Final Report for the April 2009 Gulf of Alaska Line-Transect Survey (Goals) in the Navy Training Exercise Area

Little is known about the occurrence of cetaceans found in offshore waters in the Gulf of Alaska; however, whaling records and a few recent surveys have shown this area to be important habitat. The United States Navy maintains a maritime training area in the central Gulf of Alaska, east of Kodiak Island, and has requested additional information on marine mammal presence and use of this area. To determine the occurrence and distribution of marine mammals in and around the Navy training area, a line-transect visual and acoustic survey was conducted 10-20 April 2009 from the NOAA R/V Oscar Dyson. The primary survey area encompassed nearshore, shelf and offshore pelagic waters of the central Gulf of Alaska. Survey lines were designed to provide equal coverage of the nearshore and offshore habitat.Funded by Naval Postgraduate School.N00244-09-P-096

Paleobiology Database User Guide Version 1.0

The Paleobiology Database is an online, non-governmental, non-profit public resource for paleontological data. It is organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. This volume is designed to be a comprehensive guide for Paleobiology Database users, both General and Contributory. It covers most database uses from data retrieval and mapping to data contribution of all types. It contains numerous examples to illustrate database use as well as definitions of terms and additional links to numerous other sources. We hope that this user guide will help all users access the great volume of data in the Paleobiology Database and lead others to start and continue to add data to the system

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants

Whole-genome sequence-based analysis of thyroid function

Tiina Paunio on työryhmän UK10K Consortium jäsen.Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N = 2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF >= 1%) associated with TSH and FT4 (N = 16,335). For TSH, we identify a novel variant in SYN2 (MAF = 23.5%, P = 6.15 x 10(-9)) and a new independent variant in PDE8B (MAF = 10.4%, P = 5.94 x 10(-14)). For FT4, we report a low-frequency variant near B4GALT6/ SLC25A52 (MAF = 3.2%, P = 1.27 x 10(-9)) tagging a rare TTR variant (MAF = 0.4%, P = 2.14 x 10(-11)). All common variants explain >= 20% of the variance in TSH and FT4. Analysis of rare variants (MAFPeer reviewe

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.MAK is funded by an NIHR Research Professorship and receives funding from the Wellcome Trust, Great Ormond Street Children's Hospital Charity, and Rosetrees Trust. E.M. received funding from the Rosetrees Trust (CD-A53) and Great Ormond Street Hospital Children's Charity. K.G. received funding from Temple Street Foundation. A.M. is funded by Great Ormond Street Hospital, the National Institute for Health Research (NIHR), and Biomedical Research Centre. F.L.R. and D.G. are funded by Cambridge Biomedical Research Centre. K.C. and A.S.J. are funded by NIHR Bioresource for Rare Diseases. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). We acknowledge support from the UK Department of Health via the NIHR comprehensive Biomedical Research Centre award to Guy's and St. Thomas' National Health Service (NHS) Foundation Trust in partnership with King's College London. This research was also supported by the NIHR Great Ormond Street Hospital Biomedical Research Centre. J.H.C. is in receipt of an NIHR Senior Investigator Award. The research team acknowledges the support of the NIHR through the Comprehensive Clinical Research Network. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, Department of Health, or Wellcome Trust. E.R.M. acknowledges support from NIHR Cambridge Biomedical Research Centre, an NIHR Senior Investigator Award, and the University of Cambridge has received salary support in respect of E.R.M. from the NHS in the East of England through the Clinical Academic Reserve. I.E.S. is supported by the National Health and Medical Research Council of Australia (Program Grant and Practitioner Fellowship)

Catches of Humpback Whales in the Southern Ocean, 1947-1973

We review catches of humpback whales (Megaptera novaeangliae) in the Southern Ocean during the period following World War II, with an emphasis on Areas IV, V and VI (the principal regions of illegal Soviet whaling on this species). Where possible, we summarize legal and illegal Soviet catches by year, Area and factory fleet, and also include information on takes by other nations. Soviet humpback catches between 1947 and 1973 totaled 48702 and break down as follows: 649 (Area I), 1412 (Area II), 921 (Area III), 8779 (Area IV), 22569 (Area V) and 7195 (Area VI), with 7177 catches not assignable to area. In all, at least 72542 humpback whales were killed by all operations (Soviet plus other nations) after World War 2 in Areas IV (27201), V (38146) and VI (7195). More than a third of these (25474 whales, of which 25192 came from Areas V and VI) were taken in just two seasons, 1959/60 and 1960/61. The impact of these takes, and of those from Area IV in the late 1950\u27s, is evident in the sometimes dramatic declines in catches at shore stations in Australia, New Zealand and Norfolk Island. When compared to recent estimates of abundance, the large removals from Areas IV and V indicate that the populations in these regions remain well below pre-exploitation levels despite reported strong growth rates off eastern and western Australia. Populations in many areas of Oceania continue to be small, indicating that the catches from Area VI and eastern Area V had long-term impacts on recovery

Movements of satellite-monitored humpback whales from New Caledonia

Knowledge of the local and migratory movements of humpback whales (Megaptera novaeangliae) from New Caledonia is very limited. To investigate this topic, we attached satellite-monitored tags to 12 whales off southern New Caledonia. Tag longevity ranged from 1 to 52 days (X = 22.5 days). Tagged whales generally moved to the south or southeast, with several spending time in a previously unknown seamount habitat named Antigonia before resuming movement, generally toward Norfolk Island or New Zealand. However, 1 female with a calf traveled the entire length of the western coast of New Caledonia (~450 km) and then west in the direction of the Chesterfield Reefs, a 19th century American (“Yankee”) whaling ground. None of the New Caledonia whales traveled to or toward eastern Australia, which is broadly consistent with the low rate of interchange observed from photo-identification comparisons between these 2 areas. The connections between New Caledonia and New Zealand, together with the relatively low numbers of whales seen in these places generally, support the idea that whales from these 2 areas constitute a single population that remains small and unrecovered