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Search Results: 1 - 10 of 225575 matches for " Todd R Disotell "
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Human genomic variation
Todd R Disotell
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-5-comment2004
Abstract: On June 26, 2000 at the White House, Craig Venter, Celera Genomics' president and chief scientific officer, announced that the complete human genome had been assembled, using the whole-genome shotgun-sequencing method, in only nine months [1]. But what did he mean by 'the' human genome? In fact, the Celera research group sequenced a composite genome composed of three females and two males who identified themselves as African-American, Asian, Caucasian, and Hispanic. During his announcement, Venter explained that this sampling and the sequences generated from it, "help illustrate that the concept of race has no genetic or scientific basis." Numerous articles have appeared in the popular press since then with titles such as 'Do Races Differ? Not Really, Genes Show' [2]. Do Celera's data indeed demonstrate this?Celera's method of whole-genome shotgun sequencing allowed for the rapid discovery of hundreds of thousands of single nucleotide polymorphisms (SNPs). SNPs are less variable than microsatellite markers which have previously been widely used to characterize human molecular variation and evolution (see, for example, [3,4]), although they are also much more common and less mutationally complex [5,6]. In September 1998, the US National Center for Biotechnology Information (NCBI) created the Single Nucleotide Polymorphism database (dbSNP [7,8]) in order to gather widely disparate research groups' efforts into a common format that was readily accessible. Two years on, Celera launched its SNP database [9]. The first release of this database (September 2000) contains 2.4 million unique SNPs that are not found in the public databases [9]. So, taking these together with 400,000 non-redundant SNPs from the public databases, there now are over 2.8 million SNPs characterized throughout the human genome. Will this new resource tell us anything new about human variation?Prior to the SNP-gathering efforts, what was known about the patterns of human variation? Since the initial
'Chumanzee' evolution: the urge to diverge and merge
Todd R Disotell
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-11-240
Abstract: The popular and scientific press gave extensive coverage to the recent analysis by Patterson et al. [1] of the human and chimpanzee genomes, in which they conclude that after initially splitting, our lineage continued to hybridize with chimpanzees for more than a million years. While the Washington Post noted that "Human ancestors may have interbred with chimpanzees" [2], Slate.com asked more bluntly: "Did humans mate with chimps? And are we their offspring?" [3].Given the extraordinary similarity of the chimpanzee and human genomes, scientists and the public alike have often asked such questions. An extensive review of the literature has yet to turn up a credible report of such crosses. In the 1920s, a Soviet scientist, Il'ya Ivanovich Ivanov, with the assistance of the Institut Pasteur at one of their field stations in French Guinea, unsuccessfully artificially inseminated three chimpanzees with human sperm [4]. He then tried to continue his experiments at the primate center at Sukhum in the then Soviet Republic of Georgia, where he intended to artificially inseminate human volunteers with ape sperm. He was arrested by the Soviet secret police on charges unrelated to this project and was never able to carry it out [4].Through their own sequencing efforts and data mining, Patterson et al. [1] have put together an alignment of human, chimpanzee, gorilla, orangutan, and macaque sequences that covers almost 20 Mb, which is 800 times larger than any previous analysis. But it is not just the size of the dataset that is important, it is the phylogenetic distribution. Most recent analyses of the human and chimpanzee genomes compare them with the mouse genome, which seems to be evolving at a different rate and under different constraints. By adding the very closely related gorilla, moderately close orangutan, and somewhat more distant macaque, the timing and processes of primate evolution can be more effectively studied. It is difficult, to nearly impossible, to infer whet
Discovering human history from stomach bacteria
Todd R Disotell
Genome Biology , 2003, DOI: 10.1186/gb-2003-4-5-213
Abstract: Charles Darwin recognized that the distribution and form of parasites was evolutionarily significant. He noted, for instance, that "... the Pediculi [lice] collected in different countries from the different races of man ... differ, not only in colour, but in the structure of their claws and limbs. In every case in which many specimens were obtained the differences were constant" [1]. More recently, several research groups [2-7] have found interesting correlations between the evolutionary relationships among various bacterial and viral strains hosted by humans and the pattern of migrations of modern humans throughout the world.A particularly interesting case is that of Helicobacter pylori, a Gram-negative bacterium associated with gastritis, peptic ulcers, and gastric cancer that may infect up to half of all humans [8]. The discovery that a bacterial infection could lead to what were considered chronic diseases [8] was a striking example of the fact that infectious diseases have not yet been conquered. The continuing acquired immune deficiency syndrome (AIDS) epidemic, outbreaks of Ebola in Central Africa, and the current spread of West Nile Virus in the United States and of severe acute respiratory syndrome (SARS) from Asia provide evidence of the pervasiveness and health consequences of infectious agents even in the age of vaccination and antimicrobial and antiviral therapies. Many infectious diseases are thought to have arisen concurrently with the development of agriculture and the rise of urban living. If, instead, many pathogens' relationships with humans are much older, it would not be surprising to find deeper evolutionary associations between humans and their microbial and viral invaders.The evolutionary history of H. pylori may provide an example of the coevolution of a bacterium and its only known host. The H. pylori genome is relatively small at 1.67 megabases, with a minimal complement of metabolic genes [9]. Variation between H. pylori isolates from di
Panmixia postponed: ancestry-related assortative mating in contemporary human populations
Andrew S Burrell, Todd R Disotell
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-11-245
Abstract: The past 500 years have been characterized by unprecedented episodes of human migration and admixture, particularly in the Americas. Technological innovations have to a certain extent reduced the impact of geography on human behavior, raising the possibility of a truly global population. At a local level, however, geographic, demographic, linguistic, cultural and even legal barriers now, and in the past, limit and circumscribe human mate choices. For example, cultural biases towards patrilocal or matrilocal marriage (where the married couple set up home in the place of origin of the man or woman, respectively) can lead to the differential structuring of male or female genetic variation [1]. Caste systems can similarly lead to the stratification of genetic structure within societies [2]. The patterns of divergence and admixture that characterize human populations are the result of complex cultural and evolutionary processes, but can also negatively influence the outcomes of biomedical studies associating disease susceptibilities and other biomedical traits with particular genes [3].In this context, a paper by Risch et al. [4] in Genome Biology is especially interesting in that they used 'ancestry informative markers' (AIMs) to document the genetic signature of assortative mating in contemporary human populations. These genetic markers document the contribution of particular ancestral groups to an individual's genetic make-up. Surprisingly, in view of the fact that such ancestral contributions may not be physically obvious or even known to the individual or their intended spouse, Risch et al. find that ancestral make-up is positively correlated with spouse choice within both populations studied, but find no correlation with socioeconomic or geographic origins that might explain the correlation. The work raises interesting questions about the cultural factors influencing human population genomic structure as well as the evolutionary and biomedical significance of such
The monkey's perspective
Todd R Disotell, Anthony J Tosi
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-9-226
Abstract: The recently published draft of the rhesus macaque (Macaca mulatta) genome from the Rhesus Macaque Genome Sequencing and Analysis Consortium [1] follows that of the chimpanzee [2] by only a year and a half, and now gives us three primate genome sequences, including our own. Of the 2.87 gigabases sequenced at 5.2-fold coverage, and containing approximately 20,000 predicted genetic loci, regions of the macaque genome that could be aligned to the human genome sequence were 93.5% identical (90.76% when small insertions and deletions are included). Compared with the human-chimpanzee difference of 98.77%, which sometimes gives sequences that are too similar to draw meaningful comparisons, and the human-mouse difference of 69.1%, which gives sequences often too divergent to be useful, the macaque sequences provide Goldilocks' 'just right' for many types of analyses.One of the hopes and justifications for sequencing the chimpanzee genome was that it would allow us to identify the genetic changes 'that make us human'. Once chimpanzee genome sequences started to become available, papers quickly appeared, searching for unique genetic changes along the human lineage after we separated from chimpanzees. In the absence of other primate genome sequences, the mouse was used for comparison with chimpanzee and human [3]. However, given the relatively deep evolutionary divergence of the mouse and primate lineages, of the order of at least 70 million years ago, so many changes could have occurred either along the mouse lineage or on the long branch leading to the common ancestor of humans and chimpanzees that we cannot with much confidence estimate what nucleotide was present in any position in that ancestor. Thus, we were not able to reasonably estimate whether a given difference between the chimp and human genomes had occurred in the human lineage or in the chimpanzee lineage (Figure 1). Using the macaque genome as a comparison, however, we can now place changes on a lineage far more
No evidence of a Neanderthal contribution to modern human diversity
Jason A Hodgson, Todd R Disotell
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-2-206
Abstract: One of the most intriguing questions in human evolution revolves around the Neanderthals, who were the first human-like fossil species to be discovered, more than 150 years ago. What were they like and why did they disappear 30,000 years ago? Do we carry any of their genes? Three hypotheses have been proposed to explain the origin of anatomically modern humans (Homo sapiens) and their relation to so-called 'archaic' humans such as the Neanderthals (Homo neanderthalensis) (Figure 1). One is the well known 'out of Africa' or 'recent replacement' theory [1,2]; this says that H. sapiens evolved in Africa and migrated from there relatively recently, expanding over the world and displacing those archaic humans, such as the Neanderthals, who had evolved independently in Eurasia. An older hypothesis suggests that the evolution of modern humans occurred in both Africa and Eurasia, with gene flow between the various populations; this is known as the 'multiregional' model [3-5]. A Neanderthal genome project based on DNA from fossil specimens is now under way and aims to provide us with much more information about what the Neanderthals might have been like. In particular, it should provide a definitive answer to whether there was any genetic intermixing between them and the modern humans who coexisted with them in Europe for up to 6,000 years [6] and perhaps longer in Western Asia.Mitochondrial DNA, which is inherited through the maternal line, has been a favored DNA sequence for determining relationships between human populations, and there is a large amount of data on the mitochondrial DNA sequences present in humans of many different ethnic groups from all over the world. In 1997, Krings and colleagues [7] first amplified and sequenced mitochondrial DNA (mtDNA) from a Neanderthal fossil – in fact, the original Neanderthal specimen. By late 2007, 14 other specimens had yielded mitochondrial sequences that could be compared (Figure 2 and Table 1). Several have yielded sequence
A mobile element-based evolutionary history of guenons (tribe Cercopithecini)
Jinchuan Xing, Hui Wang, Yuhua Zhang, David A Ray, Anthony J Tosi, Todd R Disotell, Mark A Batzer
BMC Biology , 2007, DOI: 10.1186/1741-7007-5-5
Abstract: We identified 151 novel Alu insertion loci from 11 species of tribe Cercopithecini, and used these insertions and 17 previously reported loci to infer a phylogenetic tree of the tribe Cercopithecini. Our results robustly supported the following relationships: (i) Allenopithecus is the basal lineage within the tribe; (ii) Cercopithecus lhoesti (L'Hoest's monkey) forms a clade with Chlorocebus aethiops (African green monkey) and Erythrocebus patas (patas monkey), supporting a single arboreal to terrestrial transition within the tribe; (iii) all of the Cercopithecus except C. lhoesti form a monophyletic group; and (iv) contrary to the common belief that Miopithecus is one of the most basal lineages in the tribe, M. talapoin (talapoin) forms a clade with arboreal members of Cercopithecus, and the terrestrial group (C. lhoesti, Chlorocebus aethiops and E. patas) diverged from this clade after the divergence of Allenopithecus. Some incongruent loci were found among the relationships within the arboreal Cercopithecus group. Several factors, including incomplete lineage sorting, concurrent polymorphism and hybridization between species may have contributed to the incongruence.This study presents one of the most robust phylogenetic hypotheses for the tribe Cercopithecini and demonstrates the advantages of SINE insertions for phylogenetic studies.Guenons (tribe Cercopithecini) are a species-rich group of primates with a distribution throughout sub Saharan Africa. With their diverse morphology, ecology, behavior and social organizations, guenons have attracted considerable attention from both primatologists and evolutionary biologists [1,2]. In addition, some species in the tribe (e.g. Chlorocebus aethiops) have been widely used in biomedical studies [3-5]. Based on Groves' classification [6], the tribe Cercopithecini consists of five genera (Erythrocebus, Chlorocebus, Cercopithecus, Miopithecus and Allenopithecus) comprising 36 species. The evolutionary history of guenons may
Demographic changes and marker properties affect detection of human population differentiation
Jennifer B Listman, Robert T Malison, Atapol Sughondhabirom, Bao-Zhu Yang, Ryan L Raaum, Nuntika Thavichachart, Kittipong Sanichwankul, Henry R Kranzler, Sookjaroen Tangwonchai, Apiwat Mutirangura, Todd R Disotell, Joel Gelernter
BMC Genetics , 2007, DOI: 10.1186/1471-2156-8-21
Abstract: Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African) while both successfully distinguished Hmong from Thai and Chinese.Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.Genetic characterization and differentiation of populations are often necessary for the conduct of valid case-control association studies [1-5], determining the role of ancestry in phenotypic differences [6,7], assigning population groups for valid linkage analysis [8], examining the distribution of neutral genetic variation among populations, and inferring migration histories [9-11]. Such differentiation has been accomplished with relative ease between major continental populations [10,12-15], but it has been asserted that population differentiation within a continent may not be possible; and when it appears to be so, may actually be an artifact of study design [16].The ubiquity and frequently highly variable nature of short tandem repeat polymorphisms (STRs or microsatellites) have made them desirable markers for measuring population
Regionally and climatically restricted patterns of distribution of genetic diversity in a migratory bat species, Miniopterus schreibersii (Chiroptera: Vespertilionidae)
Ra?it Bilgin, Ahmet Karata?, Emrah ?oraman, Todd Disotell, Juan Morales
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-209
Abstract: Our results showed differentiation in mitochondrial DNA coupled with weaker nuclear differentiation. We found evidence for restriction of lineages to geographical areas for hundreds of generations. The results showed that the most likely ancestral haplotype was restricted to the same geographic area (the Balkans) for at least 6,000 years. We were able to delineate the migration routes during the population expansion process, which followed the coasts and the inland for different nested mitochondrial clades. Hence, we were able to describe a scenario showing how multiple biotic and abiotic events including glacial periods, climate and historical dispersal patterns complemented each other in causing regional and local differentiation within a species.The geographic transitions between continents can result in species diversification and endemism, forming regions of allopatry, and contact zones for divergent flora and fauna. Sulawesi, for instance, an island located between Continental Asia and Australia, has elements of both faunal assemblages within its boundaries, hosting an elevated number of species and endemics [1]. Mexico, as another example, being located in a transition zone between tropical central America, and temperate North America is considered to be a megadiversity country [2]. Within the temperate zones, southeastern Europe and Anatolia are located within a similar geographical transition centered in between Europe, Asia and Africa (Figure 1a). As such, this region comprises an interesting area for investigation as a zone of allopatry with geographical barriers to gene flow [3,4], a contact zone for divergent biota from different continents and climatic regimes, and a refugium for the entire western Palearctics [5,6].In this study, we examined the nuclear and mitochondrial genetic structure of the bent-winged bat, Miniopterus schreibersii, in southeastern Europe and Anatolia. M. schreibersii is a colonial, cave-dwelling [7], and polytypic species with o
T. van Strien, K. van der Leer, A. Leerintveld, B. Bregman, Hofwijck. Het gedicht en de buitenplaats van Constantijn Huygens, Leerintveld, A., Bregman, B., ed.
R. Todd
BMGN : Low Countries Historical Review , 2003,
Abstract:
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