HapPart: partitioning algorithm for multiple haplotyping from haplotype conflict graph

Each chromosome in the human genome has two copies. The haplotype assembly challenge entails reconstructing two haplotypes (chromosomes) using aligned fragments genomic sequence. Plants viz. wheat, paddy and banana have more than two chromosomes. Multiple haplotype reconstruction has been a major research topic. For reconstructing multiple haplotypes for a polyploid organism, several approaches have been designed. The researchers are still fascinated to the computational challenge. This article introduces a partitioning algorithm, HapPart for dividing the fragments into k-groups focusing on reducing the computational time. HapPart uses minimum error correction curve to determine the value of k at which the growth of gain measures for two consecutive values of k-multiplied by its diversity is maximum. Haplotype conflict graph is used for constructing all possible number of groups. The dissimilarity between two haplotypes represents the distance between two nodes in graph. For merging two nodes with the minimum distance between them this algorithm ensures minimum error among fragments in same group. Experimental results on real and simulated data show that HapPart can partition fragments efficiently and with less computational time

The genomic basis of adaptation in threespine stickleback fish

Evolutionary biology consists in the study of the evolutionary processes responsible of the diversification and adaptation of life forms over time. When adapting to a new environment (or changes in their local environment), populations have to adapt through natural selection. Until recently, the study of adaptation was focusing on fathoming the consequences of natural selection at the phenotypic level and how phenotypic evolution is linked to genetic changes. The development of new genetic and genomic tools in the last 20 years, like high-throughput sequencing technologies, now allows the construction of reference genomes in a variety of non-model organisms and the investigation of the genomic basis of adaptation. In my thesis, I investigated the genomic basis of adaptation by exploring the consequences of natural selection at the molecular level using the threespine stickleback fish (Gasterosteus acualeatus) as a model. In more detail, my work focused on three main topics: the genomic basis of parallel adaptation to acidic versus basic lochs of North Uist (Outer Hebrides, Scotland); the maintenance of standing genetic variation in Atlantic stickleback fish, and the characterization of reproductive isolation at the genomic level between parapatric stickleback populations of the Misty watershed (Vancouver Island, British Columbia, Canada)

Local adaptation by birds to human-altered habitats: the great tit and the house sparrow as model species

[eng] Human-altered environments have expanded rapidly in the past decades and made a huge impact on living organisms. Inhabiting in such a habitat can modify different traits in animals, allowing for a better adaptation to these human-altered environments. In the first part of this thesis I investigated patterns of recent (contemporary) adaptation to urban habitats, focusing on the role of behavioural, genetic and epigenetic variation in great tits. In the second part of the thesis I investigated patterns of adaptation to human-made habitats in a larger time-scale, focusing on the origin and expansion of the house sparrow, which has been for ages a human commensalism. I additionally checked the effect of methylation variation on the rapid expansion and high phenotypic variation of house sparrow in the Palearctic region. Regarding the great tit I found that urban-dwelling birds are more explorative in novel environments and bolder in front of new objects than forest individuals. I found several epigenetic modifications and genetic polymorphisms possibly related to novelty seeking behaviour in the great tits. Our results suggested that epigenetics adjustment can be different in the urban-dwelling great tits in comparison to the forest birds. Furthermore, we investigated the possible polymorphisms in the Melanocortin-1 gene in the great tit to relate it with the size of the black belly stripe, which had previously been found to differ between urban and forest individuals. However, results showed that there is no polymorphism in this gene in relation to the size of the black belly stripe. In relation to the house sparrow, we found that the commensalism of this species with humans has a single origin and probably initiated in the Middle East. Then, it expanded rapidly in the Palearctic region with the aid of agriculture and human civilizations expansion. In addition, we discovered that the genome-wide methylation pattern of house sparrows has a general stability within five subspecies in the Middle East but we found high level of variation at the individual level within populations which likely happened randomly rather than due to selection. Our results indicate that variation in DNA methylation does not strictly follow subspecies designations. We have detected correlation between methylation level and some morphological traits such as standardized bill length and we suggest that part of the high morphological variation in the native populations of the house sparrow is influenced by differentially methylated regions in specific loci throughout the genome. We also detected seven differentially methylated loci diverged by subspecies and also three loci differentiated by commensal or non-commensal statu

Dynamics of Hybrid Zones at a Continental Scale

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional hybrid zones where hybridization spans generations Herein, I explored hybrid zones in two species complexes of reptiles across Eastern, Central, and Southwestern North America. Hybrid zones can influence evolutionary trajectories, and understanding the mechanisms underlying their formation is important for defining appropriate management strategies and can help avoid actions that would inadvertently lead to new hybrid zones. Chapter I assessed differential introgression in a complex of terrestrial turtles, the American Box Turtles (Terrapene spp.), from a contemporary hybrid zone in the southeastern United States. Transcriptomic loci were correlated with environmental predictors to evaluate mechanisms engendering maladapted hybrids and adaptive introgression. Selection against hybrids predominated for inter-specifics but directional introgression did so in conspecifics. Outlier loci also primarily correlated with temperature, reflecting the temperature dependency of ectotherms and underscoring their vulnerability to climate change. Chapter II performed a robust assessment of recently developed machine learning (M-L) approaches to delimit four Terrapene species and evaluate the impact of data filtering and M-L parameter choices. Parameter selections were varied to determine their effects in resolving clusters. The results provide necessary recommendations on using M-L for species delimitation in species complexes defined by secondary contact. These data exemplify usage of M-L software in a phylogenetically complex group. Chapter III describes an R package to visualize some of the analyses from Chapter I. Current software to generate genomic clines does not include functions to visualize the results. Thus, I wrote an API (application programming interface) that does so and also performs other genomic and geographic cline-related tasks. Chapter IV examines historical and contemporary phylogeographic patterns in the Massasaugas (Sistrurus spp.), a type of dwarf rattlesnake found across the Southwest and Central Great Plains. In the Southwest, S. tergeminus tergeminus and S. t. edwardsii putatively diverged in the absence of strong physiographic barriers and physical glaciers, suggesting primary divergence. In contrast, a disjunct population of S. t. tergeminus in Missouri reflects potentially historical secondary contact with S. catenatus. These taxa represent contrasting examples of divergence resulting from alternative phylogeographic processes and contextualizes evolutionarily significant and management units. Combined, the four chapters present population genomic data to elucidate impacts of phylogeographic processes on hybrid zones at a continental scale. The data will promote effective conservation management strategies, as many species in the focal regions have been affected by anthropogenic pressures. In this sense, the results can be extrapolated to co-distributed taxa with similar phylogeographic histories

DNA-based methods: technology solutions to evaluate ecosystem function (Part of 'Understanding ecosystems and resilience using DNA: Chief Scientist’s Group report')

Isolation of genetic material from environmental samples (soil, water sediment), so called eDNA is now routine. These samples provide insight into the macro and micro ecology of the ecosystem from which they are isolated. Targeting specific sequences from specific species allows non-invasive sampling of organisms of interest. Information derived from DNA can be used to support conservation efforts and it also allows the tracking of pathogens and invasive species. More generic approaches allow us to profile bacterial, fungal, algal, plant or animal species. From these data we can perform multi-dimensional analysis, addressing key environmental questions. For example, a bacterial profile can report on the presence of pathogens or the impact of pollutants. Quantitative genetic approaches and Next Generation Sequencing technology that supports the use of eDNA, represents a mature technology with validated applications throughout the healthcare industry. New innovations will provide additional, enhanced utility and cost efficiencies, supporting increased spatial and temporal resolution monitoring with the potential to provide real time surveillance. Currently, these eDNA approaches have been deployed as adjuncts to established approaches limiting the potential benefits gained. Our recommendation is for a new generation of biomonitoring approaches to be adopted based on the full potential proved by eDNA. The potential of these novel eDNA approaches combined with good ecological knowledge and interpretation will provide the tools needed to realise ‘A Green Future’, and deliver the “Plan to Improve the Environment”. Since the technology is well established, the major hurdles to exploiting eDNA tools are in transferring from research tools to regulatory and industrial implementation. Our recommendation therefore are focused around a four step process to fast-track this objective: 1. Define and specify the explicit need or question. 2. Establish a transparent ‘AGILE’ assessments and validation processes. 3. Liaise between UKRI and BEIS to establish funding pipeline from research concept to product. 4. Engage with the industrial sectors to deliver products and services for the environmental sector

Interspecific Hybridization in Plant Biology

Many crop gene pools are derived from a small number of founders. As a consequence of long histories of strong directional selection, crop gene pools have narrow genetic diversity available to provide inherent solutions to changing needs or challenges. Notoriously, plants can mate across taxonomically-determined species boundaries, and interspecific hybridization is widely used in plant genetics research. Interspecific hybridizations have conferred practical improvements to crops, some of which are unexpected based on the phenotypes of the parents. Genomics has provided insights into the fundamental consequences of interspecific hybridization for plant biology. Additionally, genomics has allowed the development of molecular tools for dissecting the genetic control of phenotypic variation in interspecific hybrid populations and manipulating interspecific introgressions in crop improvement. This Research Topic aims to publish peer-reviewed research to interspecific hybridization and its consequences, both fundamental and applied. While such work is prominent in plants, consideration will also be given to salient work in other taxa. A key threshold for publication will be the extent to which findings are of cross-cutting interest and importance, i.e. not only to those working on the target taxon but to a wide range of biological scientists.Peer reviewe

Osteoarthritis: genetics and phenotypes in all their complexity

The genetic epidemiology of ostheoarthritis, using genome-wide association studies and other omics to elucidate teh pathology of this common joint disorder

Book of Abstracts of MICROBIOTEC09

Sítio da conferência: http://www.deb.uminho.pt/microbiotec09/This book contains the abstracts presented at the 3rd joint meeting of the Portuguese Society of Microbiology and The Portuguese Society of Biotechnology - MicroBiotec09, held in Vilamoura, Portugal, over 3 days, from the 28th to the 30th of November, 2009. MicroBiotec09 comes in the sequence of previous conferences organized by each society, since 1982, date of the I Encontro Nacional de Biotecnologia (Lisbon), till 2005, date of the first joint meeting - MICRO'05 + BIOTEC'05 (Póvoa de Varzim). Following this joint meeting, another - MICRO 07 + BIOTEC 07 + XXIII JPG took place in Lisbon (2007). MicroBiotec09 is a joint organization of “Sociedade Portuguesa de Biotecnologia”, “Sociedade Portuguesa de Microbiologia”, Institute for Biotechnology and Bioengineering (Universidade do Minho – Departamento de Engenharia Biológica) and Centro de Recursos Microbiológicos (Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia – Departamento de Ciências da Vida). MicroBiotec09 brings together both young and established researchers and end users to discuss recent developments in different areas of Biotechnology and Microbiology. The conference program has thus been divided in 8 major sessions: Microbial Physiology, Molecular Biology and Functional Genomics; Cell and Tissue Engineering, Biomaterials and Nanobiotechnologies; Clinical Microbiology and Epidemiology; Environmental Microbiology and Biotechnology; Health and Pharmaceutical Biotechnology; Cellular Microbiology and Pathogenesis; Industrial and Food Microbiology and Biotechnology; Bioinformatics, Comparative Genomics and Evolution. A special session to celebrate the 200th anniversary of Charles Darwin's birth and the 150th anniversary of the publication of his landmark work “On the Origin of Species by Means of Natural Selection” will also take place. A total of 295 abstracts are included in the book, consisting of 6 invited lecturers, 10 oral presentations and 44 short oral presentations given in 3 parallel sessions, along with 4 slots for viewing poster presentations. All abstracts have been reviewed and we are grateful to the members of scientific and organizing committees for their evaluations. It was an intensive task since 328 submitted abstracts were received. It has been an honor for us to contribute to setting up MicroBiotec09 during an intensive period of 6 months. We wish to thank the authors who have contributed to yield a high scientific standard to the program. We are thankful to the sponsors who have contributed decisively to this event. We also extend our gratefulness to all those who, through their dedicated efforts, have assisted us in this task. On behalf of the Scientific and Organizing Committees we wish you that together with an interesting reading, the scientific program and the social moments organized will be memorable for all.Fundação para a Ciência e a Tecnologia (FCT

RNA, the Epicenter of Genetic Information

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information. Key Features Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other. Integrates the influences of biochemistry and genetics on the landscape of molecular biology. Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress. Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA. Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology. Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers