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PubMed2006

Nonneutral evolution of organelle genes in Silene vulgaris.

Knowledge of mitochondrial gene evolution in angiosperms has taken a dramatic shift within the past decade, from universal slow rates of nucleotide change to a growing realization of high variation in rates among lineages. Additionally, evidence of paternal inheritance of plant mitochondria and recombination among mitochondrial genomes within heteroplasmic individuals has led to speculation about the potential for independent evolution of organellar genes. We report intraspecific mitochondrial and chloroplast sequence variation in a cosmopolitan sample of 42 Silene vulgaris individuals. There was remarkably high variation in two mitochondrial genes (atp1, atp9) and additional variation within a third gene (cob). Tests for patterns of nonneutral evolution were significant for atp1 and atp9, indicative of the maintenance of balanced polymorphisms. Two chloroplast genes (matK, ndhF) possessed less, but still high, variation and no divergence from neutral expectations. Phylogenetic patterns of organelle genes in both the chloroplast and mitochondria were incongruent, indicating the potential for independent evolutionary trajectories. Evidence indicated reassociation among cytoplasmic genomes and recombination between mitochondrial genes and within atp1, implying transient heteroplasmy in ancestral lineages. Although the mechanisms for long-term maintenance of mitochondrial polymorphism are currently unknown, frequency-dependent selection on linked cytoplasmic male sterility genes is a potential candidate.

Base Sequence↗

PubMed2006

Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes.

We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length L. The population evolves in a maximally rugged fitness landscape with a large number of local optima. We find that whether the evolutionary trajectory is deterministic or stochastic depends on the effective mutational distance d(eff) up to which the population can spread in genotype space. For d(eff) = L, the deterministic quasi-species theory operates while for d(eff) < 1, the evolution is completely stochastic. Between these two limiting cases, the dynamics are described by a local quasi-species theory below a crossover time T(x) while above T(x) the population gets trapped at a local fitness peak and manages to find a better peak via either stochastic tunneling or double mutations. In the stochastic regime d(eff) < 1, we identify two subregimes associated with clonal interference and uphill adaptive walks, respectively. We argue that our findings are relevant to the interpretation of evolution experiments with microbial populations.

Adaptation, Biological↗

PubMed2026

Research Progress in the Cytogenetics of Sweetpotato and Its Wild Relatives.

Cultivated sweetpotato (Ipomoea batatas (L.) Lam.), a hexaploid (2n = 6x = 90) crop, is the most economically important species within the morning glory genus Ipomoea (Convolvulaceae). Fourteen diploid Ipomoea species and several polyploid accessions have been confirmed to be closely related to sweetpotato, often termed its wild relatives. These wild species harbor abundant elite genes beneficial to sweetpotato improvement and thereby serve as indispensable germplasm reservoirs for breeding programs. In addition, several wild taxa are proposed as potential ancestors of domesticated sweetpotato. Nevertheless, the evolutionary origin and genomic architecture of cultivated sweetpotato have not yet been fully resolved. Cytological investigations, particularly chromosome karyotyping and meiotic pairing analyses, have been pivotal in unravelling the genomic architecture and evolutionary trajectories of polyploid taxa. Herein, we systematically summarize advances in chromosome counting, genome size, karyotyping, and meiotic pairing research on sweetpotato and its wild relatives.

Ipomoea↗

PubMed2001

Family- and population-level responses to atmospheric CO2 concentration: gas exchange and the allocation of C, N, and biomass in Plantago lanceolata (Plantaginaceae).

To ascertain the inheritance of responses to changing atmospheric CO(2) content, we partitioned response to elevated CO(2) in Plantago lanceolata between families and populations in 18 families in two populations. Plants were grown in 35 Pa and 71 Pa partial pressure of CO(2) (pCO(2)) in open-top chambers. We measured above- and belowground mass, carbon (C), nitrogen (N), hexose sugar, and gas exchange properties in both CO(2) treatments. Families within populations differed in mass, mass allocation, root : shoot ratios, aboveground percentage N, C : N ratio, and gas exchange properties. The CO(2) × family interaction is the main indicator of potential evolutionary responses to changing CO(2). Significant CO(2) × family interactions were observed for N content, C : N ratio, and photosynthetic rate (A: instantaneous light-saturated carbon assimilation capacity), intercellular CO(2) concentration, transpiration rate (E), and water use efficiency (WUE = A/E), but not for stomatal conductance. Families differed significantly in acclimation across time. The ratio of A in elevated vs. ambient growth CO(2), when measured at a common internal CO(2) partial pressure was 0.79, indicating down-regulation of A under CO(2) enrichment. Mass, C : N ratio, percentage, C (%C), and soluble sugar all increased significantly but overall %N did not change. Increases in %C and sugar were significant and were coincident with redistribution of N aboveground. The observed variation among populations and families in response to CO(2) is evidence of genetic variation in response and therefore of the potential for novel evolutionary trajectories with rising atmospheric CO(2).

Journal Article↗

PubMed2004

Convergence to a novel environment: comparative method versus experimental evolution.

Laboratory adaptation allows researchers to contrast temporal studies of experimental evolution with comparative studies. The comparative method is here taken to mean the inference of microevolutionary processes from comparisons among contemporaneous populations of diverse origins, from one or multiple species. The data contrasted here come from Drosophila subobscura populations that were introduced to the laboratory at several different times and from two different locations. Two questions were addressed. First, can we correctly infer evolutionary dynamics from comparative data collected simultaneously from disparate populations? In most cases, we could, except for the character of starvation resistance. Second, are the evolutionary dynamics inferred from the comparative approach similar to those revealed by temporal studies of experimental evolution? For fecundity characters, they were. Overall the results show that both comparative and temporal studies are useful, though the former can be uninformative for characters with complex evolutionary trajectories.

Adaptation, Biological↗

PubMed2004

Population variation in the cost and benefit of tolerance and resistance against herbivory in Datura stramonium.

In this study we examine the hypothesis that divergent natural selection produces genetic differentiation among populations in plant defensive strategies (tolerance and resistance) generating adaptive variation in defensive traits against herbivory. Controlled genetic material (paternal half-sib families) from two populations of the annual Datura stramonium genetically differentiated in tolerance and resistance to herbivory were used. This set of paternal half-sib families was planted at both sites of origin and the pattern of genotypic selection acting on tolerance and resistance was determined, as well as the presence and variation in the magnitude of allocational costs of tolerance. Selection analyses support the adaptive differentiation hypothesis. Tolerance was favored at the site with higher average level of tolerance, and resistance was favored at the site with higher average level of resistance. The presence of significant environmentally dependent costs of tolerance was in agreement with site variation in the adaptive value of tolerance. Our results support the expectation that environmentally dependent costs of plant defensive strategies can generate differences among populations in the evolutionary trajectory of defensive traits and promote the existence of a selection mosaic. The pattern of contrasting selection on tolerance suggests that, in some populations of D. stramonium, tolerance may alter the strength of reciprocal coevolution between plant resistance and natural enemies.

Adaptation, Biological↗

PubMed2005

Reproduction and hybrid load in all-hybrid populations of Rana esculenta water frogs in Denmark.

All-hybrid populations of the water frog, Rana esculenta, are exceptional in consisting of independently and to some extent sexually reproducing interspecific hybrids. In most of its range R. esculenta reproduces hemiclonally with one of the parental species, R. lessonae or R. ridibunda, but viable populations of diploid and triploid hybrids, in which no individuals of the parental species have been found, exist in the northern part of the range. We test the hypothesis that nonhybrids arise every year in these all-hybrid populations, but die during larval development. Microsatellite markers were used to determine the genotypes of adults and abnormal and healthy offspring in three all-hybrid populations of R. esculenta in Denmark. Of all eggs and larvae, 63% developed abnormally or died, with some being nonhybrid (genomes matching one of the parental species), many being aneuploid (with noninteger chromosome sets), a few being tetraploid, and many eggs possibly being unfertilized. The 37% surviving and apparently healthy froglets were all diploid or triploid hybrids. In all three populations, gametogenesis matched the pattern previously described for all-hybrid R. esculenta populations in which most triploid adults have two R. lessonae genomes. This pattern was surprising for the one population in which triploid adults had two R. ridibunda genomes, because here it leads to a deficiency of gametes with an R. lessonae genome and should compromise the stability of this population. We conclude that faulty gametogenesis and mating between frogs with incompatible gametes induce a significant hybrid load in all-hybrid populations of R. esculenta, and we discuss compensating advantages and potential evolutionary trajectories to reduce this hybrid load.

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↗

PubMed2006

From more to fewer? Testing an allegedly pervasive trend in the evolution of morphological structure.

While evolutionary trends have long received much attention and have been widely disputed, new methods are now allowing the testing of directional hypotheses with increased rigor. Here, we test a general hypothesis about the way many kinds of discrete characters are thought to evolve, termed oligomerization. This is the tendency for serial structures (such as arthropod body and appendage segments) or armature (such as spines) to evolve primarily through loss and fusion. Focusing on the Crustacea, we use maximum likelihood methods to test for directional evolution in a large sample (> 500) of discrete traits, analyzed against molecular-based phylogenies. We find evidence for a significant trend toward trait loss, in accordance with the reduction principle. However, this trend is far from ubiquitous, with many characters exhibiting a reconstructed bias toward gains. These results suggest that caution must be used before drawing conclusions about which taxa are "primitive" or about the directionality of morphological shifts in the absence of phylogenetic analysis. Nevertheless, oligomerization-as a trend rather than a law-may be an important process that influences evolutionary trajectories from both morphological and functional perspectives.

Animals↗

PubMed1996

The challenge of managing laboratory information in a managed care environment.

This article considers some of the major changes that are occurring in pathology and pathology informatics in response to the shift to managed care in the United States. To better understand the relationship between information management in clinical laboratories and managed care, a typology of integrated delivery systems is presented. Following this is a discussion of the evolutionary trajectory for the computer networks that serve these large consolidated healthcare delivery organizations. The most complex of these computer networks is a community health information network. Participation in the planning and deployment of community health information networks will be important for pathologists because information management within pathology will be inexorably integrated into the larger effort by integrated delivery systems to share clinical, financial, and administrative data on a regional basis. Finally, four laboratory information management challenges under managed care are discussed, accompanied by possible approaches to each of them. The challenges presented are (1) organizational integration of departmental information systems such as the laboratory information system; (2) weakening of the best-of-breed approach to laboratory information system selection; (3) the shift away from the centralized laboratory paradigm; and (4) the development of rule-based systems to monitor and control laboratory utilization.

Community Networks↗

PubMed1998

Variation in female life-history traits among Alaskan populations of the threespine stickleback, Gasterosteus aculeatus L. (Pisces: Gasterosteidae)

Life-history characteristics of female threespine stickleback (Gasterosteus aculeatus) were examined in 12 populations, 11 freshwater and one anadromous, within the Cook Inlet region of Alaska. Because this area has been deglaciated during the last 20 000 years, the freshwater populations are recently derived, probably independently, from the local marine or anadromous stickleback. Freshwater threespine stickleback have undergone considerable morphological evolution within this region, apparently in response to environmental factors including predatory regimes and environmental productivity. Our freshwater study populations were selected to sample this range of morphological variation in order to determine whether life-history traits and morphologies have followed similar evolutionary trajectories. Freshwater populations could be categorized generally into one of three ecomorphotypes: those inhabiting relatively productive lakes having one or more piscivorous fishes present, and in which the stickleback exhibit a fully developed pelvic girdle; those inhabiting low-calcium lakes that lack piscivorous fishes, and in which the pelvic structures are incomplete; those living in streams with piscivorous fishes, in which the stickleback have fully developed pelvic girdles. The anadromous population constituted a fourth ecomorphotype that lives in marine waters, and is robustly armored. The freshwater populations showed considerable variation in all life-history traits assessed, and this variation generally corresponded to our ecomorphological classifications. Nevertheless, within each ecomorphotype there was sufficient variation to suggest that morphological and life-history traits may not always respond in the same manner in response to the same selective regime.Copyright 1998 The Linnean Society of London

Journal Article↗

PubMedDate not supplied

[Computer simulation of different types of evolutionary process].

The computer model of two alternative variants of biological evolution is proposed. The first variant supposes random while the second--directed change of individual features, thus corresponding to the Darwinian and non-Darwinian evolution. The evolution of fish communities in fresh waters serves as a particular example. The model is executed using object-oriented method of programming and mathematical apparatus of fuzzy logics. The investigation of the model showed that process of Darwinian evolution is connected with significantly greater species diversity and variability of evolutionary process trajectories than non-Darwinian one. On the other hand, non-Darwinian type of evolution provides fast achievement of high individual fitness, especially under conditions of constant environment. Non-Darwinian type evolution failed in big evolutionary alteration (for example, transition to predation); while the Darwinian evolution under the same conditions can produce such alterations though it took more time and many extinct species. Phylogenetic tree of Darwinian evolution is always more complex than of non-Darwinian one under the same conditions.

Animals↗

PubMed2026

Co-occurrence of bronchiolar adenoma and lung adenocarcinoma: a study of nine cases revealing distinct clonal origins via integrated histologic, immunophenotypic and molecular analysis.

PURPOSE: This study sought to elucidate the possible biological association between BA and lung adenocarcinoma through an analysis of cases in which both lesions coexist within the same specimen. METHODS: In our cohort, the BA and lung cancer components of nine concurrent-type BAs were microdissected using the Millisect system and subjected to whole-exome sequencing (WES). Their histopathological, immunohistochemical, and genomic profiles were comparatively evaluated. RESULTS: Histopathologically, the BA regions of concurrent-type BAs exhibited a classic bilayered architecture, composed of continuous luminal and basal cell layers. The adjacent monolayered concurrent components were diagnosed as adenocarcinoma in situ (AIS, N = 4), minimally invasive adenocarcinoma (MIA, N = 2), and invasive adenocarcinoma (ADC, N = 3). Immunohistochemically, both luminal and basal cells in BA regions expressed thyroid transcription factor 1 (TTF1), albeit with more heterogeneous staining intensity compared to that observed in tumor components. Molecularly, EGFR mutations were the most frequently identified in either BA or tumor components, or in both (Case 9). In BA components, mutations included exon 19 p.S752F, exon 19 deletions (p.L747_T751delinsP and p.E746_T751delinsVP), and compound G719C/S768I mutations. Tumor components harbored exon 28 S1130C, exon 19 indel (p.E746_S752delins), and exon 18 p.G719C mutations. Notably, only three cases demonstrated limited overlap of mutations and copy number variations (CNVs) between the two components. Phylogenetic analysis revealed that six cases shared truncal alterations in genes including KMT2A, PIK3CA, SETD2, MITF, PBRM1, and SRSF3, one case harbored a shared canonical EGFR mutation (p.G719C), with an additional p.S768I alteration uniquely detected in the BA component. CONCLUSION: There is insufficient evidence to support BA as a premalignant lesion for lung adenocarcinoma base on morphological and molecular variables, and they may represent distinct pathological entities.

Concurrent-type bronchiolar adenoma↗

PubMed2004

Evolution and stability of the G-matrix on a landscape with a moving optimum.

In quantitative genetics, the genetic architecture of traits, described in terms of variances and covariances, plays a major role in determining the trajectory of evolutionary change. Hence, the genetic variance-covariance matrix (G-matrix) is a critical component of modern quantitative genetics theory. Considerable debate has surrounded the issue of G-matrix constancy because unstable G-matrices provide major difficulties for evolutionary inference. Empirical studies and analytical theory have not resolved the debate. Here we present the results of stochastic models of G-matrix evolution in a population responding to an adaptive landscape with an optimum that moves at a constant rate. This study builds on the previous results of stochastic simulations of G-matrix stability under stabilizing selection arising from a stationary optimum. The addition of a moving optimum leads to several important new insights. First, evolution along genetic lines of least resistance increases stability of the orientation of the G-matrix relative to stabilizing selection alone. Evolution across genetic lines of least resistance decreases G-matrix stability. Second, evolution in response to a continuously changing optimum can produce persistent maladaptation for a correlated trait, even if its optimum does not change. Third, the retrospective analysis of selection performs very well when the mean G-matrix (G) is known with certainty, indicating that covariance between G and the directional selection gradient beta is usually small enough in magnitude that it introduces only a small bias in estimates of the net selection gradient. Our results also show, however, that the contemporary G-matrix only serves as a rough guide to G. The most promising approach for the estimation of G is probably through comparative phylogenetic analysis. Overall, our results show that directional selection actually can increase stability of the G-matrix and that retrospective analysis of selection is inherently feasible. One major remaining challenge is to gain a sufficient understanding of the G-matrix to allow the confident estimation of G.

Adaptation, Biological↗

PubMed2004

Tracking the trajectories of evolution.

This article proposes a method of visualizing and measuring evolution in artificial life simulations. The evolving population of agents is treated as a dynamical system. The proposed method is inspired by the notion of trajectory. The article provides examples of tracking of trajectories of evolutionary systems in the spaces of genotypes, strategies, and some global characteristics. Visualization similar to a bifurcation diagram is used to represent results of a series of simulations.

Artificial Intelligence↗

PubMed2003

Encephalization and allometric trajectories in the genus Homo: evidence from the Neandertal and modern lineages.

The term "encephalization" is commonly used to describe an enlargement in brain size, considered as either absolute endocranial volumes or relative values in relation to body size. It is widely recognized that a considerable endocranial expansion occurred throughout the evolution of the genus Homo. This article aims to evaluate whether this phenomenon was the outcome of distinct evolutionary lineages, reaching similar brain expansions but through different trajectories. Endocranial morphology was studied in a sample of fossil hominines by multivariate approaches using both traditional metrics and geometric morphometrics. The analysis was focused on the transition from a generalized archaic pattern within the genus Homo to the modern morphology and compared with changes that occurred along the Neandertal lineage. The main result was the identification of two different evolutionary trajectories, in which a similar expansion in endocranial size has been reached by different changes in shape. Along the Neandertal lineage we observed maintenance of an "archaic" endocranial model, in which a large amount of variability is based on a single allometric trend. By contrast, when modern endocasts were compared with nonmodern ones, we found important differences apparently led by a parietal expansion. In this light, the origin of our species may have represented the opportunity to surpass the constraints imposed on encephalization by the ontogenetic pattern shared by nonmodern Homo representatives.

Animals↗

PubMed2005

Niche construction through phenological plasticity: life history dynamics and ecological consequences.

The ability of an organism to alter the environment that it experiences has been termed 'niche construction'. Plants have several ways whereby they can determine the environment to which they are exposed at different life stages. This paper discusses three of these: plasticity in dispersal, flowering timing and germination timing. It reviews pathways through which niche construction alters evolutionary and ecological trajectories by altering the selective environment to which organisms are exposed, the phenotypic expression of plastic characters, and the expression of genetic variation. It provides examples whereby niche construction creates positive or negative feedbacks between phenotypes and environments, which in turn cause novel evolutionary constraints and novel life-history expression.

Biological Evolution↗

PubMed2001

Complex adaptive systems, aging and longevity.

Mortality and reproduction are intimately entwined in the study of aging and longevity. I apply the modern theory of complex adaptive systems (nonlinear, stochastic, dynamic methods) to questions of aging and longevity. I begin by highlighting major questions that must be answered in order to obtain a deeper understanding of aging. These are: (i) What should (in an evolutionary sense) mortality trajectories look like? (ii) Why does caloric restriction slow aging? (iii) Why does reproduction cause delayed mortality? (iv) Why does compensatory growth cause delayed mortality? I show how dynamic state variable models based on stochastic dynamic programming (Clark & Mangel, 2000) can be used to embed genetic theories of senescence (either mutation accumulation or antagonistic pleiotropy) in the somatic environment, as George Williams called for in 1957, and how they make the disposable soma theory of aging operational. Such models will allow unification of genetic and phenotypic theories of aging.

Adaptation, Physiological↗