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Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
The Neotropical genus Mesoconius Enderlein, 1922 is revised with the redescription or diagnosis of 20 previously described South American species, the description of one new species of the M. infestus group (M. triunfo sp. nov.) from Mexico and the description of 32 new species in four species groups from Andean South America (M. eques group: M. albiseta sp. nov., M. albitergum sp. nov., M. anchitarsus sp. nov., M. cosanga sp. nov., M. epandribarba sp. nov., M. hirsutimamma sp. nov., M. nigripleuron sp. nov., M. noteques sp. nov., M. pasachoa sp. nov., M. rufipleuron sp. nov. and M. suzukii sp. nov.; M. infestus group: M. acca sp. nov., M. albipedis sp. nov., M. nigricephala sp. nov. and M. notacca sp. nov.; M. nono group: M. aurantium sp. nov., M. bipleuron sp. nov., M. garyi sp. nov., M. nono sp. nov., M. reinai sp. nov., M. uchumachi sp. nov., M. woytkowskii sp. nov. and M. zorro sp. nov.; M. oblitus group: M. apa sp. nov., M. apicalis sp. nov., M. gelbifacies sp. nov., M. keili sp. nov., M. lobopoda sp. nov., M. nigra sp. nov., M. quadritheca sp. nov., M. rex sp. nov. and M. ruficrus sp. nov.). Calobata eques Schiner, 1868 is transferred from Cliobata Enderlein, 1923 to Mesoconius and all South American species previously treated as Zelatractodes Enderlein, 1922 are transferred to Mesoconius. Mesoconius aeripennis Enderlein, 1922 is synonymized with M. eques, M. enderleini Frey, 1927 is synonymized with M. infestus Enderlein, 1922 and Aristobata melini Frey, 1927 is synonymized with M. filipes (Enderlein, 1922). Mesoconius garleppi (Enderlein, 1922) is newly recognized as a subjective junior homonym and given the replacement name Mesoconius ottoi nom. nov. A maximum likelihood tree is provided for 29 species of Mesoconius sequenced for the barcode region of CO1 and a key is provided for all South American species of Mesoconius.
The genus Rudolfina Roháček, 1987 is revised and redefined with the description of the following nine new species, all from the New World: R. bucki sp. nov. (Mexico), R. exuberata sp. nov. (widespread, from USA to Brazil), R. howdeni sp. nov. (Mexico), R. megepandria sp. nov. (Mexico), R. newtoni sp. nov. (Mexico), R. pauca sp. nov. (Guatemala, Mexico), R. pilosa sp. nov. (Mexico), R. remiforma sp. nov. (Mexico) and R. tumida sp. nov. (Mexico, USA). Rudolfina is compared to closely related genera in the Archiceroptera genus complex, which in turn is recognized as part of a large, mostly Neotropical clade including Robustagramma Marshall & Cui, 2005, Pterogramma Spuler, 1924, Aptilotella Duda, 1924, Bitheca Marshall, 1987, Bromeloecia Spuler, 1924 and Archiceroptera Papp, 1977.
The Sclerocoelus galapagensis group is defined and revised, including the description of S. galapagensis new species from the Galapagos Islands; S. caribensis new species from the Caribbean and adjacent areas; S. brasilensis new species from Brazil, Ecuador, Colombia, and Panama; S. hemorrhoidal is new species from Ecuador and Venezuela; and S. andensis new species from Argentina, Bolivia, and Venezuela. The south Atlantic species Sclerocoelus subbrevipennis (Frey), new combination, is redescribed as a member of the S. galapagensis group, and is considered the sister species to the rest of the species group. A key to species, character matrix, and cladogram are provided.
The New World species formerly placed in Borborillus Duda (Sphaeroceridae: Copromyzinae) are transfemdto Norrbomia Papp. These are: N. lacteipennis (Malloch), n. comb., N. fumipennis (Stenhammar), n. comb., N. frigipennis (Spuler), n. comb., N. scripta (Malloch), n. comb., and N. sordida (Zetteretedt). Norrbomia fulvipennis, N. singusta, N. mexicana, N. triglabra, and N. yukonensis are described as new. Borborus articus Malloch is synonymized with N. fumipennis, and Borborus singularis Spuler is synonymized with N. scripta. All ten New World species of Norrbomia are keyed, illustrated and described. Their relationships are discussed and a cladogram is provided. Species in two of the defined clades are kleptoparasitic on dung rolling scarab beetles.
The new genus Sclerocoelus is described for a large group of New World species including Sclerocoelus sordipes (Adams) new combination, Sclerocoelus regularis (Malloch) new combination, Sclerocoelus plumiseta (Duda) new combination, and about 40 undescribed species. The widespread Nearctic species Limosina sordipes Adams is redescribed and designated as the type species of Sclerocoelus. Lectotypes are designated for Limosina sordipes Adams and Limosina evanescens Tucker. The new genus Druciatus is described for a group of 7 undescribed species fiom Central America, South America, and the Caribbean. The type species, Druciatus ovisternus n.sp., is described from Dominica and the Dominican Republic.
Druciatus nigritarsus new species is described from St. Vincent, Guyana, Ecuador and Peru, D. trisetus new species is described from Ecuador, Brazil and Guyana, D. dissidens and D. latisternus new species are described from Costa Rica, D. angustus new species is described from Mexico, D. campbelli new species is described from Guatemala, and D. petilus new species is described from Ecuador. A key is provided to the eight species in the genus Druciatus.
