Investigating The Evolutionary Patterns Of The Hybrid Incompatibility Genes Hmr And Lhr And Selective Constraint In The Drosophila Genome
DOWNLOAD
Download Investigating The Evolutionary Patterns Of The Hybrid Incompatibility Genes Hmr And Lhr And Selective Constraint In The Drosophila Genome PDF/ePub or read online books in Mobi eBooks. Click Download or Read Online button to get Investigating The Evolutionary Patterns Of The Hybrid Incompatibility Genes Hmr And Lhr And Selective Constraint In The Drosophila Genome book now. This website allows unlimited access to, at the time of writing, more than 1.5 million titles, including hundreds of thousands of titles in various foreign languages. If the content not found or just blank you must refresh this page
Investigating The Evolutionary Patterns Of The Hybrid Incompatibility Genes Hmr And Lhr And Selective Constraint In The Drosophila Genome
DOWNLOAD
Author : Jun Wang
language : en
Publisher:
Release Date : 2007
Investigating The Evolutionary Patterns Of The Hybrid Incompatibility Genes Hmr And Lhr And Selective Constraint In The Drosophila Genome written by Jun Wang and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with categories.
Genetic Molecular Analysis Of Hybrid Incompatibility In Drosophila
DOWNLOAD
Author : Arundhati Shamoni Maheshwari
language : en
Publisher:
Release Date : 2012
Genetic Molecular Analysis Of Hybrid Incompatibility In Drosophila written by Arundhati Shamoni Maheshwari and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Over evolutionary time genomes diverge by acquiring new mutations, some of which isolate species by erecting reproductive barriers. The study of such genes sheds light on how fundamental developmental processes diverge and result in new species. Hybrid incompatibility (HI) genes contribute to speciation by causing the sterility and inviability of interspecific offspring. The Hmr (Hybrid male rescue) and Lhr (Lethal hybrid rescue) genes are a major cause of hybrid lethality between Drosophila melanogaster and its sibling species D. simulans. Hybrid sons from this cross are normally inviable; however by mutating either the D. melanogaster ortholog of Hmr or the D. simulans ortholog of Lhr, viable adult hybrid sons are recovered. Like other HI genes, both Lhr and Hmr are rapidly evolving under selection. In the first study, I asked whether the evolutionary history of selection for Hmr is confined to the hybridizing lineages. I conducted a population genetic survey of Hmr alleles from two sister species D. yakuba and D. santomea, whose common ancestor diverged from the common ancestor of D. melanogaster and D. simulans approximately 10 Myrs ago. I found that Hmr has diverged recurrently under positive selection in multiple independent speciation events, suggesting that Hmr is likely to be functionally diverging in multiple species. In the second study, I examined the molecular nature of functional divergence for the HI gene, Lhr. Strikingly, I found that despite rapid evolution of the Lhr coding sequence, hybrid lethal activity is not a derived function specific to one lineage, but instead a conserved function shared by both Lhr orthologs. Examination of the heterochromatic localization patterns of Lhr orthologs also failed to reveal any evidence of functional divergence. Instead I discovered that regulatory divergence underlies the asymmetric hybrid lethal activities of Lhr orthologs. In the last study, I identified Lhr2, a D. simulans Lhr allele with a highly unusual coding sequence, as a hybrid rescue mutation. I used it to identify a conserved region in the C-terminus of the LHR protein that is critical for hybrid incompatibility. Using the Lhr2 allele I was able to assay the effect of an indel polymorphism that was segregating in the common ancestor of D. melanogaster and D. simulans on hybrid incompatibility. Notably, I found that this indel polymorphism contributes significantly to the functional divergence of Lhr.
Genetic Functional Analysis Of Hybrid Incompatibility Genes In Drosophila
DOWNLOAD
Author : Tawny Nicole Cuykendall
language : en
Publisher:
Release Date : 2015
Genetic Functional Analysis Of Hybrid Incompatibility Genes In Drosophila written by Tawny Nicole Cuykendall and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
Reproductive isolating mechanisms maintain species boundaries by preventing gene flow and act either before or after mating. Hybrid incompatibility (HI) is an example of a post-zygotic barrier and includes hybrid lethality and sterility. Mating of D. melanogaster females with D. simulans males, which diverged ~3 million years ago, produce viable but sterile daughters, and sons which die as 3rd instar larvae. Lethality is caused by an epistatic interaction in the hybrid background between D. melanogaster Hybrid male rescue (Hmr) and D. simulans Lethal hybrid rescue (Lhr). There is evidence that additional unknown factors contribute this lethal interaction in hybrids. In collaboration with members of the Barbash lab, I performed a screen using the Bloomington Deficiency Kit to identify putative HI factors. We found that there are no additional major-effect HI genes in the D. melanogaster autosomal genome, however, additional HI factors on the X chromosome are required for lethality. HI genes are typically characeterized by rapid evolution driven by selection.!! Likewise, Hmr exhibits extensive coding sequence divergence between D. melanogaster and D. simulans. In order to identify the forces driving selection, it is necessary to first describe the intraspecific function of Hmr. I used immunofluorescence and fluorescent in situ hybridization (FISH) to characterize the nuclear localization of the encoded protein and found that Hmr is heterochromatic and localizes to specific satellite sequences. Using functional genomics techniques, I showed that Hmr regulates the transcript abundance of transposable elements (TEs), which comprise a large portion of heterochromatin. In addition, genome-wide profiling of H3K9me3 enrichment and RNA Polymerase II occupancy in Hmr mutants showed that Hmr likely silences TEs posttranscriptionally. The heterochromatic properties of Hmr, as well as its role in TE regulation, are largely conserved between the orthologs. However, the D. melanogaster and D. simulans genomes have diverged in TE content, density, and activity. TEs are highly dynamic and rapidly evolving, and it is possible that the sequence evolution of TEs and other rapidly evolving repetitive elements has contributed to the divergence of Hmr.!
Genetic And Molecular Analysis Of Lethal Hybrid Rescue A Major Effect Gene In D Melanogaster D Simulans Hybrid Incompatibility
DOWNLOAD
Author : Nicholas Joseph Brideau
language : en
Publisher:
Release Date : 2010
Genetic And Molecular Analysis Of Lethal Hybrid Rescue A Major Effect Gene In D Melanogaster D Simulans Hybrid Incompatibility written by Nicholas Joseph Brideau and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Post-zygotic hybrid incompatibility (HI) refers to barriers such as sterility and inviability that affect the reproductive success of zygotes from interspecies matings. Although the genetic basis for HI has been studied for decades, very few major-effect genes have been identified. Crosses between Drosophila melanogaster and its sibling species D. simulans produce incompatible hybrids. In the cross of D. melanogaster females to D. simulans males, the F1 daughters are semi-viable but sterile, and the sons are inviable. The D. simulans gene Lethal hybrid rescue (Lhr) was identified as contributing to these incompatibilities, on the basis that loss-of-function mutations suppress hybrid male inviability. I have investigated several properties of Lhr in order to understand how it causes HI. I found that LHR physically interacts with another HI protein, Hybrid male rescue (HMR), as well as heterochromatin proteins HP1 and HP6. Furthermore, LHR directly binds to the chromo-shadow domain of HP1 through a potentially novel HP1-interacting motif. Consistent with binding to HP1, LHR localizes to heterochromatic regions of polytene chromosomes. I have discovered that the pericentric localization of LHR depends on both HP1 and HP5, and that this localization may not be critical for causing hybrid male inviability. It was previously reported that Lhr is evolving rapidly in a manner consistent with positive selection. To understand how the divergence of Lhr affects its functions and interactions, I investigated the properties of other Lhr orthologs. First, I found that the yeast two-hybrid interactions with HMR, HP1 and HP6 are conserved for six additional LHR orthologs, and despite the extensive sequence divergence among LHR orthologs, that the properties of the HP1-interacting domain are also conserved. Second, three LHR orthologs co-localize with HP1 at heterochromatic regions of polytene chromosomes when expressed in D. melanogaster. And finally, I also found that the ability to induce hybrid male lethality, that was previously attributed to only D. simulans Lhr, is conserved for D. melanogaster Lhr. These results demonstrate that despite the extensive sequence divergence among Lhr orthologs, many properties remain conserved. Overall, my work contributes to understanding the function of Lhr in both pure species and in hybrids.
Recurrent And Recent Selection In The Drosophila Melanogaster Genome
DOWNLOAD
Author :
language : en
Publisher:
Release Date : 2008
Recurrent And Recent Selection In The Drosophila Melanogaster Genome written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with categories.
Mutation, recombination, selection, and genetic drift shape patterns of genetic variation. Population geneticists traditionally investigate the contributions of these forces to sequence evolution without respect to the chromosomal context of the gene of interest, i.e., without respect to structural proteins and their corresponding dynamics characteristic of a particular chromosomal location. The ontogeny of this dissertation work begins with such a traditional approach and ends with a reconsideration. Chapter one describes five genes that evolved de novo along the D. melanogaster lineage or in the ancestor of D. melanogaster/D. simulans. These five genes are largely X-linked and expressed in a testis-biased pattern. Moreover, all de novo genes with homologous sequence in D. simulans exhibit an excess of amino acid divergence. Two previously described novel genes that evolved along the D. melanogaster lineage via shuffling of both functional and noncoding elements (Sdic, hydra) also exhibit a pattern of adaptive protein evolution, and more surprisingly, share both a testis-biased expression pattern and a chromosomal location with one of the de novo genes identified in our study. The unexpected co-occurrence of these three genes at the base of the X chromosome raises the possibility that particular features of a chromosomal region may facilitate the evolution of novel genes. The insight that physical location potentially contributes to the likelihood of novel gene evolution and consequently, adaptive protein evolution, challenged me to consider how chromosome structure may influence evolutionary forces such as selection. A rigorous investigation of this research question requires within- and between-species sequence data examined in a context of comprehensive information about chromosome dynamics. At the inception of my dissertation work, our understanding of chromatin biology was still in its infancy. Consequently, I took a "surrogate approach" by investigating the role of selection in shaping patterns of polymorphism and divergence at proteins that remodel chromatin. I began by investigating protein divergence between sister species D. melanogaster and D. simulans, and discovered a surprising amount of adaptive protein evolution at those loci encoding the Dosage Compensation Complex (DCC) proteins along the D. melanogaster lineage. Next, I investigated chromatin remodeling factors within D. melanogaster, and found evidence of spatially varying selection at several. My final chapter is a first step towards understanding the functional consequences of natural variation at these proteins. Specifically, I describe preliminary evidence of stress tolerance variation associated with coding variation at the histone acetyltransferase, chameau. Documenting signatures of selection both within and between species at chromatin remodeling factors strongly implicate chromatin dynamics as an underappreciated biological function targeted by selection and motivates deeper and more direct investigations of the functional and evolutionary mechanisms driving evolution of chromatin dynamics.
The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna
DOWNLOAD
Author : Satyaki Prasad Rajavasireddy
language : en
Publisher:
Release Date : 2014
The Hybrid Incompatibility Gene Lethal Hybrid Rescue Represses Repetitive Dna written by Satyaki Prasad Rajavasireddy and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Heterochromatin keeps in check selfish elements such as transposable elements (TEs) and satellite DNAs, which can wreak havoc on a genome by mobilizing and increasing their copy number, leading to genomic instability and sterility. Heterochromatin proteins (HPs) that mediate repression of selfish DNA may therefore be in an eternal arms race with selfish DNA. This arms race might explain the extensive sequence divergence discovered in some HPs which cause post-zygotic reproductive isolation. However, evidence for this model is limited. For my thesis work, I studied Lhr, a strong candidate gene, to test this model. Lhr encodes a rapidly evolving, HP1a interacting, HP that causes lethality in hybrids between D. melanogaster and D. simulans. To determine Lhr's normal function we knocked-out Lhr via homologous recombination in D. melanogaster. I discovered that Lhr mutant females have reduced fertility. Using mRNA-Seq, I found that Lhr regulates the steady state levels of many different satellite and TE transcripts. ChIP data argue that this increase is due to a defective post-transcriptional pathway. However, my analysis of small RNA-Seq data shows that small RNAs targeting most misregulated transposable elements are not affected and suggests instead that Lhr functions independently or downstream of the small RNA pathway. To address the effects of extensive sequence divergence of Lhr between D. melanogaster and D. simulans, I performed a RNA-Seq comparison of wildtype and Lhr mutant D. simulans lines. I discovered that loss of Lhr upregulates different transposable elements in D. melanogaster and D. simulans. Further, comparing the two species, I made the striking observation that localization of Lhr protein has expanded in D. melanogaster to encompass two satellites which account for nearly 6% of the D. melanogaster genome, but only 0.7% in the inferred ancestor of D. melanogaster and D. simulans. Finally, I found that Lhr is required for expression of heterochromatic genes, suggesting that it helps the host genes in D. melanogaster to adapt to the greatly expanded heterochromatic content of this species. My studies uncover an important component of the machinery that an organism uses to repress TEs and satellites, and to adapt to changes in selfish DNA. My work further demonstrates that each Lhr ortholog has adapted to repress different selfish elements in each species and provides support for the arms race model.
The Genetics Of Hybrid Incompatibility Early In The Speciation Continuum
DOWNLOAD
Author : Eric T. Watson
language : en
Publisher:
Release Date : 2017
The Genetics Of Hybrid Incompatibility Early In The Speciation Continuum written by Eric T. Watson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with Biodiversity categories.
Species are discrete groups of organisms that are reproductively isolated from other related groups of organisms. Variation in the strength of reproductive isolation between closely related taxa falls along a 'speciation continuum', from weakly isolated structured populations to fully isolated sister species. Efforts to understand the genetics of speciation have focused primarily on developmental defects in hybrids (intrinsic postzygotic isolation) leading to sterility or inviability. Once speciation is complete, species continue to diverge as a result of mutation, genetic drift, and selection, and new forms of reproductive isolation may continue to accumulate. Therefore, at later stages in the 'speciation continuum', it is unclear whether a given isolating barrier is a cause, or a consequence of speciation. In my dissertation, I focus on the genetics of intrinsic postzygotic isolation occurring early in the 'speciation continuum' at the onset of speciation. In chapter 1, I highlight where the assumptions of dominance theory are particularly problematic in marsupials, where X inactivation uniformly results in silencing the paternal X. I then present evidence of Haldane's rule for sterility but not for viability in marsupials, as well as the first violations of Haldane's rule for these traits among all mammals. Marsupials represent a large taxonomic group possessing heteromorphic sex chromosomes, where the dominance theory cannot explain Haldane's rule. In this light, I evaluate alternative explanations for the pre- ponderance of male sterility in interspecific hybrids, including faster male evolution, X-Y interactions, and genomic conflict hypotheses. In chapter 2, I revisit three mechanisms highlighted by Rose and Doolittle (1983) as a convenient conceptual scaffold for understanding the variety of ways TEs might directly, or indirectly, cause reproductive incompatibility. In chapter 3, I describe an example of hybrid incompatibility (called "still") segregating in F1 hybrids between populations of T. castaneum, whereby affected offspring exhibit a suite of maladaptive traits upon eclosion from the pupal stage. To investigate the genetic cause of the still phenotype, I sequenced the genomes of still and normal siblings using pooled-DNA and employed a genome scan approach that compares allele frequencies between extremely discordant sib pairs (still vs normal) to identify discordant alleles. In total, I identified 97 genes with significantly discordant non-synonymous SNPs between still and normal siblings. An additional 355 genes possess nucleotide changes that are either synonymous, or non-coding (i.e. occur in introns or within 1000kb upstream or downstream). Interestingly, a set of 19 candidate loci were recently identified as candidate phosphine resistance genes. Phosphine is an insecticidal fumigant which acts as a metabolic toxin by targeting redox reactions, and is used worldwide in grain storage and processing facilities. The Chicago population was collected over 7 decades aco, predating the use of phosphine, while Tanzania populations were potentially subjected to 30 years, or roughly 330 generations of routine phosphine exposure before it was collected and kept in the laboratory. I discuss this observation in light of the role of genetic conflict in generating hybrid incompatibilities, especially where they are still segregating early in the 'speciation continuum'. vi Table of Contents Acknowledgements....................................................................................
Investigating Patterns Of Parallel Genetic Change In Repeated Adaptation
DOWNLOAD
Author : Sara Lynn Sheeley
language : en
Publisher:
Release Date : 2010
Investigating Patterns Of Parallel Genetic Change In Repeated Adaptation written by Sara Lynn Sheeley and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Drosophila categories.
In contrast with D. melanogaster, which segregates functionally distinct variants in Adh that represent local adaptation to climate, D. americana segregates little variation. This is surprising, especially because Adh of D. americana is found near a polymorphic chromosomal rearrangement that does segregate geographically-structured alleles across the species' range. In Chapter 4, I report similarities at the Phosphoglucomutase (Pgm) locus in the two species, including a shared excess of nonsynonymous variants and the presence of clinal alleles. However, while variation at Pgm of D. melanogaster is proposed to underlie local adaptation, variation at Pgm of D. americana appears to be predominantly neutral. In Chapter 5, I investigate the role of positive selection in sequence evolution in the D. americana homologs of a group of genes thought to underlie local adaptation to climate in D. melanogaster . The two species share a large geographic range and exhibit levels of sequence variation that indicate a similar effective population size, but D. melanogaster appears to undergo more frequent fixation of advantageous alleles. Approximately half of all amino acid divergence in D. melanogaster is attributable to positive selection, but I find no signs of positive selection in the investigated genes in D. americana . Overall, the results reveal little or no parallel evolution at the single genes analyzed. This lack of parallel evolution is likely a result of the high complexity of adaptation to climate as well as contingency.
Deep Homology
DOWNLOAD
Author : Lewis I. Held, Jr
language : en
Publisher: Cambridge University Press
Release Date : 2017-02-16
Deep Homology written by Lewis I. Held, Jr and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-02-16 with Business & Economics categories.
A comparison of the genetic circuits of Homo sapiens and Drosophila reveals the evidence for deep homology.
Genetic Analysis Of Postzygotic Isolation And Recombination Rate Differences In Drosophila
DOWNLOAD
Author : M. Victoria Cattani
language : en
Publisher:
Release Date : 2012
Genetic Analysis Of Postzygotic Isolation And Recombination Rate Differences In Drosophila written by M. Victoria Cattani and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
"My dissertation research explores the genetics of hybrid incompatibilities and, separately, the evolution of recombination rates in D. melanogaster and its sibling species. In Chapter 1, I show that a hybrid lethality factor(s) in the pericentric heterochromatin of the D. mauritiana X chromosome, hybrid lethal on the X (hlx), is incompatible with a factor(s) in the same ~26-kb autosomal region from both D. sechellia and D. simulans, Suppressor of hlx (Su[hlx]). By combining genetic and phylogenetic information, I infer that hlx-Su(hlx) hybrid lethality is most likely caused by a derived-ancestral incompatibility. In Chapter 2, I map a recessive factor to the pericentromeric heterochromatin of the X chromosome in D. simulans and D. mauritiana, heterochromatin hybrid lethal (hhl), that causes lethality in F1 hybrid females with D. melanogaster. Using small segments of the D. melanogaster X chromosome duplicated onto the Y chromosome, I then map a dominant factor that causes hybrid lethality to a small 24- gene region of the D. melanogaster X and provide evidence suggesting that it interacts with hhlmau. In Chapter 3, I estimate crossover frequencies for seven segments that tile across the euchromatic length of the D. mauritiana X chromosome when introgressed into the genetic backgrounds of D. simulans and D. sechellia. My analyses suggest that both cis- and trans-acting factors contribute to differences in the genetic control of crossover frequencies on the X among the D. simulans clade species. In Chapter 4, I perform an evolutionary screen of meiotic genes to identify potential candidate genes that might contribute to species differences in the rate of crossing over. I then use a transgenic approach to introduce the D. mauritiana allele of mei-218 into D. melanogaster flies homozygous for a loss-of-function mutation at mei-218 and ask if the D. mauritiana mei-218 allele produces a D. mauritiana-like map in otherwise D. melanogaster flies. I show that the highly divergent meiosis gene, mei-218, is responsible for most of the 1.55-fold phenotypic difference in genetic map length of chromosome 2 between D. melanogaster and D. mauritiana"--Leaves vii-viii.