Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Investigating uneven recovery of repatriated bobcats (Lynx rufus) in a mined landscape: space use, habitat use and condition in coal country

Abstract ContextBobcats (Lynx rufus) were extirpated from Ohio, USA, during the mid-1800s. Genetic evidence indicates that they recolonised from neighbouring states. Initial re-establishment occurred almost simultaneously in two spatially distinct areas of a coal-mined landscape in the 1980s. Relative population growth was apparently higher in the eastern than in the southern area. AimsUnderstanding the reasons for the disparity in population dynamics and sustainability is essential for proper bobcat management. It also addresses substantial knowledge gaps in vertebrate carnivore ecology on mined land. We hypothesised that the characteristics of mined land in the eastern Ohio area provided bobcats with greater resources, enabling a more rapid recovery. MethodsWe trapped bobcats and took body measurements and weights to determine condition indices. We attached GPS radio-collars and used locations to determine annual home-range and core-area sizes, home-range and core-area overlap, and habitat selection using remotely sensed land cover data and mine permit records. We compared factors between the two bobcat population areas. Key resultsBody condition indices were higher, and home ranges and core areas of males and females were smaller, for eastern Ohio bobcats. Home-range overlap did not differ for any dyad type. Selection of mined land by habitat type differed at the home-range level, with eastern bobcats selecting more mined habitats and southern bobcats showing an opposite tendency. ConclusionsAn interaction may exist between landscape features of former surface mines and bobcat recovery. Results suggest more favourable habitat conditions in the eastern area, which featured more mined land and more older, less regulated mines, than in the southern area. These conditions may support a higher bobcat reproductive success. ImplicationsThe first bobcat harvest season in Ohio is under development by authorities. We recommend the regulation of eastern and southern Ohio as separate bobcat management units; the southern population should remain protected, and the eastern population should be managed conservatively as a source population to further colonise southern Ohio. Our data suggest that surface-mined land can be conducive to the restoration and conservation of species. </jats:p

Author Correction: Roadkill and space use data predict vehicle-strike hotspots and mortality rates in a recovering bobcat (Lynx rufus) population

An amendment to this paper has been published and can be accessed via a link at the top of the paper.</jats:p

Author Correction: Roadkill and space use data predict vehicle-strike hotspots and mortality rates in a recovering bobcat (Lynx rufus) population (Scientific Reports, (2019), 9, 1, (15391), 10.1038/s41598-019-50931-5)

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Roadkill and space use data predict vehicle-strike hotspots and mortality rates in a recovering bobcat (Lynx rufus) population

AbstractRoadways pose challenges for conserving wide-ranging animal species. As bobcat (Lynx rufus) populations recover in Ohio, an accurate evaluation of population metrics is critical to understanding future population trajectories. In this study, we integrated multiple datasets to examine overall road mortality rates in Ohio. First, we utilized a long-term vehicle-strike dataset (1978–2017) to determine landscape and local predictors of road mortality. We found that bobcats were killed at higher rates on interstates regardless of surrounding landscape composition, but that landscape variables were useful at predicting mortality on lower-traffic roads. To explore road avoidance behaviors, we used GPS telemetry data from 18 individuals to compare road crossings along trajectory paths with random road crossings simulated using Correlated Random Walks. Bobcats exhibited avoidance of certain route types (county, municipal, and US routes). Finally, by integrating traffic volume data, road crossing behavior, and accounting for the proportion of each route type present in the study area, we estimated that a minimum of 6% and up to 18% of the bobcat population in Ohio is lost to vehicle-strikes annually. To fully understand the population level impacts of this mortality, we recommend further monitoring of age structure and sex of roadkill animals. Our results identify potential areas for mitigation of vehicle-strikes and emphasize the importance of accounting for road mortality when making management decisions for Ohio’s recovering bobcat population.</jats:p

Roadkill and Space Use Data Predict Vehicle-Strike Hotspots and Mortality Rates in a Recovering Bobcat (Lynx Rufus) Population

© 2019, The Author(s). Roadways pose challenges for conserving wide-ranging animal species. As bobcat (Lynx rufus) populations recover in Ohio, an accurate evaluation of population metrics is critical to understanding future population trajectories. In this study, we integrated multiple datasets to examine overall road mortality rates in Ohio. First, we utilized a long-term vehicle-strike dataset (1978–2017) to determine landscape and local predictors of road mortality. We found that bobcats were killed at higher rates on interstates regardless of surrounding landscape composition, but that landscape variables were useful at predicting mortality on lower-traffic roads. To explore road avoidance behaviors, we used GPS telemetry data from 18 individuals to compare road crossings along trajectory paths with random road crossings simulated using Correlated Random Walks. Bobcats exhibited avoidance of certain route types (county, municipal, and US routes). Finally, by integrating traffic volume data, road crossing behavior, and accounting for the proportion of each route type present in the study area, we estimated that a minimum of 6% and up to 18% of the bobcat population in Ohio is lost to vehicle-strikes annually. To fully understand the population level impacts of this mortality, we recommend further monitoring of age structure and sex of roadkill animals. Our results identify potential areas for mitigation of vehicle-strikes and emphasize the importance of accounting for road mortality when making management decisions for Ohio’s recovering bobcat population

The responsibility to share:sharing the responsibility

The transcriptome, promoterome, and phenome clone sets described in this special issue of Genome Research are among the first of a new breed of clones. Their novel features affect how distributors on the path from originator to end user handle such resources. These new features are individual design, collective use, large scale, and flexibility. Whereas pre-genome clones bore random lengths of genomic DNA or cDNA from random locations in the genome or transcriptome, each of these post-genome clones bears a specialized vector harboring a tailored sequence that the originator selected and/or designed down to the last base pair.These clone sets are intended for collective use in two senses. Firstly, an entire set may be used in one experiment with the aim of identifying the subset that elicits some detectable phenotype in vivo. Secondly, an entire community of scientists (e.g., the worm community) may use the same clone set to identify further subsets of clones that each elicit other phenotypes. When they share their data, its combined scientific value increases disproportionately.The scale of these experiments is orders of magnitude greater than those studying one clone at a time. Since the 1970s, constructs have been arduously created by restriction and ligation. This technology is now being displaced by less-arduous in vitro recombination-based methods that permit systematic approaches to the study of defined sequences. Recombination-based cloning makes it far easier to derive subclones and swap specific sequences (representing, for example, orthologous protein domains or epitope tags). This flexibility means that initial clone sets will become the basis for many rounds of subcloning to permit finer experimental definition of function. The simplicity of these methods and the growth of bioinformatics and robotics facilitate production of large-scale clone sets whose experimental value increases geometrically, but only if distribution is timely, accurate, and efficient.Therefore, whereas the genome project used large numbers of clones for just one main purpose, post-genome molecular biology requires large clone sets for many inter-related purposes. This then creates opportunities—and problems—not only for investigative biologists, but also for infrastructure biologists (defined as those who created the machinery to facilitate the genome project that now needs adaptation to post-genomic biology).This Commentary explores how the distribution infrastructure may respond to this new breed of clones in the current policy framework. Distribution is undertaken by a number of specialist organizations globally. The authors of this Commentary are drawn from public sector organizations that may be working under not-for-profit policies and from the private sector. In some ways, we compete with each other, but our joint authorship—a first, as far as we are aware—reflects perhaps the most important feature of the response required by post-genome biology, the requirement for greater coordination