Drafting Human Ancestry: What Does the Neanderthal Genome Tell Us about Hominid Evolution? Commentary on Green et al. (2010)

Ten years after the first draft versions of the human genome wereannounced, technical progress in both DNA sequencing and ancient DNAanalyses has allowed a research team around Ed Green and Svante Pa¨a¨bo tocomplete this task from infinitely more difficult hominid samples: a fewpieces of bone originating from our closest, albeit extinct, relatives, theNeanderthals. Pulling the Neanderthal sequences out of a sea of contaminatingenvironmental DNA impregnating the bones and at the same timeavoiding the problems of contamination with modern human DNA is in itselfa remarkable accomplishment. However, the crucial question in the long runis, what can we learn from such genomic data about hominid evolution? Pay-Per-View Download To access this article as a PDF pay-per-view download via BioOne, please click here

Vertebrate DNA in Fecal Samples from Bonobos and Gorillas: Evidence for Meat Consumption or Artefact?

Background: Deciphering the behavioral repertoire of great apes is a challenge for several reasons. First, due to their elusive behavior in dense forest environments, great ape populations are often difficult to observe. Second, members of the genus Pan are known to display a great variety in their behavioral repertoire; thus, observations from one population are not necessarily representative for other populations. For example, bonobos (Pan paniscus) are generally believed to consume almost no vertebrate prey. However, recent observations show that at least some bonobo populations may consume vertebrate prey more commonly than previously believed. We investigated the extent of their meat consumption using PCR amplification of vertebrate mitochondrial DNA (mtDNA) segments from DNA extracted from bonobo feces. As a control we also attempted PCR amplifications from gorilla feces, a species assumed to be strictly herbivorous. Principal Findings: We found evidence for consumption of a variety of mammalian species in about 16% of the samples investigated. Moreover, 40% of the positive DNA amplifications originated from arboreal monkeys. However, we also found duiker and monkey mtDNA in the gorilla feces, albeit in somewhat lower percentages. Notably, the DNA sequences isolated from the two ape species fit best to the species living in the respective regions. This result suggests that the sequences are of regional origin and do not represent laboratory contaminants. Conclusions: Our results allow at least three possible and mutually not exclusive conclusions. First, all results may represent contamination of the feces by vertebrate DNA from the local environment. Thus, studies investigating a species' diet from feces DNA may be unreliable due to the low copy number of DNA originating from diet items. Second, there is some inherent difference between the bonobo and gorilla feces, with only the later ones being contaminated. Third, similar to bonobos, for which the consumption of monkeys has only recently been documented, the gorilla population investigated (for which very little observational data are as yet available) may occasionally consume small vertebrates. Although the last explanation is speculative, it should not be discarded a-priori given that observational studies continue to unravel new behaviors in great ape species

Road blocks on paleogenomes - polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA

Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought

Understanding unconventional medicine

The phenomenon of unconventional medicine is an important feature of any contemporary society. Considering the increasing popularity of various forms of non-biomedical methods of healing among various groups of people, the necessity of an in-depth investigation of traditional, complementary and alternative therapies continues to grow. Existing terminology along with prevalence rates, legal status and historical development, vary greatly in European countries. The main reason behind the compilation of this publication was, therefore, to provide an overview of the field of unconventional medicine in Slovakia, where social science research into medicine has largely been neglected and only limited data exist in relation to medical practices and products, not associated with standard healthcare. Despite various concerns and controversies that have been raised regarding alternative medicine, the intent of the book is not to provoke criticism, the representatives of which are sufficiently represented in the public debate. Likewise, it does not try to reinforce the idealized and non-critical image of unconventional therapies, adopted by a number of alternative healthcare practitioners and providers. Rather than contribute to the polarization of the topic, the purpose of this monography is to provide a comprehensive understanding of the historical background of unconventional therapies, the main trends in this area, the patterns and reasons for the use of alternative medicine and the factors determining the efficacy of alternative therapies. The first section briefly introduces the historical development of the most notable forms of unconventional medicine in Slovakia, while highlighting various institutionalization and professionalization strategies, that have dominated over the last few decades. The second section mainly concerns a representative survey, investigating the patterns and trends of unconventional medicine use and concentrates on the execution of data on prevalence and types of non-conventional medicine, examining attitudes towards different topics related to alternative healthcare. Lastly, the book briefly enters the ongoing discussion as to how unconventional medicine might work and how efficacy is negotiated between the different actors involved in the healing process

Die infragenerische Gliederung der Gattung Bomarea Mirb. und die Revision der Untergattungen Sphaerine (Herb.) Baker und Wichuraea (M. Roemer) Baker (Alstroemeriaceae)

Die Gattung Bomarea wurde seit BAKER 1888 nicht mehr revidiert. Seither hat die Zahl gültig veröffentlichter Namen von 105 auf 280 zugenommen. Eine neue Revision ist dringend erforderlich. Ausgedehnte Feldstudien in Peru bilden die Grundlage für die Inangriffnahme dieses Projekts. In der vorliegenden Arbeit wird die taxonomische Geschichte der Gattung rekonstruiert. Bomarea wird gegen die nahe verwandte Alstroemeria abgegrenzt. HUNZIKER (1973) hatte Bomarea sogar eingezogen. Die meisten Autoren erkennen aber beide Gattungen als selbstständig an (KILLIP 1936; NEUENDORF 1977; SMITH & GEREAU 1991; AAGESEN & SANSO 1998). Die wichtigsten Unterschiede zwischen den beiden Gattungen bestehen im Fruchtbau sowie in den Chromosomenzahlen. Die Basiszahl ist in Alstroemeria x = 8 und on Bomarea x = 9. Die 4 bekannten Untergattungen werden überwiegend an Hand von Merkmalen des Ovariums und der Frucht definiert. Die entscheidenden Kriterien zur Identifikation der 4 Untergattungen sind folgende: Bei Bomarea s.str. ist das Ovarium immer unterständig, die Frucht ist dehiszent; Die Arten von Sphaerine sind nicht windend, das Ovarium ist unterständig, die Frucht indehiszent, das Perikarp ist dünn, saftig, und kräftig gefärbt; In Wichuraea ist das Ovarium halbunterständig, die Frucht ist dehiszent; Die Arten des Subgenus Baccata sind immer windend, das Ovarium ist unterständig, die Frucht ist indehiszent mit einer dicken, fleischigen Fruchtwand (HOFREITER & TILLICH 2002). Feldstudien in Peru zeigten innerhalb einer Population eine hohe Variabilität der Merkmale. Die Merkmals-Variabilität ist bei den Arten der Untergattung Wichuraea an höchsten, bei Sphaerine am niedrigsten. Die Verbreitungs- und Evolutionsmuster in Bomarea unterscheiden sich nach den verschiedenen Höhenstufen und ökologischen Bedingungen. Es sind 7 verschiedene Lebensformtypen entstanden. Der Lebensformtyp „windend wachsend in Nebelwäldern“ besiedelt bis auf die Wälder in der Pantepuiregion und im Küstengebirge von Brasilien alle in Südamerika vorkommenden Nebelwaldgebiete. Die Ausbreitungsbarrieren konnten in der Eiszeit überwunden werden, und der im Vergleich zum Tiefland stärker strukturierte Lebensraum hat dazu beigetragen, mehr Arten entstehen zu lassen. Die windenden Tieflandarten haben trotz ihres größeren Verbreitungsgebietes eine weit geringere Artenzahl als die Nebelwaldarten. Die aufrecht wachsenden Nebelwaldarten haben im Süden die Grenze der Nebelwälder erreicht, und ihre Verbreitungsgrenze ist identisch mit der Grenze der windenden Nebelwaldarten. Warum sie nicht nördlich der Amotape-Huancabamba-Region vorkommen ist nicht geklärt, warum sie insgesamt weniger weit verbreitet sind als die windenden Nebelwaldrandarten erklärt sich durch die Verbreitungsmuster der Früchte fressenden Vögel. Die Huancabamba-Niederung stellt keine Ausbreitungsbarriere dar. Es wurde keine Art gefunden die nur nördlich oder südlich bis zur Grenze der Niederung vorkommt. Die Amotape-Huancabamba-Region stellt dagegen ein Diversitätszentrum der Gattung dar. Das zweite Diversitätszentrum ist die Cordillera Central in Peru. Die aufrecht wachsenden Hochgebirgsarten konnten sich teilweise aufgrund geologischer Barrieren nicht so weit ausbreiten, teilweise weil sich die ökologischen Bedingungen in den offenen Lebensräumen stärker ändern als in den Wäldern. Diese Lebensform ist mehrmals unabhängig entstanden. Die Trockengebiete wurden ebenfalls mehrmals unabhängig besiedelt, aber nur von wenigen, teilweise gering verbreiteten Arten. Die Bomarea-Floren in allen Regionen erweisen sich als polyphyletisch. Der aufrecht wachsende Lebensformtyp ist mehrmals entstanden, weil der für diese Lebensform nötige Habitattyp im Gesamtareal der Gattung stark fragmentiert ist. Der Lebensformtyp windend in Nebelwäldern wachsend ist nur einmal entstanden, weil sein Habitat nahezu kontinuierlich im Areal vorkommt oder zumindest während der letzten Eiszeit vorkam. Die Schwestergruppe der Alstroemeriaceae sind die Luzuriagaceae. Innerhalb der Alstroemeriaceae sind die Sphaerinen den Luzuriagaceae am ähnlichsten. Alstroemeria ist sicher monophyletisch, Bomarea ist ebenfalls monophyletisch oder paraphyletisch zu Alstroemeria. Die Alstroemeriaceae gehören ihrer Abstammung nach der austral-antarktischen Flora an

Simultaneous barcode sequencing of diverse museum collection specimens using a mixed RNA bait set

A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.publishedVersio

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

<p>Abstract</p> <p>Background</p> <p>DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (<it>Equus caballus</it>) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets.</p> <p>Results</p> <p>In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (<it>Equus przewalski</it>) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.</p> <p>Conclusions</p> <p>Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.</p

Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.publishedVersio