A palynological study of changing woodland limits on the Nidderdale moors

Observations have been made on the stratigraphy of peat deposits at a number of sites varying in aspect and altitude on an area of upland moorland in the West Riding of Yorkshire. Pollen diagrams have been prepared from these sites and a sequence of local pollen zones established. These zones have been subdivided on the basis of changing frequencies in the pollen of species considered to be cultural indicators. An absolute chronology has been established for the pollen diagrams from a series of eight radiocarbon dates. Attempts have been made to relate the sequence of subzones to established archaeological periods and, more recently, to documented historical events. A survey of surface pollen samples was carried out from the moorland and from within the remaining woodland communities on its flanks. The results of this survey have been used in the ecological interpretation of the fossil pollen diagrams. The early forest history of the area and the gradual decline of trees since 2,000 B.C. has been traced. It has been shown that both soil deterioration and human factors have been significant in the reduction of woodland and the establishment of heath

Opening the Woods: Towards a Quantification of Neolithic Clearance Around the Somerset Levels and Moors

Environmental reconstructions from pollen records collected within archaeological landscapes have traditionally taken a broadly narrative approach, with few attempts made at hypothesis testing or formal assessment of uncertainty. This disjuncture between the traditional interpretive approach to palynological data and the requirement for detailed, locally specific reconstructions of the landscapes in which people lived has arguably hindered closer integration of palaeoecological and archaeological datasets in recent decades. Here we implement a fundamentally different method for reconstructing past land cover from pollen records to the landscapes of and around the Somerset Levels and Moors — the Multiple Scenario Approach (MSA) — to reconstruct land cover for a series of 200-year timeslices covering the period 4200–2000 cal BC. Modelling of both archaeological and sediment chronologies enables integration of reconstructed changes in land cover with archaeological evidence of contemporary Neolithic human activity. The MSA reconstructions are presented as a series of land cover maps and as graphs of quantitative measures of woodland clearance tracked over time. Our reconstructions provide a more nuanced understanding of the scale and timing of Neolithic clearance than has previously been available from narrative based interpretations of pollen data. While the archaeological record tends to promote a view of long-term continuity in terms of the persistent building of wooden structures in the wetlands, our new interpretation of the palynological data contributes a more dynamic and varying narrative. Our case study demonstrates the potential for further integration of archaeological and palynological datasets, enabling us to get closer to the landscapes in which people lived

Genotype-by-Environment Interactions and Adaptation to Local Temperature Affect Immunity and Fecundity in Drosophila melanogaster

Natural populations of most organisms harbor substantial genetic variation for resistance to infection. The continued existence of such variation is unexpected under simple evolutionary models that either posit direct and continuous natural selection on the immune system or an evolved life history “balance” between immunity and other fitness traits in a constant environment. However, both local adaptation to heterogeneous environments and genotype-by-environment interactions can maintain genetic variation in a species. In this study, we test Drosophila melanogaster genotypes sampled from tropical Africa, temperate northeastern North America, and semi-tropical southeastern North America for resistance to bacterial infection and fecundity at three different environmental temperatures. Environmental temperature had absolute effects on all traits, but there were also marked genotype-by-environment interactions that may limit the global efficiency of natural selection on both traits. African flies performed more poorly than North American flies in both immunity and fecundity at the lowest temperature, but not at the higher temperatures, suggesting that the African population is maladapted to low temperature. In contrast, there was no evidence for clinal variation driven by thermal adaptation within North America for either trait. Resistance to infection and reproductive success were generally uncorrelated across genotypes, so this study finds no evidence for a fitness tradeoff between immunity and fecundity under the conditions tested. Both local adaptation to geographically heterogeneous environments and genotype-by-environment interactions may explain the persistence of genetic variation for resistance to infection in natural populations

Whole genome sequencing reveals a 7 base-pair deletion in DMD exon 42 in a dog with muscular dystrophy

Dystrophin is a key cytoskeletal protein coded by the Duchenne muscular dystrophy (DMD) gene located on the X-chromosome. Truncating mutations in the DMD gene cause loss of dystrophin and the classical DMD clinical syndrome. Spontaneous DMD gene mutations and associated phenotypes occur in several other species. The mdx mouse model and the golden retriever muscular dystrophy (GRMD) canine model have been used extensively to study DMD disease pathogenesis and show efficacy and side effects of putative treatments. Certain DMD gene mutations in high-risk, the so-called hot spot areas can be particularly helpful in modeling molecular therapies. Identification of specific mutations has been greatly enhanced by new genomic methods. Whole genome, next generation sequencing (WGS) has been recently used to define DMD patient mutations, but has not been used in dystrophic dogs. A dystrophin-deficient Cavalier King Charles Spaniel (CKCS) dog was evaluated at the functional, histopathological, biochemical, and molecular level. The affected dog’s phenotype was compared to the previously reported canine dystrophinopathies. WGS was then used to detect a 7 base pair deletion in DMD exon 42 (c.6051-6057delTCTCAAT mRNA), predicting a frameshift in gene transcription and truncation of dystrophin protein translation. The deletion was confirmed with conventional PCR and Sanger sequencing. This mutation is in a secondary DMD gene hotspot area distinct from the one identified earlier at the 5′ donor splice site of intron 50 in the CKCS breed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00335-016-9675-2) contains supplementary material, which is available to authorized users

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

Rhabdomyosarcoma Incidence and Survival in Whites, Blacks, and Hispanics from 1973-2013: Analysis from the Surveillance, Epidemiology, and End Results Program

Purpose Our objectives were to 1) determine the difference in Rhabdomyosarcoma (RMS) incidence and survival between different race/ethnicity groups, and 2) evaluate the difference in survival of RMS between children and adults of these race/ethnicity groups, using the Surveillance, Epidemiology, and End Results Program (SEER) database between 1973-2013. Patients and Methods We analyzed racial characteristic and incidence data from 4,280 patients diagnosed with RMS, between 1973-2013, that were reported to the SEER database. Survival and hazard analyses were conducted on 4,268 patients with known follow-up data, with end point being death from any cause. Results Over the 40-year study period overall RMS incidence rates have experienced a statistically significant decline (APC: -0.78, 95% CI: -1.28 – -0.28). Whites have experienced a significant decline in incidence rates (APC: -1.05, 95% CI: -1.60 – -0.50). Though not statistically significant, incidence rates in Blacks and Hispanics have trended upwards. While adjusted survival was not predicted by race, survival did significantly differ among racial/ethnic groups in children, with Hispanics and “Others” having the lowest 5- and 10-year survival rates (65% and 58% verses 58% and 56%, respectively). Black race/ethnicity was also shown to be a predictor for mortality for the time period 1990-2013. Conclusion Racial/ethnic minorities have worse RMS clinical presentation and incidence rates than Whites. While overall survival is not predicted by race, being an ethnic minority child diagnosed with RMS is predictive of survival. These disparities point towards a genetic component in RMS that has not yet been described

Rhabdomyosarcoma Incidence and Survival in Whites, Blacks, and Hispanics from 1973-2013: Analysis from the Surveillance, Epidemiology, and End Results Program

Purpose Our objectives were to 1) determine the difference in Rhabdomyosarcoma (RMS) incidence and survival between different race/ethnicity groups, and 2) evaluate the difference in survival of RMS between children and adults of these race/ethnicity groups, using the Surveillance, Epidemiology, and End Results Program (SEER) database between 1973-2013. Patients and Methods We analyzed racial characteristic and incidence data from 4,280 patients diagnosed with RMS, between 1973-2013, that were reported to the SEER database. Survival and hazard analyses were conducted on 4,268 patients with known follow-up data, with end point being death from any cause. Results Over the 40-year study period overall RMS incidence rates have experienced a statistically significant decline (APC: -0.78, 95% CI: -1.28 – -0.28). Whites have experienced a significant decline in incidence rates (APC: -1.05, 95% CI: -1.60 – -0.50). Though not statistically significant, incidence rates in Blacks and Hispanics have trended upwards. While adjusted survival was not predicted by race, survival did significantly differ among racial/ethnic groups in children, with Hispanics and “Others” having the lowest 5- and 10-year survival rates (65% and 58% verses 58% and 56%, respectively). Black race/ethnicity was also shown to be a predictor for mortality for the time period 1990-2013. Conclusion Racial/ethnic minorities have worse RMS clinical presentation and incidence rates than Whites. While overall survival is not predicted by race, being an ethnic minority child diagnosed with RMS is predictive of survival. These disparities point towards a genetic component in RMS that has not yet been described