Field Museum of Natural History

About: Field Museum of Natural History is a(n) archive organization based out in Chicago, Illinois, United States. It is known for research contribution in the topic(s): Population & Monophyly. The organization has 777 authors who have published 2997 publication(s) receiving 134503 citation(s). The organization is also known as: Field Museum & The Field Museum.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

A higher-level phylogenetic classification of the Fungi

Abstract: A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis.

Abstract: In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.

Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations

Abstract: Aim Glaciation and deglaciation and the accompanying lowering and rising of sea levels during the late Pleistocene are known to have greatly affected land mass configurations in Southeast Asia. The objective of this report is to provide a series of maps that estimate the areas of exposed land in the Indo-Australian region during periods of the Pleistocene when sea levels were below present day levels. Location The maps presented here cover tropical Southeast Asia and Austral-Asia. The east–west coverage extends 8000 km from Australia to Sri Lanka. The north–south coverage extends 5000 km from Taiwan to Australia. Methods Present-day bathymetric depth contours were used to estimate past shore lines and the locations of the major drowned river systems of the Sunda and Sahul shelves. The timing of sea level changes associated with glaciation over the past 250,000 years was taken from multiple sources that, in some cases, account for tectonic uplift and subsidence during the period in question. Results This report provides a series of maps that estimate the areas of exposed land in the Indo-Australian region during periods of 17,000, 150,000 and 250,000 years before present. The ancient shorelines are based on present day depth contours of 10, 20, 30, 40, 50, 75, 100 and 120 m. On the maps depicting shorelines at 75, 100 and 120 m below present levels the major Pleistocene river systems of the Sunda and Sahul shelves are depicted. Estimates of the number of major sea level fluctuation events and the duration of time that sea levels were at or below the illustrated level are provided. Main conclusions Previous reconstructions of sea-level change during the Pleistocene have emphasized the maximum lows. The perspective provided here emphasizes that sea levels were at their maximum lows for relatively short periods of time but were at or below intermediate levels (e.g. at or below 40 m below present-day levels) for more than half of each of the time periods considered.

Reconstructing the early evolution of Fungi using a six-gene phylogeny

Abstract: The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.