.5 Myr. These estimates agree well with the last rise of the Northern Andes and the Panama isthmus.

Animals↗
PubMed2004

Ecological and morphological patterns in communities of land snails of the genus Mandarina from the Bonin Islands.

The land snail genus Mandarina has undergone extensive radiation within the Bonin Islands in the west Pacific. The preferred above-ground vegetation heights of sympatric species were clearly different. They separated into arboreal, semi-arboreal, exposed ground and sheltered ground ecotypes. Shells of species with different ecotypes differ markedly, but shells of species with the same ecotype are very similar to each other. Shell morphologies of some phylogenetically distantly related species with the same ecotype were indistinguishable. Character evolution estimated parsimoniously using a phylogenetic tree suggests that the speciation among sympatric species is accompanied by ecological and morphological diversification. In addition, species coexistence of Mandarina is related to niche differentiation. The above findings suggest that ecological interactions among species contribute to the ecological and morphological diversification and radiation of these land snails in this depauperate environment.

Animal Structures↗
PubMed2002

Asian migration to Australia: food and health consequences.

Australia's food and health patterns are inextricably and increasingly linked with Asia. Indigenous Australians arrived in the continent via Asia and have linguistic connections with people who settled in south India; there was interaction and food trade between both South-East Asia and China and northern indigenous Australians over thousands of years. After European settlement in 1788, there have been several and increasing (apart from the period of the infamous White Australian Policy following the Colonial period and Independence, with Federation, in 1901) waves of Asian migration, notably during the gold rush (Chinese), the building of the overland Telegraph (Afghans), the Colombo Plan and Asian student education in Australia from the 1950s onwards (South-Eeast Asians), and with refugees (Vietnamese and mainland Chinese), and business (late twentieth century) and progressive family reunion. Each wave has injected additional food cultural elements and caused a measure of health change for migrants and host citizens. Of principal advantage to Australia has been the progressive diversification of the food supply and associated health protection. This has increased food security and sustainability. The process of Australian eating patterns becoming Asianized is evident through market garden development (and the introduction of new foods), fresh food markets and groceries, restaurants and the development of household cooking skills (often taught by student boarders). Most of the diversification has been with grain (rice), legumes (soy), greens, root vegetables, and various 'exotic fruits'. Food acculturation with migration is generally bi-directional. Thus, for Asians in Australia, there has been a decrease in energy expenditure (and a lower plane of energy throughput), an increase in food energy density (through increased fat and sugary drink intakes), and a decrease in certain health protective foods (lentils, soy, greens) and beverages (tea). This sets the stage for 'eco-diseases'. In a population probably genetically programmed (but modifiably) in utero to abdominal obesity, diabetes (type II and gestational) and cardiovascular disease, these conditions may be rapidly acquired on migration, along with certain cancers (breast, colo-rectal and prostate). Thus, whilst Asian migration to Australia has provided health opportunities for host citizens, there have been threats to migrant citizens in regard to nutrition-related health.

Acculturation↗
PubMed2001

Molecular correlates in AIDS patients following antiretroviral therapy: diversified T-cell receptor repertoires and in vivo control of cytomegalovirus replication.

OBJECTIVES: To evaluate whether successful, long-term immune reconstitution in vivo can be achieved in end-stage AIDS patients following antiretroviral therapy (ART). METHODS: A 1-year prospective study of changes of CD4+ and CD8+ T-cell surface phenotypes, T-cell receptor (TCR) repertoires and capacity to control in vivo replication of cytomegalovirus (CMV) was performed in five treatment-naive end-stage AIDS patients (median CD4+ T-cell counts of 19 cells/microL) following therapy. Proportions of CD45RA+, CD45RO+ and CD28+ cells within the CD4+ and CD8+ subsets, were determined by flow cytometry. Changes in TCR Vbeta repertoires within the CD4+ and CD8+ T-cell compartments were evaluated using CDR3 spectratyping. CMV replication was determined by a sensitive polymerase chain reaction (PCR) assay using whole blood. RESULTS: Following ART, proportionate increases in 'naive' (CD45RA+) and 'memory' (CD45RO+) T cells were observed within both CD4+ and CD8+ T-cell subsets, while increased numbers of CD28+ T cells were mainly observed within the CD4+ subset. Diversification of CD4+ and CD8+ TCR repertoires was established concomitantly with renewed in vivo control of CMV replication. CONCLUSIONS: An important degree of molecular and functional immune recovery is possible in end-stage AIDS patients introduced to therapy. Diversification of TCR repertoires and the in vivo restoration of immunocompetence to control opportunistic infections clearly show that an important degree of molecular immune reconstitution is established following the initiation of ART even in late-stage AIDS.

ATP-Binding Cassette Transporters↗