Mapping copy number variation by population-scale genome sequencing

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.     

Ecology drives a global network of gene exchange connecting the human microbiome

Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.     

The earliest evidence for anatomically modern humans in northwestern Europe

The earliest anatomically modern humans in Europe are thought to have appeared around 43,000-42,000 calendar years before present (43-42 kyr cal BP), by association with Aurignacian sites and lithic assemblages assumed to have been made by modern humans rather than by Neanderthals. However, the actual physical evidence for modern humans is extremely rare, and direct dates reach no farther back than about 41-39 kyr cal BP, leaving a gap. Here we show, using stratigraphic, chronological and archaeological data, that a fragment of human maxilla from the Kent's Cavern site, UK, dates to the earlier period. The maxilla (KC4), which was excavated in 1927, was initially diagnosed as Upper Palaeolithic modern human. In 1989, it was directly radiocarbon dated by accelerator mass spectrometry to 36.4-34.7 kyr cal BP. Using a Bayesian analysis of new ultrafiltered bone collagen dates in an ordered stratigraphic sequence at the site, we show that this date is a considerable underestimate. Instead, KC4 dates to 44.2-41.5 kyr cal BP. This makes it older than any other equivalently dated modern human specimen and directly contemporary with the latest European Neanderthals, thus making its taxonomic attribution crucial. We also show that in 13 dental traits KC4 possesses modern human rather than Neanderthal characteristics; three other traits show Neanderthal affinities and a further seven are ambiguous. KC4 therefore represents the oldest known anatomically modern human fossil in northwestern Europe, fills a key gap between the earliest dated Aurignacian remains and the earliest human skeletal remains, and demonstrates the wide and rapid dispersal of early modern humans across Europe more than 40 kyr ago.     

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.     

Discovery of the milliped Scytonotus granulatus (Say, 1821) in Oklahoma and Alabama, with a review of its distribution (Polydesmida: Polydesmidae)

Scytonotus granulatus (Say, 1821) (Polydesmida: Polydesmidae), the most widely ranging polydesmid species in North America and the 4th most widely distributed indigenous continental milliped, is recorded from LeFlore and Latimer Counties, Oklahoma, and Jackson County, Alabama, the 1st records from these states. It also occurs in Logan and Independence Counties, Arkansas. The Latimer County record corresponds approximately to the terminus of the eastern forested biome and extends the distributions of the species and the genus some 255 miles (408 km) westward; along with literature records from Shawnee County, Kansas, and Cass County, Nebraska, it constitutes the western range limits. The projected overall distribution extends around 1100 miles (1760 km) east-west and 985 miles (1576 km) north-south and encompasses parts of Ontario, Québec, and 19 states, including all of Pennsylvania, West Virginia, Ohio, Indiana, and Illinois. New localities are detailed as are those from Missouri and that from Dare County, on the Outer Banks of North Carolina.     

Distribution of the milliped Virgoiulus minutus (Brandt, 1841): first records from Mississippi, Oklahoma, and Texas (Julida: Blaniulidae)

Virgoiulus minutus (Brandt 1841) (Julida: Blaniulidae), the only indigenous representative of the family in the New World, occurs, or can be expected, in parts or all of 24 states east of the Central Plains plus the District of Columbia; it is documented for the 1st time from Mississippi, Oklahoma, and Texas. The northern-, southern-, and westernmost localities are in Berrien County, Michigan; Putnam County, Florida; and Angelina/Rusk Counties, Texas, respectively. New England, Utah, Wyoming, Canada, and Mexico are deleted from the range, and specific localities are reported to augment previous generalized citations; those from Mexico represent misidentifications of Nopoiulus kochii (Gervais, 1847), an introduced European species that is recorded from Mexico City, Distrito Federal. Records of V. minutus from Pennsylvania, Virginia, South Carolina, Georgia, Alabama, West Virginia, Ohio, Illinois, Michigan, and Missouri are the 1st definite localities from these states; a sample from ""Anechar,"" believed to be a misspelling of ""Arrochar,"" a neighborhood in Staten Island, is considered the 1st definite record from New York. The published statement of occurrence in Delaware in general is the only known record of an indigenous diplopod from this state.     

Composition and distribution of the milliped tribe Pachydesmini west of the Mississippi River (Polydesmida: Xystodesmidae)

The xystodesmid milliped tribe Pachydesmini is supported by the autapomorphic absence of bold aposematic pigmentations and possibly also by relative somatic inflexibility; it comprises 3 component genera: Pachydesmus Cook, 1895; Dicellarius Chamberlin, 1920; and Thrinaxoria Chamberlin and Hoffman, 1950. Three representatives occur west of the Mississippi River— P. clarus (Chamberlin), P. crassicutis crassicutis (Wood), and T. lampra (Chamberlin). New localities are documented in Louisiana and Texas, and literature records are summarized for these states and Arkansas; records of P. clarus from Cherokee County, Texas, are the westernmost in this state for the east-Nearctic xystodesmid fauna. An apparently allopatric population of P. crassicutis crassicutis occurs in Evangeline and Lafayette Parishes, Louisiana. These are the first records of this species from west of the Mississippi River, and new localities of this form are cited from east of the watercourse. Thrinaxoria lampra , known previously in Texas from only Gregg County, is documented from Bowie, Cass, Harrison, Rusk, Sabine, and Titus Counties plus Webster Parish, Louisiana. Diagnoses and pertinent anatomical illustrations are provided for each species including the first cyphopod drawings for P. clarus and T. lampra ; occurrences west of the river are depicted on a map. A new tribal diagnosis is published along with a distribution map.     

Note on fungi in small mammals from the Nothofagus Forest in Argentina

Fungal spores from the same taxa of fungi that occur in the Pacific Northwest are reported from digestive tracts of31 rodents of 5 genera from the Nothofagus forest of southern Argentina. Mycophagy (fungal feeding) by forest rodents has been well documented in North America (Fogel and Trappe 1978, Maser et al. 1978, Mclntire 1984, and others), Europe (Blaschke and B?umler 1986, Durrieu et al. 1984), and Australia (Malajczuk et al. 1987). The purpose of this note is to report fungi consumed by rodents of the Argentine Andinian Patagonic forest (see Dimitri 1972,McQueen 1977, and Ward 1965 for a discussion of this forest), where mycorrhizal fungi may be an important part of the forest-rodent ecology (Cabrera and Yepes 1960, Pearson 1983, 1948, Pearson and Pearson 1982).     

Note on food habits of the Screech Owl and the Burrowing Owl of southeastern Oregon

Diets of the Common Screech Owl ( Otus asio ) and Burrowing Owl ( Athene cunicularia ) from the Great Basin, Malheur County, southeastern Oregon, were studied. Although there was considerable overlap in the diets of these owls, there were differences related to habitat use.     

Prey choices and foraging efficiency of recently fledged California Gulls at Mono Lake, California

We studied the foraging biology of recently fledged California Gulls ( Larus californicus ) at Mono Lake during August-September 1991. We made behavioral observations to collect information on the relative proportions of different prey types in the diet of these birds and took plankton tows to determine the relative abundance of each prey in the water column. These data show that alkali flies ( Ephydra hians ) were the primary constituent of the diet and that they were eaten at a much higher rate than one would expect based on their abundance. We also determined the number of feeding attempts and successful captures made during each behavioral observation. From these, we calculated the bird's feeding efficiencies on emergent adult alkali flies and on all other prey types combined. We found that foraging efficiencies on emergent flies were very high and significantly greater than those obtained on other prey types. These results suggest that flies were actively sought in preference to the alternative prey type, brine shrimp ( Artemia monica ), presumably because they are easier to capture and of greater nutritional value.