Evolution of Ribosomal DNA (Rdna) Genetic Structure in Colonial Californian Populations of Avena Barbata

DNA samples from 980 plants of Avena barbata from 48 ecologically diverse sites in California and Oregon were assayed to determine their genotype for two duplicated loci governing rDNA variants. More than 40 different rDNA genotypes were observed among which 5 made up 96% of our sample in environmentally homogeneous sites; predominant genotypes were less frequent and recombinant genotypes were more frequent in environmentally heterogeneous sites. The spatial distribution of each predominant rDNA genotype was nearly an exact overlay on both macro- and microgeographical scales of a distinctive habitat and also of the distribution of an eight-locus morphological-allozyme variant genotype. In all, seven different habitat-genotype combinations (ecotypes) were distinguishable on the basis of their morphological-allozyme-rDNA genotypes. None of these seven genotypes has been found in ancestral Spanish populations; thus the above predominant multilocus genotypes (ecotypes) of the colonial populations evidently evolved subsequent to the recent introduction (within 150-200 generations) of A. barbata to California. The precise associations of specific alleles and genotypes of the morphological allozyme and rDNA loci with different specifiable habitats leads us to the conclusion that natural selection favoring particular multilocus combinations of alleles in different habitats was the main guiding force in shaping the internal genetic structure of local populations as well as the overall adaptive landscape of A. barbata over California and Oregon.     

Evolution of Multilocus Genetic Structure in Avena Hirtula and Avena Barbata

Avena barbata, an autotetraploid grass, is much more widely adapted than Avena hirtula, its diploid ancestor. We have determined the 14-locus genotype of 754 diploid and 4751 tetraploid plants from 10 and 50 Spanish sites, respectively. Allelic diversity is much greater in the tetraploid (52 alleles) than in the diploid (38 alleles): the extra alleles of the tetraploid were present in nonsegregating heteroallelic quadriplexes. Seven loci were monomorphic for the same allele (genotypically 11) in all populations of the diploid: five of these loci were also monomorphic for the same allele (genotypically 1111) in all populations of the tetraploid whereas two loci each formed a heteroallelic quadriplex (1122) that was monomorphic or predominant in the tetraploid. Seven of the 14 loci formed one or more highly successful homoallelic and/or heteroallelic quadriplexes in the tetraploid. We attribute much of the greater heterosis and wider adaptedness of the tetraploid to favorable within-locus interactions and interlocus (epistatic) interactions among alleles of the loci that form heteroallelic quadriplexes. It is difficult to account for the observed patterns in which genotypes are distributed ecogeographically except in terms of natural selection favoring particular alleles and genotypes in specific habitats. We conclude that natural selection was the predominant integrating force in shaping the specific genetic structure of different local populations as well as the adaptive landscape of both the diploid and tetraploid.     

Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.     

The Bioarchaeology of Identity in Spanish Colonial Florida: Social and Evolutionary Transformation before, during, and after Demographic Collapse

In this article, I consider the effects of Spanish missionization on indigenous identity and biological interaction patterns. Odontometric data were recorded for 26 skeletal samples dating to three time periods: precontact (C.E. 1200–1400), early mission (C.E. 1600–1650), and late mission (C.E. 1650–1700). Population genetic analyses generated estimates of regional genetic variation (F_ST) and intersample genetic distances. Genetic variation during the precontact period was limited despite documented linguistic and cultural variation. Variation increased during the early mission period, indicating a decline in between-group interaction despite inclusion within a single colonial sociopolitical framework. During the late mission period, variation declined significantly, indicating a dramatic reduction in between-group variability consistent with genetic drift and gene flow between communities. I discuss these results in terms of archaeological and historical models of postcolonial transformation and suggest an emerging polyethnic community was resident in La Florida preceding the subsequent diaspora caused by burgeoning European military conflict in eastern North America.     

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins: Deciphering Gene Trajectories and Changes in Biochemical Properties

Extreme halophilic Archaea thrive in high salt, where, through proteomic adaptation, they cope with the strong osmolarity and extreme ionic conditions of their environment. In spite of wide fundamental interest, however, studies providing insights into this adaptation are scarce, because of practical difficulties inherent to the purification and characterization of halophilic enzymes. In this work, we describe the evolutionary history of malate dehydrogenases (MalDH) within Halobacteria (a class of the Euryarchaeota phylum). We resurrected nine ancestors along the inferred halobacterial MalDH phylogeny, including the Last Common Ancestral MalDH of Halobacteria (LCAHa) and compared their biochemical properties with those of five modern halobacterial MalDHs. We monitored the stability of these various MalDHs, their oligomeric states and enzymatic properties, as a function of concentration for different salts in the solvent. We found that a variety of evolutionary processes, such as amino acid replacement, gene duplication, loss of MalDH gene and replacement owing to horizontal transfer resulted in significant differences in solubility, stability and catalytic properties between these enzymes in the three Halobacteriales, Haloferacales, and Natrialbales orders since the LCAHa MalDH. We also showed how a stability trade-off might favor the emergence of new properties during adaptation to diverse environmental conditions. Altogether, our results suggest a new view of halophilic protein adaptation in Archaea.     

Composition and growth of subtidal parvosilvosa from Californian kelp forests

Summary 1. Ecological studies of the kelp forests of Pacific North America have understandably stressed the larger vegetational components. An important vegetational component, previously neglected, is a taxonomically complex turf or parvosilvosa (Gislén 1930), composed of small algae and microscopic reproductive or developmental forms of larger algae.2. This report considers the ecological importance of this smaller plant component within the framework of the overall vegetational structure. Both diving studies and the cultivation of experimental material in the laboratory under controlled conditions have been utilized to probe the questions involved.3. Rocks and shells covered with representative algal turf have been cultured in the laboratory in naturally or artificially-illuminated tanks provided with a continuous supply of filtered seawater, and the resulting species composition has been compared with that occurring in nature.4. Both luxuriant forms of previously collected material and new forms have been observed in these cultures. Certain of these algae grow extremely well in culture and in some cases continue to reproduce, generating successive crops of plants. Growth rates under laboratory conditions for a few species have been measured and approach what might be expected in the field.5. Elective culture results suggest that many benthic algae may well exist for periods of time as resting or resistant stages, awaiting favorable environmental conditions. Stages such as those postulated have been produced in the laboratory.6. Complete taxonomic or ecological surveys of subtidal areas, and particularly the deeper benthic regions near the lower limits of plant distribution would benefit from culture studies of the type described. Subtidal benthic algae also lend themselves readily to experimental manipulation, and the results obtained to date, although preliminary, suggest possible experimental approache to subtidal ecology.

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Komposition und Wachstum von Parvosilvosa aus dem untergetauchten Gezeitenbereich kalifornischer Tangwälder

Kurzfassung Als Parvosilvosa werden taxonomisch komplexe, rasenartige Pflanzenbestände bezeichnet, die aus kleinen Algen und mikroskopischen Entwicklungsstadien größerer Algen bestehen. Die vorliegende Untersuchung erörtert die ökologische Bedeutung dieser Pflanzenkomponente als Teil der örtlichen Gesamtflora; sie basiert auf Schwimmtauch-Studien und Laboratoriumsexperimenten. Mit Parvosilvosa bedeckte Felsstücke und Molluskenschalen wurden unter Laboratoriumsbedingungen natürlichem und künstlichem Licht ausgesetzt. In den Kulturen konnten sowohl luxurierende Formen von bereits aus dem Biotop bekanntem Material als auch neue Formen festgestellt werden. Einige dieser Algen wuchsen sehr gut in Kultur und schritten zur sexuellen Fortpflanzung. Offenbar existieren viele benthonische Algen zeitweise in Form von Ruhestadien. Unter günstigen Bedingungen — wie sie beispielsweise in unseren Kulturen geboten werden — wachsen sie dann zu adulten Pflanzen heran. Die Erfassung des gesamten Algenbestandes eines Biotops dürfte durch die hier angewandten Methoden erleichtert werden. Die durchgeführten Untersuchungen ergeben neue Ansatzpunkte für experimentelle Arbeiten im Litoral.

     

Allelic Association: Linkage Disequilibrium Structure and Gene Mapping

The linkage disequilibrium (LD) structure of the human genome is now well understood and characterised for a number of human populations. The LD structure underpins the design and execution of candidate gene and genome-wide association mapping studies. Successful association mapping studies completed to date provide vital new insights into the genetic influences on common diseases, such as diabetes, some cancers and heart disease. The LD structure also presents new avenues of research into the genetic history of human populations, the effects of natural selection and the impact of recombination on the genomic landscape. This review introduces this exciting and complex field by encompassing this range of topics.     

Pyrimidine Pools and Macromolecular Composition of Pyrimidine-Limited Escherichia coli

The growth rate of a pyrimidine-requiring strain was controlled by limiting the concentration of exogenous orotic acid. As the steady state, pyrimidine-limited growth rate was decreased, the intracellular pyrimidine pools and the total nucleic acid per unit mass of culture also decreased. The ratio of deoxyribonucleic acid to protein remained constant, whereas the ratio of ribonucleic acid to protein decreased 30% over a threefold variation in growth rate (50- to 150-min doubling times). The intracellular uridine triphosphate and cytosine triphosphate pools also decreased (although not coordinately), and the pyrimidine biosynthetic enzymes were derepressed. Cell size was unaffected by pyrimidine-mediated variation of the growth rate.     

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

Current tools used in the reconstruction of ancestral gene orders often fall into event-based and adjacency-based methods according to the principles they follow. Event-based methods such as GRAPPA are very accurate but with extremely high complexity, while more recent methods based on gene adjacencies such as InferCARsPro is relatively faster, but often produces an excessive number of chromosomes. This issue is mitigated by newer methods such as GapAdj, however it sacrifices a considerable portion of accuracy. We recently developed an adjacency-based method in the probabilistic framework called PMAG to infer ancestral gene orders. PMAG relies on calculating the conditional probabilities of gene adjacencies that are found in the leaf genomes using the Bayes'' theorem. It uses a novel transition model which accounts for adjacency changes along the tree branches as well as a re-rooting procedure to prevent any information loss. In this paper, we improved PMAG with a new method to assemble gene adjacencies into valid gene orders, using an exact solver for traveling salesman problem (TSP) to maximize the overall conditional probabilities. We conducted a series of simulation experiments using a wide range of configurations. The first set of experiments was to verify the effectiveness of our strategy of using the better transition model and re-rooting the tree under the targeted ancestral genome. PMAG was then thoroughly compared in terms of three measurements with its four major competitors including InferCARsPro, GapAdj, GASTS and SCJ in order to assess their performances. According to the results, PMAG demonstrates superior performance in terms of adjacency, distance and assembly accuracies, and yet achieves comparable running time, even all TSP instances were solved exactly. PMAG is available for free at http://phylo.cse.sc.edu.     

Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter‐ and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.     

Plant-soil Interactions: Ecological Aspects and Evolutionary Implications

Building on the concept of plants as ecosystem engineers, and on published information on effects of particular plant species on soils, we review the evidence that such effects can provide a positive feedback to such plants. Based on case studies involving dune formation by Marram grass, N supply by N2-fixing plants, depression of N availability by ericaceous plants, islands of fertility in deserts, mull- and mor-forming temperate forest trees, and formation of peatbogs, as well as similar other cases, we conclude that there is strong evidence for plant-soil feedbacks in a variety of ecosystems. We argue, moreover, that these feedbacks could have played a role in the evolution of the plant species in question. These ideas are based mainly on correlative observations, and need further testing.     

Ion and Osmoregulation in Prenatal Elasmobranchs: Evolutionary Implications

The elasmobranchs represent a fascinating series of experimentsin the evolution of maternal support for developing embryos.In oviparous species, eggs are enclosed in a tough, fibrouscapsule. The capsule is very permeable and the embryonic tissuesare bathed in a solution ionically similar to sea water withinhours of oviposition. In the primitively viviparous speciesSqualus acanthias, early embryos in egg capsules are retainedin utero and are bathed in a solution similar to maternal plasma.Several months into the 22 month gestation period the embryosare capable of independent iono- and osmoregulation in a uterinesolution that resembles sea water. Embryos of more advancedviviparous species develop in a solution that is similar tomaternal plasma. Iono- and osmoregulation by these embryos wouldappear to beminimal. It is clear that in the oviparous elasmobranchs,the ability of the egg/embryo to maintain salts and urea atappropriate levels is present at the earliest stage of development.The ability of prenatal elasmobranch embryos to iono- and osmoregulatewould allow the evolution ofa diverse array of reproductivestrategies in the elasmobranchs.     

Intensive Farming: Evolutionary Implications for Parasites and Pathogens

An increasing number of scientists have recently raised concerns about the threat posed by human intervention on the evolution of parasites and disease agents. New parasites (including pathogens) keep emerging and parasites which previously were considered to be 'under control' are re-emerging, sometimes in highly virulent forms. This re-emergence may be parasite evolution, driven by human activity, including ecological changes related to modern agricultural practices. Intensive farming creates conditions for parasite growth and transmission drastically different from what parasites experience in wild host populations and may therefore alter selection on various traits, such as life-history traits and virulence. Although recent epidemic outbreaks highlight the risks associated with intensive farming practices, most work has focused on reducing the short-term economic losses imposed by parasites, such as application of chemotherapy. Most of the research on parasite evolution has been conducted using laboratory model systems, often unrelated to economically important systems. Here, we review the possible evolutionary consequences of intensive farming by relating current knowledge of the evolution of parasite life-history and virulence with specific conditions experienced by parasites on farms. We show that intensive farming practices are likely to select for fast-growing, early-transmitted, and hence probably more virulent parasites. As an illustration, we consider the case of the fish farming industry, a branch of intensive farming which has dramatically expanded recently and present evidence that supports the idea that intensive farming conditions increase parasite virulence. We suggest that more studies should focus on the impact of intensive farming on parasite evolution in order to build currently lacking, but necessary bridges between academia and decision-makers.     

Allelic Diversity and Its Implications for the Rate of Adaptation

Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided.     

Craniometric Relationships of Plains Populations: Historical and Evolutionary Implications

Abstract

Large skeletal samples from cemeteries in the Northern Plains near Mobridge, South Dakota have made possible the accurate determination of craniometric relationships between populations ancestoral to the historic Arikara. There is considerable change throughout the approximately 200 years represented, due primarily to gene flow from adjacent Siouan speaking groups. Arikara crania from the Northern Plains are seen to be morphologically similar to earlier crania further south, in particular St. Helena materials in northeastern Nebraska. This offers Support for the archaeological hypothesis that Coalescent Tradition cultures grew out of the Central Plains Tradition. Early crania from the Northern Plains are markedly different from those in the Central Plains and more similar to historic Mandan. The craniometric evidence argues for biological continuity rather than replacement in the Plains area.     

Ecological and Evolutionary Implications of Bird Pollination

This paper addresses the question of how, and under what ecologicalcircumstances, bird pollination will be optimal for a plant,and which or how many of the available nectar-feeding bird specieswill be optimal pollen vectors. Pollination by birds is energetically expensive for the plants,and should accur only when birds can mediate optimal patternsof pollen flow and seed set. Each nectar-feeding bird has potentialadvantages and disadvantages as a pollen vector, related toits size, morphology, and foraging behavior. Which availablebird is the optimal pollinator depends on the plant's growthhabit, spatial distribution, and breeding system. The variousadaptations shown by plants favoring one pollinator over anotherall revolve around the secretion of nectar and the manner ofpresenting it to the birds. However, other aspects of plantmorphology, physiology, ecology, or life cycle may affect theproduction and presentation of nectar, and influence plant-pollinatorcoevolution. Many question remain regarding the interrelationsbetween pollination and the total biology of the plant; birdpollination systems may prove fruitful in yielding meaningfulanswers.     

Genotypic and Allelic Variability in CYP19A1 among Populations of African and European Ancestry

CYP19A1 facilitates the bioconversion of estrogens from androgens. CYP19A1 intron single nucleotide polymorphisms (SNPs) may alter mRNA splicing, resulting in altered CYP19A1 activity, and potentially influencing disease susceptibility. Genetic studies of CYP19A1 SNPs have been well documented in populations of European ancestry; however, studies in populations of African ancestry are limited. In the present study, ten ‘candidate’ intronic SNPs in CYP19A1 from 125 African Americans (AA) and 277 European Americans (EA) were genotyped and their frequencies compared. Allele frequencies were also compared with HapMap and ASW 1000 Genomes populations. We observed significant differences in the minor allele frequencies between AA and EA in six of the ten SNPs including rs10459592 (p<0.0001), rs12908960 (p<0.0001), rs1902584 (p = 0.016), rs2470144 (p<0.0001), rs1961177 (p<0.0001), and rs6493497 (p = 0.003). While there were no significant differences in allele frequencies between EA and CEU in the HapMap population, a 1.2- to 19-fold difference in allele frequency for rs10459592 (p = 0.004), rs12908960 (p = 0.0006), rs1902584 (p<0.0001), rs2470144 (p = 0.0006), rs1961177 (p<0.0001), and rs6493497 (p = 0.0092) was observed between AA and the Yoruba (YRI) population. Linkage disequilibrium (LD) blocks and haplotype clusters that is unique to the EA population but not AA was also observed. In summary, we demonstrate that differences in the allele frequencies of CYP19A1 intron SNPs are not consistent between populations of African and European ancestry. Thus, investigations into whether CYP19A1 intron SNPs contribute to variations in cancer incidence, outcomes and pharmacological response seen in populations of different ancestry may prove beneficial.     

Genotypic and kin discrimination in a solitary Hymenopterous parasitoid: Implications for speciation

In Hymenopterous parasitoids, host discrimination enables a female to avoid ovipositing in an already parasitized host. A female recognizes such hosts by the presence of external or internal pheromone markings that differ depending on whether the host has been parasitized by the same female, a conspecific or a female of another species. If the ability to recognize hosts parasitized by genetically distant females does exist and results in a change in acceptance, this behaviour would have an impact on sympatric speciation. We tested this hypothesis in Anaphes victus Huber (Hymenoptera: Mymaridae) by examining two special cases of intraspecific discrimination: the recognition of different biotypes (i.e. genotypic discrimination) and the recognition of close relatives (i.e. kin discrimination). Female A. victus had to choose between two categories of parasitized eggs in petri dishes. They were able to discriminate between biotypes and always preferred to oviposit in eggs parasitized by females of other biotypes rather than by females of their own biotype. Females were also able to discriminate between their sisters and unrelated conspecifics and preferred to oviposit in eggs parasitized by unrelated females, but did not discriminate between their sisters and themselves. These results suggest that there is a polymorphic genetic component in host discrimination and that such a preference could induce a reduction in gene flow between populations. That this discrimination system shares many analogies with the complex system of communication of social Hymenoptera is discussed.