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PubMed2001

Mechanisms of rapid sympatric speciation by sex reversal and sexual selection in cichlid fish.

Mechanisms of speciation in cichlid fish were investigated by analyzing population genetic models of sexual selection on sex-determining genes associated with color polymorphisms. The models are based on a combination of laboratory experiments and field observations on the ecology, male and female mating behavior, and inheritance of sex-determination and color polymorphisms. The models explain why sex-reversal genes that change males into females tend to be X-linked and associated with novel colors, using the hypothesis of restricted recombination on the sex chromosomes, as suggested by previous theory on the evolution of recombination. The models reveal multiple pathways for rapid sympatric speciation through the origin of novel color morphs with strong assortative mating that incorporate both sex-reversal and suppressor genes. Despite the lack of geographic isolation or ecological differentiation, the new species coexists with the ancestral species either temporarily or indefinitely. These results may help to explain different patterns and rates of speciation among groups of cichlids, in particular the explosive diversification of rock-dwelling haplochromine cichlids.

Animals↗
PubMed1997

An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera.

We have studied the potential reasons for a conspicuous deviation of substitution rates in Dipteran ribosomal genes. Systematic pairwise relative-rate tests reveal that a significant increase in substitution rate is characteristic for Diptera, but not for the other insects analyzed. Estimation of sequence change in specific lineages reveals that most of these substitutions took place during the evolution of the Dipteran stem lineage. When related to the paleontologically documented periods of absolute time, the substitution rate in the stem lineage of the Diptera underwent an at least 20-fold increase compared to other insect groups and subsequently dropped by a factor of 10 before the diversification of the major Dipteran subgroups. Systematic comparisons of nucleotide composition show that this episodic change in substitution rate was accompanied by a significant increase in A+T content of Dipteran rDNA. Our data suggest that the episodic evolution of the Dipteran rDNA has most probably been caused by a change of directional mutation pressure which must have occurred during the evolution of the stem lineage of the Diptera.

Animals↗
PubMed2005

Rapid cladogenesis in marine fishes revisited.

Lineages that underwent rapid cladogenesis are attractive systems for the study of mechanisms underlying taxonomic, ecological, morphological, and behavioral diversification. Recently developed statistical methods provide insights into historical patterns of diversity and allow distinguishing bursts of cladogenesis from stochastic background rates in the presence of confounding factors such as extinction and incomplete taxon sampling. Here, we compare the dynamics of speciation in several marine fish lineages some of which were previously proposed to have undergone significant changes of cladogenesis through time. We tested for evidence of episodes of rapid cladogenesis using the constant rate and Monte Carlo constant rate tests that are robust to incomplete taxon sampling. These tests employ the statistic gamma to measure the relative position of internal node in a chronogram. For the first time, we conducted a comparative analysis to address the behavior of the statistic under different chronogram-constructing methods (Langley-Fitch, nonparametric rate smoothing, and penalized likelihood). Although estimates of gamma sometimes differ widely among methods, acceptance or rejection of the constant rate model within a particular clade appears to be robust to the choice of method. Bursts of cladogenesis were detected in 14 of 34 studied datasets. Some of these were previously proposed to represent marine fish "radiations," whereas others are identified anew. Our results indicate that the wider application of tree shape methods that are able to detect significantly elevated rates of speciation is useful to more precisely define clades that underwent episodes of rapid cladogenesis in marine fish clades. Contrasting the patterns of phylogenetic diversification in marine fish lineages may facilitate the identification of common evolutionary trajectories versus idiosyncrasies, and ultimately help towards a better understanding of the factors and processes underlying speciation in the marine realm.

Animals↗
PubMed2001

Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup.

Genes involved in male fertility are potential targets for sexual selection, and their evolution may play a role in reproductive isolation and speciation. Here we describe a new Drosophila melanogaster gene, ocnus (ocn), that encodes a protein abundant in testes nuclear extracts. RT-PCR indicates that ocn transcription is limited to males and is specific to testes. ocn shares homology with another testis-specific gene, janusB (janB), and is located just distal to janB on chromosome 3. The two genes also share homology with the adjacent janusA (janA) gene, suggesting that multiple duplication events have occurred within this region of the genome. We cloned and sequenced these three genes from species of the D. melanogaster species subgroup. Phylogenetic analysis based on protein-encoding sequences predicts a duplication pattern of janA --> janA janB --> janA janB ocn, with the latter event occurring after the divergence of the D. melanogaster and Drosophila obscura species groups. We found significant heterogeneity in the rates of evolution among the three genes within the D. melanogaster species subgroup as measured by the ratio of nonsynonymous to synonymous substitutions, suggesting that diversification of gene function followed each duplication event and that each gene evolved under different selective constraints. All three genes showed faster rates of evolution than genes encoding proteins with metabolic function. These results are consistent with previous studies that have detected an increased rate of evolution in genes with reproductive function.

Animals↗
PubMed2007

The causes of evolutionary radiations in archipelagoes: passerine birds in the Lesser Antilles.

To investigate why some lineages undergo evolutionary radiation, we compare the passerine avifaunas of the Hawaiian and Galapagos archipelagoes, which have supported well-known radiations of birds, with those of the Lesser Antilles, which have not. We focus on four steps required for the buildup of diversity through allopatric speciation and secondary sympatry: genetic divergence in isolation, persistence of island populations, recolonization of source islands, and ecological compatibility in secondary sympatry. Analysis of genetic divergence among island populations in the Lesser Antilles reveals evidence of both prolonged independent evolution and re-expansion of differentiated island populations through the archipelago but little evidence of secondary sympatry of divergent genetic lineages. Archipelagoes with high rates of colonization from continental or nearby large-island sources might fail to promote evolutionary radiations because colonists fill ecological space and constrain diversification through competition. However, morphological analysis demonstrated similar divergence between allopatric populations in species in Hawaii, Galapagos, and the Lesser Antilles, although the rate of divergence between secondarily sympatric species evidently is more rapid in Hawaii and the Galapagos. Alternatively, endemic buildup of diversity might be facilitated by the relative absence of pathogens in Hawaii and Galapagos that otherwise could prevent the secondary sympatry of populations owing to disease-mediated competition.

Animals↗
PubMed2000

The alpha-mannosidases: phylogeny and adaptive diversification.

alpha-Mannosidase enzymes comprise a class of gylcoside hydrolases involved in the maturation and degradaton of glycoprotein-linked oligosaccharides. Various alpha-mannosidase enzymatic activities are encoded by an ancient and ubiquitous gene superfamily. A comparative sequence analysis was employed here to characterize the evolutionary relationships and dynamics of the alpha-mannosidase superfamily. A series of lineage-specific BLAST searches recovered the first ever recognized archaean and eubacterial alpha-mannosidase sequences, in addition to numerous eukaryotic sequences. Motif-based alignment and subsequent phylogenetic analysis of the entire superfamily revealed the presence of three well-supported monophyletic clades that represent discrete alpha-mannosidase families. The comparative method was used to evaluate the phylogenetic distribution of alpha-mannosidase functional variants within families. Results of this analysis demonstrate a pattern of functional diversification of alpha-mannosidase paralogs followed by conservation of function among orthologs. Nucleotide polymorphism among the most closely related pair of duplicated genes was analyzed to evaluate the role of natural selection in the functional diversification of alpha-mannosidase paralogs. Ratios of nonsynonymous and synonymous variation show an increase in the rate of nonsynonymous change after duplication and a relative excess of fixed nonsynonymous changes between the two groups of paralogs. These data point to a possible role for positive Darwinian selection in the evolution of alpha-mannosidase functional diversification following gene duplication.

Amino Acid Sequence↗
PubMed1993

Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha).

Patterns of evolutionary relationships among haplotype clades of sequences of the mitochondrial cytochrome b DNA gene are examined for five genera of arboreal rodents of the Caviomorph family Echimyidae from the Amazon Basin. Data are available for 798 bp of sequence from a total of 24 separate localities in Peru, Venezuela, Bolivia, and Brazil for Mesomys, Isothrix, Makalata, Dactylomys, and Echimys. Sequence divergence, corrected for multiple hits, is extensive, ranging from less than 1% for comparisons within populations of over 20% among geographic units within genera. Both the degree of differentiation and the geographic patterning of the variation suggest that more than one species composes the Amazonian distribution of the currently recognized Mesomys hispidus, Isothrix bistriata, Makalata didelphoides, and Dactylomys dactylinus. There is general concordance in the geographic range of haplotype clades for each of these taxa, and the overall level of differentiation within them is largely equivalent. These observations suggest that a common vicariant history underlies the respective diversification of each genus. However, estimated times of divergence based on the rate of third position transversion substitutions for the major clades within each genus typically range above 1 million years. Thus, allopatric isolation precipitating divergence must have been considerably earlier than the late Pleistocene forest fragmentation events commonly invoked for Amazonian biota.

Animals↗
PubMed2004

Hybridization and adaptive radiation.

Whether interspecific hybridization is important as a mechanism that generates biological diversity is a matter of controversy. Whereas some authors focus on the potential of hybridization as a source of genetic variation, functional novelty and new species, others argue against any important role, because reduced fitness would typically render hybrids an evolutionary dead end. By drawing on recent developments in the genetics and ecology of hybridization and on principles of ecological speciation theory, I develop a concept that reconciles these views and adds a new twist to this debate. Because hybridization is common when populations invade new environments and potentially elevates rates of response to selection, it predisposes colonizing populations to rapid adaptive diversification under disruptive or divergent selection. I discuss predictions and suggest tests of this hybrid swarm theory of adaptive radiation and review published molecular phylogenies of adaptive radiations in light of the theory.

Journal Article↗
PubMed2001

The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae).

Beetles in the weevil subfamilies Scolytinae and Platypodinae are unusual in that they burrow as adults inside trees for feeding and oviposition. Some of these beetles are known as ambrosia beetles for their obligate mutualisms with asexual fungi--known as ambrosia fungi--that are derived from plant pathogens in the ascomycete group known as the ophiostomatoid fungi. Other beetles in these subfamilies are known as bark beetles and are associated with free-living, pathogenic ophiostomatoid fungi that facilitate beetle attack of phloem of trees with resin defenses. Using DNA sequences from six genes, including both copies of the nuclear gene encoding enolase, we performed a molecular phylogenetic study of bark and ambrosia beetles across these two subfamilies to establish the rate and direction of changes in life histories and their consequences for diversification. The ambrosia beetle habits have evolved repeatedly and are unreversed. The subfamily Platypodinae is derived from within the Scolytinae, near the tribe Scolytini. Comparison of the molecular branch lengths of ambrosia beetles and ambrosia fungi reveals a strong correlation, which a fungal molecular clock suggests spans 60 to 21 million years. Bark beetles have shifted from ancestral association with conifers to angiosperms and back again several times. Each shift to angiosperms is associated with elevated diversity, whereas the reverse shifts to conifers are associated with lowered diversity. The unusual habit of adult burrowing likely facilitated the diversification of these beetle-fungus associations, enabling them to use the biomass-rich resource that trees represent and set the stage for at least one origin of eusociality.

Agriculture↗
PubMed1996

Variable expression and geographic distribution of Mycoplasma agalactiae surface epitopes demonstrated with monoclonal antibodies.

Species-specific monoclonal antibodies (MAbs) were developed against Mycoplasma agalactiae reference strain PG2 and French isolate P89 to study the in vitro expression of surface epitopes and to probe the antigenic profiles of 245 field isolates originating from 10 different countries. Colony immunostaining with MAbs on clonal lineage showed that 4 out of 9 species-specific epitopes exhibited a high rate of variation, demonstrating that M. agalactiae possesses a capacity for phenotypic diversification of its surface antigenicity. The emphasis was on dot immunobinding screening of the field isolates with MAbs recognizing permanently expressed epitopes. Eight different profiles could be defined. Great differences in epitope conservation were demonstrated with some area-specific strains completely lacking certain specific determinants. These results indicate that the antigenic variability of M. agalactiae relies not only upon surface switching mechanisms but also upon true epitope differences, partially related to the geographic origin of the isolates.

Animal Husbandry↗
PubMed1989

Improving the bottom line. Strategies for diversification.

Prospective pricing is on the rise. Operating surpluses have vanished. Cash flow has become a trickle. Credit ratings have been reduced. The cost of liability insurance has gone through the overhead. Regulatory red tape is strangling creativity. There aren't enough nurses, money or hours in the day to deal with all the problems. Why would anyone in his right mind want to run a hospital?

Financial Management↗
PubMed2006

TprK sequence diversity accumulates during infection of rabbits with Treponema pallidum subsp. pallidum Nichols strain.

The tprK gene in Treponema pallidum undergoes antigenic variation. In all T. pallidum isolates examined to date, except the Nichols type strain, heterogeneous tprK sequences have been identified. This heterogeneity is localized to seven variable (V) regions, and tprK sequence diversity accumulates with serial passage in naïve rabbits. The T. pallidum Nichols genome described a single tprK sequence, and after decades of independent passage, only minor tprK sequence diversity is seen among the Nichols strains from different laboratories. We hypothesized that T. pallidum Nichols is capable of only limited tprK diversification. To address this hypothesis, we passaged the T. pallidum Nichols strain in naïve rabbits at the peak of infection (rapid passage) or after the adaptive immune response had cleared most organisms in vivo (slow passage). After 22 rapid passages (9- to 10-day intervals), no tprK V region sequence changes were observed. In contrast, after two slow passages (30- to 35-day intervals), three V regions had sequences that were completely different from that of the original inoculum. New sequences were observed in all seven V regions by the fifth slow passage. In contrast to the rapid-passaged Nichols strain, rapid-passaged Chicago C, a clonal strain isolated from the highly diverse parent Chicago strain, developed significant tprK diversification. These findings suggest that tprK variation can occur, but at a lower rate, in Nichols and that immune pressure may be required for accumulation of bacteria with diverse tprK sequences. Adaptation to growth in rabbits may explain the limited repertoire of V region sequences seen in the Nichols strain.

Amino Acid Sequence↗
PubMed1987

Comparative analysis of avian embryonic growth.

The relationships between weight (W) and age (t) of embryos of 27 species of birds are described by parabolic equations of the form W = a*(t-i)b*, where a*,b*, and i are constants and i accounts for a time lag before the onset of parabolic growth. A simple transformation gives values of a and b for the equation dW/dt = aWb. Some mathematical properties of the parabolic equation, relating growth rate (dW/dt) to weight and age, extrapolating different curves to their intersection (point of divergence), and relating the length of the incubation period to constants of the parabolic equation and to hatching weight, are described. Fitted constants for most species formed a cluster in the vicinity of a = 0.4-0.5 and b = 0.65-0.75, within which one could not differentiate precocial and altricial species, nor among precocial families. Pelagic seabirds consistently had reduced values of b and were the only group with i greater than 0 (5-19 days). The relation between fitted constants and incubation periods is discussed. The rate at which embryo growth rate decreases with respect to size (b) is directly related to the rate of accumulation of dry matter in the tissues, suggesting that both express an underlying program of development. This study emphasizes the relationship between growth rate and development of the embryo, illustrates the degree of evolutionary flexibility and diversification within and among taxonomic groups, and reveals the sensitivity of the very young embryo to environmental conditions.

Animals↗
PubMed2006

Ecological mechanisms favouring behavioural diversification in the absence of morphological diversification: a theoretical examination using brook charr (Salvelinus fontinalis).

1. Behavioural diversification is thought to be an important initial step in the origin of resource polymorphisms. We developed a model for young brook charr (Salvelinus fontinalis Mitchill) to examine four mechanisms that could generate a U-shaped relationship between growth rate (fitness) and the proportion of time spent moving that would favour alternative foraging tactics in the absence of obvious differences in body size and shape. 2. Recently emerged brook charr of similar size and shape inhabit still-water pools along the sides of streams. Some individuals tend to sit and wait for crustacean prey at the pool substrate near the bank, while others tend to search actively for insect prey at the pool surface away from the bank. 3. The ecological mechanisms modelled were (i) the relationship between the rate of prey capture and the proportion of time spent moving is curvilinear, such that net rate of energy gain is maximized at two different levels of activity; (ii) switching between foraging locations and, hence, tactics involves lost opportunity and travel costs; (iii) switching between prey types and, hence, tactics involves a learning cost; and (iv) foraging success is status-dependent with individuals switching between tactics having a lower status than those specializing at a tactic. 4. Singly, no mechanism predicted the U-shaped relationship between growth rate and the proportion of time spent moving. Together, a U-shaped relationship was obtained, indicating that the behavioural diversification and diversifying selection observed in the field may be a consequence of multiple, subtle mechanisms.

Animals↗
PubMed2004

Evolutionary trace analysis of scorpion toxins specific for K-channels.

Scorpion alpha-K(+) channel toxins are a large family of polypeptides with a similar structure but diverse pharmacological activities. Despite many structural and functional data available at present, little progress has been made in understanding the toxin's molecular basis responsible for the functional diversification. In this paper, we report the first complete cDNA sequences of toxins belonging to subfamily 6 and identify five new members, called alpha-KTx 6.6-6.10. By analyzing the rates of mutations that occurred in the corresponding cDNAs, we suggest that accelerated evolution in toxin-coding regions may be associated with the functional diversification of this subfamily. To pinpoint sites probably involved in the functional diversity of alpha-KTx family, we analyzed this family of sequences using the evolutionary trace method. This analysis highlighted one channel-binding surface common for all the members. This surface is composed of one conserved lysine residue at position 29 assisted by other residues at positions 10, 26, 27, 32, 34, and 36. Of them, the positions 29, 32, and 34 have been reported to be the most major determinants of channel specificity. Interestingly, another contrary surface was also observed at a higher evolutionary time cut-off value, which may be involved in the binding of ERG (ether-a-go-go-related gene) channel-specific toxins. The good match between the trace residues and the functional epitopes of the toxins suggested that the evolutionary trace results reported here can be applied to predict channel-binding sites of the toxins. Because, the side-chain variation in the trace positions is strongly linked with the functional alteration and channel-binding surface transfer of alpha-KTx family, we conclude that our findings should also be important for the rational design of new toxins targeting a given potassium channel with high selectivity.

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↗
PubMed2004

Ecological constraints on diversification in a model adaptive radiation.

Taxonomic diversification commonly occurs through adaptive radiation, the rapid evolution of a single lineage into a range of genotypes or species each adapted to a different ecological niche. Radiation size (measured as the number of new types) varies widely between phylogenetically distinct taxa and between replicate radiations within a single taxon where the ecological opportunities available seem to be identical. Here we show how variation in energy input (productivity) and environmental disturbance combine to determine the extent of diversification in a single radiating lineage of Pseudomonas fluorescens adapting to laboratory conditions. Diversity peaked at intermediate rates of both productivity and disturbance and declined towards the extremes in a manner reminiscent of well-known ecological patterns. The mechanism responsible for the decrease in diversity arises from pleiotropic fitness costs associated with niche specialization, the effects of which are modulated by gradients of productivity and disturbance. Our results indicate that ecological gradients may constrain the size of adaptive radiations, even in the presence of the strong diversifying selection associated with ecological opportunity, by decoupling evolutionary diversification from ecological coexistence.

Animals↗
PubMed2000

Mating systems of diploid and allotetraploid populations of Tragopogon (Asteraceae). II. Artificial populations.

Polyploidization has long been recognized as an important force in the diversification of plants. Theoretical models predict that polyploids may be expected to exhibit higher rates of self-fertilization than do closely related diploid species. Wild populations of the neopolyploid Tragopogon mirus (4n) exhibited slightly higher rates of outcrossing than did populations of one of its progenitors, T. dubius (2n). In the current study, outcrossing rates in populations of T. dubius and T. mirus were estimated using artificial arrays constructed to maximize the chances of detecting outcrossing events. The artificial diploid population is more highly outcrossing (t=0.727; family-level estimates range from 0.00 to 1. 32) than the tetraploid population (t=0.591; family-level estimates range from 0.00 to 1.14), although the difference between them is not statistically significant. The results of this study, combined with those of the previous work on wild populations, suggest that mating systems in these species vary more among populations than between ploidal levels. This could be because of the relatively recent origins of the tetraploid species; there may have been insufficient time since the formations of the tetraploids for shifts in mating systems to occur.

Alleles↗