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Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.
Pubmed ID: 41474552
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A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.
View all literature mentionsAndrew Carnegie founded the Carnegie Institution of Washington in 1902 as an organization for scientific discovery. His intention was for institution to be home to exceptional individualsmen and women with imagination and extraordinary dedication capable of working at the cutting edge of their fields. Today, Carnegie scientists work in six scientific departments on the West and East Coasts. Carnegie investigators are leaders in the fields of plant biology, developmental biology, Earth and planetary sciences, astronomy, and global ecology. They seek answers to questions about the structure of the universe, the formation of our solar system and other planetary systems, the behavior and transformation of matter when subjected to extreme conditions, the origin of life, the function of genes, and the development of organisms from single-celled egg to adult. The Carnegie Institution for Science is headquartered in Washington, D.C. It is an endowed, independent, nonprofit institution. Significant additional support comes from federal grants and private donations. A board of trustees, consisting of leaders in business, the sciences, education, and public service, oversees Carnegie''s operations. Each of the six departments has its own scientific director who manages day-to-day operations under the leadership of Richard A. Meserve, Carnegie president. In addition to the scientists on staff, there is a constantly changing roster of pre- and postdoctoral fellows and associates, as well as visiting investigators, at each facility. Each of the six departments is independently managed by a director, who is aided by support staff. Carnegie is also involved in education at the lower levels.
View all literature mentionsNIH is the nations medical research agency - making important medical discoveries that improve health and save lives. The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the primary Federal agency for conducting and supporting medical research. Helping to lead the way toward important medical discoveries that improve peoples health and save lives, NIH scientists investigate ways to prevent disease as well as the causes, treatments, and even cures for common and rare diseases. NIH research impacts: * child and teen health, * men's health, * minority health, * seniors' health, * women's health, and * wellness and lifestyle issues. Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsDatabase of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria.
View all literature mentionsThe mission of the Department of Energy is to ensure America''s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. Goal 1: Transform our Energy Systems - Catalyze the timely, material, and efficient transformation of the nation''s energy system and secure U.S. leadership in clean energy technologies. Goal 2: The Science and Engineering Enterprise - Maintain a vibrant U.S. effort in science and engineering as a cornerstone of our economic prosperity, with clear leadership in strategic areas. Goal 3: Secure Our Nation - Enhance nuclear security through defense, nonproliferation, and environmental efforts. Goal 4: Management and Operational Excellence - Establish an operational and adaptable framework that combines the best wisdom of all Department stakeholders to maximize mission success.
View all literature mentionsAn independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process.
View all literature mentionsSource code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.
View all literature mentionsSoftware Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.
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