Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity.
We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae, Nodaviridae, and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.
Journal Article Patterns of Mitochondrial DNA Divergence in North American Crested Titmice Get access Frank B. Gill, Frank B. Gill The Academy of Natural Sciences. Philadelphia, PA 19103 Search for other works by this author on: Oxford Academic Google Scholar Beth Slikas Beth Slikas The Academy of Natural Sciences. Philadelphia, PA 19103 Search for other works by this author on: Oxford Academic Google Scholar The Condor, Volume 94, Issue 1, 1 February 1992, Pages 20–28, https://doi.org/10.2307/1368792 Published: 01 February 1992 Article history Received: 19 March 1991 Accepted: 13 September 1991 Published: 01 February 1992
IN THE INTRODUCTION to Hawaiian Birdlife, Andrew Berger (1972) wrote with frustration and dismay about his futile search for several species of endemic Hawaiian birds that had been described by collectors in the 1890s, but apparently were extinct by the mid-20th century. He bemoaned the fact that the ecology and behavior of those birds could never be studied. In fact, the loss of diversity and the gaps in our knowledge of the ecology and evolution of Hawaii's birds both are far greater than Berger could have imagined. During the past three decades, paleontological efforts spearheaded by Storrs Olson and Helen James have unearthed an unsuspected number and diversity of extinct birds. Bones collected from sand dunes, lava tubes, sinkholes, and former lakebeds have approximately doubled the number of endemic Hawaiian species. Among the fossil taxa collected and described by Olson and James are at least 15 new species in the spectacular honeycreeper radiation (tribe Drepanidini); several species of raptors unknown in the historical avifauna, including an eagle, a harrier, and a radiation of bird-eating owls; and many flightless birds, including rails, ibises, ducks, and geese (Olson and James 1982a, b, 1991; James and Olson 1991). Olson and James have demonstrated that the historically recorded Hawaiian avifauna, although spectacular, is a meager and biased sample of the fauna that existed prehistorically (i.e. before 1778, the year of the arrival of James Cook in the Hawaiian Islands). Radiocarbon dating of bones of extinct birds and presence of extinct birds in some archaeological sites have shown that extinctions on Hawaii occurred after humans colonized the archipelago, -1,600 years ago (Olson and James 1982a, b; James et al. 1987, Burney et al. 2001). That pattern of massive, rapid extinction of endemic birds following human colonization has been found on oceanic islands throughout the
Microplastics (particles less than 5 mm) numerically dominate marine debris and occur from coastal waters to mid‐ocean gyres, where surface circulation concentrates them. Given the prevalence of plastic marine debris (PMD) and the rise in plastic production, the impacts of plastic on marine ecosystems will likely increase. Microscopic life (the “Plastisphere”) thrives on these tiny floating “islands” of debris and can be transported long distances. Using next‐generation DNA sequencing, we characterized bacterial communities from water and plastic samples from the North Pacific and North Atlantic subtropical gyres to determine whether the composition of different Plastisphere communities reflects their biogeographic origins. We found that these communities differed between ocean basins – and to a lesser extent between polymer types – and displayed latitudinal gradients in species richness. Our research reveals some of the impacts of microplastics on marine biodiversity, demonstrates that the effects and fate of PMD may vary considerably in different parts of the global ocean, and suggests that PMD mitigation will require regional management efforts.
3 O. Blinkova 1,2 , K. Rosario 3 , L. Li 1,2 , A. Kapoor 1,2 , B. Slikas 1,2 , F. Bernardin 1,2 , 4 M. Breitbart 3 and E. Delwart 1,2 * 5 6 1. Blood Systems Research Institute, San Francisco, California. 7 2. Dept. of Laboratory Medicine, University of California, San Francisco, 8 California. 9 3. University of South Florida, College of Marine Science, 140 7 th Avenue 10 South St. Petersburg, Florida. 11 12 *Communicating author: BSRI, 270 Masonic Ave, San Francisco, CA 94118 13
A small number of cetaceans have adapted to an entirely freshwater environment, having colonized rivers in Asia and South America from an ancestral origin in the marine environment. This includes the 'river dolphins', early divergence from the odontocete lineage, and two species of true dolphins (Family Delphinidae). Successful adaptation to the freshwater environment may have required increased demands in energy involved in processes such as the mitochondrial osmotic balance. For this reason, riverine odontocetes provide a compelling natural experiment in adaptation of mammals from marine to freshwater habitats. Here we present initial evidence of positive selection in the NADH dehydrogenase subunit 2 of riverine odontocetes by analyses of full mitochondrial genomes, using tests of selection and protein structure modeling. The codon model with highest statistical support corresponds to three discrete categories for amino acid sites, those under positive, neutral, and purifying selection. With this model we found positive selection at site 297 of the NADH dehydrogenase subunit 2 (dN/dS>1.0,) leading to a substitution of an Ala or Val from the ancestral state of Thr. A phylogenetic reconstruction of 27 cetacean mitogenomes showed that an Ala substitution has evolved at least four times in cetaceans, once or more in the three 'river dolphins' (Families Pontoporidae, Lipotidae and Inidae), once in the riverine Sotalia fluviatilis (but not in its marine sister taxa), once in the riverine Orcaella brevirostris from the Mekong River (but not in its marine sister taxa) and once in two other related marine dolphins. We located the position of this amino acid substitution in an alpha-helix channel in the trans-membrane domain in both the E. coli structure and Sotalia fluviatilis model. In E. coli this position is located in a helix implicated in a proton translocation channel of respiratory complex 1 and may have a similar role in the NADH dehydrogenases of cetaceans.
