Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

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Michael H. Kohn

2008-01-01

Full Text Available While it remains a matter of some debate, rapid sequence evolution of the coding sequences of duplicate genes is characteristic for early phases past duplication, but long established duplicates generally evolve under constraint, much like the rest of the coding genome. As for coding sequences, it may be possible to infer evolutionary rate, selection, and constraint via contrasts between duplicate gene divergence in the 5 prime regions and in the corresponding synonymous site divergence in the coding regions. Finding elevated rates for the 5 prime regions of duplicated genes, in addition to the coding regions, would enable statements regarding the early processes of duplicate gene evolution. Here, 1 kb of each of the 5 prime regulatory regions of Drosophila melanogaster duplicate gene pairs were mapped onto one another to isolate shared sequence blocks. Genetic distances within shared sequence blocks (d5’ were found to increase as a function of synonymous (dS, and to a lesser extend, amino-acid (dA site divergence between duplicates. The rate d5’/dS was found to rapidly decay from values > 1 in young duplicate pairs (dS 0.8. Such rapid rates of 5 prime evolution exceeding 1 (~neutral predominantly were found to occur in duplicate pairs with low amino-acid site divergence and that tended to be co-regulated when assayed on microarrays. Conceivably, functional redundancy and relaxation of selective constraint facilitates subsequent positive selection on the 5 prime regions of young duplicate genes. This might promote the evolution of new functions (neofunctionalization or division of labor among duplicate genes (subfunctionalization. In contrast, similar to the vast portion of the non-coding genome, the 5 prime regions of long-established gene duplicates appear to evolve under selective constraint, indicating that these long-established gene duplicates have assumed critical functions.

Conductive solar wind models in rapidly diverging flow geometries

International Nuclear Information System (INIS)

Holzer, T.E.; Leer, E.

1980-01-01

A detailed parameter study of conductive models of the solar wind has been carried out, extending the previous similar studies of Durney (1972) and Durney and Hundhausen (1974) by considering collisionless inhibition of thermal conduction, rapidly diverging flow geometries, and the structure of solutions for the entire n 0 -T 0 plane (n 0 and T 0 are the coronal base density and temperature). Primary emphasis is placed on understanding the complex effects of the physical processes operative in conductive solar wind models. There are five points of particular interest that have arisen from the study: (1) neither collisionless inhibition of thermal conduction nor rapidly diverging flow geometries can significantly increase the solar wind speed at 1 AU; (2) there exists a firm upper limit on the coronal base temperature consistent with observed values of the coronal base pressure and solar wind mass flux density; (3) the principal effect of rapidly diverging flow geometries is a decrease in the solar wind mass flux density at 1 AU and an increase in the mass flux density at the coronal base; (4) collisionless inhibition of thermal conduction can lead to a solar wind flow speed that either increases or decreases with increasing coronal base density (n 0 ) and temperature (T 0 , depending on the region of the n 0 -T 0 plane considered; (5) there is a region of the n 0 -T/sub o/ plane at high coronal base densities where low-speed, high-mass-flux, transonic solar wind flows exist: a region not previously considered

Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation.

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Bay, Rachael A; Arnegard, Matthew E; Conte, Gina L; Best, Jacob; Bedford, Nicole L; McCann, Shaugnessy R; Dubin, Matthew E; Chan, Yingguang Frank; Jones, Felicity C; Kingsley, David M; Schluter, Dolph; Peichel, Catherine L

2017-11-06

Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Contrasting patterns of genetic divergence in two sympatric pseudo-metallophytes: Rumex acetosa L. and Commelina communis L.

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Ye M

2012-06-01

Full Text Available Abstract Background Patterns of genetic divergence between populations of facultative metallophytes have been investigated extensively. However, most previous investigations have focused on a single plant species making it unclear if genetic divergence shows common patterns or, conversely, is species-specific. The herbs Rumex acetosa L. and Commelina communis L. are two pseudo-metallophytes thriving in both normal and cupriferous soils along the middle and lower reaches of the Yangtze River in China. Their non-metallicolous and metallicolous populations are often sympatric thus providing an ideal opportunity for comparative estimation of genetic structures and divergence under the selective pressure derived from copper toxicity. Results In the present study, patterns of genetic divergence of R. acetosa and C. communis , including metal tolerance, genetic structure and genetic relationships between populations, were investigated and compared using hydroponic experiments, AFLP, ISSR and chloroplast genetic markers. Our results show a significant reduction in genetic diversity in metallicolous populations of C. communis but not in R. acetosa . Moreover, genetic differentiation is less in R. acetosa than in C. communis , the latter species also shows a clustering of its metallicolous populations. Conclusions We propose that the genetic divergences apparent in R. acetosa and C. communis , and the contrasting responses of the two species to copper contamination, might be attributed to the differences in their intrinsic physiological and ecological properties. No simple and generalised conclusions on genetic divergence in pseudo-metallophytes can thus be drawn.

Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

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Ciofi, C.; Beaumont, M. A.; Swingland, I. R.; Bruford, M. W.

1999-01-01

In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world's largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Komodo shows by far the largest values of genetic divergence and is proposed that it should be a separate conservation management unit. Other populations, surviving either on small islands with substantially reduced genetic variability, or in isolated patches, are identified as particularly vulnerable to stochastic threats and habitat loss. Our results provide an example of how data defining intraspecific levels of genetic divergence can provide information to help management plans, ensure the maintenance of genetic variability across populations and identify evolutionary potential within endangered species.

Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

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Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

2013-07-01

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana.

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Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin

2008-10-01

Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.

Speciation in rapidly diverging systems: lessons from Lake Malawi.

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Danley, P D; Kocher, T D

2001-05-01

Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand- and rock-dwellers, each adapted to a major benthic macrohabitat. Among the rock-dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.

Potencial de melhoramento e divergência genética de cultivares de milho-pipoca Potential to breeding and genetic divergence in popcorn cultivars

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Glauco Vieira Miranda

2003-06-01

Full Text Available O objetivo deste trabalho foi avaliar o potencial de melhoramento e a divergência genética de nove cultivares tropicais de milho-pipoca. A divergência genética foi estimada por meio da técnica de análise multivariada e as cultivares foram agrupadas com base na distância generalizada de Mahalanobis (DGM, utilizando o método de otimização de Tocher e a dispersão gráfica. Com produtividade de grãos acima de 3 t/ha, destacaram-se as cultivares CMS 43, IAC 112, Viçosa, CMS 42 e Branco, e com índices de capacidade de expansão acima de 24 (v/v, as cultivares IAC 112, RS 20 e Zélia. As estimativas da DGM indicaram (RS 20 e Beija-flor e (Rosa-claro e RS 20 os pares de cultivares mais distantes geneticamente, e (IAC 112 e Viçosa e (Branco e CMS 42, os pares mais similares. Foram identificados três ou quatro grupos divergentes dependendo do método de agrupamento. Para o melhoramento de milho-pipoca, as cultivares com maiores potenciais são RS 20, Zélia, IAC 112 e Beija-flor. As cultivares apresentam divergência genética.The objective of this paper was to evaluate the potential of breeding and genetic divergence in nine tropical popcorn cultivars. The genetic divergence was estimated using multivariate analysis techniques and the cultivars were grouped based in Mahalanobis' generalized distance (MGD, using Tocher's optimization and graphic dispersion. The best cultivars concerning the yield grain above 3 ton/ha were CMS 43, IAC 112, Viçosa, CMS 42 and Branco, and to popping expansion above 24 (v/v were IAC 112, RS 20 and Zélia. The estimates of MGD indicated the pairs genetically more distant (RS 20, Beija-flor and (Rosa-claro, RS 20 as well as pairs genetically more similar (IAC 112, Viçosa and (Branco, CMS 42. Tree or four genetic divergences groups were formed depending on the method. To popcorn breeding, cultivars with best potential are RS 20, Zélia, IAC 112, and Beija-flor. The cultivars show genetic divergence.

Genetic Divergence in Eucalyptus camaldulensis Progenies in the Savanna Biome in Mato Grosso, Brazil.

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Reginaldo Brito da Costa

Full Text Available Assessing the parental genetic differences and their subsequent prediction of progeny performance is an important first step to assure the efficiency of any breeding program. In this study, we estimate the genetic divergence in Eucalyptus camaldulensis based on the morphological traits of 132 progenies grown in a savanna biome. Thus, a field experiment was performed using a randomized block design and five replications to compare divergences in total height, commercial height, diameter at breast height, stem form and survival rate at 48 months. Tocher's clustering method was performed using the Mahalanobis and Euclidian distances. The Mahalanobis distance seemed more reliable for the assessed parameters and clustered all of the progenies into fourteen major groups. The most similar progenies (86 accessions were clustered into Group I, while the most dissimilar (1 progeny represented Group XIV. The divergence analysis indicated that promising crosses could be made between progenies allocated in different groups for high genetic divergence and for favorable morphological traits.

GENETIC DIVERGENCE AMONG COTTON GENOTYPES GROWN IN THE MAIN SEASON AND OFF SEASON

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THIAGO ALEXANDRE SANTANA GILIO

2017-01-01

Full Text Available The objective of this work was to evaluate the agronomic performance and estimate the genetic divergence of 18 cotton genotypes grown in the main season (sowed in December, 2012 and off season (sowed in January, 2013, considering their agronomic characteristics and resistance to Ramularia leaf spot. A randomized block experimental design was used, with five replications. The characteristics evaluated were plant height, first branch height, position of first fruiting branch, height of first fruiting branch, length between nodes, number of nodes, average number of bolls per plant, average boll weight, area under the disease progress curve (AUDPC related to the Ramularia leaf spot severity, weight of 100 - seed from the plant middle third, fiber percentage, average production per plant, yield and cotton fiber quality. The results were subjected to individual and joint analysis of variance and the genetic divergence was estimated according to multivariate procedures (Mahalanobis' generalized distance and Tocher's optimization method. The dissimilarity matrices were summed to estimate the genetic divergence, considering both growing periods. Genetic variability was found among the genotypes evaluated, in both the main season and off season. The characteristic that most contributed to the genetic divergence in the main season was the production per plant and, in the off season, was the fiber percentage. According to the results of the present work, the crosses between the genotypes BRS - 335 and FMT - 707; FM - 910 and FMT - 707; and IMA - 08 - 12427 and FMT - 707 are recommended.

Interspecific genetic divergence in grey mullets from the Goa region

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Menezes, M.R.; Martins, M.; Naik, S.

Genetic divergence and phylogenetic relationships among Mugil cephalus, Liza subviridis and Valamugil cunnesius were investigated by examining the electrophoretic patterns of ten enzymes and sarcoplasmic proteins. Among the 19 loci detected, eight...

Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation

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Duim, Birgitta; van der Graaf-van Bloois, Linda; Wagenaar, Jaap A; Zomer, Aldert L

2018-01-01

Abstract Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1–5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution. PMID:29608720

Increased genetic divergence between two closely related fir species in areas of range overlap

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Wang, Jing; Abbott, Richard J; Ingvarsson, Pär K; Liu, Jianquan

2014-01-01

Because of introgressive hybridization, closely related species can be more similar to each other in areas of range overlap (parapatry or sympatry) than in areas where they are geographically isolated from each other (allopatry). Here, we report the reverse situation based on nuclear genetic divergence between two fir species, Abies chensiensis and Abies fargesii, in China, at sites where they are parapatric relative to where they are allopatric. We examined genetic divergence across 126 amplified fragment length polymorphism (AFLP) markers in a set of 172 individuals sampled from both allopatric and parapatric populations of the two species. Our analyses demonstrated that AFLP divergence was much greater between the species when comparisons were made between parapatric populations than between allopatric populations. We suggest that selection in parapatry may have largely contributed to this increased divergence. PMID:24772279

High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens.

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Hu, Xin-Sheng; Yeh, Francis C; Hu, Yang; Deng, Li-Ting; Ennos, Richard A; Chen, Xiaoyang

2017-02-22

Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G st  = 0.05 ± 0.049). The smallest divergence is among African populations (G st  = 0.0081 ± 0.0025), with increased divergence among non-African populations (G st  = 0.0217 ± 0.0109) and then among African and non-African populations (G st  = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.

Genetic Divergence in Ducks for Economic Traits | Kalita | Animal ...

African Journals Online (AJOL)

D2 Statistics was used to identify the genetic divergence in 4 groups of duck, namely Khaki Campbell (KC), Desi (D), Khaki Campbell x Desi (KC x D) and Desi x Khaki Campbell (D x KC) reared under rural conditions at the Siphajar, Darrang District, Assam, India. The study showed that both Khaki Campbell and Desi or ...

Divergência genética entre progênies de café robusta Genetic divergence among robusta coffe progenies

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Milana Gonçalves Ivoglo

2008-12-01

Full Text Available Estudou-se a divergência genética de 21 progênies de meios-irmãos - 19 do grupo Congolês e duas do grupo Guineano - de introduções do germoplasma de café robusta (Coffea canephora do IAC. O estudo baseou-se em análises multivariadas de 14 características morfo-agronômicas, com o propósito de selecionar as progênies mais divergentes, visando à definição de população-base para posterior seleção e produção de híbridos. Avaliou-se também a importância das características discriminantes para análises de divergência, visando ao descarte das variáveis, segundo suas contribuições relativas. O experimento foi plantado e desenvolvido em campo experimental localizado no Pólo Regional do Nordeste Paulista, Mococa (SP, em blocos casualizados, com 21 tratamentos e 24 repetições. O agrupamento dos genótipos foi realizado com base nos métodos de Tocher e UPGMA. A matriz de dissimilaridade genética foi obtida por meio da distância generalizada de Mahalanobis, que serviu de base para a formação dos grupos. Os métodos empregados foram eficientes em detectar ampla variabilidade genética entre as progênies avaliadas. Vários grupos dissimilares foram identificados. As progênies IAC 2262, IAC 2290, IAC 2286, IAC 2292 e IAC 2291 são indicadas para compor programas de intercruzamentos, por terem sido consideradas as mais promissoras na obtenção de populações segregantes ou híbridos heteróticos. As características que menos contribuíram para a divergência genética foram, hierarquicamente: diâmetro da copa antes da poda, altura da planta antes da poda e área foliar.It was studied genetic divergence of 21 half-sib progenies, being 19 of the Congolês group and two of the Guineano group, introductions of germoplasma robust (Coffea canephora, based in 14 morpho-agronomic traits and multivariate procedures. It's aims to select the lineages most divergent for definition of population-base for posterior reciprocal

GENETIC DIVERGENCE AND MORPHO - AGRONOMIC PERFORMANCE OF JATROPHA CURCAS L. CLONES FOR SELECTION OF CLONAL VARIETIES

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ADRIANA QUEIROZ DE ALMEIDA

2016-01-01

Full Text Available The knowledge about genetic diversity of jatropha crop is important for genetic conservation resources and breeding of this species. The aim of this study was to evaluate the genetic diversity and performance of jatropha clones through morphological characterization to selection of clonal varieties for biofuels production. The clones were obtained through shoot cuttings from previous selection in a population of half - sibs progenies. The morphoagronomic analyses of clones was carried out at 180 days after transplantation and were evaluated plant height, stem diameter, number of primary branches and number of secondary branches, number of bunches and number of fruits per plant. Evaluating clones performance, significant results were found for the number of secondary branches. About analysis of genetic diversity, the measures of dissimilarity genetic varied from 0.62 to 13.11, this way, the UFRBPR14 and UFRBPR15 clones were more divergent. The Tocher method was efficient to verify formation of four groups. The characteristics that most contributed to the divergence among clones were branches number, height and number of bunches, and, stem diameter had lower contribution. The jatropha clones differed only in the secondary branches number and multivariate analysis showed divergence among the jatropha clones with formation of four groups. Also, branches number, plant height and number of bunches were characteristic that contributed to genetic divergence.

Divergent plate motion drives rapid exhumation of (ultra)high pressure rocks

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Liao, Jie; Malusà, Marco G.; Zhao, Liang; Baldwin, Suzanne L.; Fitzgerald, Paul G.; Gerya, Taras

2018-06-01

Exhumation of (ultra)high pressure [(U)HP] rocks by upper-plate divergent motion above an unbroken slab, first proposed in the Western Alps, has never been tested by numerical methods. We present 2D thermo-mechanical models incorporating subduction of a thinned continental margin beneath either a continental or oceanic upper plate, followed by upper-plate divergent motion away from the lower plate. Results demonstrate how divergent plate motion may trigger rapid exhumation of large volumes of (U)HP rocks directly to the Earth's surface, without the need for significant overburden removal by erosion. Model exhumation paths are fully consistent with natural examples for a wide range of upper-plate divergence rates. Exhumation rates are systematically higher than the divergent rate imposed to the upper plate, and the modeled size of exhumed (U)HP domes is invariant for different rates of upper-plate divergence. Major variations are instead predicted at depth for differing model scenarios, as larger amounts of divergent motion may allow mantle-wedge exhumation to shallow depth under the exhuming domes. The transient temperature increase, due to ascent of mantle-wedge material in the subduction channel, has a limited effect on exhumed continental (U)HP rocks already at the surface. We test two examples, the Cenozoic (U)HP terranes of the Western Alps (continental upper plate) and eastern Papua New Guinea (oceanic upper plate). The good fit between model predictions and the geologic record in these terranes encourages the application of these models globally to pre-Cenozoic (U)HP terranes where the geologic record of exhumation is only partly preserved.

Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes.

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Streicher, Jeffrey W; McEntee, Jay P; Drzich, Laura C; Card, Daren C; Schield, Drew R; Smart, Utpal; Parkinson, Christopher L; Jezkova, Tereza; Smith, Eric N; Castoe, Todd A

2016-07-01

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern-local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation-not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male-biased dispersal. © 2016 The Author(s).

Divergência genética entre cultivares de gérbera utilizando marcadores RAPD Genetic divergence among cultivars of gerbera using RAPD markers

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Rodrigo Kelson Silva Rezende

2009-11-01

Full Text Available No processo de produção comercial de mudas de gérbera, a cor da flor é uma das principais características morfológicas de interesse agronômico, sendo uma característica importante em programas de melhoramento genético. A utilização de marcadores moleculares pode servir para direcionar cruzamentos, confirmar novos híbridos ou genótipos mutantes e identificar novos genótipos para fins comerciais. Nesse contexto, o objetivo deste trabalho foi analisar a divergência genética entre seis cultivares de Gerbera jamesonii ('Jaguar Yellow', 'Jaguar Cream', 'Jaguar Lemon', 'Jaguar Salmon Pastel', 'Jaguar Red', 'Jaguar Deep Rose'. A análise de divergência genética entre as cultivares de gérbera foi realizada utilizando-se 21 primers, os quais amplificaram 37 fragmentos polimórficos de DNA, que foram usados para estimar o coeficiente de Jaccard, o qual apresentou uma média de 0,38, variando de 0,28 a 0,56. A estrutura genética entre as cultivares foi estimada pelo UPGMA, revelando dois grupos distintos, a 38% de similaridade genética. A maior similaridade genética encontrada (56% foi entre as cultivares 'Jaguar Yellow' e 'Jaguar Lemon'. Os resultados demonstram que a técnica RAPD oferece uma maneira rápida, relativamente barata e útil para a caracterização da divergência genética entre as diferentes cultivares de Gerbera jamesonii com relação à cor da flor.During the commercial production of gerbera seedlings, flower color is one of the main morphological aspects that have an agronomic interest and becoming an important feature in genetic breeding programs. The use of molecular markers may serve to direct crossings, new hybrids and mutants, besides confirm and identify new genotypes for commercial purposes. In that context, this work aimed to analyze the genetic divergence among six cultivars of Gerbera jamesonii ('Jaguar Yellow', 'Jaguar Cream', 'Jaguar Lemon', 'Jaguar Salmon Pastel', 'Jaguar Red', 'Jaguar Deep Rose'. The

Genetic divergence analysis in pumpkin

International Nuclear Information System (INIS)

Quamruzzaman, A.M.; Moniruzzaman, M.

2013-01-01

Genetic divergence among 18 punpkin genotypes was estimated using Mahalanohis's 1) statistic. Altogether lour clusters were formed where cluster I contained the highest number of genotypes (8) and cluster II contained the lowest (I). The highest intra-cluster distance was observed h.ir cluster I (0.83 I) and the lowest for clustcr IV (0.65 I). The highest inter-cluster distance was observed between cluster I and 11(24.346). Cluster II recorded the highest mean for fruit number/plant, TSS, fruit yield and niinitnuiii III cavity length and cavity diameter. Cluster III had the second highest mean for fruit diameter, fruit number/plant, individual unit weight, fruit yield and the fewest number of days to 1st Female flowering, earliness being a desirable trait. These crosses may produce new recombinants with desirable traits. (author)

Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20-year field experiment.

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Herrera, Carlos M; Bazaga, Pilar

2016-06-01

Little is known on the potential of ecological disturbance to cause genetic and epigenetic changes in plant populations. We take advantage of a long-term field experiment initiated in 1986 to study the demography of the shrub Lavandula latifolia , and compare genetic and epigenetic characteristics of plants in two adjacent subplots, one experimentally disturbed and one left undisturbed, 20 years after disturbance. Experimental setup was comparable to an unreplicated 'Before-After-Control-Impact' (BACI) design where a single pair of perturbed and control areas were compared. When sampled in 2005, plants in the two subplots had roughly similar ages, but they had established in contrasting environments: dense conspecific population ('Undisturbed' subpopulation) versus open area with all conspecifics removed ('Disturbed' subpopulation). Plants were characterized genetically and epigenetically using amplified fragment length polymorphism (AFLP) and two classes of methylation-sensitive AFLP (MSAP) markers. Subpopulations were similar in genetic diversity but differed in epigenetic diversity and multilocus genetic and epigenetic characteristics. Epigenetic divergence between subpopulations was statistically unrelated to genetic divergence. Bayesian clustering revealed an abrupt linear boundary between subpopulations closely coincident with the arbitrary demarcation line between subplots drawn 20 years back, which supports that genetic and epigenetic divergence between subpopulations was caused by artificial disturbance. There was significant fine-scale spatial structuring of MSAP markers in both subpopulations, which in the Undisturbed one was indistinguishable from that of AFLP markers. Genetic differences between subpopulations could be explained by divergent selection alone, while the concerted action of divergent selection and disturbance-driven appearance of new methylation variants in the Disturbed subpopulation is proposed to explain epigenetic differences. This

Genetic, ecological and morphological divergence between populations of the endangered Mexican Sheartail hummingbird (Doricha eliza.

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Yuyini Licona-Vera

Full Text Available The Mexican Sheartail (Doricha eliza, an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.

Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

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Hellberg, M E; Moy, G W; Vacquier, V D

2000-03-01

Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea).

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Santamaria, Carlos A; Mateos, Mariana; DeWitt, Thomas J; Hurtado, Luis A

2016-03-01

Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show evidence of hybridization. Populations are highly isolated, some of which appear to be very small; thus, the effects of drift are expected to reduce the efficiency of selection. Large genetic divergences among lineages, marked environmental differences in their ranges, reproductive isolation, and/or high isolation of populations may have resulted in morphological differences in L. occidentalis, not detected yet by traditional taxonomy. We used landmark-based geometric morphometric analyses to test for differences in body shape among highly divergent lineages of L. occidentalis, and among populations within these lineages. We analyzed a total of 492 individuals from 53 coastal localities from the southern California Bight to Central Mexico, including the Gulf of California. We conducted discriminant function analyses (DFAs) on body shape morphometrics to assess morphological variation among genetically differentiated lineages and their populations. We also tested for associations between phylogeny and morphological variation, and whether genetic divergence is correlated to multivariate morphological divergence. We detected significant differences in body shape among highly divergent lineages, and among populations within these lineages. Nonetheless, neither lineages nor populations can be discriminated on the basis of body shape, because correct classification rates of cross

The effects of medieval dams on genetic divergence and demographic history in brown trout populations

DEFF Research Database (Denmark)

Hansen, Michael Møller; Limborg, Morten; Ferchaud, A.-L.

2014-01-01

Background: Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River......, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally...... genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results: Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence...

Genetic divergence is decoupled from ecological diversification in the Hawaiian Nesosydne planthoppers.

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Roesch Goodman, Kari; Welter, Stephen C; Roderick, George K

2012-09-01

Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history using mitochondrial and multiple independent microsatellite loci in a species whose geographic distribution on the island of Hawaii enabled us to observe the chronology of divergence in its very earliest stages. We found that genetic divergence is associated with geographic features but not different plant hosts and that divergence times are very recent and on the same timescales as the dynamic geology of the island. Our results suggest an important role for geography in the dynamics of the early stages of divergence. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations.

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Hansen, Michael M; Limborg, Morten T; Ferchaud, Anne-Laure; Pujolar, José-Martin

2014-06-05

Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600-800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600-800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.

Extensive genetic divergence among Diptychus maculatus populations in northwest China

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Meng, Wei; Yang, Tianyan; Hai, Sa; Ma, Yanwu; Cai, Lingang; Ma, Xufa; Gao, Tianxiang; Guo, Yan

2015-05-01

D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity ( h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences ( k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other ( P<0.01). The largest F st value was between Yurungkash River population and Muzat River population, while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

NARCIS (Netherlands)

Shahin, A.; Smulders, M.J.M.; Tuyl, van J.M.; Arens, P.F.P.; Bakker, F.T.

2014-01-01

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

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Brunner Sylvia

2008-05-01

Full Text Available Abstract Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

Multivariate genetic divergence among sugarcane clones by multivariate analysis associated with mixed models

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Valéria Rosa Lopes

2014-02-01

Full Text Available This work had the aim to evaluate the genetic divergence in sugarcane clones using the methodology of graphic dispersion by principal components analysis associated to linear mixed models, indentifying the more divergent and productive genotypes with more precision, for a subsequent combination. 138 sugarcane clones of the RB97 series of the Sugarcane Breeding Program of the Universidade Federal do Parana, more two standard cultivars were evaluated in three environments, with two replications. The two first components explained 96% of the total variation, sufficiently for explaining the divergence found. The variable that contributed the most to de divergence was kilogram of brix per plot (BKP followed by brix, mass of 10 stalks and number of stalks per plot. The more divergent sugarcane clones were RB975008, RB975112, RB975019, RB975153 and RB975067 and the more productive clones were RB975269, RB977533, RB975102, RB975317 and RB975038.

Genetic divergence among cupuaçu accessions by multiscale bootstrap resampling

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Vinicius Silva dos Santos

2015-06-01

Full Text Available This study aimed at investigating the genetic divergence of eighteen accessions of cupuaçu trees based on fruit morphometric traits and comparing usual methods of cluster analysis with the proposed multiscale bootstrap resampling methodology. The data were obtained from an experiment conducted in Tomé-Açu city (PA, Brazil, arranged in a completely randomized design with eighteen cupuaçu accessions and 10 repetitions, from 2004 to 2011. Genetic parameters were estimated by restricted maximum likelihood/best linear unbiased prediction (REML/BLUP methodology. The predicted breeding values were used in the study on genetic divergence through Unweighted Pair Cluster Method with Arithmetic Mean (UPGMA hierarchical clustering and Tocher’s optimization method based on standardized Euclidean distance. Clustering consistency and optimal number of clusters in the UPGMA method were verified by the cophenetic correlation coefficient (CCC and Mojena’s criterion, respectively, besides the multiscale bootstrap resampling technique. The use of the clustering UPGMA method in situations with and without multiscale bootstrap resulted in four and five clusters, respectively, while the Tocher’s method resulted in seven clusters. The multiscale bootstrap resampling technique proves to be efficient to assess the consistency of clustering in hierarchical methods and, consequently, the optimal number of clusters.

Divergência genética entre cinco genótipos de melão rendilhado Genetic divergence among five muskmelon cultivars

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Adriana Antonieta do Nascimento Rizzo

2002-06-01

Full Text Available Estimou-se a divergência genética entre cinco genótipos de melão rendilhado (Cucumis melo var. reticulatus Naud. (JAB-20, JAB-21, JAB-22, JAB-23 e 'Bônus nº 2' e determinou-se qual a contribuição relativa das 16 características avaliadas [nº médio de flores masculinas, hermafroditas/planta; produção total de frutos/m², peso médio dos frutos comerciáveis; diâmetro médio transversal e longitudinal do fruto (DMTF e DMLF; diâmetro médio transversal da inserção do pedúculo (DMTP; espessura média do mesocarpo e epicarpo (EMM e EME; diâmetro médio longitudinal e transversal do lóculo (DMTL e DMLL; proporção da cavidade (PC; desprendimento de sementes (DS; teor de sólidos solúveis totais (SST, pH e acidez titulável (AT] na divergência gen��tica. Obtiveram-se dois grupos de similaridade: I- JAB-20, JAB-21 e 'Bônus nº2' e II- JAB-22 e JAB-23. As características DMLF, DMTP, DMLL, DS e SST foram as que mais contribuíram para a divergência genética entre os genótipos.The genetic divergence of five cultivars of muskmelon was estimated (Cucumis melo var. reticulatus Naud (JAB-20, JAB-21, JAB-22, JAB-23 and 'Bônus nº2' and the relative contribution of each 16 characteristics were determined (number of male flowers per plant; total production of fruit, weight of fruits; longitudinal and transversal diameters of fruits; thickness and color of flesh and skin; longitudinal and transversal loculos diameter of fruits; seed loosing; netting thickness; and % total solvers solids, pH and total acidity in genetic divergence. Two groups of similarity were formed between the genitors by the values of D², one of then was constituted of the JAB-20 and JAB-21 and 'Bônus nº 2' genotypes, and another of the JAB-22 and JAB-23. The characteristics of longitudinal loculos diameters, longitudinal diameter of fruits, transversal diameter of peduncle insertion, % total solvers solids and seed loosing contributed to for genetic

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

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Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

Genetic divergence among hybrids of 'Cravo' mandarin with 'Pêra' sweet orange Divergência genética entre híbridos de tangerina 'Cravo' com laranja 'Pêra'

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Roberto Pedroso de Oliveira

2003-02-01

Full Text Available Molecular markers have been used as tools in breading programs of sexual hybridation, allowing the genetic characterization of a large number of genotypes. The RADP markers are the most used since the employed techniques are simple and of low cost. To evaluate the genetic divergence among F1 hybrids of 'Cravo' mandarin (Citrus reticulata Blanco and 'Pêra' sweet orange (C. sinensis (L. Osbeck, this study analyses the variability and similarity of the hybrids among themselves and with their parents. Random Amplified Polimorfic DNA marker analysis, with 102 primers, were applied to a population composed of 94 hybrids and their parents. Multivariate genetic divergence analysis of the principal components and Tocher grouping were carried out only considering the polymorphic fragments. Genetic distances were calculated by the arithmetic complement of the Jaccard index. Bidimensional dispersion graphs among hybrid and parent distances and of the divergence analysis by principal components were constructed. High genetic similarity among Cravo and Pêra varieties and their hybrids was verified, showing a casual distribution from the hybrids in relation to the parents, but in intermediary positions. The principal component analysis showed little applicability in the study of hybrid genetic divergence. The hybrids and parents were classified in groups based on the genetic similarity, using the Tocher optimization method.Os marcadores moleculares têm sido utilizados como ferramentas em programas de melhoramento por hibridação sexual, permitindo a caracterização genética de grande número de genótipos. Os marcadores moleculares RAPD são os mais utilizados pois as técnicas empregadas são simples e de baixo custo. Avaliou-se a divergência genética entre híbridos F1 de tangerina 'Cravo' (Citrus reticulata Blanco com laranja 'Pêra' (C. sinensis (L. Osbeck e estudou-se a variabilidade e a similaridade desses materiais entre si e em relação aos

Rapid divergence of mussel populations despite incomplete barriers to dispersal.

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Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia L; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul Hamid A; Gillespie, Rosemary G; Becking, Leontine E

2018-04-01

Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence. © 2018 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Meiotic Consequences of Genetic Divergence Across the Murine Pseudoautosomal Region.

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Dumont, Beth L

2017-03-01

The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X / Y segregation is buffered against the accumulation of homology-disrupting mutations. Here, I investigate the interplay of PAR evolution and function in two interfertile house mouse subspecies characterized by structurally divergent PARs, Mus musculus domesticus and M. m. castaneus Using cytogenetic methods to visualize the sex chromosomes at meiosis, I show that intersubspecific F 1 hybrids harbor an increased frequency of pachytene spermatocytes with unsynapsed sex chromosomes. This high rate of asynapsis is due, in part, to the premature release of synaptic associations prior to completion of prophase I. Further, I show that when sex chromosomes do synapse in intersubspecific hybrids, recombination is reduced across the paired region. Together, these meiotic defects afflict ∼50% of spermatocytes from F 1 hybrids and lead to increased apoptosis in meiotically dividing cells. Despite flagrant disruption of the meiotic program, a subset of spermatocytes complete meiosis and intersubspecific F 1 males remain fertile. These findings cast light on the meiotic constraints that shape sex chromosome evolution and offer initial clues to resolve the paradox raised by the rapid evolution of this functionally significant locus. Copyright © 2017 by the Genetics Society of America.

Genetic divergence of a sympatric lake-resident-anadromous three-spined stickleback Gasterosteus aculeatus species pair.

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Drevecky, C J; Falco, R; Aguirre, W E

2013-07-01

The genetic relationship between sympatric, morphologically divergent populations of anadromous and lake-resident three-spined stickleback Gasterosteus aculeatus in the Jim Creek drainage of Cook Inlet, Alaska, was examined using microsatellite loci and mitochondrial d-loop sequence data. Resident samples differed substantially from sympatric anadromous samples in the Jim Creek drainage with the magnitude of the genetic divergence being similar to that between allopatric resident and anadromous populations in other areas. Resident samples were genetically similar within the Jim Creek drainage, as were the anadromous samples surveyed. Neighbour-joining and Structure cluster analysis grouped the samples into four genetic clusters by ecomorph (anadromous v. all resident) and geographic location of the resident samples (Jim Creek, Mat-Su and Kenai). There was no evidence of hybridization between resident and anadromous G. aculeatus in the Jim Creek drainage, which thus appear to be reproductively isolated. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

Divergence and genetic variability among superior rubber tree genotypes Divergência e variabilidade genética de genótipos superiores de seringueira

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Lígia Regina Lima Gouvêa

2010-02-01

Full Text Available The objective of this work was to estimate the genetic variability and divergence among 22 superior rubber tree (Hevea sp. genotypes of the IAC 400 series. Univariate and multivariate analyses were performed using eight quantitative traits (descriptors, including yield. In the univariate analyses, the estimated parameters were: genetic and environmental variances; genetic and environmental coefficients of variation; and the variation index. The Mahalanobis generalized distance, the Tocher agglomerative method and canonical variables were used for the multivariate analyses. In the univariate analyses, variability was verified among the genotypes for all the variables evaluated. The Tocher method grouped the genotypes into 11 clusters of dissimilarity. The first four canonical variables explained 87.93% of the cumulative variation. The highest genetic variability was found in rubber yield-related traits, which contributed the most to the genetic divergence. The most divergent pairs of genotypes are suggested for crossbreeding. The genotypes evaluated are suitable for breeding and may be used to continue the IAC rubber tree breeding program.O objetivo deste trabalho foi estimar a divergência e a variabilidade genética entre 22 genótipos superiores de seringueira (Hevea sp. da série IAC 400. Análises univariadas e multivariadas foram realizadas com oito caracteres quantitativos (descritores, incluindo produtividade. Na análise univariada, os parâmetros estimados foram: variâncias genética e ambiental, coeficientes de variação genética e ambiental, e índice de variação. A distância generalizada de Mahalanobis, o método aglomerativo de Tocher e variáveis canônicas foram utilizados nas análises multivariadas. Nas análises univariadas, verificou-se variabilidade entre os genótipos para todas as variáveis avaliadas. O método de Tocher agrupou os genótipos em 11 grupos de dissimilaridade. As quatro primeiras variáveis can

Complex patterns of genetic and phenotypic divergence in an island bird and the consequences for delimiting conservation units.

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Phillimore, A B; Owens, I P F; Black, R A; Chittock, J; Burke, T; Clegg, S M

2008-06-01

Substantial phenotypic and genetic variation is often found below the species level and this may be useful in quantifying biodiversity and predicting future diversification. However, relatively few studies have tested whether different aspects of intraspecific variation show congruent patterns across populations. Here, we quantify several aspects of divergence between 13 insular populations of an island endemic bird, the Vanuatu white-eye (Zosterops flavifrons). The components of divergence studied are mitochondrial DNA (mtDNA), nuclear DNA microsatellites and morphology. These different aspects of divergence present subtly different scenarios. For instance, an mtDNA phylogenetic tree reveals a potential cryptic species on the most southerly island in Vanuatu and considerable divergence between at least two other major phylogroups. Microsatellite loci suggest that population genetic divergence between insular populations, both between and within phylogroups, is substantial, a result that is consistent with a low level of interisland gene flow. Finally, most populations were found to be strongly morphologically divergent, but no single population was morphologically diagnosable from all others. Taken together, our results show that, although many measures of divergence are concordant in this system, the number of divergent units identified varies widely depending on the characters considered and approach used. A continuum of divergence and a degree of discordance between different characters are both to be expected under simple models of evolution, but they present problems in terms of delimiting conservation units.

Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

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Julianne M O'Reilly-Wapstra

Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

Divergência genética entre acessos de feijão-de-vagem de hábito de crescimento indeterminado Genetic divergence among climbing snap bean accessions

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Flávia B. Abreu

2004-09-01

ão-de-vagem.The search for snap bean cultivars presenting better production and quality is of crucial relevance due to the agricultural importance of this crop in the Rio de Janeiro State, Brazil. The determination of genetic divergence by multivariate analysis, through which several characters can be simultaneously dimensioned, is a rather advantageous technique since it allows to identify sources of variability, to evaluate the importance of characters for genetic divergence, and to identify genetic combinations with greater chances of success before crossings are performed. Multivariate analysis techniques allowed us to verify that common bean accessions presenting undetermined growth habits, originated from the UENF germplasm bank, show variability in relation to the evaluated traits. The Tocher optimization method allowed the formation of two groups; however, sub grouping by the same method has confirmed the occurrence of variability among group 1 accessions, from the formation of six subgroups. No relationship between genetic diversity and geographic origin of the accesses was found by using this method. The genetic divergence observed among the common bean accesses was quantified by three canonic variables, which explained around 79% of the total available variation. Discarding the variables of lower relative importance allowed us to identify the traits that have truly contributed to the determination of the genetic divergence: 100-seed weight, days for flowering, pod diameter, pod length, total number of beans and average number of beans. Accesses UENF-1429, UENF-1432, UENF-1442, UENF-1445 and UENF-1448 showed a good performance for the evaluated traits and genetic divergence, being indicated for use in breeding programs of snap beans.

Genetic divergence through joint analysis of morphoagronomic and molecular characters in accessions of Jatropha curcas.

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Pestana-Caldas, C N; Silva, S A; Machado, E L; de Souza, D R; Cerqueira-Pereira, E C; Silva, M S

2016-10-05

The aim of this study was to investigate the genetic divergence between accessions of Jatropha curcas through joint analysis of morphoagronomic and molecular characters. To this end, we investigated 11 morphoagronomic characters and performed molecular genotyping, using 23 inter-simple sequence repeat (ISSR) primers in 46 accessions of J. curcas. We calculated the contribution of each character on divergence using analysis of variance. The grouping among accessions was performed using the Ward-MLM (modified location model) method, using morphoagronomic and molecular data, whereas the cophenetic correlation was obtained based on Gower's algorithm. There were significant differences in all growth-related characteristics: number of primary and secondary branches per plant, plant height, and stem diameter. For characters related to grain production, differences were found for number of fruit clusters per plant and number of inflorescence clusters per plant and average number of seeds per fruit. The greatest phenotypic variation was found in plant height (59.67- 222.33 cm), whereas the smallest variation was found in average number of seeds per fruit (0-2.90), followed by the number of fruit clusters per plant (0-8.67). In total, 94 polymorphic ISSR fragments were obtained. The genotypic grouping identified six groups, indicating that there is genetic divergence among the accessions. The most promising crossings for future hybridization were identified among accessions UFRB60 and UFVJC45, and UFRB61 and UFVJC18. In conclusion, the joint analysis of morphoagronomic characters and ISSR markers is an efficient method to assess the genetic divergence in J. curcas.

GENETIC DIVERGENCE AMONG Passiflora cristalina Vanderpl & Zappi. GENOTYPES BASED ON FLOWER AND FRUIT CHARACTERISTICS

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GREICIELE FARIAS DA SILVEIRA

Full Text Available ABSTRACT This study aimed to evaluate the genetic divergence among Passiflora cristalina genotypes and quantify the relative contribution of 30 flower and fruit characteristics, seeking to support the preservation and characterization of genetic resources of the species for preservation and use in future breeding programs. We evaluated 150 fruit and 150 flowers collected in 15 genotypes with naturally occurring in the municipality of Alta Floresta, MT. The characterization of genotypes was performed through 30 morphological characteristics of flowers and fruits, 21 of these for flower and 9 for fruit. Data were evaluated using the principal components and cluster methods obtained by UPGMA method from the similarity matrix (Euclidian mean distance, using the Genes software. By principal component analysis, it has been found that the first three components have absorbed 52.11% of the accumulated variation. The characteristics that most contributed to the discrimination of genotypes were fresh fruit weight, stigma length, length of corona filaments, fruit width, petal width and pulp weight, which are more responsive for the selection of P.cristalina genotypes. Smaller contributions to diversity were obtained from anther width, bract width and fruit length. The smallest contributions for diversity were obtained from the following characteristics: anther width, bract width and fruit length. Through UPGMA clustering method, it was found that there is a large genetic divergence among genotypes analyzed because all genotypes were grouped with over 50% of dissimilarity. This study identified genotypes 4, 5 and 9 as the most divergent and therefore the most suitable for breeding in future breeding programs and genetic conservation of the species.

Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird

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Wiley, Anne E.; Welch, Andreanna J.; Ostrom, P.H.; James, Helen F.; Stricker, C.A.; Fleischer, R.C.; Gandhi, H.; Adams, J.; Ainley, D.G.; Duvall, F.; Holmes, N.; Hu, D.; Judge, S.; Penniman, J.; Swindle, K.A.

2012-01-01

Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels (Pterodroma sandwichensis) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (?? 13C, ?? 15N and ??D, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with ?? ST = 0. 50 (p Feather ??D varied from -69 to 53???. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies. ?? 2011 Springer-Verlag (outside the USA).

Ecological divergence and evolutionary transition of resprouting types in Banksia attenuata.

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He, Tianhua

2014-08-01

Resprouting is a key functional trait that allows plants to survive diverse disturbances. The fitness benefits associated with resprouting include a rapid return to adult growth, early flowering, and setting seed. The resprouting responses observed following fire are varied, as are the ecological outcomes. Understanding the ecological divergence and evolutionary pathways of different resprouting types and how the environment and genetics interact to drive such morphological evolution represents an important, but under-studied, topic. In the present study, microsatellite markers and microevolutionary approaches were used to better understand: (1) whether genetic differentiation is related to morphological divergence among resprouting types and if so, whether there are any specific genetic variations associated with morphological divergence and (2) the evolutionary pathway of the transitions between two resprouting types in Banksia attenuata (epicormic resprouting from aerial stems or branch; resprouting from a underground lignotuber). The results revealed an association between population genetic differentiation and the morphological divergence of postfire resprouting types in B. attenuata. A microsatellite allele has been shown to be associated with epicormic populations. Approximate Bayesian Computation analysis revealed a likely evolutionary transition from epicormic to lignotuberous resprouting in B. attenuata. It is concluded that the postfire resprouting type in B. attenuata is likely determined by the fire's characteristics. The differentiated expression of postfire resprouting types in different environments is likely a consequence of local genetic adaptation. The capacity to shift the postfire resprouting type to adapt to diverse fire regimes is most likely the key factor explaining why B. attenuata is the most widespread member of the Banksia genus.

Rapid male-specific regulatory divergence and down regulation of spermatogenesis genes in Drosophila species hybrids.

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Jennifer Ferguson

Full Text Available In most crosses between closely related species of Drosophila, the male hybrids are sterile and show postmeiotic abnormalities. A series of gene expression studies using genomic approaches have found significant down regulation of postmeiotic spermatogenesis genes in sterile male hybrids. These results have led some to suggest a direct relationship between down regulation in gene expression and hybrid sterility. An alternative explanation to a cause-and-effect relationship between misregulation of gene expression and male sterility is rapid divergence of male sex regulatory elements leading to incompatible interactions in an interspecies hybrid genome. To test the effect of regulatory divergence in spermatogenesis gene expression, we isolated 35 fertile D. simulans strains with D. mauritiana introgressions in either the X, second or third chromosome. We analyzed gene expression in these fertile hybrid strains for a subset of spermatogenesis genes previously reported as significantly under expressed in sterile hybrids relative to D. simulans. We found that fertile autosomal introgressions can cause levels of gene down regulation similar to that of sterile hybrids. We also found that X chromosome heterospecific introgressions cause significantly less gene down regulation than autosomal introgressions. Our results provide evidence that rapid male sex gene regulatory divergence can explain misexpression of spermatogenesis genes in hybrids.

Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

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Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

2016-09-01

Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers.

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Streitberger, K; Schweizer, M; Kropatsch, R; Dekomien, G; Distl, O; Fischer, M S; Epplen, J T; Hertwig, S T

2012-10-01

As a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders' preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

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Wong, Mark K L; Woodman, James D; Rowell, David M

2017-07-01

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Comparative epigenetic and genetic spatial structure of the perennial herb Helleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence.

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Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

2017-08-16

Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations. © 2017 Botanical Society of America.

Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex

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Daza-Vamenta, Riza; Glusman, Gustavo; Rowen, Lee; Guthrie, Brandon; Geraghty, Daniel E.

2004-01-01

The major histocompatibility complex (MHC) is comprised of the class I, class II, and class III regions, including the MHC class I and class II genes that play a primary role in the immune response and serve as an important model in studies of primate evolution. Although nonhuman primates contribute significantly to comparative human studies, relatively little is known about the genetic diversity and genomics underlying nonhuman primate immunity. To address this issue, we sequenced a complete rhesus macaque MHC spanning over 5.3 Mb, and obtained an additional 2.3 Mb from a second haplotype, including class II and portions of class I and class III. A major expansion of from six class I genes in humans to as many as 22 active MHC class I genes in rhesus and levels of sequence divergence some 10-fold higher than a similar human comparison were found, averaging from 2% to 6% throughout extended portions of class I and class II. These data pose new interpretations of the evolutionary constraints operating between MHC diversity and T-cell selection by contrasting with models predicting an optimal number of antigen presenting genes. For the clinical model, these data and derivative genetic tools can be implemented in ongoing genetic and disease studies that involve the rhesus macaque. PMID:15289473

Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis

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Ornelas Juan

2011-02-01

Full Text Available Abstract Background Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Results Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma, and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Conclusions Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the

Genetic Divergence and signatures of natural election in marginal populations of a Keystone, long-lived conifer, Eastern White Pine (Pinus strobus) from Northern Ontario

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Vikram E. Chhatre; Om P. Rajora

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations...

Heterosis and genetic distance in rapeseed (Brasica napus L.). Use of different indicators of genetic divergence in 7x7 diallel

OpenAIRE

Lefort-Buson, Marianne; Guillot-Lemoine, Brigitte; Dattée, Yvette

1986-01-01

The paper deals with a comparison of different indicators of genetic divergence between rapeseed parental lines : the relationship coefficient defined by MALÈCOT the generalized distance D2 of Mahalanobis, and a new G2 parameter close to HANSON & CASAS' R2. The purpose of the authors is to discuss the advantages of their simultaneous use in the prediction of both heterosis values and F1 performances of hybrids from parental lines. Relationships between heterosis values and genetic distanc...

Rapid evolution of the intersexual genetic correlation for fitness in Drosophila melanogaster.

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Collet, Julie M; Fuentes, Sara; Hesketh, Jack; Hill, Mark S; Innocenti, Paolo; Morrow, Edward H; Fowler, Kevin; Reuter, Max

2016-04-01

Sexual antagonism (SA) arises when male and female phenotypes are under opposing selection, yet genetically correlated. Until resolved, antagonism limits evolution toward optimal sex-specific phenotypes. Despite its importance for sex-specific adaptation and existing theory, the dynamics of SA resolution are not well understood empirically. Here, we present data from Drosophila melanogaster, compatible with a resolution of SA. We compared two independent replicates of the "LHM " population in which SA had previously been described. Both had been maintained under identical, controlled conditions, and separated for around 200 generations. Although heritabilities of male and female fitness were similar, the intersexual genetic correlation differed significantly, being negative in one replicate (indicating SA) but close to zero in the other. Using population sequencing, we show that phenotypic differences were associated with population divergence in allele frequencies at nonrandom loci across the genome. Large frequency changes were more prevalent in the population without SA and were enriched at loci mapping to genes previously shown to have sexually antagonistic relationships between expression and fitness. Our data suggest that rapid evolution toward SA resolution has occurred in one of the populations and open avenues toward studying the genetics of SA and its resolution. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

The genetic structure of populations from Haiti and Jamaica reflect divergent demographic histories.

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Simms, Tanya M; Rodriguez, Carol E; Rodriguez, Rosa; Herrera, Rene J

2010-05-01

The West Indies represent an amalgamation of African, European and in some cases, East Asian sources, but the contributions from each ethnic group remain relatively unexplored from a genetic perspective. In the present study, we report, for the first time, allelic frequency data across the complete set of 15 autosomal STR loci for general collections from Haiti and Jamaica, which were subsequently used to examine the genetic diversity present in each island population. Our results indicate that although both Haiti and Jamaica display genetic affinities with the continental African collections, a stronger African signal is detected in Haiti than in Jamaica. Although only minimal contributions from non-African sources were observed in Haiti, Jamaica displays genetic input from both European and East Asian sources, an admixture profile similar to other New World collections of African descent analyzed in this report. The divergent genetic signatures present in these populations allude to the different migratory events of Africans, Europeans, and East Asians into the New World.

Ecological and genetic divergence between two lineages of Middle American túngara frogs Physalaemus (= Engystomops pustulosus

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Ron Santiago R

2010-05-01

Full Text Available Abstract Background Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. Here we combine population genetic methods (microsatellites with phylogenetic information (mtDNA to define genetic population clusters of the wide-spread Neotropical túngara frog (Physalaemus pustulosus. We measure gene flow and migration within and between population clusters and compare genetic diversity between population clusters. By applying ecological niche modeling we determine whether the two most divergent genetic groups of the túngara frog (1 inhabit different habitats, and (2 are separated geographically by unsuitable habitat across a gap in the distribution. Results Most population structure is captured by dividing all sample localities into two allopatric genetic lineages. The Northern genetic lineage (NW Costa Rica is genetically homogenous while the Southern lineage (SW Costa Rica and Panama is sub-divided into three population clusters by both microsatellite and mtDNA analyses. Gene flow is higher within the Northern lineage than within the Southern lineage, perhaps due to increased landscape heterogeneity in the South. Niche modeling reveals differences in suitable habitat between the Northern and Southern lineages: the Northern lineage inhabits dry/pine-oak forests, while the Southern lineage is confined to tropical moist forests. Both lineages seem to have had little movement across the distribution gap, which persisted during the last glacial maximum. The lack of movement was more pronounced for the Southern lineage than for the Northern lineage. Conclusions This study confirms the finding of previous studies that túngara frogs diverged into two allopatric genetic lineages north and south of the gap in the distribution in central Costa Rica several million years ago. The allopatric distribution is attributed to unsuitable habitat and probably other unknown ecological factors

Divergent Cumulative Cultural Evolution

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Marriott, Chris; Chebib, Jobran

2016-01-01

Divergent cumulative cultural evolution occurs when the cultural evolutionary trajectory diverges from the biological evolutionary trajectory. We consider the conditions under which divergent cumulative cultural evolution can occur. We hypothesize that two conditions are necessary. First that genetic and cultural information are stored separately in the agent. Second cultural information must be transferred horizontally between agents of different generations. We implement a model with these ...

Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

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Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

2018-05-02

Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

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Chunping Liu

Full Text Available Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE, whereas it has a scattered and patchy distribution in South China (SC. In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM. Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278 among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

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Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

Science.gov (United States)

Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Development of Microsatellite Markers in the Branched Broomrape Phelipanche ramosa L. (Pomel and Evidence for Host-Associated Genetic Divergence

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Valérie Le Corre

2014-01-01

Full Text Available Phelipanche ramosa is a parasitic plant that infects numerous crops worldwide. In Western Europe it recently expanded to a new host crop, oilseed rape, in which it can cause severe yield losses. We developed 13 microsatellite markers for P. ramosa using next-generation 454 sequencing data. The polymorphism at each locus was assessed in a sample of 96 individuals collected in France within 6 fields cultivated with tobacco, hemp or oilseed rape. Two loci were monomorphic. At the other 11 loci, the number of alleles and the expected heterozygosity ranged from 3 to 6 and from 0.31 to 0.60, respectively. Genetic diversity within each cultivated field was very low. The host crop from which individuals were collected was the key factor structuring genetic variation. Individuals collected on oilseed rape were strongly differentiated from individuals collected on hemp or tobacco, which suggests that P. ramosa infecting oilseed rape forms a genetically diverged race. The microsatellites we developed will be useful for population genetics studies and for elucidating host-associated genetic divergence in P. ramosa.

Divergência genética entre linhagens de matrizes de corte por meio de análise de agrupamento Genetic divergence in meat-type hens using cluster analysis

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Marcos Yamaki

2008-05-01

Full Text Available Este trabalho foi realizado com o objetivo de avaliar a divergência genética de três linhagens de matrizes de corte do Programa de Melhoramento Genético da UFV. Foram avaliados dados de 270 aves, 90 de cada linhagem, para estudo das características dias para o primeiro ovo (DPPO, taxa de postura da 22ª à 56ª semana (TP, peso médio individual na 32ª (PMI1, 40ª (PMI2, 48ª (PMI3, 56ª (PMI4 e 64ª semanas de idade (PMI5; e peso médio do ovo, obtido pela média da pesagem de três ovos na 32ª (PMO1, 40ª (PMO2, 48ª (PMO3, 56ª (PMO4 e 64ª semanas de idade (PMO5. Para avaliar a divergência, foram utilizados dois métodos: hierárquico do vizinho mais próximo e otimização de Tocher. Pelo método hierárquico do vizinho mais próximo, utilizando-se a distância de Mahalanobis ao quadrado (D² como medida de dissimilaridade, formou-se um único grupo. Pelo método de otimização de Tocher, foram formados dois grupos, comprovando que os dois métodos foram discordantes na avaliação da divergência genética de linhas de aves de corte. As características que apresentaram as contribuições relativas mais expressivas para a divergência foram, respectivamente, PMO1 (25,71%, DDPO (21,76%, PMI4 (17,65% e PMI2 (13,04%.Genetic divergence among three lineages of meat-type hens from the Genetic Breeding Program of the Universidade Federal de Viçosa was evaluated for the following traits: days at first egg (DPPO, egg production rate (TP from 22nd to 56th week, body weight on the 32nd (PMI1, on 40th (PMI2, at 48th (PMI3, at 56th (PMI4 and at the 64th week (PMI5, egg weight on the 32nd (PMO1, on 40th (PMO2, at 48th (PMO3, at 56th (PMO4 and at the 64th week (PMO5. Traits were measured on 270 hens (90 of each lineage and two different methods were used to evaluate genetic divergence. For the single linkage hierarchical method, using the squared Mahalanobis distance (D² as the dissimilarity measure, only one single group was formed. When

The influence of life-history strategy on genetic differentiation and lineage divergence in darters (Percidae: Etheostomatinae).

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Fluker, Brook L; Kuhajda, Bernard R; Harris, Phillip M

2014-11-01

Recent studies determined that darters with specialized breeding strategies can exhibit deep lineage divergence over fine geographic scales without apparent physical barriers to gene flow. However, the extent to which intrinsic characteristics interact with extrinsic factors to influence population divergence and lineage diversification in darters is not well understood. This study employed comparative phylogeographic and population genetic methods to investigate the influence of life history on gene flow, dispersal ability, and lineage divergence in two sympatric sister darters with differing breeding strategies. Our results revealed highly disparate phylogeographic histories, patterns of genetic structure, and dispersal abilities between the two species suggesting that life history may contribute to lineage diversification in darters, especially by limiting dispersal among large river courses. Both species also showed striking differences in demographic history, indicating that extrinsic factors differentially affected each species during the Pleistocene. Collectively, our results indicate that intrinsic and extrinsic factors have influenced levels of gene flow among populations within both species examined. However, we suggest that life-history strategy may play a more important role in lineage diversification in darters than previously appreciated, a finding that has potentially important implications for understanding diversification of the rich North American freshwater fish fauna. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae).

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Jaros, Ursula; Tribsch, Andreas; Comes, Hans Peter

2018-02-12

Disentangling the relative roles of past fragmentation (vicariance), colonization (dispersal) and post-divergence gene flow in the genetic divergence of continental island organisms remains a formidable challenge. Amplified fragment length polymorphisms (AFLPs) were used to (1) gain further insights into the biogeographical processes underlying the Pleistocene diversification of the Aegean Nigella arvensis complex; (2) evaluate the role of potential key factors driving patterns of population genetic variability (mating system, geographical isolation and historical contingencies); and (3) test the robustness of conclusions previously drawn from chloroplast (cp) DNA. Genetic diversity was analysed for 235 AFLP markers from 48 populations (497 individuals) representing 11 taxa of the complex using population genetic methods and Bayesian assignment tests. Most designated taxa are identifiable as genetically distinct units. Both fragmentation and dispersal-driven diversification processes occurred at different geological time scales, from Early to Late Pleistocene, specifically (1) sea barrier-induced vicariant speciation in the Cyclades, the Western Cretan Strait and Ikaria; and (2) bi-regional colonizations of the 'Southern Aegean Island Arc' from the Western vs. Eastern Aegean mainland, followed by allopatric divergences in Crete vs. Rhodos and Karpathos/Kasos. Outcrossing island taxa experienced drift-related demographic processes that are magnified in the two insular selfing species. Population genetic differentiation on the mainland seems largely driven by dispersal limitation, while in the Central Aegean it may still be influenced by historical events (island fragmentation and sporadic long-distance colonization). The biogeographical history of Aegean Nigella is more complex than expected for a strictly allopatric vicariant model of divergence. Nonetheless, the major phylogeographical boundaries of this radiation are largely congruent with the geography and

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations.

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Wang, Yuchen; Lu, Dongsheng; Chung, Yeun-Jun; Xu, Shuhua

2018-01-01

Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied. We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant. These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

Rapid recent human evolution and the accumulation of balanced genetic polymorphisms.

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Wills, Christopher

2011-01-01

All evolutionary change can be traced to alterations in allele frequencies in populations over time. DNA sequencing on a massive scale now permits us to follow the genetic consequences as our species has diverged from our close relatives and as we have colonized different parts of the world and adapted to them. But it has been difficult to disentangle natural selection from many other factors that alter frequencies. These factors include mutation and intragenic reciprocal recombination, gene conversion, segregation distortion, random drift, and gene flow between populations (these last two are greatly influenced by splits and coalescences of populations over time). The first part of this review examines recent studies that have had some success in dissecting out the role of natural selection, especially in humans and Drosophila. Among many examples, these studies include those that have followed the rapid evolution of traits that may permit adaptation to high altitude in Tibetan and Andean populations. In some cases, directional selection has been so strong that it may have swept alleles close to fixation in the span of a few thousand years, a rapidity of change that is also sometimes encountered in other organisms. The second part of the review summarizes data showing that remarkably few alleles have been carried completely to fixation during our recent evolution. Some of the alleles that have not reached fixation may be approaching new internal equilibria, which would indicate polymorphisms that are maintained by balancing selection. Finally, the review briefly examines why genetic polymorphisms, particularly those that are maintained by negative frequency dependence, are likely to have played an important role in the evolution of our species. A method is suggested for measuring the contribution of these polymorphisms to our gene pool. Such polymorphisms may add to the ability of our species to adapt to our increasingly complex and challenging environment. �

Genetic Divergence and Signatures of Natural Selection in Marginal Populations of a Keystone, Long-Lived Conifer, Eastern White Pine (Pinus strobus) from Northern Ontario

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Chhatre, Vikram E.; Rajora, Om P.

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (N e) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and N e than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and N e between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance. PMID:24859159

Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, Eastern White Pine (Pinus strobus) from Northern Ontario.

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Chhatre, Vikram E; Rajora, Om P

2014-01-01

Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (Ne) and higher genetic differentiation than central populations. We tested these hypotheses using eastern white pine (Pinus strobus) as a model for keystone, long-lived widely-distributed plants. All 614 eastern white pine trees, in a complete census of two populations each of marginal old-growth, central old-growth, and central second-growth, were genotyped at 11 microsatellite loci. The central populations had significantly higher allelic and genotypic diversity, latent genetic potential (LGP) and Ne than the marginal populations. However, heterozygosity and fixation index were similar between them. The marginal populations were genetically diverged from the central populations. Model testing suggested predominant north to south gene flow in the study area with curtailed gene flow to northern marginal populations. Signatures of natural selection were detected at three loci in the marginal populations; two showing divergent selection with directional change in allele frequencies, and one balancing selection. Contrary to the general belief, no significant differences were observed in genetic diversity, differentiation, LGP, and Ne between old-growth and second-growth populations. Our study provides information on the dynamics of migration, genetic drift and selection in central versus marginal populations of a keystone long-lived plant species and has broad evolutionary, conservation and adaptation significance.

Genetic divergence among populations and accessions of the spineless peach palm from Pampa Hermosa landrace used in the heart-of-palm agribusiness in Brazil.

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Alves-Pereira, Alessandro; Clement, Charles R; Picanço-Rodrigues, Doriane

2012-04-01

Although originally domesticated for its fruit, exploitation of the peach palm (Bactris gasipaes Kunth) in the production of gourmet heart-of-palm has also become an important activity, hence the need for improved material for large-scale production, on employing the Pampa Hermosa landrace as the seed source. In this study 11 microsatellite markers were used to evaluate genetic divergence among 96 elite plants representing four populations of spineless peach palm from the above cited source. Genetic variability was high (H(T) = 0.82). The low levels of divergence [F(ST) (0.023), G(ST)' (0.005)] and the high number of migrants (Nm - 3.8 to 52.2) indicated significant interpopulation gene flow. Some of the plants presented high levels of genetic divergence, but the plants were grouped independently of their geographic origins. When combined with morpho-agronomic evaluation, the results found could substantially contribute towards mounting an efficient tool for obtaining superior genotypes with wide genetic variability for improvement programs.

Genetic divergence among populations and accessions of the spineless peach palm from Pampa Hermosa landrace used in the heart-of-palm agribusiness in Brazil

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Alessandro Alves-Pereira

2012-01-01

Full Text Available Although originally domesticated for its fruit, exploitation of the peach palm (Bactris gasipaes Kunth in the production of gourmet heart-of-palm has also become an important activity, hence the need for improved material for large-scale production, on employing the Pampa Hermosa landrace as the seed source. In this study 11 microsatellite markers were used to evaluate genetic divergence among 96 elite plants representing four populations of spineless peach palm from the above cited source. Genetic variability was high (H T = 0.82. The low levels of divergence [F ST (0.023, G ST' (0.005] and the high number of migrants (Nm -3.8 to 52.2 indicated significant interpopulation gene flow. Some of the plants presented high levels of genetic divergence, but the plants were grouped independently of their geographic origins. When combined with morpho-agronomic evaluation, the results found could substantially contribute towards mounting an efficient tool for obtaining superior genotypes with wide genetic variability for improvement programs.

The puzzle of Italian rice origin and evolution: determining genetic divergence and affinity of rice germplasm from Italy and Asia.

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Xingxing Cai

Full Text Available The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (H(e = 0.63-0.65 in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships.

Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan.

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Hiraoka, Koichi; Tomaru, Nobuhiro

2009-05-01

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species' range. Although population differentiation was very low (F (ST) = 0.027; R (ST) = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H (E) = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.

Genetic structure and divergence in populations of Lutzomyia cruciata, a phlebotomine sand fly (Diptera: Psychodidae) vector of Leishmania mexicana in southeastern Mexico.

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Pech-May, Angélica; Marina, Carlos F; Vázquez-Domínguez, Ella; Berzunza-Cruz, Miriam; Rebollar-Téllez, Eduardo A; Narváez-Zapata, José A; Moo-Llanes, David; Ibáñez-Bernal, Sergio; Ramsey, Janine M; Becker, Ingeborg

2013-06-01

The low dispersal capacity of sand flies could lead to population isolation due to geographic barriers, climate variation, or to population fragmentation associated with specific local habitats due to landscape modification. The phlebotomine sand fly Lutzomyia cruciata has a wide distribution throughout Mexico and is a vector of Leishmania mexicana in the southeast. The aim of this study was to evaluate the genetic diversity, structure, and divergence within and among populations of Lu. cruciata in the state of Chiapas, and to infer the intra-specific phylogeny using the 3' end of the mitochondrial cytochrome b gene. We analyzed 62 sequences from four Lu. cruciata populations and found 26 haplotypes, high genetic differentiation and restricted gene flow among populations (Fst=0.416, Nm=0.701, p<0.001). The highest diversity values were recorded in populations from Loma Bonita and Guadalupe Miramar. Three lineages (100% bootstrap and 7% overall divergence) were identified using a maximum likelihood phylogenetic analysis which showed high genetic divergence (17.2-22.7%). A minimum spanning haplotype network also supported separation into three lineages. Genetic structure and divergence within and among Lu. cruciata populations are hence affected by geographic heterogeneity and evolutionary background. Data obtained in the present study suggest that Lu. cruciata in the state of Chiapas consists of at least three lineages. Such findings may have implications for vector capacity and hence for vector control strategies. Copyright © 2013 Elsevier B.V. All rights reserved.

Regulatory divergence of X-linked genes and hybrid male sterility in mice.

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Oka, Ayako; Shiroishi, Toshihiko

2014-01-01

Postzygotic reproductive isolation is the reduction of fertility or viability in hybrids between genetically diverged populations. One example of reproductive isolation, hybrid male sterility, may be caused by genetic incompatibility between diverged genetic factors in two distinct populations. Genetic factors involved in hybrid male sterility are disproportionately located on the X chromosome. Recent studies showing the evolutionary divergence in gene regulatory networks or epigenetic effects suggest that the genetic incompatibilities occur at much broader levels than had previously been thought (e.g., incompatibility of protein-protein interactions). The latest studies suggest that evolutionary divergence of transcriptional regulation causes genetic incompatibilities in hybrid animals, and that such incompatibilities preferentially involve X-linked genes. In this review, we focus on recent progress in understanding hybrid sterility in mice, including our studies, and we discuss the evolutionary significance of regulatory divergence for speciation.

Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean.

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Deli, Temim; Kalkan, Evrim; Karhan, Selahattin Ünsal; Uzunova, Sonya; Keikhosravi, Alireza; Bilgin, Raşit; Schubart, Christoph D

2018-04-11

Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187). Our results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes

Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

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Ali, Sajid; Rodriguez-Algaba, Julian; Thach, Tine; Sørensen, Chris K.; Hansen, Jens G.; Lassen, Poul; Nazari, Kumarse; Hodson, David P.; Justesen, Annemarie F.; Hovmøller, Mogens S.

2017-01-01

We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales. PMID:28676811

Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

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Sajid Ali

2017-06-01

Full Text Available We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales.

Rapid detection of genetic modification for GMO monitoring in agriculture

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Petrović Sofija

2015-01-01

Full Text Available Transgenic technology has expanded the ways of new genetic variability creation. Genetically modified organisms (GMOs are organisms which total genome is altered in a way that could not happen in nature. GM crops recorded a steady increase in its share in agricultural production. However, for the most part, GMO in agriculture has been limited to two cultivars - soy and corn, and the two genetic modifications, the total herbicide resistance and pest of the Lepidoptera genus. In order to monitor cultivation and trade of GMOs, tests of different precision are used, qualitatively and/or quantitatively determining the presence of genetic modification. Tests for the rapid determination of the presence of GM are suitable, since they can be implemented quickly and accurately, in terms of declared sensitivity, outside or in the laboratory. The example of the use of rapid tests demonstrates their value in use for rapid and efficient monitoring.

A potential third Manta Ray species near the Yucat?n Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico

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Hinojosa-Alvarez, Silvia; Walter, Ryan P.; Diaz-Jaimes, Pindaro; Galv?n-Maga?a, Felipe; Paig-Tran, E. Misty

2016-01-01

We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0....

East-west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

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Guay, P.-J.; Chesser, R.T.; Mulder, R.A.; Afton, A.D.; Paton, D.C.; McCracken, K.G.

2010-01-01

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (??ST = 0. 747), one nuclear intron (??ST = 0.193) and eight microsatellite loci (FST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews' (Austral Avian Record 2:83-107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other. ?? 2010 Springer Science+Business Media B.V.

Estudo da divergência genética entre seis linhas de aves Legorne utilizando técnicas de análise multivariada Genetic divergence study among six Leghorn lines by multivariate analysis

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A.V. Pires

2002-06-01

Full Text Available A divergência genética entre seis linhas de aves Legorne (L1, L2, L3, L4, L5 e L6, desenvolvidas pela UFV, foi avaliada utilizando análise de variáveis canônicas e o método de agrupamento de Tocher. Foram incluídas no estudo oito características: peso corporal na 40ª semana (PC40, na 48ª semana (PC48, na 56ª semana (PC56; peso do ovo na 40ª semana (PO40, na 44ª semana (PO44, na 52ª semana (PO52, na 60ª semana (PO60 e taxa de postura da 40ª a 62ª semana (TP. Foi observada diferença entre as linhas quanto às características estudadas. A linha L4 mostrou-se divergente das demais, apresentando a menor média canônica, e foi alocada em grupo distinto das outras pelo teste de Tocher. O desempenho das diferentes linhas foi também avaliado por meio da análise de variância multivariada, usando o teste do maior autovalor de Roy, e por meio do teste de Roy para comparações múltiplas. Verificou-se divergência genética entre as linhas da UFV, sendo PC40 a característica que mais contribuiu para a divergência.Genetic divergence among six Leghorn lines (L1, L2, L3, L4, L5 e L6, developed by Universidade Federal de Viçosa, Brazil, was evaluated using canonical variate analysis and grouping method of Tocher. Eight traits were used: body weight at 40 weeks, at 48 weeks, at 56 weeks; egg weight at 40 weeks, at 44 weeks, at 52 weeks, at 60 weeks and laying ratio from 40 to 62 weeks of age. Significant differences were observed among lines for the studied traits. The line L4 was divergent in comparison with the other ones, showed the smallest canonical mean and was allocated in a different group. The performance of different genetic groups was also evaluated by multivariate analysis of variance, using Roy test of the largest eigenvalue and the Roy principle for multiple comparisons. Genetic divergence among UFV's lines was observed and body weight at 40 weeks was the trait that more contributed for this divergence.

The estimation of genetic divergence

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Holmquist, R.; Conroy, T.

1981-01-01

Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

Divergência genética entre acessos e cultivares de mamoneira por meio de estatística multivariada Genetic divergence on castor bean accesses and cultivars through multivariate analysis

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Mauro Nóbrega da Costa

2006-11-01

Full Text Available O objetivo deste trabalho foi avaliar a divergência genética entre acessos e cultivares de mamoneira (Ricinus communis L. e utilizá-la como critério na escolha de genitores que viabilizem, a partir de hibridações, a formação de populações segregantes. Os tratamentos foram representados pelos acessos BRA 4871, BRA 2968, BRA 5550 e BRA 7722 Papo-de-gia, e as cultivares BRS 188 Paraguaçu, BRS 149 Nordestina, IAC-80, Mirante-10 e Pernambucana Melhorada. As características analisadas foram: início do florescimento (FR, número de racemos por planta (NRP, comprimento efetivo do racemo primário (CR, altura de planta (AP, potencial produtivo (PP e teor de óleo nas sementes (TO. A divergência genética foi estimada por meio de estatística multivariada, com base em variáveis canônicas e análise de agrupamento, tendo-se empregado a distância euclidiana média. Houve a formação de dois grupos: o grupo I formado por oito genótipos e o grupo II por apenas um genótipo, a cultivar Mirante-10. Apesar de a cultivar Mirante-10 ter sido a mais divergente, não deve ser recomendada para hibridação, por sua baixa média de desempenho. As demais cultivares também apresentam restrições para hibridação, por serem bastante similares. As variáveis que mais contribuíram para a divergência genética foram FR, AP, TO e CR.This work aimed to evaluate genetic divergence among castor bean (Ricinus communis L. cultivars, in order to enable the choice of parents which make the formation of segregating populations possible. Accesses BRA 4871, BRA 2968, BRA 5550 and BRA 7722 Papo-de-gia, and cultivars BRS 188 Paraguaçu, BRS 149 Nordestina, IAC-80, Mirante-10 and Pernambucana Melhorada were evaluated. Characteristics analyzed were: days to flowering, number of racemes per plant, length of pistillate region of main raceme, plant height, potential yield, and seed oil content. The genetic divergence among accesses and cultivars was studied by

Divergência genética entre populações de cebola com base em marcadores morfológicos Genetic divergence in onion populations based on morphological markers

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Rosa Lía Barbieri

2005-04-01

Full Text Available Bulbos de 16 acessos do Banco Ativo de Germoplasma de Cebola (Allium cepa da Embrapa Clima Temperado foram avaliados quanto a peso, diâmetro, altura, coloração das túnicas externas, formato, uniformidade e conservação pós-colheita nas condições ambientais de Pelotas - RS, com o objetivo de estimar a divergência genética entre populações de cebola. Os dados obtidos foram submetidos a análises de agrupamento e de componentes principais. Foi evidenciada a presença de variabilidade genética para os caracteres considerados. Os acessos foram divididos em três grupos: o primeiro reuniu 13 acessos incluindo todas as variedades locais e as variedades comerciais com bulbos de coloração marrom; o segundo formado por uma variedade local de bulbos roxos; e o terceiro grupo reunindo as duas variedades comerciais de bulbos brancos. Os caracteres que mais contribuíram para a divergência entre os acessos foram a cor, o peso e a conservação pós-colheita.Bulbs of 16 acessions from Onion Gene Bank of Embrapa Clima Temperado were evaluated for weight, diameter, length, skin color, shape, uniformity, and post harvest conservation in Pelotas, RS, Brazil. The objective of this work was to estimate genetic divergence in onion populations. The obtained data were submitted to principal component and cluster analysis. There was genetic variability for evaluated traits. Acessions were separated in three clusters. One cluster had 13 populations including all landraces and cultivars with brown skin color; the second cluster had the landrace with violet bulbs; and the third cluster had the two cultivars with white bulbs. Skin color, weight and post harvest of bulbs showed the highest contribution to divergence among acessions.

Genetic and morphological divergence among Cooper's Hawk (Accipiter cooperii) populations breeding in north-central and western North America

Science.gov (United States)

Sonsthagen, Sarah A.; Rosenfield, Robert N.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William C.; Driscoll, Timothy G.; Bozek, Michael A.; Sloss, Brian L.; Talbot, Sandra L.

2012-01-01

Cooper's Hawk (Accipiter cooperii) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits (PST) and genetic markers (FST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite FST= 0.031-0.050; mitochondrial DNA ΦST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits (PST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of FST and ΦST interpopulation estimates. Comparison of PSTand FSTestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

Behavioural divergence, interfertility and speciation: a review.

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Pillay, Neville; Rymer, Tasmin L

2012-11-01

Behavioural compatibility between mates is fundamental for maintaining species boundaries and is achieved through appropriate communication between males and females. A breakdown in communication will lead to behavioural divergence and reduced interfertility. In this review, we summarise the current knowledge on male signals and female perception of these signals, integrating the literature from several taxa. We advocate that signaller-perceiver coevolution, which is usually under strong stabilising selection to enable mating, forms the basis of species-specific mate recognition systems. The mechanisms (phylogeny, geography, ecology, biology) shaping signaller-perceiver systems are briefly discussed to demonstrate the factors underpinning the evolution of signaller-perceiver couplings. Since divergence and diversification of communication systems is driven by changes in the mechanical properties of sensory pathways and morphology of sensory organs, we highlight signal modalities (auditory, olfactory, visual, tactile) and their importance in communication, particularly in mate selection. Next, using available examples and generating a stylised model, we suggest how disruption (biological, ecological, stochastic) of signaller-perceiver systems drives behavioural divergence and consequently results in reduced interfertility and speciation. Future studies should adopt an integrative approach, combining multiple parameters (phylogeny, adaptive utility of communication systems, genetics and biomechanical/biochemical properties of signals and perception) to explore how disruption of signaller-perceiver systems results in behavioural divergence and reduced interfertility. Finally, we question the impact that rapid environmental change will have on disruption of communication systems, potentially interfering with signaller-perceiver couplings. Copyright © 2012 Elsevier B.V. All rights reserved.

Genetic divergence of the common bean (Phaseolus vulgaris L.) group Carioca using morpho-agronomic traits by multivariate analysis.

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Gonçalves Ceolin, Ana Cristina; Gonçalves-Vidigal, Maria Celeste; Soares Vidigal Filho, Pedro; Vinícius Kvitschal, Marcus; Gonela, Adriana; Alberto Scapim, Carlos

2007-03-01

The objective of this study was to evaluate the genetic divergence among the common bean group Carioca by the Tocher method (based on Mahalanobis distance) and graphic dispersion of canonic variables, aiming to identify populations with wide genetic variability. Eighteen genotypes were evaluated in four seasons using a randomized block design with four replications. The mean weight of 100 seeds, in three experiments, and the mean number of pods per plant, in one experiment, were the most important characteristics for the genetic divergence, representing more than 46% of the total variation in the first canonic variable. The first two canonic variables were sufficient to explain about 88.23% of the total variation observed in the average of the four environments. The results showed that CNFC 8008 and CNFC 8009 genotypes presented the best yield averages in all the experiments. While Pérola, Princesa and CNFC 8005 cultivars were the most dissimilar for morpho-agronomic traits. Therefore, the combinations of PérolaxCNFC 8008, CNFC 8005xCNFC 8009, PérolaxCNFC 8009, PrincesaxCNFC 8008 and PrincesaxCNFC 8009 were indicated for interpopulational breeding.

Rapid Genetic Analysis in Congenital Hyperinsulinism

DEFF Research Database (Denmark)

Christesen, Henrik Thybo; Brusgaard, Klaus; Alm, Jan

2007-01-01

BACKGROUND: In severe, medically unresponsive congenital hyperinsulinism (CHI), the histological differentiation of focal versus diffuse disease is vital, since the surgical management is completely different. Genetic analysis may help in the differential diagnosis, as focal CHI is associated...... with a paternal germline ABCC8 or KCNJ11 mutation and a focal loss of maternal chromosome 11p15, whereas a maternal mutation, or homozygous/compound heterozygous ABCC8 and KCNJ11 mutations predict diffuse-type disease. However, genotyping usually takes too long to be helpful in the absence of a founder mutation....... METHODS: In 4 patients, a rapid genetic analysis of the ABBC8 and KCNJ11 genes was performed within 2 weeks on request prior to the decision of pancreatic surgery. RESULTS: Two patients had no mutations, rendering the genetic analysis non-informative. Peroperative multiple biopsies showed diffuse disease...

Worldwide variation in hip fracture incidence weakly aligns with genetic divergence between populations.

Science.gov (United States)

Wallace, I J; Botigué, L R; Lin, M; Smaers, J B; Henn, B M; Grine, F E

2016-09-01

This study investigates the influence of genetic differentiation in determining worldwide heterogeneity in osteoporosis-related hip fracture rates. The results indicate that global variation in fracture incidence exceeds that expected on the basis of random genetic variance. Worldwide, the incidence of osteoporotic hip fractures varies considerably. This variability is believed to relate mainly to non-genetic factors. It is conceivable, however, that genetic susceptibility indeed differs across populations. Here, we present the first quantitative assessment of the effects of genetic differentiation on global variability in hip fracture rates. We investigate the observed variance in publically reported age-standardized rates of hip fracture among 28 populations from around the world relative to the expected variance given the phylogenetic relatedness of these populations. The extent to which these variances are similar constitutes a "phylogenetic signal," which was measured using the K statistic. Population genetic divergence was calculated using a robust array of genome-wide single nucleotide polymorphisms. While phylogenetic signal is maximized when K > 1, a K value of only 0.103 was detected in the combined-sex fracture rate pattern across the 28 populations, indicating that fracture rates vary more than expected based on phylogenetic relationships. When fracture rates for the sexes were analyzed separately, the degree of phylogenetic signal was also found to be small (females: K = 0.102; males: K = 0.081). The lack of a strong phylogenetic signal underscores the importance of factors other than stochastic genetic diversity in shaping worldwide heterogeneity in hip fracture incidence.

Genetic divergence and its implication in breeding of desired plant type in coriander -Coriandrum sativum L.-

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Singh S.P.

2005-01-01

Full Text Available Seventy germplasm lines of coriander (Coriandrum sativum L. of diverse eco-geographical origin were undertaken in present investigation to determine the genetic divergence following multivariate and canonical analysis for seed yield and its 9 component traits. The 70 genotypes were grouped into 9 clusters depending upon the genetic architecture of genotypes and characters uniformity and confirmed by canonical analysis. Seventy percent of total genotypes (49/70 were grouped in 4 clusters (V, VI, VIII and IX, while apparent diversity was noticed for 30 percent genotypes (21/70 that diverged into 5 clusters (I, II, III, FV, and VII. The maximum inter cluster distance was between I and IV (96.20 followed by III and IV (91.13 and I and VII (87.15. The cluster VI was very unique having genotypes of high mean values for most of the component traits. The cluster VII had highest seeds/umbel (35.3 ± 2.24, and leaves/plant (12.93 ± 0.55, earliest flowering (65.05 ± 1.30 and moderately high mean values for other characters. Considering high mean and inter cluster distance breeding plan has been discussed to select desirable plant types.

Deep genetic divergence between disjunct Refugia in the Arctic-Alpine King's Crown, Rhodiola integrifolia (Crassulaceae.

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Eric G DeChaine

Full Text Available Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King's Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia, and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia. Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome.

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer.

Science.gov (United States)

Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A

2016-07-01

Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution.

Genetic divergence in the Indian mackerel Rastrelliger kanagurta (Cuv) from the coastal waters of Peninsular India and the Andaman Sea

Digital Repository Service at National Institute of Oceanography (India)

Menezes, M.R.; Naik, S.; Martins, M.

Genetic divergence in the Indian mackerel Rastrelliger kanagurta (Cuv) from the west coast (Goa), east coast (Madras) and the Andaman Sea was estimated, using allozyme markers. Skeletal muscle and eye proteins were electrophoretically analysed for 5...

The Genetic Basis of Baculum Size and Shape Variation in Mice

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Nicholas G. Schultz

2016-05-01

Full Text Available The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.

Phenotypic Divergence in the Reproductive Traits of Marbled ...

African Journals Online (AJOL)

Overall, the results indicated some level of phenotypic divergence of the fish ... divergence cannot be partitioned between fishing mortality, genetic .... female fish was estimated from the egg counts ..... that greatly improved the quality of the.

A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico.

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Hinojosa-Alvarez, Silvia; Walter, Ryan P; Diaz-Jaimes, Pindaro; Galván-Magaña, Felipe; Paig-Tran, E Misty

2016-01-01

We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0.78%) from the currently recognized Manta birostris and M. alfredi species, and (2) a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris , or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.

Genetic Divergence and Chemotype Diversity in the Fusarium Head Blight Pathogen Fusarium poae.

Science.gov (United States)

Vanheule, Adriaan; De Boevre, Marthe; Moretti, Antonio; Scauflaire, Jonathan; Munaut, Françoise; De Saeger, Sarah; Bekaert, Boris; Haesaert, Geert; Waalwijk, Cees; van der Lee, Theo; Audenaert, Kris

2017-08-23

Fusarium head blight is a disease caused by a complex of Fusarium species. F. poae is omnipresent throughout Europe in spite of its low virulence. In this study, we assessed a geographically diverse collection of F. poae isolates for its genetic diversity using AFLP (Amplified Fragment Length Polymorphism). Furthermore, studying the mating type locus and chromosomal insertions, we identified hallmarks of both sexual recombination and clonal spread of successful genotypes in the population. Despite the large genetic variation found, all F. poae isolates possess the nivalenol chemotype based on Tri7 sequence analysis. Nevertheless, Tri gene clusters showed two layers of genetic variability. Firstly, the Tri1 locus was highly variable with mostly synonymous mutations and mutations in introns pointing to a strong purifying selection pressure. Secondly, in a subset of isolates, the main trichothecene gene cluster was invaded by a transposable element between Tri5 and Tri6 . To investigate the impact of these variations on the phenotypic chemotype, mycotoxin production was assessed on artificial medium. Complex blends of type A and type B trichothecenes were produced but neither genetic variability in the Tri genes nor variability in the genome or geography accounted for the divergence in trichothecene production. In view of its complex chemotype, it will be of utmost interest to uncover the role of trichothecenes in virulence, spread and survival of F. poae .

Evaluation of genetic divergence among clones of conilon coffee after scheduled cycle pruning.

Science.gov (United States)

Dalcomo, J M; Vieira, H D; Ferreira, A; Lima, W L; Ferrão, R G; Fonseca, A F A; Ferrão, M A G; Partelli, F L

2015-11-30

Coffea canephora genotypes from the breeding program of Instituto Capixaba de Pesquisa e Extensão Rural were evaluated, and genetic diversity was estimated with the aim of future improvement strategies. From an initial group of 55 genotypes, 18 from the region of Castelo, ES, were selected, and three clones of the cultivars "Vitória" and "robusta tropical." Upon completion of the scheduled cycle pruning, 17 morphoagronomic traits were measured in the 22 genotypes selected. The principal components method was used to evaluate the contributions relative to the traits. The genetic dissimilarity matrix was obtained through Mahalanobis generalized distance, and genotypes were grouped using the hierarchical method based on the mean of the distances. The most promising clones of Avaliação Castelo were AC02, AC03, AC12, AC13, AC22, AC24, AC26, AC27, AC28, AC29, AC30, AC35, AC36, AC37, AC39, AC40, AC43, and AC46. These methods detected high genetic variability, grouping, by similarity, the genotypes in five groups. The trait that contributed the least to genetic divergence was the number of leaves in plagiotropic branches; however, this was not eliminated, because discarding it altered the groups. There are superior genotypes with potential for use in the next stages of the breeding program, aimed at both the composition of clonal variety and hybridizations.

Ecological and Genetic Divergences with Gene Flow of Two Sister Species (Leucomeris decora and Nouelia insignis) Driving by Climatic Transition in Southwest China.

Science.gov (United States)

Zhao, Yujuan; Yin, Genshen; Pan, Yuezhi; Gong, Xun

2018-01-01

Understanding of the processes of divergence and speciation is a major task for biodiversity researches and may offer clearer insight into mechanisms generating biological diversity. Here, we employ an integrative approach to explore genetic and ecological differentiation of Leucomeris decora and Nouelia insignis distributed allopatrically along the two sides of the biogeographic boundary 'Tanaka Line' in Southwest China. We addressed these questions using ten low-copy nuclear genes and nine plastid DNA regions sequenced among individuals sampled from 28 populations across their geographic ranges in China. Phylogenetic, coalescent-based population genetic analyses, approximate Bayesian computation (ABC) framework and ecological niche models (ENMs) were conducted. We identified a closer phylogenetic relationship in maternal lineage of L. decora with N. insignis than that between L . decora and congeneric Leucomeris spectabilis . A deep divergence between the two species was observed and occurred at the boundary between later Pliocene and early Pleistocene. However, the evidence of significant chloroplast DNA gene flow was also detected between the marginal populations of L. decora and N. insignis . Niche models and statistical analyses showed significant ecological differentiation, and two nuclear loci among the ten nuclear genes may be under divergent selection. These integrative results imply that the role of climatic shift from Pliocene to Pleistocene may be the prominent factor for the divergence of L . decora and N . insignis , and population expansion after divergence may have given rise to chloroplast DNA introgression. The divergence was maintained by differential selection despite in the face of gene flow.

Divergência genética entre progênies de maracujazeiro- amarelo com base em características das plântulas Genetic divergence among yellow passion fruit progenies based on seed traits

Directory of Open Access Journals (Sweden)

Jacson Rondinelli da Silva Negreiros

2008-03-01

Full Text Available O objetivo do presente trabalho foi avaliar a diversidade genética entre 24 populações de maracujazeiro-amarelo, discriminando os caracteres mais importantes na avaliação da divergência genética, com base em características das plântulas. Foram coletadas sementes de frutos obtidos a partir de polinização natural de vinte e quatro populações segregantes de meios-irmãos de maracujazeiro-amarelo. Utilizou-se delineamento experimental inteiramente casualizado, em vinte e quatro tratamentos (populações segregantes, com quatro repetições, considerando-se como unidade experimental cada grupo de 50 sementes. Aos 28 dias, avaliaram-se a porcentagem de germinação e o índice de velocidade de emergência (IVE. Aos 45 dias, avaliaram-se porcentagem de sobrevivência, altura das plântulas, comprimento de raiz, número de folhas e massa da matéria seca total das plântulas. Os dados obtidos foram submetidos à análise de variância, e as médias foram agrupadas pelo método de Scott & Knott. A diversidade genética foi estudada de acordo com o método de agrupamento de Tocher, baseado na distância de Mahalanobis (D² e variáveis canônicas. As características que mais contribuíram para a divergência genética foram porcentagem de germinação, número de folhas e IVE. A população 20 pode ser recomendada para hibridação com as outras populações devido à sua alta divergência e também altas taxas de germinação e vigor de sementes.The genetic diversity was studied among passion fruit (Passiflora edulis f. flavicarpa progenies, discriminating the characters most important of seed traits for genetic divergence evaluation. Seeds were extracted of fruits gotten by natural pollination of twenty four half-sib segregant populations. The experiment was outlined as an entirely randomized design with twenty four treatments (segregant populations, four replications and 50 seeds per experimental unit. The germination percentage and the

Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium.

Directory of Open Access Journals (Sweden)

Pim Bongaerts

2010-05-01

Full Text Available Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a approximately 30 m depth range at three locations on the Great Barrier Reef (n = 336. The populations were assessed for genetic structure using a combination of mitochondrial (putative control region and nuclear (three microsatellites markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium. Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.

Segmenting the human genome based on states of neutral genetic divergence.

Science.gov (United States)

Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

2013-09-03

Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

Science.gov (United States)

Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

2011-12-01

Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

Understanding of research, genetics and genetic research in a rapid ethical assessment in north west Cameroon.

Science.gov (United States)

Kengne-Ouafo, Jonas A; Millard, James D; Nji, Theobald M; Tantoh, William F; Nyoh, Doris N; Tendongfor, Nicholas; Enyong, Peter A; Newport, Melanie J; Davey, Gail; Wanji, Samuel

2016-05-01

There is limited assessment of whether research participants in low-income settings are afforded a full understanding of the meaning of medical research. There may also be particular issues with the understanding of genetic research. We used a rapid ethical assessment methodology to explore perceptions surrounding the meaning of research, genetics and genetic research in north west Cameroon. Eleven focus group discussions (including 107 adults) and 72 in-depth interviews were conducted with various stakeholders in two health districts in north west Cameroon between February and April 2012. Most participants appreciated the role of research in generating knowledge and identified a difference between research and healthcare but gave varied explanations as to this difference. Most participants' understanding of genetics was limited to concepts of hereditary, with potential benefits limited to the level of the individual or family. Explanations based on supernatural beliefs were identified as a special issue but participants tended not to identify any other special risks with genetic research. We demonstrated a variable level of understanding of research, genetics and genetic research, with implications for those carrying out genetic research in this and other low resource settings. Our study highlights the utility of rapid ethical assessment prior to complex or sensitive research. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza.

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Ying Wu

Full Text Available Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown.We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i all three triploid hybrids are stable in both chromosome number and gross structure; (ii stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner.Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic instabilities at the molecular level. These novel hybrids might

Rapid Recombination Mapping for High-Throughput Genetic Screens in Drosophila

OpenAIRE

Sapiro, Anne L.; Ihry, Robert J.; Buhr, Derek L.; Konieczko, Kevin M.; Ives, Sarah M.; Engstrom, Anna K.; Wleklinski, Nicholas P.; Kopish, Kristin J.; Bashirullah, Arash

2013-01-01

Mutagenesis screens are a staple of classical genetics. Chemical-induced mutations, however, are often difficult and time-consuming to identify. Here, we report that recombination analysis with pairs of dominant visible markers provides a rapid and reliable strategy to map mutations in Drosophila melanogaster. This method requires only two generations and a total of six crosses in vials to estimate the genetic map position of the responsible lesion with high accuracy. This genetic map positio...

Divergência genética e subcoleção representativa de populações da traça-do-tomateiro Genetic divergence and representative tomato pinworm populations subcollection

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Gisele Rodrigues Moreira

2004-05-01

Full Text Available O objetivo deste trabalho foi estudar a divergência genética e propor uma subcoleção representativa da traça-do-tomateiro, Tuta absoluta (TDT. O experimento foi conduzido com quatro populações do inseto procedentes de Uberlândia, MG, Viçosa, MG, Camocim de São Félix, PE, e Santa Teresa, ES, e cinco acessos de tomateiro, 'Santa Clara', 'Moneymaker', TOM-601, PI 126445 (Lycopersicon hirsutum f. typicum e PI 134417 (L. hirsutum f. glabratum. Foi realizada análise de agrupamento (método de Tocher, usando a distância de Mahalanobis como medida de dissimilaridade e verificada a importância relativa dos caracteres da TDT para a divergência genética entre populações por meio do método de Singh. As populações de cada grupo obtido pela análise de agrupamento foram combinadas e, para cada caráter, foi realizado o teste t de Student para uma média. Existe variabilidade genética entre populações da TDT provenientes de diferentes localidades do Brasil, quando estão infestando Lycopersicon spp. A mortalidade larval teve maior contribuição para a divergência genética entre as populações, com exceção de PI 134417, cujo caráter de maior contribuição foi o número de pupas fêmeas. Propõe-se uma subcoleção da TDT tomando-se por base a combinação das populações de Santa Teresa e Uberlândia.This work aimed to study the genetic diversity and to propose a representative tomato pinworm, Tuta absoluta (TDT, subcollection. Populations of insect originally from Uberlândia, MG, Viçosa (MG, Camocim de São Félix, PE, and Santa Teresa, ES, Brazil, and five tomato accessions, 'Santa Clara', 'Moneymaker', TOM-601, PI 126445 (Lycopersicon hirsutum f. typicum and PI 134417 (L. hirsutum f. glabratum were used. Grouping analysis (Tocher method, using the Mahalanobis distance as dissimilarity measurement was performed and the relative importance of TDT characters to the genetic divergence among populations was evaluated by Singh

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana).

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Shih, Kai-Ming; Chang, Chung-Te; Chung, Jeng-Der; Chiang, Yu-Chung; Hwang, Shih-Ying

2018-01-01

Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana , disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, F ST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana . Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana , but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana , was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population

Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana

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Kai-Ming Shih

2018-02-01

Full Text Available Double digest restriction site-associated DNA sequencing (ddRADseq is a tool for delivering genome-wide single nucleotide polymorphism (SNP markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals of K. davidiana var. formosana. Principal component analysis (PCA, individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE. However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals. This study has produced highly informative population genomic data for the understanding of

Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

DEFF Research Database (Denmark)

Ali, Sajid; Rodriguez Algaba, Julian; Thach, Tine

2017-01-01

population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease...... that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia......; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent...

Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

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Mallikarjuna Rao eKovi

2015-11-01

Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico

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Silvia Hinojosa-Alvarez

2016-11-01

Full Text Available We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1 a group of mtDNA haplotypes divergent (0.78% from the currently recognized Manta birostris and M. alfredi species, and (2 a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris, or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (<100,000 YBP following fit to an Isolation-with-Migration model, with additional support for asymmetrical gene flow from M. birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.

Assessing genetic divergence in interspecific hybrids of Aechmea gomosepala and A. recurvata var. recurvata using inflorescence characteristics and sequence-related amplified polymorphism markers.

Science.gov (United States)

Zhang, F; Ge, Y Y; Wang, W Y; Shen, X L; Yu, X Y

2012-12-03

Conventional hybridization and selection techniques have aided the development of new ornamental crop cultivars. However, little information is available on the genetic divergence of bromeliad hybrids. In the present study, we investigated the genetic variability in interspecific hybrids of Aechmea gomosepala and A. recurvata var. recurvata using inflorescence characteristics and sequence-related amplified polymorphism (SRAP) markers. The morphological analysis showed that the putative hybrids were intermediate between both parental species with respect to inflorescence characteristics. The 16 SRAP primer combinations yield 265 bands, among which 154 (57.72%) were polymorphic. The genetic similarity was an average of 0.59 and ranged from 0.21 to 0.87, indicating moderate genetic divergence among the hybrids. The unweighted pair group method with arithmetic average (UPGMA)-based cluster analysis distinguished the hybrids from their parents with a genetic distance coefficient of 0.54. The cophenetic correlation was 0.93, indicating a good fit between the dendrogram and the original distance matrix. The two-dimensional plot from the principal coordinate analysis showed that the hybrids were intermediately dispersed between both parents, corresponding to the results of the UPGMA cluster and the morphological analysis. These results suggest that SRAP markers could help to identify breeders, characterize F(1) hybrids of bromeliads at an early stage, and expedite genetic improvement of bromeliad cultivars.

Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

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Kevin C. Deitz

2016-09-01

Full Text Available Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.

Genetic and non-genetic factors affecting rabbit doe sexual receptivity as estimated from one generation of divergent selection

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M. Theau.Clément

2015-09-01

Full Text Available Sexual receptivity of rabbit does at insemination greatly influences fertility and is generally induced by hormones or techniques known as “biostimulation”. Searching for more sustainable farming systems, an original alternative would be to utilise the genetic pathway to increase the does’receptivity. The purpose of the present study was to identify genetic and non-genetic factors that influence rabbit doe sexual receptivity, in the context of a divergent selection experiment over 1 generation. The experiment spanned 2 generations: the founder generation (G0 consisting of 140 rabbit does, and the G1 generation comprising 2 divergently selected lines (L and H lines with 70 does each and 2 successive batches from each generation. The selection rate of the G0 females to form the G1 lines was 24/140. The selection tests consisted of 16 to 18 successive receptivity tests at the rate of 3 tests per week. On the basis of 4716 tests from 275 females, the average receptivity was 56.6±48.2%. A batch effect and a test operator effect were revealed. The contribution of females to the total variance was 20.0%, whereas that of bucks was only 1.1%. Throughout the experiment, 18.2% of does expressed a low receptivity (< 34%, 50.7% a medium one and 33.1% a high one (>66%. Some does were frequently receptive, whereas others were rarely receptive. The repeatability of sexual receptivity was approximately 20%. The results confirmed the high variability of sexual receptivity of non-lactating rabbit does maintained without any biostimulation or hormonal treatment. A lack of selection response on receptivity was observed. Accordingly, the heritability of receptivity was estimated at 0.01±0.02 from an animal model and at 0.02±0.03 from a  sire and dam model. The heritability of the average receptivity of a doe was calculated as 0.04. In agreement with the low estimated heritability, the heritability determined was no different from zero

Rates of genomic divergence in humans, chimpanzees and their lice.

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Johnson, Kevin P; Allen, Julie M; Olds, Brett P; Mugisha, Lawrence; Reed, David L; Paige, Ken N; Pittendrigh, Barry R

2014-02-22

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.

Transcriptome-wide patterns of divergence during allopatric evolution.

Science.gov (United States)

Pereira, Ricardo J; Barreto, Felipe S; Pierce, N Tessa; Carneiro, Miguel; Burton, Ronald S

2016-04-01

Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level. © 2016 John Wiley & Sons Ltd.

Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

Science.gov (United States)

Aleixandre, Pau; Hernández Montoya, Julio; Milá, Borja

2013-01-01

The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving

Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia.

Science.gov (United States)

Pettengill, James B; Moeller, David A

2012-09-01

The origins of hybrid zones between parapatric taxa have been of particular interest for understanding the evolution of reproductive isolation and the geographic context of species divergence. One challenge has been to distinguish between allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative divergence histories. Here, we use complementary phylogeographic and population genetic analyses to investigate the recent divergence of two subspecies of Clarkia xantiana and the formation of a hybrid zone within the narrow region of sympatry. We tested alternative phylogeographic models of divergence using approximate Bayesian computation (ABC) and found strong support for a secondary contact model and little support for a model allowing for gene flow throughout the divergence process (i.e. primary intergradation). Two independent methods for inferring the ancestral geography of each subspecies, one based on probabilistic character state reconstructions and the other on palaeo-distribution modelling, also support a model of divergence in allopatry and range expansion leading to secondary contact. The membership of individuals to genetic clusters suggests geographic substructure within each taxon where allopatric and sympatric samples are primarily found in separate clusters. We also observed coincidence and concordance of genetic clines across three types of molecular markers, which suggests that there is a strong barrier to gene flow. Taken together, our results provide evidence for allopatric divergence followed by range expansion leading to secondary contact. The location of refugial populations and the directionality of range expansion are consistent with expectations based on climate change since the last glacial maximum. Our approach also illustrates the utility of combining phylogeographic hypothesis testing with species distribution modelling and fine-scale population genetic analyses for inferring

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

Science.gov (United States)

Charruau, P; Fernandes, C; Orozco-terWengel, P; Peters, J; Hunter, L; Ziaie, H; Jourabchian, A; Jowkar, H; Schaller, G; Ostrowski, S; Vercammen, P; Grange, T; Schlötterer, C; Kotze, A; Geigl, E-M; Walzer, C; Burger, P A

2011-01-01

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity. PMID:21214655

Genetic divergence in populations of Lutzomyia ayacuchensis, a vector of Andean-type cutaneous leishmaniasis, in Ecuador and Peru.

Science.gov (United States)

Kato, Hirotomo; Cáceres, Abraham G; Gomez, Eduardo A; Mimori, Tatsuyuki; Uezato, Hiroshi; Hashiguchi, Yoshihisa

2015-01-01

Haplotype and gene network analyses were performed on mitochondrial cytochrome oxidase I and cytochrome b gene sequences of Lutzomyia (Lu.) ayacuchensis populations from Andean areas of Ecuador and southern Peru where the sand fly species transmit Leishmania (Leishmania) mexicana and Leishmania (Viannia) peruviana, respectively, and populations from the northern Peruvian Andes, for which transmission of Leishmania by Lu. ayacuchensis has not been reported. The haplotype analyses showed higher intrapopulation genetic divergence in northern Peruvian Andes populations and less divergence in the southern Peru and Ecuador populations, suggesting that a population bottleneck occurred in the latter populations, but not in former ones. Importantly, both haplotype and phylogenetic analyses showed that populations from Ecuador consisted of clearly distinct clusters from southern Peru, and the two populations were separated from those of northern Peru. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Rapid recombination mapping for high-throughput genetic screens in Drosophila.

Science.gov (United States)

Sapiro, Anne L; Ihry, Robert J; Buhr, Derek L; Konieczko, Kevin M; Ives, Sarah M; Engstrom, Anna K; Wleklinski, Nicholas P; Kopish, Kristin J; Bashirullah, Arash

2013-12-09

Mutagenesis screens are a staple of classical genetics. Chemical-induced mutations, however, are often difficult and time-consuming to identify. Here, we report that recombination analysis with pairs of dominant visible markers provides a rapid and reliable strategy to map mutations in Drosophila melanogaster. This method requires only two generations and a total of six crosses in vials to estimate the genetic map position of the responsible lesion with high accuracy. This genetic map position can then be reliably used to identify the mutated gene through complementation testing with an average of nine deficiencies and Sanger sequencing. We have used this approach to successfully map a collection of mutations from an ethyl methanesulfonate-based mutagenesis screen on the third chromosome. We propose that this method also may be used in conjunction with whole-genome sequencing, particularly when multiple independent alleles of the mutated locus are not available. By facilitating the rapid identification of mutated genes, our mapping strategy removes a primary obstacle to the widespread use of powerful chemical mutagenesis screens to understand fundamental biological phenomena.

Rapid identification of Enterobacter hormaechei and Enterobacter cloacae genetic cluster III.

Science.gov (United States)

Ohad, S; Block, C; Kravitz, V; Farber, A; Pilo, S; Breuer, R; Rorman, E

2014-05-01

Enterobacter cloacae complex bacteria are of both clinical and environmental importance. Phenotypic methods are unable to distinguish between some of the species in this complex, which often renders their identification incomplete. The goal of this study was to develop molecular assays to identify Enterobacter hormaechei and Ent. cloacae genetic cluster III which are relatively frequently encountered in clinical material. The molecular assays developed in this study are qPCR technology based and served to identify both Ent. hormaechei and Ent. cloacae genetic cluster III. qPCR results were compared to hsp60 sequence analysis. Most clinical isolates were assigned to Ent. hormaechei subsp. steigerwaltii and Ent. cloacae genetic cluster III. The latter was proportionately more frequently isolated from bloodstream infections than from other material (P < 0·05). The qPCR assays detecting Ent. hormaechei and Ent. cloacae genetic cluster III demonstrated high sensitivity and specificity. The presented qPCR assays allow accurate and rapid identification of clinical isolates of the Ent. cloacae complex. The improved identifications obtained can specifically assist analysis of Ent. hormaechei and Ent. cloacae genetic cluster III in nosocomial outbreaks and can promote rapid environmental monitoring. An association was observed between Ent. cloacae cluster III and systemic infection that deserves further attention. © 2014 The Society for Applied Microbiology.

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

Science.gov (United States)

Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

2016-08-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

Sds-page based genetic divergence in safflower (carthamus tinctorius l.)

International Nuclear Information System (INIS)

Shinwari, Z.K.; Rehman, H.; Rabbani, M.A.

2014-01-01

Safflower (Carthamus tinctorius L.) germplasm, comprising of 116 accessions was characterized using Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) of seed storage proteins. The germplasm was acquired from different countries of the world. Total seed proteins were separated through electrophoresis polyacrylamide gels using standard protocols. Eighteen (60%) of the protein bands detected were polymorphic, the rest being monomorphic. Eight bands (14, 17, 18, 19, 20, 23, 24 and 25) were more than 80% common in all accessions. Similarity coefficients among the accessions ranged from 0.00 to 1.00. Accessions 16327 and 26752 were the most divergent genotypes having maximum dissimilarity with all the other accessions used. Unweighted Pair Group Method with Arithmetic averages (UPGMA) was used which is based on dissimilarity matrix. The dendrogram obtained separated all accessions into four main clusters (I, II, III and IV) and two independent individual genotypes. Four major clusters comprised of 23, 75, 8 and 8 accessions, respectively. This technique did not reveal genetic variability of significant value in safflower genotypes, hence advanced molecular and biochemical markers are recommended for further studies. This study will be helpful for the future breeding program of safflower accessions. (author)

Insulin-like signaling (IIS) responses to temperature, genetic background, and growth variation in garter snakes with divergent life histories.

Science.gov (United States)

Reding, Dawn M; Addis, Elizabeth A; Palacios, Maria G; Schwartz, Tonia S; Bronikowski, Anne M

2016-07-01

The insulin/insulin-like signaling pathway (IIS) has been shown to mediate life history trade-offs in mammalian model organisms, but the function of this pathway in wild and non-mammalian organisms is understudied. Populations of western terrestrial garter snakes (Thamnophis elegans) around Eagle Lake, California, have evolved variation in growth and maturation rates, mortality senescence rates, and annual reproductive output that partition into two ecotypes: "fast-living" and "slow-living". Thus, genes associated with the IIS network are good candidates for investigating the mechanisms underlying ecological divergence in this system. We reared neonates from each ecotype for 1.5years under two thermal treatments. We then used qPCR to compare mRNA expression levels in three tissue types (brain, liver, skeletal muscle) for four genes (igf1, igf2, igf1r, igf2r), and we used radioimmunoassay to measure plasma IGF-1 and IGF-2 protein levels. Our results show that, in contrast to most mammalian model systems, igf2 mRNA and protein levels exceed those of igf1 and suggest an important role for igf2 in postnatal growth in reptiles. Thermal rearing treatment and recent growth had greater impacts on IGF levels than genetic background (i.e., ecotype), and the two ecotypes responded similarly. This suggests that observed ecotypic differences in field measures of IGFs may more strongly reflect plastic responses in different environments than evolutionary divergence. Future analyses of additional components of the IIS pathway and sequence divergence between the ecotypes will further illuminate how environmental and genetic factors influence the endocrine system and its role in mediating life history trade-offs. Copyright © 2016 Elsevier Inc. All rights reserved.

Capacidade combinatória, divergência genética entre linhagens de milho e correlação com heterose Combining ability, genetic divergence among maize lines and correlation with heterosis

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Maria Elisa Ayres Guidetti Zagatto Paterniani

2008-01-01

Full Text Available Objetivou-se avaliar o desempenho de híbridos simples de milho (Zea mays L., obtidos de cruzamentos dialélicos entre linhagens divergentes, estimar a capacidade de combinação das linhagens e verificar se a divergência genética entre as linhagens, obtida por marcadores moleculares, é correlacionada com a heterose dos híbridos simples no campo. Trinta e seis híbridos resultantes de um dialelo parcial foram avaliados em Campinas e em Mococa e as 12 linhagens parentais somente em Campinas, a fim de se calcular a heterose dos híbridos. O delineamento experimental empregado foi o de blocos ao acaso, com três repetições e 2 testemunhas comerciais. Avaliaram-se os caracteres: altura da planta (AP, altura da espiga (AE e massa de grãos (MG. Análises de variância foram efetuadas, sendo as médias comparadas entre si pelo teste de Tukey a 5%. A capacidade de combinação das linhagens foi obtida de acordo com o método de Geraldi e Miranda Filho. Estimaram-se as correlações entre heterose, produtividade e capacidade específica de combinação com divergência genética obtida por AFLP e SSR. Destacou-se o híbrido PM624 x IP398, e as linhagens VER266 e L105 revelaram efeitos positivos da capacidade de combinação para produtividade. As estimativas de heterose variaram de -559 a 6.320 kg ha-1. Não houve correlação entre heterose, capacidade específica de combinação e produtividade dos híbridos com a distância genética por AFLP e SSR, indicando que não é possível fazer inferências sobre o comportamento dos híbridos de milho a partir da divergência genética entre as linhagens parentais.The objectives of this research were to evaluate single cross hybrids of maize (Zea mays L. obtained from partial diallel crosses among contrasting inbred lines, to estimate the combining ability of the lines and to verify whether the genetic diversity among those lines assessed by moleculars markers is correlated with single cross hybrid

Rapid genetic erosion in pollutant-exposed experimental chironomid populations

Energy Technology Data Exchange (ETDEWEB)

Nowak, Carsten [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: cnowak@senckenberg.de; Vogt, Christian [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: vogt@bio.uni-frankfurt.de; Pfenninger, Markus [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: pfenninger@bio.uni-frankfurt.de; Schwenk, Klaus [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: k.schwenk@bio.uni-frankfurt.de; Oehlmann, Joerg [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: oehlmann@bio.uni-frankfurt.de; Streit, Bruno [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: streit@bio.uni-frankfurt.de; Oetken, Matthias [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: oetken@bio.uni-frankfurt.de

2009-03-15

Few studies have evaluated how effectively environmental contamination may reduce genetic diversity of a population. Here, we chose a laboratory approach in order to test if tributyltin (TBT) exposure at environmentally relevant concentrations leads to reduced genetic variation in the midge Chironomus riparius. Two TBT-exposed and two unexposed experimental populations were reared simultaneously in the laboratory for 12 generations. We recorded several life-history traits in each generation and monitored genetic variation over time using five variable microsatellite markers. TBT-exposed strains showed increased larval mortality (treatments: 43.8%; controls: 27.8%), slightly reduced reproductive output, and delayed larval development. Reduction of genetic variation was strongest and only significant in the TBT-exposed strains (treatments: -45.9%, controls: -24.4% of initial heterozygosity) after 12 generations. Our findings document that chemical pollution may lead to a rapid decrease in genetic diversity, which has important implications for conservation strategies and ecological management in polluted environments. - Chronic TBT exposure reduces allelic variation at five variable microsatellite loci in experimental populations of Chironomus riparius.

Rapid genetic erosion in pollutant-exposed experimental chironomid populations

International Nuclear Information System (INIS)

Nowak, Carsten; Vogt, Christian; Pfenninger, Markus; Schwenk, Klaus; Oehlmann, Joerg; Streit, Bruno; Oetken, Matthias

2009-01-01

Few studies have evaluated how effectively environmental contamination may reduce genetic diversity of a population. Here, we chose a laboratory approach in order to test if tributyltin (TBT) exposure at environmentally relevant concentrations leads to reduced genetic variation in the midge Chironomus riparius. Two TBT-exposed and two unexposed experimental populations were reared simultaneously in the laboratory for 12 generations. We recorded several life-history traits in each generation and monitored genetic variation over time using five variable microsatellite markers. TBT-exposed strains showed increased larval mortality (treatments: 43.8%; controls: 27.8%), slightly reduced reproductive output, and delayed larval development. Reduction of genetic variation was strongest and only significant in the TBT-exposed strains (treatments: -45.9%, controls: -24.4% of initial heterozygosity) after 12 generations. Our findings document that chemical pollution may lead to a rapid decrease in genetic diversity, which has important implications for conservation strategies and ecological management in polluted environments. - Chronic TBT exposure reduces allelic variation at five variable microsatellite loci in experimental populations of Chironomus riparius

Partial status epilepticus - rapid genetic diagnosis of Alpers' disease.

LENUS (Irish Health Repository)

McCoy, Bláthnaid

2011-11-01

We describe four children with a devastating encephalopathy characterised by refractory focal seizures and variable liver dysfunction. We describe their electroencephalographic, radiologic, genetic and pathologic findings. The correct diagnosis was established by rapid gene sequencing. POLG1 based Alpers\\' disease should be considered in any child presenting with partial status epilepticus.

A Rapid Systematic Review of Outcomes Studies in Genetic Counseling.

Science.gov (United States)

Madlensky, Lisa; Trepanier, Angela M; Cragun, Deborah; Lerner, Barbara; Shannon, Kristen M; Zierhut, Heather

2017-06-01

As healthcare reimbursement is increasingly tied to value-of-service, it is critical for the genetic counselor (GC) profession to demonstrate the value added by GCs through outcomes research. We conducted a rapid systematic literature review to identify outcomes of genetic counseling. Web of Science (including PubMed) and CINAHL databases were systematically searched to identify articles meeting the following criteria: 1) measures were assessed before and after genetic counseling (pre-post design) or comparisons were made between a GC group vs. a non-GC group (comparative cohort design); 2) genetic counseling outcomes could be assessed independently of genetic testing outcomes, and 3) genetic counseling was conducted by masters-level genetic counselors, or non-physician providers. Twenty-three papers met the inclusion criteria. The majority of studies were in the cancer genetic setting and the most commonly measured outcomes included knowledge, anxiety or distress, satisfaction, perceived risk, genetic testing (intentions or receipt), health behaviors, and decisional conflict. Results suggest that genetic counseling can lead to increased knowledge, perceived personal control, positive health behaviors, and improved risk perception accuracy as well as decreases in anxiety, cancer-related worry, and decisional conflict. However, further studies are needed to evaluate a wider array of outcomes in more diverse genetic counseling settings.

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana.

Science.gov (United States)

Luo, Y; Widmer, A; Karrenberg, S

2015-02-01

Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest.

Science.gov (United States)

Bracewell, Ryan R; Bentz, Barbara J; Sullivan, Brian T; Good, Jeffrey M

2017-11-17

Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations. This striking progression of reproductive isolation is coupled with extensive gene specialization, natural selection, and elevated genetic differentiation on both sex chromosomes. Closely related populations isolated by hybrid male sterility also show fixation of alternative neo-Y haplotypes that differ in structure and male-specific gene content. Our results suggest that neo-sex chromosome evolution can drive rapid functional divergence between closely related populations irrespective of ecological drivers of divergence.

Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco.

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Pau Aleixandre

Full Text Available The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis, and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands

Genetic divergence among accessions of melon from traditional agriculture of the Brazilian Northeast.

Science.gov (United States)

Aragão, F A S; Torres Filho, J; Nunes, G H S; Queiróz, M A; Bordallo, P N; Buso, G S C; Ferreira, M A; Costa, Z P; Bezerra Neto, F

2013-12-06

The genetic divergence of 38 melon accessions from traditional agriculture of the Brazilian Northeast and three commercial hybrids were evaluated using fruit descriptors and microsatellite markers. The melon germplasm belongs to the botanic varieties cantalupensis (19), momordica (7), conomon (4), and inodorus (3), and to eight genotypes that were identified only at the species level. The fruit descriptors evaluated were: number of fruits per plant (NPF), fruit mass (FM; kg), fruit longitudinal diameter (LD; cm), fruit transversal diameter (TD; cm), shape index based on the LD/TD ratio, flesh pulp thickness, cavity thickness (CT; cm), firmness fruit pulp (N), and soluble solids (SS; °Brix). The results showed high variability for all descriptors, especially for NPF, LD, and FM. The grouping analysis based on fruit descriptors produced eight groups without taxonomic criteria. The LD (22.52%), NPF (19.70%), CT (16.13%), and SS (9.57%) characteristics were the descriptors that contributed the most to genotype dissimilarity. The 17 simple sequence repeat polymorphic markers amplified 41 alleles with an average of 2.41 alleles and three genotypes per locus. Some markers presented a high frequency for the main allele. The genetic diversity ranged from 0.07 to 0.60, the observed heterozygosity had very low values, and the mean polymorphism information content was 0.32. Molecular genetic similarity analyses clustered the accessions in 13 groups, also not following taxonomic ranks. There was no association between morphoagronomic and molecular groupings. In conclusion, there was great variability among the accessions and among and within botanic groups.

Genetic divergence of physiological-quality traits of seeds in a population of peppers.

Science.gov (United States)

Pessoa, A M S; Barroso, P A; do Rêgo, E R; Medeiros, G D A; Bruno, R L A; do Rêgo, M M

2015-10-16

Brazil has a great diversity of Capsicum peppers that can be used in breeding programs. The objective of this study was to evaluate genetic variation in traits related to the physiological quality of seeds of Capsicum annuum L. in a segregating F2 population and its parents. A total of 250 seeds produced by selfing in the F1 generation resulting from crosses between UFPB 77.3 and UFPB 76 were used, with 100 seeds of both parents used as additional controls, totaling 252 genotypes. The seeds were germinated in gerboxes containing substrate blotting paper moistened with distilled water. Germination and the following vigor tests were evaluated: first count, germination velocity index, and root and shoot lengths. Data were subjected to analysis of variance, and means were compared by Scott and Knott's method at 1% probability. Tocher's clustering based on Mahalanobis distance and canonical variable analysis with graphic dispersion of genotypes were performed, and genetic parameters were estimated. All variables were found to be significant by the F test (P ≤ 0.01) and showed high heritability and a CVg/CVe ratio higher than 1.0, indicating genetic differences among genotypes. Parents (genotypes 1 and 2) formed distinct groups in all clustering methods. Genotypes 3, 104, 153, and 232 were found to be the most divergent according to Tocher's clustering method, and this was mainly due to early germination, which was observed on day 14, and would therefore be selected. Understanding the phenotypic variability among these 252 genotypes will serve as a basis for continuing the breeding program within this family.

Convergence from divergence

Science.gov (United States)

Costin, Ovidiu; Dunne, Gerald V.

2018-01-01

We show how to convert divergent series, which typically occur in many applications in physics, into rapidly convergent inverse factorial series. This can be interpreted physically as a novel resummation of perturbative series. Being convergent, these new series allow rigorous extrapolation from an asymptotic region with a large parameter, to the opposite region where the parameter is small. We illustrate the method with various physical examples, and discuss how these convergent series relate to standard methods such as Borel summation, and also how they incorporate the physical Stokes phenomenon. We comment on the relation of these results to Dyson’s physical argument for the divergence of perturbation theory. This approach also leads naturally to a wide class of relations between bosonic and fermionic partition functions, and Klein-Gordon and Dirac determinants.

Mind the gut : Genomic insights to population divergence and gut microbial composition of two marine keystone species

NARCIS (Netherlands)

Fietz, Katharina; Rye Hintze, Christian Olaf; Skovrind, Mikkel; Kjærgaard Nielsen, Tue; Limborg, Morten T; Krag, Marcus A; Palsbøll, Per J; Hestbjerg Hansen, Lars; Rask Møller, Peter; Gilbert, M Thomas P

2018-01-01

BACKGROUND: Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ecological adaptive potential are classically viewed at the genetic level, it

Chained Kullback-Leibler Divergences

Science.gov (United States)

Pavlichin, Dmitri S.; Weissman, Tsachy

2017-01-01

We define and characterize the “chained” Kullback-Leibler divergence minw D(p‖w) + D(w‖q) minimized over all intermediate distributions w and the analogous k-fold chained K-L divergence min D(p‖wk−1) + … + D(w2‖w1) + D(w1‖q) minimized over the entire path (w1,…,wk−1). This quantity arises in a large deviations analysis of a Markov chain on the set of types – the Wright-Fisher model of neutral genetic drift: a population with allele distribution q produces offspring with allele distribution w, which then produce offspring with allele distribution p, and so on. The chained divergences enjoy some of the same properties as the K-L divergence (like joint convexity in the arguments) and appear in k-step versions of some of the same settings as the K-L divergence (like information projections and a conditional limit theorem). We further characterize the optimal k-step “path” of distributions appearing in the definition and apply our findings in a large deviations analysis of the Wright-Fisher process. We make a connection to information geometry via the previously studied continuum limit, where the number of steps tends to infinity, and the limiting path is a geodesic in the Fisher information metric. Finally, we offer a thermodynamic interpretation of the chained divergence (as the rate of operation of an appropriately defined Maxwell’s demon) and we state some natural extensions and applications (a k-step mutual information and k-step maximum likelihood inference). We release code for computing the objects we study. PMID:29130024

Neurogenomics and the role of a large mutational target on rapid behavioral change.

Science.gov (United States)

Stanley, Craig E; Kulathinal, Rob J

2016-11-08

Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast

Genetic divergence between Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum (Siluriformes: Pimelodidae in the Paraná River Basin

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TS. Bignotto

Full Text Available Pseudoplatystoma corruscans (Spix and Agassiz, 1829 and Pseudoplatystoma reticulatum (Eingenmann and Eigenmann, 1889 are large migratory catfishes of high biological importance and great commercial value in South America. Because fertile crossbreeds can be artificially produced in hatcheries, a high genetic proximity between these two Pimelodidae species is conceivable. Possible escape of crossbred specimens from pisciculture stations is a serious environmental concern. Despite their importance, knowledge of P. corruscans and P. reticulatum biology, ecology, population diversity and genetics is limited. In the present work, the genetic divergence between P. corruscans and P. reticulatum populations from the Paraná River Basin was analyzed on the basis of polymorphisms in ISSR fragments and in the hypervariable sequence of the mitochondrial DNA (mtDNA control region. Estimates of intraspecific haplotype (h > 0.5 and nucleotide diversities (π < 0.01 indicate that P. corruscans and P. reticulatum have survived a historical population decline, followed by a demographic expansion. The interspecific polymorphisms within the mtDNA control region and ISSR fragments were suitable as diagnostic molecular markers and could be used to discriminate the two species. A unique Pseudoplatystoma specimen, captured in the Upper Paraná River Floodplain, was identified by these DNA diagnostic markers as a hybrid P. reticulatum x P. corruscans, which possibly escaped from pisciculture. The integrity of the natural population of P. corruscans in the Upper Paraná River is at risk of genetic introgression or homogenization due to the presence of hybrids and the transposition of P. reticulatum upstream through the Canal da Piracema at Itaipu Dam. Data presented herein improve the understanding of the genetic relatedness between P. corruscans and P. reticulatum and represent potential tools for future programs of conservation and surveillance of genetic introgression

Morphological divergence and flow-induced phenotypic plasticity in a native fish from anthropogenically altered stream habitats.

Science.gov (United States)

Franssen, Nathan R; Stewart, Laura K; Schaefer, Jacob F

2013-11-01

Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently diverged in reservoir habitats compared with streams; individuals from reservoirs were shallower bodied with smaller heads compared with individuals from streams. Significant population-level differences in morphology persisted in offspring but morphological variation compared with field-collected individuals was limited to the head region. Populations demonstrated dissimilar flow-induced phenotypic plasticity when reared under flow, but phenotypic plasticity in response to flow variation was an unlikely explanation for observed phenotypic divergence in the field. Our results, together with previous investigations, suggest the environmental conditions currently thought to drive morphological change in reservoirs (i.e., predation and flow regimes) may not be the sole drivers of phenotypic change.

The roles of calving migration and climate change in the formation of the weak genetic structure in the Tibetan antelope (Pantholops hodgsonii).

Science.gov (United States)

Chen, Jiarui; Lin, Gonghua; Qin, Wen; Yan, Jingyan; Zhang, Tongzuo; Su, Jianping

2018-05-31

Geographical barriers and distance can reduce gene exchange among animals, resulting in genetic divergence of geographically isolated populations. The habitats of Tibetan antelope (Pantholops hodgsonii) has a geographical range of approximately 1,600 km across the Qinghai-Tibet Plateau (QTP) with a series tall mountains and big rivers. However, previously studies indicated that there was little genetic differentiation among their geographically delineated populations. To better understand the genetic structure of P. hodgsonii populations, we collected 145 samples from the three major calving regions considering their various calving grounds and migration routes. We used a combination of mitochondrial sequences (Cyt b, ATPase, D-loop and COX I) to investigate the genetic structure and the evolutionary divergence of the populations. Significant, albeit weak, genetic differentiation was detected among the three geographical populations. Analysis of the genetic divergence process revealed that the animals gradually entered into a period of rapid genetic differentiation since approximately 60,000 years ago. The calving migration of P. hodgsonii cannot be the main cause of their weak genetic structure since such cannot fully homogenize the genetic pool. Instead, the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Genetic Divergence between Freshwater and Marine Morphs of Alewife (Alosa pseudoharengus): A ‘Next-Generation’ Sequencing Analysis

Science.gov (United States)

Czesny, Sergiusz; Epifanio, John; Michalak, Pawel

2012-01-01

Alewife Alosa pseudoharengus, a small clupeid fish native to Atlantic Ocean, has recently (∼150 years ago) invaded the North American Great Lakes and despite challenges of freshwater environment its populations exploded and disrupted local food web structures. This range expansion has been accompanied by dramatic changes at all levels of organization. Growth rates, size at maturation, or fecundity are only a few of the most distinct morphological and life history traits that contrast the two alewife morphs. A question arises to what extent these rapidly evolving differences between marine and freshwater varieties result from regulatory (including phenotypic plasticity) or structural mutations. To gain insights into expression changes and sequence divergence between marine and freshwater alewives, we sequenced transcriptomes of individuals from Lake Michigan and Atlantic Ocean. Population specific single nucleotide polymorphisms were rare but interestingly occurred in sequences of genes that also tended to show large differences in expression. Our results show that the striking phenotypic divergence between anadromous and lake alewives can be attributed to massive regulatory modifications rather than coding changes. PMID:22438868

Genetic divergence among pumpkin landraces

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Rebeca Lourenço de Oliveira

2016-04-01

Full Text Available Estimating the genetic variability in germplasm collections is important not only for conserving genetic resources, but also for plant breeding purposes. However, generating a large number of different categories data (qualitative and quantitative often complicate the analysis and results interpretation, resulting in an incomplete distinction of accessions. This study reports the characterization and evaluation of 14 pumpkin (Cucurbita moschata accessions collected from farms in the northern region of Rio de Janeiro state. Genetic diversity among accessions was also estimated using qualitative and quantitative variables considering joint analysis. The plants were grown under field conditions in a randomized block design with three replications and six plants per plot. Eight qualitative traits (leaf size; seed shape; seed color; color of the fruit pulp; hollow; fruit shape; skin color, and fruit skin texture and eight quantitative traits (fruit weight; fruit length; fruit diameter; soluble solids, 100 seed weight, and wall thickness measured in the middle and in the lower stem were evaluated. The data were analyzed considering the Gower distance, and cluster analysis was performed using unweighted pair group method with arithmetic mean (UPGMA. Variability among accessions was observed considering morphoagronomic data. The Gower distance together with UPGMA cluster allowed for good discrimination between accessions in the groups, demonstrating that the simultaneous analysis of qualitative and quantitative data is feasible and may increase the understanding of the variation among accessions.

Moving Speciation Genetics Forward: Modern Techniques Build on Foundational Studies in Drosophila.

Science.gov (United States)

Castillo, Dean M; Barbash, Daniel A

2017-11-01

The question of how new species evolve has been examined at every level, from macroevolutionary patterns of diversification to molecular population genetic analyses of specific genomic regions between species pairs. Drosophila has been at the center of many of these research efforts. Though our understanding of the speciation process has grown considerably over the past few decades, very few genes have been identified that contribute to barriers to reproduction. The development of advanced molecular genetic and genomic methods provides promising avenues for the rapid discovery of more genes that contribute to speciation, particularly those involving prezygotic isolation. The continued expansion of tools and resources, especially for species other than Drosophila melanogaster , will be most effective when coupled with comparative approaches that reveal the genetic basis of reproductive isolation across a range of divergence times. Future research programs in Drosophila have high potential to answer long-standing questions in speciation. These include identifying the selective forces that contribute to divergence between populations and the genetic basis of traits that cause reproductive isolation. The latter can be expanded upon to understand how the genetic basis of reproductive isolation changes over time and whether certain pathways and genes are more commonly involved. Copyright © 2017 by the Genetics Society of America.

Genetic divergence of Etlingera elatior based on agro-morphological features for cut flowers

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Charleston Gonçalves

2014-09-01

Full Text Available Despite the wide acceptability Torch Ginger (Etlingera elatior by the consumer market and its cultivation are still restrict­ed due to the high mass of inflorescences (over 1 kg, which complicates the process of harvesting, handling, packaging and transportation. The objective of this work was to characterize agromorphological and estimate the genetic divergence among Etlingera elatior ( Jack R.M. Sm. with standard cut flower. A stand of 75 genotypes resulting from crosses between genotypes at random from the collection of germplasm with variability inflorescences of commercial interest, they keep on growing in the Research and Development of Ubatuba. Seventeen descriptors were evaluated on the leaf, inflorescence and infrutescence. The inflorescence mass, length and diameter of the flowering stem, height and flower diameter were selected as the most important descriptors for selecting accessions with standard marketing as cut flower. We selected 12 promising accessions, with characteristics appropriate to the market and with good combination of shapes and coloring bracts.

Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): founder effects, vicariance, or both?

Science.gov (United States)

Wörheide, Gert; Epp, Laura S; Macis, Luciana

2008-01-26

An increasing number of studies demonstrate that genetic differentiation and speciation in the sea occur over much smaller spatial scales than previously appreciated given the wide distribution range of many morphologically defined coral reef invertebrate species and the presumed dispersal-enhancing qualities of ocean currents. However, knowledge about the processes that lead to population divergence and speciation is often lacking despite being essential for the understanding, conservation, and management of marine biodiversity. Sponges, a highly diverse, ecologically and economically important reef-invertebrate taxon, exhibit spatial trends in the Indo-West Pacific that are not universally reflected in other marine phyla. So far, however, processes generating those unexpected patterns are not understood. We unraveled the phylogeographic structure of the widespread Indo-Pacific coral reef sponge Leucetta chagosensis across its known geographic range using two nuclear markers: the rDNA internal transcribed spacers (ITS 1&2) and a fragment of the 28S gene, as well as the second intron of the ATP synthetase beta subunit-gene (ATPSb-iII). This enabled the detection of several deeply divergent clades congruent over both loci, one containing specimens from the Indian Ocean (Red Sea and Maldives), another one from the Philippines, and two other large and substructured NW Pacific and SW Pacific clades with an area of overlap in the Great Barrier Reef/Coral Sea. Reciprocally monophyletic populations were observed from the Philippines, Red Sea, Maldives, Japan, Samoa, and Polynesia, demonstrating long-standing isolation. Populations along the South Equatorial Current in the south-western Pacific showed isolation-by-distance effects. Overall, the results pointed towards stepping-stone dispersal with some putative long-distance exchange, consistent with expectations from low dispersal capabilities. We argue that both founder and vicariance events during the late Pliocene and

Genetic divergence among toxic and non-toxic cyanobacteria of the dry zone of Sri Lanka.

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Liyanage, Harshini M; Magana Arachchi, Dhammika N; Chandrasekaran, Naduviladath V

2016-01-01

Sri Lanka has rich cyanobacterial diversity, however, only few studies have been conducted to identify the potential toxin producers in water bodies used for human consumption. As the detection of cyanotoxin is vital in water quality management, a study was done by employing 16S rRNA gene to explore the genetic divergence, phylogenetic relationships and potential toxin producing cyanobacteria in reservoirs and well waters in the dry zone of Sri Lanka. Forty five, 16S rRNA gene sequences were assayed and phylogenetic tree was constructed. Among 45 isolates, 20 isolates were classified as unidentified cyanobacteria and considered as novel cyanobacterial genera. Of 25 identified isolates, seven isolates were identified up to species level. With 16S rRNA phylogeny, 20 unidentified cyanobacterial isolates were able to place on their taxonomic positions up to order level. Results revealed that water samples understudy had vast cyanobacterial diversity with potential microcystin (MC) and cylindrospermopsin (CYN) producers and eleven clusters clearly demonstrated five cyanobacterial orders with more than 90% similarity irrespective to their toxicity which showed the suitability of 16S rRNA gene for taxonomic differentiation. Sixteen isolates had the potential to produce MC and two isolates to produce CYN. Findings of the study confirm the rich cyanobacterial diversity and the divergence among the potential cyanotoxin producers in the dry zone water bodies of Sri Lanka.

Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus.

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Kindler, Eveline; Arlettaz, Raphaël; Heckel, Gerald

2012-11-01

The grasshopper Oedaleus decorus is a thermophilic insect with a large, mostly south-Palaearctic distribution range, stretching from the Mediterranean regions in Europe to Central-Asia and China. In this study, we analyzed the extent of phylogenetic divergence and the recent evolutionary history of the species based on 274 specimens from 26 localities across the distribution range in Europe. Phylogenetic relationships were determined using sequences of two mitochondrial loci (ctr, ND2) with neighbour-joining and Bayesian methods. Additionally, genetic differentiation was analyzed based on mitochondrial DNA and 11 microsatellite markers using F-statistics, model-free multivariate and model-based Bayesian clustering approaches. Phylogenetic analyses detected consistently two highly divergent, allopatrically distributed lineages within O. decorus. The divergence among these Western and Eastern lineages meeting in the region of the Alps was similar to the divergence of each lineage to the sister species O. asiaticus. Genetic differentiation for ctr was extremely high between Western and Eastern grasshopper populations (F(ct)=0.95). Microsatellite markers detected much lower but nevertheless very significant genetic structure among population samples. The nuclear data also demonstrated a case of cytonuclear discordance because the affiliation with mitochondrial lineages was incongruent in Northern Italy. Taken together these results provide evidence of an ancient separation within Oedaleus and either historical introgression of mtDNA among lineages and/or ongoing sex-specific gene flow in this grasshopper. Our study stresses the importance of multilocus approaches for unravelling the history and status of taxa of uncertain evolutionary divergence. Copyright © 2012 Elsevier Inc. All rights reserved.

Convergent evolution and divergent selection: lizards at the White Sands ecotone.

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Rosenblum, Erica Bree

2006-01-01

Ecological transition zones, where organismal phenotypes result from a delicate balance between selection and migration, highlight the interplay of local adaptation and gene flow. Here, I study the response of an entire species assemblage to natural selection across a common ecotone. Three lizard species, distributed along a dramatic environmental gradient in substrate color, display convergent adaptation of blanched coloration on the gypsum dunes of White Sands National Monument. I investigate the role of gene flow in modulating phenotypic response to selection by quantifying color variation and genetic variation across the ecotone. I find species differences in degree of background matching and in genetic connectivity of populations across the ecotone. Differences among species in phenotypic response to selection scale precisely to levels of genetic isolation. Species with higher levels of gene flow across the ecotone exhibit less dramatic responses to selection. Results also reveal a strong signal of ecologically mediated divergence for White Sands lizards. For all species, phenotypic variation is better explained by habitat similarity than genetic similarity. Convergent evolution of blanched coloration at White Sands clearly reflects the action of strong divergent selection; however, adaptive response appears to be modulated by gene flow and demographic history and can be predicted by divergence-with-gene-flow models.

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

International Nuclear Information System (INIS)

Nugoli, Mélanie; Theillet, Charles; Chuchana, Paul; Vendrell, Julie; Orsetti, Béatrice; Ursule, Lisa; Nguyen, Catherine; Birnbaum, Daniel; Douzery, Emmanuel JP; Cohen, Pascale

2003-01-01

Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved

Comparative genomics using microarrays reveals divergence and loss of virulence-associated genes in host-specific strains of the insect pathogen Metarhizium anisopliae.

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Wang, Sibao; Leclerque, Andreas; Pava-Ripoll, Monica; Fang, Weiguo; St Leger, Raymond J

2009-06-01

Many strains of Metarhizium anisopliae have broad host ranges, but others are specialists and adapted to particular hosts. Patterns of gene duplication, divergence, and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain Ma2575. As expected, major life processes are highly conserved, presumably due to purifying selection. However, up to 7% of Ma2575 genes were highly divergent or absent in specialist strains. Many of these sequences are conserved in other fungal species, suggesting that there has been rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, indicative of reductive evolution. These included several involved in toxin biosynthesis and sugar metabolism in root exudates, suggesting that specialists are losing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist cricket pathogen Ma443 contained extra insertion elements that might play a role in generating evolutionary novelty. This study throws light on the abundance of orphans in genomes, as 15% of orphan sequences were found to be rapidly evolving in the Ma2575 lineage.

The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

Energy Technology Data Exchange (ETDEWEB)

Podsiadlowski, L.; Carapelli, A.; Nardi, F.; Dallai, R.; Koch,M.; Boore, J.L.; Frati, F.

2005-12-01

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

Sympatric and allopatric divergence of MHC genes in threespine stickleback.

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Blake Matthews

2010-06-01

Full Text Available Parasites can strongly affect the evolution of their hosts, but their effects on host diversification are less clear. In theory, contrasting parasite communities in different foraging habitats could generate divergent selection on hosts and promote ecological speciation. Immune systems are costly to maintain, adaptable, and an important component of individual fitness. As a result, immune system genes, such as those of the Major Histocompatibility Complex (MHC, can change rapidly in response to parasite-mediated selection. In threespine stickleback (Gasterosteus aculeatus, as well as in other vertebrates, MHC genes have been linked with female mating preference, suggesting that divergent selection acting on MHC genes might influence speciation. Here, we examined genetic variation at MHC Class II loci of sticklebacks from two lakes with a limnetic and benthic species pair, and two lakes with a single species. In both lakes with species pairs, limnetics and benthics differed in their composition of MHC alleles, and limnetics had fewer MHC alleles per individual than benthics. Similar to the limnetics, the allopatric population with a pelagic phenotype had few MHC alleles per individual, suggesting a correlation between MHC genotype and foraging habitat. Using a simulation model we show that the diversity and composition of MHC alleles in a sympatric species pair depends on the amount of assortative mating and on the strength of parasite-mediated selection in adjacent foraging habitats. Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes.

Divergência genética em linhagens de melancia Genetic divergence in watermelon lines

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Flávio de França Souza

2005-06-01

Full Text Available A divergência genética entre 31 genótipos de melancia foi avaliada por meio da análise de variáveis canônicas e de técnicas de agrupamento (Tocher e método hierárquico de Ward baseadas na distância generalizada de Mahalanobis (D²ii'. Trinta linhagens, obtidas a partir de acessos coletados no Nordeste brasileiro e a cultivar 'Crimson Sweet' foram avaliadas quanto ao número de dias para o aparecimento da primeira flor masculina e da primeira flor feminina (NDM e NDF; número do nó da primeira flor masculina e da primeira flor feminina (NGM e NGF; número de frutos por planta (NFP; comprimento de rama principal (CRP; peso médio de fruto (PMF; teor de sólidos solúveis (TSS; diâmetro transversal e longitudinal do fruto (DTF e DLF e espessura média de casca (EMC. O experimento foi realizado em delineamento de blocos ao acaso com três repetições, compostas por parcelas de sete plantas. As características que mais contribuíram para a divergência entre as linhagens foram número de frutos por planta, diâmetro longitudinal, teor de sólidos solúveis e peso médio de fruto. Foram formados três grupos por meio do método de otimização de Tocher, três por meio do método hierárquico de Ward e quatro grupos pela dispersão gráfica baseada nas duas primeiras variáveis canônicas. Neste caso, o grupo I compôs-se de sete linhagens de Pernambuco e uma da Bahia; o grupo II reuniu todas as 21 linhagens do Maranhão; os grupos III e IV foram compostos pela linhagem 97-0247.008 (Pernambuco e pela cultivar Crimson Sweet, respectivamente. As linhagens 87-019.021 e 87-019.022 foram as mais semelhantes, enquanto a linhagem 87-019.023 e 'Crimson Sweet' apresentaram maior dissimilaridade pela distância generalizada Mahalanobis (D²ii'. Os cruzamentos mais promissores serão aqueles realizados entre Crimson Sweet e as linhagens do grupo II. Cruzamentos entre Crimson Sweet e as linhagens do grupo I serão interessantes para a obtenção de

Rapid and repeated origin of insular gigantism and dwarfism in Australian tiger snakes.

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Keogh, J Scott; Scott, Ian A W; Hayes, Christine

2005-01-01

It is a well-known phenomenon that islands can support populations of gigantic or dwarf forms of mainland conspecifics, but the variety of explanatory hypotheses for this phenomenon have been difficult to disentangle. The highly venomous Australian tiger snakes (genus Notechis) represent a well-known and extreme example of insular body size variation. They are of special interest because there are multiple populations of dwarfs and giants and the age of the islands and thus the age of the tiger snake populations are known from detailed sea level studies. Most are 5000-7000 years old and all are less than 10,000 years old. Here we discriminate between two competing hypotheses with a molecular phylogeography dataset comprising approximately 4800 bp of mtDNA and demonstrate that populations of island dwarfs and giants have evolved five times independently. In each case the closest relatives of the giant or dwarf populations are mainland tiger snakes, and in four of the five cases, the closest relatives are also the most geographically proximate mainland tiger snakes. Moreover, these body size shifts have evolved extremely rapidly and this is reflected in the genetic divergence between island body size variants and mainland snakes. Within south eastern Australia, where populations of island giants, populations of island dwarfs, and mainland tiger snakes all occur, the maximum genetic divergence is only 0.38%. Dwarf tiger snakes are restricted to prey items that are much smaller than the prey items of mainland tiger snakes and giant tiger snakes are restricted to seasonally available prey items that are up three times larger than the prey items of mainland tiger snakes. We support the hypotheses that these body size shifts are due to strong selection imposed by the size of available prey items, rather than shared evolutionary history, and our results are consistent with the notion that adaptive plasticity also has played an important role in body size shifts. We suggest

Cryptic Genetic Variation in Evolutionary Developmental Genetics

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Annalise B. Paaby

2016-06-01

Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

A climate for speciation: rapid spatial diversification within the Sorex cinereus complex of shrews

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Hope, Andrew G.; Speer, Kelly A.; Demboski, John R.; Talbot, Sandra L.; Cook, Joseph A.

2012-01-01

The cyclic climate regime of the late Quaternary caused dramatic environmental change at high latitudes. Although these events may have been brief in periodicity from an evolutionary standpoint, multiple episodes of allopatry and divergence have been implicated in rapid radiations of a number of organisms. Shrews of the Sorex cinereus complex have long challenged taxonomists due to similar morphology and parapatric geographic ranges. Here, multi-locus phylogenetic and demographic assessments using a coalescent framework were combined to investigate spatiotemporal evolution of 13 nominal species with a widespread distribution throughout North America and across Beringia into Siberia. For these species, we first test a hypothesis of recent differentiation in response to Pleistocene climate versus more ancient divergence that would coincide with pre-Pleistocene perturbations. We then investigate the processes driving diversification over multiple continents. Our genetic analyses highlight novel diversity within these morphologically conserved mammals and clarify relationships between geographic distribution and evolutionary history. Demography within and among species indicates both regional stability and rapid expansion. Ancestral ecological differentiation coincident with early cladogenesis within the complex enabled alternating and repeated episodes of allopatry and expansion where successive glacial and interglacial phases each promoted divergence. The Sorex cinereus complex constitutes a valuable model for future comparative assessments of evolution in response to cyclic environmental change.

Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae: Founder effects, vicariance, or both?

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Epp Laura S

2008-01-01

Full Text Available Abstract Background An increasing number of studies demonstrate that genetic differentiation and speciation in the sea occur over much smaller spatial scales than previously appreciated given the wide distribution range of many morphologically defined coral reef invertebrate species and the presumed dispersal-enhancing qualities of ocean currents. However, knowledge about the processes that lead to population divergence and speciation is often lacking despite being essential for the understanding, conservation, and management of marine biodiversity. Sponges, a highly diverse, ecologically and economically important reef-invertebrate taxon, exhibit spatial trends in the Indo-West Pacific that are not universally reflected in other marine phyla. So far, however, processes generating those unexpected patterns are not understood. Results We unraveled the phylogeographic structure of the widespread Indo-Pacific coral reef sponge Leucetta chagosensis across its known geographic range using two nuclear markers: the rDNA internal transcribed spacers (ITS 1&2 and a fragment of the 28S gene, as well as the second intron of the ATP synthetase beta subunit-gene (ATPSb-iII. This enabled the detection of several deeply divergent clades congruent over both loci, one containing specimens from the Indian Ocean (Red Sea and Maldives, another one from the Philippines, and two other large and substructured NW Pacific and SW Pacific clades with an area of overlap in the Great Barrier Reef/Coral Sea. Reciprocally monophyletic populations were observed from the Philippines, Red Sea, Maldives, Japan, Samoa, and Polynesia, demonstrating long-standing isolation. Populations along the South Equatorial Current in the south-western Pacific showed isolation-by-distance effects. Overall, the results pointed towards stepping-stone dispersal with some putative long-distance exchange, consistent with expectations from low dispersal capabilities. Conclusion We argue that both

Finite Divergence

DEFF Research Database (Denmark)

Hansen, Michael Edberg; Pandya, P. K.; Chaochen, Zhou

1995-01-01

the framework of duration calculus. Axioms and proof rules are given. Patterns of occurrence of divergence are classified into dense divergence, accumulative divergence and discrete divergence by appropriate axioms. Induction rules are given for reasoning about discrete divergence...

Divergência genética entre acessos de batata-doce utilizando caracteres fenotípicos de raiz Genetic divergence among sweet potato accessions based on root traits

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Giovani O da Silva

2012-12-01

Full Text Available Estudos de quantificação da divergência genética entre acessos e caracterização dos recursos genéticos têm sido de grande importância em programas de melhoramento, auxiliando na identificação de genitores e no conhecimento do material genético disponível. Os objetivos do presente trabalho foram: (1 avaliar os acessos de batata-doce pertencentes ao banco de germoplasma da Embrapa com base em caracteres de raiz; (2 calcular a importância relativa dos caracteres morfo-agronômicos quantitativos na discriminação dos acessos e, (3 obter indicações das combinações híbridas mais promissoras para cruzamentos. Foi avaliada uma coleção de 11 clones pertencentes ao Banco Ativo de Germoplasma da Embrapa por meio de um experimento conduzido na Embrapa SPM/EN, em Canoinhas-SC. Os acessos foram cultivados em condições de campo no delineamento em blocos ao acaso com quatro repetições, onde a parcela experimental foi composta por 10 plantas. As plantas de cada parcela foram colhidas e avaliadas para 12 caracteres fenotípicos de raiz. O estudo indicou que os caracteres número e massa total de raízes e peso específico foram os que mais contribuíram para a divergência genética. A maioria dos acessos é bastante similar quanto aos caracteres quantitativos avaliados. Porém, há a possibilidade de ganhos com a heterose, geração de variabilidade genética e de progênies superiores cruzando-se os acessos dos diferentes grupamentos formados; pois os genótipos mais contrastantes '1228', '051-1' e '1270' foram agrupados entre os melhores para várias características como massa e número total de raízes, massa comercial de raízes; os dois primeiros apresentaram elevado peso específico e o '1270' apresentou coloração alaranjada intensa, indicativo de alto teor de β-caroteno.The estimation of the genetic divergence among accessions of a germplasm bank, as well as their characterization are very important in breeding programs in

Are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild rice Oryza rufipogon?

Science.gov (United States)

Zhao, Yao; Vrieling, Klaas; Liao, Hui; Xiao, Manqiu; Zhu, Yongqing; Rong, Jun; Zhang, Wenju; Wang, Yuguo; Yang, Ji; Chen, Jiakuan; Song, Zhiping

2013-11-01

Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (mh  = 0.0002-0.0013, mc  = 0.007-0.029), indicating IBD and resulting in a high level of population divergence (FST  = 0.343). High within-population genetic variation (HE  = 0.377-0.515), relatively large effective population sizes (Ne  = 96-158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon. © 2013 John Wiley & Sons Ltd.

The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus

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Thébaud Christophe

2010-05-01

Full Text Available Abstract Background Oceanic islands provide unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. Assessing the relative importance of selective and neutral factors in driving population divergence is central to understanding how such divergence may lead to speciation in small oceanic islands, where opportunities for gene flow and population mixing are potentially high. Here we report a case of genetic and morphological structure in the Mascarene grey white-eye (Zosterops borbonicus a species that shows a striking, geographically structured plumage polymorphism on the topographically and ecologically complex island of Réunion, yet is monotypic on the relatively uniform neighbouring island of Mauritius. Results Analysis of 276 AFLP loci in 197 individuals revealed prolonged independent evolution of Réunion and Mauritius populations, which is congruent with previous mtDNA assessments. Furthermore, populations on Réunion showed significant differentiation into three main genetic groups separating lowland from highland areas despite the small geographic distances involved. Genetic differentiation along the altitudinal gradient is consistent with morphometric analysis of fitness-related traits. Birds in the highlands were larger, yet had relatively smaller beaks than in the lowlands, suggesting the role of selection in shaping morphology and restricting gene flow along the gradient. No genetic differentiation between plumage morphs was detected in neutral markers, suggesting that plumage differences are of recent origin. Conclusions Our results suggest a dual role of vicariance and natural selection in differentiating populations of a passerine bird in an oceanic island at very small spatial scales. We propose a combination of past microallopatry driven by volcanic activity and selection-constrained dispersal along steep ecological gradients to explain the striking levels of population

Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations.

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Szövényi, P; Terracciano, S; Ricca, M; Giordano, S; Shaw, A J

2008-12-01

Several lines of evidence suggest that recent long-distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi-Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (IM and MIGRATE) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F(ST) = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long-range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000-289,000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi-Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.

Adaptive divergence in resistance to herbivores in Datura stramonium

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Guillermo Castillo

2015-11-01

Full Text Available Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations of Datura stramonium, we compared the degree of phenotypic differentiation (PST of leaf resistance traits (trichome density, atropine and scopolamine concentration against neutral genetic differentiation (FST at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher than FST across the range of trait heritability values. In contrast, genetic differentiation in trichome density was different from FST only when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits in D. stramonium.

Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

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Gregersen Finn

2010-11-01

Full Text Available Abstract Background Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions. Results We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (QST was larger than estimated genetic drift levels (microsatellite FST between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the

Phylogeography of Rhodiola kirilowii (Crassulaceae: a story of Miocene divergence and quaternary expansion.

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Jian-Qiang Zhang

Full Text Available The evolution and current distribution of the Sino-Tibetan flora have been greatly affected by historical geological events, such as the uplift of the Qinghai-Tibetan Plateau (QTP, and Quaternary climatic oscillations. Rhodiola kirilowii, a perennial herb with its distribution ranging from the southeastern QTP and the Hengduan Mountains (HM to adjacent northern China and central Asia, provides an excellent model to examine and disentangle the effect of both geological orogeny and climatic oscillation on the evolutionary history of species with such distribution patterns. We here conducted a phylogeographic study using sequences of two chloroplast fragments (trnL-F and trnS-G and internal transcribed spacers in 29 populations of R. kirilowii. A total of 25 plastid haplotypes and 12 ITS ribotypes were found. Molecular clock estimation revealed deep divergence between the central Asian populations and other populations from the HM and northern China; this split occurred ca. 2.84 million year ago. The majority of populations from the mountains of northern China were dominated by a single haplotype or ribotype, while populations of the HM harbored both high genetic diversity and high haplotype diversity. This distribution pattern indicates that HM was either a diversification center or a refugium for R. kirilowii during the Quaternary climatic oscillations. The present distribution of this species on mountains in northern China may have resulted from a rapid glacial population expansion from the HM. This expansion was confirmed by the mismatch distribution analysis and negative Tajima's D and Fu's FS values, and was dated to ca. 168 thousand years ago. High genetic diversity and population differentiation in both plastid and ITS sequences were revealed; these imply restricted gene flow between populations. A distinct isolation-by-distance pattern was suggested by the Mantel test. Our results show that in old lineages, populations may harbour

Design and testing of low-divergence elliptical-jet nozzles

Energy Technology Data Exchange (ETDEWEB)

Rouly, Etienne; Warkentin, Andrew; Bauer, Robert [Dalhousie University, Halifax (China)

2015-05-15

A novel approach was developed to design and fabricate nozzles to produce high-pressure low-divergence fluid jets. Rapid-prototype fabrication allowed for myriad experiments investigating effects of different geometric characteristics of nozzle internal geometry on jet divergence angle and fluid distribution. Nozzle apertures were elliptical in shape with aspect ratios between 1.00 and 2.45. The resulting nozzle designs were tested and the lowest elliptical jet divergence angle was 0.4 degrees. Nozzle pressures and flowrates ranged from 0.32 to 4.45 MPa and 13.6 to 37.9 LPM, respectively. CimCool CimTech 310 machining fluid was used in all experiments at a Brix concentration of 6.6 percent.

Integrating paleoecology and genetics of bird populations in two sky island archipelagos.

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McCormack, John E; Bowen, Bonnie S; Smith, Thomas B

2008-06-27

Genetic tests of paleoecological hypotheses have been rare, partly because recent genetic divergence is difficult to detect and time. According to fossil plant data, continuous woodland in the southwestern USA and northern Mexico became fragmented during the last 10,000 years, as warming caused cool-adapted species to retreat to high elevations. Most genetic studies of resulting 'sky islands' have either failed to detect recent divergence or have found discordant evidence for ancient divergence. We test this paleoecological hypothesis for the region with intraspecific mitochondrial DNA and microsatellite data from sky-island populations of a sedentary bird, the Mexican jay (Aphelocoma ultramarina). We predicted that populations on different sky islands would share common, ancestral alleles that existed during the last glaciation, but that populations on each sky island, owing to their isolation, would contain unique variants of postglacial origin. We also predicted that divergence times estimated from corrected genetic distance and a coalescence model would post-date the last glacial maximum. Our results provide multiple independent lines of support for postglacial divergence, with the predicted pattern of shared and unique mitochondrial DNA haplotypes appearing in two independent sky-island archipelagos, and most estimates of divergence time based on corrected genetic distance post-dating the last glacial maximum. Likewise, an isolation model based on multilocus gene coalescence indicated postglacial divergence of five pairs of sky islands. In contrast to their similar recent histories, the two archipelagos had dissimilar historical patterns in that sky islands in Arizona showed evidence for older divergence, suggesting different responses to the last glaciation. This study is one of the first to provide explicit support from genetic data for a postglacial divergence scenario predicted by one of the best paleoecological records in the world. Our results

Rapid screening for targeted genetic variants via high-resolution melting curve analysis.

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Chambliss, Allison B; Resnick, Molly; Petrides, Athena K; Clarke, William A; Marzinke, Mark A

2017-03-01

Current methods for the detection of single nucleotide polymorphisms (SNPs) associated with aberrant drug-metabolizing enzyme function are hindered by long turnaround times and specialized techniques and instrumentation. In this study, we describe the development and validation of a high-resolution melting (HRM) curve assay for the rapid screening of variant genotypes for targeted genetic polymorphisms in the cytochrome P450 enzymes CYP2C9, CYP2C19, and CYP3A5. Sequence-specific primers were custom-designed to flank nine SNPs within the genetic regions of aforementioned drug metabolizing enzymes. PCR amplification was performed followed by amplicon denaturation by precise temperature ramping in order to distinguish genotypes by melting temperature (Tm). A standardized software algorithm was used to assign amplicons as 'reference' or 'variant' as compared to duplicate reference sequence DNA controls for each SNP. Intra-assay (n=5) precision of Tms for all SNPs was ≤0.19%, while inter-assay (n=20) precision ranged from 0.04% to 0.21%. When compared to a reference method of Sanger sequencing, the HRM assay produced no false negative results, and overcall frequency ranged from 0% to 26%, depending on the SNP. Furthermore, HRM genotyping displayed accuracy over input DNA concentrations ranging from 10 to 200 ng/μL. The presented assay provides a rapid method for the screening for genetic variants in targeted CYP450 regions with a result of 'reference' or 'variant' available within 2 h from receipt of extracted DNA. The method can serve as a screening approach to rapidly identify individuals with variant sequences who should be further investigated by reflexed confirmatory testing for aberrant cytochrome P450 enzymatic activity. Rapid knowledge of variant status may aid in the avoidance of adverse clinical events by allowing for dosing of normal metabolizer patients immediately while identifying the need to wait for confirmatory testing in those patients who are

Antigenic and genetic characterization of a divergent African virus, Ikoma lyssavirus.

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Horton, Daniel L; Banyard, Ashley C; Marston, Denise A; Wise, Emma; Selden, David; Nunez, Alejandro; Hicks, Daniel; Lembo, Tiziana; Cleaveland, Sarah; Peel, Alison J; Kuzmin, Ivan V; Rupprecht, Charles E; Fooks, Anthony R

2014-05-01

In 2009, a novel lyssavirus (subsequently named Ikoma lyssavirus, IKOV) was detected in the brain of an African civet (Civettictis civetta) with clinical rabies in the Serengeti National Park of Tanzania. The degree of nucleotide divergence between the genome of IKOV and those of other lyssaviruses predicted antigenic distinction from, and lack of protection provided by, available rabies vaccines. In addition, the index case was considered likely to be an incidental spillover event, and therefore the true reservoir of IKOV remained to be identified. The advent of sensitive molecular techniques has led to a rapid increase in the discovery of novel viruses. Detecting viral sequence alone, however, only allows for prediction of phenotypic characteristics and not their measurement. In the present study we describe the in vitro and in vivo characterization of IKOV, demonstrating that it is (1) pathogenic by peripheral inoculation in an animal model, (2) antigenically distinct from current rabies vaccine strains and (3) poorly neutralized by sera from humans and animals immunized against rabies. In a laboratory mouse model, no protection was elicited by a licensed rabies vaccine. We also investigated the role of bats as reservoirs of IKOV. We found no evidence for infection among 483 individuals of at least 13 bat species sampled across sites in the Serengeti and Southern Kenya.

Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep

NARCIS (Netherlands)

Epps, CW; Palsboll, PJ; Wehausen, JD; Roderick, GK; Ramey, RR; McCullough, DR

2005-01-01

The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been

Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

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Brekke, Thomas D.; Steele, Katherine A.; Mulley, John F.

2017-01-01

Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait. PMID:29242387

gPGA: GPU Accelerated Population Genetics Analyses.

Directory of Open Access Journals (Sweden)

Chunbao Zhou

Full Text Available The isolation with migration (IM model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC simulations of gene genealogies. But computational burden of IM program has placed limits on its application.With strong computational power, Graphics Processing Unit (GPU has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA, which we call gPGA.Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.

Local divergence and curvature divergence in first order optics

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Mafusire, Cosmas; Krüger, Tjaart P. J.

2018-06-01

The far-field divergence of a light beam propagating through a first order optical system is presented as a square root of the sum of the squares of the local divergence and the curvature divergence. The local divergence is defined as the ratio of the beam parameter product to the beam width whilst the curvature divergence is a ratio of the space-angular moment also to the beam width. It is established that the beam’s focusing parameter can be defined as a ratio of the local divergence to the curvature divergence. The relationships between the two divergences and other second moment-based beam parameters are presented. Their various mathematical properties are presented such as their evolution through first order systems. The efficacy of the model in the analysis of high power continuous wave laser-based welding systems is briefly discussed.

Rapid Increase of Genetically Diverse Methicillin-Resistant Staphylococcus aureus, Copenhagen, Denmark

DEFF Research Database (Denmark)

Bartels, Mette Damkjær; Boye, Kit; Larsen, Anders Rhod

2007-01-01

In Copenhagen, methicillin-resistant Staphylococcus aureus (MRSA) accounted for <15 isolates per year during 1980-2002. However, since 2003 an epidemic increase has been observed, with 33 MRSA cases in 2003 and 110 in 2004. We analyzed these 143 cases epidemiologically and characterized isolates ...... and soft tissue infections dominated. CO-MRSA with diverse genetic backgrounds is rapidly emerging in a low MRSA prevalence area. Udgivelsesdato: October...

Pharmacogenetics of clopidogrel: comparison between a standard and a rapid genetic testing.

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Saracini, Claudia; Vestrini, Anna; Galora, Silvia; Armillis, Alessandra; Abbate, Rosanna; Giusti, Betti

2012-06-01

CYP2C19 variant alleles are independent predictors of clopidogrel response variability and occurrence of major adverse cardiovascular events in high-risk vascular patients on clopidogrel therapy. Increasing evidence suggests a combination of platelet function testing with CYP2C19 genetic testing may be more effective in identifying high-risk individuals for alternative antiplatelet therapeutic strategies. A crucial point in evaluating the use of these polymorphisms in clinical practice, besides test accuracy, is the cost of the genetic test and rapid availability of the results. One hundred acute coronary syndrome patients were genotyped for CYP2C19*2,*3,*4,*5, and *17 polymorphisms with two platforms: Verigene(®) and the TaqMan(®) system. Genotyping results obtained by the classical TaqMan approach and the rapid Verigene approach showed a 100% concordance for all the five polymorphisms investigated. The Verigene system had shorter turnaround time with respect to TaqMan. The cost of reagents for TaqMan genotyping was lower than that for the Verigene system, but the effective manual staff involvement and the relative cost resulted in higher cost for TaqMan than for Verigene. The Verigene system demonstrated good performance in terms of turnaround time and cost for the evaluation of the clopidogrel poor metabolizer status, giving genetic information in suitable time (206 min) for a therapeutic strategy decision.

Genetic divergence of roundup ready (RR) soybean cultivars ...

African Journals Online (AJOL)

The aim of this study was to estimate the genetic diversity in 74 RR soybean cultivars from different Brazilian breeding programs. ... chosen SSR markers were effective in assessing the genetic diversity among genotypes, besides proving to be ...

Divergence in male sexual odor signal and genetics across populations of the red mason bee, Osmia bicornis, in Europe.

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Conrad, Taina; Paxton, Robert J; Assum, Günter; Ayasse, Manfred

2018-01-01

In some insect species, females may base their choice for a suitable mate on male odor. In the red mason bee, Osmia bicornis, female choice is based on a male's odor bouquet as well as its thorax vibrations, and its relatedness to the female, a putative form of optimal outbreeding. Interestingly, O. bicornis can be found as two distinct color morphs in Europe, which are thought to represent subspecies and between which we hypothesize that female discrimination may be particularly marked. Here we investigated (i) if these two colors morphs do indeed represent distinct, reproductively differentiated populations, (ii) how odor bouquets of male O. bicornis vary within and between populations, and (iii) whether variation in male odor correlates with genetic distance, which might represent a cue by which females could optimally outbreed. Using GC and GC-MS analysis of male odors and microsatellite analysis of males and females from 9 populations, we show that, in Denmark, an area of subspecies sympatry, the two color morphs at any one site do not differ, either in odor bouquet or in population genetic differentiation. Yet populations across Europe are distinct in their odor profile as well as being genetically differentiated. Odor differences do not, however, mirror genetic differentiation between populations. We hypothesize that populations from Germany, England and Denmark may be under sexual selection through female choice for local odor profiles, which are not related to color morph though which could ultimately lead to population divergence and speciation.

Along the speciation continuum: Quantifying intrinsic and extrinsic isolating barriers across five million years of evolutionary divergence in California jewelflowers.

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Christie, Kyle; Strauss, Sharon Y

2018-05-01

Understanding the relative roles of intrinsic and extrinsic reproductive barriers, and their interplay within the geographic context of diverging taxa, remains an outstanding challenge in the study of speciation. We conducted a comparative analysis of reproductive isolation in California Jewelflowers (Streptanthus, s.l., Brassicaceae) by quantifying potential barriers to gene flow at multiple life history stages in 39 species pairs spanning five million years of evolutionary divergence. We quantified nine potential pre- and postzygotic barriers and explored patterns of reproductive isolation in relation to genetic distance. Intrinsic postzygotic isolation was initially weak, increased at intermediate genetic distances, and reached a threshold characterized by complete genetic incompatibility. Climatic niche differences were strong at shallow genetic distances, and species pairs with overlapping ranges showed slight but appreciable phenological isolation, highlighting the potential for ecological barriers to contribute to speciation. Geographic analyses suggest that speciation is not regionally allopatric in the California Jewelflowers, as recently diverged taxa occur in relatively close proximity and display substantial range overlap. Young pairs are characterized by incomplete intrinsic postzygotic isolation, suggesting that extrinsic barriers or fine-scale spatial segregation are more important early in the divergence process than genetic incompatibilities. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms.

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Pérez-Portela, R; Bumford, A; Coffman, B; Wedelich, S; Davenport, M; Fogg, A; Swenarton, M K; Coleman, F; Johnston, M A; Crawford, D L; Oleksiak, M F

2018-03-22

Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish's long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (F ST p-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.

SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis.

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Han, Zhengzhou; Ma, Xinye; Wei, Min; Zhao, Tong; Zhan, Ruoting; Chen, Weiwen

2018-04-25

Chrysanthemum indicum L., an important ancestral species of the flowering plant chrysanthemum, can be used as medicine and for functional food development. Due to the lack of hereditary information for this species and the difficulty of germplasm identification, we herein provide new genetic insight from the perspective of intraspecific transcriptome comparison and present single sequence repeat (SSR) molecular marker recognition technology. Through the study of a diploid germplasm (DIWNT) and a tetraploid germplasm (DIWT), the following outcome were obtained. (1) A significant difference in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations for specific homologous genes was observed using the OrthoMCL method for the identification of homologous gene families between the two cytotypes. Ka/Ks analysis of common, single-copy homologous family members also revealed a greater difference among genes that experienced positive selection than among those experiencing positive selection. (2) Of more practical value, 2575 SSR markers were predicted and partly verified. We used TaxonGap as a visual tool to inspect genotype uniqueness and screen for high-performance molecular loci; we recommend four primers of 65 randomly selected primers with a combined identification success rate of 88.6% as priorities for further development of DNA fingerprinting of C. indicum germplasm. The SSR technology based on next-generation sequencing was proved to be successful in the identification of C. indicum germplasms. And the information on the intraspecfic genetic divergence generated by transcriptome comparison deepened the understanding of this complex species' nature.

Morphological and genetic divergence between Agave inaequidens, A. cupreata and the domesticated A. hookeri. Analysis of their evolutionary relationships.

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Carmen J Figueredo-Urbina

Full Text Available Agave inaequidens and A. cupreata are wild species with some populations under incipient management, while A. hookeri is exclusively cultivated, used for producing the fermented beverage pulque. These species are closely related and sympatric members of the Crenatae group, but taxonomists have previously hypothesized that A. inaequidens is the most probable ancestor of A. hookeri. Our study aims at evaluating patterns of morphological and genetic divergence among populations of the three species, in order to analyze their ecological and possible evolutionary relationships. We studied 24 agave populations, 16 of them of Agave inaequidens, four of A. cupreata and four of A. hookeri. Population morphometric and genetics studies were performed using 39 morphological characters and 10 nuclear microsatellites, respectively. We estimated levels of morphological and genetic diversity and dissimilarity, as well as genetic structure and gene flow among populations and species. The three species were clearly differentiated by general plant size, lateral teeth, terminal spines, flowers and fruit size. The largest plants were those of A. hookeri followed by A. inaequidens and the smallest were A. cupreata. Multivariate analyses indicated greater morphological similarity between A. hookeri and cultivated A. inaequidens, while A. cupreata consistently appeared as a separate group. We identified similar levels of morphological diversity index (MDI in the three species, but higher genetic diversity in A. inaequidens (MDI = 0.401-0.435; HE = 0.704-0.733, than in A. cupreata (MDI = 0.455-0.523; HE = 0.480-0.510 and the predominantly vegetative propagated crop A. hookeri (MDI = 0.335-0.688; HE = 0.450-0.567, a pattern consistent with our expectations. The morphological and genetic similarities between cultivated A. inaequidens and A. hookeri support the hypothetical evolutionary relationships among these species, but studies with cpDNA and SNPs, and including other

Morphological and genetic divergence between Agave inaequidens, A. cupreata and the domesticated A. hookeri. Analysis of their evolutionary relationships.

Science.gov (United States)

Figueredo-Urbina, Carmen J; Casas, Alejandro; Torres-García, Ignacio

2017-01-01

Agave inaequidens and A. cupreata are wild species with some populations under incipient management, while A. hookeri is exclusively cultivated, used for producing the fermented beverage pulque. These species are closely related and sympatric members of the Crenatae group, but taxonomists have previously hypothesized that A. inaequidens is the most probable ancestor of A. hookeri. Our study aims at evaluating patterns of morphological and genetic divergence among populations of the three species, in order to analyze their ecological and possible evolutionary relationships. We studied 24 agave populations, 16 of them of Agave inaequidens, four of A. cupreata and four of A. hookeri. Population morphometric and genetics studies were performed using 39 morphological characters and 10 nuclear microsatellites, respectively. We estimated levels of morphological and genetic diversity and dissimilarity, as well as genetic structure and gene flow among populations and species. The three species were clearly differentiated by general plant size, lateral teeth, terminal spines, flowers and fruit size. The largest plants were those of A. hookeri followed by A. inaequidens and the smallest were A. cupreata. Multivariate analyses indicated greater morphological similarity between A. hookeri and cultivated A. inaequidens, while A. cupreata consistently appeared as a separate group. We identified similar levels of morphological diversity index (MDI) in the three species, but higher genetic diversity in A. inaequidens (MDI = 0.401-0.435; HE = 0.704-0.733), than in A. cupreata (MDI = 0.455-0.523; HE = 0.480-0.510) and the predominantly vegetative propagated crop A. hookeri (MDI = 0.335-0.688; HE = 0.450-0.567), a pattern consistent with our expectations. The morphological and genetic similarities between cultivated A. inaequidens and A. hookeri support the hypothetical evolutionary relationships among these species, but studies with cpDNA and SNPs, and including other member of the

Genomic islands of divergence are not affected by geography of speciation in sunflowers.

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Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

2013-01-01

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

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Resnyk, Christopher W.; Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.; Simon, Jean; Le Bihan-Duval, Elisabeth; Duclos, Michel J.; Cogburn, Larry A.

2015-01-01

Genetic selection for enhanced growth rate in meat-type chickens (Gallus domesticus) is usually accompanied by excessive adiposity, which has negative impacts on both feed efficiency and carcass quality. Enhanced visceral fatness and several unique features of avian metabolism (i.e., fasting hyperglycemia and insulin insensitivity) mimic overt symptoms of obesity and related metabolic disorders in humans. Elucidation of the genetic and endocrine factors that contribute to excessive visceral fatness in chickens could also advance our understanding of human metabolic diseases. Here, RNA sequencing was used to examine differential gene expression in abdominal fat of genetically fat and lean chickens, which exhibit a 2.8-fold divergence in visceral fatness at 7 wk. Ingenuity Pathway Analysis revealed that many of 1687 differentially expressed genes are associated with hemostasis, endocrine function and metabolic syndrome in mammals. Among the highest expressed genes in abdominal fat, across both genotypes, were 25 differentially expressed genes associated with de novo synthesis and metabolism of lipids. Over-expression of numerous adipogenic and lipogenic genes in the FL chickens suggests that in situ lipogenesis in chickens could make a more substantial contribution to expansion of visceral fat mass than previously recognized. Distinguishing features of the abdominal fat transcriptome in lean chickens were high abundance of multiple hemostatic and vasoactive factors, transporters, and ectopic expression of several hormones/receptors, which could control local vasomotor tone and proteolytic processing of adipokines, hemostatic factors and novel endocrine factors. Over-expression of several thrombogenic genes in abdominal fat of lean chickens is quite opposite to the pro-thrombotic state found in obese humans. Clearly, divergent genetic selection for an extreme (2.5–2.8-fold) difference in visceral fatness provokes a number of novel regulatory responses that govern

Genetic diversity among 16 genotypes of Coffea arabica in the Brazilian cerrado.

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Machado, C M S; Pimentel, N S; Golynsk, A; Ferreira, A; Vieira, H D; Partelli, F L

2017-09-21

For the selection of coffee plants that have favorable characteristics, it is necessary to evaluate variables related to production. Knowledge of the genetic divergence of arabica coffee is of extreme importance, as this knowledge can be associated with plant breeding programs in order to combine genetic divergence with good productive performance. The objective of this study was to evaluate the genetic divergence among 16 genotypes of Coffea arabica with the purpose of identifying the most dissimilar genotypes for the establishment of breeding programs and adaptation to the Brazilian cerrado. The genetic divergence was evaluated using multivariate procedures, the analysis of the average grouping unweighted pair group method with arithmetic mean (UPGMA) and main components in 2013 and 2014. Eight characters were evaluated in an experiment conducted in Morrinhos, Goiás. The presence of genetic divergence among the 16 C. arabica genotypes under cerrado conditions was recorded. The formation of UPGMA groups for the evaluated characteristics was pertinent due to the number of genotypes. The first three major components accounted for 81.77% of the total variance. The genotype H-419-3-4-4-13(C-241) of low size was the most divergent, followed by Catucaí 2 SL and Catiguá MG2, according to the main components.

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

Science.gov (United States)

Sutphin, George L.; Mahoney, J. Matthew; Sheppard, Keith; Walton, David O.; Korstanje, Ron

2016-01-01

The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species—humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/. PMID:27812085

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

Directory of Open Access Journals (Sweden)

George L Sutphin

2016-11-01

Full Text Available The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

Genetic influences on alcohol use behaviors have diverging developmental trajectories: a prospective study among male and female twins.

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Meyers, Jacquelyn L; Salvatore, Jessica E; Vuoksimaa, Eero; Korhonen, Tellervo; Pulkkinen, Lea; Rose, Richard J; Kaprio, Jaakko; Dick, Danielle M

2014-11-01

17-year-old females with twin brothers. We found divergent developmental trajectories for alcohol-specific and externalizing behavior-related genetic influences on alcohol use behaviors; in early adolescence, genetic influences on alcohol use behaviors are largely nonspecific, and later in adolescence and young adulthood, alcohol-specific genetic influences on alcohol use are more influential. Importantly, within these overall trajectories, several interesting sex differences emerged. We found that the relationship between genetic risk and problematic drinking across development is moderated by the individual's sex and his/her cotwin's sex. AUD-GR influenced adolescent alcohol outcomes in females more than in males and by age 22, EXT-GR influenced AD criteria more for males than females. In addition, the association between genetic risk and intoxication frequency was greater among 14- and 17-year-old females with male cotwins. Copyright © 2014 by the Research Society on Alcoholism.

Divergent synthesis and optoelectronic properties of oligodiacetylene building blocks

NARCIS (Netherlands)

Pilzak, G.S.; Lagen, van B.; Sudhölter, E.J.R.; Zuilhof, H.

2008-01-01

A new and divergent synthetic route to oligodiacetylene (ODA) building blocks has been developed via Sonogashira reactions under a reductive atmosphere. These central building blocks provide a new way for rapid preparation of long ODAs. In addition, we report on their optoelectronic properties which

[Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

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Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

2014-10-01

Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax.

Divergence in male sexual odor signal and genetics across populations of the red mason bee, Osmia bicornis, in Europe.

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Taina Conrad

Full Text Available In some insect species, females may base their choice for a suitable mate on male odor. In the red mason bee, Osmia bicornis, female choice is based on a male's odor bouquet as well as its thorax vibrations, and its relatedness to the female, a putative form of optimal outbreeding. Interestingly, O. bicornis can be found as two distinct color morphs in Europe, which are thought to represent subspecies and between which we hypothesize that female discrimination may be particularly marked. Here we investigated (i if these two colors morphs do indeed represent distinct, reproductively differentiated populations, (ii how odor bouquets of male O. bicornis vary within and between populations, and (iii whether variation in male odor correlates with genetic distance, which might represent a cue by which females could optimally outbreed. Using GC and GC-MS analysis of male odors and microsatellite analysis of males and females from 9 populations, we show that, in Denmark, an area of subspecies sympatry, the two color morphs at any one site do not differ, either in odor bouquet or in population genetic differentiation. Yet populations across Europe are distinct in their odor profile as well as being genetically differentiated. Odor differences do not, however, mirror genetic differentiation between populations. We hypothesize that populations from Germany, England and Denmark may be under sexual selection through female choice for local odor profiles, which are not related to color morph though which could ultimately lead to population divergence and speciation.

Rapid genetic turnover in populations of the insect pest Bemisia tabaci Middle East: Asia Minor 1 in an agricultural landscape.

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Dinsdale, A; Schellhorn, N A; De Barro, P; Buckley, Y M; Riginos, C

2012-10-01

Organisms differ greatly in dispersal ability, and landscapes differ in amenability to an organism's movement. Thus, landscape structure and heterogeneity can affect genetic composition of populations. While many agricultural pests are known for their ability to disperse rapidly, it is unclear how fast and over what spatial scale insect pests might respond to the temporally dynamic agricultural landscapes they inhabit. We used population genetic analyses of a severe crop pest, a member of the Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidea) cryptic species complex known as Middle East-Asia Minor 1 (commonly known as biotype B), to estimate spatial and temporal genetic diversity over four months of the 2006-2007 summer growing season. We examined 559 individuals from eight sites, which were scored for eight microsatellite loci. Temporal genetic structure greatly exceeded spatial structure. There was significant temporal change in local genetic composition from the beginning to the end of the season accompanied by heterozygote deficits and inbreeding. This temporal structure suggests entire cohorts of pests can occupy a large and variable agricultural landscape but are rapidly replaced. These rapid genetic fluctuations reinforce the concept that agricultural landscapes are dynamic mosaics in time and space and may contribute to better decisions for pest and insecticide resistance management.

Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana.

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Tanaka, Kentaro M; Hopfen, Corinna; Herbert, Matthew R; Schlötterer, Christian; Stern, David L; Masly, John P; McGregor, Alistair P; Nunes, Maria D S

2015-05-01

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes, and anal plates exhibit striking differences between Drosophila mauritiana and D. simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits. Copyright © 2015 by the Genetics Society of America.

Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus.

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Anssi Karvonen

Full Text Available Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus).

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Karvonen, Anssi; Lucek, Kay; Marques, David A; Seehausen, Ole

2015-01-01

Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka populations

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Habicht Christopher

2011-02-01

Full Text Available Abstract Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance and ecology (spawning habitat and timing driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second

Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets.

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García-Pereira, María Jesús; Caballero, Armando; Quesada, Humberto

2010-05-01

Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony

Divergent Selection and Then What Not: The Conundrum of Missing Reproductive Isolation in Misty Lake and Stream Stickleback

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Katja Räsänen

2012-01-01

Full Text Available In ecological speciation, reproductive isolation evolves as a consequence of adaptation to different selective environments. A frequent contributor to this process is the evolution of positive assortative mate choice between ecotypes. We tested this expectation for lake and inlet stream threespine stickleback (Gasterosteus aculeatus from the Misty system (Vancouver Island, Canada, which show strong genetically based adaptive divergence and little genetic exchange in nature. This, and work on other stickleback systems, led us to expect positive assortative mating. Yet, our standard “no-choice” laboratory experiment on common-garden fish revealed no evidence for this—despite divergence in traits typically mediating assortative mating in stickleback. These results remind us that divergent natural selection may not inevitably lead to the evolution of positive assortative mate choice. The apparent lack of strong and symmetric reproductive barriers in this system presents a conundrum: why are such barriers not evident despite strong adaptive divergence and low gene flow in nature?

Divergent structural brain abnormalities between different genetic subtypes of children with Prader-Willi syndrome.

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Lukoshe, Akvile; White, Tonya; Schmidt, Marcus N; van der Lugt, Aad; Hokken-Koelega, Anita C

2013-10-22

Prader-Willi syndrome (PWS) is a complex neurogenetic disorder with symptoms that indicate not only hypothalamic, but also a global, central nervous system (CNS) dysfunction. However, little is known about developmental differences in brain structure in children with PWS. Thus, our aim was to investigate global brain morphology in children with PWS, including the comparison between different genetic subtypes of PWS. In addition, we performed exploratory cortical and subcortical focal analyses. High resolution structural magnetic resonance images were acquired in 20 children with genetically confirmed PWS (11 children carrying a deletion (DEL), 9 children with maternal uniparental disomy (mUPD)), and compared with 11 age- and gender-matched typically developing siblings as controls. Brain morphology measures were obtained using the FreeSurfer software suite. Both children with DEL and mUPD showed smaller brainstem volume, and a trend towards smaller cortical surface area and white matter volume. Children with mUPD had enlarged lateral ventricles and larger cortical cerebrospinal fluid (CSF) volume. Further, a trend towards increased cortical thickness was found in children with mUPD. Children with DEL had a smaller cerebellum, and smaller cortical and subcortical grey matter volumes. Focal analyses revealed smaller white matter volumes in left superior and bilateral inferior frontal gyri, right cingulate cortex, and bilateral precuneus areas associated with the default mode network (DMN) in children with mUPD. Children with PWS show signs of impaired brain growth. Those with mUPD show signs of early brain atrophy. In contrast, children with DEL show signs of fundamentally arrested, although not deviant brain development and presented few signs of cortical atrophy. Our results of global brain measurements suggest divergent neurodevelopmental patterns in children with DEL and mUPD.

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

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Martina Temunović

Full Text Available Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM. We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Divergência genética entre genótipos de alface por meio de marcadores AFLP Genetics divergence among lettuce genotypes by AFLP markers

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Cristina Soares de Sousa

2007-01-01

Full Text Available Considerando a restrita diversidade de espécies disponíveis para nutrir a carência de vitaminas no Brasil, Kerr e colaboradores, desde 1981, vêm desenvolvendo pesquisas para melhoramento genético de hortaliças ricas em vitamina A. Dentre elas, obtiveram uma cultivar de alface, denominada Uberlândia 10.000 com 10.200 UI de vitamina A em 100 gramas de folha fresca. Este trabalho objetivou comparar o grau de divergência genética entre a cultivar Uberlândia 10.000 e seus parentais para avaliar a eficiência da seleção utilizada, por meio da técnica AFLP. Foram utilizados os seguintes genótipos de alface: Maioba, Salad Bowl-Mimosa, Moreninha-de-Uberlândia, Vitória de Santo Antão, Uberlândia 10.000 lisa 8.ª e 9.ª geração e Uberlândia 10.000 crespa 8.ª e 9.ª geração. A técnica AFLP foi eficiente para identificar genótipos muito próximos e para estudos de progênies em alface. O primer PR15 permitiu a separação da forma lisa e crespa com 1,8% de divergência genética e a oitava da nona geração com apenas 0,71%. Com o estudo da filogenia da cultivar pode-se observar que o programa de melhoramento foi desenvolvido com sucesso, pois a cultivar obtida Uberlândia 10.000 possui alto teor de vitamina A e 92% de similaridade com o parental Vitória de Santo Antão. O primer PR11 conseguiu identificar polimorfismo entre cultivares de alta e baixa resistência à septoriose, sugerindo a possibilidade destas bandas estarem relacionadas à resistência.Considering the restricted diversity of species available to counteract vitamin deficiencies in Brazil, Kerr and coworkers have been engaged since 1981, in developing genetic improved garden vegetables rich in vitamin A. One of these vegetables is the lettuce cultivar Uberlândia 10,000, which contains 10,200 UI of vitamin A per 100 grams of fresh leaves. This study compares the genetic diversity between Uberlândia 10,000 and its parental, evaluating selection efficiency through

Ethanol yields and cell wall properties in divergently bred switchgrass genotypes

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Genetic modification of herbaceous plant cell walls to increase biofuels yields from harvested biomass is a primary bioenergy research goal. The focus of much of this research has been on cell wall lignin concentration. Using switchgrass genotypes developed by divergent breeding for ruminant diges...

Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle.

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Fox, Charles W; Wagner, James D; Cline, Sara; Thomas, Frances Ann; Messina, Frank J

2009-05-01

Independent populations subjected to similar environments often exhibit convergent evolution. An unresolved question is the frequency with which such convergence reflects parallel genetic mechanisms. We examined the convergent evolution of egg-laying behavior in the seed-feeding beetle Callosobruchus maculatus. Females avoid ovipositing on seeds bearing conspecific eggs, but the degree of host discrimination varies among geographic populations. In a previous experiment, replicate lines switched from a small host to a large one evolved reduced discrimination after 40 generations. We used line crosses to determine the genetic architecture underlying this rapid response. The most parsimonious genetic models included dominance and/or epistasis for all crosses. The genetic architecture underlying reduced discrimination in two lines was not significantly different from the architecture underlying differences between geographic populations, but the architecture underlying the divergence of a third line differed from all others. We conclude that convergence of this complex trait may in some cases involve parallel genetic mechanisms.

A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

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Borja Milá

Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks.

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Mark Ravinet

Full Text Available Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L. forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12, we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an

Male sex interspecies divergence and down regulation of expression of spermatogenesis genes in Drosophila sterile hybrids.

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Sundararajan, Vignesh; Civetta, Alberto

2011-01-01

Male sex genes have shown a pattern of rapid interspecies divergence at both the coding and gene expression level. A common outcome from crosses between closely-related species is hybrid male sterility. Phenotypic and genetic studies in Drosophila sterile hybrid males have shown that spermatogenesis arrest is postmeiotic with few exceptions, and that most misregulated genes are involved in late stages of spermatogenesis. Comparative studies of gene regulation in sterile hybrids and parental species have mainly used microarrays providing a whole genome representation of regulatory problems in sterile hybrids. Real-time PCR studies can reject or reveal differences not observed in microarray assays. Moreover, differences in gene expression between samples can be dependant on the source of RNA (e.g., whole body vs. tissue). Here we survey expression in D. simulans, D. mauritiana and both intra and interspecies hybrids using a real-time PCR approach for eight genes expressed at the four main stages of sperm development. We find that all genes show a trend toward under expression in the testes of sterile hybrids relative to parental species with only the two proliferation genes (bam and bgcn) and the two meiotic class genes (can and sa) showing significant down regulation. The observed pattern of down regulation for the genes tested can not fully explain hybrid male sterility. We discuss the down regulation of spermatogenesis genes in hybrids between closely-related species within the contest of rapid divergence experienced by the male genome, hybrid sterility and possible allometric changes due to subtle testes-specific developmental abnormalities.

Landscape genetic approaches to guide native plant restoration in the Mojave Desert

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Shryock, Daniel F.; Havrilla, Caroline A.; DeFalco, Lesley; Esque, Todd C.; Custer, Nathan; Wood, Troy E.

2016-01-01

Restoring dryland ecosystems is a global challenge due to synergistic drivers of disturbance coupled with unpredictable environmental conditions. Dryland plant species have evolved complex life-history strategies to cope with fluctuating resources and climatic extremes. Although rarely quantified, local adaptation is likely widespread among these species and potentially influences restoration outcomes. The common practice of reintroducing propagules to restore dryland ecosystems, often across large spatial scales, compels evaluation of adaptive divergence within these species. Such evaluations are critical to understanding the consequences of large-scale manipulation of gene flow and to predicting success of restoration efforts. However, genetic information for species of interest can be difficult and expensive to obtain through traditional common garden experiments. Recent advances in landscape genetics offer marker-based approaches for identifying environmental drivers of adaptive genetic variability in non-model species, but tools are still needed to link these approaches with practical aspects of ecological restoration. Here, we combine spatially-explicit landscape genetics models with flexible visualization tools to demonstrate how cost-effective evaluations of adaptive genetic divergence can facilitate implementation of different seed sourcing strategies in ecological restoration. We apply these methods to Amplified Fragment Length Polymorphism (AFLP) markers genotyped in two Mojave Desert shrub species of high restoration importance: the long-lived, wind-pollinated gymnosperm Ephedra nevadensis, and the short-lived, insect-pollinated angiosperm Sphaeralcea ambigua. Mean annual temperature was identified as an important driver of adaptive genetic divergence for both species. Ephedra showed stronger adaptive divergence with respect to precipitation variability, while temperature variability and precipitation averages explained a larger fraction of adaptive

Ground state energies from converging and diverging power series expansions

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Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E.; Su, Q.; Grobe, R.

2016-01-01

It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh–Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state’s spatial extension is comparable to L. Once the binding strength is so strong that the ground state’s extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

Ground state energies from converging and diverging power series expansions

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Lisowski, C.; Norris, S.; Pelphrey, R.; Stefanovich, E., E-mail: eugene-stefanovich@usa.net; Su, Q.; Grobe, R.

2016-10-15

It is often assumed that bound states of quantum mechanical systems are intrinsically non-perturbative in nature and therefore any power series expansion methods should be inapplicable to predict the energies for attractive potentials. However, if the spatial domain of the Schrödinger Hamiltonian for attractive one-dimensional potentials is confined to a finite length L, the usual Rayleigh–Schrödinger perturbation theory can converge rapidly and is perfectly accurate in the weak-binding region where the ground state’s spatial extension is comparable to L. Once the binding strength is so strong that the ground state’s extension is less than L, the power expansion becomes divergent, consistent with the expectation that bound states are non-perturbative. However, we propose a new truncated Borel-like summation technique that can recover the bound state energy from the diverging sum. We also show that perturbation theory becomes divergent in the vicinity of an avoided-level crossing. Here the same numerical summation technique can be applied to reproduce the energies from the diverging perturbative sums.

Genetic divergence among accessions of Axonopus jesuiticus x A. scoparius based on morphological and agronomical traits

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SIMONE M. SCHEFFER-BASSO

2014-03-01

Full Text Available This study had the objective of assessing the genetic divergence in giant missionary grass (Axonopus jesuiticus x A. scoparius germplasm based on morphological and agronomic traits. Five accessions were evaluated in the field: V14337, V14403, V14404, V14405 and V14406. Three contrasting groups were formed using the UPGMA clustering method: V14337 and V14404 formed one group, V14403 and V14405 formed another, and V14406 was isolated from the other accessions. The most striking traits for the identification of the accessions were the height of the plant and the change color of the leaf. Only V14406 accession had purplish green leaves. The other four accessions differed with regards to plant height and dry matter production, with superiority of V14337 and V14404 accessions. The high similarity, as assessed by the mean Euclidean distance, suggests that V14337 and V14404 share the same genotype. The genotypic variability among accessions indicates their potential use in breeding programs.

Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes

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Bruno F. Melo

2018-04-01

Full Text Available Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.

Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories.

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Avigdor, Bracha Erlanger; Cimino-Mathews, Ashley; DeMarzo, Angelo M; Hicks, Jessica L; Shin, James; Sukumar, Saraswati; Fetting, John; Argani, Pedram; Park, Ben H; Wheelan, Sarah J

2017-12-21

Heterogeneity within and among tumors in a metastatic cancer patient is a well-established phenomenon that may confound treatment and accurate prognosis. Here, we used whole-exome sequencing to survey metastatic breast cancer tumors from 5 patients in a rapid autopsy program to construct the origin and genetic development of metastases. Metastases were obtained from 5 breast cancer patients using a rapid autopsy protocol and subjected to whole-exome sequencing. Metastases were evaluated for sharing of somatic mutations, correlation of copy number variation and loss of heterozygosity, and genetic similarity scores. Pathological features of the patients' disease were assessed by immunohistochemical analyses. Our data support a monoclonal origin of metastasis in 3 cases, but in 2 cases, metastases arose from at least 2 distinct subclones in the primary tumor. In the latter 2 cases, the primary tumor presented with mixed histologic and pathologic features, suggesting early divergent evolution within the primary tumor with maintenance of metastatic capability in multiple lineages. We used genetic and histopathological evidence to demonstrate that metastases can be derived from a single or multiple independent clones within a primary tumor. This underscores the complexity of breast cancer clonal evolution and has implications for how best to determine and implement therapies for early- and late-stage disease.

Thrust characteristics of a series of convergent-divergent exhaust nozzles at subsonic and supersonic flight speeds

Science.gov (United States)

Fradenburgh, Evan A; Gorton, Gerald C; Beke, Andrew

1954-01-01

An experimental investigation of a series of four convergent-divergent exhaust nozzles was conducted in the Lewis 8-by-6 foot supersonic wind tunnel at Mach numbers of 0.1, 0.6, 1.6, and 2.0 over a range of nozzle pressure ratios. The thrust characteristics of these nozzles were determined by a pressure-integration technique. From a thrust standpoint, a nozzle designed to give uniform parallel flow at the exit had no advantage over the simple geometric design with conical convergent and divergent sections. The rapid-divergent nozzles might be competitive with the more gradual-divergent nozzles since the relatively short length of these nozzles would be advantageous from a weight standpoint and might result in smaller thrust losses due to friction. The thrusts, with friction losses neglected, were predicted satisfactorily by one-dimensional theory for the nozzles with relatively gradual divergence. The thrusts of the rapid-divergent designs were several percentages below the theoretical values at the design pressure ratio or above, while at low pressure ratios there was a considerable effect of free-stream Mach number, with thrusts considerably above theoretical values at subsonic speeds and somewhat above theoretical values at supersonic speeds. This Mach numb effect appeared to be related to the variation of the model base pressure with free-stream Mach number.

Demographic histories of adaptively diverged riparian and non-riparian species of Ainsliaea (Asteraceae) inferred from coalescent analyses using multiple nuclear loci.

Science.gov (United States)

Mitsui, Yuki; Setoguchi, Hiroaki

2012-12-28

Understanding demographic histories, such as divergence time, patterns of gene flow, and population size changes, in ecologically diverging lineages provide implications for the process and maintenance of population differentiation by ecological adaptation. This study addressed the demographic histories in two independently derived lineages of flood-resistant riparian plants and their non-riparian relatives [Ainsliaea linearis (riparian) and A. apiculata (non-riparian); A. oblonga (riparian) and A. macroclinidioides (non-riparian); Asteraceae] using an isolation-with-migration (IM) model based on variation at 10 nuclear DNA loci. The highest posterior probabilities of the divergence time parameters were estimated to be ca. 25,000 years ago for A. linearis and A. apiculata and ca. 9000 years ago for A. oblonga and A. macroclinidioides, although the confidence intervals of the parameters had broad ranges. The likelihood ratio tests detected evidence of historical gene flow between both riparian/non-riparian species pairs. The riparian populations showed lower levels of genetic diversity and a significant reduction in effective population sizes compared to the non-riparian populations and their ancestral populations. This study showed the recent origins of flood-resistant riparian plants, which are remarkable examples of plant ecological adaptation. The recent divergence and genetic signatures of historical gene flow among riparian/non-riparian species implied that they underwent morphological and ecological differentiation within short evolutionary timescales and have maintained their species boundaries in the face of gene flow. Comparative analyses of adaptive divergence in two sets of riparian/non-riparian lineages suggested that strong natural selection by flooding had frequently reduced the genetic diversity and size of riparian populations through genetic drift, possibly leading to fixation of adaptive traits in riparian populations. The two sets of riparian

Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow

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Aneil F. Agrawal

2011-01-01

Full Text Available The evolution of intrinsic postmating isolation has received much attention, both historically and in recent studies of speciation genes. Intrinsic isolation often stems from between-locus genetic incompatibilities, where alleles that function well within species are incompatible with one another when brought together in the genome of a hybrid. It can be difficult for such incompatibilities to originate when populations diverge with gene flow, because deleterious genotypic combinations will be created and then purged by selection. However, it has been argued that if genes underlying incompatibilities are themselves subject to divergent selection, then they might overcome gene flow to diverge between populations, resulting in the origin of incompatibilities. Nonetheless, there has been little explicit mathematical exploration of such scenarios for the origin of intrinsic incompatibilities during ecological speciation with gene flow. Here we explore theoretical models for the origin of intrinsic isolation where genes subject to divergent natural selection also affect intrinsic isolation, either directly or via linkage disequilibrium with other loci. Such genes indeed overcome gene flow, diverge between populations, and thus result in the evolution of intrinsic isolation. We also examine barriers to neutral gene flow. Surprisingly, we find that intrinsic isolation sometimes weakens this barrier, by impeding differentiation via ecologically based divergent selection.

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species

DEFF Research Database (Denmark)

Pearce, S L; Clarke, D F; East, P D

2017-01-01

BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptom......BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics......, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100...... lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show...

Mechanisms by Which Phenotypic Plasticity Affects Adaptive Divergence and Ecological Speciation.

Science.gov (United States)

Nonaka, Etsuko; Svanbäck, Richard; Thibert-Plante, Xavier; Englund, Göran; Brännström, Åke

2015-11-01

Phenotypic plasticity is the ability of one genotype to produce different phenotypes depending on environmental conditions. Several conceptual models emphasize the role of plasticity in promoting reproductive isolation and, ultimately, speciation in populations that forage on two or more resources. These models predict that plasticity plays a critical role in the early stages of speciation, prior to genetic divergence, by facilitating fast phenotypic divergence. The ability to plastically express alternative phenotypes may, however, interfere with the early phase of the formation of reproductive barriers, especially in the absence of geographic barriers. Here, we quantitatively investigate mechanisms under which plasticity can influence progress toward adaptive genetic diversification and ecological speciation. We use a stochastic, individual-based model of a predator-prey system incorporating sexual reproduction and mate choice in the predator. Our results show that evolving plasticity promotes the evolution of reproductive isolation under diversifying environments when individuals are able to correctly select a more profitable habitat with respect to their phenotypes (i.e., adaptive habitat choice) and to assortatively mate with relatively similar phenotypes. On the other hand, plasticity facilitates the evolution of plastic generalists when individuals have a limited capacity for adaptive habitat choice. We conclude that plasticity can accelerate the evolution of a reproductive barrier toward adaptive diversification and ecological speciation through enhanced phenotypic differentiation between diverging phenotypes.

Foundations of genetic algorithms 1991

CERN Document Server

1991-01-01

Foundations of Genetic Algorithms 1991 (FOGA 1) discusses the theoretical foundations of genetic algorithms (GA) and classifier systems.This book compiles research papers on selection and convergence, coding and representation, problem hardness, deception, classifier system design, variation and recombination, parallelization, and population divergence. Other topics include the non-uniform Walsh-schema transform; spurious correlations and premature convergence in genetic algorithms; and variable default hierarchy separation in a classifier system. The grammar-based genetic algorithm; condition

Phylogeography of the sandy beach amphipod Haustorioides japonicus along the Sea of Japan: Paleogeographical signatures of cryptic regional divergences

Science.gov (United States)

Takada, Yoshitake; Sakuma, Kay; Fujii, Tetsuo; Kojima, Shigeaki

2018-01-01

Recent findings of genetic breaks within apparently continuous marine populations challenge the traditional vicariance paradigm in population genetics. Such "invisible" boundaries are sometimes associated with potential geographic barriers that have forced divergence of an ancestral population, habitat discontinuities, biogeographic disjunctions due to environmental gradients, or a combination of these factors. To explore the factors that influence the genetic population structure of apparently continuous populations along the Sea of Japan, the sandy beach amphipod Haustorioides japonicus was examined. We sampled a total of 300 individuals of H. japonicus from the coast of Japan, and obtained partial sequences of the mitochondrial COI gene. The sequences from 19 local populations were clustered into five groups (Northwestern Pacific, Northern, Central, Southern Sea of Japan, and East China Sea) based on a spatial genetic mixture analysis and a minimum-spanning network. AMOVA and pairwise Fst tests further supported the significant divergence of the five groups. Phylogenetic analysis revealed the relationship among the haplotypes of H. japonicus and outgroups, which inferred the northward range expansion of the species. A relaxed molecular-clock Bayesian analysis inferred the early-to middle-Pleistocene divergence of the populations. Among the five clusters, the Central Sea of Japan showed the highest values for genetic diversity indices indicating the existence of a relatively stable and large population there. The hypothesis is also supported by Bayesian Skyline Plots that showed sudden population expansion for all the clusters except for Central Sea of Japan. The present study shows genetic boundaries between the Sea of Japan and the neighboring seas, probably due to geographic isolation during the Pleistocene glacial periods. We further found divergence between the populations along the apparently continuous coast of the Sea of Japan. Historical changes in the

Genetic heterogeneity of murine coronaviruses

International Nuclear Information System (INIS)

Lai, M.M.C.; Fleming, J.O.; Stohlman, S.A.; Fujiwara, K.

1983-01-01

Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. Two strains, MHV-K and MHV-D, which were isolated in Japan and, which cause anaplasia and necrosis of bone marrow and diarrhea, respectively, were found to be closely related to MHV-A59, the prototype MHV. Two other MHV strains, isolated from nude mice, were found to have diverged extensively from the known MHV strains. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. Genetic divergence during persistent infection may be one of the mechanisms by which the MHV diverges. (Author)

Genetic heterogeneity of murine coronaviruses

Energy Technology Data Exchange (ETDEWEB)

Lai, M M.C.; Fleming, J O; Stohlman, S A; Fujiwara, K

1983-12-01

Several mouse hepatitis viruses (MHV) with different pathogenicity were studied by oligonucleotide fingerprinting. Two strains, MHV-K and MHV-D, which were isolated in Japan and, which cause anaplasia and necrosis of bone marrow and diarrhea, respectively, were found to be closely related to MHV-A59, the prototype MHV. Two other MHV strains, isolated from nude mice, were found to have diverged extensively from the known MHV strains. The MHVs isolated from separate cloned neuroblastoma cell lines persistently infected with JHM strain were also found to have diverged more markedly than the corresponding virus maintained under the conditions of lytic infection. Genetic divergence during persistent infection may be one of the mechanisms by which the MHV diverges.

Natural transformation of Vibrio parahaemolyticus: A rapid method to create genetic deletions.

Science.gov (United States)

Chimalapati, Suneeta; de Souza Santos, Marcela; Servage, Kelly; De Nisco, Nicole J; Dalia, Ankur B; Orth, Kim

2018-03-19

The Gram-negative bacterium Vibrio parahaemolyticus is an opportunistic human pathogen and the leading cause of seafood borne acute gastroenteritis worldwide. Recently, this bacterium was implicated as the etiologic agent of a severe shrimp disease with consequent devastating outcomes to shrimp farming. In both cases, acquisition of genetic material via horizontal transfer provided V. parahaemolyticus with new virulence tools to cause disease. Dissecting the molecular mechanisms of V. parahaemolyticus pathogenesis often requires manipulating its genome. Classically, genetic deletions in V. parahaemolyticus are performed using a laborious, lengthy, multi-step process. Herein, we describe a fast and efficient method to edit this bacterium's genome based on V. parahaemolyticus natural competence. Although this method is similar to one previously described, V. parahaemolyticus requires counter selection for curing of acquired plasmids due to its recalcitrant nature of retaining extrachromosomal DNA. We believe this approach will be of use to the Vibrio community. Importance Spreading of Vibrios throughout the world correlates with increased global temperatures. As they spread, they find new niches to survive, proliferate and invade. Therefore, genetic manipulation of Vibrios is of utmost importance for studying these species. Herein, we have delineated and validated a rapid method to create genetic deletions in Vibrio parahaemolyticus This study provides insightful methodology for studies with other Vibrio species. Copyright © 2018 American Society for Microbiology.

Multivariate analysis in a genetic divergence study of Psidium guajava.

Science.gov (United States)

Nogueira, A M; Ferreira, M F S; Guilhen, J H S; Ferreira, A

2014-12-18

The family Myrtaceae is widespread in the Atlantic Forest and is well-represented in the Espírito Santo State in Brazil. In the genus Psidium of this family, guava (Psidium guajava L.) is the most economically important species. Guava is widely cultivated in tropical and subtropical countries; however, the widespread cultivation of only a small number of guava tree cultivars may cause the genetic vulnerability of this crop, making the search for promising genotypes in natural populations important for breeding programs and conservation. In this study, the genetic diversity of 66 guava trees sampled in the southern region of Espírito Santo and in Caparaó, MG, Brazil were evaluated. A total of 28 morphological descriptors (11 quantitative and 17 multicategorical) and 18 microsatellite markers were used. Principal component, discriminant and cluster analyses, descriptive analyses, and genetic diversity analyses using simple sequence repeats were performed. Discrimination of accessions using molecular markers resulted in clustering of genotypes of the same origin, which was not observed using morphological data. Genetic diversity was detected between and within the localities evaluated, regardless of the methodology used. Genetic differentiation among the populations using morphological and molecular data indicated the importance of the study area for species conservation, genetic erosion estimation, and exploitation in breeding programs.

Genetic diversity in maize genotypes with and without a topdressing of nitrogen fertilizer = Divergência genética de genótipos de milho com e sem adubação nitrogenada em cobertura

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Karen Cristina Leite Silva

2015-06-01

Full Text Available The use of genetic diversity as a basis for identifying combinations which are superior to the parents, with a greater heterozygosity, is important in view of the difficulty when selecting promising genotypes for a breeding program. Given the above, the aim of this work was to evaluate genetic diversity in maize genotypes with and without a topdressing of nitrogen fertiliser, using characteristics of the growth stage of the crop. Two field experiments were carried out in Gurupi, in the south of the state of Tocantins, Brazil (TO, one with and another without a topdressing of N fertilizer (1 - no N topdressing, 2 - 150 kg N ha-1. The treatments consisted of 12 genotypes (six open-pollinated populations, and six S5 strains. In applying the technique of clustering to the genotypes, the Generalised Mahalanobis Distance (D2 was adopted as dissimilarity measure. To establish similar groups, the agglomerative hierarchical method of optimisation proposed by Tocher was applied. In addition, Singh’s criterion was used to quantify the relative contribution to genetic divergence of the characteristics under evaluation. The characteristics, Chlorophyll-a and total chlorophyll, displayed the greatest contribution to genetic divergence, when there was no topdressing of nitrogen fertiliser and with the use of 150 kg N ha-1 respectively. A topdressing of nitrogen influenced both the vegetative development of the genotypes, and the expression of their genetic variability. = A utilização da divergência genética como base para a identificação de combinações superiores aos progenitores, apresentando maior heterozigose, faz-se importante diante da dificuldade de escolha de genótipos promissores em um programa de melhoramento. Com base no exposto, objetivou-se com este trabalho avaliar a divergência genética de genótipos de milho com e sem adubação nitrogenada em cobertura, utilizando características do estágio vegetativo da cultura, no sul do Estado

Characterization of genetic diversity of bird-of-paradise accessions

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Alessandro Aparecido Brito dos Santos

2018-04-01

Full Text Available This study aimed to characterize genetic diversity in the bird-of-paradise (Strelitzia reginae collection at the Universidade do Estado de Mato Grosso Carlos Alberto Reyes Maldonado (UNEMAT by estimating genetic divergence among genotypes based on agronomic characteristics. Seven agronomic characters were evaluated with average Euclidean distance. The UPGMA (Unweighted Pair Group Method with Arithmetic Mean hierarchical clustering method was used between groups, as well as Tocher’s optimization clustering method and principal component analysis (PCA, in order to classify the genotypes with maximum similarity between groups. Measures of genetic dissimilarity with average Euclidean distance verified the existence of genetic variability among accessions since the amplitude of dissimilarity values ranged from 1.09 to 36.97. Tocher’s clustering method verified the formation of two distinct groups. UPGMA hierarchical clustering, based on the dissimilarity matrix, verified the formation of three groups with 30% cutoff point. Based on the main components analysis, we verified genetic divergence between the bird-of-paradise accessions in the UNEMAT Collection. The most promising combinations for future crosses in breeding programs comprise accessions 1, 11, and 23 and accession 1 as the most divergent among the accessions evaluated.

Ecological, morphological and genetic divergence of sympatric North Atlantic killer whale populations

DEFF Research Database (Denmark)

Foote, Andrew D; Newton, Jason; Piertney, Stuart B

2009-01-01

promoting divergence. Here we use morphological traits, nitrogen stable isotope ratios and tooth wear to characterize two disparate types of North Atlantic killer whale. We find a highly specialist type, which reaches up to 8.5 m in length and a generalist type which reaches up to 6.6 m in length...

Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq.

Science.gov (United States)

Dennenmoser, Stefan; Vamosi, Steven M; Nolte, Arne W; Rogers, Sean M

2017-01-01

Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), an abundant euryhaline fish in northwestern North America, high genetic connectivity among brackish-water (estuarine) and freshwater (tributary) habitats of coastal rivers does not preclude the build-up of neutral genetic differentiation and emergence of different life history strategies. Because these two habitats present different osmotic niches, we predicted high genetic differentiation at known teleost candidate genes underlying salinity tolerance and osmoregulation. We applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to explore adaptive divergence between two estuarine and two tributary habitats. Paired-end sequence reads were mapped against genomic contigs of European Cottus, and the gene content of candidate regions was explored based on comparisons with the threespine stickleback genome. Genes showing signals of repeated differentiation among brackish-water and freshwater habitats included functions such as ion transport and structural permeability in freshwater gills, which suggests that local adaptation to different osmotic niches might contribute to genomic divergence among habitats. Overall, the presence of both repeated and unique signatures of differentiation across many loci scattered throughout the genome is consistent with polygenic adaptation from standing genetic variation and locally variable selection pressures in the early stages of life history divergence. © 2016 John Wiley & Sons Ltd.

Potencial agronômico e divergência genética entre genótipos de berinjela nas condições do Caribe Colombiano Agronomic potential and genetic divergence among eggplant genotypes in the Colombian Caribbean region

Directory of Open Access Journals (Sweden)

Hermes Aramendiz-Tatis

2011-06-01

Full Text Available Foram avaliados 24 genótipos (híbridos, cultivares e variedades locais de berinjela quanto às características produtivas no Caribe Colombiano para quantificar a divergência genética entre estes e indicar possíveis cruzamentos. Visa-se dar início a um programa de melhoramento genético da cultura na região, considerando a divergência genética e as características agronômicas desses genótipos. Utilizou-se delineamento em blocos casualizados, com três repetições. As variáveis estudadas foram comprimento do fruto, número de frutos por planta, massa média do fruto, rendimento, firmeza do fruto e altura da planta. Os dados foram submetidos à análise de variância univariada e estatísticas multivariadas utilizando-se diferentes métodos de agrupamento hierárquico e as variáveis canônicas. As médias foram agrupadas pelo teste de Scott-Knott. Verificou-se elevada divergência entre os genótipos estudados. Quando se considerou isoladamente os híbridos, as cultivares e as variedades locais, observou-se maior variabilidade entre os híbridos seguido das cultivares e, por fim, das variedades locais. O método UPGMA foi mais fidedigno no agrupamento que os métodos Ward e Vizinho Mais Próximo, pois obteve maior valor de Coeficiente de Correlação Cofenética. Pelos critérios pseudo-F e pseudo-t² verificou-se que o ponto de máximo foi atingido quando da forma��ão de quatro grupos, sendo este considerado o número ideal de grupos para o UPGMA. Houve concordância entre os grupos formados pelo UPGMA e pelas variáveis canônicas. Com os resultados pode-se inferir que os cruzamentos CC08 x CC02; CC08 x EU01 e CC08 x C016 têm grande potencial visando à produção e a firmeza do fruto.We evaluated 24 genotypes (hybrids, cultivars and landraces of eggplant related to yield traits in the Colombian Caribbean region, to quantify the genetic divergence among these genotypes and to indicate possible crosses. With the results of

Divergence in morphology, but not habitat use, despite low genetic differentiation among insular populations of the lizard Anolis lemurinus in Honduras

Science.gov (United States)

Logan, M.L.; Montgomery, Chad E.; Boback, Scott M.; Reed, R.N.; Campbell, J.A.

2012-01-01

Studies of recently isolated populations are useful because observed differences can often be attributed to current environmental variation. Two populations of the lizard Anolis lemurinus have been isolated on the islands of Cayo Menor and Cayo Mayor in the Cayos Cochinos Archipelago of Honduras for less than 15 000 y. We measured 12 morphometric and 10 habitat-use variables on 220 lizards across these islands in 2 y, 2008 and 2009. The goals of our study were (1) to explore patterns of sexual dimorphism, and (2) to test the hypothesis that differences in environment among islands may have driven divergence in morphology and habitat use despite genetic homogeneity among populations. Although we found no differences among sexes in habitat use, males had narrower pelvic girdles and longer toe pads on both islands. Between islands, males differed in morphology, but neither males nor females differed in habitat use. Our data suggest that either recent selection has operated differentially on males despite low genetic dill'erentiation, or that they display phenotypic plasticity in response to environmental variation. We suggest that patterns may be driven by variation in intrapopulation density or differences in predator diversity among islands.

Diverging Cohesion?

DEFF Research Database (Denmark)

Charron, Nicholas

2016-01-01

– which we define here as a combination of impartial bureaucratic practices, corruption and the rule of law – limits, and in some cases reverses the tendency towards greater divergence linked to trade. Countries with high levels of state capacity – that is, those that have greater government effectiveness......, stronger rule of law and lower corruption – experience lower levels of divergence, as they have the mechanisms to counterbalance the strong centripetal forces linked to openness. This claim is tested on countries that have experienced relatively high levels of increases in levels of economic and political......Why do increases in globalisation in the face of European expansion lead to sharp levels of regional divergences in wealth in some countries but not in others? The central crux of this paper is that convergence/divergence trends in European states are conditioned by ‘state capacity’. State capacity...

Low genetic and phenotypic divergence in a contact zone between freshwater and marine sticklebacks: gene flow constrains adaptation

DEFF Research Database (Denmark)

Pedersen, Susanne Holst; Ferchaud, Anne-Laure; Bertelsen, Mia Smedegaard

2017-01-01

Background: Distinct hybrid zones and phenotypic and genomic divergence is often observed between marine and freshwater threespine sticklebacks (Gasterosteus aculeatus). Nevertheless, cases also exist where marinefreshwater divergence is diffuse despite seemingly similar environmental settings...

Redundancy and divergence in the amyloid precursor protein family.

Science.gov (United States)

Shariati, S Ali M; De Strooper, Bart

2013-06-27

Gene duplication provides genetic material required for functional diversification. An interesting example is the amyloid precursor protein (APP) protein family. The APP gene family has experienced both expansion and contraction during evolution. The three mammalian members have been studied quite extensively in combined knock out models. The underlying assumption is that APP, amyloid precursor like protein 1 and 2 (APLP1, APLP2) are functionally redundant. This assumption is primarily supported by the similarities in biochemical processing of APP and APLPs and on the fact that the different APP genes appear to genetically interact at the level of the phenotype in combined knockout mice. However, unique features in each member of the APP family possibly contribute to specification of their function. In the current review, we discuss the evolution and the biology of the APP protein family with special attention to the distinct properties of each homologue. We propose that the functions of APP, APLP1 and APLP2 have diverged after duplication to contribute distinctly to different neuronal events. Our analysis reveals that APLP2 is significantly diverged from APP and APLP1. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Uso do algoritmo de Gower na determinação da divergência genética entre acessos de tomateiro do grupo cereja = Using Gower’s algorithm on the genetic divergence determination among cherry tomato accessions

Directory of Open Access Journals (Sweden)

Mariella Camargo Rocha

2010-07-01

Full Text Available A análise conjunta de variáveis qualitativas e quantitativas tem sido apontada como ferramenta útil na estimativa da divergência genética entre os acessos de uma coleção de germoplasma. O presente trabalho teve como objetivos caracterizar uma coleção de germoplasma de tomateiro do grupo cereja, com base em descritores qualitativos e quantitativos e utilizar o algoritmo de Gower na quantificação da divergência genética. Estudaram-se 40 acessos de tomateiro cereja, cultivados em manejo orgânico nas condições de Seropédica, Estado do Rio de Janeiro. Foram utilizados quatro descritores qualitativos relacionados aos frutos e nove descritores quantitativos. Os dados foram analisados de forma conjunta pelo algoritmo de Gower. Detectou-se variabilidade para coloração, formato e número de lóculos do fruto. A coloração vermelha foi observada em 25 acessos testados, registrando-se também a produção de frutos amarelos, laranjas e marrons. Para número de lóculos, foi registrada a ocorrência de frutosbi, tri, tetra e pluriloculares (com até sete lóculos. O método UPGMA foi o que obteve o maior coeficiente de correlação cofenética (0,80, observando-se a formação de sete grupos. Os grupos formados permitiram a distinção de frutos classificados como cereja e outros que não se adequaram a esta definição, por estarem acima do diâmetro equatorial proposto para esta classe. The joint analysis of qualitative and quantitative variables has been considered a useful tool to estimate the genetic divergence among accessions of a gene bank. The purpose of this research was: (i to characterize a collection of cherry tomatoes, using quantitative and qualitative descriptors, and (ii to use Gower’s algorithm to quantify genetic divergence among genotypes, employing a joint descriptors analysis. Forty accessions of organically grown cherry tomato were studied in Seropedica, Rio de Janeiro, Brazil. Fourqualitative fruit descriptors

History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei).

Science.gov (United States)

Bagley, Robin K; Sousa, Vitor C; Niemiller, Matthew L; Linnen, Catherine R

2017-02-01

Divergent host use has long been suspected to drive population differentiation and speciation in plant-feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double-digest restriction-associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a widespread pest that uses multiple Pinus hosts throughout its range in eastern North America. Because this species has a broad range and specializes on host plants known to have migrated extensively during the Pleistocene, we first assess overall genetic structure using model-based and model-free clustering methods and identify three geographically distinct genetic clusters. Next, using a composite-likelihood approach based on the site frequency spectrum and a novel strategy for maximizing the utility of linked RAD markers, we infer the population topology and date divergence to the Pleistocene. Based on existing knowledge of Pinus refugia, estimated demographic parameters and patterns of diversity among sawfly populations, we propose a Pleistocene divergence scenario for N. lecontei. Finally, using Mantel and partial Mantel tests, we identify a significant relationship between genetic distance and geography in all clusters, and between genetic distance and host use in two of three clusters. Overall, our results indicate that Pleistocene isolation, dispersal limitation and ecological divergence all contribute to genomewide differentiation in this species and support the hypothesis that host use is a common driver of population divergence in host-specialized insects. © 2016 John Wiley & Sons Ltd.

A rapid method for establishment of a reverse genetics system for canine parvovirus.

Science.gov (United States)

Yu, Yongle; Su, Jun; Wang, Jigui; Xi, Ji; Mao, Yaping; Hou, Qiang; Zhang, Xiaomei; Liu, Weiquan

2017-12-01

Canine parvovirus (CPV) is an important and highly prevalent pathogen of dogs that causes acute hemorrhagic enteritis disease. Here, we describe a rapid method for the construction and characterization of a full-length infectious clone (rCPV) of CPV. Feline kidney (F81) cells were transfected with rCPV incorporating an engineered EcoR I site that served as a genetic marker. The rescued virus was indistinguishable from that of wild-type virus in its biological properties.

Genetic divergence of bean genotypes to infestation of Zabrotes subfasciatus (Bohemann (Coleoptera: Bruchidae

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Eduardo Neves Costa

2013-12-01

Full Text Available The aim of this work was to evaluate the genetics divergence of bean genotypes in relation to the oviposition, feeding and development of Zabrotes subfasciatus, determining the degrees of resistance to the weevil. The genotypes used were: IAC Carioca-Tybatã, IAC Fortaleza, IAPAR 81, IAC Carioca-Eté, IAC Galante, IAC Harmonia, IAC Una, IAC Diplomata, BRS Supremo and RAZ 49. Tests were performed in laboratory under controlled humidity, temperature and photophase conditions. In free choice test, 10 g of bean genotypes seeds were distributed in circular openings placed equidistant from each other in aluminum trays, where 70 couples were released. The attractiveness was evaluated 24 hours and seven days after the experiment started, and then the number of eggs was evaluated. In non choice test, 10 g of seeds were used where seven couples of Z. subfasciatus, 24 hours-old, were released, remaining seven days, and after the adults retreat, the total number eggs, viable and unviable eggs, the number and percentage of emerged adults, weight, longevity and period from egg to adult of males and females, sex ratio, dry mass and dry mass consumed by insect were evaluated. In the genotype IAC Harmonia was observed the lower oviposition; RAZ 49 was the most non preference-type resistant for feeding and/or antibiosis-type resistant; BRS Supremo, IAC Carioca-Eté and IAPAR 81 are no preference for feeding and/or antibiosis-type moderate resistant; IAC Galante is susceptible and the other genotypes are highly susceptible to Z. subfasciatus

Functional divergence caused by ancient positive selection of a Drosophila hybrid incompatibility locus.

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Daniel A Barbash

2004-06-01

Full Text Available Interspecific hybrid lethality and sterility are a consequence of divergent evolution between species and serve to maintain the discrete identities of species. The evolution of hybrid incompatibilities has been described in widely accepted models by Dobzhansky and Muller where lineage-specific functional divergence is the essential characteristic of hybrid incompatibility genes. Experimentally tractable models are required to identify and test candidate hybrid incompatibility genes. Several Drosophila melanogaster genes involved in hybrid incompatibility have been identified but none has yet been shown to have functionally diverged in accordance with the Dobzhansky-Muller model. By introducing transgenic copies of the X-linked Hybrid male rescue (Hmr gene into D. melanogaster from its sibling species D. simulans and D. mauritiana, we demonstrate that Hmr has functionally diverged to cause F1 hybrid incompatibility between these species. Consistent with the Dobzhansky-Muller model, we find that Hmr has diverged extensively in the D. melanogaster lineage, but we also find extensive divergence in the sibling-species lineage. Together, these findings implicate over 13% of the amino acids encoded by Hmr as candidates for causing hybrid incompatibility. The exceptional level of divergence at Hmr cannot be explained by neutral processes because we use phylogenetic methods and population genetic analyses to show that the elevated amino-acid divergence in both lineages is due to positive selection in the distant past-at least one million generations ago. Our findings suggest that multiple substitutions driven by natural selection may be a general phenomenon required to generate hybrid incompatibility alleles.

Mechanisms of peripheral phylogeographic divergence in the indo-Pacific: lessons from the spiny lobster Panulirus homarus.

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Farhadi, Ahmad; Jeffs, Andrew G; Farahmand, Hamid; Rejiniemon, Thankappan Sarasam; Smith, Greg; Lavery, Shane D

2017-08-18

There is increasing recognition of the concordance between marine biogeographic and phylogeographic boundaries. However, it is still unclear how population-level divergence translates into species-level divergence, and what are the principal factors that first initiate that divergence, and then maintain reproductive isolation. This study examines the likely forces driving population and lineage divergences in the broadly-distributed Indo-Pacific spiny lobster Panulirus homarus, which has peripheral divergent lineages in the west and east. The study focuses particularly on the West Indian Ocean, which is emerging as a region of unexpected diversity. Mitochondrial control region (mtCR) and COI sequences as well as genotypes of 9 microsatellite loci were examined in 410 individuals from 17 locations grouped into 7 regions from South Africa in the west, and eastward across to Taiwan and the Marquesas Islands. Phylogenetic and population-level analyses were used to test the significance and timing of divergences and describe the genetic relationships among populations. Analyses of the mtCR revealed high levels of divergence among the seven regions (Ф ST  = 0.594, P Indo-Pacific that helps drive some of the regions' recognized biogeographic boundaries.

Differential divergences of obligately insect-pathogenic Entomophthora species from fly and aphid hosts.

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Jensen, Annette Bruun; Eilenberg, Jørgen; López Lastra, Claudia

2009-11-01

Three DNA regions (ITS 1, LSU rRNA and GPD) of isolates from the insect-pathogenic fungus genus Entomophthora originating from different fly (Diptera) and aphid (Hemiptera) host taxa were sequenced. The results documented a large genetic diversity among the fly-pathogenic Entomophthora and only minor differences among aphid-pathogenic Entomophthora. The evolutionary time of divergence of the fly and the aphid host taxa included cannot account for this difference. The host-driven divergence of Entomophthora, therefore, has been much greater in flies than in aphids. Host-range differences or a recent host shift to aphid are possible explanations.

Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations.

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Tobler, M; Plath, M; Riesch, R; Schlupp, I; Grasse, A; Munimanda, G K; Setzer, C; Penn, D J; Moodley, Y

2014-05-01

The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution). © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Conservation and Divergence in the Candida Species Biofilm Matrix Mannan-Glucan Complex Structure, Function, and Genetic Control.

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Dominguez, Eddie; Zarnowski, Robert; Sanchez, Hiram; Covelli, Antonio S; Westler, William M; Azadi, Parastoo; Nett, Jeniel; Mitchell, Aaron P; Andes, David R

2018-04-03

Candida biofilms resist the effects of available antifungal therapies. Prior studies with Candida albicans biofilms show that an extracellular matrix mannan-glucan complex (MGCx) contributes to antifungal sequestration, leading to drug resistance. Here we implement biochemical, pharmacological, and genetic approaches to explore a similar mechanism of resistance for the three most common clinically encountered non- albicans Candida species (NAC). Our findings reveal that each Candida species biofilm synthesizes a mannan-glucan complex and that the antifungal-protective function of this complex is conserved. Structural similarities extended primarily to the polysaccharide backbone (α-1,6-mannan and β-1,6-glucan). Surprisingly, biochemical analysis uncovered stark differences in the branching side chains of the MGCx among the species. Consistent with the structural analysis, similarities in the genetic control of MGCx production for each Candida species also appeared limited to the synthesis of the polysaccharide backbone. Each species appears to employ a unique subset of modification enzymes for MGCx synthesis, likely accounting for the observed side chain diversity. Our results argue for the conservation of matrix function among Candida spp. While biogenesis is preserved at the level of the mannan-glucan complex backbone, divergence emerges for construction of branching side chains. Thus, the MGCx backbone represents an ideal drug target for effective pan- Candida species biofilm therapy. IMPORTANCE Candida species, the most common fungal pathogens, frequently grow as a biofilm. These adherent communities tolerate extremely high concentrations of antifungal agents, due in large part, to a protective extracellular matrix. The present studies define the structural, functional, and genetic similarities and differences in the biofilm matrix from the four most common Candida species. Each species synthesizes an extracellular mannan-glucan complex (MGCx) which

Eco-evo-devo in the Study of Adaptive Divergence: Examples from Threespine Stickleback (Gasterosteus aculeatus).

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Jamniczky, Heather A; Barry, Tegan N; Rogers, Sean M

2015-07-01

The tight fit between form and function in organisms suggests the influence of adaptive evolution in biomechanics; however, the prevalence of adaptive traits, the mechanisms by which they arise and the corresponding responses to selection are subjects of extensive debate. We used three-dimensional microcomputed tomography and geometric morphometrics to characterize the structure of phenotypic covariance within the G. aculeatus trophic apparatus and its supporting structures in wild and controlled crosses of fish from two different localities. Our results reveal that while the structure of phenotypic covariance is conserved in marine and freshwater forms, it may be disrupted in the progeny of artificial crosses or during rapid adaptive divergence events. We discuss these results within the context of integrating covariance structure with quantitative genetics, toward establishing predictive links between genes, development, biomechanics, and the environment. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

The Integrated Genomic Architecture and Evolution of Dental Divergence in East African Cichlid Fishes (Haplochromis chilotes x H. nyererei

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C. Darrin Hulsey

2017-09-01

Full Text Available The independent evolution of the two toothed jaws of cichlid fishes is thought to have promoted their unparalleled ecological divergence and species richness. However, dental divergence in cichlids could exhibit substantial genetic covariance and this could dictate how traits like tooth numbers evolve in different African Lakes and on their two jaws. To test this hypothesis, we used a hybrid mapping cross of two trophically divergent Lake Victoria species (Haplochromis chilotes × Haplochromis nyererei to examine genomic regions associated with cichlid tooth diversity. Surprisingly, a similar genomic region was found to be associated with oral jaw tooth numbers in cichlids from both Lake Malawi and Lake Victoria. Likewise, this same genomic location was associated with variation in pharyngeal jaw tooth numbers. Similar relationships between tooth numbers on the two jaws in both our Victoria hybrid population and across the phylogenetic diversity of Malawi cichlids additionally suggests that tooth numbers on the two jaws of haplochromine cichlids might generally coevolve owing to shared genetic underpinnings. Integrated, rather than independent, genomic architectures could be key to the incomparable evolutionary divergence and convergence in cichlid tooth numbers.

Genetic characterization of a core collection of flax (Linum usitatissimum L.) suitable for association mapping studies and evidence of divergent selection between fiber and linseed types.

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Soto-Cerda, Braulio J; Diederichsen, Axel; Ragupathy, Raja; Cloutier, Sylvie

2013-05-06

Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax. Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (F(ST) = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r²) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species. Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a

Host-driven divergence in the parasitic plant Orobanche minor Sm. (Orobanchaceae).

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Thorogood, C J; Rumsey, F J; Harris, S A; Hiscock, S J

2008-10-01

Many parasitic angiosperms have a broad host range and are therefore considered to be host generalists. Orobanche minor is a nonphotosynthetic root parasite that attacks a range of hosts from taxonomically disparate families. In the present study, we show that O. minor sensu lato may comprise distinct, genetically divergent races isolated by the different ecologies of their hosts. Using a three-pronged approach, we tested the hypothesis that intraspecific taxa O. minor var. minor and O. minor ssp. maritima parasitizing either clover (Trifolium pratense) or sea carrot (Daucus carota ssp.gummifer), respectively, are in allopatric isolation. Morphometric analysis revealed evidence of divergence but this was insufficient to define discrete, host-specific taxa. Intersimple sequence repeat (ISSR) marker-based data provided stronger evidence of divergence, suggesting that populations were isolated from gene flow. Phylogenetic analysis, using sequence-characterized amplified region (SCAR) markers derived from ISSR loci, provided strong evidence for divergence by clearly differentiating sea carrot-specific clades and mixed-host clades. Low levels of intrapopulation SCAR marker sequence variation and floral morphology suggest that populations on different hosts are probably selfing and inbreeding. Morphologically cryptic Orobanche taxa may therefore be isolated from gene flow by host ecology. Together, these data suggest that host specificity may be an important driver of allopatric speciation in parasitic plants.

Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae.

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Lim, K Yoong; Kovarik, Ales; Matyasek, Roman; Chase, Mark W; Knapp, Sandra; McCarthy, Elizabeth; Clarkson, James J; Leitch, Andrew R

2006-12-01

Combining phylogenetic reconstructions of species relationships with comparative genomic approaches is a powerful way to decipher evolutionary events associated with genome divergence. Here, we reconstruct the history of karyotype and tandem repeat evolution in species of diploid Nicotiana section Alatae. By analysis of plastid DNA, we resolved two clades with high bootstrap support, one containing N. alata, N. langsdorffii, N. forgetiana and N. bonariensis (called the n = 9 group) and another containing N. plumbaginifolia and N. longiflora (called the n = 10 group). Despite little plastid DNA sequence divergence, we observed, via fluorescent in situ hybridization, substantial chromosomal repatterning, including altered chromosome numbers, structure and distribution of repeats. Effort was focussed on 35S and 5S nuclear ribosomal DNA (rDNA) and the HRS60 satellite family of tandem repeats comprising the elements HRS60, NP3R and NP4R. We compared divergence of these repeats in diploids and polyploids of Nicotiana. There are dramatic shifts in the distribution of the satellite repeats and complete replacement of intergenic spacers (IGSs) of 35S rDNA associated with divergence of the species in section Alatae. We suggest that sequence homogenization has replaced HRS60 family repeats at sub-telomeric regions, but that this process may not occur, or occurs more slowly, when the repeats are found at intercalary locations. Sequence homogenization acts more rapidly (at least two orders of magnitude) on 35S rDNA than 5S rDNA and sub-telomeric satellite sequences. This rapid rate of divergence is analogous to that found in polyploid species, and is therefore, in plants, not only associated with polyploidy.

Divergent clonal selection dominates medulloblastoma at recurrence

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Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

2016-01-01

The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

Point-of-care genetic testing for personalisation of antiplatelet treatment (RAPID GENE): a prospective, randomised, proof-of-concept trial.

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Roberts, Jason D; Wells, George A; Le May, Michel R; Labinaz, Marino; Glover, Chris; Froeschl, Michael; Dick, Alexander; Marquis, Jean-Francois; O'Brien, Edward; Goncalves, Sandro; Druce, Irena; Stewart, Alexandre; Gollob, Michael H; So, Derek Y F

2012-05-05

Prospective assessment of pharmacogenetic strategies has been limited by an inability to undertake bedside genetic testing. The CYP2C19*2 allele is a common genetic variant associated with increased rates of major adverse events in individuals given clopidogrel after percutaneous coronary intervention (PCI). We used a novel point-of-care genetic test to identify carriers of the CYP2C19*2 allele and aimed to assess a pharmacogenetic approach to dual antiplatelet treatment after PCI. Between Aug 26, 2010, and July 7, 2011, 200 patients were enrolled into our prospective, randomised, proof-of-concept study. Patients undergoing PCI for acute coronary syndrome or stable angina were randomly assigned to rapid point-of-care genotyping or to standard treatment. Individuals in the rapid genotyping group were screened for the CYP2C19*2 allele. Carriers were given 10 mg prasugrel daily, and non-carriers and patients in the standard treatment group were given 75 mg clopidogrel daily. The primary endpoint was the proportion of CYP2C19*2 carriers with high on-treatment platelet reactivity (P2Y12 reactivity unit [PRU] value of more than 234) after 1 week of dual antiplatelet treatment, which is a marker associated with increased adverse cardiovascular events. Interventional cardiologists and data analysts were masked to genetic status and treatment. Patients were not masked to treatment allocation. All analyses were by intention to treat. This study is registered with ClinicalTrials.gov, NCT01184300. After randomisation, 187 patients completed follow-up (91 rapid genotyping group, 96 standard treatment). 23 individuals in each group carried at least one CYP2C19*2 allele. None of the 23 carriers in the rapid genotyping group had a PRU value of more than 234 at day 7, compared with seven (30%) given standard treatment (p=0·0092). The point-of-care genetic test had a sensitivity of 100% (95% CI 92·3-100) and a specificity of 99·3% (96·3-100). Point-of-care genetic testing after

Widespread utility of highly informative AFLP molecular markers across divergent shark species.

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Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

2006-01-01

Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks.

Natural and sexual selection giveth and taketh away reproductive barriers: models of population divergence in guppies.

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Labonne, Jacques; Hendry, Andrew P

2010-07-01

The standard predictions of ecological speciation might be nuanced by the interaction between natural and sexual selection. We investigated this hypothesis with an individual-based model tailored to the biology of guppies (Poecilia reticulata). We specifically modeled the situation where a high-predation population below a waterfall colonizes a low-predation population above a waterfall. Focusing on the evolution of male color, we confirm that divergent selection causes the appreciable evolution of male color within 20 generations. The rate and magnitude of this divergence were reduced when dispersal rates were high and when female choice did not differ between environments. Adaptive divergence was always coupled to the evolution of two reproductive barriers: viability selection against immigrants and hybrids. Different types of sexual selection, however, led to contrasting results for another potential reproductive barrier: mating success of immigrants. In some cases, the effects of natural and sexual selection offset each other, leading to no overall reproductive isolation despite strong adaptive divergence. Sexual selection acting through female choice can thus strongly modify the effects of divergent natural selection and thereby alter the standard predictions of ecological speciation. We also found that under no circumstances did divergent selection cause appreciable divergence in neutral genetic markers.

The power to detect recent fragmentation events using genetic differentiation methods.

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Michael W Lloyd

Full Text Available Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution.

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Garrigan, Daniel; Kingan, Sarah B; Geneva, Anthony J; Vedanayagam, Jeffrey P; Presgraves, Daven C

2014-09-04

Drosophila mauritiana is an Indian Ocean island endemic species that diverged from its two sister species, Drosophila simulans and Drosophila sechellia, approximately 240,000 years ago. Multiple forms of incomplete reproductive isolation have evolved among these species, including sexual, gametic, ecological, and intrinsic postzygotic barriers, with crosses among all three species conforming to Haldane's rule: F(1) hybrid males are sterile and F(1) hybrid females are fertile. Extensive genetic resources and the fertility of hybrid females have made D. mauritiana, in particular, an important model for speciation genetics. Analyses between D. mauritiana and both of its siblings have shown that the X chromosome makes a disproportionate contribution to hybrid male sterility. But why the X plays a special role in the evolution of hybrid sterility in these, and other, species remains an unsolved problem. To complement functional genetic analyses, we have investigated the population genomics of D. mauritiana, giving special attention to differences between the X and the autosomes. We present a de novo genome assembly of D. mauritiana annotated with RNAseq data and a whole-genome analysis of polymorphism and divergence from ten individuals. Our analyses show that, relative to the autosomes, the X chromosome has reduced nucleotide diversity but elevated nucleotide divergence; an excess of recurrent adaptive evolution at its protein-coding genes; an excess of recent, strong selective sweeps; and a large excess of satellite DNA. Interestingly, one of two centimorgan-scale selective sweeps on the D. mauritiana X chromosome spans a region containing two sex-ratio meiotic drive elements and a high concentration of satellite DNA. Furthermore, genes with roles in reproduction and chromosome biology are enriched among genes that have histories of recurrent adaptive protein evolution. Together, these genome-wide analyses suggest that genetic conflict and frequent positive natural

Gene duplication and divergence affecting drug content in Cannabis sativa.

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Weiblen, George D; Wenger, Jonathan P; Craft, Kathleen J; ElSohly, Mahmoud A; Mehmedic, Zlatko; Treiber, Erin L; Marks, M David

2015-12-01

Cannabis sativa is an economically important source of durable fibers, nutritious seeds, and psychoactive drugs but few economic plants are so poorly understood genetically. Marijuana and hemp were crossed to evaluate competing models of cannabinoid inheritance and to explain the predominance of tetrahydrocannabinolic acid (THCA) in marijuana compared with cannabidiolic acid (CBDA) in hemp. Individuals in the resulting F2 population were assessed for differential expression of cannabinoid synthase genes and were used in linkage mapping. Genetic markers associated with divergent cannabinoid phenotypes were identified. Although phenotypic segregation and a major quantitative trait locus (QTL) for the THCA/CBDA ratio were consistent with a simple model of codominant alleles at a single locus, the diversity of THCA and CBDA synthase sequences observed in the mapping population, the position of enzyme coding loci on the map, and patterns of expression suggest multiple linked loci. Phylogenetic analysis further suggests a history of duplication and divergence affecting drug content. Marijuana is distinguished from hemp by a nonfunctional CBDA synthase that appears to have been positively selected to enhance psychoactivity. An unlinked QTL for cannabinoid quantity may also have played a role in the recent escalation of drug potency. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis.

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Jiufeng Sun

Full Text Available Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb] was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection

Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis

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Sun, Jiufeng; Huang, Yan; Huang, Huaiqiu; Liang, Pei; Wang, Xiaoyun; Mao, Qiang; Men, Jingtao; Chen, Wenjun; Deng, Chuanhuan; Zhou, Chenhui; Lv, Xiaoli; Zhou, Juanjuan; Zhang, Fan; Li, Ran; Tian, Yanli; Lei, Huali; Liang, Chi; Hu, Xuchu; Xu, Jin; Li, Xuerong; XinbingYu

2013-01-01

Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb]) was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs) showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C) showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection worldwide. Thus, the

Quantum skew divergence

Energy Technology Data Exchange (ETDEWEB)

Audenaert, Koenraad M. R., E-mail: koenraad.audenaert@rhul.ac.uk [Department of Mathematics, Royal Holloway University of London, Egham TW20 0EX, United Kingdom and Department of Physics and Astronomy, University of Ghent, S9, Krijgslaan 281, B-9000 Ghent (Belgium)

2014-11-15

In this paper, we study the quantum generalisation of the skew divergence, which is a dissimilarity measure between distributions introduced by Lee in the context of natural language processing. We provide an in-depth study of the quantum skew divergence, including its relation to other state distinguishability measures. Finally, we present a number of important applications: new continuity inequalities for the quantum Jensen-Shannon divergence and the Holevo information, and a new and short proof of Bravyi's Small Incremental Mixing conjecture.

Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

Science.gov (United States)

Baillie, Shauna M.; Muir, Andrew M.; Hansen, Michael J.; Krueger, Charles C.; Bentzen, Paul

2016-01-01

BackgroundAdaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycushthat considers variation as a cline rather than discriminatory among ecotypes. Genetic and phenotypic traits organized along common ecological gradients of water depth and geographic distance provide important insights into diversification processes in a lake with high levels of human disturbance from over-fishing.ResultsFour putative lake trout ecotypes could not be distinguished using population genetic methods, despite morphological differences. Neutral genetic partitioning in lake trout was stronger along a gradient of water depth, than by locality or ecotype. Contemporary genetic migration patterns were consistent with isolation-by-depth. Historical gene flow patterns indicated colonization from shallow to deep water. Comparison of phenotypic (Pst) and neutral genetic variation (Fst) revealed that morphological traits related to swimming performance (e.g., buoyancy, pelvic fin length) departed more strongly from neutral expectations along a depth gradient than craniofacial feeding traits. Elevated phenotypic variance with increasing water depth in pelvic fin length indicated possible ongoing character release and diversification. Finally, differences in early growth rate and asymptotic fish length across depth strata may be associated with limiting factors attributable to cold deep-water environments.ConclusionWe provide evidence of reductions in gene flow and divergent natural selection associated with water depth in Lake Superior. Such information is relevant for documenting intraspecific biodiversity in the largest freshwater lake

Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

Science.gov (United States)

Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

2012-03-01

Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

On Hölder Projective Divergences

KAUST Repository

Nielsen, Frank

2017-03-16

We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

On Hölder Projective Divergences

KAUST Repository

Nielsen, Frank; Sun, Ke; Marchand-Maillet, Stephane

2017-01-01

We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

Genetic Divergence and Heritability of 42 Coloured Upland Rice Genotypes (Oryzasativa) as Revealed by Microsatellites Marker and Agro-Morphological Traits

Science.gov (United States)

Ahmad, Faiz; Hanafi, Mohamed Musa; Hakim, Md Abdul; Rafii, Mohd Y.; Arolu, Ibrahim Wasiu; Akmar Abdullah, Siti Nor

2015-01-01

Coloured rice genotypes have greater nutritious value and consumer demand for these varieties is now greater than ever. The documentation of these genotypes is important for the improvement of the rice plant. In this study, 42 coloured rice genotypes were selected for determination of their genetic divergence using 25 simple sequence repeat (SSR) primers and 15 agro-morphological traits. Twenty-one out of the 25 SSR primers showed distinct, reproducible polymorphism. A dendrogram constructed using the SSR primers clustered the 42 coloured rice genotypes into 7 groups. Further, principle component analysis showed 75.28% of total variations were explained by the first—three components. All agro-morphological traits showed significant difference at the (p≤0.05) and (p≤0.01) levels. From the dendrogram constructed using the agro-morphological traits, all the genotypes were clustered into four distinct groups. Pearson’s correlation coefficient showed that among the 15 agro-morphological traits, the yield contributing factor had positive correlation with the number of tillers, number of panicles, and panicle length. The heritability of the 15 traits ranged from 17.68 to 99.69%. Yield per plant and harvest index showed the highest value for both heritability and genetic advance. The information on the molecular and agro-morphological traits can be used in rice breeding programmes to improve nutritional value and produce higher yields. PMID:26393807

Genetic divergence and phylogenetic relationships in grey mullets (Teleostei: Mugilidae) based on PCR-RFLP analysis of mtDNA segments.

Science.gov (United States)

Papasotiropoulos, V; Klossa-Kilia, E; Kilias, G; Alahiotis, S

2002-04-01

The genetic differentiation and phylogenetic relationships among five species of the Mugilidae family (Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens) were investigated at the mtDNA level, on samples taken from Messolongi lagoon-Greece. RFLP analysis of three PCR-amplified mtDNA gene segments (12s rRNA, 16s rRNA, and CO I) was used. Ten, eight, and nine restriction enzymes were found to have at least one recognition site at 12s rRNA, 16s rRNA, and CO I genes, respectively. Several fragment patterns were revealed to be species-specific, and thus they could be useful in species taxonomy as diagnostic markers, as well as for further evolutionary studies. Seven different haplotypes were detected. The greatest amount of genetic differentiation was observed at the interspecific level, while little variation was revealed at the intraspecific level. The highest values of nucleotide sequence divergence were observed between M. cephalus and all the other species, while the lowest was found between C. labrosus and L. saliens. Dendrograms obtained by the three different methods (UPGMA, Neighbor-Joining, and Dollo parsimony), were found to exhibit in all cases the same topology. According to this, the most distinct species is M. cephalus, while the other species are clustered in two separate groups, thefirst one containing L. aurata and L. ramada, the other L. saliens and C. labrosus. This last clustering makes the monophyletic origin of the genus Liza questionable.

Genetic divergence and diversity in the Mona and Virgin Islands Boas, Chilabothrus monensis (Epicrates monensis) (Serpentes: Boidae), West Indian snakes of special conservation concern.

Science.gov (United States)

Rodríguez-Robles, Javier A; Jezkova, Tereza; Fujita, Matthew K; Tolson, Peter J; García, Miguel A

2015-07-01

Habitat fragmentation reduces the extent and connectivity of suitable habitats, and can lead to changes in population genetic structure. Limited gene flow among isolated demes can result in increased genetic divergence among populations, and decreased genetic diversity within demes. We assessed patterns of genetic variation in the Caribbean boa Chilabothrus monensis (Epicrates monensis) using two mitochondrial and seven nuclear markers, and relying on the largest number of specimens of these snakes examined to date. Two disjunct subspecies of C. monensis are recognized: the threatened C. m. monensis, endemic to Mona Island, and the rare and endangered C. m. granti, which occurs on various islands of the Puerto Rican Bank. Mitochondrial and nuclear markers revealed unambiguous genetic differences between the taxa, and coalescent species delimitation methods indicated that these snakes likely are different evolutionary lineages, which we recognize at the species level, C. monensis and C. granti. All examined loci in C. monensis (sensu stricto) are monomorphic, which may indicate a recent bottleneck event. Each population of C. granti exclusively contains private mtDNA haplotypes, but five of the seven nuclear genes assayed are monomorphic, and nucleotide diversity is low in the two remaining markers. The faster pace of evolution of mtDNA possibly reflects the present-day isolation of populations of C. granti, whereas the slower substitution rate of nuDNA may instead mirror the relatively recent episodes of connectivity among the populations facilitated by the lower sea level during the Pleistocene. The small degree of overall genetic variation in C. granti suggests that demes of this snake could be managed as a single unit, a practice that would significantly increase their effective population size. Copyright © 2015 Elsevier Inc. All rights reserved.

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.

Science.gov (United States)

Schlebusch, Carina M; Malmström, Helena; Günther, Torsten; Sjödin, Per; Coutinho, Alexandra; Edlund, Hanna; Munters, Arielle R; Vicente, Mário; Steyn, Maryna; Soodyall, Himla; Lombard, Marlize; Jakobsson, Mattias

2017-11-03

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Genetic studies of Australian Trichomya hirsuta (Bivalvia: Mytilidae suggest antitropical divergence of this species

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Donald J. Colgan

2018-03-01

Full Text Available The hairy mussel Trichomya hirsuta (Lamarck, 1819 has disjunct known ranges in northeast Asia and Australia. There are substantial DNA sequence divergences for mitochondrial cytochrome c oxidase subunit I and 16S ribosomal RNA between specimens from these ranges showing that neither is likely to derive from a recent colonization. The most recent common ancestor of the observed haplotypes may have lived as long ago as the early Pliocene. It is, however, suggested here that the mussels from the two regions continue to be regarded, tentatively, as conspecific because intraspecific divergence of mitochondrial DNA sequences can be very high in Mytilidae. The present knowledge of fossil history suggests that the direction of colonization in Trichomya may have been from the Southern to the Northern Hemisphere in contrast with migrations of other genera of Mytilidae.

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

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Wang Xiao-Wei

2012-10-01

Full Text Available Abstract Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the transcriptomes of two invasive whiteflies species, Middle East Asia Minor 1 (MEAM1 and Mediterranean (MED, respectively. Results More than 16 million reads of 74 base pairs in length were obtained for the Asia II 3 species using the Illumina sequencing platform. These reads were assembled into 52,535 distinct sequences (mean size: 466 bp and 16,596 sequences were annotated with an E-value above 10-5. Protein family comparisons revealed obvious diversification among the transcriptomes of these species suggesting species-specific adaptations during whitefly evolution. On the contrary, substantial conservation of the whitefly transcriptomes was also evident, despite their differences. The overall divergence of coding sequences between the orthologous gene pairs of Asia II 3 and MEAM1 is 1.73%, which is comparable to the average divergence of Asia II 3 and MED transcriptomes (1.84% and much higher than that of MEAM1 and MED (0.83%. This is consistent with the previous phylogenetic analyses and crossing experiments suggesting these are distinct species. We also identified hundreds of highly diverged genes and compiled sequence identify data into gene functional groups and found the most divergent gene classes are Cytochrome P450, Glutathione metabolism and Oxidative phosphorylation. These results strongly suggest that the divergence of genes related to metabolism might be the driving force of the MEAM1 and Asia II 3 differentiation. We also analyzed single nucleotide polymorphisms within the orthologous gene pairs of indigenous and invasive whiteflies which are helpful for

Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini).

Science.gov (United States)

Brand, Philipp; Ramírez, Santiago R; Leese, Florian; Quezada-Euan, J Javier G; Tollrian, Ralph; Eltz, Thomas

2015-08-28

Insects rely more on chemical signals (semiochemicals) than on any other sensory modality to find, identify, and choose mates. In most insects, pheromone production is typically regulated through biosynthetic pathways, whereas pheromone sensory detection is controlled by the olfactory system. Orchid bees are exceptional in that their semiochemicals are not produced metabolically, but instead male bees collect odoriferous compounds (perfumes) from the environment and store them in specialized hind-leg pockets to subsequently expose during courtship display. Thus, the olfactory sensory system of orchid bees simultaneously controls male perfume traits (sender components) and female preferences (receiver components). This functional linkage increases the opportunities for parallel evolution of male traits and female preferences, particularly in response to genetic changes of chemosensory detection (e.g. Odorant Receptor genes). To identify whether shifts in pheromone composition among related lineages of orchid bees are associated with divergence in chemosensory genes of the olfactory periphery, we searched for patterns of divergent selection across the antennal transcriptomes of two recently diverged sibling species Euglossa dilemma and E. viridissima. We identified 3185 orthologous genes including 94 chemosensory loci from five different gene families (Odorant Receptors, Ionotropic Receptors, Gustatory Receptors, Odorant Binding Proteins, and Chemosensory Proteins). Our results revealed that orthologs with signatures of divergent selection between E. dilemma and E. viridissima were significantly enriched for chemosensory genes. Notably, elevated signals of divergent selection were almost exclusively observed among chemosensory receptors (i.e. Odorant Receptors). Our results suggest that rapid changes in the chemosensory gene family occurred among closely related species of orchid bees. These findings are consistent with the hypothesis that strong divergent selection

Divergence in function and expression of the NOD26-like intrinsic proteins in plants

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Feng Ying

2009-07-01

Full Text Available Abstract Background NOD26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further investigate the evolutionary mechanisms being responsible for the functional diversification of the NIP genes. To better understand this process, a comprehensive analysis including the phylogenetic, positive selection, functional divergence, and transcriptional analysis was carried out. Results The origination of NIPs could be dated back to the primitive land plants, and their diversification would be no younger than the emergence time of the moss P. patens. The rapid proliferation of NIPs in plants may be primarily attributed to the segmental chromosome duplication produced by polyploidy and tandem duplications. The maximum likelihood analysis revealed that NIPs should have experienced strong selective pressure for adaptive evolution after gene duplication and/or speciation, prompting the formation of distinct NIP groups. Functional divergence analysis at the amino acid level has provided strong statistical evidence for shifted evolutionary rate and/or radical change of the physiochemical properties of amino acids after gene duplication, and DIVERGE2 has identified the critical amino acid sites that are thought to be responsible for the divergence for further investigation. The expression of plant NIPs displays a distinct tissue-, cell-type-, and developmental specific pattern, and their responses to various stress treatments are quite different also. The differences in organization of cis-acting regulatory elements in the promoter regions may partially explain their distinction in expression. Conclusion A number of analyses both at the DNA and amino acid sequence levels have provided strong evidences that plant NIPs have

Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

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Lígia Regina Lima Gouvêa

2010-01-01

Full Text Available Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC, Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (H T' = 0.58 and high gene differentiation (Gst' = 0.61 were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability.

String perturbation theory diverges

International Nuclear Information System (INIS)

Gross, D.J.; Periwal, V.

1988-01-01

We prove that perturbation theory for the bosonic string diverges for arbitrary values of the coupling constant and is not Borel summable. This divergence is independent of the existence of the infinities that occur in the theory due to the presence of tachyons and dilaton tadpoles. We discuss the physical implications of such a divergence

Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

Science.gov (United States)

Ravinet, Mark; Harrod, Chris; Eizaguirre, Christophe; Prodöhl, Paulo A

2014-06-01

Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.

Randomized trial of proactive rapid genetic counseling versus usual care for newly diagnosed breast cancer patients.

Science.gov (United States)

Schwartz, Marc D; Peshkin, Beth N; Isaacs, Claudine; Willey, Shawna; Valdimarsdottir, Heiddis B; Nusbaum, Rachel; Hooker, Gillian; O'Neill, Suzanne; Jandorf, Lina; Kelly, Scott P; Heinzmann, Jessica; Zidell, Aliza; Khoury, Katia

2018-04-02

Breast cancer patients who carry BRCA1/BRCA2 gene mutations may consider bilateral mastectomy. Having bilateral mastectomy at the time of diagnosis not only reduces risk of a contralateral breast cancer, but can eliminate the need for radiation therapy and yield improved reconstruction options. However, most patients do not receive genetic counseling or testing at the time of their diagnosis. In this trial, we tested proactive rapid genetic counseling and testing (RGCT) in newly diagnosed breast cancer patients in order to facilitate pre-surgical genetic counseling and testing. We recruited newly diagnosed breast cancer patients at increased risk for carrying a BRCA1/2 mutation. Of 379 eligible patients who completed a baseline survey, 330 agreed to randomization in a 2:1 ratio to RGCT (n = 220) versus UC (n = 108). Primary outcomes were genetic counseling and testing uptake and breast cancer surgical decisions. RGCT led to higher overall (83.8% vs. 54.6%; p genetic counseling uptake compared to UC. Despite higher rates of genetic counseling, RGCT did not differ from UC in overall (54.1% vs. 49.1%, p > 0.10) or pre-surgical (30.6% vs. 27.4%, p > 0.10) receipt of genetic test results nor did they differ in uptake of bilateral mastectomy (26.6% vs. 21.8%, p > 0.10). Although RGCT yielded increased genetic counseling participation, this did not result in increased rates of pre-surgical genetic testing or impact surgical decisions. These data suggest that those patients most likely to opt for genetic testing at the time of diagnosis are being effectively identified by their surgeons.

Interspecific genetic divergence in sciaenids from Japan and its adjacent waters

Digital Repository Service at National Institute of Oceanography (India)

Menezes, M.R.; Taniguchi, N.

enzymes. The allele frequencies of 21 loci were estimated to calculate the genetic distances (D). The average D value among the sciaenid species increased in proportion to the level of taxonomic category. Relationships estimated by genetic markers well...

Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

OpenAIRE

Ciofi, C.; Beaumont, M. A.; Swingland, I. R.; Bruford, M. W.

1999-01-01

In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world's largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Kom...

Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship.

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Jessica Cande

Full Text Available In Drosophila, male flies perform innate, stereotyped courtship behavior. This innate behavior evolves rapidly between fly species, and is likely to have contributed to reproductive isolation and species divergence. We currently understand little about the neurobiological and genetic mechanisms that contributed to the evolution of courtship behavior. Here we describe a novel behavioral difference between the two closely related species D. yakuba and D. santomea: the frequency of wing rowing during courtship. During courtship, D. santomea males repeatedly rotate their wing blades to face forward and then back (rowing, while D. yakuba males rarely row their wings. We found little intraspecific variation in the frequency of wing rowing for both species. We exploited multiplexed shotgun genotyping (MSG to genotype two backcross populations with a single lane of Illumina sequencing. We performed quantitative trait locus (QTL mapping using the ancestry information estimated by MSG and found that the species difference in wing rowing mapped to four or five genetically separable regions. We found no evidence that these loci display epistasis. The identified loci all act in the same direction and can account for most of the species difference.

Divergence at neutral and non-neutral loci in Drosophila buzzatii populations and their hybrids

DEFF Research Database (Denmark)

Andersen, Ditte Holm; Pertoldi, Cino; Loeschcke, Volker

2008-01-01

The impact of intraspecific hybridisation on fitness and morphological traits depends on the history of natural selection and genetic drift, which may have led to differently coadapted gene-complexes in the parental populations. The divergence at neutral and non-neutral loci between populations can...... populations of Drosophila buzzatii, one between populations from Argentina and the Canary Islands (separated for 200 years), and the other between populations from Argentina and Australia (separated for 80 years). We observed the highest divergence at neutral loci between the Argentinean and Canary Island...

The large-scale blast score ratio (LS-BSR pipeline: a method to rapidly compare genetic content between bacterial genomes

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Jason W. Sahl

2014-04-01

Full Text Available Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR.Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors.Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated

Urbanization Is Associated with Divergence in Pace-of-Life in Great Tits

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Anne Charmantier

2017-05-01

Full Text Available As an extension of the classic life history theory, the recently highlighted pace-of-life syndrome hypothesis predicts the coevolution of behavioral, physiological and life-history traits. For instance, bolder and shyer individuals do not only differ in personality profiles, but also in neuro-endocrinology and breeding patterns. While theory predicts that bolder (i.e., proactive, more aggressive individuals should colonize more rapidly urbanized habitats than shyer (i.e., reactive, less aggressive individuals, it is also predicted that across generations, adaptive selection processes could favor shyer individuals that are more sensitive to novel environmental cues. Here we compared two personality traits (handling aggression, exploration score in a novel environment, one physiological trait related to stress response (breath rate and four breeding traits (lay date, clutch size, hatching success and fledging success in a rural and an urban study population of Mediterranean great tits Parus major. Mixed models revealed strong phenotypic divergence between forest and city in most traits explored, in particular in personality, whereby urban great tits were more reactive to stress and faster explorers compared to rural birds (yet not more aggressive. Urban birds also laid smaller broods earlier in spring compared to their rural conspecifics, and city broods resulted in lower hatching success yet interestingly fledging success was similar. Nest-box centered measures of anthropogenic (artificial light, pedestrians, and cars perturbation and resource abundance allowed us to go beyond the classical forest/city comparison by exploring the phenotypic variation across an urbanization gradient. This revealed that high urbanization in nest-box surroundings was associated overall with earlier breeding and smaller clutches, but also with faster breath rate, although these trends showed strong annual variation. Ongoing rapid urbanization and non-random gene flow

A Rapid Aeroelasticity Optimization Method Based on the Stiffness characteristics

OpenAIRE

Yuan, Zhe; Huo, Shihui; Ren, Jianting

2018-01-01

A rapid aeroelasticity optimization method based on the stiffness characteristics was proposed in the present study. Large time expense in static aeroelasticity analysis based on traditional time domain aeroelasticity method is solved. Elastic axis location and torsional stiffness are discussed firstly. Both torsional stiffness and the distance between stiffness center and aerodynamic center have a direct impact on divergent velocity. The divergent velocity can be adjusted by changing the cor...

[The significance of pedigree genetic screening and rapid immunological parameters in the diagnosis of primary hemophagocytic lymphohistiocytosis].

Science.gov (United States)

Zhang, J; Wang, Y N; Wang, J S; Wu, L; Wei, N; Fu, L; Gao, Z; Chen, J H; Pei, R J; Wang, Z

2016-07-01

To investigate the significance of pedigree genetic screening and rapid immunological parameters in the diagnosis of primary hemophagocytic lymphohistiocytosis (HLH). Four cases of primary HLH patients with PRF1, UNC13D and SH2D1A gene mutations were conducted pedigree investigation, including family genetic screening and detections of immunological parameters (NK cell activity, CD107a degranulation and expression of HLH related defective protein), to evaluate the significance of these different indicators in the diagnosis of primary HLH and explore their correlations. The DNA mutations of the four families included missense mutation c.T172C (p.S58P) and non- frameshift deletions c.1083_1094del (p.361_365del), missense mutation c.C1349T (p.T450M) and frameshift mutation c.1090_1091delCT (p.T364fsX93) in PRF1 gene, missense mutation c.G2588A (p.G863D) in UNC13D gene and hemizygous mutation c.32T>G (p.I11S) in SH2D1A gene. The patients and their family members presented decreased NK cell activities. Individuals who carried mutations of PRF1 gene and SH2D1A gene showed low expression of perforin (PRF1) and signaling lymphocytic activation molecule associated protein (SAP). And the patient with UNC13D gene mutation and his family member with identical mutation showed significant reducing cytotoxic degranulation function (expression of CD107a). Pedigree genetic screening and rapid detection of immunological parameters might play an important role in the diagnosis of primary HLH, and both of them had good consistency. As an efficient detection means, the rapid immunological detection indicators would provide reliable basis for the early diagnosis of the primary HLH.

NOTE - Characterization of genetic variability among common bean genotypes by morphological descriptors

Directory of Open Access Journals (Sweden)

Marilene Santos de Lima

2012-01-01

Full Text Available The purpose of this study was to characterize the genetic variability in 100 genotypes of the Active Germplasm Bank of common bean of the Federal University of Viçosa, by morphological descriptors, classify them in groups of genetic similarity and to identify the degree of relevance of descriptors of genetic divergence. The genotypes were evaluated based on 22 quantitative and qualitative morphological descriptors. The highyielding genotypes V 7936, Gold Gate, LM 95103904, 1829 S 349 Venezuela, and PF 9029975, CNFC 9454 andFe 732015, with upright growth, have potential for use as parents in common bean breeding programs. By genetic divergence analysis, the genotypes were clustered in eight groups of genetic dissimilarity. By methods of principal components, 9 of the 22 descriptors were eliminated, for being redundant or little variable, suggesting that 10-20 morphological descriptors can be used in studies of characterization of genetic variation.

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

Science.gov (United States)

Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

2012-09-01

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

Molecular analysis and genetic diversity of Aedes albopictus (Diptera, Culicidae) from China.

Science.gov (United States)

Ruiling, Zhang; Peien, Leng; Xuejun, Wang; Zhong, Zhang

2018-05-01

Aedes albopictus is one of the most invasive species, which can carry Dengue virus, Yellow fever virus and more than twenty arboviruses. Based on mitochondrial gene cytochrome c oxidase I (COI) and samples collected from 17 populations, we investigated the molecular character and genetic diversity of Ae. albopictus from China. Altogether, 25 haplotypes were detected, including 10 shared haplotypes and 15 private haplotypes. H1 was the dominant haplotype, which is widely distributed in 13 populations. Tajima'D value of most populations was significantly negative, demonstrating that populations experienced rapid range expansion recently. Most haplotypes clustered together both in phylogenetic and median-joining network analysis without clear phylogeographic patterns. However, neutrality tests revealed shallow divergences among Hainan and Guangxi with other populations (0.15599 ≤ F ST ≤ 0.75858), which probably due to interrupted gene flow, caused by geographical isolations. In conclusion, Ae. albopictus populations showed low genetic diversity in China.

Condition dependence and the nature of genetic variation for male sex comb bristle number in Drosophila melanogaster.

Science.gov (United States)

Ahuja, Abha; De Vito, Scott; Singh, Rama S

2011-04-01

Genetic architecture of variation underlying male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila, was examined. First, in order to test for condition dependence, diet was manipulated in a set of ten Drosophila melanogaster full-sib families. We confirmed heightened condition dependent expression of sex comb bristle number and its female homologue (distal transverse row bristles) as compared to non-sex sternopleural bristles. Significant genotype by environment effects were detected for the sex traits indicating a genetic basis for condition dependence. Next we measured sex comb bristle number and sternopleural bristle number, as well as residual mass, a commonly used condition index, in a set of thirty half-sib families. Sire effect was not significant for sex comb and sternopleural bristle number, and we detected a strong dominance and/or maternal effect or X chromosome effect for both traits. A strong sire effect was detected for condition and its heritability was the highest as compared to sex comb and sternopleural bristles. We discuss our results in light of the rapid response to divergent artificial selection for sex comb bristle number reported previously. The nature of genetic variation for male sex traits continues to be an important unresolved issue in evolutionary biology.

Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates of selection and QTL mapping.

Science.gov (United States)

Ågren, Jon; Oakley, Christopher G; Lundemo, Sverre; Schemske, Douglas W

2017-03-01

To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic trade-offs. To this end, we conducted field experiments for three years using recombinant inbred lines (RILs) derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped quantitative trait loci (QTL). There was strong selection for early flowering in Italy, but weak selection in Sweden. Eleven distinct flowering time QTL were detected, and for each the Italian genotype caused earlier flowering. Twenty-seven candidate genes were identified, two of which (FLC and VIN3) appear under major flowering time QTL in Italy. Seven of eight QTL in Italy with narrow credible intervals colocalized with previously reported fitness QTL, in comparison to three of four in Sweden. The results demonstrate that the magnitude of selection on flowering time differs strikingly between our study populations, that the genetic basis of flowering time variation is multigenic with some QTL of large effect, and suggest that divergence in flowering time between ecotypes is due mainly to conditional neutrality. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

k-Means Clustering with Hölder Divergences

KAUST Repository

Nielsen, Frank

2017-10-24

We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

k-Means Clustering with Hölder Divergences

KAUST Repository

Nielsen, Frank; Sun, Ke; Marchand-Maillet, Sté phane

2017-01-01

We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

Genetic diversity in India and the inference of Eurasian population expansion.

Science.gov (United States)

Xing, Jinchuan; Watkins, W Scott; Hu, Ya; Huff, Chad D; Sabo, Aniko; Muzny, Donna M; Bamshad, Michael J; Gibbs, Richard A; Jorde, Lynn B; Yu, Fuli

2010-01-01

Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored. To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans. Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia. © 2010 Xing et al.; licensee BioMed Central Ltd.

Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae).

Science.gov (United States)

Ober, Karen A; Heider, Thomas N

2010-08-27

Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae

Directory of Open Access Journals (Sweden)

Ober Karen A

2010-08-01

Full Text Available Abstract Background Harpalinae is a species rich clade of carabid beetles with many unusual morphological forms and ecological interactions. How this diversity evolved has been difficult to reconstruct, perhaps because harpalines underwent a rapid burst of diversification early in their evolutionary history. Here we investigate the tempo of evolution in harpalines using molecular divergence dating techniques and explore the rates of lineage accumulation in harpalines and their sister group. Results According to molecular divergence date estimates, harpalines originated in the mid Cretaceous but did not diversify extensively until the late Cretaceous or early Paleogene about 32 million years after their origin. In a relatively small window of time, harpalines underwent rapid speciation. Harpalines have a relative high net diversification rate and increased cladogenesis in some regions of the clade. We did not see a significant decrease in diversification rate through time in the MCCR test, but a model of diversification with two shift points to lower diversification rates fit the harpaline lineage accumulation through time the best. Conclusions Our results indicate harpalines are significantly more diverse and have higher diversification than their sistergroup. Instead of an immediate burst of explosive diversification, harpalines may have had a long "fuse" before major lineages diversified during the early Paleogene when other taxa such as mammals, birds, and some flowering plants were also rapidly diversifying.

Divergent unprotected peptide macrocyclisation by palladium-mediated cysteine arylation.

Science.gov (United States)

Rojas, Anthony J; Zhang, Chi; Vinogradova, Ekaterina V; Buchwald, Nathan H; Reilly, John; Pentelute, Bradley L; Buchwald, Stephen L

2017-06-01

Macrocyclic peptides are important therapeutic candidates due to their improved physicochemical properties in comparison to their linear counterparts. Here we detail a method for a divergent macrocyclisation of unprotected peptides by crosslinking two cysteine residues with bis-palladium organometallic reagents. These synthetic intermediates are prepared in a single step from commercially available aryl bis-halides. Two bioactive linear peptides with cysteine residues at i , i + 4 and i , i + 7 positions, respectively, were cyclised to introduce a diverse array of aryl and bi-aryl linkers. These two series of macrocyclic peptides displayed similar linker-dependent lipophilicity, phospholipid affinity, and unique volume of distributions. Additionally, one of the bioactive peptides showed target binding affinity that was predominantly affected by the length of the linker. Collectively, this divergent strategy allowed rapid and convenient access to various aryl linkers, enabling the systematic evaluation of the effect of appending unit on the medicinal properties of macrocyclic peptides.

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand.

Science.gov (United States)

Kutanan, Wibhu; Kampuansai, Jatupol; Fuselli, Silvia; Nakbunlung, Supaporn; Seielstad, Mark; Bertorelle, Giorgio; Kangwanpong, Daoroong

2011-06-15

The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. © 2011 Kutanan et al; licensee BioMed Central Ltd.

Hyperreal Numbers for Infinite Divergent Series

OpenAIRE

Bartlett, Jonathan

2018-01-01

Treating divergent series properly has been an ongoing issue in mathematics. However, many of the problems in divergent series stem from the fact that divergent series were discovered prior to having a number system which could handle them. The infinities that resulted from divergent series led to contradictions within the real number system, but these contradictions are largely alleviated with the hyperreal number system. Hyperreal numbers provide a framework for dealing with divergent serie...

The divergence theorem for divergence measure vectorfields on sets with fractal boundaries

Czech Academy of Sciences Publication Activity Database

Šilhavý, Miroslav

2009-01-01

Roč. 14, č. 5 (2009), s. 445-455 ISSN 1081-2865 Institutional research plan: CEZ:AV0Z10190503 Keywords : divergence measure vectorfields * fractal s * divergence theorem Subject RIV: BA - General Mathematics Impact factor: 1.065, year: 2009

The Patchwork Divergence Theorem

OpenAIRE

Dray, Tevian; Hellaby, Charles

1994-01-01

The divergence theorem in its usual form applies only to suitably smooth vector fields. For vector fields which are merely piecewise smooth, as is natural at a boundary between regions with different physical properties, one must patch together the divergence theorem applied separately in each region. We give an elegant derivation of the resulting "patchwork divergence theorem" which is independent of the metric signature in either region, and which is thus valid if the signature changes. (PA...

Evolution of pygmy angelfishes: Recent divergences, introgression, and the usefulness of color in taxonomy

KAUST Repository

Gaither, Michelle R.

2014-05-01

The pygmy angelfishes (genus Centropyge, family Pomacanthidae) are brightly colored species that occupy reef habitats in every tropical ocean. Some species are rarely observed because they occur below conventional scuba depths. Their striking coloration can command thousands of U.S. dollars in the aquarium trade, and closely related species are often distinguished only by coloration. These factors have impeded phylogenetic resolution, and every phylogeographic survey to date has reported discordance between coloration, taxonomy, and genetic partitions. Here we report a phylogenetic survey of 29 of the 34 recognized species (N= 94 plus 23 outgroups), based on two mtDNA and three nuclear loci, totaling 2272. bp. The resulting ML and Baysian trees are highly concordant and indicate that the genus Centropyge is paraphyletic, consistent with a previous analysis of the family Pomacanthidae. Two recognized genera (Apolemichthys and Genicanthus) nest within Centropyge, and two subgenera (Xiphypops and Paracentropyge) comprise monophyletic lineages that should be elevated to genus level. Based on an age estimate of 38. Ma for the family Pomacanthidae, Centropyge diverged from the closest extant genus Pygoplites about 33. Ma, three deep lineages within Centropyge diverged about 18-28. Ma, and four species complexes diverged 3-12. Ma. However, in 11 of 13 cases, putative species in these complexes are indistinguishable based on morphology and genetics, being defined solely by coloration. These cases indicate either emerging species or excessive taxonomic splitting based on brightly colored variants. © 2014 Elsevier Inc.

Is mitochondrial DNA divergence of near easter crested newts, Triturus karelinii group, reflected by differentiation of skull shape

NARCIS (Netherlands)

Ivanovic, A.; Uzum, N.; Wielstra, B.M.; Olgun, K.; Litvinchuk, S.N.; Kalezic, M.L.; Arntzen, J.W.

2013-01-01

The Eurasian Triturus karelinii group of crested newts comprises three distinct, geographically coherent mitochondrial DNA lineages, designated as the eastern, central and western lineage. These three lineages are genetically as diverged as other, morphologically well-differentiated crested newt

Evolution under domestication: ongoing artificial selection and divergence of wild and managed Stenocereus pruinosus (Cactaceae) populations in the Tehuacan Valley, Mexico.

Science.gov (United States)

Parra, Fabiola; Casas, Alejandro; Peñaloza-Ramírez, Juan Manuel; Cortés-Palomec, Aurea C; Rocha-Ramírez, Víctor; González-Rodríguez, Antonio

2010-09-01

The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations. Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations. Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours other than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (H(E) = 0.743) was higher than in wild (H(E) = 0.726) and cultivated (H(E) = 0.700) populations. Most of the genetic variation (90.58 %) occurred within populations. High gene flow (Nm(FST) > 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations. Traditional management of S. pruinosus involves

Novel divergent nidovirus in a python with pneumonia.

Science.gov (United States)

Bodewes, Rogier; Lempp, Charlotte; Schürch, Anita C; Habierski, Andre; Hahn, Kerstin; Lamers, Mart; von Dörnberg, Katja; Wohlsein, Peter; Drexler, Jan Felix; Haagmans, Bart L; Smits, Saskia L; Baumgärtner, Wolfgang; Osterhaus, Albert D M E

2014-11-01

The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin-neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales. © 2014 The Authors.

Divergência genética em tomate estimada por marcadores RAPD em comparação com descritores multicategóricos Genetic divergence among tomato accessions using RAPD markers and its comparison with multicategoric descriptors

Directory of Open Access Journals (Sweden)

Leandro SA Gonçalves

2008-09-01

Full Text Available A estimativa da variabilidade genética existente em um banco de germoplasma é importante não só para a conservação dos recursos genéticos, mas também para aplicações no melhoramento de plantas. O presente trabalho teve como objetivo estudar a divergência genética entre 78 acessos de uma coleção de germoplasma de tomateiro, com base em 74 marcadores RAPD e correlacionar esses resultados àqueles da caracterização morfoagronômica realizada para 27 descritores. Foi utilizado o agrupamento hierárquico UPGMA para analisar os dados, observando-se a formação de 13 grupos. Esses grupos foram correlacionados a cinco descritores (hábito de crescimento, tipo de folha, cor do fruto, número de lóculos e formato do fruto. Alguns grupos apresentaram peculiaridades, a exemplo do grupo IV, que reuniu acessos com frutos no formato de pêra; o grupo VII com acessos resistentes a murcha-bacteriana e o grupo IX, que englobou acessos com folhas do tipo batata. As análises por bootstrap revelaram poucos agrupamentos consistentes. Houve correlação positiva e altamente significativa entre as matrizes geradas pelos 27 descritores qualitativos e pelos marcadores RAPD (t = 14,02. A correlação de Mantel (r = 0,39 foi altamente significativa, porém de baixa magnitude. O baixo valor verificado para esta correlação sugere que ambas as etapas de caracterização (morfoagronômica e molecular são importantes para um conhecimento mais amplo e melhor discriminação entre os acessos de tomate.The estimation of genetic variability in a germplasm bank is important not only for the conservation of the genetic resources, but also for applications in plant breeding. The genetic divergence among 78 tomato accessions was studied, based on 74 RAPD markers. Also, a correlation between the molecular profile and 27 morphological and agronomic data was performed. Cluster analysis (UPGMA, used to study the data, resulted in 13 groups that were correlated with

Divergence of iron metabolism in wild Malaysian yeast.

Science.gov (United States)

Lee, Hana N; Mostovoy, Yulia; Hsu, Tiffany Y; Chang, Amanda H; Brem, Rachel B

2013-12-09

Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ.

Science.gov (United States)

Resnyk, C W; Carré, W; Wang, X; Porter, T E; Simon, J; Le Bihan-Duval, E; Duclos, M J; Aggrey, S E; Cogburn, L A

2017-08-16

Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today's broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens. We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold). Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate. The present analyses of the visceral fat transcriptome in

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

KAUST Repository

Huang, Chao-Li; Pu, Pei-Hua; Huang, Hao-Jen; Sung, Huang-Mo; Liaw, Hung-Jiun; Chen, Yi-Min; Chen, Chien-Ming; Huang, Ming-Ban; Osada, Naoki; Gojobori, Takashi; Pai, Tun-Wen; Chen, Yu-Tin; Hwang, Chi-Chuan; Chiang, Tzen-Yuh

2015-01-01

Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification. © Huang et al.

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

KAUST Repository

Huang, Chao-Li

2015-03-15

Background: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. Results: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. Conclusion: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification. © Huang et al.

Divergence, recombination and retention of functionality during protein evolution

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Xu Yanlong O

2005-09-01

Full Text Available Abstract We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates. These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality -- even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

On infrared divergences

International Nuclear Information System (INIS)

Parisi, G.

1979-01-01

The structure of infrared divergences is studied in superrenormalizable interactions. It is conjectured that there is an extension of the Bogoliubov-Parasiuk-Hepp theorem which copes also with infrared divergences. The consequences of this conjecture on the singularities of the Borel transform in a massless asymptotic free field theory are discussed. The application of these ideas to gauge theories is briefly discussed. (Auth.)

Homogenous Population Genetic Structure of the Non-Native Raccoon Dog (Nyctereutes procyonoides) in Europe as a Result of Rapid Population Expansion

Science.gov (United States)

Drygala, Frank; Korablev, Nikolay; Ansorge, Hermann; Fickel, Joerns; Isomursu, Marja; Elmeros, Morten; Kowalczyk, Rafał; Baltrunaite, Laima; Balciauskas, Linas; Saarma, Urmas; Schulze, Christoph; Borkenhagen, Peter; Frantz, Alain C.

2016-01-01

The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species’ dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large ‘central’ population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations. PMID:27064784

String loop divergences and effective lagrangians

International Nuclear Information System (INIS)

Fischler, W.; Klebanov, I.; Susskind, L.

1988-01-01

We isolate logarithmic divergences from bosonic string amplitudes on a disc. These divergences are compared with 'tadpole' divergences in the effective field theory, with a covariant cosmological term implied by the counting of string coupling constants. We find an inconsistency between the two. This might be a problem in eliminating divergences from the bosonic string. (orig.)

Statistical inference based on divergence measures

CERN Document Server

Pardo, Leandro

2005-01-01

The idea of using functionals of Information Theory, such as entropies or divergences, in statistical inference is not new. However, in spite of the fact that divergence statistics have become a very good alternative to the classical likelihood ratio test and the Pearson-type statistic in discrete models, many statisticians remain unaware of this powerful approach.Statistical Inference Based on Divergence Measures explores classical problems of statistical inference, such as estimation and hypothesis testing, on the basis of measures of entropy and divergence. The first two chapters form an overview, from a statistical perspective, of the most important measures of entropy and divergence and study their properties. The author then examines the statistical analysis of discrete multivariate data with emphasis is on problems in contingency tables and loglinear models using phi-divergence test statistics as well as minimum phi-divergence estimators. The final chapter looks at testing in general populations, prese...

Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

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Robinson, J.; Snider, M.; Duke, J.; Moyer, G.R.

2014-01-01

 The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina

Enhancing creative cognition with a rapid right-parietal neurofeedback procedure.

Science.gov (United States)

Agnoli, Sergio; Zanon, Marco; Mastria, Serena; Avenanti, Alessio; Corazza, Giovanni Emanuele

2018-02-14

The present article describes an innovative neurofeedback training (NFT) procedure aimed at increasing creative cognition through the enhancement of specific brain activities previously associated with divergent thinking. We designed and tested two NFT protocols based on training alpha and beta EEG oscillations selectively measured over the right parietal region. A total of 80 participants were involved, 40 in the alpha NFT protocol and 40 in the beta NFT protocol. The NFT loop was closed on a video stream that would advance only when oscillation power exceeded a normalized threshold. The total duration of the protocol was two hours in a single day, hence its classification as rapid. Changes in ideational fluency and originality, measured with a divergent thinking task, were compared between participants receiving real video feedback and participants receiving sham feedback. We controlled for individual differences in creative achievement level. Results showed that the protocols were effective at enhancing alpha and beta activities in the targeted area. Differences between the two protocols emerged in their effectiveness at promoting divergent thinking. While no significant changes in originality resulted from the rapid alpha NFT, increases in both originality and fluency emerged as a consequence of the rapid beta NFT. These results were particularly evident in participants starting with a low creative achievement level. Possible interpretations and future directions are proposed and discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Divergent thinking and constructing episodic simulations.

Science.gov (United States)

Addis, Donna Rose; Pan, Ling; Musicaro, Regina; Schacter, Daniel L

2016-01-01

Divergent thinking likely plays an important role in simulating autobiographical events. We investigated whether divergent thinking is differentially associated with the ability to construct detailed imagined future and imagined past events as opposed to recalling past events. We also examined whether age differences in divergent thinking might underlie the reduced episodic detail generated by older adults. The richness of episodic detail comprising autobiographical events in young and older adults was assessed using the Autobiographical Interview. Divergent thinking abilities were measured using the Alternative Uses Task. Divergent thinking was significantly associated with the amount of episodic detail for imagined future events. Moreover, while age was significantly associated with imagined episodic detail, this effect was strongly related to age-related changes in episodic retrieval rather than divergent thinking.

Ecological explanations to island gigantism: dietary niche divergence, predation, and size in an endemic lizard.

Science.gov (United States)

Runemark, Anna; Sagonas, Kostas; Svensson, Erik I

2015-08-01

Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard (Podarcis gaigeae) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.

Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

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Schwartz, Tonia S; Bronikowski, Anne M

2013-02-01

The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

Ancient geographical barriers drive differentiation among Sonneratia caseolaris populations and recent divergence from S. lanceolata

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Yuchen Yang

2016-10-01

Full Text Available Glacial vicariance is thought to influence population dynamics and speciation of many marine organisms. Mangroves, a plant group inhabiting intertidal zones, were also profoundly influenced by Pleistocene glaciations. In this study, we investigated phylogeographic patterns of a widespread mangrove species Sonneratia caseolaris and a narrowly distributed, closely related species S. lanceolata to infer their divergence histories and related it to historical geological events. We sequenced two chloroplast fragments and five nuclear genes for one population of S. lanceolata and 12 populations of S. caseolaris across the Indo-West Pacific (IWP region to evaluate genetic differentiation and divergence time among them. Phylogenetic analysis based on sequences of nuclear ribosomal internal transcribed spacer (nrITS and a nuclear gene rpl9 for all Sonneratia species indicate that S. lanceolata individuals are nested within S. caseolaris. We found strong genetic structure among geographic regions (South China Sea, the Indian Ocean and eastern Australia inhabited by S. caseolaris. We estimated that divergence between the Indo-Malesia and Australasia populations occurred 4.035 million years ago (MYA, prior to the onset of Pleistocene. BARRIERS analysis suggested that complex geographic features in the IWP region had largely shaped the phylogeographic patterns of S. caseolaris. Furthermore, haplotype analyses provided convincing evidence for secondary contact of the South China Sea (SCS and the Indian Ocean lineages at the Indo-Pacific boundary. Demographic history inference under isolation and migration (IM model detected substantial gene flow from the Sri Lanka populations to the populations in the Java Island. Moreover, multi-locus sequence analysis indicated that S. lanceolata was most closely related to the Indian Ocean populations of S. caseolaris and the divergence time between them was 2.057 MYA, coinciding with the onset of the Pleistocene

Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth.

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Crawford, Nicholas; Prendergast, D'Arcy; Oehlert, John W; Shaw, Gary M; Stevenson, David K; Rappaport, Nadav; Sirota, Marina; Tishkoff, Sarah A; Sondheimer, Neal

2018-03-01

To examine linkages between mitochondrial genetics and preterm birth by assessing the risk for preterm birth associated with the inheritance of nuclear haplotypes that are ancestrally distinct from mitochondrial haplogroup. Genome-wide genotyping studies of cohorts of preterm and term individuals were evaluated. We determined the mitochondrial haplogroup and nuclear ancestry for individuals and developed a scoring for the degree to which mitochondrial ancestry is divergent from nuclear ancestry. Infants with higher degrees of divergent mitochondrial ancestry were at increased risk for preterm birth (0.124 for preterm vs 0.105 for term infants; Pancestry correlated with earlier delivery within the primary study population, but this finding was not replicated in secondary cohorts born preterm. Individuals with divergent patterns of mitochondrial and nuclear ancestry are at increased risk for preterm birth. These findings may in part explain the higher rates of preterm birth in African Americans and in individuals with a matrilineal family history of preterm birth. Copyright © 2017 Elsevier Inc. All rights reserved.

Divergence in sex steroid hormone signaling between sympatric species of Japanese threespine stickleback.

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Jun Kitano

Full Text Available Sex steroids mediate the expression of sexually dimorphic or sex-specific traits that are important both for mate choice within species and for behavioral isolation between species. We investigated divergence in sex steroid signaling between two sympatric species of threespine stickleback (Gasterosteus aculeatus: the Japan Sea form and the Pacific Ocean form. These sympatric forms diverge in both male display traits and female mate choice behaviors, which together contribute to asymmetric behavioral isolation in sympatry. Here, we found that plasma levels of testosterone and 17β-estradiol differed between spawning females of the two sympatric forms. Transcript levels of follicle-stimulating hormone-β (FSHβ gene were also higher in the pituitary gland of spawning Japan Sea females than in the pituitary gland of spawning Pacific Ocean females. By contrast, none of the sex steroids examined were significantly different between nesting males of the two forms. However, combining the plasma sex steroid data with testis transcriptome data suggested that the efficiency of the conversion of testosterone into 11-ketotestosterone has likely diverged between forms. Within forms, plasma testosterone levels in males were significantly correlated with male body size, a trait important for female mate choice in the two sympatric species. These results demonstrate that substantial divergence in sex steroid signaling can occur between incipient sympatric species. We suggest that investigation of the genetic and ecological mechanisms underlying divergence in hormonal signaling between incipient sympatric species will provide a better understanding of the mechanisms of speciation in animals.

Zebra Alphaherpesviruses (EHV-1 and EHV-9: Genetic Diversity, Latency and Co-Infections

Directory of Open Access Journals (Sweden)

Azza Abdelgawad

2016-09-01

Full Text Available Alphaherpesviruses are highly prevalent in equine populations and co-infections with more than one of these viruses’ strains frequently diagnosed. Lytic replication and latency with subsequent reactivation, along with new episodes of disease, can be influenced by genetic diversity generated by spontaneous mutation and recombination. Latency enhances virus survival by providing an epidemiological strategy for long-term maintenance of divergent strains in animal populations. The alphaherpesviruses equine herpesvirus 1 (EHV-1 and 9 (EHV-9 have recently been shown to cross species barriers, including a recombinant EHV-1 observed in fatal infections of a polar bear and Asian rhinoceros. Little is known about the latency and genetic diversity of EHV-1 and EHV-9, especially among zoo and wild equids. Here, we report evidence of limited genetic diversity in EHV-9 in zebras, whereas there is substantial genetic variability in EHV-1. We demonstrate that zebras can be lytically and latently infected with both viruses concurrently. Such a co-occurrence of infection in zebras suggests that even relatively slow-evolving viruses such as equine herpesviruses have the potential to diversify rapidly by recombination. This has potential consequences for the diagnosis of these viruses and their management in wild and captive equid populations.

Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass.

Science.gov (United States)

Wang, Le; Wan, Zi Yi; Lim, Huan Sein; Yue, Gen Hua

2016-08-01

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the 'genomic islands' scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene. © 2016 John Wiley & Sons Ltd.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

KAUST Repository

Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh

2014-01-01

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

KAUST Repository

Huang, Chao-Li

2014-11-11

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Genetic diversity of Casearia sylvestris populations in remnants of the Atlantic Forest.

Science.gov (United States)

Araujo, F L; Siqueira, M V B M; Grando, C; Viana, J P G; Pinheiro, J B; Alves-Pereira, A; Campos, J B; Brancalion, P H S; Zucchi, M I

2017-01-23

Guaçatonga (Casearia sylvestris) is a native plant of the Atlantic Forest, with high medicinal potential and relevance for reforestation programs. The aim of this study was to characterize, with microsatellite markers, two populations of C. sylvestris from remaining areas of the Atlantic Forest in the State of São Paulo. High allelic variation was found in both populations (N A = 101 and 117; A R = 12.5 and 14.4), although with high endogamy coefficients (f = 0.640 and 0.363). Estimates of genetic structure suggested the presence of considerable genetic divergence between the populations (F ST = 0.103); however, there was no spatial genetic structure within the populations. Genetic divergence may have occurred due to decreased gene flow between the fragmented populations as the result of deforestation. The results of this study demonstrate the importance of genetic diversity and its characterization in native plants within remaining forest areas for the management and restoration of such areas.

Divergence and Adaptive Capacity of Marine Keystone Species

DEFF Research Database (Denmark)

Fietz, Katharina

A multitude of anthropogenic actions ranging from overexploitation, pollution, and eutrophication to the introduction of invasive species impact the marine environment today (Jansson & Dahlberg 1999; Islam & Tanaka 2004; Pauly et al. 2005; Molnar et al. 2008). In combination with rapid environmen......A multitude of anthropogenic actions ranging from overexploitation, pollution, and eutrophication to the introduction of invasive species impact the marine environment today (Jansson & Dahlberg 1999; Islam & Tanaka 2004; Pauly et al. 2005; Molnar et al. 2008). In combination with rapid...... and effective conservation actions. In this thesis, I took a population genetic approach to shed light on the above features of three different keystone organisms in the North Atlantic and Baltic Sea ecosystems. In Chapter 2, my colleagues and I combined modern and historic nuclear and mitochondrial genetic...

Genetic analysis of seed proteins contents in cowpea ( Vigna ...

African Journals Online (AJOL)

In order to select cowpea genotypes with high food value, 10 varieties were genetically screened in Ngaoundéré (Cameroon) for seed crude protein and its soluble fractions contents. Five divergent lines were studied through a 5 x 5 half diallel cross mating. The genotypes presented a significant genetic variability for these ...

Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis.

Science.gov (United States)

Wang, Baosheng; Mao, Jian-Feng; Zhao, Wei; Wang, Xiao-Ru

2013-01-01

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.

Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations.

Science.gov (United States)

Tavares, Mara Garcia; Pietrani, Nathalia Teixeira; de Castro Durvale, Maxwell; Resende, Helder Canto; de Oliveira Campos, Lucio Antonio

2013-03-01

Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (Ho) ranged from 0.03-0.21, while the expected heterozygosity (He) ranged from 0.23-0.47. The genetic distances among populations ranged from 0.03-0.45. The FST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata.

Niche evolution and adaptive radiation: Testing the order of trait divergence

Science.gov (United States)

Ackerly, D.D.; Schwilk, D.W.; Webb, C.O.

2006-01-01

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (?? niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (?? niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This ?? niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (?? niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the ?? niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of ?? niche traits might be a common feature of niche evolution in

The devil is in the details: genetic variation in introduced populations and its contributions to invasion.

Science.gov (United States)

Dlugosch, Katrina M; Anderson, Samantha R; Braasch, Joseph; Cang, F Alice; Gillette, Heather D

2015-05-01

The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself. © 2015 John Wiley & Sons Ltd.

Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences.

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Keskin, Emre; Atar, Hasan Huseyin

2012-04-01

Mitochondrial DNA sequence variation in 655 bpfragments of the cytochrome oxidase c subunit I gene, known as the DNA barcode, of European anchovy (Engraulis encrasicolus) was evaluated by analyzing 1529 individuals representing 16 populations from the Black Sea, through the Marmara Sea and the Aegean Sea to the Mediterranean Sea. A total of 19 (2.9%) variable sites were found among individuals, and these defined 10 genetically diverged populations with an overall mean distance of 1.2%. The highest nucleotide divergence was found between samples of eastern Mediterranean and northern Aegean (2.2%). Evolutionary history analysis among 16 populations clustered the Mediterranean Sea clades in one main branch and the other clades in another branch. Diverging pattern of the European anchovy populations correlated with geographic dispersion supports the genetic structuring through the Black Sea-Marmara Sea-Aegean Sea-Mediterranean Sea quad.

Evolutionary divergence in sexual signals: Insights from within and among barn swallow populations

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Wilkins, Matthew Reed

A wealth of studies across diverse animal groups indicate the importance of sexual selection in shaping phenotypes within and across breeding populations. In recent decades, much research has focused on how divergent sexual selection pressures among populations may lead to speciation. For my first dissertation chapter, I performed a literature review on the causes and consequences of evolutionary divergence in acoustic signals and developed the acoustic window conceptual framework for understanding the contributions of selection, genetic drift, and evolutionary constraint to signal divergence. Further, I found that sexual selection explains acoustic differences between recently diverged populations of the best-studied taxa. However, the relative contributions of ecological selection, sexual selection, and drift to acoustic divergence have not typically been considered within the same study systems. The remainder of my dissertation used the Northern Hemisphere-distributed barn swallow ( Hirundo rustica) species complex as a model system to study sender-receiver dynamics, intra- and intersexual selection pressures, and visual and acoustic signal interactions at the local scale, and signal divergence across populations at the global scale. From song recordings taken across 19 sampling sites, spanning five of six described subspecies, I demonstrated considerable conservation in song structure. However, temporal traits were highly divergent across subspecies, and in particular, the speed of the terminal trill of songs. In a detailed study of the multimodal communication system of the barn swallow (including visual and acoustic traits), I demonstrated that males and females use different types of signals to mediate competition and mate choice. One of the only exceptions to this rule was trill rate, which was also implicated in song divergence across populations. In order to test the function of trill rate in communication, I performed a two-year playback study within the

Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni

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Dávila José A

2007-12-01

Full Text Available Abstract Background The forests of the upper Amazon basin harbour some of the world's highest anuran species richness, but to date we have only the sparsest understanding of the distribution of genetic diversity within and among species in this region. To quantify region-wide genealogical patterns and to test for the presence of deep intraspecific divergences that have been documented in some other neotropical anurans, we developed a molecular phylogeny of the wide-spread terrestrial leaflitter frog Eleutherodactylus ockendeni (Leptodactylidae from 13 localities throughout its range in Ecuador using data from two mitochondrial genes (16S and cyt b; 1246 base pairs. We examined the relation between divergence of mtDNA and the nuclear genome, as sampled by five species-specific microsatellite loci, to evaluate indirectly whether lineages are reproductively isolated where they co-occur. Our extensive phylogeographic survey thus assesses the spatial distribution of E. ockendeni genetic diversity across eastern Ecuador. Results We identified three distinct and well-supported clades within the Ecuadorean range of E. ockendeni: an uplands clade spanning north to south, a northeastern and central lowlands clade, and a central and southeastern clade, which is basal. Clades are separated by 12% to 15% net corrected p-distance for cytochrome b, with comparatively low sequence divergence within clades. Clades marginally overlap in some geographic areas (e.g., Napo River basin but are reproductively isolated, evidenced by diagnostic differences in microsatellite PCR amplification profiles or DNA repeat number and coalescent analyses (in MDIV best modelled without migration. Using Bayesian (BEAST and net phylogenetic estimates, the Southeastern Clade diverged from the Upland/Lowland clades in the mid-Miocene or late Oligocene. Lowland and Upland clades speciated more recently, in the early or late Miocene. Conclusion Our findings uncover previously

Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

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Lauber, Chris; Gorbalenya, Alexander E

2012-04-01

Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

Intraspecific ecological niche divergence and reproductive shifts foster cytotype displacement and provide ecological opportunity to polyploids.

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Karunarathne, Piyal; Schedler, Mara; Martínez, Eric J; Honfi, Ana I; Novichkova, Anastasiia; Hojsgaard, Diego

2018-05-11

Niche divergence between polyploids and their lower ploidy progenitors is one of the primary mechanisms fostering polyploid establishment and adaptive divergence. However, within-species chromosomal and reproductive variability have usually been neglected in community ecology and biodiversity analyses even though they have been recognized to play a role in the adaptive diversification of lineages. We used Paspalum intermedium, a grass species with diverging genetic systems (diploidy vs. autopolyploidy, allogamy vs. autogamy and sexuality vs. apomixis), to recognize the causality of biogeographic patterns, adaptation and ecological flexibility of cytotypes. Chromosome counts and flow cytometry were used to characterize within-species genetic systems diversity. Environmental niche modelling was used to evaluate intraspecific ecological attributes associated with environmental and climatic factors and to assess correlations among ploidy, reproductive modes and ecological conditions ruling species' population dynamics, range expansion, adaptation and evolutionary history. Two dominant cytotypes non-randomly distributed along local and regional geographical scales displayed niche differentiation, a directional shift in niche optima and signs of disruptive selection on ploidy-related ecological aptitudes for the exploitation of environmental resources. Ecologically specialized allogamous sexual diploids were found in northern areas associated with higher temperature, humidity and productivity, while generalist autogamous apomictic tetraploids occurred in southern areas, occupying colder and less productive environments. Four localities with a documented shift in ploidy and four mixed populations in a zone of ecological transition revealed an uneven replacement between cytotypes. Polyploidy and contrasting reproductive traits between cytotypes have promoted shifts in niche optima, and increased ecological tolerance and niche divergence. Ecologically specialized diploids

Genetic characterization of the ABO blood group in Neandertals

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Bertranpetit Jaume

2008-12-01

Full Text Available Abstract Background The high polymorphism rate in the human ABO blood group gene seems to be related to susceptibility to different pathogens. It has been estimated that all genetic variation underlying the human ABO alleles appeared along the human lineage, after the divergence from the chimpanzee lineage. A paleogenetic analysis of the ABO blood group gene in Neandertals allows us to directly test for the presence of the ABO alleles in these extinct humans. Results We have analysed two male Neandertals that were retrieved under controlled conditions at the El Sidron site in Asturias (Spain and that appeared to be almost free of modern human DNA contamination. We find a human specific diagnostic deletion for blood group O (O01 haplotype in both Neandertal individuals. Conclusion These results suggest that the genetic change responsible for the O blood group in humans predates the human and Neandertal divergence. A potential selective event associated with the emergence of the O allele may have therefore occurred after humans separated from their common ancestor with chimpanzees and before the human-Neandertal population divergence.

Divergence within and among Seaweed Siblings (Fucus vesiculosus and F. radicans) in the Baltic Sea.

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Ardehed, Angelica; Johansson, Daniel; Sundqvist, Lisa; Schagerström, Ellen; Zagrodzka, Zuzanna; Kovaltchouk, Nikolaj A; Bergström, Lena; Kautsky, Lena; Rafajlovic, Marina; Pereyra, Ricardo T; Johannesson, Kerstin

2016-01-01

Closely related taxa provide significant case studies for understanding evolution of new species but may simultaneously challenge species identification and definition. In the Baltic Sea, two dominant and perennial brown algae share a very recent ancestry. Fucus vesiculosus invaded this recently formed postglacial sea 8000 years ago and shortly thereafter Fucus radicans diverged from this lineage as an endemic species. In the Baltic Sea both species reproduce sexually but also recruit fully fertile new individuals by asexual fragmentation. Earlier studies have shown local differences in morphology and genetics between the two taxa in the northern and western Bothnian Sea, and around the island of Saaremaa in Estonia, but geographic patterns seem in conflict with a single origin of F. radicans. To investigate the relationship between northern and Estonian distributions, we analysed the genetic variation using 9 microsatellite loci in populations from eastern Bothnian Sea, Archipelago Sea and the Gulf of Finland. These populations are located in between earlier studied populations. However, instead of bridging the disparate genetic gap between N-W Bothnian Sea and Estonia, as expected from a simple isolation-by-distance model, the new populations substantially increased overall genetic diversity and showed to be strongly divergent from the two earlier analysed regions, showing signs of additional distinct populations. Contrasting earlier findings of increased asexual recruitment in low salinity in the Bothnian Sea, we found high levels of sexual reproduction in some of the Gulf of Finland populations that inhabit extremely low salinity. The new data generated in this study supports the earlier conclusion of two reproductively isolated but very closely related species. However, the new results also add considerable genetic and morphological complexity within species. This makes species separation at geographic scales more demanding and suggests a need for more

Divergence within and among Seaweed Siblings (Fucus vesiculosus and F. radicans in the Baltic Sea.

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Angelica Ardehed

Full Text Available Closely related taxa provide significant case studies for understanding evolution of new species but may simultaneously challenge species identification and definition. In the Baltic Sea, two dominant and perennial brown algae share a very recent ancestry. Fucus vesiculosus invaded this recently formed postglacial sea 8000 years ago and shortly thereafter Fucus radicans diverged from this lineage as an endemic species. In the Baltic Sea both species reproduce sexually but also recruit fully fertile new individuals by asexual fragmentation. Earlier studies have shown local differences in morphology and genetics between the two taxa in the northern and western Bothnian Sea, and around the island of Saaremaa in Estonia, but geographic patterns seem in conflict with a single origin of F. radicans. To investigate the relationship between northern and Estonian distributions, we analysed the genetic variation using 9 microsatellite loci in populations from eastern Bothnian Sea, Archipelago Sea and the Gulf of Finland. These populations are located in between earlier studied populations. However, instead of bridging the disparate genetic gap between N-W Bothnian Sea and Estonia, as expected from a simple isolation-by-distance model, the new populations substantially increased overall genetic diversity and showed to be strongly divergent from the two earlier analysed regions, showing signs of additional distinct populations. Contrasting earlier findings of increased asexual recruitment in low salinity in the Bothnian Sea, we found high levels of sexual reproduction in some of the Gulf of Finland populations that inhabit extremely low salinity. The new data generated in this study supports the earlier conclusion of two reproductively isolated but very closely related species. However, the new results also add considerable genetic and morphological complexity within species. This makes species separation at geographic scales more demanding and suggests a

Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome.

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Tao, Yun; Zeng, Zhao-Bang; Li, Jian; Hartl, Daniel L; Laurie, Cathy C

2003-08-01

Hybrid male sterility (HMS) is a rapidly evolving mechanism of reproductive isolation in Drosophila. Here we report a genetic analysis of HMS in third-chromosome segments of Drosophila mauritiana that were introgressed into a D. simulans background. Qualitative genetic mapping was used to localize 10 loci on 3R and a quantitative trait locus (QTL) procedure (multiple-interval mapping) was used to identify 19 loci on the entire chromosome. These genetic incompatibilities often show dominance and complex patterns of epistasis. Most of the HMS loci have relatively small effects and generally at least two or three of them are required to produce complete sterility. Only one small region of the third chromosome of D. mauritiana by itself causes a high level of infertility when introgressed into D. simulans. By comparison with previous studies of the X chromosome, we infer that HMS loci are only approximately 40% as dense on this autosome as they are on the X chromosome. These results are consistent with the gradual evolution of hybrid incompatibilities as a by-product of genetic divergence in allopatric populations.

On the Critical Role of Divergent Selection in Evolvability

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Joel Lehman

2016-08-01

Full Text Available An ambitious goal in evolutionary robotics is to evolve increasingly complex robotic behaviors with minimal human design effort. Reaching this goal requires evolutionary algorithms that can unlock from genetic encodings their latent potential for evolvability. One issue clouding this goal is conceptual confusion about evolvability, which often obscures the aspects of evolvability that are important or desirable. The danger from such confusion is that it may establish unrealistic goals for evolvability that prove unproductive in practice. An important issue separate from conceptual confusion is the common misalignment between selection and evolvability in evolutionary robotics. While more expressive encodings can represent higher-level adaptations (e.g. sexual reproduction or developmental systems that increase long-term evolutionary potential (i.e. evolvability, realizing such potential requires gradients of fitness and evolvability to align. In other words, selection is often a critical factor limiting increasing evolvability. Thus, drawing from a series of recent papers, this article seeks to both (1 clarify and focus the ways in which the term evolvability is used within artificial evolution, and (2 argue for the importance of one type of selection, i.e. divergent selection, for enabling evolvability. The main argument is that there is a fundamental connection between divergent selection and evolvability (on both the individual and population level that does not hold for typical goal-oriented selection. The conclusion is that selection pressure plays a critical role in realizing the potential for evolvability, and that divergent selection in particular provides a principled mechanism for encouraging evolvability in artificial evolution.

Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen

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Lucía Graña-Miraglia

2017-09-01

Full Text Available Genome sequencing has been useful to gain an understanding of bacterial evolution. It has been used for studying the phylogeography and/or the impact of mutation and recombination on bacterial populations. However, it has rarely been used to study gene turnover at microevolutionary scales. Here, we sequenced Mexican strains of the human pathogen Acinetobacter baumannii sampled from the same locale over a 3 year period to obtain insights into the microevolutionary dynamics of gene content variability. We found that the Mexican A. baumannii population was recently founded and has been emerging due to a rapid clonal expansion. Furthermore, we noticed that on average the Mexican strains differed from each other by over 300 genes and, notably, this gene content variation has accrued more frequently and faster than the accumulation of mutations. Moreover, due to its rapid pace, gene content variation reflects the phylogeny only at very short periods of time. Additionally, we found that the external branches of the phylogeny had almost 100 more genes than the internal branches. All in all, these results show that rapid gene turnover has been of paramount importance in producing genetic variation within this population and demonstrate the utility of genome sequencing to study alternative forms of genetic variation.

Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

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Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

2011-01-01

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback.

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David A Marques

2016-02-01

Full Text Available Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this.

Extensive shared polymorphism at non-MHC immune genes in recently diverged North American prairie grouse

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Minias, Piotr; Bateson, Zachary W.; Whittingham, Linda A.; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O.

2018-01-01

Gene polymorphisms shared between recently diverged species are thought to be widespread and most commonly reflect introgression from hybridization or retention of ancestral polymorphism through incomplete lineage sorting. Shared genetic diversity resulting from incomplete lineage sorting is usually maintained for a relatively short period of time, but under strong balancing selection it may persist for millions of years beyond species divergence (balanced trans-species polymorphism), as in the case of the major histocompatibility complex (MHC) genes. However, balancing selection is much less likely to act on non-MHC immune genes. The aim of this study was to investigate the patterns of shared polymorphism and selection at non-MHC immune genes in five grouse species from Centrocercus and Tympanuchus genera. For this purpose, we genotyped five non-MHC immune genes that do not interact directly with pathogens, but are involved in signaling and regulate immune cell growth. In contrast to previous studies with MHC, we found no evidence for balancing selection or balanced trans-species polymorphism among the non-MHC immune genes. No haplotypes were shared between genera and in most cases more similar allelic variants sorted by genus. Between species within genera, however, we found extensive shared polymorphism, which was most likely attributable to introgression or incomplete lineage sorting following recent divergence and large ancestral effective population size (i.e., weak genetic drift). Our study suggests that North American prairie grouse may have attained relatively low degree of reciprocal monophyly at nuclear loci and reinforces the rarity of balancing selection in non-MHC immune genes.

Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation.

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Macdonald, K A; Pryce, J E; Spelman, R J; Davis, S R; Wales, W J; Waghorn, G C; Williams, Y J; Marett, L C; Hayes, B J

2014-03-01

Residual feed intake (RFI), as a measure of feed conversion during growth, was estimated for around 2,000 growing Holstein-Friesian heifer calves aged 6 to 9 mo in New Zealand and Australia, and individuals from the most and least efficient deciles (low and high RFI phenotypes) were retained. These animals (78 New Zealand cows, 105 Australian cows) were reevaluated during their first lactation to determine if divergence for RFI observed during growth was maintained during lactation. Mean daily body weight (BW) gain during assessment as calves had been 0.86 and 1.15 kg for the respective countries, and the divergence in RFI between most and least efficient deciles for growth was 21% (1.39 and 1.42 kg of dry matter, for New Zealand and Australia, respectively). At the commencement of evaluation during lactation, the cows were aged 26 to 29 mo. All were fed alfalfa and grass cubes; it was the sole diet in New Zealand, whereas 6 kg of crushed wheat/d was also fed in Australia. Measurements of RFI during lactation occurred for 34 to 37 d with measurements of milk production (daily), milk composition (2 to 3 times per week), BW and BW change (1 to 3 times per week), as well as body condition score (BCS). Daily milk production averaged 13.8 kg for New Zealand cows and 20.0 kg in Australia. No statistically significant differences were observed between calf RFI decile groups for dry matter intake, milk production, BW change, or BCS; however a significant difference was noted between groups for lactating RFI. Residual feed intake was about 3% lower for lactating cows identified as most efficient as growing calves, and no negative effects on production were observed. These results support the hypothesis that calves divergent for RFI during growth are also divergent for RFI when lactating. The causes for this reduced divergence need to be investigated to ensure that genetic selection programs based on low RFI (better efficiency) are robust. Copyright © 2014 American Dairy

Collinearity, convergence and cancelling infrared divergences

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Lavelle, Martin; McMullan, David

2006-01-01

The Lee-Nauenberg theorem is a fundamental quantum mechanical result which provides the standard theoretical response to the problem of collinear and infrared divergences. Its argument, that the divergences due to massless charged particles can be removed by summing over degenerate states, has been successfully applied to systems with final state degeneracies such as LEP processes. If there are massless particles in both the initial and final states, as will be the case at the LHC, the theorem requires the incorporation of disconnected diagrams which produce connected interference effects at the level of the cross-section. However, this aspect of the theory has never been fully tested in the calculation of a cross-section. We show through explicit examples that in such cases the theorem introduces a divergent series of diagrams and hence fails to cancel the infrared divergences. It is also demonstrated that the widespread practice of treating soft infrared divergences by the Bloch-Nordsieck method and handling collinear divergences by the Lee-Nauenberg method is not consistent in such cases

No boundaries: genomes, organisms, and ecological interactions responsible for divergence and reproductive isolation.

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Etges, William J

2014-01-01

Revealing the genetic basis of traits that cause reproductive isolation, particularly premating or sexual isolation, usually involves the same challenges as most attempts at genotype-phenotype mapping and so requires knowledge of how these traits are expressed in different individuals, populations, and environments, particularly under natural conditions. Genetic dissection of speciation phenotypes thus requires understanding of the internal and external contexts in which underlying genetic elements are expressed. Gene expression is a product of complex interacting factors internal and external to the organism including developmental programs, the genetic background including nuclear-cytotype interactions, epistatic relationships, interactions among individuals or social effects, stochasticity, and prevailing variation in ecological conditions. Understanding of genomic divergence associated with reproductive isolation will be facilitated by functional expression analysis of annotated genomes in organisms with well-studied evolutionary histories, phylogenetic affinities, and known patterns of ecological variation throughout their life cycles. I review progress and prospects for understanding the pervasive role of host plant use on genetic and phenotypic expression of reproductive isolating mechanisms in cactophilic Drosophila mojavensis and suggest how this system can be used as a model for revealing the genetic basis for species formation in organisms where speciation phenotypes are under the joint influences of genetic and environmental factors. © The American Genetic Association. 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Rapid growth and genetic diversity retention in an isolated reintroduced black bear population in the central appalachians

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Murphy, Sean M.; Cox, John J.; Clark, Joseph D.; Augustine, Benjamin J.; Hast, John T.; Gibbs, Dan; Strunk, Michael; Dobey, Steven

2015-01-01

Animal reintroductions are important tools of wildlife management to restore species to their historical range, and they can also create unique opportunities to study population dynamics and genetics from founder events. We used non-invasive hair sampling in a systematic, closed-population capture-mark-recapture (CMR) study design at the Big South Fork (BSF) area in Kentucky during 2010 and Tennessee during 2012 to estimate the demographic and genetic characteristics of the black bear (Ursus americanus) population that resulted from a reintroduced founding population of 18 bears in 1998. We estimated 38 (95% CI: 31–66) and 190 (95% CI: 170–219) bears on the Kentucky and Tennessee study areas, respectively. Based on the Tennessee abundance estimate alone, the mean annual growth rate was 18.3% (95% CI: 17.4–19.5%) from 1998 to 2012. We also compared the genetic characteristics of bears sampled during 2010–2012 to bears in the population during 2000–2002, 2–4 years following reintroduction, and to the source population. We found that the level of genetic diversity since reintroduction as indicated by expected heterozygosity (HE) remained relatively constant (HE(source, 2004) = 0.763, HE(BSF, 2000–2002) = 0.729, HE(BSF, 2010–2012) = 0.712) and the effective number of breeders (NB) remained low but had increased since reintroduction in the absence of sufficient immigration (NB(BSF, 2000–2002) = 12, NB(BSF, 2010–2012)  = 35). This bear population appears to be genetically isolated, but contrary to our expectations, we did not find evidence of genetic diversity loss or other deleterious genetic effects typically observed from small founder groups. We attribute that to high initial genetic diversity in the founder group combined with overlapping generations and rapid population growth. Although the population remains relatively small, the reintroduction using a small founder group appears to be demographically and genetically

Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

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Wan Hongjian

2012-09-01

Full Text Available Abstract Background Pepper (Capsicum annuum L. is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS-leucine-rich repeat (LRR gene family is the largest class of known disease resistance genes (R genes effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs. Results A total of 78 R gene analogues (CaRGAs were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR-NBS-LRR (CaRGAs I to IV and TIR-NBS-LRR (CaRGAs V to VII subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in

Semantic search during divergent thinking.

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Hass, Richard W

2017-09-01

Divergent thinking, as a method of examining creative cognition, has not been adequately analyzed in the context of modern cognitive theories. This article casts divergent thinking responding in the context of theories of memory search. First, it was argued that divergent thinking tasks are similar to semantic fluency tasks, but are more constrained, and less well structured. Next, response time distributions from 54 participants were analyzed for temporal and semantic clustering. Participants responded to two prompts from the alternative uses test: uses for a brick and uses for a bottle, for two minutes each. Participants' cumulative response curves were negatively accelerating, in line with theories of search of associative memory. However, results of analyses of semantic and temporal clustering suggested that clustering is less evident in alternative uses responding compared to semantic fluency tasks. This suggests either that divergent thinking responding does not involve an exhaustive search through a clustered memory trace, but rather that the process is more exploratory, yielding fewer overall responses that tend to drift away from close associates of the divergent thinking prompt. Copyright © 2017 Elsevier B.V. All rights reserved.

Genitores potenciais para hibridações identificados por divergência genética em feijão carioca Bean parents for hybridization identified by genetic divergence in "carioca" bean

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Nerinéia Dalfollo Ribeiro

2003-06-01

Full Text Available Noventa genótipos de feijão carioca (Phaseolus vulgaris L. foram avaliados, em dois anos agrícolas, em Santa Maria, RS, a fim de definir quais características agromorfológicas constituem-se como melhores descritores, realizar agrupamento em função de dissimilaridade genética e de definir quais combinações híbridas mais promissoras serão obtidas para o desenvolvimento de populações segregantes. Dos 20 caracteres agromorfológicos avaliados, apenas nove (ferrugem nos legumes, acamamento, nota geral, cor do tegumento, rendimento de grãos, massa de 100 sementes, altura de inserção do primeiro legume, altura de inserção do último legume e número de sementes por legume apresentaram maior contribuição para a divergência genética. Os genótipos de feijão carioca foram agrupados pelo método hierárquico de ligação completa. Populações segregantes, com variabilidade genética superior, podem ser obtidas com hibridações entre o genótipo ESAL 550 com genótipos do grupo 2 (LH-6, 17-4-32, R-78, H-4-5 e R-102 e/ou com genótipos do grupo 3 (FT 97-188, Cati-Taquari, CII-328, Carioca Precoce, FT 97-41, LH-11, FT 91-4067, Iapar 31, CI 102, Carioca MG, CII-54 e R-102.Carioca bean genotypes (Phaseolus vulgaris L. were evaluated in two growing seasons in Santa Maria, RS, Brazil. The objectives of this work were to evaluate which morpho-agronomic characteristics were the best descriptors, to group the genotypes in relation to genetic diversity and to determine which hybrid combinations are promissing to obtain higher segregation populations in carioca bean. From the 20 morpho-agronomic characteristics evaluated, only seven (pod rust, lodging, general note, colour of seed tegument, grain yield, 100 seed weight, height of first and final pod insertion and number of seeds per pod showed higher contribution to genetic diversity. The evaluated carioca bean genotypes were clustered by the complete linkage method. The following hybrid

Genetic component of flammability variation in a Mediterranean shrub.

Science.gov (United States)

Moreira, B; Castellanos, M C; Pausas, J G

2014-03-01

Recurrent fires impose a strong selection pressure in many ecosystems worldwide. In such ecosystems, plant flammability is of paramount importance because it enhances population persistence, particularly in non-resprouting species. Indeed, there is evidence of phenotypic divergence of flammability under different fire regimes. Our general hypothesis is that flammability-enhancing traits are adaptive; here, we test whether they have a genetic component. To test this hypothesis, we used the postfire obligate seeder Ulex parviflorus from sites historically exposed to different fire recurrence. We associated molecular variation in potentially adaptive loci detected with a genomic scan (using AFLP markers) with individual phenotypic variability in flammability across fire regimes. We found that at least 42% of the phenotypic variation in flammability was explained by the genetic divergence in a subset of AFLP loci. In spite of generalized gene flow, the genetic variability was structured by differences in fire recurrence. Our results provide the first field evidence supporting that traits enhancing plant flammability have a genetic component and thus can be responding to natural selection driven by fire. These results highlight the importance of flammability as an adaptive trait in fire-prone ecosystems. © 2014 John Wiley & Sons Ltd.

Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

Science.gov (United States)

Zhang, Linbin; Sun, Tianai; Woldesellassie, Fitsum; Xiao, Hailian; Tao, Yun

2015-03-01

Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

Population Divergence in Venom Bioactivities of Elapid Snake Pseudonaja textilis: Role of Procoagulant Proteins in Rapid Rodent Prey Incapacitation

Science.gov (United States)

Skejić, Jure; Hodgson, Wayne C.

2013-01-01

This study looked at how toxic proteins in venoms of adult Australian eastern Brown snakes Pseudonaja textilis from South Australian and Queensland populations interact with physiological functions of the lab SD rat Rattus norvegicus. Circulatory collapse and incoagulable blood occurred instantly after injection of venom under the dorsal skin of anaesthetised and mechanically ventilated rats in an imitation of a P. textilis bite. Intravenous injection of purified P. textilis (Mackay, QLD) venom prothrombin activator proteins caused instant failure of circulation, testifying of high toxicity of these proteins and suggesting their role in rapid incapacitation of rodent prey. The hypothesis is further supported by circulatory collapse occurring instantly despite artificial respiration in envenomed rats and the finding of extremely high venom procoagulant potency in rat plasma. LC-MS and physiology assays revealed divergent venom composition and biological activity of South Australian (Barossa locality) and Queensland (Mackay locality) populations, which may be driven by selection for different prey. The Queensland venom of P. textilis was found to be more procoagulant and to exhibit predominately presynaptic neurotoxicity, while the South Australian venom contained diverse postsynaptic type II and III α-neurotoxins in addition to the presynaptic neurotoxins and caused significantly faster onset of neuromuscular blockade in the rat phrenic nerve-diaphragm preparation. LC-MS analysis found evidence of multiple coagulation factor X-like proteins in P. textilis venoms, including a match to P. textilis coagulation factor X isoform 2, previously known to be expressed only in the liver. PMID:23691135

Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats

Directory of Open Access Journals (Sweden)

van Oppen Madeleine JH

2011-10-01

Full Text Available Abstract Background Divergent natural selection across environmental gradients has been acknowledged as a major driver of population and species divergence, however its role in the diversification of scleractinian corals remains poorly understood. Recently, it was demonstrated that the brooding coral Seriatopora hystrix and its algal endosymbionts (Symbiodinium are genetically partitioned across reef environments (0-30 m on the far northern Great Barrier Reef. Here, we explore the potential mechanisms underlying this differentiation and assess the stability of host-symbiont associations through a reciprocal transplantation experiment across habitats ('Back Reef', 'Upper Slope' and 'Deep Slope', in combination with molecular (mtDNA and ITS2-DGGE and photo-physiological analyses (respirometry and HPLC. Results The highest survival rates were observed for native transplants (measured 14 months after transplantation, indicating differential selective pressures between habitats. Host-symbiont assemblages remained stable during the experimental duration, demonstrating that the ability to "shuffle" or "switch" symbionts is restricted in S. hystrix. Photo-physiological differences were observed between transplants originating from the shallow and deep habitats, with indirect evidence of an increased heterotrophic capacity in native deep-water transplants (from the 'Deep Slope' habitat. Similar photo-acclimatisation potential was observed between transplants originating from the two shallow habitats ('Back Reef' and 'Upper Slope', highlighting that their genetic segregation over depth may be due to other, non-photo-physiological traits under selection. Conclusions This study confirms that the observed habitat partitioning of S. hystrix (and associated Symbiodinium is reflective of adaptive divergence along a depth gradient. Gene flow appears to be reduced due to divergent selection, highlighting the potential role of ecological mechanisms, in addition to

Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae)

DEFF Research Database (Denmark)

Trénel, P.; Hansen, Michael Møller; Nordmand, S.

2008-01-01

-Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based...... Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron-Paute deflection. F-statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses...... impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation (RST > FST) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance...

Worldwide genetic differentiation in the common fouling barnacle, Amphibalanus amphitrite

KAUST Repository

Chen, Hsi-Nien

2014-10-21

© 2014, © 2014 Taylor & Francis. Amphibalanus amphitrite is a common fouling barnacle distributed globally in tropical and subtropical waters. In the present study, the genetic (mitochondrial cytochrome oxidase subunit I) and morphological differentiation in A. amphitrite from 25 localities around the world were investigated. The results revealed three clades within A. amphitrite with a genetic divergence of ~ 4% among clades, whereas there were no diagnostic morphological differences among clades. Clade 1 is widely distributed in both temperate and tropical waters, whereas Clade 3 is currently restricted to the tropical region. The deep divergence among clades suggests historical isolation within A. amphitrite; thus, the present geographical overlaps are possibly a result of the combined effects of rising sea level and human-mediated dispersals. This study highlights the genetic differentiation that exists in a common, widely distributed fouling organism with great dispersal potential; future antifouling research should take into account the choice of lineages.

Linear energy divergences in Coulomb gauge QCD

OpenAIRE

Andrasi, A.

2011-01-01

The structure of linear energy divergences is analysed on the example of one graph to 3-loop order. Such dangerous divergences do cancel when all graphs are added, but next to leading divergences do not cancel out.

Accelerating dynamic genetic conservation efforts: Use of FT-IR spectroscopy for the rapid identification of trees resistant to destructive pathogens

Science.gov (United States)

C. Villari; R.A. Sniezko; L.E. Rodriguez-Saona; P. Bonello

2017-01-01

A strong focus on tree germplasm that can resist threats such as non-native insects and pathogens, or a changing climate, is fundamental for successful genetic conservation efforts. However, the unavailability of tools for rapid screening of tree germplasm for resistance to critical pathogens and insect pests is becoming an increasingly serious bottleneck. Here we...

Rapid Genetic and Epigenetic Alterations under Intergeneric Genomic Shock in Newly Synthesized Chrysanthemum morifolium × Leucanthemum paludosum Hybrids (Asteraceae)

Science.gov (United States)

Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Chen, Fadi

2014-01-01

The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5–50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses. PMID:24407856

Rapid genetic and epigenetic alterations under intergeneric genomic shock in newly synthesized Chrysanthemum morifolium x Leucanthemum paludosum hybrids (Asteraceae).

Science.gov (United States)

Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Chen, Fadi

2014-01-01

The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5-50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses.

Guises and disguises of quadratic divergences

Energy Technology Data Exchange (ETDEWEB)

Cherchiglia, A.L., E-mail: adriano@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Vieira, A.R., E-mail: arvieira@fisica.ufmg.br [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Hiller, Brigitte, E-mail: brigitte@teor.fis.uc.pt [Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, 3004-516 Coimbra (Portugal); Baêta Scarpelli, A.P., E-mail: scarpelli.apbs@dpf.gov.br [Setor Técnico-Científico, Departamento de Polícia Federal, Rua Hugo D’Antola, 95 - Lapa, São Paulo (Brazil); Sampaio, Marcos, E-mail: marcos.sampaio@durham.ac.uk [Departamento de Física, ICEx, Universidade Federal de Minas Gerais, P.O. BOX 702, 30.161-970, Belo Horizonte, MG (Brazil); Centre for Particle Theory, Department of Mathematical Sciences, Durham University, South Road Durham DH1 3LE (United Kingdom)

2014-12-15

In this contribution, we present a new perspective on the control of quadratic divergences in quantum field theory, in general, and in the Higgs naturalness problem, in particular. Our discussion is essentially based on an approach where UV divergences are parameterized, after being reduced to basic divergent integrals (BDI) in one internal momentum, as functions of a cutoff and a renormalization group scale λ. We illustrate our proposal with well-known examples, such as the gluon vacuum self energy of QCD and the Higgs decay in two photons within this approach. We also discuss frameworks in effective low-energy QCD models, where quadratic divergences are indeed fundamental.

Genetic divergence among Psidium accessions based on biochemical and agronomic variables

Directory of Open Access Journals (Sweden)

Carlos Antonio Fernandes Santos

2011-01-01

Full Text Available Sixty-nine Psidium accessions collected in six Brazilian states were analyzed by two non-hierarchical clusteringmethods and principal components (PC, to provide orientation for breeding programs. The variables ascorbic acid, b-carotene,lycopene, total phenols, total flavonoids, antioxidant activity, titrable acidity, soluble solids, total soluble sugars, moisture content,lateral and transversal fruit diameter, fruit pulp and seed weighs, and plant fruit number and weight were analyzed. Specific groups were observed for the araçazeiros accessions, by the Tocher and the k-means methods, as well as by the three-dimensionaldispersion of the four PCs. The clustering separated accessions of araçazeiros from the guava. There was no specific grouping interms of States of origin, indicating the absence of barriers in the guava propagation accessions. Analyses suggested the collectionof a greater number of guava germplasm samples from a smaller number of regions and divergent accessions with high nutritionalcompound levels to develop new cultivars.

Computer recognition of divergences in Feynman graphs

Energy Technology Data Exchange (ETDEWEB)

Calmet, J

1973-05-01

The program described recognizes whether or not a graph is divergent. It determines the kind of the divergences found: vacuum polarizations, electron self energies and vertices. it does not consider infrared divergences. The programming language used is REDUCE. A LISP version is also available. The nature of the divergences and their counter terms was extensively used to write down this program, therefore it is limited to the case of quantum electrodynamics. (auth)

Sexual imprinting on ecologically divergent traits leads to sexual isolation in sticklebacks.

Science.gov (United States)

Kozak, Genevieve M; Head, Megan L; Boughman, Janette W

2011-09-07

During sexual imprinting, offspring learn parental phenotypes and then select mates who are similar to their parents. Imprinting has been thought to contribute to the process of speciation in only a few rare cases; this is despite imprinting's potential to generate assortative mating and solve the problem of recombination in ecological speciation. If offspring imprint on parental traits under divergent selection, these traits will then be involved in both adaptation and mate preference. Such 'magic traits' easily generate sexual isolation and facilitate speciation. In this study, we show that imprinting occurs in two ecologically divergent stickleback species (benthics and limnetics: Gasterosteus spp.). Cross-fostered females preferred mates of their foster father's species. Furthermore, imprinting is essential for sexual isolation between species; isolation was reduced when females were raised without fathers. Daughters imprinted on father odour and colour during a critical period early in development. These traits have diverged between the species owing to differences in ecology. Therefore, we provide the first evidence that imprinting links ecological adaptation to sexual isolation between species. Our results suggest that imprinting may facilitate the evolution of sexual isolation during ecological speciation, may be especially important in cases of rapid diversification, and thus play an integral role in the generation of biodiversity.

Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event.

Science.gov (United States)

Plath, Martin; Hermann, Bernd; Schröder, Christiane; Riesch, Rüdiger; Tobler, Michael; García de León, Francisco J; Schlupp, Ingo; Tiedemann, Ralph

2010-08-23

Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations

GENETIC, PATHOGENIC AND TOXIGENIC VARIABILITY OF F

African Journals Online (AJOL)

Vesna Krnjaja

2012-03-08

Mar 8, 2012 ... The same authors concluded that natural populations of F. proliferatum in Iran were probably genetically divergent and included isolates representing a potential risk for disease development. Elmer (1991) and Elmer et al. (1999) collected 110 and. 77 isolates of F. proliferatum from asparagus originating.

Phenotypic divergence along geographic gradients reveals potential for rapid adaptation of the White-nose Syndrome pathogen, Pseudogymnoascus destructans, in North America.

Science.gov (United States)

Forsythe, Adrian; Giglio, Victoria; Asa, Jonathan; Xu, Jianping

2018-06-18

White-nose Syndrome (WNS) is an ongoing epizootic affecting multiple species of North American bats, caused by epidermal infections of the psychrophilic filamentous fungus, Pseudogymnoascus destructans Since its introduction from Europe, WNS has spread rapidly across eastern North America and resulted in high mortality rates in bats. At present, the mechanisms behind its spread and the extent of its adaptation to different geographic and ecological niches remain unknown. The objective of this study was to examine the geographic patterns of phenotypic variation and the potential evidence for adaptation among strains representing broad geographic locations in eastern North America. The morphological features of these strains were evaluated on artificial medium, and the viability of asexual arthroconidia of representative strains were investigated after storage at high (23°C), moderate (14°C), and low (4°C) temperatures at different lengths of times. Our analyses identified evidence for a geographic pattern of colony morphology changes among the clonal descendants of the fungus, with trait values correlated with increased distance from the epicenter of WNS. Our genomic comparisons of three representative isolates revealed novel genetic polymorphisms and suggested potential candidate mutations that might be related to some of the phenotypic changes. These results show that even though this pathogen arrived in North America only recently and reproduces asexually, there has been substantial evolution and phenotypic diversification during its rapid clonal expansion. Importance The causal agent of White-nose Syndrome in bats is Pseudogymnoascus destructans , a filamentous fungus recently introduced from its native range in Europe. Infections caused by P. destructans have progressed across the eastern parts of Canada and the United States over the last ten years. It is not clear how the disease is spread as the pathogen is unable to grow above 23°C and ambient

Properties of classical and quantum Jensen-Shannon divergence

NARCIS (Netherlands)

J. Briët (Jop); P. Harremoës (Peter)

2009-01-01

htmlabstractJensen-Shannon divergence (JD) is a symmetrized and smoothed version of the most important divergence measure of information theory, Kullback divergence. As opposed to Kullback divergence it determines in a very direct way a metric; indeed, it is the square of a metric. We consider a

Rapidity resummation for B-meson wave functions

Directory of Open Access Journals (Sweden)

Shen Yue-Long

2014-01-01

Full Text Available Transverse-momentum dependent (TMD hadronic wave functions develop light-cone divergences under QCD corrections, which are commonly regularized by the rapidity ζ of gauge vector defining the non-light-like Wilson lines. The yielding rapidity logarithms from infrared enhancement need to be resummed for both hadronic wave functions and short-distance functions, to achieve scheme-independent calculations of physical quantities. We briefly review the recent progress on the rapidity resummation for B-meson wave functions which are the key ingredients of TMD factorization formulae for radiative-leptonic, semi-leptonic and non-leptonic B-meson decays. The crucial observation is that rapidity resummation induces a strong suppression of B-meson wave functions at small light-quark momentum, strengthening the applicability of TMD factorization in exclusive B-meson decays. The phenomenological consequence of rapidity-resummation improved B-meson wave functions is further discussed in the context of B → π transition form factors at large hadronic recoil.

Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)

DEFF Research Database (Denmark)

Jacobsen, Magnus W.; Hansen, Michael Møller; Orlando, Ludovic

2012-01-01

colonized Denmark following the last glacial maximum, Bayesian Serial SimCoal analysis showed consistency with a scenario of long-term stability, resulting from a rapid initial sixfold population expansion. The findings illustrate the utility of mitogenome data for resolving recent intraspecific divergence...

Environmental and genetic factors affecting faecal worm egg counts ...

African Journals Online (AJOL)

Environmental and genetic factors affecting faecal worm egg counts in Merinos divergently selected for reproduction. ... The fixed effect of birth year x sex interaction was significant, with rams showing higher mean values for FWEC than ewes ...

Evolution under domestication: ongoing artificial selection and divergence of wild and managed Stenocereus pruinosus (Cactaceae) populations in the Tehuacán Valley, Mexico

Science.gov (United States)

Parra, Fabiola; Casas, Alejandro; Peñaloza-Ramírez, Juan Manuel; Cortés-Palomec, Aurea C.; Rocha-Ramírez, Víctor; González-Rodríguez, Antonio

2010-01-01

Background and Aims The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations. Methods Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations. Key Results Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours others than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (HE = 0·743) was higher than in wild (HE = 0·726) and cultivated (HE = 0·700) populations. Most of the genetic variation (90·58 %) occurred within populations. High gene flow (NmFST > 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations. Conclusions

Genetic divergence between two sympatric species of the Lutzomyia longipalpis complex in the paralytic gene, a locus associated with insecticide resistance and lovesong production

Directory of Open Access Journals (Sweden)

RMMA Lins

2008-11-01

Full Text Available The sandfly Lutzomyia longipalpis s.l. is the main vector of American Visceral Leishmaniasis. L. longipalpis s.l. is a species complex but until recently the existence of cryptic sibling species among Brazilian populations was a controversial issue. A fragment of paralytic (para, a voltage dependent sodium channel gene associated with insecticide resistance and courtship song production in Drosophila, was isolated and used as a molecular marker to study the divergence between two sympatric siblings of the L. longipalpis complex from Sobral, Brazil. The results revealed para as the first single locus DNA marker presenting fixed differences between the two species in this locality. In addition, two low frequency amino-acid changes in an otherwise very conserved region of the channel were observed, raising the possibility that it might be associated with incipient resistance in this vector. To the best of our knowledge, the present study represents the first population genetics analysis of insecticide resistance genes in this important leishmaniasis vector.

Genetic diversity in Monoporeia affinis at polluted and reference sites of the Baltic Bothnian Bay.

Science.gov (United States)

Guban, Peter; Wennerström, Lovisa; Elfwing, Tina; Sundelin, Brita; Laikre, Linda

2015-04-15

The amphipod Monoporeia affinis plays an important role in the Baltic Sea ecosystem as prey and as detritivore. The species is monitored for contaminant effects, but almost nothing is known about its genetics in this region. A pilot screening for genetic variation at the mitochondrial COI gene was performed in 113 individuals collected at six sites in the northern Baltic. Three coastal sites were polluted by pulp mill effluents, PAHs, and trace metals, and two coastal reference sites were without obvious connection to pollution sources. An off-coastal reference site was also included. Contaminated sites showed lower levels of genetic diversity than the coastal reference ones although the difference was not statistically significant. Divergence patterns measured as ΦST showed no significant differentiation within reference and polluted groups, but there was significant genetic divergence between them. The off-coastal sample differed significantly from all coastal sites and also showed lower genetic variation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

Science.gov (United States)

Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

2015-02-15

WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparative analysis of the full genome of Helicobacter pylori isolate Sahul64 identifies genes of high divergence.

Science.gov (United States)

Lu, Wei; Wise, Michael J; Tay, Chin Yen; Windsor, Helen M; Marshall, Barry J; Peacock, Christopher; Perkins, Tim

2014-03-01

Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to play a functional role in persistence and colonization of diverse human populations. To provide further genomic evidence in the lineage of H. pylori and to further characterize diverse strains of this pathogen in different human populations, we report the finished genome sequence of Sahul64, an H. pylori strain isolated from an indigenous Australian. Our analysis identified genes that were highly divergent compared to the 38 publically available genomes, which include genes involved in the biosynthesis and modification of lipopolysaccharide, putative prophage genes, restriction modification components, and hypothetical genes. Furthermore, the virulence-associated vacA locus is a pseudogene and the cag pathogenicity island (cagPAI) is not present. However, the genome does contain a gene cluster associated with pathogenicity, including dupA. Our analysis found that with the addition of Sahul64 to the 38 genomes, the core genome content of H. pylori is reduced by approximately 14% (∼170 genes) and the pan-genome has expanded from 2,070 to 2,238 genes. We have identified three putative horizontally acquired regions, including one that is likely to have been acquired from the closely related Helicobacter cetorum prior to speciation. Our results suggest that Sahul64, with the absence of cagPAI, highly divergent cell envelope proteins, and a predicted nontransportable VacA protein, could be more highly adapted to ancient indigenous Australian people but with lower virulence potential compared to other sequenced and cagPAI-positive H. pylori strains.

Jensen divergence based on Fisher’s information

International Nuclear Information System (INIS)

Sánchez-Moreno, P; Zarzo, A; Dehesa, J S

2012-01-01

The measure of Jensen–Fisher divergence between probability distributions is introduced and its theoretical grounds set up. This quantity, in contrast to the remaining Jensen divergences, grasps the fluctuations of the probability distributions because it is controlled by the (local) Fisher information, which is a gradient functional of the distribution. So it is appropriate and informative when studying the similarity of distributions, mainly for those having oscillatory character. The new Jensen–Fisher divergence shares with the Jensen–Shannon divergence the following properties: non-negativity, additivity when applied to an arbitrary number of probability densities, symmetry under exchange of these densities, vanishing under certain conditions and definiteness even when these densities present non-common zeros. Moreover, the Jensen–Fisher divergence is shown to be expressed in terms of the relative Fisher information as the Jensen–Shannon divergence does in terms of the Kullback–Leibler or relative Shannon entropy. Finally, the Jensen–Shannon and Jensen–Fisher divergences are compared for the following three large, non-trivial and qualitatively different families of probability distributions: the sinusoidal, generalized gamma-like and Rakhmanov–Hermite distributions, which are closely related to the quantum-mechanical probability densities of numerous physical systems. (paper)

Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean.

Science.gov (United States)

Davies, S W; Treml, E A; Kenkel, C D; Matz, M V

2015-01-01

Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo-West Pacific, is the centre of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we characterized the population genetic structure of two ecologically important congeneric species of reef-building corals across greater Micronesia, from Palau to the Marshall Islands. Genetic divergences between islands followed an isolation-by-distance pattern, with Acropora hyacinthus exhibiting greater genetic divergences than A. digitifera, suggesting different migration capabilities or different effective population sizes for these closely related species. We inferred dispersal distance using a biophysical larval transport model, which explained an additional 15-21% of the observed genetic variation compared to between-island geographical distance alone. For both species, genetic divergence accumulates and genetic diversity diminishes with distance from the Coral Triangle, supporting the hypothesis that Micronesian islands act as important stepping stones connecting the central Pacific with the species-rich Coral Triangle. However, for A. hyacinthus, the species with lower genetic connectivity, immigration from the subequatorial Pacific begins to play a larger role in shaping diversity than input from the Coral Triangle. This work highlights the enormous dispersal potential of broadcast-spawning corals and identifies the biological and physical drivers that influence coral genetic diversity on a regional scale. © 2014 John Wiley & Sons Ltd.

Journal of Genetics | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Genetics; Volume 94; Issue 4. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. Subhash C. Lakhotia. Review Article, Special section in honour of Mary F. Lyon Volume 94 Issue 4 ...

Evaluation of genetic diversity among soybean (Glycine max) genotypes using univariate and multivariate analysis.

Science.gov (United States)

Oliveira, M M; Sousa, L B; Reis, M C; Silva Junior, E G; Cardoso, D B O; Hamawaki, O T; Nogueira, A P O

2017-05-31

The genetic diversity study has paramount importance in breeding programs; hence, it allows selection and choice of the parental genetic divergence, which have the agronomic traits desired by the breeder. This study aimed to characterize the genetic divergence between 24 soybean genotypes through their agronomic traits, using multivariate clustering methods to select the potential genitors for the promising hybrid combinations. Six agronomic traits evaluated were number of days to flowering and maturity, plant height at flowering and maturity, insertion height of the first pod, and yield. The genetic divergence evaluated by multivariate analysis that esteemed first the Mahalanobis' generalized distance (D 2 ), then the clustering using Tocher's optimization methods, and then the unweighted pair group method with arithmetic average (UPGMA). Tocher's optimization method and the UPGMA agreed with the groups' constitution between each other, the formation of eight distinct groups according Tocher's method and seven distinct groups using UPGMA. The trait number of days for flowering (45.66%) was the most efficient to explain dissimilarity between genotypes, and must be one of the main traits considered by the breeder in the moment of genitors choice in soybean-breeding programs. The genetic variability allowed the identification of dissimilar genotypes and with superior performances. The hybridizations UFU 18 x UFUS CARAJÁS, UFU 15 x UFU 13, and UFU 13 x UFUS CARAJÁS are promising to obtain superior segregating populations, which enable the development of more productive genotypes.

Verbal and visual divergent thinking in aging.

Science.gov (United States)

Palmiero, Massimiliano; Nori, Raffaella; Piccardi, Laura

2017-04-01

According to the peak and decline model divergent thinking declines at a specific age (in or after middle age). However, if divergent thinking declines steadily in aging still has to be clarified. In order to explore the age-related changes in verbal and visual divergent thinking, in the present study a sample of 159 participants was divided in five age groups: young adults (18-35 years), middle-aged adults (36-55), young old (56-74), old (75-85) and the oldest-old (86-98). Two divergent thinking tasks were administered: the alternative uses for cardboard boxes, aimed at assessing verbal ideational fluency, flexibility and originality; the completion drawing task, aimed at assessing visual ideational fluency, flexibility and originality. Results showed that after peaking in the young adult group (20-35 years) all components of verbal and visual divergent thinking stabilized in the middle-aged adult group (36-55 years) and then started declining in the young old group (56-75). Interestingly, all components were found to be preserved after declining. Yet, verbal and visual divergent thinking were found at the same extent across age groups, with the exception of visual ideational fluency, that was higher in the young old group, the old group and the oldest-old group than verbal ideational fluency. These results support the idea that divergent thinking does not decline steadily in the elderly. Given that older people can preserve to some extent verbal and visual divergent thinking, these findings have important implications for active aging, that is, divergent thinking might be fostered in aging in order to prevent the cognitive decline.

Quadratic divergences and dimensional regularisation

International Nuclear Information System (INIS)

Jack, I.; Jones, D.R.T.

1990-01-01

We present a detailed analysis of quadratic and quartic divergences in dimensionally regulated renormalisable theories. We perform explicit three-loop calculations for a general theory of scalars and fermions. We find that the higher-order quartic divergences are related to the lower-order ones by the renormalisation group β-functions. (orig.)

Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences.

Science.gov (United States)

Guo, Guo-Ye; Chen, Fang; Shi, Xiao-Dong; Tian, Yin-Shuai; Yu, Mao-Qun; Han, Xue-Qin; Yuan, Li-Chun; Zhang, Ying

2016-01-01

Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Does rapid genetic counseling and testing in newly diagnosed breast cancer patients cause additional psychosocial distress? Results from a randomized clinical trial

NARCIS (Netherlands)

Wevers, M.R.; Ausems, M.G.E.M.; Verhoef, S.; Bleiker, E.M.A.; Hahn, D.E.E.; Brouwer, T.; Hogervorst, F.B.L.; van der Luijt, R.B.; van Dalen, T.; Theunissen, E.B.; van Ooijen, B.; de Roos, M.A.; Borgstein, P.J.; Vrouenraets, B.C.; Vriens, E.; Bouma, W.H.; Rijna, H.; Vente, J.P.; Kieffer, J.M.; Valdimarsdottir, H.B.; Rutgers, E.J.Th.; Witkamp, A.J.; Aaronson, N.K.

2016-01-01

Purpose: Female breast cancer patients carrying a BRCA1/2 mutation have an increased risk of second primary breast cancer. Rapid genetic counseling and testing (RGCT) before surgery may influence choice of primary surgical treatment. In this article, we report on the psychosocial impact of RGCT.

All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza.

Science.gov (United States)

Huang, Zhongyun; Young, Nelson D; Reagon, Michael; Hyma, Katie E; Olsen, Kenneth M; Jia, Yulin; Caicedo, Ana L

2017-06-01

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the 'agricultural weed syndrome', making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the USA, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genomewide divergence scans between weed groups from the USA and South Asia, and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed-crop pairs, but are not shared among all weed-crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms. © 2017 John Wiley & Sons Ltd.

Population divergence in venom bioactivities of elapid snake Pseudonaja textilis: role of procoagulant proteins in rapid rodent prey incapacitation.

Directory of Open Access Journals (Sweden)

Jure Skejić

Full Text Available This study looked at how toxic proteins in venoms of adult Australian eastern Brown snakes Pseudonaja textilis from South Australian and Queensland populations interact with physiological functions of the lab SD rat Rattus norvegicus. Circulatory collapse and incoagulable blood occurred instantly after injection of venom under the dorsal skin of anaesthetised and mechanically ventilated rats in an imitation of a P. textilis bite. Intravenous injection of purified P. textilis (Mackay, QLD venom prothrombin activator proteins caused instant failure of circulation, testifying of high toxicity of these proteins and suggesting their role in rapid incapacitation of rodent prey. The hypothesis is further supported by circulatory collapse occurring instantly despite artificial respiration in envenomed rats and the finding of extremely high venom procoagulant potency in rat plasma. LC-MS and physiology assays revealed divergent venom composition and biological activity of South Australian (Barossa locality and Queensland (Mackay locality populations, which may be driven by selection for different prey. The Queensland venom of P. textilis was found to be more procoagulant and to exhibit predominately presynaptic neurotoxicity, while the South Australian venom contained diverse postsynaptic type II and III α-neurotoxins in addition to the presynaptic neurotoxins and caused significantly faster onset of neuromuscular blockade in the rat phrenic nerve-diaphragm preparation. LC-MS analysis found evidence of multiple coagulation factor X-like proteins in P. textilis venoms, including a match to P. textilis coagulation factor X isoform 2, previously known to be expressed only in the liver.

Genetics researchers’ and iRB professionals’ attitudes toward genetic research review: a comparative analysis

Science.gov (United States)

Edwards, Karen L.; Lemke, Amy A.; Trinidad, Susan B.; Lewis, Susan M.; Starks, Helene; Snapinn, Katherine W.; Griffin, Mary Quinn; Wiesner, Georgia L.; Burke, Wylie

2012-01-01

Purpose Genetic research involving human participants can pose challenging questions related to ethical and regulatory standards for research oversight. However, few empirical studies describe how genetic researchers and institutional review board (IRB) professionals conceptualize ethical issues in genetic research or where common ground might exist. Methods Parallel online surveys collected information from human genetic researchers (n = 351) and IRB professionals (n = 208) regarding their views about human participant oversight for genetic protocols. Results A range of opinions were observed within groups on most issues. In both groups, a minority thought it likely that people would be harmed by participation in genetic research or identified from coded genetic data. A majority of both groups agreed that reconsent should be required for four of the six scenarios presented. Statistically significant differences were observed between groups on some issues, with more genetic researcher respondents trusting the confidentiality of coded data, fewer expecting harms from reidentification, and fewer considering reconsent necessary in certain scenarios. Conclusions The range of views observed within and between IRB and genetic researcher groups highlights the complexity and unsettled nature of many ethical issues in genome research. Our findings also identify areas where researcher and IRB views diverge and areas of common ground. PMID:22241102

Genetic characterization of natural populations of pineapple guava (Acca sellowiana, with heterologous microsatellites markers

Directory of Open Access Journals (Sweden)

Karine Louise dos Santos

2011-12-01

Full Text Available Pineapple guava (Acca sellowiana is a native species from south Brazil and northeast Uruguay, and due to the unique flavor of its fruits, it is an income-generating alternative to small farmers. Knowledge on genetic diversity is an important tool for genetic improvement and conservation. Aiming to increase the knowledge with regarde to the species genetic diversity, fi ve natural populations of A. sellowiana were analyzed through microsatellites markers developed from Eucalyptus grandis W. Hill ex Maiden x E. urophylla S.T. Blake complex. Using 10 pairs of selected markers, 122 plants were characterized. The mean values for expected and observed heterozigosity were 0.42 and 0.47, respectively. The fˆ estimates did not differ from zero to four out of the five populations evaluated, suggesting a small inbreeding effect. In addition, private alleles and high genetic divergence was observed. the average genetic divergence among the populations was st Fˆ = 0,13 e st Rˆ = 0,14, mostly due to the incidenceof rare or exclusive alleles among some populations.

Sex chromosome turnover contributes to genomic divergence between incipient stickleback species.

Directory of Open Access Journals (Sweden)

Kohta Yoshida

2014-03-01

Full Text Available Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.

An experimental test of alternative population augmentation scenarios.

Science.gov (United States)

Kronenberger, John A; Gerberich, Jill C; Fitzpatrick, Sarah W; Broder, E Dale; Angeloni, Lisa M; Funk, W Chris

2018-01-19

Human land use is fragmenting habitats worldwide and inhibiting dispersal among previously connected populations of organisms, often leading to inbreeding depression and reduced evolutionary potential in the face of rapid environmental change. To combat this augmentation of isolated populations with immigrants is sometimes used to facilitate demographic and genetic rescue. Augmentation with immigrants that are genetically and adaptively similar to the target population effectively increases population fitness, but if immigrants are very genetically or adaptively divergent, augmentation can lead to outbreeding depression. Despite well-cited guidelines for the best practice selection of immigrant sources, often only highly divergent populations remain, and experimental tests of these riskier augmentation scenarios are essentially nonexistent. We conducted a mesocosm experiment with Trinidadian guppies (Poecilia reticulata) to test the multigenerational demographic and genetic effects of augmenting 2 target populations with 3 types of divergent immigrants. We found no evidence of demographic rescue, but we did observe genetic rescue in one population. Divergent immigrant treatments tended to maintain greater genetic diversity, abundance, and hybrid fitness than controls that received immigrants from the source used to seed the mesocosms. In the second population, divergent immigrants had a slightly negative effect in one treatment, and the benefits of augmentation were less apparent overall, likely because this population started with higher genetic diversity and a lower reproductive rate that limited genetic admixture. Our results add to a growing consensus that gene flow can increase population fitness even when immigrants are more highly divergent and may help reduce uncertainty about the use of augmentation in conservation. © 2018 Society for Conservation Biology.

Habitat fragmentation causes rapid genetic differentiation and ...

African Journals Online (AJOL)

... city buildings. These results were supported by multiple statistical analyses including Mantel's test, PCOORDA and AMOVA. Genetic enrichment and epigenetic variation studies can be included in habitat fragmentation analysis and its implications in inducing homogenization and susceptibility in natural plant populations.

Worldwide genetic differentiation in the common fouling barnacle, Amphibalanus amphitrite

KAUST Repository

Chen, Hsi-Nien; Tsang, Ling Ming; Chong, Ving Ching; Chan, Benny K.K.

2014-01-01

differentiation in A. amphitrite from 25 localities around the world were investigated. The results revealed three clades within A. amphitrite with a genetic divergence of ~ 4% among clades, whereas there were no diagnostic morphological differences among clades

Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow.

Science.gov (United States)

Sachdeva, Himani; Barton, Nicholas H

2017-06-01

Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.