Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Tarsal organ morphology and the phylogeny of goblin spiders (Araneae, Oonopidae), with notes on basal genera

Based on a survey of a wide variety of oonopid genera and outgroups, we hypothesize new synapomorphies uniting the Oonopidae (minus the South African genus Calculus Purcell, which is transferred to the Orsolobidae). The groundplan of the tarsal organ in Oonopidae is hypothesized to be an exposed organ with a distinctive, longitudinal ridge originating from the proximal end of the organ, and a serially dimorphic pattern of 4-4-3-3 raised receptors on legs I IV, respectively. Such organs typify the diverse, basal, and ancient genus Orchestina Simon. Several other genera whose members resemble Orchestina in retaining two plesiomorphic features (an H-shaped, transverse eye arrangement and a heavily sclerotized, thick-walled sperm duct within the male palp) are united by having tarsal organs that are partly (in the case of Cortestina Knoflach) or fully capsulate (in the case of Sulsula Simon, Xiombarg Brignoli, and Unicorn Platnick and Brescovit). The remaining oonopids are united by the loss of the heavily sclerotized palpal sperm duct, presumably reflecting a significant transformation in palpal mechanics. Within that large assemblage, a 4-4-3-3 tarsal organ receptor pattern and an H-shaped eye arrangement seem to be retained only in the New Zealand genus Kapitia Forster; the remaining genera are apparently united by a reduction in the tarsal organ pattern to 3-3-2-2 raised receptors on legs I IV and by the acquisition of a clumped eye arrangement. Three subfamilies of oonopids are recognized: Orchestininae Chamberlin and Ivie (containing only Orchestina; Ferchestina Saaristo and Marusik is placed as a junior synonym of Orchestina), Sulsulinae, new subfamily (containing Sulsula, Xiombarg, Unicorn, and Cortestina), and Oonopinae Simon (containing all the remaining genera, including those previously placed in the Gamasomorphinae). The type species of Sulsula and Kapitia, S. pauper (O. P.-Cambridge) and K. obscura Forster, are redescribed, and the female of S. pauper is described for the first time. A new sulsuline genus, Dalmasula, is established for Sulsula parvimana Simon and four new species from Namibia and South Africa

Gavarilla, a new genus of jumping spider from Brazil, and description of two new species of the genera Capeta Ruiz & Brescovit and Amatorculus Ruiz & Brescovit (Araneae, Salticidae, Sitticinae) Gavarilla, um novo gênero de aranha papa-mosca do Brasil, e descrição de duas espécies novas dos gêneros Capeta Ruiz & Brescovit, 2005 e Amatorculus Ruiz & Brescovit (Araneae, Salticidae, Sitticinae)

Gavarilla gen. nov. from Northeastern Brazil is proposed to include two new species: the type species Gavarilla ianuzziae sp. nov. from the State of Sergipe and Gavarilla arretada sp. nov. from the State of Maranhão. The genus presents the standard sitticine dentition and is presumably related to the genera Aillutticus Galiano, 1987, Nosferattus Ruiz & Brescovit, 2005, Capeta Ruiz & Brescovit, 2005 and Amatorculus Ruiz & Brescovit, 2005, with which it shares the similar high, rounded carapace. Two new species, Capeta cachimbo and Amatorculus cristinae, are also described from the State of Pará, and Amatorculus stygius Ruiz & Brescovit, 2005 is recorded for the first time from the State of Minas Gerais.<br>Gavarilla gen. nov. do Nordeste do Brasil é proposto para incluir duas espécies novas: a espécie-tipo Gavarilla ianuzziae sp. nov. de Sergipe e Gavarilla arretada sp. nov. do Maranhão. O gênero apresenta a dentição padrão dos siticíneos e está provavelmente relacionado aos gêneros Aillutticus Galiano, 1987, Nosferattus Ruiz & Brescovit, 2005, Capeta Ruiz & Brescovit, 2005 e Amatorculus Ruiz & Brescovit, 2005, com os quais compartilha a carapaça alta e arredondada. Duas espécies novas, Capeta cachimbo e Amatorculus cristinae, também são descritas para o Pará, e Amatorculus stygius Ruiz & Brescovit, 2005 é registrado pela primeira vez para o Estado de Minas Gerais