Evolutionary medicine is a growing field focusing on the evolutionary basis of human diseases and their changes through time. The introduction of concepts of long- and short-term evolution into the medical curricula is essential to acknowledge the variability of human biology.
Methods
Three courses of the EM taught at the University of Zurich and the University of Adelaide are presented by giving their general descriptions, full curricula, and the results of anonymized student evaluations.
Results
The presented courses meet a growing need and were positively received by the students. Most importantly, they seem to stimulate critical thinking about issues relating to health and evolution.
Conclusions
The incorporation of these topics into curricula will allow future practitioners of health-related professions to apply principles of human evolution and its forces in their work.
Keywords Disease Curricula Evolutionary medicine Medical school
Phylogenetic trees have become increasingly essential across biology disciplines. Consequently, learning about phylogenetic trees has become an important component of biology education and an area of interest for biology education research. Construction tasks, in which students generate phylogenetic trees from some type of data, are often used for instruction. However, the impact of these exercises on student learning is uncertain, in part due to our fragmented knowledge of what students construct during the tasks. The goal of this project was to develop a more robust method for describing student-generated phylogenetic trees, which will support future investigations that attempt to link construction tasks with student learning.
Results
Through iterative examination of data from an introductory biology course, we developed a method for describing student-generated phylogenetic trees in terms of style, conventionality, and accuracy. Students used the diagonal style more often than the bracket style for construction tasks. The majority of phylogenetic trees were constructed conventionally, and variable orientation of branches was the most common unconventional feature. In addition, the majority of phylogenetic trees were generated correctly (no errors) or adequately (minor errors only) in terms of accuracy. Suggesting extant taxa are descended from other extant taxa was the most common major error, while empty branches and extra nodes were very common minor errors.
Conclusions
The method we developed to describe student-constructed phylogenetic trees uncovered several trends that warrant further investigation. For example, while diagonal and bracket phylogenetic trees contain equivalent information, student preference for using the diagonal style could impact comprehension. In addition, despite a lack of explicit instruction, students generated phylogenetic trees that were largely conventional and accurate. Surprisingly, accuracy and conventionality were also dependent on each other. Our method for describing phylogenetic trees constructed by students is based on data from one introductory biology course at one institution, and the results are likely limited. We encourage researchers to use our method as a baseline for developing a more generalizable tool, which will support future investigations that attempt to link construction tasks with student learning.
Keywords
Phylogenetic trees Cladograms Conceptual models Construction tasks Evolution Tree thinking
We investigate Quantum Darwinism and the emergence of a classical world from the quantum one in connection with the spectral properties of the environment. We use a microscopic model of quantum environment in which, by changing a simple system parameter, we can modify the information back flow from environment into the system, and therefore its non-Markovian character. We show that the presence of memory effects hinders the emergence of classical objective reality, linking these two apparently unrelated concepts via a unique dynamical feature related to decoherence factors.
Heart fossilization is possible and informs the evolution of cardiac outflow tract in vertebrates
Lara Maldanis, Murilo Carvalho, Mariana Ramos Almeida, Francisco Idalécio Freitas, José Artur Ferreira Gomes de Andrade, Rafael Silva Nunes, Carlos Eduardo Rochitte, Ronei Jesus Poppi, Raul Oliveira Freitas, Fábio Rodrigues, Sandra Siljeström, Frederico Alves Lima, Douglas Galante, Ismar S Carvalho, Carlos Alberto Perez, Marcelo Rodrigues de Carvalho, Jefferson Bettini, Vincent Fernandez, José Xavier-Neto
Elucidating cardiac evolution has been frustrated by lack of fossils. One celebrated enigma in cardiac evolution involves the transition from a cardiac outflow tract dominated by a multi-valved conus arteriosus in basal actinopterygians, to an outflow tract commanded by the non-valved, elastic, bulbus arteriosus in higher actinopterygians.We demonstrate that cardiac preservation is possible in the extinct fish Rhacolepis buccalis from the Brazilian Cretaceous. Using X-ray synchrotron microtomography, we show that Rhacolepis fossils display hearts with a conus arteriosus containing at least five valve rows. This represents a transitional morphology between the primitive, multivalvar, conal condition and the derived, monovalvar, bulbar state of the outflow tract in modern actinopterygians. Our data rescue a long-lost cardiac phenotype (119-113 Ma) and suggest that outflow tract simplification in actinopterygians is compatible with a gradual, rather than a drastic saltation event. Overall, our results demonstrate the feasibility of studying cardiac evolution in fossils.
Modern research has majorly advanced our understanding of how the heart works, and has led to new therapies for cardiac diseases. However, little is known about how the heart has evolved throughout the history of animals with backbones – a group that is collectively referred to as vertebrates. This is partly because the heart is made from soft muscle tissue, which does not fossilize as often as harder tissues such as bones.
Even though fossils of soft tissues are rare, paleontologists have already unearthed fossils of other soft organs such as the stomach and umbilical cord. These discoveries suggested that there was hope of finding fossil hearts, and now Maldanis, Carvalho et al. have indeed discovered fossil hearts in two specimens of an extinct species of bony fish called Rhacolepis buccalis. These fish were alive over 113 million years ago during the Cretaceous period, in an area that is now modern-day Brazil.
Like all known vertebrates, these R. buccalis fossils have valves between the heart and the major artery that carries blood out of the heart. Such valves are vital because they prevent pumped blood from flowing back into the heart. However, oddly, R. buccalis fossils show five of these valves, which is more than any advanced bony fish that is alive today. Comparing this with the situation in other fish species suggests that vertebrate hearts gradually evolved to become progressively simpler.
This discovery shows that it is possible to study heart evolution with fossils. Maldanis, Carvalho et al. hope that their findings will stimulate researchers from all over the world to examine the fossils of well-preserved animals in search of clues to help reconstruct the major steps in the evolution of the vertebrate heart.
A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.
Citation: Doolittle WF, Brunet TDP (2016) What Is the Tree of Life? PLoS Genet 12(4): e1005912. doi:10.1371/journal.pgen.1005912
Editor: Susan M. Rosenberg, Baylor College of Medicine, UNITED STATES
Funding: This work was supported by the Natural Sciences and Engineering Research Council of Canada, grant number GLDSU/447989—2013. The funders had no role in the preparation of the article.
Competing interests: The authors have declared that no competing interests exist.
The collective dynamics of multicellular systems arise from the interplay of a few fundamental elements: growth, division and apoptosis of single cells; their mechanical and adhesive interactions with neighboring cells and the extracellular matrix; and the tendency of polarized cells to move. Micropatterned substrates are increasingly used to dissect the relative roles of these fundamental processes and to control the resulting dynamics. Here we show that a unifying computational framework based on the cellular Potts model can describe the experimentally observed cell dynamics over all relevant length scales. For single cells, the model correctly predicts the statistical distribution of the orientation of the cell division axis as well as the final organisation of the two daughters on a large range of micropatterns, including those situations in which a stable configuration is not achieved and rotation ensues. Large ensembles migrating in heterogeneous environments form non-adhesive regions of inward-curved arcs like in epithelial bridge formation. Collective migration leads to swirl formation with variations in cell area as observed experimentally. In each case, we also use our model to predict cell dynamics on patterns that have not been studied before.
Author Summary
The collective dynamics of many cells is more than the sum of its parts. For example, large cell collectives often form streams, swirls or bridges that cannot be achieved by single cells. Yet the dynamic processes of single cells, especially their response to adhesive and mechanical cues, stays an essential element of the collective cell dynamics. Here we introduce a comprehensive modeling framework that allows us to predict cellular dynamics from the level of single cells up to the level of large cell collectives on the same footing. We focus on cellular dynamics on adhesive micropatterns as an especially successful approach to investigate and control complex cell behaviour. Our model successfully predicts a large range of experimentally observed phenomena, allows us to investigate the relative importance of the different cellular processes and in the future can be used to design new adhesive micropatterns that promote desired cell dynamics.
Citation: Albert PJ, Schwarz US (2016) Dynamics of Cell Ensembles on Adhesive Micropatterns: Bridging the Gap between Single Cell Spreading and Collective Cell Migration. PLoS Comput Biol 12(4): e1004863. doi:10.1371/journal.pcbi.1004863
Editor: Feilim Mac Gabhann, Johns Hopkins University, UNITED STATES
Received: August 31, 2015; Accepted: March 11, 2016; Published: April 7, 2016
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: This work was supported by the European Union’s Seventh Framework Programme through the MEHTRICS-project (Micropattern Enhanced High Throughput RNA Interference for Cell Screening, http://www.mehtrics.com, grant agreement 278758). We also acknowledge support by the EcTop B programme (cytoskeleton) of the cluster of excellence CellNetworks. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network’s units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function.
• A model for time-compensated sun compass used by monarch butterflies is developed
• Neural oscillations encoding solar azimuth and time of day are proposed
• Special integration of neural oscillations enables correction to southwest flight
• The model explains flight simulator tracks and supports northeast remigration
Summary
Migrating eastern North American monarch butterflies use a time-compensated sun compass to adjust their flight to the southwest direction. Although the antennal genetic circadian clock and the azimuth of the sun are instrumental for proper function of the compass, it is unclear how these signals are represented on a neuronal level and how they are integrated to produce flight control. To address these questions, we constructed a receptive field model of the compound eye that encodes the solar azimuth. We then derived a neural circuit model that integrates azimuthal and circadian signals to correct flight direction. The model demonstrates an integration mechanism, which produces robust trajectories reaching the southwest regardless of the time of day and includes a configuration for remigration. Comparison of model simulations with flight trajectories of butterflies in a flight simulator shows analogous behaviors and affirms the prediction that midday is the optimal time for migratory flight.
Received: September 2, 2015; Received in revised form: February 11, 2016; Accepted: March 15, 2016; Published: April 14, 2016
A 2.4% Determination of the Local Value of the Hubble Constant
Adam G. Riess, Lucas M. Macri, Samantha L. Hoffmann, Dan Scolnic, Stefano Casertano, Alexei V. Filippenko, Brad E. Tucker, Mark J. Reid, David O. Jones, Jeffrey M. Silverman, Ryan Chornock, Peter Challis, Wenlong Yuan, Ryan J. Foley
Laura A. Hug, Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, Alex W. Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A. Relman, Kari M. Finstad, Ronald Amundson, Brian C. Thomas & Jillian F. Banfield
The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches 2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships 3,4,5 or on the known, well-classified diversity of life with an emphasis on eukaryotes 6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts 7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.
Early approaches to describe the tree of life distinguished organisms based on their physical characteristics and metabolic features. Molecular methods dramatically broadened the diversity that could be included in the tree because they circumvented the need for direct observation and experimentation by relying on sequenced genes as markers for lineages. Gene surveys, typically using the small subunit ribosomal RNA (SSU rRNA) gene, provided a remarkable and novel view of the biological world 1,9,10, but questions about the structure and extent of diversity remain. Organisms from novel lineages have eluded surveys, because many are invisible to these methods due to sequence divergence relative to the primers commonly used for gene amplification 7,11. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts 7.
Whole genome reconstruction was first accomplished in 1995 (ref. 12), with a near-exponential increase in the number of draft genomes reported each subsequent year. There are 30,437 genomes from all three domains of life—Bacteria, Archaea and Eukarya—which are currently available in the Joint Genome Institute's Integrated Microbial Genomes database (accessed 24 September 2015). Contributing to this expansion in genome numbers are single cell genomics 13 and metagenomics studies. Metagenomics is a shotgun sequencing-based method in which DNA isolated directly from the environment is sequenced, and the reconstructed genome fragments are assigned to draft genomes 14. New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes 7,15. These genome- (rather than gene) based approaches provide information about metabolic potential and a variety of phylogenetically informative sequences that can be used to classify organisms 16. Here, we have constructed a tree of life by making use of genomes from public databases and 1,011 newly reconstructed genomes that we recovered from a variety of environments (see Methods).
To render this tree of life, we aligned and concatenated a set of 16 ribosomal protein sequences from each organism. This approach yields a higher-resolution tree than is obtained from a single gene, such as the widely used 16S rRNA gene16. The use of ribosomal proteins avoids artefacts that would arise from phylogenies constructed using genes with unrelated functions and subject to different evolutionary processes. Another important advantage of the chosen ribosomal proteins is that they tend to be syntenic and co-located in a small genomic region in Bacteria and Archaea, reducing binning errors that could substantially perturb the geometry of the tree. Included in this tree is one representative per genus for all genera for which high-quality draft and complete genomes exist (3,083 organisms in total).
Despite the methodological challenges, we have included representatives of all three domains of life. Our primary focus relates to the status of Bacteria and Archaea, as these organisms have been most difficult to profile using macroscopic approaches, and substantial progress has been made recently with acquisition of new genome sequences 7,8,13. The placement of Eukarya relative to Bacteria and Archaea is controversial 1,4,5,17,18. Eukaryotes are believed to be evolutionary chimaeras that arose via endosymbiotic fusion, probably involving bacterial and archaeal cells 19. Here, we do not attempt to confidently resolve the placement of the Eukarya. We position them using sequences of a subset of their nuclear-encoded ribosomal proteins, an approach that classifies them based on the inheritance of their information systems as opposed to lipid or other cellular structures 5.
Figure 1 presents a new view of the tree of life. This is one of a relatively small number of three-domain trees constructed from molecular information so far, and the first comprehensive tree to be published since the development of genome-resolved metagenomics. We highlight all major lineages with genomic representation, most of which are phylum-level branches (see Supplementary Fig. 1 for full bootstrap support values). However, we separately identify the Classes of the Proteobacteria, because the phylum is not monophyletic (for example, the Deltaproteobacteria branch away from the other Proteobacteria, as previously reported2,20).
Studies of the effects of mass extinctions on ancient ecosystems have focused on changes in taxic diversity, morphological disparity, abundance, behaviour and resource availability as key determinants of group survival. Crucially, the contribution of life history traits to survival during terrestrial mass extinctions has not been investigated, despite the critical role of such traits for population viability. We use bone microstructure and body size data to investigate the palaeoecological implications of changes in life history strategies in the therapsid forerunners of mammals before and after the Permo-Triassic Mass Extinction (PTME), the most catastrophic crisis in Phanerozoic history. Our results are consistent with truncated development, shortened life expectancies, elevated mortality rates and higher extinction risks amongst post-extinction species. Various simulations of ecological dynamics indicate that an earlier onset of reproduction leading to shortened generation times could explain the persistence of therapsids in the unpredictable, resource-limited Early Triassic environments, and help explain observed body size distributions of some disaster taxa (e.g., Lystrosaurus). Our study accounts for differential survival in mammal ancestors after the PTME and provides a methodological framework for quantifying survival strategies in other vertebrates during major biotic crises.
Many bacteria, including important pathogens, move by projecting grappling-hook–like extensions called type IV pili from their cell bodies. After these pili attach to other cells or objects in their environment, the bacteria retract the pili to pull themselves forward. Chang et al. used electron cryotomography of intact cells to image the protein machines that extend and retract the pili, revealing where each protein component resides. Putting the known structures of the individual proteins in place like pieces of a three-dimensional puzzle revealed insights into how the machine works, including evidence that ATP hydrolysis by cytoplasmic motors rotates a membrane-embedded adaptor that slips pilin subunits back and forth from the membrane onto the pilus.
Science, this issue p. 10.1126/science.aad2001
Structured Abstract
INTRODUCTION
Type IVa pili are bacterial cell surface structures that perform critical functions in motility, surface adhesion, virulence, and biofilm formation. Type IVa pili are anchored in the cell envelope and pull cells forward through cycles of extension, adhesion to surfaces, and retraction, all powered by the type IVa pilus machine (T4PM). Although the structures and connectivities of the 10 core T4PM proteins and minor pilins have already been determined, the overall architecture of the T4PM and its extension and retraction mechanisms have not.
RATIONALE
To elucidate the architecture of the intact T4PM, we directly imaged T4PMs within intact Myxococcus xanthus cells by cryo–electron tomography. Mutants that either lacked T4PM components or contained individual T4PM proteins fused to a tag were then imaged. Difference maps revealed the locations of all components of the T4PM machine. Hypothetical models were then built by fitting the known atomic structures of the components together in their relative positions.
RESULTS
Both piliated and nonpiliated T4PMs are multilayered structures that span the entire cell envelope. T4PMs include an outer membrane pore, three interconnected periplasmic ring structures and another in the cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. The PilQ secretin forms the outer membrane pore; TsaP forms a periplasmic ring around PilQ; periplasmic domains of PilQ together with PilP constitute the mid-periplasmic ring; and the globular domains of PilO and PilN constitute the lower periplasmic ring and connect via coiled coils across the inner membrane to PilM, which forms the cytoplasmic ring. The cytoplasmic domains of the inner membrane protein PilC form the cytoplasmic dome on the T4PM axis inside the PilM ring. The short stem in the nonpiliated state is composed of minor pilins and PilA, the major subunit of the pilus. In the piliated state, the pilus extends from the cell exterior through the PilQ pore and the periplasmic rings to PilC in the inner membrane. In the piliated structure, the hexameric adenosine triphosphatases (ATPases) PilB and PilT bind in a mutually exclusive manner to the base of the T4PM, where they appear as the cytoplasmic disc during extensions and retractions, respectively.
Next, we asked whether the known atomic structures of the proteins could be fit within the map where our imaging results indicated, while still satisfying all known constraints of size, connectivities, and interfaces. This successful effort resulted in “pseudo-atomic” working models of both states of the T4PM. The models suggest that through ATP hydrolysis, PilB rotates PilC, incrementally moving it into positions that facilitate incorporation of new PilA subunits one by one from the inner membrane onto the base of the growing helical pilus. Pilus retraction is driven by replacement of PilB with PilT, which rotates PilC into positions that promote PilA departure from the base of the pilus back into the membrane.
CONCLUSION
We determined the architecture of the T4PM in the piliated and nonpiliated states and mapped all known components onto this architecture, producing a complete structural map of the T4PM. The results illustrate how the structure and function of macromolecular complexes that defy purification and traditional structural approaches can nonetheless be interrogated through cryo–electron tomography of intact cells and model building.
Abstract
Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo–electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.
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PERGUNTA CAUSTICANTE DESTE BLOGGER:
No Abstract os autores não mencionaram o fato, Fato, FATO da evolução das fímbrias. Antes, se limitaram tão somente a descrever a complexidade de máquina biológica que são as fímbrias.
Ora, e Darwin e seus atuais discípulos fundamentalistas não conseguem explicar a extrema complexidade arquitetônica de uma "simples" fímbria, podem explicar a diversidade e complexidade de toda história evolutiva das espécies?
Pano rápido!
Resposta substanciada pelas montanhas de evidências consideradas pelo rigor do contexto de justificação teórica: NÃO!
Texto Silvio Anunciação Imagens Antoninho Perri Edição de Imagens Paulo José Cavalheri
O professor da Unicamp Marcos Nogueira Eberlin será o primeiro cientista sul-americano a receber a medalha J. J. Thomson, conferida bianualmente pela Fundação Internacional de Espectrometria de Massa (IMSF, na sigla em inglês). A escolha de Marcos Eberlin foi feita após votação dos representantes de 39 sociedades de espectrometria de massa afiliadas. Conforme a IMSF seu nome foi escolhido entre 17 candidatos indicados graças aos relevantes serviços para o desenvolvimento e propagação da espectrometria de massas. A medalha será entregue em agosto na cidade de Toronto, no Canadá, durante a 21ª Conferência Internacional de Espectrometria de Massas.
David Gordon1,2,*, John Huddleston1,2,*, Mark J. P. Chaisson1,*, Christopher M. Hill1,*, Zev N. Kronenberg1,*, Katherine M. Munson1, Maika Malig1, Archana Raja1,2, Ian Fiddes3, LaDeana W. Hillier4, Christopher Dunn5, Carl Baker1, Joel Armstrong3, Mark Diekhans3, Benedict Paten3, Jay Shendure1,2, Richard K. Wilson4, David Haussler3, Chen-Shan Chin5, Evan E. Eichler1,2,†
Access to complete, high-quality genomes of nonhuman primates will also help us understand human biology. Gordon et al. used long-read sequencing technology to improve genome data on our close relative the gorilla. Sequencing from a single individual decreased assembly fragmentation and recovered previously missed genes and noncoding loci. Mapping short-read sequences from additional gorillas helped reconstruct a “pan” gorilla sequence documenting genetic variation. Comparison with human genomes revealed species-specific differences ranging in size from one to thousands of bases in length, including some that are likely to affect gene regulation.
The accurate sequence and assembly of genomes is critical to our understanding of evolution and genetic variation. Despite advances in short-read sequencing technology that have decreased cost and increased throughput, whole-genome assembly of mammalian genomes remains problematic because of the presence of repetitive DNA.
RATIONALE
The goal of this study was to sequence and assemble the genome of the western lowland gorilla by using primarily single-molecule, real-time (SMRT) sequencing technology and a novel assembly algorithm that takes advantage of long (>10 kbp) sequence reads. We specifically compare the properties of this assembly to gorilla genome assemblies that were generated by using more routine short sequence read approaches in order to determine the value and biological impact of a long-read genome assembly.
RESULTS
We generated 74.8-fold SMRT whole-genome shotgun sequence from peripheral blood DNA isolated from a western lowland gorilla (Gorilla gorilla gorilla) named Susie. We applied a string graph assembly algorithm, Falcon, and consensus algorithm, Quiver, to generate a 3.1-Gbp assembly with a contig N50 of 9.6 Mbp. Short-read sequence data from an additional six gorilla genomes was mapped so as to reduce indel errors and improve the accuracy of the final assembly. We estimate that 98.9% of the gorilla euchromatin has been assembled into 1854 sequence contigs. The assembly represents an improvement in contiguity: >800-fold with respect to the published gorilla genome assembly and >180-fold with respect to a more recently released upgrade of the gorilla assembly. Most of the sequence gaps are now closed, considerably increasing the yield of complete gene models. We estimate that 87% of the missing exons and 94% of the incomplete genes are recovered. We find that the sequence of most full-length common repeats is resolved, with the most significant gains occurring for the longest and most G+C–rich retrotransposons. Although complex regions such as the major histocompatibility locus are accurately sequenced and assembled, both heterochromatin and large, high-identity segmental duplications are not because read lengths are insufficiently long to traverse these repetitive structures. The long-read assembly produces a much finer map of structural variation down to 50 bp in length, facilitating the discovery of thousands of lineage-specific structural variant differences that have occurred since divergence from the human and chimpanzee lineages. This includes the disruption of specific genes and loss of predicted regulatory regions between the two species. We show that use of the new gorilla genome assembly changes estimates of divergence and diversity, resulting in subtle but substantial effects on previous population genetic inferences, such as the timing of species bottlenecks and changes in the effective population size over the course of evolution.
CONCLUSION
The genome assembly that results from using the long-read data provides a more complete picture of gene content, structural variation, and repeat biology, improving population genetic and evolutionary inferences. Long-read sequencing technology now makes it practical for individual laboratories to generate high-quality reference genomes for complex mammalian genomes.
Almost a spider: a 305-million-year-old fossil arachnid and spider origins
Russell J. Garwood, Jason A. Dunlop, Paul A. Selden, Alan R. T. Spencer, Robert C. Atwood, Nghia T. Vo, Michael Drakopoulos
Published 30 March 2016.DOI: 10.1098/rspb.2016.0125
Abstract
Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasieri gen. et sp. nov. from the Late Carboniferous (Stephanian, ca 305–299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography reconstruction. The latter is a first for siderite-hosted fossils and has allowed us to investigate fine anatomical details. Although distinctly spider-like in habitus, this remarkable fossil lacks a key diagnostic character of Araneae: spinnerets on the underside of the opisthosoma. It also lacks a flagelliform telson found in the recently recognized, spider-related, Devonian–Permian Uraraneida. Cladistic analysis resolves our new fossil as sister group to the spiders: the spider stem-group comprises the uraraneids and I. brasieri. While we are unable to demonstrate the presence of spigots in this fossil, the recovered phylogeny suggests the earliest character to evolve on the spider stem-group is the secretion of silk. This would have been followed by the loss of a flagelliform telson, and then the ability to spin silk using spinnerets. This last innovation defines the true spiders, significantly post-dates the origins of silk, and may be a key to the group's success. The Montceau-les-Mines locality has previously yielded a mesothele spider (with spinnerets). Evidently, Late Palaeozoic spiders lived alongside Palaeozoic arachnid grades which approached the spider condition, but did not express the full suite of crown-group autapomorphies.
Por que sou ‘pós-darwinista’? Porque já fui evolucionista de carteirinha. Hoje, sou cético da teoria macroevolutiva como verdade científica. Contudo, meu ceticismo ao ‘dogma central’ darwinista não é baseado em relatos da criação de textos sagrados. Foi a séria e conflituosa consideração do debate que ocorre intramuros e nas publicações científicas há muitos anos sobre a insuficiência epistêmica da teoria geral da evolução. Eu fui ateu marxista-leninista. Hoje, não tenho mais fé cega no ateísmo. Não creio mais na interpretação literal dos dogmas de Darwin aceitos ‘a priori’ e defendidos ideologicamente com unhas e dentes pela Nomenklatura científica. A Ciência me deu esta convicção. Aprendi na universidade: quando uma teoria científica não é apoiada pelas evidências, ela deve ser revista ou simplesmente descartada. Sou pós-darwinista me antecipando à iminente e eminente ruptura paradigmática em biologia evolutiva. Chegou a hora de dizer adeus a Darwin. Mestre em História da Ciência – PUC-SP. CV Plataforma Lattes: http://lattes.cnpq.br/6602620537249723
