Phylogeography of Rattus norvegicus in the South Atlantic Ocean

Acknowledgments Funding for sample collection was provided by the Shackleton Scholarship Fund, Antarctic Research Trust, the Wyoming Biodiversity Institute, PVE/CAPES (Proposal 235453) and Fundação para a Ciência e a Tecnologia (SFRH/BPD/88854/2012). Thanks to Martin Collins, Andy Black, Darren Christie and the Government of South Georgia and South Sandwich Islands for the provision of samples from South Georgia, Annalea Beard for providing the rat sample from St Helena Island, Joaquim Tapisso, Rita Monarca and Ana Cerveira for samples from Portugal, and Emily Puckett for help validating South American SNP haplotypes. Funding for DNA sequencing was provided by Island LandCare, the University of Auckland. Thanks to two anonymous reviewers for the constructive comments.Peer reviewedPublisher PD

The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi

Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or “SNP chips”, enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species

Addressing student attrition within higher education online programs through a collaborative community of practice

Student retention is a key strategic issue in higher education affecting student experience, university funding, and reputation. It is critical for institutions to identify factors that impact upon student success, build effective strategies to enhance student outcomes, and respond to the emerging evidence-base of distance student engagement. The University of Tasmania has one of the highest attrition rates in Australia, at 28 percent for commencing bachelor students. Studying by distance is a known risk factor affecting attrition and it is vital that we understand the challenges that 'at risk' distance students face when they engage in higher education and how to best support them for success. This study describes a Community of Practice approach that identified four key challenges to reduce student attrition in online degree programs: (i) the importance of knowing your students, (ii) the difficulty in getting reliable data, (iii) the need for 'belonging' for online students and early, meaningful engagement, and (iv) student access to known academics. With no magic bullet to reduce student attrition rates, we present a range of targeted and connected early interventions designed to support students to succeed and enhance their learning experience

Phylogenetic Species Identification in <i>Rattus</i> Highlights Rapid Radiation and Morphological Similarity of New Guinean Species

<div><p>The genus <i>Rattus</i> is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in <i>Rattus</i> but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 <i>Rattus</i> species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean <i>Rattus</i> clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, <i>R. leucopus</i>/<i>R</i>. cf. <i>verecundus</i> and <i>R. steini/R</i>. <i>praetor</i>. Additionally, our results showed that <i>R. praetor</i>, <i>R. niobe</i> and <i>R</i>. <i>verecundus</i> each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of <i>Rattus</i> in the Australo-Papuan region.</p></div

The presence of monophyletic species across the trees compared with nominal species designations.

<p>The tree estimation methods are represented as: R = RAxML; P = PHYML; B = MrBayes. The evidence for monophyly is represented as: M =  monophyletic species with good support (≥90% bootstrap; ≥0.95 posterior probability); m =  monophyletic species with moderate support (70–90% bootstrap; 0.80–0.95 posterior probability); l =  monophyletic species with low support; x =  non-monophyletic species; -  = species not present in tree; s =  single sample.</p

Sample location map showing South East Asia, Australia, New Guinea and the western Pacific region.

<p>The middle pane is a more detailed view of New Guinea (comprising Papua, a province of Indonesia, and Papua New Guinea) and the bottom pane is a map of Papua New Guinea showing some major features, including the provinces, mentioned in the text. Note that given the scales involved the sample positions are approximate.</p

ML tree for COI based on 162 taxa with sequence lengths of 655 bp.

<p>As explained in the caption for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0098002#pone-0098002-g003" target="_blank">Fig. 3</a>, monophyletic species are named on the tree while other species are colour coded. Note the changed positions and species make-up shown in the boxes and see further discussion of this in the text. Bootstrap support of ≥70% and Bayesian posterior probabilities ≥0.80 are shown as symbols in the order RAxML/PHYML/MrBayes.</p

Sample identification history.

<p>ID is the species identification. AMSV # is the voucher number used by the Australian Museum Sydney. SAM # is the tissue accession number used by the South Australian Museum.</p><p>*indicates that the vouchers were examined but the samples were not included in the current analyses because their sequences are the same haplotype as <i>R. exulans</i> ExPN025 which was included.</p