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Rapid evolution of a polyphenic threshold.

Polyphenisms are thought to play an important role in the evolution of phenotypic diversity and the origin of morphological and behavioral novelties. However, the extent to which polyphenic developmental mechanisms evolve in natural populations is unknown. Here we contrast patterns of male phenotype expression in native and exotic and ancestral and descendant populations of the horn polyphenic beetle, Onthophagus taurus. Males in this species express two alternative morphologies in response to larval feeding conditions. Favorable conditions cause males to grow larger than a threshold body size and to develop a pair of horns on their heads. Males that encounter relatively poor conditions do not reach this threshold size and remain hornless. We show that exotic and native populations of O. taurus differ significantly in the body size threshold that separates alternative male phenotypes. Comparison with archival museum collections and additional samples obtained from the native range of O. taurus suggests that allometric differences between exotic and native populations do not reflect preexisting variation in the native range of this species. Instead, our data suggest that threshold divergences between exotic and native populations have evolved in less than 40 years since the introduction to a new habitat and have proceeded in opposite directions in two exotic ranges of this species. Finally, we show that the kind and magnitude of threshold divergence between native and exotic populations are similar to differences normally observed between species. Our results support the view that certain components of the developmental control mechanism that underlie polyphenic development can evolve rapidly in natural populations and may provide important avenues for phenotypic differentiation and diversification in nature. We discuss the role of developmental control mechanisms in the origin of allometric diversification and explore potential evolutionary mechanisms that could drive scaling relationship evolution in nature.

Adaptation, Biological↗
PubMed2006

Development of the neonatal B and T cell repertoire in swine: implications for comparative and veterinary immunology.

Birth in all higher vertebrates is at the center of the critical window of development in which newborns transition from dependence on innate immunity to dependence on their own adaptive immunity, with passive maternal immunity bridging this transition. Therefore we have studied immunological development through fetal and early neonatal life. In swine, B cells appear earlier in fetal development than T cells. B cell development begins in the yolk sac at the 20th day of gestation (DG20), progresses to fetal liver at DG30 and after DG45 continues in bone marrow. The first wave of developing T cells is gammadelta cells expressing a monomorphic Vdelta rearrangement. Thereafter, alphabeta T cells predominate and at birth, at least 19 TRBV subgroups are expressed, 17 of which appear highly homologous with those in humans. In contrast to the T cell repertoire and unlike humans and mice, the porcine pre-immune VH (IGHV-D-J) repertoire is highly restricted, depending primarily on CDR3 for diversity. The V-KAPPA (IGKV-J) repertoire and apparently also the V-LAMBDA (IGLV-J) repertoire, are also restricted. Diversification of the pre-immune B cell repertoire of swine and the ability to respond to both T-dependent and T-independent antigen depends on colonization of the gut after birth in which colonizing bacteria stimulate with Toll-like receptor ligands, especially bacterial DNA. This may explain the link between repertoire diversification and the anatomical location of primary lymphoid tissue like the ileal Peyers patches. Improper development of adaptive immunity can be caused by infectious agents like the porcine reproductive and respiratory syndrome virus that causes immune dysregulation resulting in immunological injury and autoimmunity.

Allergy and Immunology↗
PubMed2004

Dynamics of HIV-1 recombination in its natural target cells.

Genetic recombination is believed to assist HIV-1 diversification and escape from host immunity and antiviral therapies, yet this process remains largely unexamined within the natural target-cell populations. We developed a method for measuring HIV-1 recombination directly that employs reporter viruses bearing functional enhanced yellow fluorescent protein (YFP) and enhanced cyan fluorescent protein (CFP) genes in which recombination produces a modified GFP gene and GFP fluorescence in the infected cells. These reporter viruses allow simultaneous quantification of the dynamics of HIV-1 infection, coinfection, and recombination in cell culture and in animal models by flow-cytometric analysis. Multiround infection assays revealed that productive cellular coinfection was subject to little functional inhibition. As a result, generation of recombinants proceeded according to the square of the infection rate during HIV-1 replication in T lymphocytes and within human thymic grafts in severe combined immunodeficient (SCID)-hu (Thy/Liv) mice. These results suggest that increases in viral load may confer a compounding risk of virus escape by means of recombinational diversification. A single round of replication in T lymphocytes in culture generated an average of nine recombination events per virus, and infection of macrophages led to approximately 30 crossover events, making HIV-1 up to an order of magnitude more recombinogenic than recognized previously and demonstrating that the infected cell exerts a profound influence on the frequency of recombination.

Animals↗
PubMed2004

Phylogenetic expression of Galalpha1-4Gal on avian glycoproteins: glycan differentiation inscribed in the early history of modern birds.

Glycoproteins containing Galalpha1-4Gal (galabiose) had been rarely found in vertebrates, except in a few species of birds and amphibians. We had previously reported that pigeon (Columba livia) egg white and serum glycoproteins are rich in N-glycans with Galalpha1-4Gal at nonreducing termini. To investigate the origin of Galalpha1-4Gal expression in avian evolution, we examined the presence of Galalpha1-4Gal glycoproteins in egg whites from 20 orders, 88 families, 163 genera, and 181 species of birds, as probed by Western blot with Griffonia simplicifolia-I lectin (terminal alpha-Gal/GalNAc-specific) and anti-P(1) mAb (Galalpha1-4Galbeta1-4GlcNAcbeta1-specific). One of the significant observations is the total absence of Galalpha1-4Gal glycoproteins in Struthioniformes (four species), Tinamiformes (three species), Craciformes (two species), Galliformes (14 species), and Anseriformes (10 species), which are phylogenetically separated from other orders at earlier stage of modern bird diversification (100-65 million years ago). The presence or absence of Galalpha1-4Gal glycoproteins in other avian orders varied by the species (104 species positive, and 44 species negative), even though some of them belong to the same order or family. Our results revealed that the expression of Galalpha1-4Gal glycoproteins is not rare among avians, and is correlated with the phylogeny. The expression was most likely differentiated at earlier stage of diversification in modern birds, but some birds might have lost the facility for the expression relatively recently.

Animals↗
PubMed2004

Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait.

Epistatic gene interactions are believed to be a major factor in the genetic architecture of evolutionary diversification. In Arabidopsis thaliana, the FRI and FLC genes mechanistically interact to control flowering time, and here we show that this epistatic interaction also contributes to a latitudinal cline in this life history trait within the species. Two major FLC haplogroups (FLC(A) and FLC(B)) are associated with flowering time variation in A. thaliana in field conditions, but only in the presence of putatively functional FRI alleles. Significant differences in latitudinal distribution of FLC haplogroups in Eurasia and North Africa also depend on the FRI genotype. There is significant linkage disequilibrium between FRI and FLC despite their location on separate chromosomes. Although no nonsynonymous polymorphisms differentiate FLC(A) and FLC(B), vernalization induces the expression of an alternatively spliced FLC transcript that encodes a variant protein with a radical amino acid replacement associated with the two FLC haplogroups. Numerous polymorphisms differentiating the FLC haplogroups also occur in intronic regions implicated in the regulation of FLC expression. The features of the regulatory gene interaction between FRI and FLC in contributing to the latitudinal cline in A. thaliana flowering time are consistent with the maintenance of this interaction by epistatic selection. These results suggest that developmental genetic pathways and networks provide the molecular basis for epistasis, contributing to ecologically important phenotypic variation in natural populations and to the process of evolutionary diversification.

Alternative Splicing↗
PubMed2005

Timing the origin and expansion of the Mexican tropical dry forest.

Macroevolution examines the temporal patterns of biological diversity in deep time. When combined with biogeography, it can provide unique information about the historical changes in the distribution of communities and biomes. Here I document temporal and spatial changes of diversity in the genus Bursera and relate them to the origin and expansion of the tropical dry forests of Mexico. Bursera is very old, highly adapted to warm dry conditions, and a dominant member of the Mexican tropical dry forest. These characteristics make it a useful indicator of the history of this vegetation. I used a time-calibrated phylogeny to estimate Bursera's diversification rate at different times over the last 60 million years. I also reconstructed the geographic center and time of origin of all species and nodes from information on current distributions. Results show that between 30 and 20 million years ago, Bursera began a relatively rapid diversification. This suggests that conditions were favorable for its radiation and thus, very probably for the establishment of the dry forest as well. The oldest lineages diverged mostly in Western Mexico, whereas the more recent lineages diverged in the south-central part of the country. This suggests that the tropical dry forest probably first established in the west and then expanded south and east. The timing of the radiations in these areas corresponds to that suggested for formations of the mountainous systems in Western and Central Mexico, which have been previously recognized as critical for the persistence of the Mexican dry forest.

Biological Evolution↗
PubMed2005

Male genital size reflects a tradeoff between attracting mates and avoiding predators in two live-bearing fish species.

Male genitalia may experience more rapid, divergent evolution than any other animal character, but why? Research during the past several decades has culminated in the view that genital diversification primarily results from postmating sexual selection (e.g., sperm competition or cryptic female choice). However, the potential roles of premating sexual selection (e.g., mate choice) and natural selection have received little attention. We examined the possible importance of these mechanisms by investigating divergence in male genitalia among populations differing in predator regime for two species of live-bearing fish (Gambusia affinis in Texas and Gambusia hubbsi in The Bahamas). When controlled for body size, males exhibited a larger gonopodium (sperm-transfer organ) in predator-free environments than in predatory environments, a trend that persisted across space (multiple populations), time (multiple years), and species. By conducting laboratory experiments with G. affinis, we found that premating sexual selection seems to favor larger male genitalia (females exhibited mating preference for males having larger gonopodia), but natural selection in the presence of predatory fishes seems to favor reduced genital size (larger gonopodium size was associated with reduced burst-swimming performance, an important antipredator behavior). Although postmating sexual selection is widely presumed to be the most important mechanism driving genital diversification, these findings suggest that alternative mechanisms, particularly for organisms that cannot retract their genitalia, may also prove important.

Analysis of Variance↗
PubMed2005

Activation-induced deaminase cloning, localization, and protein extraction from young VH-mutant rabbit appendix.

Studies in mouse, human, and chicken suggest that activation-induced deaminase (AID) is involved in three known processes leading to antibody diversification: somatic hypermutation, gene conversion, and class-switch recombination. Developing rabbit appendix provides a particularly good site for studying all three of these B cell maturation events. We report here successful cloning of rabbit AID and isolation of AID protein from rabbit appendix-cell nuclear and cytoplasmic extracts. We succeeded in identifying and locating AID protein in cells by immunohistochemical and immunofluorescent staining techniques and examined colocalization of AID and other molecules important for Ab diversification. This report extends our knowledge about AID to a mammalian species that uses gene conversion to diversify rearranged Ig genes. Although much work remains to understand fully the mechanism of action of AID and its association with other cellular components, the rabbit system now offers a particularly useful model for future studies of these dynamics.

Amino Acid Sequence↗
PubMed2005

Critical review of host specificity and its coevolutionary implications in the fig/fig-wasp mutualism.

Figs (Ficus spp., Moraceae) and their pollinating wasps (Agaonidae, Chalcidoidea) constitute perhaps the most tightly integrated pollination mutualism that is known. Figs are characterized by extraordinarily high global and local species diversity. It has been proposed that the diversification of this mutualism has occurred through strict-sense coadaptation and cospeciation between pairs of fig and wasp species that are associated in highly specific one-to-one relationships. However, existing studies cast doubt on the generality of this proposition. Here, we review our current knowledge of the evolutionary history of the fig/fig-wasp mutualism. We critically examine the idea that codivergence between figs and their pollinators has been dominated by strict-sense cospeciation. We present phylogenetic and population genetic data from neotropical fig and fig wasp species that suggest that a more accurate model for diversification in this mutualism is that of groups of genetically well defined wasp species coevolving with genetically less well defined (frequently hybridizing) groups of figs. Last, we use our results to assess previously proposed hypotheses on models of speciation in this mutualism.

Animals↗
PubMed2005

Variable lymphocyte receptors in hagfish.

A previously uncharacterized type of variable lymphocyte receptors (VLR) was identified recently in the Sea lamprey. This jawless vertebrate generates an extensive VLR repertoire through differential insertion of neighboring diverse leucine-rich repeat (LRR) cassettes into an incomplete germ-line VLR gene. We report here VLR homologs from two additional lamprey species and the presence of two types of VLR genes in hagfish, the only other order of contemporary jawless vertebrates. As in the Sea lamprey, the incomplete hagfish germ-line VLR-A and -B genes are modified in lymphocyte-like cells to generate highly diverse repertoires of VLR-A and -B proteins via a presently undetermined mechanism. This jawless-fish mode of VLR diversification starkly contrasts with the rearrangement of Ig V(D)J gene segments used by all jawed vertebrates to produce diverse repertoires of T and B lymphocyte antigen receptors. The development of two very different strategies for receptor diversification at the dawn of vertebrate evolution approximately 500 million years ago attests to the fitness value of a lymphocyte-based system of anticipatory immunity.

Amino Acid Motifs↗
PubMed2005

Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America.

Because of a dearth of Cenozoic grass fossils, the timing of the taxonomic diversification of modern subclades within the grass family (Poaceae) and the rise to ecological dominance of open-habitat grasses remain obscure. Here, I present data from 99 Eocene to Miocene phytolith assemblages from the North American continental interior (Colorado, Nebraska, Wyoming, and Montana/Idaho), constituting the only high-resolution mid-Cenozoic record of grasses. Analyses of these assemblages show that open-habitat grasses had undergone considerable taxonomic diversification by the earliest Oligocene (34 million years ago) but that they did not become ecologically dominant in North America until 7-11 million years later (Late Oligocene or Early Miocene). This pattern of decoupling suggests that environmental changes (e.g., climate changes), rather than taxonomic radiations within Poaceae, provided the key opportunity for open-habitat grasses to expand in North America.

Demography↗
PubMed2006

Chemically engineered extracts as an alternative source of bioactive natural product-like compounds.

The access to libraries of molecules with interesting biomolecular properties is a limiting step in the drug discovery process. By virtue of a long molecular evolution process, natural products are recognized as biologically validated starting points in structural space for library development. We introduce here a strategy to generate natural product-like libraries. A semisynthetic mixture of compounds was produced by diversification of a natural product extract through the chemical transformation of common chemical functionalities in natural products into chemical functionalities rarely found in nature. The resulting mixture showed antifungal activity against Candida albicans, whereas the starting extract did not show such activity. Bioguided fractionation led to the isolation of a previously undescribed active semisynthetic pyrazole. The result illustrates how biological activity can be generated by designed chemical diversification of a natural product mixture, and represents the proof of principle of an alternative strategy for producing natural product-like libraries from natural products libraries.

Antifungal Agents↗
PubMed2001

Antigen polymorphism in Borrelia hermsii, a clonal pathogenic bacterium.

The relapsing fever spirochete, Borrelia hermsii, escapes immune selection by alternating expression of surface lipoprotein alleles. The switch results from a duplicative transposition of one of several surface lipoprotein-encoding nucleotide sequences into the singular expression site. These nucleotide sequences constitute a large gene family whose diversity originated, in some cases, before the major divergences of Borrelia species. We have examined the B. hermsii vsp subfamily of alleles, which are carried on linear plasmids within each cell and maintained in several diverse copies as an antigenic archive. Each encodes a distinct serotype-specific protein. We sequenced more than 90% of the alleles within a single strain-B. hermsii strain HS1. A preponderance of allelic mosaicism suggests that intragenic recombination, coupled with selection imposed by host immune response, has driven diversification of the archived ensemble of vsp alleles. The recombinational diversification of vsp alleles generates change in the associated serotypes of the magnitude (30-40% amino acid differentiation) necessary for overcoming cross-reactivity of neutralizing antibodies. We conclude that evolution of vsp has occurred by punctuated occurrence of allelic differentiation, rather than by gradual selection of incremental point mutations that do not meet the threshold for antigenic diversity.

Antigens, Bacterial↗
PubMed2001

Global biodiversity and the ancient carbon cycle.

Paleontological data for the diversity of marine animals and land plants are shown to correlate significantly with a concurrent measure of stable carbon isotope fractionation for approximately the last 400 million years. The correlations can be deduced from the assumption that increasing plant diversity led to increasing chemical weathering of rocks and therefore an increasing flux of carbon from the atmosphere to rocks, and nutrients from the continents to the oceans. The CO(2) concentration dependence of photosynthetic carbon isotope fractionation then indicates that the diversification of land plants led to decreasing CO(2) levels, while the diversification of marine animals derived from increasing nutrient availability. Under the explicit assumption that global biodiversity grows with global biomass, the conservation of carbon shows that the long-term fluctuations of CO(2) levels were dominated by complementary changes in the biological and fluid reservoirs of carbon, while the much larger geological reservoir remained relatively constant in size. As a consequence, the paleontological record of biodiversity provides an indirect estimate of the fluctuations of ancient CO(2) levels.

Animals↗
PubMed2002

Sympatric speciation by sexual conflict.

It is well established that sexual conflict can drive an endless coevolutionary chase between the sexes potentially leading to genetic divergence of isolated populations and allopatric speciation. We present a simple mathematical model that shows that sexual conflict over mating rate can result in two other general regimes. First, rather than "running away" from males, females can diversify genetically into separate groups, effectively "trapping" the males in the middle at a state characterized by reduced mating success. Female diversification brings coevolutionary chase to the end. Second, under certain conditions, males respond to female diversification by diversifying themselves. This response results in the formation of reproductively isolated clusters of genotypes that emerge sympatrically.

Adaptation, Physiological↗
PubMed2002

Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment.

Gene-family evolution mostly relies on gene duplication coupled with functional diversification of gene products. However, other evolutionary mechanisms may also be important in generating protein diversity. The ubiquitous membrane intrinsic protein (MIP) gene family is an excellent model system to search for such alternative evolutionary mechanisms. MIPs are proteins that transport water, glycerol, and small solutes across cell membranes in all living organisms. We reconstructed the molecular phylogeny of MIPs based on amino acid sequence data by using neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The recovered trees show an early and distinct separation of water and glycerol transporters, i.e., aquaporins (AQPs), and aquaglyceroporins. The latter are absent from plants. As expected, gene duplication and functional diversification account for most of the diversity of animal and plant members of the family. However, in contrast to this model, we find that the sister group of plant glycerol transporters are bacterial AQPs. This relationship suggests first that plant glycerol transporters may resulted from a single event of horizontal gene transfer from bacteria, which we have estimated to have occurred approximately 1,200 million years ago, at the origin of plants, and second that bacterial AQPs were likely recruited to transport glycerol in plants because of their absence of aquaglyceroporins. This striking example of adaptive evolution at the molecular level was demonstrated further by finding convergent or parallel replacements at particular amino acid positions related to water- and glycerol-transporting specificity.

Amino Acid Sequence↗
PubMed2002

Modularity, individuality, and evo-devo in butterfly wings.

Modularity in animal development is thought to have facilitated morphological diversification, but independent change of those traits integrated within a module might be restricted. Correlations among traits describe potential developmental constraints on evolution. These have often been postulated to explain patterns of morphological variation and have been examined theoretically but seldom analyzed experimentally. Here, we use artificial selection to explore the modular organization of butterfly wing patterns and the extent to which their evolution is constrained by the genetic correlations among repeated pattern elements. We show that, in Bicyclus anynana butterflies, despite the evidence that all eyespots are developmentally coupled, the response to selection for increased size of one individual eyespot can proceed in a manner largely independent from selection imposed on another eyespot. We argue that among-eyespot correlations are unlikely to have constrained the evolutionary diversification of butterfly wing patterns but might be important when only limited time is available for adaptive evolution to occur. The ease with which we have been able to produce independent responses to artificial selection on different eyespots may be linked to a legacy of natural selection favoring individuality. Our results are discussed within the context of the evolution of modularity and individuality of serially repeated morphological traits.

Animals↗
PubMed2024

Teleost Hox code defines regional identities competent for the formation of dorsal and anal fins.

The dorsal and anal fins can vary widely in position and length along the anterior-posterior axis in teleost fishes. However, the molecular mechanisms underlying the diversification of these fins remain unknown. Here, we used genetic approaches in zebrafish and medaka, in which the relative positions of the dorsal and anal fins are opposite, to demonstrate the crucial role of hox genes in the patterning of the teleost posterior body, including the dorsal and anal fins. By the CRISPR-Cas9-induced frameshift mutations and positional cloning of spontaneous dorsalfinless medaka, we show that various hox mutants exhibit the absence of dorsal or anal fins, or a stepwise posterior extension of these fins, with vertebral abnormalities. Our results indicate that multiple hox genes, primarily from hoxc-related clusters, encompass the regions responsible for the dorsal and anal fin formation along the anterior-posterior axis. These results further suggest that shifts in the anterior boundaries of hox expression which vary among fish species, lead to diversification in the position and size of the dorsal and anal fins, similar to how modulations in Hox expression can alter the number of anatomically distinct vertebrae in tetrapods. Furthermore, we show that hox genes responsible for dorsal fin formation are different between zebrafish and medaka. Our results suggest that a novel mechanism has occurred during teleost evolution, in which the gene network responsible for fin formation might have switched to the regulation downstream of other hox genes, leading to the remarkable diversity in the dorsal fin position.

Animals↗