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Characidium is a Neotropical fish genus. Its distribution ranges from eastern Panama to northern Argentina, and it is an important component of the Neotropical ichthyofauna present in the major rivers of South America. We here provide an approximation to the dispersal and historical distributions of Characidium. The biogeographic history of five species of the genus was analyzed through nuclear RAG-2 and mitochondrial 16S genes and a time-calibrated phylogenetic analysis using three outgroup species. A biogeographical reconstruction was performed to estimate ancestral geographic ranges and infer the historical events that impacted the geographic distributions of Characidium species. Our results showed Characidium as a monophyletic group. The molecular clock suggests that the most recent common ancestor of Characidium originated during the Eocene, about 50.2 Mya. In addition, different dispersion and vicariance events could be inferred, which possibly gave rise to the present geographical distribution of the genus. Our results point to the rise of the Andean mountains and sea fluctuations as being important events in the formations and delimitation of different rivers, which influenced the distribution of South American ichthyofauna.
Pubmed ID: 27741308 RIS Download
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NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsThe Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, via the Internet. Through a global network of countries and organizations, GBIF promotes and facilitates the mobilization, access, discovery and use of information about the occurrence of organisms over time and across the planet. GBIF provides three core services and products: # An information infrastructure an Internet-based index of a globally distributed network of interoperable databases that contain primary biodiversity data information on museum specimens, field observations of plants and animals in nature, and results from experiments so that data holders across the world can access and share them # Community-developed tools, standards and protocols the tools data providers need to format and share their data # Capacity-building the training, access to international experts and mentoring programs that national and regional institutions need to become part of a decentralized network of biodiversity information facilities. GBIF and its many partners work to mobilize the data, and to improve search mechanisms, data and metadata standards, web services, and the other components of an Internet-based information infrastructure for biodiversity. GBIF makes available data that are shared by hundreds of data publishers from around the world. These data are shared according to the GBIF Data Use Agreement, which includes the provision that users of any data accessed through or retrieved via the GBIF Portal will always give credit to the original data publishers. * Explore Species: Find data for a species or other group of organisms. Information on species and other groups of plants, animals, fungi and micro-organisms, including species occurrence records, as well as classifications and scientific and common names. * Explore Countries: Find data on the species recorded in a particular country, territory or island. Information on the species recorded in each country, including records shared by publishers from throughout the GBIF network. * Explore Datasets: Find data from a data publisher, dataset or data network. Information on the data publishers, datasets and data networks that share data through GBIF, including summary information on 10028 datasets from 419 data publishers.
View all literature mentionsThe California Academy of Sciences is a multifaceted scientific institution committed to leading-edge research, to educational outreach, and to finding new and innovative ways to engage and inspire the public. This world-class scientific and cultural institution is based in San Francisco and recently opened a new facility in Golden Gate Park that houses an aquarium, a planetarium a natural history museum and a 4-story rainforest all under one roof. The new facility is also home to the Academy''s staff of world-class scientists, an education department that provides a wide range of student and teacher services, and an extensive science library with over 26 million specimens and artifacts. The Academy is an international center for scientific education and research and is at the forefront of efforts to understand and protect the diversity of Earth''s living things. The Academy has a staff of over 50 professional educators and Ph.D.-level scientists, supported by more than 100 Research and Field Associates and over 300 Fellows. It hosts 11 fields of research, including anthropology, aquatic biology, botany, comparative genomics, entomology, geology, herpetology, ichthyology, invertebrate zoology,mammalogy and ornithology. The Academy''s research collections, which are among the world''s largest, include more than 26 million specimensessential tools for comparative studies on the history and future of the natural world.
View all literature mentionsFishNet is a collaborative effort by natural history museums and other biodiversity institutions to establish a global network of Ichthyology collections. There is an open invitation for any institution with a fish collection to join. The current portal is an outgrowth of the original FishNet project with improvements in network stability, georeferencing capabilities, and technical support. Users are provided access to searchable, mappable and downloadable data that are cached on a regular basis from participating institutions who have published their data via the DiGIR or TAPIR protocols with a Darwin Core schema. FishNet is also one of four (along with MaNIS, HerpNET, and ORNIS) vertebrate network portals that provide access to specimen collection records from around the world. These web portals, together, comprise VertNet and serve georeferenced, taxon-based data from 72 global institutions. VertNet is a cooperative project working to maintain and expand these distributed database projects. Future plans for VertNet include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. :Sponsors: This resource is supported by the National Science Foundation :.
View all literature mentionsA graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.
View all literature mentionsA cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
View all literature mentionsMultiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
View all literature mentionsOpen source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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