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PubMed2005

Evolutionary history of the synbranchid eels (Teleostei: Synbranchidae) in Central America and the Caribbean islands inferred from their molecular phylogeny.

Swamp eels of the genera Synbranchus and Ophisternon are secondary freshwater fishes whose biogeography provides evidence of their long residence in Mesoamerica, while their impoverished species-level taxonomy might suggest a more recent diversification or a conservative morphology. We have inferred the phylogenetic relationships of Synbranchus marmoratus and Ophisternon aenigmaticum from 45 drainages throughout South, Central America, and Cuba based on mitochondrial genes (cytochrome b and ATPase 8/6). Phylogeographic analysis supported the monophyly of Mesoamerican O. aenigmaticum although our results suggest that S. marmoratus is not a monophyletic group. We found a evolutionary differentiated Synbranchus mtDNA lineage inhabiting Las Perlas islands (Pacific Panama) that appeared to be taxonomically distinct and separated for a long period of time from the main Synbranchus clade. Major synbranchid clades were also corroborated with the nuclear RAG-1 gene (1171-bp). Application of two fish-based mtDNA clocks (1.05-1.3% pairwise divergence/million year (Ma)), is in accordance with the Gondwanian origin suggested for the Synbranchidae. The mtDNA lineages exhibited a remarkable geographic structure in Central America suggesting that vicariance has most likely promoted the Synbranchus and Ophisternon mtDNA diversification. Although our data indicate the importance of the Pacific area in Synbranchus differentiation, the mtDNA divergence between South and Central American Synbranchus is too small to support Cretaceous colonization via the proto-Antillean bridge suggested by Rosen [Syst. Zool. 24 (1976) 431]. Instead, our phylogeographic results suggest that Ophisternon and Synbranchus mtDNA clades most likely colonized Central America during the Miocene (12.7-23Ma) prior the final closure of the Isthmus of Panama (3.3Ma).

Adenosine Triphosphatases↗
PubMed2005

Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans.

Studies of Neotropical birds, and their distributions and areas of endemism, in particular, have been central in the formulation of hypotheses proposed to explain the high species diversity in the Neotropics. We used mtDNA sequence data (ATPase 6 and 8, COI, and cyt b) to reconstruct the species-level phylogenies for two genera, Pionopsitta (Aves: Psittacidae) and Pteroglossus (Aves: Ramphastidae), compare our results with previous morphology-based phylogenetic analyses, and estimate the absolute timing of lineage and biogeographic divergences. Both the Pionopsitta and Pteroglossus phylogenies support a hypothesis of area relationships in which a divergence of the Serra do Mar (Atlantic Forest, Brazil) region of endemism is followed by the divergence of cis- and trans-Andean regions, then a split between the upper and lower Amazon basin, next the divergence of the Guyana area, and finally diversification of taxa in the upper Amazon basin's areas of endemism. Phylogenies of both genera support a hypothesis of area relationships that is similar to that proposed by Prum [XIX International Ornithological Congress (1988), 2562] for high-vagility species, but while they agree on the relative timing of area divergence (vicariance) events, they yield different absolute time estimates for those divergences when the typical avian mtDNA clock calibration is used. Taken at face value, the time estimates indicate that both genera began to diversify before the start of the Pleistocene, and that climatic and habitat shifts alone do not account for the diversification of these taxa.

Animals↗
PubMed2005

Biogeography and divergence times in the mulberry family (Moraceae).

The biogeographical history of the mulberry family (Moraceae) was investigated using phylogenetic inferences from nuclear and chloroplast DNA, molecular dating with multiple fossil calibrations, and independent geological evidence. The Moraceae are centered in the tropics which has invited the hypothesis that the family has Gondwanan origins and extant distribution is the result of vicariance due to the break-up of Gondwana. However, the cosmopolitan distribution of Moraceae suggests a more complicated biogeographical history. The timing and location of Moraceae diversification also bears on the origin of the fig pollination mutualism, a model for the study of coevolution and specialization. Recent molecular dating of pollinating fig wasps suggested that an ancient Gondwanan origin coupled with vicariance and dispersal could account for the present day distribution of the mutualism. Here, we provide the first assessment of this hypothesis based on dating of figs and their relatives. Minimum age estimates suggest that the Moraceae had diversified by at least the mid-Cretaceous and major clades including the figs may have radiated during the Tertiary after the break-up of Gondwanaland. Molecular evidence together with Eurasian fossils suggest that the early diversification of Moraceae in Eurasia and subsequent migration into the southern hemisphere is at least as plausible as the Gondwanan hypothesis. These findings invite a reevaluation of the biogeography of fig pollination and highlight the need for incorporating multiple sources of evidence in biogeographical reconstructions.

Cell Nucleus↗
PubMed2006

Hybrid origin of the Pliocene ancestor of wild goats.

Recent theories on speciation suggest that interspecific hybridization is an important mechanism for explaining adaptive radiation. According to this view, hybridization can promote the rapid transfer of adaptations between different species; the hybrid population thus invades new habitats and diversifies into a variety of new species. Although hybridization is well accepted as a fairly common mechanism for diversification in plants, its role in the evolution of animals is more controversial, because reduced fitness would typically condemn animal hybrids to an evolutionary dead-end. Here, we examine DNA sequences of four mitochondrial and four nuclear genes selected for resolving phylogenetic relationships between goats, sheep, and their allies. Our analyses provide evidence of strong discordance for the position of Capra between mitochondrial and nuclear phylogenies. We suggest that the common ancestor of wild goats arose from interspecific hybridization, and that the mitochondrial genome of a species better adapted to life at high altitudes was transferred via this route into the common ancestor of Capra. We propose that the acquisition of more efficient mitochondria has conferred a selective advantage on goats, allowing their rapid adaptive radiation during the Plio-Pleistocene epoch. Our study therefore agrees with theories that predict an important role for interspecific hybridization in the evolution and diversification of animal species.

Altitude↗
PubMed2006

Evolution of host specialization in the Adelgidae (Insecta: Hemiptera) inferred from molecular phylogenetics.

The Adelgidae form a small group of insects in the Aphidoidea. They are cyclically parthenogenetic with host alternating, multiple-generation complex life cycles and are restricted to certain host genera in the Pinaceae. Species that host alternate always have Picea as the primary host where sexual reproduction and gall formation occur, and another genus in the Pinaceae as the secondary host where a series of parthenogenetic generations are produced. Other species that do not host alternate complete their entire life cycle on one host and only reproduce parthenogenetically. We studied relationships within Adelgidae using DNA sequences from the mitochondrial COI, COII, and cytb genes, and the nuclear EF1alpha gene. Analysis of the combined data resulted in a well-resolved phylogeny in which the major adelgid clades correspond neatly to their association with secondary host genera. Specialization on each secondary host genus occurred only once and was followed by diversification on the host genus. Molecular dating of divergence times in the Adelgidae suggest that diversification among host genera occurred in the Late Cretaceous and Early Tertiary when the Pinaceae genera were diverging. It is not clear, however, whether the Adelgidae and Pinaceae co-diversified because the relationships among the Pinaceae genera are not fully resolved. We discuss implications for adelgid taxonomy, life cycle evolution, and evolution of the interaction between adelgids and their host plants.

Animals↗
PubMed2003

Why are parasite contingency genes often associated with telomeres?

Contingency genes are common in pathogenic microbes and enable, through pre-emptive mutational events, rapid, clonal switches in phenotype that are conducive to survival and proliferation in hosts. Antigenic variation, which is a highly successful survival strategy employed by eubacterial and eukaryotic pathogens, involves large repertoires of distinct contingency genes that are expressed differentially, enabling evasion of host acquired immunity. Most, but not all, antigenic variation systems make extensive use of subtelomeres. Study of model systems has shown that subtelomeres have unusual properties, including reversible silencing of genes mediated by proteins binding to the telomere, and engagement in ectopic recombination with other subtelomeres. There is a general theory that subtelomeric location confers a capacity for gene diversification through such recombination, although experimental evidence is that there is no increased mitotic recombination at such loci and that sequence homogenisation occurs. Possible benefits of subtelomeric location for pathogen contingency systems are reversible gene silencing, which could contribute to systems for gene switching and mutually exclusive expression, and ectopic recombination, leading to gene family diversification. We examine, in several antigenic variation systems, what possible benefits apply.

Animals↗
PubMed1998

Antigenic variation and the murine immune response to Giardia lamblia.

The protozoan parasite Giardia lamblia is an important causative agent of acute or chronic diarrhoea in humans and various animals. During infection, the parasite survives the host's reactions by undergoing continuous antigenic variation of its major surface antigen, named VSP (variant surface protein). The VSPs form a unique family of cysteine-rich proteins that are extremely heterogeneous in size. The relevance of antigenic variation for the survival in the host has been most successfully studied by performing experimental infections in a combined mother/offspring mouse system and by using the G. lamblia clone GS/M-83-H7 (human isolate) as model parasite. In-vivo antigenic variation of G. lamblia clone GS/M-83-H7 is characterised by a diversification of the intestinal parasite population into a complex mixture of different variant antigen types. It could be shown that maternally transferred lactogenic anti-VSP IgA antibodies exhibit cytotoxic activity on the Giardia variant-specific trophozoites in suckling mice, and thus express a modulatory function on the proliferative parasite population characteristics. Complementarily, in-vitro as well as in-vivo experiments in adult animals indicated that non-immunological factors such as intestinal proteases may interfere into the process of antigen variation in that they favour proliferation of those variant antigen-type populations which resist the hostile physiological conditions within the intestine. These observations suggest that an interplay between immunological and physiological factors, rather than one of these two factor alone, modulates antigenic diversification of a G. lamblia population within an experimental murine host and thus influences the survival rate and strategy of the parasite.

Animals↗
PubMed2005

Isoforms of terminal deoxynucleotidyltransferase: developmental aspects and function.

The immune system develops in a series of programmed developmental stages. Although recombination-activating gene (RAG) and nonhomologous end-joining (NHEJ) proteins are indispensable in the generation of immunoglobulins and T-cell receptors (TCRs), most CDR3 diversity is contributed by nontemplated addition of nucleotides catalyzed by the nuclear enzyme terminal deoxynucleotidyltransferase (TdT) and most nucleotide deletion is performed by exonucleases at V(D)J joins. Increasing TdT expression continuing into adult life results in N region addition and diversification of the T and B cell repertoires. In several species including mice and humans, there are multiple isoforms of TdT resulting from alternative mRNA splicing. The short form (TdTS) produces N additions during TCR and B-cell receptor (BCR) gene rearrangements. Other long isoforms, TdTL1 and TdTL2, have 3' --> 5' exonuclease activity. The two forms of TdT therefore have distinct and opposite functions in lymphocyte development. The enzymatic activities of the splice variants of TdT play an essential role in the diversification of lymphocyte repertoires by modifying the composition and length of the gene segments involved in the production of antibodies and T-cell receptors.

Alternative Splicing↗
PubMed1997

Immunoglobulin VH gene replacements in a T-cell lymphoblastic lymphoma.

We have analysed the rearrangement status of the immunoglobulin heavy (IgH) chain locus during progression of a T-cell lymphoblastic lymphoma displaying multiple IgH rearrangements as demonstrated by variable heavy (VH) gene family specific polymerase chain reaction (PCR) analysis. The tumor was found to undergo diversification at the IgH locus between diagnosis and relapse through a mechanism of VH to VHDJH replacement. In subsets of the tumor at relapse, two separate VH gene segments were found to have replaced the VH gene utilized by a VHDJH rearrangement identified at diagnosis. The observed VH gene replacement events appear to have been mediated by a heptamer sequence homologous to the heptamer of the recombination signal sequence (RSS) located internally in the VH gene segment. These results support the notion that VH replacements contribute to the diversification of immunoglobulin genes.

Adult↗
PubMed1999

Gene-conversion in rabbit B-cell ontogeny and during immune responses in splenic germinal centers.

Combinatorial diversity is limited in rabbits because only a few V(H) genes rearrange. Most diversification of the primary repertoire is generated by somatic hypermutation and gene conversion-like changes of rearranged V(H) in B cells that migrate to appendix and other gut associated lymphoid tissues (GALT) of young rabbits. The changes are referred to as gene conversion-like because the non-reciprocal nature of the alterations introduced has not yet been demonstrated. There are many similarities between rabbits and chickens in how their B cells develop and diversify their repertoires. However, although the majority of rabbit B cells may have rearranged and diversified their V genes early in life, some B cells in adult rabbits have rearranged VH sequences that are identical or nearly identical to germline sequences. We found these cells in splenic germinal centers (GC) on days 7 and 10 after immunization of normal adult rabbits with DNP-BGG. By day 15, all rearranged V(H) sequences were diversified. We find an overall pattern of splenic precursor cells whose germline or near germline sequences change both by gene conversion and point mutations during early divisions and mainly by point mutations during later divisions. These events, in parallel with diversification of light chain sequences, may produce the diverse combining sites that serve as substrates for further affinity maturation by selection either within GC or later among emigrant cells in sites such as bone marrow. Some of the sequences altered by gene conversion in splenic germinal centers may also produce new members of the B-cell repertoire in adult rabbits comparable to those produced in GALT of neonatal rabbits.

Animals↗
PubMed2001

Correlated patterns of neuron differentiation and Hox gene expression in the hindbrain: a comparative analysis.

Hindbrain neurons are organized into coherent subpopulations with characteristic projection patterns and functions. Many of these serve vital functions that have been conserved throughout the vertebrate radiation, but diversification to modified or highly specialized functions has also occurred. The differentiation of identifiable neuron groups in specific spatial domains must involve the regional expression of determinants within the hindbrain neuroepithelium. The Hox genes are involved in longitudinal regionalization of the neural tube, and their expression patterns in the hindbrain are closely related to the rhombomeres which partition the hindbrain into morphogenetic units. Hox gene expression also exhibits conserved patterning as well as phylogenetic variation. One plausible mechanism that may have contributed to evolutionary diversification in hindbrain neuron populations is therefore the emergence of species-specific differences in Hox gene expression. This article presents a comparative overview of the regional patterning of selected Hox genes and hindbrain neuron populations in several embryologically important species. Although tantalizing correlations exist, the relationship between Hox genes and neuronal patterning is complex, and complicated by dynamic features in each. Much more comparative and developmental data must be obtained before the link between Hox gene expression and hindbrain neuron patterning can be elucidated satisfactorily in an evolutionary context.

Animals↗
PubMed2000

The family of light-harvesting-related proteins (LHCs, ELIPs, HLIPs): was the harvesting of light their primary function?

Light-harvesting complex proteins (LHCs) and early light-induced proteins (ELIPs) are essential pigment-binding components of the thylakoid membrane and are encoded by one of the largest and most complex higher plant gene families. The functional diversification of these proteins corresponded to the transition from extrinsic (phycobilisome-based) to intrinsic (LHC-based) light-harvesting antenna systems during the evolution of chloroplasts from cyanobacteria, yet the functional basis of this diversification has been elusive. Here, we propose that the original function of LHCs and ELIPs was not to collect light and to transfer its energy content to the reaction centers but to disperse the absorbed energy of light in the form of heat or fluorescence. These energy-dispersing proteins are believed to have originated in cyanobacteria as one-helix, highly light-inducible proteins (HLIPs) that later acquired four helices through two successive gene duplication steps. We suggest that the ELIPs arose first in this succession, with a primary function in energy dispersion for protection of photosynthetic pigments from photo-oxidation. We consider the LHC I and II families as more recent and very successful evolutionary additions to this family that ultimately attained a new function, thereby replacing the ancestral extrinsic light-harvesting system. Our model accounts for the non-photochemical quenching role recently shown for higher plant psbS proteins.

Evolution, Molecular↗
PubMed2001

Characterization of three GLOBOSA-like MADS-box genes from maize: evidence for ancient paralogy in one class of floral homeotic B-function genes of grasses.

Floral homeotic B-function genes are involved in specifying the identity of petals and stamens during flower development in higher eudicotyledonous plants. Monocotyledonous plants belonging to the grass family (Poaceae) have very similar B-function genes, except that these genes specify lodicules rather than petals. All B-function genes known so far are members of the MADS-box gene family encoding transcription factors. In some eudicot model systems such as Arabidopsis and Antirrhinum, the B-function is provided by heterodimeric protein complexes encoded by one DEF- and one GLO-like gene. In several different lineages of flowering plant species, however, more than one DEF- or GLO-like gene is found. A known example is the monocot model system rice, which contains two GLO-like genes, termed OSMADS2 and OSMADS4. Duplications of floral homeotic genes may have played a critical role in the diversification of floral homeotic functions and thus the evolution of flowers. In order to date the gene duplication event that gave rise to these two genes, we cloned cDNAs of three different GLO-like genes from maize, a distant relative of rice within the Poaceae family. Phylogeny reconstructions and chromosomal mapping indicate that one of these genes, named ZMM16, is orthologous to OSMADS2, and that the other two, ZMM18 and ZMM29, are probably orthologous to OSMADS4. The gene duplication which gave rise to OSMADS2- and OSMADS4-like genes occurred probably after the split of the lineages that resulted in extant Liliaceae and Poaceae, but before the separation of the lineages that gave rise to extant maize and rice about 50 MYA. Northern and in situ hybridization studies demonstrated that the maize genes are expressed in lodicules, stamens and carpels throughout spikelet development in male and female inflorescences. The GLO-like genes from rice have very similar patterns of mRNA accumulation. In addition, ZMM16 shows also weak expression in vegetative organs. Conservation of the expression in lodicules and stamens is in perfect agreement with a floral homeotic B-function of the GLO-like genes in grasses. The conserved expression in carpels is discussed. Moreover, circumstantial evidence for a functional diversification of GLO-like genes in grasses is provided.

Amino Acid Sequence↗
PubMedDate not supplied

Structural and serological analysis of cross-reactive idiotypes: comparison of heavy and light chain families of anti-arsonate antibodies.

The amino acid sequences of VH and VL regions of 16 cross-reactive idiotype-positive (CRI+) and ten CRI-negative (CRI-) monoclonal anti-arsonate antibodies from a range of laboratories were compared. Analysis of the data demonstrates the existence of several pairs of hybridoma proteins (within CRI+ and CRI- families) which have identical or very similar sequences for VH and VL. This strongly suggests the existence of at least 4 germ-line genes in A/J mice coding for CRI+VH, CRI+VL, CRI-VH and CRI-VL regions. The CRI+ family, however, consists of VH structures which represent either (1) germ-line sequences, (2) VHVL variants with a few substitutions, or (3) VHVL variants with extensive substitutions. The latter two consist of antibodies which have lost either the CRI or arsonate binding capacities. The CRI- family consists of two very different groups. The first group appears to be the product of CRI- VHVL germ-line genes and their variants. The second group contains antibodies coded by CRI+ germ-line genes but which, due to somatic diversification, become CRI-. Comparison of VHVL of all anti-arsonate antibodies clearly indicates that light chain selection by the heavy chain is a non-random process. Also, there appears to be a parallel diversification of VH and VL. Comparative data on H and L chain structures and serological evidence obtained by three monoclonal antiidiotypic antibodies indicates that formation of the original cross-reactive idiotypic determinant(s) requires an equal contribution for both H and L chains; moreover, CRI consists of a single (or few) idiotopes.

Amino Acid Sequence↗
PubMed2004

A postmitotic role for Isl-class LIM homeodomain proteins in the assignment of visceral spinal motor neuron identity.

LIM homeobox genes have a prominent role in the regulation of neuronal subtype identity and distinguish motor neuron subclasses in the embryonic spinal cord. We have investigated the role of Isl-class LIM homeodomain proteins in motor neuron diversification using mouse genetic methods. All spinal motor neuron subtypes initially express both Isl1 and Isl2, but Isl2 is rapidly downregulated by visceral motor neurons. Mouse embryos lacking Isl2 function exhibit defects in the migration and axonal projections of thoracic level motor neurons that appear to reflect a cell-autonomous switch from visceral to somatic motor neuron character. Additional genetic mutations that reduce or eliminate both Isl1 and Isl2 activity result in more pronounced defects in visceral motor neuron generation and erode somatic motor neuron character. Thus, an early phase of high Isl expression and activity in newly generated motor neurons permits the diversification of visceral and somatic motor neuron subtypes in the developing spinal cord.

Acetylcholinesterase↗
PubMed1999

Ectopic gene expression and homeotic transformations in arthropods using recombinant Sindbis viruses.

BACKGROUND: The morphological diversity of arthropods makes them attractive subjects for studying the evolution of developmental mechanisms. Comparative analyses suggest that arthropod diversity has arisen largely as a result of changes in expression patterns of genes that control development. Direct analysis of how a particular gene functions in a given species during development is hindered by the lack of broadly applicable techniques for manipulating gene expression. RESULTS: We report that the Arbovirus Sindbis can be used to deliver high levels of gene expression in vivo in a number of non-host arthropod species without causing cytopathic effects in infected cells or impairing development. Using recombinant Sindbis virus, we investigated the function of the homeotic gene Ultrabithorax in the development of butterfly wings and beetle embryos. Ectopic Ultrabithorax expression in butterfly forewing imaginal discs was sufficient to cause the transformation of characteristic forewing properties in the adult, including scale morphology and pigmentation, to those of the hindwing. Expression of Ultrabithorax in beetle embryos outside of its endogenous expression domain affected normal development of the body wall cuticle and appendages. CONCLUSIONS: The homeotic genes have long been thought to play an important role in the diversification of arthropod appendages. Using recombinant Sindbis virus, we were able to investigate homeotic gene function in non-model arthropod species. We found that Ultrabithorax is sufficient to confer hindwing identity in butterflies and alter normal development of anterior structures in beetles. Recombinant Sindbis virus has broad potential as a tool for analyzing how the function of developmental genes has changed during the diversification of arthropods.

Animals↗
PubMedDate not supplied

Multigene analyses identify the three earliest lineages of extant flowering plants.

Flowering plants (angiosperms) are by far the largest, most diverse, and most important group of land plants, with over 250,000 species and a dominating presence in most terrestrial ecosystems. Understanding the origin and early diversification of angiosperms has posed a long-standing botanical challenge [1]. Numerous morphological and molecular systematic studies have attempted to reconstruct the early history of this group, including identifying the root of the angiosperm tree. There is considerable disagreement among these studies, with various groups of putatively basal angiosperms from the subclass Magnoliidae having been placed at the root of the angiosperm tree (reviewed in [2-4]). We investigated the early evolution of angiosperms by conducting combined phylogenetic analyses of five genes that represent all three plant genomes from a broad sampling of angiosperms. Amborella, a monotypic, vessel-less dioecious shrub from New Caledonia, was clearly identified as the first branch of angiosperm evolution, followed by the Nymphaeales (water lillies), and then a clade of woody vines comprising Schisandraceae and Austrobaileyaceae. These findings are remarkably congruent with those from several concurrent molecular studies [5-7] and have important implications for whether or not the first angiosperms were woody and contained vessels, for interpreting the evolution of other key characteristics of basal angiosperms, and for understanding the timing and pattern of angiosperm origin and diversification.

Biological Evolution↗
PubMed2003

Immunity through DNA deamination.

Functional antibody genes assembled by V(D)J joining are subsequently diversified by somatic hypermutation, gene conversion and class-switch recombination. Recent evidence indicates that all three processes are caused by the deamination of cytosine to uracil at sites within the immunoglobulin (Ig) loci, with the pattern of diversification depending on the pathway used for resolving the initiating dU-dG lesion. Whereas DNA deamination targeted to the endogenous Ig locus triggers a program of somatic gene diversification that underpins adaptive immunity, deamination targeted to foreign DNA might have arisen initially as a form of innate immunity. Furthermore, the observation that members of the DNA deaminase family can target inappropriate genes suggests they might also contribute to mutations during genome evolution, as well as in cancer.

Animals↗