749 research outputs found
A genomic view on the adaptation and diversification of natural populations
Earlier studies in evolutionary genetics focused on a few model organisms such as
fruit flies or mice that are limited when it comes to answering evolutionary and
ecological questions. In contrast, genetic studies of natural populations have now
become common and can provide a more realistic understanding of how natural
selection, genetic drift, mutation, and gene flow shape the patterns of phenotypic
and genetic diversity, as well as adaptation and diversification across a range of
environmental conditions. This dissertation illustrates how current genomic tools
can be effectively used to (1) study the evolutionary history of species along altitudinal
gradients, and (2) understand the genetic basis of adaptive phenotypes in populations
inhabiting high-altitude habitats. In the first research paper, we compared
whole-genome resequencing data of Eastern honey bee (Apis cerana) populations
from high and low altitudes in southwestern China. We identified several regions of
the genome that appeared to have been under positive selection in highland bee
populations. Candidate loci in these genomic regions included genes related to reproduction
and feeding behavior. In the second paper, we generated a transcriptome
reference for the Neotropical frogs of the genus Oreobates by sequencing RNA
from one individual of the La Paz robber frog (Oreobates cruralis). In the third
paper, we used that transcriptome to selectively target and enrich ~18,000 genes
across species of Oreobates collected along the Andean Mountains, in South America.
We found that highland species have smaller effective populations and accumulate
nonsynonymous mutations faster than species sampled at lower altitudes. These
mutations can be targeted by natural selection and contribute to the adaptation and
differentiation of populations in mountain environments. In the fourth and final
paper, we pointed out that genomics has to be integrated with other sources of evidence
to understand evolutionary and ecological processes more deeply than was
thought in the past
Lessons learned from organizing and teaching virtual phylogenetics workshops
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Root and floral effects of flavonoid transport via an Arabidopsis MATE family transporter
Amongst their numerous roles in plants, flavonoid pigments are hypothesised to affect growth and development via interactions with components of auxin transport networks. Accordingly, our previous work showed that a multidrug and toxin efflux family transporter (FFT) alters root and seed characteristics and was required for full fertility in Arabidopsis. FFT is transcribed in guard cells throughout the plant and inactivation of FFT caused a significant perturbation in flavonoid profile in floral organs. Indeed, SEM and viability staining of mutant flowers reveal reduced anther dehiscence and a proportion of defective pollen, while siliques are smaller with fewer seeds than in WT. Null mutant seedlings grow faster and bolt sooner than WT, and seed size and mucilage are also affected. We are currently quantifying in more detail the flavonoid content of fft plants, and investigating the effect of externally applied auxin, flavonols and an auxin transport inhibitor. Finally, since we see FFT- promoter-GUS induced staining in vegetative tissues, including hydathode guard cells, we are also examining the abiotic stress response in the fft mutant. Co-expressed genes are involved in drought response including salt and osmotic stress
Human brain evolution and the "Neuroevolutionary Time-depth Principle:" Implications for the Reclassification of fear-circuitry-related traits in DSM-V and for studying resilience to warzone-related posttraumatic stress disorder.
The DSM-III, DSM-IV, DSM-IV-TR and ICD-10 have judiciously minimized discussion of etiologies to distance clinical psychiatry from Freudian psychoanalysis. With this goal mostly achieved, discussion of etiological factors should be reintroduced into the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-V). A research agenda for the DSM-V advocated the "development of a pathophysiologically based classification system". The author critically reviews the neuroevolutionary literature on stress-induced and fear circuitry disorders and related amygdala-driven, species-atypical fear behaviors of clinical severity in adult humans. Over 30 empirically testable/falsifiable predictions are presented. It is noted that in DSM-IV-TR and ICD-10, the classification of stress and fear circuitry disorders is neither mode-of-acquisition-based nor brain-evolution-based. For example, snake phobia (innate) and dog phobia (overconsolidational) are clustered together. Similarly, research on blood-injection-injury-type-specific phobia clusters two fears different in their innateness: 1) an arguably ontogenetic memory-trace-overconsolidation-based fear (hospital phobia) and 2) a hardwired (innate) fear of the sight of one's blood or a sharp object penetrating one's skin. Genetic architecture-charting of fear-circuitry-related traits has been challenging. Various, non-phenotype-based architectures can serve as targets for research. In this article, the author will propose one such alternative genetic architecture. This article was inspired by the following: A) Nesse's "Smoke-Detector Principle", B) the increasing suspicion that the "smooth" rather than "lumpy" distribution of complex psychiatric phenotypes (including fear-circuitry disorders) may in some cases be accounted for by oligogenic (and not necessarily polygenic) transmission, and C) insights from the initial sequence of the chimpanzee genome and comparison with the human genome by the Chimpanzee Sequencing and Analysis Consortium published in late 2005. Neuroevolutionary insights relevant to fear circuitry symptoms that primarily emerge overconsolidationally (especially Combat related Posttraumatic Stress Disorder) are presented. Also introduced is a human-evolution-based principle for clustering innate fear traits. The "Neuroevolutionary Time-depth Principle" of innate fears proposed in this article may be useful in the development of a neuroevolution-based taxonomic re-clustering of stress-triggered and fear-circuitry disorders in DSM-V. Four broad clusters of evolved fear circuits are proposed based on their time-depths: 1) Mesozoic (mammalian-wide) circuits hardwired by wild-type alleles driven to fixation by Mesozoic selective sweeps; 2) Cenozoic (simian-wide) circuits relevant to many specific phobias; 3) mid Paleolithic and upper Paleolithic (Homo sapiens-specific) circuits (arguably resulting mostly from mate-choice-driven stabilizing selection); 4) Neolithic circuits (arguably mostly related to stabilizing selection driven by gene-culture co-evolution). More importantly, the author presents evolutionary perspectives on warzone-related PTSD, Combat-Stress Reaction, Combat-related Stress, Operational-Stress, and other deployment-stress-induced symptoms. The Neuroevolutionary Time-depth Principle presented in this article may help explain the dissimilar stress-resilience levels following different types of acute threat to survival of oneself or one's progency (aka DSM-III and DSM-V PTSD Criterion-A events). PTSD rates following exposure to lethal inter-group violence (combat, warzone exposure or intentionally caused disasters such as terrorism) are usually 5-10 times higher than rates following large-scale natural disasters such as forest fires, floods, hurricanes, volcanic eruptions, and earthquakes. The author predicts that both intentionally-caused large-scale bioevent-disasters, as well as natural bioevents such as SARS and avian flu pandemics will be an exception and are likely to be followed by PTSD rates approaching those that follow warzone exposure. During bioevents, Amygdala-driven and locus-coeruleus-driven epidemic pseudosomatic symptoms may be an order of magnitude more common than infection-caused cytokine-driven symptoms. Implications for the red cross and FEMA are discussed. It is also argued that hospital phobia as well as dog phobia, bird phobia and bat phobia require re-taxonomization in DSM-V in a new "overconsolidational disorders" category anchored around PTSD. The overconsolidational spectrum category may be conceptualized as straddling the fear circuitry spectrum disorders and the affective spectrum disorders categories, and may be a category for which Pitman's secondary prevention propranolol regimen may be specifically indicated as a "morning after pill" intervention. Predictions are presented regarding obsessive-compulsive disorder (OCD) (e.g., female-pattern hoarding vs. male-pattern hoarding) and "culture-bound" acute anxiety symptoms (taijin-kyofusho, koro, shuk yang, shook yong, suo yang, rok-joo, jinjinia-bemar, karoshi, gwarosa, Voodoo death). Also discussed are insights relevant to pseudoneurological symptoms and to the forthcoming Dissociative-Conversive disorders category in DSM-V, including what the author terms fright-triggered acute pseudo-localized symptoms (i.e., pseudoparalysis, pseudocerebellar imbalance, psychogenic blindness, pseudoseizures, and epidemic sociogenic illness). Speculations based on studies of the human abnormal-spindle-like, microcephaly-associated (ASPM) gene, the microcephaly primary autosomal recessive (MCPH) gene, and the forkhead box p2 (FOXP2) gene are made and incorporated into what is termed "The pre-FOXP2 Hypothesis of Blood-Injection-Injury Phobia." Finally, the author argues for a non-reductionistic fusion of "distal (evolutionary) neurobiology" with clinical "proximal neurobiology," utilizing neurological heuristics. It is noted that the value of re-clustering fear traits based on behavioral ethology, human-phylogenomics-derived endophenotypes and on ontogenomics (gene-environment interactions) can be confirmed or disconfirmed using epidemiological or twin studies and psychiatric genomics
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community
The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in
The GMOD Drupal Bioinformatic Server Framework
Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS)
A second horizon scan of biogeography:golden ages, Midas touches, and the Red Queen
Are we entering a new ‘Golden Age’ of biogeography, with continued development of infrastructure
and ideas? We highlight recent developments, and the challenges and opportunities they bring, in
light of the snapshot provided by the 7th biennial meeting of the International Biogeography Society
(IBS 2015). We summarize themes in and across 15 symposia using narrative analysis and word
clouds, which we complement with recent publication trends and ‘research fronts’. We find that
biogeography is still strongly defined by core sub-disciplines that reflect its origins in botanical,
zoological (particularly bird and mammal), and geographic (e.g., island, montane) studies of the
1800s. That core is being enriched by large datasets (e.g. of environmental variables, ‘omics’,
species’ occurrences, traits) and new techniques (e.g., advances in genetics, remote sensing,
modeling) that promote studies with increasing detail and at increasing scales; disciplinary
breadth is being diversified (e.g., by developments in paleobiogeography and microbiology) and
integrated through the transfer of approaches and sharing of theory (e.g., spatial modeling and
phylogenetics in evolutionary–ecological contexts). Yet some subdisciplines remain on the fringe
(e.g., marine biogeography, deep-time paleobiogeography), new horizons and new theory may be
overshadowed by popular techniques (e.g., species distribution modelling), and hypotheses, data,
and analyses may each be wanting. Trends in publication suggest a shift away from traditional
biogeography journals to multidisciplinary or open access journals. Thus, there are currently many stewardship of, the planet (e.g., Intergovernmental Science-Policy Platform on Biodiversity and
Ecosystem Services). As in the past, biogeographers doubtless will continue to be engaged by
new data and methods in exploring the nexus between biology and geography for decades into
the future. But golden ages come and go, and they need not touch every domain in a discipline
nor affect subdisciplines at the same time; moreover, what appears to be a Golden Age may
sometimes have an undesirable ‘Midas touch’. Contexts within and outwith biogeography—e.g.,
methods, knowledge, climate, biodiversity, politics—are continually changing, and at times it can
be challenging to establish or maintain relevance. In so many races with the Red Queen, we
suggest that biogeography will enjoy greatest success if we also increasingly engage with the
epistemology of our disciplinePeer reviewe
Phylogenomic and population genomic insights on the evolutionary history of coffee leaf rust within the rust fungi
Tese de doutoramento, Biologia e Ecologia das Alterações Globais (Biologia do Genoma e Evolução), Universidade de Lisboa, Faculdade de Ciências, 2018Fungi are currently responsible for more than 30% of the emerging diseases worldwide and rust fungi (Pucciniales, Basidiomycota) are one of the most destructive groups of plant pathogens. In this thesis, two genomic approaches were pursued to further our knowledge on these pathogenic fungi at the macro-evolutionary level, using phylogenomics, and micro-evolutionary level, using population genomics. At the macro-evolutionary level, a phylogenomics pipeline was developed with the aim of investigating the role of positive selection on the origin of the rusts, particularly related to their obligate biotrophic life-style and pathogenicity. With up to 30% of the ca. 1000 screened genes showing a signal of positive selection, these results revealed a pervasive role of natural selection on the origin of this fungal group, with an enrichment of functional classes involved in nutrient uptake and secondary metabolites. Furthermore, positive selection was detected on conserved amino acid sites revealing an unexpected but potentially important role of natural selection on codon usage preferences. At the micro-evolutionary level, the focus was shifted to the coffee rust, Hemileia vastatrix, which is the causal agent of leaf rust disease and the main threat to Arabic coffee production worldwide. Using RAD sequencing to produce thousands of informative SNPs for a broad and unique sampling of this species, the aim was to investigate its evolutionary history and translate population genomic insights into recommendations for disease control. The results of this work overturned most of the preconceptions about the pathogen by revealing that instead of a single unstructured and large population, H. vastatrix is most likely a complex of cryptic species with marked host specialization. Moreover, genomic signatures of hybridization and introgression occurring between these lineages were uncovered, raising the possibility that virulence factors may be quickly exchanged. The most recent “domesticated” lineage infects exclusively the most important coffee species and SNP linkage analyses revealed the presence of recombination among isolates that were previously thought to be clonal. Altogether, these results considerably raise the evolutionary potential of this pathogen to overcome disease control measures in coffee crops. To undertake most of the tasks in this project, a new computational application called TriFusion was developed to streamline the gathering, processing and visualization of big genomic data
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