scholarly journals MAXIMUM LIKELIHOOD PHYLOGENETIC RECONSTRUCTION FROM HIGH-RESOLUTION WHOLE-GENOME DATA AND A TREE OF 68 EUKARYOTES

Author(s):  
YU LIN ◽  
FEI HU ◽  
JIJUN TANG ◽  
BERNARD M. E. MORET
2021 ◽  
Author(s):  
Helgi Hilmarsson ◽  
Arvind S. Kumar ◽  
Richa Rastogi ◽  
Carlos D. Bustamante ◽  
Daniel Mas Montserrat ◽  
...  

ABSTRACTAs genome-wide association studies and genetic risk prediction models are extended to globally diverse and admixed cohorts, ancestry deconvolution has become an increasingly important tool. Also known as local ancestry inference (LAI), this technique identifies the ancestry of each region of an individual’s genome, thus permitting downstream analyses to account for genetic effects that vary between ancestries. Since existing LAI methods were developed before the rise of massive, whole genome biobanks, they are computationally burdened by these large next generation datasets. Current LAI algorithms also fail to harness the potential of whole genome sequences, falling well short of the accuracy that such high variant densities can enable. Here we introduce Gnomix, a set of algorithms that address each of these points, achieving higher accuracy and swifter computational performance than any existing LAI method, while also enabling portable models that are particularly useful when training data are not shareable due to privacy or other restrictions. We demonstrate Gnomix (and its swift phase correction counterpart Gnofix) on worldwide whole-genome data from both humans and canids and utilize its high resolution accuracy to identify the location of ancient New World haplotypes in the Xoloitzcuintle, dating back over 100 generations. Code is available at https://github.com/AI-sandbox/gnomix.


2021 ◽  
Vol 9 (8) ◽  
pp. 1629
Author(s):  
Claudia Perea ◽  
Giovanna Ciaravino ◽  
Tod Stuber ◽  
Tyler C. Thacker ◽  
Suelee Robbe-Austerman ◽  
...  

The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.


2003 ◽  
Vol 358 (1429) ◽  
pp. 223-230 ◽  
Author(s):  
Jason Raymond ◽  
Olga Zhaxybayeva ◽  
J. Peter Gogarten ◽  
Robert E. Blankenship

Reconstructing the early evolution of photosynthesis has been guided in part by the geological record, but the complexity and great antiquity of these early events require molecular genetic techniques as the primary tools of inference. Recent genome sequencing efforts have made whole genome data available from representatives of each of the five phyla of bacteria with photosynthetic members, allowing extensive phylogenetic comparisons of these organisms. Here, we have undertaken whole genome comparisons using maximum likelihood to compare 527 unique sets of orthologous genes from all five photosynthetic phyla. Substantiating recent whole genome analyses of other prokaryotes, our results indicate that horizontal gene transfer (HGT) has played a significant part in the evolution of these organisms, resulting in genomes with mosaic evolutionary histories. A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared.


Land ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 193
Author(s):  
Ali Alghamdi ◽  
Anthony R. Cummings

The implications of change on local processes have attracted significant research interest in recent times. In urban settings, green spaces and forests have attracted much attention. Here, we present an assessment of change within the predominantly desert Middle Eastern city of Riyadh, an understudied setting. We utilized high-resolution SPOT 5 data and two classification techniques—maximum likelihood classification and object-oriented classification—to study the changes in Riyadh between 2004 and 2014. Imagery classification was completed with training data obtained from the SPOT 5 dataset, and an accuracy assessment was completed through a combination of field surveys and an application developed in ESRI Survey 123 tool. The Survey 123 tool allowed residents of Riyadh to present their views on land cover for the 2004 and 2014 imagery. Our analysis showed that soil or ‘desert’ areas were converted to roads and buildings to accommodate for Riyadh’s rapidly growing population. The object-oriented classifier provided higher overall accuracy than the maximum likelihood classifier (74.71% and 73.79% vs. 92.36% and 90.77% for 2004 and 2014). Our work provides insights into the changes within a desert environment and establishes a foundation for understanding change in this understudied setting.


2018 ◽  
Vol 22 (4) ◽  
pp. 1075-1086 ◽  
Author(s):  
Feiyi Fan ◽  
Yuepeng Yan ◽  
Kun Zhao ◽  
Fei Long ◽  
Hao Zhang

2016 ◽  
Vol 43 (6Part1) ◽  
pp. 3049-3061 ◽  
Author(s):  
Nicolas Gross-Weege ◽  
David Schug ◽  
Patrick Hallen ◽  
Volkmar Schulz

2009 ◽  
Vol 39 (8) ◽  
pp. 1231-1235 ◽  
Author(s):  
R. Keers ◽  
A. E. Farmer ◽  
K. J. Aitchison

There is significant unmet need for more effective treatments for bipolar disorder. The drug discovery process is becoming prohibitively expensive. Hence, biomarker clues to assist or shortcut this process are now widely sought. Using the publicly available data from the whole genome association study conducted by the Wellcome Trust Case Control Consortium, we sought to identify groups of genetic markers (single nucleotide polymorphisms) in which each marker was independently associated with bipolar disorder, with a less stringent threshold than that set by the original investigators (p⩽1×10−4). We identified a group of markers occurring within the CACNA1C gene (encoding the alpha subunit of the calcium channel Cav1.2). We then ascertained that this locus had been previously associated with the disorder in both a smaller and a whole genome study, and that a number of drugs blocking this channel (including verapamil and diltiazem) had been trialled in the treatment of bipolar disorder. The dihydropyridine-based blockers such as nimodipine that bind specifically to Cav1.2 and are more penetrant to the central nervous system have shown some promising early results; however, further trials are indicated. In addition, migraine is commonly seen in affective disorder, and calcium channel antagonists are successfully used in the treatment of migraine. One such agent, flunarizine, is structurally related to other first-generation derivatives of antihistamines such as antipsychotics. This implies that flunarizine could be useful in the treatment of bipolar disorder, and, furthermore, that other currently licensed drugs should be investigated for antagonism of Cav1.2.


PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e66493 ◽  
Author(s):  
Thijs Bosch ◽  
Erwin Verkade ◽  
Martijn van Luit ◽  
Bruno Pot ◽  
Paul Vauterin ◽  
...  

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