Phlogeny and Biogeography of the Prayer Plant Family

Marantaceae are the second largest family in the order Zingiberales, with approximately 31 genera and 535 species. Earlier studies based on morphological and molecular characters could not confidently determine the relationships among major lineages of the family, nor could they identify the basal branch of the family tree. Phylogenetic analyses of DNA sequence data from all three genomic compartments (chloroplast: matK, ndhF, rbcL, rps16 intron, and trnL-trnF intergenic spacer; mitochondrion: cox1; nucleus: ITS region and the 5\u27-end of 26S) for a restricted set of taxa were conducted under parsimony criteria to define the root node and to assess geographical distribution patterns. Our results support the recognition of five major lineages, most of which are restricted to a single geographical region (tropical America, tropical Africa, or tropical Asia). The phylogenies and character reconstructions (Fitch parsimony optimization, Bremer ancestral areas, and DIVA) support an African origin for the family, followed by a minimum of two dispersal events to the New World tropics and four or more dispersal events to the Asian tropics. Less likely are two alternative hypotheses: (1) vicariance of a western Gondwanan group (the Americas and Africa) followed by several dispersals to Asia and Africa, or (2) an American origin followed by several dispersals to Africa and Asia. The low specific diversity in Africa may be due to higher extinction rates as a result of shrinking lowland tropical forests during the Tertiary

The Evolutionary and Biogeographic Origin and Diversification of the Tropical Monocot Order Zingiberales

Zingiberales are a primarily tropical lineage of monocots. The current pantropical distribution of the order suggests an historical Gondwanan distribution, however the evolutionary history of the group has never been analyzed in a temporal context to test if the order is old enough to attribute its current distribution to vicariance mediated by the break-up of the supercontinent. Based on a phylogeny derived from morphological and molecular characters, we develop a hypothesis for the spatial and temporal evolution of Zingiberales using Dispersal-Vicariance Analysis (DIVA) combined with a local molecular clock technique that enables the simultaneous analysis of multiple gene loci with multiple calibration points. We employ a pairwise relative rates test to assign four rate classes to 24 ingroup and 12 outgroup taxa using evidence from three gene regions (rbcL, atpB, 18S). Five nodes of in group and outgroup taxa were calibrated using fossils and previous monocot-wide age estimates. The results are compared with non-parametric rate smoothing and penalized likelihood estimates of temporal diversification. The divergence of Zingiberales from the remaining commelinid monocots is found to have occurred around 124 million years ago, with major family-level lineages becoming established in the late Cretaceous (80-110 mya) and crown lineages within each family beginning to diversify during the early to mid-Tertiary (29-64 mya). Ancestral Gondwanan vicariance combined with a potential Laurasian distribution and multiple secondary dispersal events within families during the Tertiary can explain the main biogeographic events leading to the current pantropical distribution of this tropical order

Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys

The paper describes the focus, scope and the rationale of PhytoKeys, a newly established, peer-reviewed, open-access journal in plant systematics. PhytoKeys is launched to respond to four main challenges of our time: (1) Appearance of electronic publications as amendments or even alternatives to paper publications; (2) Open Access (OA) as a new publishing model; (3) Linkage of electronic registers, indices and aggregators that summarize information on biological species through taxonomic names or their persistent identifiers (Globally Unique Identifiers or GUIDs; currently Life Science Identifiers or LSIDs); (4) Web 2.0 technologies that permit the semantic markup of, and semantic enhancements to, published biological texts. The journal will pursue cutting-edge technologies in publication and dissemination of biodiversity information while strictly following the requirements of the current International Code of Botanical Nomenclature (ICBN)

Phylogenetic Analysis of the Zingiberales Based on \u3cem\u3erbc\u3c/em\u3eL Sequences

Morphological data have been used previously to construct phylogenies of the eight families of the Zingiberales one of the most widely accepted monophyletic groups of flowering plants. To provide additional support for phylogenetic relationships within the order, and placement of the order among monocots, we present a parsimony analysis of DNA sequences from the chloroplast-encoded gene, rbcL, for 21 species of Zingiberales and proposed relatives. Five analyses with equal, and differential weights were performed. All analyses resulted in the same most parsimonious tree for taxa within the Zingiberales and the immediate outgroup. The closest sister group to the Zingiberales based on these data is a clade containing Commelinaceae/Haemodoraceae/Pontederiacea. The tree topology within the order based on rbcL sequence data is different from previous morphological analyses. The order can be divided into two sister groups, one containing the Costaceae and Marantaceae, and the other, the remaining six families. All recognized families are monophyletic with the exception of the Musaceae, which is paraphyletic with the Cannaceae. Wtih trees one and two steps longer tha the most parsimonious trees, phylogenetic resolution is rapidly lost, suggesting that the phylogenetic utility of rbcL sequence date for the Zingiberales is limited to interordinal and intrafamilial relationships

Species-time-area and phylogenetic-time-area relationships in tropical tree communities

The species-area relationship (SAR) has proven to be one of the few strong generalities in ecology. The temporal analog of the SAR, the species-time relationship (STR), has received considerably less attention. Recent work primarily from the temperate zone has aimed to merge the SAR and the STR into a synthetic and unified species-time-area relationship (STAR) as originally envisioned by Preston (1960). Here we test this framework using two tropical tree communities and extend it by deriving a phylogenetic-time-area relationship (PTAR). The work finds some support for Preston's prediction that diversity-time relationships, both species and phylogenetic, are sensitive to the spatial scale of the sampling. Contrary to the Preston's predictions we find a decoupling of diversity-area and diversity-time relationships in both forests as the time period used to quantify the diversity-area relationship changes. In particular, diversity-area and diversity-time relationships are positively correlated using the initial census to quantify the diversity-area relationship, but weakly or even negatively correlated when using the most recent census. Thus, diversity-area relationships could forecast the temporal accumulation of biodiversity of the forests, but they failed to back-cast the temporal accumulation of biodiversity suggesting a decoupling of space and time

Next-Generation Field Guides

To conserve species, we must first identify them. Field researchers, land managers, educators, and citizen scientists need up-to-date and accessible tools to identify organisms, organize data, and share observations. Emerging technologies complement traditional, book-form field guides by providing users with a wealth of multimedia data. We review technical innovations of next-generation field guides, including Web-based and stand-alone applications, interactive multiple-access keys, visual-recognition software adapted to identify organisms, species checklists that can be customized to particular sites, online communities in which people share species observations, and the use of crowdsourced data to refine machine-based identification algorithms. Next-generation field guides are user friendly; permit quality control and the revision of data; are scalable to accommodate burgeoning data; protect content and privacy while allowing broad public access; and are adaptable to ever-changing platforms and browsers. These tools have great potential to engage new audiences while fostering rigorous science and an appreciation for nature.Organismic and Evolutionary Biolog

A Well-Resolved Phylogeny of the Trees of Puerto Rico Based on DNA Barcode Sequence Data

Background: The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarilydefined species pools. Methodology/principal findings: We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with PHYLOMATIC (proportion of internal nodes resolved:constrained ML = 74%, unconstrained ML = 68%, PHYLOMATIC = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and PHYLOMATIC phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. PHYLOMATIC) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny. Conclusions/significance: With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning

„DNA barkodiranje“ za pouzdano utvrđivanje izvornosti morskih rakova, mekušaca i riba dostupnih na tržištu

Animal DNA barcoding allows researchers to identify different species by analyzing a short nucleotide sequence, typically the mitochondrial gene cox1. In this paper, we use DNA barcoding to genetically identify seafood samples that were purchased from various locations throughout Italy. We adopted a multi-locus approach to analyze the cob, 16S-rDNA and cox1 genes, and compared our sequences to reference sequences in the BOLD and GenBank online databases. Our method is a rapid and robust technique that can be used to genetically identify crustaceans, mollusks and fishes. This approach could be applied in the future for conservation, particularly for monitoring illegal trade of protected and endangered species. Additionally, this method could be used for authentication in order to detect mislabeling of commercially processed seafood.DNA barkodiranje“ omogućuje istraživačima identifikaciju različitih životinjskih vrsta analizom kratke sekvencije nukleotida, i to obično mitohondrijskog gena cox1. U ovom je radu „DNA barkodiranje“ primjenjeno za identifikaciju uzoraka morskih rakova, mekušaca i riba kupljenih na različitim lokacijama diljem Italije. Sekvencionirani su geni cob, cox1 i 16S-rDNA, a dobivene su sekvencije uspoređene s odgovarajućim sekvencijama u online bazama podataka BOLD i GenBank. Ova metoda omogućuje brzo i točno utvrđivanje genetičkog porijekla rakova, mekušaca i riba, što se može ubuduće primijeniti u svrhu zaštite ugroženih vrsta, te sprečavanje njihove ilegalne prodaje. Također se ovom metodom može utvrditi istinitost podataka na deklaracijama prehrambenih proizvoda od riba, rakova i mekušaca

„DNA barkodiranje“ za pouzdano utvrđivanje izvornosti morskih rakova, mekušaca i riba dostupnih na tržištu

Animal DNA barcoding allows researchers to identify different species by analyzing a short nucleotide sequence, typically the mitochondrial gene cox1. In this paper, we use DNA barcoding to genetically identify seafood samples that were purchased from various locations throughout Italy. We adopted a multi-locus approach to analyze the cob, 16S-rDNA and cox1 genes, and compared our sequences to reference sequences in the BOLD and GenBank online databases. Our method is a rapid and robust technique that can be used to genetically identify crustaceans, mollusks and fishes. This approach could be applied in the future for conservation, particularly for monitoring illegal trade of protected and endangered species. Additionally, this method could be used for authentication in order to detect mislabeling of commercially processed seafood.DNA barkodiranje“ omogućuje istraživačima identifikaciju različitih životinjskih vrsta analizom kratke sekvencije nukleotida, i to obično mitohondrijskog gena cox1. U ovom je radu „DNA barkodiranje“ primjenjeno za identifikaciju uzoraka morskih rakova, mekušaca i riba kupljenih na različitim lokacijama diljem Italije. Sekvencionirani su geni cob, cox1 i 16S-rDNA, a dobivene su sekvencije uspoređene s odgovarajućim sekvencijama u online bazama podataka BOLD i GenBank. Ova metoda omogućuje brzo i točno utvrđivanje genetičkog porijekla rakova, mekušaca i riba, što se može ubuduće primijeniti u svrhu zaštite ugroženih vrsta, te sprečavanje njihove ilegalne prodaje. Također se ovom metodom može utvrditi istinitost podataka na deklaracijama prehrambenih proizvoda od riba, rakova i mekušaca

Space Weather Nowcasting of Atmospheric Ionizing Radiation for Aviation Safety

There is a growing concern for the health and safety of commercial aircrew and passengers due to their exposure to ionizing radiation with high linear energy transfer (LET), particularly at high latitudes. The International Commission of Radiobiological Protection (ICRP), the EPA, and the FAA consider the crews of commercial aircraft as radiation workers. During solar energetic particle (SEP) events, radiation exposure can exceed annual limits, and the number of serious health effects is expected to be quite high if precautions are not taken. There is a need for a capability to monitor the real-time, global background radiations levels, from galactic cosmic rays (GCR), at commercial airline altitudes and to provide analytical input for airline operations decisions for altering flight paths and altitudes for the mitigation and reduction of radiation exposure levels during a SEP event. The Nowcast of Atmospheric Ionizing Radiation for Aviation Safety (NAIRAS) model is new initiative to provide a global, real-time radiation dosimetry package for archiving and assessing the biologically harmful radiation exposure levels at commercial airline altitudes. The NAIRAS model brings to bear the best available suite of Sun-Earth observations and models for simulating the atmospheric ionizing radiation environment. Observations are utilized from ground (neutron monitors), from the atmosphere (the METO analysis), and from space (NASA/ACE and NOAA/GOES). Atmospheric observations provide the overhead shielding information and the ground- and space-based observations provide boundary conditions on the GCR and SEP energy flux distributions for transport and dosimetry simulations. Dose rates are calculated using the parametric AIR (Atmospheric Ionizing Radiation) model and the physics-based HZETRN (High Charge and Energy Transport) code. Empirical models of the near-Earth radiation environment (GCR/SEP energy flux distributions and geomagnetic cut-off rigidity) are benchmarked against the physics-based CMIT (Coupled Magnetosphere- Ionosphere-Thermosphere) and SEP-trajectory models