Evolution in Australasian Mangrove Forests: Multilocus Phylogenetic Analysis of the Gerygone Warblers (Aves: Acanthizidae)

The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster

Stratified Abstraction of Access Control Policies

The shift to cloud-based APIs has made application security critically depend on understanding and reasoning about policies that regulate access to cloud resources. We present stratified predicate abstraction, a new approach that summarizes complex security policies into a compact set of positive and declarative statements that precisely state who has access to a resource. We have implemented stratified abstraction and deployed it as the engine powering AWS’s IAM Access Analyzer service, and hence, demonstrate how formal methods and SMT can be used for security policy explanation

Miocene waterfowl and other birds from central Otago, New Zealand

Copyright © The Natural History Museum 2007Abundant fossil bird bones from the lower Bannockburn Formation, Manuherikia Group, an Early-Middle Miocene lacustrine deposit, 16–19 Ma, from Otago in New Zealand, reveal the “St Bathans Fauna” (new name), a first Tertiary avifauna of land and freshwater birds from New Zealand. At least 23 species of birds are represented by bones, and probable moa, Aves: Dinornithiformes, by eggshell. Anatids dominate the fauna with four genera and five species described as new: a sixth and largest anatid species is represented by just one bone. This is the most diverse Early-Middle Miocene duck fauna known worldwide. Among ducks, two species of dendrochenines are most numerous in the fauna, but a tadornine is common as well. A diving petrel (Pelecanoididae: Pelecanoides) is described, so extending the geological range of this genus worldwide from the Pliocene to the Middle Miocene, at least. The remaining 16 taxa are left undescribed but include: a large species of gull (Laridae); two small waders (Charadriiformes, genus indet.), the size of Charadrius bicinctus and Calidris ruficollis, respectively; a gruiform represented by one specimen similar to Aptornis; abundant rail (Rallidae) bones, including a common flightless rail and a rarer slightly larger taxon, about the size of Gallirallus philippensis; an ?eagle (Accipitridae); a pigeon (Columbidae); three parrots (Psittacidae); an owlet nightjar (Aegothelidae: Aegotheles sp.); a swiftlet (Apodidae: Collocalia sp.); and three passerine taxa, of which the largest is a member of the Cracticidae. The absence of some waterbirds, such as anserines (including swans), grebes (Podicipedidae) and shags (Phalacrocoracidae), among the abundant bones, indicates their probable absence from New Zealand in the Early-Middle Miocene.T. H. Worthy, A. J. D. Tennyson, C. Jones, J. A. McNamara and B. J. Dougla

Uncovering cryptic evolutionary diversity in extant and extinct populations of the southern Australian arid zone Western and Thick-billed Grasswrens (Passeriformes: Maluridae: Amytornis)

Published online: 08 June 2013The Western and Thick-billed Grasswrens (Aves: Passeriformes: Maluridae:Amytornis textilis and A. modestus, respectively) exemplify issues surrounding the evolution, biogeography and conservation of Australia's arid and semi-arid zone fauna. The two species together have historically occurred across much of southern Australia. They showed high intraspecific taxonomic diversity and short range endemism but suffered high rates of recent anthropogenic extinction. Of 11 named and one un-named subspecies, five are extinct and three are vulnerable or critically endangered. To clarify taxonomic issues, and to understand their pre-extinction phylogeography and identify extant populations and taxa of conservation value, we sequenced ~1000 bp of the mtDNA ND2 gene from all extant populations and all but one extinct population. We confirmed reciprocal monophyly of A. modestus and A. textilis and identified strong phylogeographic structure associated with morphological divergence within each species. Populations of A. t. myall at the western edge of their range in South Australia may preserve “ghost” lineages of extinct subspecies from Western Australia as a result of ancient gene flow. Our results support recent taxonomic revisions, and highlight the critical importance of including samples of extirpated populations and extinct species to fully understand and interpret extant diversity. Conservation and management plans should recognise and seek to preserve the unique evolutionary diversity present in surviving populations.Jeremy J. Austin, Leo Joseph, Lynn P. Pedler, Andrew B. Blac

A historical overview of the classification, evolution, and dispersion of Leishmania parasites and sandflies

Background The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale. Methodology and Principal Findings Leishmania and sandfly classification has always been a controversial matter, and the increasing number of species currently described further complicates this issue. Despite several hypotheses on the origin, evolution, and distribution of Leishmania and sandflies in the Old and New World, no consistent agreement exists regarding dissemination of the actors that play roles in leishmaniasis. For this purpose, we present here three centuries of research on sandflies and Leishmania descriptions, as well as a complete description of Leishmania and sandfly fossils and the emergence date of each Leishmania and sandfly group during different geographical periods, from 550 million years ago until now. We discuss critically the different approaches that were used for Leishmana and sandfly classification and their synonymies, proposing an updated classification for each species of Leishmania and sandfly. We update information on the current distribution and dispersion of different species of Leishmania (53), sandflies (more than 800 at genus or subgenus level), and animal reservoirs in each of the following geographical ecozones: Palearctic, Nearctic, Neotropic, Afrotropical, Oriental, Malagasy, and Australian. We propose an updated list of the potential and proven sandfly vectors for each Leishmania species in the Old and New World. Finally, we address a classical question about digenetic Leishmania evolution: which was the first host, a vertebrate or an invertebrate? Conclusions and Significance We propose an updated view of events that have played important roles in the geographical dispersion of sandflies, in relation to both the Leishmania species they transmit and the animal reservoirs of the parasites

Second Language Tutoring Using Social Robots: A Large-Scale Study

We present a large-scale study of a series of seven lessons designed to help young children learn English vocabulary as a foreign language using a social robot. The experiment was designed to investigate 1) the effectiveness of a social robot teaching children new words over the course of multiple interactions (supported by a tablet), 2) the added benefit of a robot's iconic gestures on word learning and retention, and 3) the effect of learning from a robot tutor accompanied by a tablet versus learning from a tablet application alone. For reasons of transparency, the research questions, hypotheses and methods were preregistered. With a sample size of 194 children, our study was statistically well-powered. Our findings demonstrate that children are able to acquire and retain English vocabulary words taught by a robot tutor to a similar extent as when they are taught by a tablet application. In addition, we found no beneficial effect of a robot's iconic gestures on learning gains

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016