Current Search: Evolutionary genetics (x)
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- Title
- Novel Techniques in Genetic Programming.
- Creator
- Fernandez, Thomas, Furht, Borko, Florida Atlantic University, College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
- Abstract/Description
-
Three major problems make Genetic Programming unfeasible or impractical for real world problems. The first is the excessive time complexity.In nature the evolutionary process can take millions of years, a time frame that is clearly not acceptable for the solution of problems on a computer. In order to apply Genetic Programming to real world problems, it is essential that its efficiency be improved. The second is called overfitting (where results are inaccurate outside the training data). In a...
Show moreThree major problems make Genetic Programming unfeasible or impractical for real world problems. The first is the excessive time complexity.In nature the evolutionary process can take millions of years, a time frame that is clearly not acceptable for the solution of problems on a computer. In order to apply Genetic Programming to real world problems, it is essential that its efficiency be improved. The second is called overfitting (where results are inaccurate outside the training data). In a paper[36] for the Federal Reserve Bank, authors Neely and Weller state “a perennial problem with using flexible, powerful search procedures like Genetic Programming is overfitting, the finding of spurious patterns in the data. Given the well-documented tendency for the genetic program to overfit the data it is necessary to design procedures to mitigate this.” The third is the difficulty of determining optimal control parameters for the Genetic Programming process. Control parameters control the evolutionary process. They include settings such as, the size of the population and the number of generations to be run. In his book[45], Banzhaf describes this problem, “The bad news is that Genetic Programming is a young field and the effect of using various combinations of parameters is just beginning to be explored.” We address these problems by implementing and testing a number of novel techniques and improvements to the Genetic Programming process. We conduct experiments using data sets of various degrees of difficulty to demonstrate success with a high degree of statistical confidence.
Show less - Date Issued
- 2006
- PURL
- http://purl.flvc.org/fau/fd/FA00012570
- Subject Headings
- Evolutionary programming (Computer science), Genetic algorithms, Genetic programming (Computer science)
- Format
- Document (PDF)
- Title
- Cladistic analysis of juvenile and adult hominoid cranial shape variables.
- Creator
- DiVito, Thomas A. II, Dorothy F. Schmidt College of Arts and Letters, Department of Anthropology
- Abstract/Description
-
Phylogenies constructed from skeletal data often contradict those built from genetic data. This study evaluates the phylogenetic utility of adult male, female, and juvenile hominoid cranial bones. First, I used geometric morphometric methods to compare the cranial bone shapes of seven primate genera (Gorilla, Homo, Hylobates, Macaca, Nomascus, Pan, and Pongo). I then coded these shapes as continuous characters and constructed cladograms via parsimony analysis for the adult male, female, and...
Show morePhylogenies constructed from skeletal data often contradict those built from genetic data. This study evaluates the phylogenetic utility of adult male, female, and juvenile hominoid cranial bones. First, I used geometric morphometric methods to compare the cranial bone shapes of seven primate genera (Gorilla, Homo, Hylobates, Macaca, Nomascus, Pan, and Pongo). I then coded these shapes as continuous characters and constructed cladograms via parsimony analysis for the adult male, female, and juvenile character matrices. Finally, I evaluated the similarity of these cladograms to one another and to the genetic phylogeny using topological distance software. Cladograms did not differ from one another or the genetic phylogeny less than comparisons of randomly generated trees. These results suggest that cranial shapes are unlikely to provide accurate phylogenetic information, and agree with other analyses of skeletal data that fail to recover the molecular phylogeny (Collard & Wood, 2000, 2001; Springer et al., 2007).
Show less - Date Issued
- 2011
- PURL
- http://purl.flvc.org/FAU/3175013
- Subject Headings
- Cladistic analysis, Mathematics, Morphology, Mathematics, Hominids, Evolution, Evolutionary genetics, Mathematics
- Format
- Document (PDF)
- Title
- The Paranthropus face: examining a developmental model.
- Creator
- Burdelsky, Brittany A., Dorothy F. Schmidt College of Arts and Letters, Department of Anthropology
- Abstract/Description
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The Paranthropus head is characterized by features traditionally thought to be related to heavy chewing. McCollum [Science 284 (1999) : 301-305] proposed that palatal thickening is a response to developmental integration between the mandibular ramus, oral and nasal functional matrices, and the vomer, which inserts onto the premaxilla in Paranthropus and causes the palate to thicken instead of rotate during vertical expansion. I tested whether palate thickness increases as a byproduct of...
Show moreThe Paranthropus head is characterized by features traditionally thought to be related to heavy chewing. McCollum [Science 284 (1999) : 301-305] proposed that palatal thickening is a response to developmental integration between the mandibular ramus, oral and nasal functional matrices, and the vomer, which inserts onto the premaxilla in Paranthropus and causes the palate to thicken instead of rotate during vertical expansion. I tested whether palate thickness increases as a byproduct of differential increases in the sizes of the oral and nasal functional matrices compared to growth in the mandibular ramus. To do so, I collected 3D volume and landmark data from computed tomography (CT) scans of extant (Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus) and extinct taxa (Australopithecus and Paranthropus), and tested counterpart relationships for bones in the cranium using scaling analyses. Results suggest that developmental constraints related to growth counterpart relationships in the skulll are unlikely to affect palate thickness in the genus Paranthropus.
Show less - Date Issued
- 2012
- PURL
- http://purl.flvc.org/FAU/3358331
- Subject Headings
- Physical anthropology, Fossil hominids, Craniology, Human evolution, Evolutionary genetics
- Format
- Document (PDF)
- Title
- Applications of evolutionary algorithms in mechanical engineering.
- Creator
- Nelson, Kevin M., Florida Atlantic University, Huang, Ming Z., College of Engineering and Computer Science, Department of Ocean and Mechanical Engineering
- Abstract/Description
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Many complex engineering designs have conflicting requirements that must be compromised to effect a successful product. Traditionally, the engineering approach breaks up the complex problem into smaller sub-components in known areas of study. Tradeoffs occur between the conflicting requirements and a sub-optimal design results. A new computational approach based on the evolutionary processes observed in nature is explored in this dissertation. Evolutionary algorithms provide methods to solve...
Show moreMany complex engineering designs have conflicting requirements that must be compromised to effect a successful product. Traditionally, the engineering approach breaks up the complex problem into smaller sub-components in known areas of study. Tradeoffs occur between the conflicting requirements and a sub-optimal design results. A new computational approach based on the evolutionary processes observed in nature is explored in this dissertation. Evolutionary algorithms provide methods to solve complex engineering problems by optimizing the entire system, rather than sub-components of the system. Three standard forms of evolutionary algorithms have been developed: evolutionary programming, genetic algorithms and evolution strategies. Mathematical and algorithmic details are described for each of these methods. In this dissertation, four engineering problems are explored using evolutionary programming and genetic algorithms. Exploiting the inherently parallel nature of evolution, a parallel version of evolutionary programming is developed and implemented on the MasPar MP-1. This parallel version is compared to a serial version of the same algorithm in the solution of a trial set of unimodal and multi-modal functions. The parallel version had significantly improved performance over the serial version of evolutionary programming. An evolutionary programming algorithm is developed for the solution of electronic part placement problems with different assembly devices. The results are compared with previously published results for genetic algorithms and show that evolutionary programming can successfully solve this class of problem using fewer genetic operators. The finite element problem is cast into an optimization problem and an evolutionary programming algorithm is developed to solve 2-D truss problems. A comparison to LU-decomposition showed that evolutionary programming can solve these problems and that it has the capability to solve the more complex nonlinear problems. Finally, ordinary differential equations are discretized using finite difference representation and an objective function is formulated for the application of evolutionary programming and genetic algorithms. Evolutionary programming and genetic algorithms have the benefit of permitting over-constraining a problem to obtain a successful solution. In all of these engineering problems, evolutionary algorithms have been shown to offer a new solution method.
Show less - Date Issued
- 1997
- PURL
- http://purl.flvc.org/fcla/dt/12514
- Subject Headings
- Mechanical engineering, Genetic algorithms, Evolutionary programming (Computer science)
- Format
- Document (PDF)
- Title
- A Phylogeny of Mexican Ambystoma Salamanders (Caudata: Ambystomatidae) from Larval Characters.
- Creator
- Cole, Lauren A., Wyneken, Jeanette, Florida Atlantic University
- Abstract/Description
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A phylogeny of Mexican Ambystoma salamanders was constructed using larval morphology. Characters were scored for 19 ambystomatid species from Mexico and North America Twenty-five continuous characters came from external measurements of cranial and branchial features and ratios of measurements. Twenty-six categorical characters were scored from internal and external larval, branchial, and cranial features, as well as overall color and adult life history. Cladograms constructed from individual...
Show moreA phylogeny of Mexican Ambystoma salamanders was constructed using larval morphology. Characters were scored for 19 ambystomatid species from Mexico and North America Twenty-five continuous characters came from external measurements of cranial and branchial features and ratios of measurements. Twenty-six categorical characters were scored from internal and external larval, branchial, and cranial features, as well as overall color and adult life history. Cladograms constructed from individual character matrices lack major resolution beyond individual species level. The consensus cladogram did not resolve the majority of species, and was similar to consensus results from previous cladistic analysis based on molecular characters. Convergent morphology is evident in characters of geographically distant members of the clade. However, species determination was possible for all examined taxa. Neoteny is widespread in the A. tigrinum complex and, as an isolating mechanism, may be the main driver of speciation in the complex.
Show less - Date Issued
- 2007
- PURL
- http://purl.flvc.org/fau/fd/FA00000734
- Subject Headings
- Salamanders--Reproduction, Salamanders--Classification, Cladistic analysis--Mathematics, Evolutionary genetics--Mathematics, Evolution (Biology)
- Format
- Document (PDF)
- Title
- Structure-function relationships in eukaryotic and prokaryotic family 6 glycosyltransferases.
- Creator
- Tumbale, Percy., Charles E. Schmidt College of Medicine, Department of Biomedical Science
- Abstract/Description
-
Carbohydrate Active Enzyme family 6 (CA6) glycosyltransferases (GTs) are type II transmembrane proteins localized in the Golgi apparatus. CA6 GTs have a GT-A fold, a type of structure that resembles the Rossman fold and catalyze the transfer either galactose (Gal) or N-acetylgalactosamine (GalNAc) from the UDP nucleotide sugar to an non-reducing terminal Gal or GalNAc on an acceptor via an a-1,3 linkage. In this reaction, the anomeric configuration of the sugar moiety of the donor is retained...
Show moreCarbohydrate Active Enzyme family 6 (CA6) glycosyltransferases (GTs) are type II transmembrane proteins localized in the Golgi apparatus. CA6 GTs have a GT-A fold, a type of structure that resembles the Rossman fold and catalyze the transfer either galactose (Gal) or N-acetylgalactosamine (GalNAc) from the UDP nucleotide sugar to an non-reducing terminal Gal or GalNAc on an acceptor via an a-1,3 linkage. In this reaction, the anomeric configuration of the sugar moiety of the donor is retained in the product. CA6 GTs includes the histo-blood group A and B GTs, a-galactosyltransferase (a3GT), Forssman glycolipid synthase (FS), isogloboside 3 synthase (iGb3) in mammals. a3GT and its products (a-Gal epitode) are present in most mammals but are absent in humans and old world primates because of inactivating mutations. The absence of a3GT and its products results in the production of anti-a-Gal epitope natural antibodies in these species., Up to date, the catalytic mechanisms of the CA6 GTs are not well understood. Based on previous structural and mutagenesis studies of bovine aB3GT, we investigated active site residues (His315, Asp316, Ser318, His319, and Lys359) that are highly conserved among CA6 GTs. We have also investigated the role of the C-terminal region by progressive C-terminal truncations. Findings from these studies clarify the functional roles of these residues in structure, catalysis, and specificity in these enzymes and have implications for their catalytic mechanisms. GTs are useful tools in synthesis of glycans for various applications in science and medicine. Methods for the large scale production of pure glycans are continuously being developed. We created a limited randomized combinatorial library based on knowledge of structural information and sequence analysis of the enzyme and its mammalian homologues., Two GalNAc-specific variants were identified from the library and one Glc-specific variant was identified by site-direct mutagenesis. The glycosyltransferase activities of these variants are expected to be improved by further screens of libraries which are designed using the variants as templates. The mammalian CA6 GTs that have been characterized to date are metal-independent and require the divalent cation, Mn2+ for activity. In some recently-discovered bacterial CA6 GTs, the DXD sequence that is present in eukaryotic GTs is replaced by NXN. We cloned and expressed one of these proteins from Bacteroides ovatus, a bacterium that has been linked with inflammatory bowel disease. Functional characterization shows it is a metal-independent monomeric GT that efficiently catalyzes the synthesis of oligosaccharides similar to human blood group A glycan., Mutational studies indicated that despite the lack of a metal cofactor there are similarities in structure-function relationships between the bacterial and vertebrate family 6 GTs.
Show less - Date Issued
- 2009
- PURL
- http://purl.flvc.org/FAU/186686
- Subject Headings
- Molecular biology, Mathematical models, Glycotransferase genes, Biological transport, Proteins, Synthesis, Evolutionary genetics
- Format
- Document (PDF)
- Title
- Elucidation of Microbial Communities From South Florida Beaches Using 16S rRNA Sequence Analysis.
- Creator
- Ponukumati, Sushma, Esiobu, Nwadiuto, Florida Atlantic University
- Abstract/Description
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The composition of marine bacterial communities from South Florida beaches were characterized using 16S rRNA sequence analysis. To compare cultivable and noncultured populations, community genomic DNA was extracted directly from sand and seawater samples and from two cultured equivalents. Only two ofthe 86 (2.3%) direct extracted sequences and 79 of 150 (52.6%) culture sequences belong to known isolates in Ribosomal Database (version 9.0) at 95% confidence level. At low stringency (p=0.70),...
Show moreThe composition of marine bacterial communities from South Florida beaches were characterized using 16S rRNA sequence analysis. To compare cultivable and noncultured populations, community genomic DNA was extracted directly from sand and seawater samples and from two cultured equivalents. Only two ofthe 86 (2.3%) direct extracted sequences and 79 of 150 (52.6%) culture sequences belong to known isolates in Ribosomal Database (version 9.0) at 95% confidence level. At low stringency (p=0.70), the populations cluster into several unknown clads with early divergence, indicating the presence of novel well established bacterial groups. Members of phylum Bacteroidetes, Firmicuites and Proteobacteria were identified, with the latter being the most prevalent in culture. Diversity indices rank Hollywood beach > Fort Lauderdale > Hobie beach. Taxonomic representation indicates marine water as more diverse compared to dry sand and wet sand. A combination of phylogenetic markers will be needed to define the immense diversity of this niche.
Show less - Date Issued
- 2007
- PURL
- http://purl.flvc.org/fau/fd/FA00000809
- Subject Headings
- Marine microbiology--Florida, Evolutionary genetics, Biodiversity--Research, Marine biodiversity conservation
- Format
- Document (PDF)
- Title
- The behavioral, emotional, and attentional effects of human baby schema.
- Creator
- Machluf, Karin, Bjorklund, David F., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Psychology
- Abstract/Description
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Children exhibit neotenous, or physically immature, features, such as a large rounded head relative to body size, adult-sized eyes, round cheeks, a small chin, and a short narrow nose. Bowlby (1969) and others (Eibl-Eibesfeldt, 1989; Hrdy, 2005) propose that, in species whose young depend on care from an adult, these features could enhance offspring survival. Lorenz (1943) argued that adult humans are particularly attracted to these features, and that these characteristics, which he termed...
Show moreChildren exhibit neotenous, or physically immature, features, such as a large rounded head relative to body size, adult-sized eyes, round cheeks, a small chin, and a short narrow nose. Bowlby (1969) and others (Eibl-Eibesfeldt, 1989; Hrdy, 2005) propose that, in species whose young depend on care from an adult, these features could enhance offspring survival. Lorenz (1943) argued that adult humans are particularly attracted to these features, and that these characteristics, which he termed Kindchenschema or “baby schema,” trigger a cognitive system that processes and reacts specifically to infantile features for the purpose of enhancing motivation to engage in caretaking behaviors. The goal of the studies proposed here is to examine the behavioral, attentional, and emotional effects of baby schema.
Show less - Date Issued
- 2015
- PURL
- http://purl.flvc.org/fau/fd/FA00004452, http://purl.flvc.org/fau/fd/FA00004452
- Subject Headings
- Ego (Psychology), Emotions in infants, Empathy, Evolutionary psychology, Genetic psychology, Human behavior, Identity (Philosophical concept), Moral development, Parent and child
- Format
- Document (PDF)