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Evren, Özay Hasan, Ertuǧrul Yüzbaşıoǧlu, and Mehmet Yaşar Dadandı. "Determination of intra-specific genetic variation of Phlomis kurdica and Phlomis oppositiflora and investigation for the hybridity of P. x melitenense (Lamiaceae) by means of molecular markers." Biologia 70, no. 9 (September 1, 2015): 1159–71. http://dx.doi.org/10.1515/biolog-2015-0132.
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Abstract In this study, intra-specific genetic variation and inter-specific genetic relation were investigated among Phlomis oppositiflora, P. kurdica, P. × melitenense (P. kurdica × oppositiflora), P. capitata and P. kurdica × capitata by using RAPD and ISSR markers. The hybridity of P. × melitenense and P. kurdica × capitata samples was also surveyed in terms of morphological and molecular aspects. Except for two, all bands obtained from RAPD (707 bands) and ISSR (651 bands) analyses were polymorphic. The lowest genetic distance values obtained from RAPD and ISSR analyses were 0.0156 (between P. × melitenense and P. kurdica) and 0.0142 (between P. × melitenense and P. kurdica) respectively. The highest genetic distance values obtained from RAPD and ISSR analyses were 0.0866 (between P. kotschyana and P. oppositiflora) and 0.1237 (between P. kotschyana and P. kurdica × capitata) respectively. While P. kurdica indicated the highest genetic diversity (H = 0.1572; I = 0.2646) in RAPD analysis, P. capitata displayed the highest genetic diversity (H = 0.1403; I = 0.2329) in ISSR analysis. AMOVA results showed that 86% and 75% of the total variance resided within groups based on RAPD and ISSR markers, respectively. Based on the RAPD and ISSR results, both P. × melitenense and P. kurdica × capitata samples inherited species specific bands from their parental species, which confirms their hybridity. Although both P. × melitenense and P. kurdica × capitata hybrids showed a morphological mosaic between their parental phenotypes in terms of the majority of the quantitative characters examined, P. × melitenense and P. kurdica × capitata exceeded their parental phenotypes in terms of the three and 11 quantitative characters respectively. MANOVA results from the morphological data showed significant distinction among P. kurdica, P. oppositiflora, P. × melitenense, P. capitata and P. kurdica × capitata (Wilks’ Lambda = 0.003; df = 112; P < 0.01). Average pollen fertilities of P. oppositiflora, P. × melitenense, P. capitata, P. kurdica and P. kurdica × capitata were 93.44%, 68.42%, 93.28 %, 90.12% and 92.77% respectively.
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Kehayias, George. "Spatial and temporal variation of Branchiostoma lanceolatum larvae (Cephalochordata) in a hypoxic bay." Biologia 70, no. 9 (September 1, 2015): 1234–44. http://dx.doi.org/10.1515/biolog-2015-0140.
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Abstract A 12-month zooplankton survey (September 2008 to August 2009) in the hypoxic, stratified and seasonally eutrophic Amvrakikos Gulf (western Greece) revealed the presence of larvae of the Cephalochordate Branchiostoma lanceolatum. The larvae were found at almost all sampling occasions, except September and February, and presented their peak of abundance in April (426.8 ind. m−3). The oxygen depletion in the water column affected their vertical and horizontal distribution. Thus, their abundance was greater in the subsurface layers (10-20 m) which corresponds to the well oxygenated thermocline layer. An east to west increase of their abundance in the deeper layers was associated with the severity of oxygen depletion. The lower oxygen limit for their presence seems to have been 2 mg L−1 which corresponds to hypoxia. A size-specific depth distribution was noticed, with larger larvae residing in deeper strata. A diel vertical migration of the larvae in the summer was recorded, with a night ascent in shallower depths and a day descent in deeper strata. There was an apparent coexistence in space and time between the larvae and the dinoflagellate Ceratium sp., though this could not indicate a trophic interrelation between them due to the large size of the latter. The results suggest that, during their planktonic stage, the larvae utilize the water stratification within the Amvrakikos Gulf by inhabiting the depths within or close to the thermocline, where they can satisfy their oxygen and energy demands while being protected from predation.
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Sanaei, Ehsan, Marjan Seiedy, and Farzaneh Momtazi. "A uni- and multivariate analysis approach to reveal sexual size dimorphism in Iranian populations of Hypera postica (Coleoptera: Curculionidae)." Biologia 70, no. 9 (September 1, 2015): 1228–33. http://dx.doi.org/10.1515/biolog-2015-0137.
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Abstract Body size dimorphism between genders is a commonly observed phenomenon in insects, usually manifested in larger female body size. Sexual Size Dimorphism (SSD) varies from species to species, the degree and direction influenced by certain evolutionary pressures. Intraspecific variation in SSD may also occur between populations. The Hypera postica (Gyllenhal, 1813) is a well-known alfalfa plant pest that shows a degree of morphological divergence in its populations. The female alfalfa weevils are very fecund and have a larger body size compared to males. To improve our knowledge on magnitude and direction of SSD in alfalfa weevil, we studied 200 specimens of H. postica from four Iranian populations (Karaj1, Karaj2, Tuyserkan and Jovein). 10 morphological variables from three external anatomic parts (pronotum, elytra and rostrum) and 45 ratio characters were statistically analyzed in order to determine the amount of SSD in Iranian populations. In addition we investigated for morphological divergence pattern in mentioned populations. The results of this study show that a low degree of morphological divergence occurs in Iranian populations. Measured variables indicate that the SSD pattern of H. postica is compatible with the Rensch’s rule, and is related to high fecundity of females and a lack of strong sexual selection. Also it is mentioned that the larger rostrum in females may correspond to its unique role in egg laying.
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Prince, Véronique, Anne-Marie Simao-Beaunoir, and Carole Beaulieu. "Amplified ribosomal DNA restriction analysis of free-living bacteria present in the headbox of a Canadian paper machine." Canadian Journal of Microbiology 55, no. 7 (July 2009): 810–17. http://dx.doi.org/10.1139/w09-036.
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The headbox water is the main source of bacterial contamination of paper machines. Identification of these bacterial contaminants could be an asset in developing specific control methods. An amplified ribosomal DNA restriction analysis (ARDRA) was carried out to characterize the bacterial communities associated with the headbox water of a paper machine in a Canadian mill in February and July 2006. Eight bacterial genera were identified as the main colonizers present in the headbox water. The genus Meiothermus appeared to be the dominant bacterial group in the Canadian paper machine. Some variation was observed between the February and July clone libraries. Bacterial genera such as Chelatococcus and Hydrogenophilus were only detected in February or in July, respectively. Furthermore, the proportion of Tepidimonas clones in the libraries was higher in July than in February. The metabolic profile of the February and July communities, determined using Biolog EcoPlates, also suggested that temporal variation occurred within the bacterial populations that colonized the headbox of the paper machine.
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Gadagkar, Sudhindra R. "PhyloM: A Computer Program for Phylogenetic Inference from Measurement or Binary Data, with Bootstrapping." Life 12, no. 5 (May 11, 2022): 719. http://dx.doi.org/10.3390/life12050719.
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Quantitative and binary results are ubiquitous in biology. Inasmuch as an underlying genetic basis for the observed variation in these observations can be assumed, it is pertinent to infer the evolutionary relationships among the entities being measured. I present a computer program, PhyloM, that takes measurement data or binary data as input, using which, it directly generates a pairwise distance matrix that can then be subjected to the popular neighbor-joining (NJ) algorithm to produce a phylogenetic tree. PhyloM also has the option of nonparametric bootstrapping for testing the level of support for the inferred phylogeny. Finally, PhyloM also allows the user to root the tree on any desired branch. PhyloM was tested on Biolog Gen III growth data from isolates within the genus Chromobacterium and the closely related Aquitalea sp. This allowed a comparison with the genotypic tree inferred from whole-genome sequences for the same set of isolates. From this comparison, it was possible to infer parallel evolution. PhyloM is a stand-alone and easy-to-use computer program with a user-friendly graphical user interface that computes pairwise distances from measurement or binary data, which can then be used to infer phylogeny using NJ using a utility in the same program. Alternatively, the distance matrix can be downloaded for use in another program for phylogenetic inference or other purposes. It does not require any software to be installed or computer code written and is open source. The executable and computer code are available on GitHub.
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Warren, William J., Randall M. Jeter, Robert C. Kimbrough, and John C. Zak. "Population patterns and antimicrobial resistance ofAeromonasin urban playa lakes." Canadian Journal of Microbiology 50, no. 6 (June 1, 2004): 397–404. http://dx.doi.org/10.1139/w04-029.
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Bacteria belonging to the genus Aeromonas are indigenous to aquatic environments. Once regarded as unimportant human pathogens, reports of opportunistic infections caused by these organisms have appeared increasingly in the medical literature. To estimate the potential for human infection by Aeromonas where limited water resources are being used intensively, we studied the spatial and temporal variation and incidence of antimicrobial resistance among environmental isolates of Aeromonas from two urban playa lakes in Lubbock, Texas. Aeromonas population densities varied seasonally, with the highest densities occurring from mid-April to late October. The greatest range of densities was 100-fold, from 2.50 to 255.17 colony-forming units per 0.1 mL of water sample. Densities also varied with water depth, although the variation did not display a consistent pattern. One hundred fifty-one Aeromonas isolates were divided into 10 species or subspecies groups by using the BIOLOG identification system. Nine isolates displayed resistance to co-trimoxazole, tetracycline, and cefuroxime, and none was resistant to more than one of these antimicrobial agents. In summary, the results of this study showed that the densities of Aeromonas peak in the late spring and again in late summer, times when human activity around the playa lakes is also high. Thus, we infer that human exposure to these potential pathogens varies seasonally. Compared to other published studies, the incidence of antimicrobial-resistant Aeromonas is relatively low in urban playa lakes in Lubbock, Texas. Nevertheless, resistant organisms were detected.Key words: Aeromonas, water, playa, antibiotic resistance, population dynamics.
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Charlesworth, Deborah, Nicholas H. Barton, and Brian Charlesworth. "The sources of adaptive variation." Proceedings of the Royal Society B: Biological Sciences 284, no. 1855 (May 31, 2017): 20162864. http://dx.doi.org/10.1098/rspb.2016.2864.
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The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis . Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.
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Wielbo, Jerzy, Monika Marek-Kozaczuk, Agnieszka Kubik-Komar, and Anna Skorupska. "Increased metabolic potential of Rhizobium spp. is associated with bacterial competitiveness." Canadian Journal of Microbiology 53, no. 8 (August 2007): 957–67. http://dx.doi.org/10.1139/w07-053.
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Of 105 rhizobial isolates obtained from nodules of commonly cultivated legumes, we selected 19 strains on the basis of a high rate of symbiotic plant growth promotion. Individual strains within the species Rhizobium leguminosarum bv. trifolii , R. leguminosarum bv. viciae , and Rhizobium etli displayed variation not only in plasmid sizes and numbers but also in the chromosomal 16S–23S internal transcribed spacer. The strains were tagged with gusA gene and their competitiveness was examined in relation to an indigenous population of rhizobia under greenhouse conditions. A group of 9 strains was thus isolated that were competitive in relation to native rhizobia in pot experiments. Nineteen selected competitive and uncompetitive strains were examined with respect to their ability to utilize various carbon and energy sources by means of commercial Biolog GN2 microplate test. The ability of the selected strains to metabolize a wide range of nutrients differed markedly and the competitive strains were able to utilize more carbon and energy sources than uncompetitive ones. A major difference concerned the utilization of amino and organic acids, which were metabolized by most of the competitive and only a few uncompetitive strains, whereas sugars and their derivatives were commonly utilized by both groups of strains. A statistically significant correlation between the ability to metabolize a broad range of substrates and nodulation competitiveness was found, indicating that metabolic properties may be an essential trait in determining the competitiveness of rhizobia.
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Taylor, John W., David M. Geiser, Austin Burt, and Vassiliki Koufopanou. "The Evolutionary Biology and Population Genetics Underlying Fungal Strain Typing." Clinical Microbiology Reviews 12, no. 1 (January 1, 1999): 126–46. http://dx.doi.org/10.1128/cmr.12.1.126.
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SUMMARY Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.
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Karczewski, Konrad J., and Alicia R. Martin. "Analytic and Translational Genetics." Annual Review of Biomedical Data Science 3, no. 1 (July 20, 2020): 217–41. http://dx.doi.org/10.1146/annurev-biodatasci-072018-021148.
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Understanding the influence of genetics on human disease is among the primary goals for biology and medicine. To this end, the direct study of natural human genetic variation has provided valuable insights into human physiology and disease as well as into the origins and migrations of humans. In this review, we discuss the foundations of population genetics, which provide a crucial context to the study of human genes and traits. In particular, genome-wide association studies and similar methods have revealed thousands of genetic loci associated with diseases and traits, providing invaluable information into the biology of these traits. Simultaneously, as the study of rare genetic variation has expanded, so-called human knockouts have elucidated the function of human genes and the therapeutic potential of targeting them.
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Sanders, Ian R. "Intraspecific genetic variation in arbuscular mycorrhizal fungi and its consequences for molecular biology, ecology, and development of inoculum." Canadian Journal of Botany 82, no. 8 (August 1, 2004): 1057–62. http://dx.doi.org/10.1139/b04-094.
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It has been known for some time that different arbuscular mycorrhizal fungal (AMF) taxa confer differences in plant growth. Although genetic variation within AMF species has been given less attention, it could potentially be an ecologically important source of variation. Ongoing studies on variability in AMF genes within Glomus intraradices indicate that at least for some genes, such as the BiP gene, sequence variability can be high, even in coding regions. This suggests that genetic variation within an AMF may not be selectively neutral. This clearly needs to be investigated in more detail for other coding regions of AMF genomes. Similarly, studies on AMF population genetics indicate high genetic variation in AMF populations, and a considerable amount of variation seen in phenotypes in the population can be attributed to genetic differences among the fungi. The existence of high within-species genetic variation could have important consequences for how investigations on AMF gene expression and function are conducted. Furthermore, studies of within-species genetic variability and how it affects variation in plant growth will help to identify at what level of precision ecological studies should be conducted to identify AMF in plant roots in the field. A population genetic approach to studying AMF genetic variability can also be useful for inoculum development. By knowing the amount of genetic variability in an AMF population, the maximum and minimum numbers of spores that will contain a given amount of genetic diversity can be estimated. This could be particularly useful for developing inoculum with high adaptability to different environments.Key words: arbuscular mycorrhizas, symbiosis, genomics, genetic diversity, population genetics, evolutionary ecology.
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Jablonka, Eva, and Marion J. Lamb. "Précis of Evolution in Four Dimensions." Behavioral and Brain Sciences 30, no. 4 (August 2007): 353–65. http://dx.doi.org/10.1017/s0140525x07002221.
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AbstractIn his theory of evolution, Darwin recognized that the conditions of life play a role in the generation of hereditary variations, as well as in their selection. However, as evolutionary theory was developed further, heredity became identified with genetics, and variation was seen in terms of combinations of randomly generated gene mutations. We argue that this view is now changing, because it is clear that a notion of hereditary variation that is based solely on randomly varying genes that are unaffected by developmental conditions is an inadequate basis for evolutionary theories. Such a view not only fails to provide satisfying explanations of many evolutionary phenomena, it also makes assumptions that are not consistent with the data that are emerging from disciplines ranging from molecular biology to cultural studies. These data show that the genome is far more responsive to the environment than previously thought, and that not all transmissible variation is underlain by genetic differences. In Evolution in Four Dimensions (2005) we identify four types of inheritance (genetic, epigenetic, behavioral, and symbol-based), each of which can provide variations on which natural selection will act. Some of these variations arise in response to developmental conditions, so there are Lamarckian aspects to evolution. We argue that a better insight into evolutionary processes will result from recognizing that transmitted variations that are not based on DNA differences have played a role. This is particularly true for understanding the evolution of human behavior, where all four dimensions of heredity have been important.
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Rowntree, Jennifer K., David M. Shuker, and Richard F. Preziosi. "Forward from the crossroads of ecology and evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1569 (May 12, 2011): 1322–28. http://dx.doi.org/10.1098/rstb.2010.0357.
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Community genetics is a synthesis of community ecology and evolutionary biology. It examines how genetic variation within a species affects interactions among species to change ecological community structure and diversity. The use of community genetics approaches has greatly expanded in recent years and the evidence for ecological effects of genetic diversity is growing. The goal of current community genetics research is to determine the circumstances in which, and the mechanisms by which community genetic effects occur and is the focus of the papers in this special issue. We bring a new group of researchers into the community genetics fold. Using a mixture of empirical research, literature reviews and theoretical development, we introduce novel concepts and methods that we hope will enable us to develop community genetics into the future.
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Koornneef, Maarten. "A Central Role for Genetics in Plant Biology." Annual Review of Plant Biology 72, no. 1 (June 17, 2021): 1–16. http://dx.doi.org/10.1146/annurev-arplant-071720-111039.
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This article describes my involvement in the development of genetics as an essential tool in the integrated study of plant biology. My research comes from a strong background in plant genetics based on my education as a plant breeder at Wageningen University and collaborations with plant physiologists and molecular geneticists in Wageningen and the wider scientific community. It initially involved the isolation and physiological characterization of mutants defective in biosynthesis or mode of action of plant hormones, photoreceptors and traits such as flowering time in both Arabidopsis and tomato. I also generated a genetic map of Arabidopsis. Subsequently, the exploitation of natural variation became a main area of interest, including the molecular identification of underlying genetic differences. The integration of various disciplines and the adoption of Arabidopsis as a main model species contributed strongly to the impressive progress in our knowledge of plant biology over the past 40 years.
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Breslow, J. L. "Human Apolipoprotein Molecular Biology and Genetic Variation." Annual Review of Biochemistry 54, no. 1 (June 1985): 699–727. http://dx.doi.org/10.1146/annurev.bi.54.070185.003411.
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Lemaitre, H., V. S. Mattay, F. Sambataro, B. Verchinski, R. E. Straub, J. H. Callicott, R. Kittappa, et al. "Genetic Variation in FGF20 Modulates Hippocampal Biology." Journal of Neuroscience 30, no. 17 (April 28, 2010): 5992–97. http://dx.doi.org/10.1523/jneurosci.5773-09.2010.
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Woycinck Kowalski, Thayne, Larissa Brussa Reis, Tiago Finger Andreis, Patricia Ashton-Prolla, and Clévia Rosset. "Systems Biology Approaches Reveal Potential Phenotype-Modifier Genes in Neurofibromatosis Type 1." Cancers 12, no. 9 (August 26, 2020): 2416. http://dx.doi.org/10.3390/cancers12092416.
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Neurofibromatosis type (NF1) is a syndrome characterized by varied symptoms, ranging from mild to more aggressive phenotypes. The variation is not explained only by genetic and epigenetic changes in the NF1 gene and the concept of phenotype-modifier genes in extensively discussed in an attempt to explain this variability. Many datasets and tools are already available to explore the relationship between genetic variation and disease, including systems biology and expression data. To suggest potential NF1 modifier genes, we selected proteins related to NF1 phenotype and NF1 gene ontologies. Protein–protein interaction (PPI) networks were assembled, and network statistics were obtained by using forward and reverse genetics strategies. We also evaluated the heterogeneous networks comprising the phenotype ontologies selected, gene expression data, and the PPI network. Finally, the hypothesized phenotype-modifier genes were verified by a random-walk mathematical model. The network statistics analyses combined with the forward and reverse genetics strategies, and the assembly of heterogeneous networks, resulted in ten potential phenotype-modifier genes: AKT1, BRAF, EGFR, LIMK1, PAK1, PTEN, RAF1, SDC2, SMARCA4, and VCP. Mathematical models using the random-walk approach suggested SDC2 and VCP as the main candidate genes for phenotype-modifiers.
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Wagner, Günter P. "Evolutionary Genetics: The Nature of Hidden Genetic Variation Unveiled." Current Biology 13, no. 24 (December 2003): R958—R960. http://dx.doi.org/10.1016/j.cub.2003.11.042.
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Sénéchal, Sandra, and Martin Kussmann. "Genetics Meets Proteomics: Correlating the Portuguese Water Dog Blood Serum Proteome with Genetic Markers." Proteomics Insights 4 (January 2011): PRI.S6470. http://dx.doi.org/10.4137/pri.s6470.
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Blood serum is a body fluid widely used for biomarker discovery and therefore numerous studies aim at defining its proteome. The serum proteome is subject to fluctuations resulting from biological variability (eg, diurnal variations) reflecting both healthy and/or disease-related conditions. Inter-individual differences originate partly at the genetic level and may influence clinical blood profile including the serum proteome. Therefore we investigated whether serum protein abundance is genetically determined: we report the study of a cohort of 146 Portuguese Water Dogs, a dog breed whose genetic background has been well characterized. We generated protein profiles of dog sera on 1D-gels and correlated them with microsatellite markers. We detected correlations between 7 gel bands and 11 genetic regions and developed a label-free protein quantification method to identify and quantify the proteins most accountable for serum proteome variation. An association between the abundance of RBP4 in dog serum and the adiponectin gene was detected.
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Abdul-Muneer, P. M. "Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies." Genetics Research International 2014 (April 7, 2014): 1–11. http://dx.doi.org/10.1155/2014/691759.
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Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.
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Howie, Heather L., Ariel M. Hay, Karen de Wolski, Hayley Waterman, Jenna Lebedev, Xiaoyun Fu, Rachel Culp-Hill, et al. "Differences in Steap3 expression are a mechanism of genetic variation of RBC storage and oxidative damage in mice." Blood Advances 3, no. 15 (July 26, 2019): 2272–85. http://dx.doi.org/10.1182/bloodadvances.2019000605.
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Abstract Red blood cells (RBCs) are the most numerous cell type in the body and serve a vital purpose of delivering oxygen to essentially all tissues. In addition to the central role of RBCs in health and disease, RBC storage is a requirement for the >90 million units of RBC transfusions given to millions of recipients each year, worldwide. It is well known that there is genetic donor-to-donor variability in how human RBCs store, rendering blood a nonstandardized therapeutic with a wide range of biological properties from unit to unit, by the time it is transfused. As with humans, genetic variation exists in how murine RBCs, from different strains of mice, store and perform after transfusion. The genetic mechanisms for variation, in humans and mice, both remain obscure. Combining advanced metabolomics, genetics, and molecular and cellular biology approaches, we identify genetic variation in six-transmembrane epithelial antigen of prostate 3 (Steap3) expression as a critical and previously unrecognized mechanism of oxidative damage of RBCs during storage. Increased levels of Steap3 result in degradation of cellular membrane through lipid peroxidation, leading to failure of RBC homeostasis and hemolysis/clearance of RBCs. This article is the first report of a role of Steap3 in mature RBCs; it defines a new mechanism of redox biology in RBCs with a substantial effect upon RBC function and provides a novel mechanistic determinant of genetic variation of RBC storage.
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Jakobson, Christopher M., and Daniel F. Jarosz. "What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit?" Annual Review of Genetics 54, no. 1 (November 23, 2020): 439–64. http://dx.doi.org/10.1146/annurev-genet-021920-102037.
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The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
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Storz, Jay F., Jamie T. Bridgham, Scott A. Kelly, and Theodore Garland. "Genetic approaches in comparative and evolutionary physiology." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 309, no. 3 (August 1, 2015): R197—R214. http://dx.doi.org/10.1152/ajpregu.00100.2015.
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Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology.
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Roos, D. S. "GENETICS: Themes and Variations in Apicomplexan Parasite Biology." Science 309, no. 5731 (July 1, 2005): 72–73. http://dx.doi.org/10.1126/science.1115252.
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Lazzarano, Stefano, Marek Kučka, João P. L. Castro, Ronald Naumann, Paloma Medina, Michael N. C. Fletcher, Rebecka Wombacher, et al. "Genetic mapping of species differences via in vitro crosses in mouse embryonic stem cells." Proceedings of the National Academy of Sciences 115, no. 14 (March 21, 2018): 3680–85. http://dx.doi.org/10.1073/pnas.1717474115.
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Discovering the genetic changes underlying species differences is a central goal in evolutionary genetics. However, hybrid crosses between species in mammals often suffer from hybrid sterility, greatly complicating genetic mapping of trait variation across species. Here, we describe a simple, robust, and transgene-free technique to generate “in vitro crosses” in hybrid mouse embryonic stem (ES) cells by inducing random mitotic cross-overs with the drug ML216, which inhibits the DNA helicase Bloom syndrome (BLM). Starting with an interspecific F1 hybrid ES cell line between the Mus musculus laboratory mouse and Mus spretus (∼1.5 million years of divergence), we mapped the genetic basis of drug resistance to the antimetabolite tioguanine to a single region containing hypoxanthine–guanine phosphoribosyltransferase (Hprt) in as few as 21 d through “flow mapping” by coupling in vitro crosses with fluorescence-activated cell sorting (FACS). We also show how our platform can enable direct study of developmental variation by rederiving embryos with contribution from the recombinant ES cell lines. We demonstrate how in vitro crosses can overcome major bottlenecks in mouse complex trait genetics and address fundamental questions in evolutionary biology that are otherwise intractable through traditional breeding due to high cost, small litter sizes, and/or hybrid sterility. In doing so, we describe an experimental platform toward studying evolutionary systems biology in mouse and potentially in human and other mammals, including cross-species hybrids.
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McDonald, B. A., R. E. Pettway, R. S. Chen, J. M. Boeger, and J. P. Martinez. "The population genetics of Septoria tritici (teleomorph Mycosphaerella graminicola)." Canadian Journal of Botany 73, S1 (December 31, 1995): 292–301. http://dx.doi.org/10.1139/b95-259.
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The DNA-based markers of molecular genetics were combined with the analytical tools of population genetics to learn about the population biology of the wheat pathogen Mycosphaerella graminicola. DNA-based genetic markers, including restriction fragment length polymorphisms in nuclear and mitochondrial DNA, DNA fingerprints, and electrophoretic karyotypes were used in combination to show that the amount and distribution of genetic variation within and among field populations of M. graminicola is similar around the world. Measures of gametic disequilibrium suggested that the sexual stage of reproduction has a more significant impact on the genetic structure of M. graminicola populations than asexual reproduction. A field experiment conducted over a 3-year period showed that populations had a high degree of genetic stability over time. The potential effects of selection were quantified in a cultivar mixture experiment with four wheat cultivars that varied in resistance to M. graminicola. In combination, these experiments demonstrated the utility of selectively neutral genetic markers to elucidate the population genetics of fungi. Key words: genetic diversity, wheat, gene flow, RFLPs, DNA fingerprinting.
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Balaban, Evan. "Eugenics and Individual Phenotypic Variation: To What Extent Is Biology a Predictive Science?" Science in Context 11, no. 3-4 (1998): 331–56. http://dx.doi.org/10.1017/s0269889700003069.
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The ArgumentEugenics, in whatever form it may be articulated, is based on the idea that phenotypic characteristics of particular individuals can be predicted in advance. This paper argues that biology's capacity to predict many of the characteristics exhibited by an individual, especially behavioral or cognitive attributes, will always be very limited. This stems from intrinsic limitations to the methodology for relating genotypes to phenotypes, and from the nature of developmental processes which intervene between genotypes and phenotypes. While genetic studies may generate valid population predictions for conditions which impact human health, neither genetics nor developmental biology are likely to generate useful individual predictions about variation in non-disease-related human behavioral and cognitive phenotypes in the foreseeable future.
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Powell, Jeffrey. "Genetic Variation in Insect Vectors: Death of Typology?" Insects 9, no. 4 (October 11, 2018): 139. http://dx.doi.org/10.3390/insects9040139.
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The issue of typological versus population thinking in biology is briefly introduced and defined. It is then emphasized how population thinking is most relevant and useful in vector biology. Three points are made: (1) Vectors, as they exist in nature, are genetically very heterogeneous. (2) Four examples of how this is relevant in vector biology research are presented: Understanding variation in vector competence, GWAS, identifying the origin of new introductions of invasive species, and resistance to inbreeding. (3) The existence of high levels of vector genetic heterogeneity can lead to failure of some approaches to vector control, e.g., use of insecticides and release of sterile males (SIT). On the other hand, vector genetic heterogeneity can be harnessed in a vector control program based on selection for refractoriness.
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Hütt, Marc-Thorsten. "Understanding genetic variation - the value of systems biology." British Journal of Clinical Pharmacology 77, no. 4 (March 20, 2014): 597–605. http://dx.doi.org/10.1111/bcp.12266.
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Sunyaev, Shamil R., and Frederick P. Roth. "Systems biology and the analysis of genetic variation." Current Opinion in Genetics & Development 23, no. 6 (December 2013): 599–601. http://dx.doi.org/10.1016/j.gde.2013.11.010.
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GAERTNER, BRYN E., and PATRICK C. PHILLIPS. "Caenorhabditis elegans as a platform for molecular quantitative genetics and the systems biology of natural variation." Genetics Research 92, no. 5-6 (December 2010): 331–48. http://dx.doi.org/10.1017/s0016672310000601.
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SummaryOver the past 30 years, the characteristics that have made the nematode Caenorhabditis elegans one of the premier animal model systems have also allowed it to emerge as a powerful model system for determining the genetic basis of quantitative traits, particularly for the identification of naturally segregating and/or lab-adapted alleles with large phenotypic effects. To better understand the genetic underpinnings of natural variation in other complex phenotypes, C. elegans is uniquely poised in the emerging field of quantitative systems biology because of the extensive knowledge of cellular and neural bases to such traits. However, perturbations in standing genetic variation and patterns of linkage disequilibrium among loci are likely to limit our ability to tie understanding of molecular function to a broader evolutionary context. Coupling the experimental strengths of the C. elegans system with the ecological advantages of closely related nematodes should provide a powerful means of understanding both the molecular and evolutionary genetics of quantitative traits.
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Chrispeels, H. E., M. L. Klosterman, J. B. Martin, S. R. Lundy, J. M. Watkins, C. L. Gibson, and G. K. Muday. "Undergraduates Achieve Learning Gains in Plant Genetics through Peer Teaching of Secondary Students." CBE—Life Sciences Education 13, no. 4 (December 2014): 641–52. http://dx.doi.org/10.1187/cbe.14-01-0007.
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This study tests the hypothesis that undergraduates who peer teach genetics will have greater understanding of genetic and molecular biology concepts as a result of their teaching experiences. Undergraduates enrolled in a non–majors biology course participated in a service-learning program in which they led middle school (MS) or high school (HS) students through a case study curriculum to discover the cause of a green tomato variant. The curriculum explored plant reproduction and genetic principles, highlighting variation in heirloom tomato fruits to reinforce the concept of the genetic basis of phenotypic variation. HS students were taught additional activities related to molecular biology techniques not included in the MS curriculum. We measured undergraduates’ learning outcomes using pre/postteaching content assessments and the course final exam. Undergraduates showed significant gains in understanding of topics related to the curriculum they taught, compared with other course content, on both types of assessments. Undergraduates who taught HS students scored higher on questions specific to the HS curriculum compared with undergraduates who taught MS students, despite identical lecture content, on both types of assessments. These results indicate the positive effect of service-learning peer-teaching experiences on undergraduates’ content knowledge, even for non–science major students.
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Hancock, Roeland, and Thomas G. Bever. "Genetic Factors and Normal Variation in the Organization of Language." Biolinguistics 7 (March 4, 2013): 75–95. http://dx.doi.org/10.5964/bioling.8971.
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LI, X. M., R. X. QIU, C. H. SONG, Q. H. HUANG, X. D. WANG, Z. T. HU, X. Z. HE, et al. "Genotype and genetic variation of HCV infections with low-risk factors in Putian coastal regions, China." Epidemiology and Infection 145, no. 16 (October 30, 2017): 3385–97. http://dx.doi.org/10.1017/s0950268817002357.
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SUMMARYHepatitis C virus (HCV) infection is one of the leading causes of death and morbidity associated with liver disease. Risk factors identified for the transmission of HCV include contaminated blood products, intravenous drug use, body piercing, an infected mother at birth, sexual activity, and dental therapy, among others. However, the exact diversity of the HCV genotype and genetic variation among patients with low-risk factors is still unknown. In this study, we briefly described and analysed the genotype distribution and genetic variation of HCV infections with low-risk factors using molecular biology techniques. The results suggested that genotype 1b was predominant, followed by genotypes 2a and 1a. Genetic variations in the 5′ UTR sequences of HCV were identified, including point mutations, deletions, and insertions. The frequency of genetic variations in 1b was higher than in 2a. This study provides considerable value for the prevention and treatment of liver disease caused by HCV among patients with low-risk factors and for the development of HCV diagnostic reagents and vaccines.
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Melo, Diogo, Gabriel Marroig, and Jason B. Wolf. "Genomic Perspective on Multivariate Variation, Pleiotropy, and Evolution." Journal of Heredity 110, no. 4 (April 15, 2019): 479–93. http://dx.doi.org/10.1093/jhered/esz011.
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AbstractMultivariate quantitative genetics provides a powerful framework for understanding patterns and processes of phenotypic evolution. Quantitative genetics parameters, like trait heritability or the G-matrix for sets of traits, can be used to predict evolutionary response or to understand the evolutionary history of a population. These population-level approaches have proven to be extremely successful, but the underlying genetics of multivariate variation and evolutionary change typically remain a black box. Establishing a deeper empirical understanding of how individual genetic effects lead to genetic (co)variation is then crucial to our understanding of the evolutionary process. To delve into this black box, we exploit an experimental population of mice composed from lineages derived by artificial selection. We develop an approach to estimate the multivariate effect of loci and characterize these vectors of effects in terms of their magnitude and alignment with the direction of evolutionary divergence. Using these estimates, we reconstruct the traits in the ancestral populations and quantify how much of the divergence is due to genetic effects. Finally, we also use these vectors to decompose patterns of genetic covariation and examine the relationship between these components and the corresponding distribution of pleiotropic effects. We find that additive effects are much larger than dominance effects and are more closely aligned with the direction of selection and divergence, with larger effects being more aligned than smaller effects. Pleiotropic effects are highly variable but are, on average, modular. These results are consistent with pleiotropy being partly shaped by selection while reflecting underlying developmental constraints.
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Freitas, Leandro, Priciane C. C. Ribeiro, Aline S. Cancio, Marco A. Machado, Michelle C. Sampaio, Rafaela C. Forzza, and Lyderson F. Viccini. "Population demography, genetic variation and reproductive biology of two rare and endangered Neoregelia species (Bromeliaceae)." Botanical Journal of the Linnean Society 192, no. 4 (December 23, 2019): 787–802. http://dx.doi.org/10.1093/botlinnean/boz110.
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Abstract Although plant demography, genetics and reproduction are inter-related processes, few studies on rare tropical plants have attempted to integrate them. We used an integrated approach to study two endangered Neoregelia spp. from the Brazilian Atlantic Forest. The floral phenotypes of N. ibitipocensis and N. oligantha are similar, and both species are visited and pollinated only by bumblebees. Flowers of N. ibitipocensis secrete copious nectar, which bees can access only by forcing the corolla to open, whereas flowers of N. oligantha are nectarless. Neoregelia ibitipocensis is self-incompatible and pollen-limited, whereas N. oligantha is self-compatible and sets fruits spontaneously. Population growth rates indicate an increasing population size for both species, although to a lesser extent for N. oligantha. Genetic diversity as a whole was moderate; Bayesian analysis indicated a spatially structured cluster for N. ibitipocensis populations, and genetic diversity was scattered across the distribution of N. oligantha. Despite these differences, vegetative reproduction via clonal growth was the main component of population structuring in both species. Limited seed production in N. ibitipocensis and the risk of genetic drift in N. oligantha seem to be the main threats to their persistence.
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Dougherty, M. J., C. Pleasants, L. Solow, A. Wong, and H. Zhang. "A Comprehensive Analysis of High School Genetics Standards: Are States Keeping Pace with Modern Genetics?" CBE—Life Sciences Education 10, no. 3 (September 2011): 318–27. http://dx.doi.org/10.1187/cbe.10-09-0122.
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Science education in the United States will increasingly be driven by testing and accountability requirements, such as those mandated by the No Child Left Behind Act, which rely heavily on learning outcomes, or “standards,” that are currently developed on a state-by-state basis. Those standards, in turn, drive curriculum and instruction. Given the importance of standards to teaching and learning, we investigated the quality of life sciences/biology standards with respect to genetics for all 50 states and the District of Columbia, using core concepts developed by the American Society of Human Genetics as normative benchmarks. Our results indicate that the states’ genetics standards, in general, are poor, with more than 85% of the states receiving overall scores of Inadequate. In particular, the standards in virtually every state have failed to keep pace with changes in the discipline as it has become genomic in scope, omitting concepts related to genetic complexity, the importance of environment to phenotypic variation, differential gene expression, and the differences between inherited and somatic genetic disease. Clearer, more comprehensive genetics standards are likely to benefit genetics instruction and learning, help prepare future genetics researchers, and contribute to the genetic literacy of the U.S. citizenry.
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Feng, Yuanqing, Michael A. McQuillan, and Sarah A. Tishkoff. "Evolutionary genetics of skin pigmentation in African populations." Human Molecular Genetics 30, R1 (January 12, 2021): R88—R97. http://dx.doi.org/10.1093/hmg/ddab007.
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Abstract Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.
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Orzack, S. H., E. D. Parker, and J. Gladstone. "The comparative biology of genetic variation for conditional sex ratio behavior in a parasitic wasp, Nasonia vitripennis." Genetics 127, no. 3 (March 1, 1991): 583–99. http://dx.doi.org/10.1093/genetics/127.3.583.
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Abstract Using genetic markers, we tracked the sex ratio behavior of individual females of the parasitic wasp, Nasonia vitripennis, in foundress groups of size 1, 2, 4, 8 and 16. Comparison of 12 isofemale strains extracted from a natural population reveals significant between-strain heterogeneity of sex ratios produced in all sizes of foundress group. Under simple assumptions about population structure, this heterogeneity results in heterogeneity of fitnesses. The strains differ in their conditional sex ratio behavior (the sex ratio response of a female to foundress groups of different sizes). Females of some strains produce more males as foundress group size increases (up to size eight). Females of another strain produce more males when not alone but do not respond differentially to group size otherwise. Females of two other strains show no conditional sex ratio behavior. Females of only two strains behave differently in foundress groups of size 8 and 16. Correlation and regression analyses indicate that the strains differ significantly in their fit to the predictions of an evolutionarily stable strategy (ESS) model of conditional sex ratio behavior. Such heterogeneity contradicts the notion that females of this species possess conditonal sex ratio behavior that is optimal in the ESS sense. The results imply that this ESS model is useful but not sufficient for understanding the causal basis of the evolution of this behavior in this species. This is the first report on the sex ratio behavior of individual females in multiple foundress groups in any species of parasitic wasp. Data of this type (and not foundress group or "patch" sex ratios) are essential for testing evolutionary models that predict the sex ratio behaviors of individuals. We suggest that a test for an ESS model include the answers to two important questions: 1) is the model quantitatively accurate? and 2) is there reasonable evidence to indicate that natural selection has caused individuals to manifest the ESS behavior?
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Hlusko, Leslea J., Christopher A. Schmitt, Tesla A. Monson, Marianne F. Brasil, and Michael C. Mahaney. "The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution." Proceedings of the National Academy of Sciences 113, no. 33 (July 11, 2016): 9262–67. http://dx.doi.org/10.1073/pnas.1605901113.
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Developmental genetics research on mice provides a relatively sound understanding of the genes necessary and sufficient to make mammalian teeth. However, mouse dentitions are highly derived compared with human dentitions, complicating the application of these insights to human biology. We used quantitative genetic analyses of data from living nonhuman primates and extensive osteological and paleontological collections to refine our assessment of dental phenotypes so that they better represent how the underlying genetic mechanisms actually influence anatomical variation. We identify ratios that better characterize the output of two dental genetic patterning mechanisms for primate dentitions. These two newly defined phenotypes are heritable with no measurable pleiotropic effects. When we consider how these two phenotypes vary across neontological and paleontological datasets, we find that the major Middle Miocene taxonomic shift in primate diversity is characterized by a shift in these two genetic outputs. Our results build on the mouse model by combining quantitative genetics and paleontology, and thereby elucidate how genetic mechanisms likely underlie major events in primate evolution.
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Toth, Zoltan. "Genetic differentiation over a small spatial scale in the smooth newt (Lissotriton vulgaris)." Herpetological Journal, Volume 31 Number 2 (April 1, 2021): 61–69. http://dx.doi.org/10.33256/31.2.6169.
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Understanding the distribution of genetic variation is central for both population biology and conservation genetics. Genetic population structure can be primarily affected by the species’ dispersal ability, which is assumed to be limited in many amphibians. In this study, we estimated allelic differentiation metrics and FST indices to investigate genetic variation among natural breeding ponds of smooth newts (Lissotriton vulgaris) over a small spatial scale. Based on six microsatellite loci, we found a small, but significant allelic differentiation among clusters of natural breeding ponds (i.e. ‘local regions’), which result was in line with the calculation of corresponding hierarchical FST values. Analysis of molecular variance also indicated significant between-region variation in the study area. Pairwise estimations showed that only the furthermost regions differed from each other in both differentiation measures, but this difference was not attributable to geographic distances between ponds. Our results provide evidence that hierarchical genetic structure can be characteristic to breeding ponds of smooth newts on a small spatial scale in their natural breeding habitat, but dispersal distance may be less limited than previously thought in these philopatric caudates.
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Speth, Elena Bray, Neil Shaw, Jennifer Momsen, Adam Reinagel, Paul Le, Ranya Taqieddin, and Tammy Long. "Introductory Biology Students’ Conceptual Models and Explanations of the Origin of Variation." CBE—Life Sciences Education 13, no. 3 (September 2014): 529–39. http://dx.doi.org/10.1187/cbe.14-02-0020.
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Mutation is the key molecular mechanism generating phenotypic variation, which is the basis for evolution. In an introductory biology course, we used a model-based pedagogy that enabled students to integrate their understanding of genetics and evolution within multiple case studies. We used student-generated conceptual models to assess understanding of the origin of variation. By midterm, only a small percentage of students articulated complete and accurate representations of the origin of variation in their models. Targeted feedback was offered through activities requiring students to critically evaluate peers’ models. At semester's end, a substantial proportion of students significantly improved their representation of how variation arises (though one-third still did not include mutation in their models). Students’ written explanations of the origin of variation were mostly consistent with their models, although less effective than models in conveying mechanistic reasoning. This study contributes evidence that articulating the genetic origin of variation is particularly challenging for learners and may require multiple cycles of instruction, assessment, and feedback. To support meaningful learning of the origin of variation, we advocate instruction that explicitly integrates multiple scales of biological organization, assessment that promotes and reveals mechanistic and causal reasoning, and practice with explanatory models with formative feedback.
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Sun, Qinglan, Chang Shu, Wenyu Shi, Yingfeng Luo, Guomei Fan, Jingyi Nie, Yuhai Bi, et al. "VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes." Nucleic Acids Research 50, no. D1 (October 11, 2021): D888—D897. http://dx.doi.org/10.1093/nar/gkab921.
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Abstract The genomic variations of SARS-CoV-2 continue to emerge and spread worldwide. Some mutant strains show increased transmissibility and virulence, which may cause reduced protection provided by vaccines. Thus, it is necessary to continuously monitor and analyze the genomic variations of SARS-COV-2 genomes. We established an evaluation and prewarning system, SARS-CoV-2 variations evaluation and prewarning system (VarEPS), including known and virtual mutations of SARS-CoV-2 genomes to achieve rapid evaluation of the risks posed by mutant strains. From the perspective of genomics and structural biology, the database comprehensively analyzes the effects of known variations and virtual variations on physicochemical properties, translation efficiency, secondary structure, and binding capacity of ACE2 and neutralizing antibodies. An AI-based algorithm was used to verify the effectiveness of these genomics and structural biology characteristic quantities for risk prediction. This classifier could be further used to group viral strains by their transmissibility and affinity to neutralizing antibodies. This unique resource makes it possible to quickly evaluate the variation risks of key sites, and guide the research and development of vaccines and drugs. The database is freely accessible at www.nmdc.cn/ncovn.
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Hill, William G. "Sewall Wright and quantitative genetics." Genome 31, no. 1 (January 1, 1989): 190–95. http://dx.doi.org/10.1139/g89-033.
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Some aspects of Wright's great contribution to quantitative genetics and animal breeding are reviewed in relation to current research and practice. Particular aspects discussed are as follows: the utility of his definition of inbreeding coefficient in terms of the correlation of uniting gametes; the maintenance of genetic variation in the optimum model; the inter-relations between past and present animal-breeding practice and the shifting-balance theory of evolution.Key words: quantitative genetics, inbreeding coefficient, genetic variation, evolution.
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Rogatcheva, Margarita M., Laurie A. Rund, Kelly S. Swanson, Brandy M. Marron, Jonathan E. Beever, Christopher M. Counter, and Lawrence B. Schook. "Creating Porcine Biomedical Models Through Recombineering." Comparative and Functional Genomics 5, no. 3 (2004): 262–67. http://dx.doi.org/10.1002/cfg.404.
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Recent advances in genomics provide genetic information from humans and other mammals (mouse, rat, dog and primates) traditionally used as models as well as new candidates (pigs and cattle). In addition, linked enabling technologies, such as transgenesis and animal cloning, provide innovative ways to design and perform experiments to dissect complex biological systems. Exploitation of genomic information overcomes the traditional need to choose naturally occurring models. Thus, investigators can utilize emerging genomic knowledge and tools to create relevant animal models. This approach is referred to as reverse genetics. In contrast to ‘forward genetics’, in which gene(s) responsible for a particular phenotype are identified by positional cloning (phenotype to genotype), the ‘reverse genetics’ approach determines the function of a gene and predicts the phenotype of a cell, tissue, or organism (genotype to phenotype). The convergence of classical and reverse genetics, along with genomics, provides a working definition of a ‘genetic model’ organism (3). The recent construction of phenotypic maps defining quantitative trait loci (QTL) in various domesticated species provides insights into how allelic variations contribute to phenotypic diversity. Targeted chromosomal regions are characterized by the construction of bacterial artificial chromosome (BAC) contigs to isolate and characterize genes contributing towards phenotypic variation. Recombineering provides a powerful methodology to harvest genetic information responsible for phenotype. Linking recombineering with gene-targeted homologous recombination, coupled with nuclear transfer (NT) technology can provide ‘clones’ of genetically modified animals.
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Price, Courtney G., Emma M. Knee, Julie A. Miller, Diana Shin, James Mann, Deborah K. Crist, Erich Grotewold, and Jelena Brkljacic. "Following Phenotypes: An Exploration of Mendelian Genetics Using Arabidopsis Plants." American Biology Teacher 80, no. 4 (April 1, 2018): 291–300. http://dx.doi.org/10.1525/abt.2018.80.4.291.
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Arabidopsis thaliana, a model system for plant research, serves as the ideal organism for teaching a variety of basic genetic concepts including inheritance, genetic variation, segregation, and dominant and recessive traits. Rapid advances in the field of genetics make understanding foundational concepts, such as Mendel's laws, ever more important to today's biology student. Coupling these concepts with hands-on learning experiences better engages students and deepens their understanding of the topic. In our article, we present a teaching module from the Arabidopsis Biological Resource Center as a tool to engage students in lab inquiry exploring Mendelian genetics. This includes a series of protocols and assignments that guide students through growing two generations of Arabidopsis, making detailed observations of mutant phenotypes, and determining the inheritance of specific traits, thus providing a hands-on component to help teach genetics at the middle and high school level.
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Sánchez, Carmen, David Moore, Geoff Robson, and Tony Trinci. "21st century miniguide to fungal biotechnology." Mexican journal of biotechnology 5, no. 1 (December 29, 2019): 11–42. http://dx.doi.org/10.29267/mxjb.2020.5.1.11.
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Realising the biotechnological potential of fungi requires full appreciation of the molecular biology and genetics of this kingdom. We review recent advances in our understanding of fungal genetic structure as it might influence biotechnology; including introns, alternative splicing of primary transcripts, transposons (transposable elements, or TEs), heterokaryosis, ploidy and genomic variation, sequencing, annotation and comparison of fungal genomes, and gene editing. We end by indicating under-researched, but unique, aspects of fungal cell biology that offer opportunities for developing new strategies to manage the activities of fungi to our benefit. As a closing example, we discuss the potential of bioengineering fungi specifically for bioremediation of plastic wastes.
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Hill, William G. "Understanding and using quantitative genetic variation." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1537 (January 12, 2010): 73–85. http://dx.doi.org/10.1098/rstb.2009.0203.
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Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. Its basis is in statistical models and methodology, albeit based on many strong assumptions. While these are formally unrealistic, methods work. Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. Hence, new methods of prediction of merit in breeding programmes are again based on essentially numerical methods, but incorporating genomic information. Long-term selection responses are revealed in laboratory selection experiments, and prospects for continued genetic improvement are high. There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. Methods based on summary statistics and predictions rather than at the individual gene level seem likely to prevail for some time yet.
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Sarre, Stephen D., and Arthur Georges. "Genetics in conservation and wildlife management: a revolution since Caughley." Wildlife Research 36, no. 1 (2009): 70. http://dx.doi.org/10.1071/wr08066.
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In his 1994 review of conservation biology, Graeme Caughley questioned the central role for genetics in that discipline. His central theme was that there was no known case of genetic malfunction leading to the extinction of a population or species, and that driving forces such as overkill, habitat fragmentation and introduced predators as well as environmental and demographic stochasticity of small populations should be considered ahead of genetics in the debate about extinction prevention. At the time, only indirect and theoretical evidence existed for genetic contributions to the declines of wildlife and most of the debate revolved around the impact of genetic variation on fitness and long-term persistence. In addition, the application of DNA technologies to the study of wildlife was in its infancy. Though this was not Caughley’s intention, many within wildlife management took his criticisms of genetic aspects of species decline as the cue to dismiss this branch of science as of minor relevance to conservation biology. Since Caughley’s critique, there has been a revolution in genetic technologies for non-model organisms with the arrival of highly informative hypervariable DNA markers. Perhaps even more importantly, developments in DNA and gene technologies have provided the opportunity to study fundamental life-history traits such as disease resistance in more direct ways than previously possible. In concert with these tools, conservation geneticists have risen to Caughley’s challenge and demonstrated unambiguously a clear role for genetic analysis in conservation biology. Despite these impressive advances, there remains an important gap between the genetic approaches available and their uptake by managers. Bridging this gap will greatly increase the capacity of wildlife managers to generate the data necessary for sound management.
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Carvalho, Daniel C., Denise A. A. Oliveira, Iracilda Sampaio, and Luciano B. Beheregaray. "Analysis of propagule pressure and genetic diversity in the invasibility of a freshwater apex predator: the peacock bass (genus Cichla)." Neotropical Ichthyology 12, no. 1 (March 2014): 105–16. http://dx.doi.org/10.1590/s1679-62252014000100011.
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An important step in invasive biology is to assess biological variables that could be used to predict invasion success. The study of genetics, evolution, and interactions of invasive and native species in invaded ranges provides a unique opportunity to study processes in population genetics and the capability of a species' range expansion. Here, we used information from microsatellite DNA markers to test if genetic variation relates to propagule pressure in the successful invasion of an apex predator (the Amazonian cichlid Cichla) into Southeastern Brazilian River systems. Invasive populations of Cichla have negatively impacted many freshwater communities in Southeastern Brazil since the 1960s. Reduction of genetic variation was observed in all invasive populations for both Cichla kelberi (CK) and Cichla piquiti(CP). For instance, heterozygosity was lower in the invasive range when compared to native populations from the Amazon basin (CP HE= 0.179/0.44; CK HE= 0.258/0.536 respectively). Therefore, despite the successful invasion of Cichla in southeast Brazil, low genetic diversity was observed in the introduced populations. We suggest that a combination of factors, such as Cichla's reproductive and feeding strategies, the "evolutionary trap" effect and the biotic resistance hypothesis, overcome their depauperete genetic diversity, being key aspects in this apex predator invasion.