Search results for "Bayes"

The Origins of Lactase Persistence in Europe

2009

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (−13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the −13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model w…

Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and…

2010

Abstract Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA–trnH intergenic spacer, petB–petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concer…

Discrepant partitioning of genetic diversity in mouse lemurs and dwarf lemurs--biological reality or taxonomic bias?

2013

Unequal degrees of taxonomic subdivision can pose problems for research that relies on cross-taxon comparisons of biogeographic patterns. Numerous species of lemurs have been described in recent years. These descriptions were unevenly distributed over the genera of lemurs as exemplified by the closely related mouse lemurs (Microcebus spp.) and dwarf lemurs (Cheirogaleus spp.). According to previous studies, these genera display striking differences such as many versus few species, small versus large distributions, and small versus large mitochondrial divergence within and between species. We questioned if these differences reflect the biological reality or a biased taxonomic subdivision, wh…

Modern taurine cattle descended from small number of near-eastern founders.

2012

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challengin…

SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models

2015

The discovery of single nucleotide variants (SNVs) from next-generation sequencing (NGS) data typically works by aligning reads to a given genome and then creating an alignment map to interpret the presence of SNVs. Various approaches have been developed to call whether germline SNVs (or SNPs) in normal cells or somatic SNVs in cancer/tumor cells. Nonetheless, efficient callers for both germline and somatic SNVs have not yet been extensively investigated. In this paper, we present SNVSniffer, an integrated caller for germline and somatic SNVs from NGS data based on Bayesian probabilistic models. In SNVSniffer, our germline SNV calling models allele counts per site as a multinomial condition…

A Phylogenetic Analysis of Human Syntenies Revealed by Chromosome Painting in Euarchontoglires Orders

2010

To search for cytogenetic signatures that can help to clarify evolutionary affinities among the five orders within the Euarchontoglires clade, we focused on associations of conserved syntenic blocks that have been accumulated in the karyotypes of Primates (Strepsirhini and Haplorhini), five families of Rodentia, Scandentia (Tupaia belangeri), Dermoptera (Galeopterus variegatus) and Lagomorpha (Oryctolagus cuniculus). We examined available chromosome painting data to identify conserved chromosomes and chromosomal segments, and syntenic associations likely to have characterized the ancestral eutherian karyotype. The data set includes 161 characters that have been subjected to a concatenated a…

Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates.

2014

Legionella pneumophila is a strictly environmental pathogen and the etiological agent of legionellosis. It is known that non-vertical processes have a major role in the short-term evolution of pathogens, but little is known about the relevance of these and other processes in environmental bacteria. We report the whole-genome sequencing of 69 L. pneumophila strains linked to recurrent outbreaks in a single location (Alcoy, Spain) over 11 years. We found some examples where the genome sequences of isolates of the same sequence type and outbreak did not cluster together and were more closely related to sequences from different outbreaks. Our analyses identify 16 recombination events responsibl…

Deep metazoan phylogeny: When different genes tell different stories

2013

11 páginas, 4 figuras, 1 tabla.

Selective phenotyping, entropy reduction, and the mastermind game.

2011

Abstract Background With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. Results Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of p…

2021

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a we…