Time-dependent rates of molecular evolution

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

Evolution of the extinct Sabretooths and the American cheetah-like cat

The sabretooths (Smilodon and Homotherium) and the American cheetah-like cat (Miracinonyx) were the top predators in Late Pleistocene America, but became extinct about 13 thousand years ago. As the evolutionary history of these taxa remains poorly understood , we analysed their phylogenetic relationship to extant felids. In contrast to previous molecular studies , our results show that the sabretooths diverge early and are not closely related to any living cats. This supports their morphological placement in a separate subfamily (Machairodontinae). Despite its remarkable morphological similarity to the African cheetah (Acinonyx jubatus), Miracinonyx appears to have evolved from a puma-like ancestor, presumably in response to similar ecological pressures.

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.

'Nothing exists for one cause' : putting biology back into evolution

The opening phrase of the title is from Charles Darwin’s notebooks (Schweber 1977). It is a double reminder, firstly that mainstream evolutionary theory is not just about describing nature but is particularly looking for mechanisms or ‘causes’, and secondly, that there will usually be several causes affecting any particular outcome. The second part of the title is our concern at the almost universal rejection of the idea that biological mechanisms are sufficient for macroevolutionary changes, thus rejecting a cornerstone of Darwinian evolutionary theory. Our primary aim here is to consider ways of making it easier to develop and to test hypotheses about evolution. Formalizing hypotheses can help generate tests. In an absolute sense, some of the discussion by scientists about evolution is little better than the lack of reasoning used by those advocating intelligent design. Our discussion here is in a Popperian framework where science is defined by that area of study where it is possible, in principle, to find evidence against hypotheses – they are in principle falsifiable. However, with time, the boundaries of science keep expanding. In the past, some aspects of evolution were outside the current boundaries of falsifiable science, but increasingly new techniques and ideas are expanding the boundaries of science and it is appropriate to re-examine some topics. It often appears that over the last few decades there has been an increasingly strong assumption to look first (and only) for a physical cause. This decision is virtually never formally discussed, just an assumption is made that some physical factor ‘drives’ evolution. It is necessary to examine our assumptions much more carefully. What is meant by physical factors ‘driving’ evolution, or what is an ‘explosive radiation’. Our discussion focuses on two of the six mass extinctions, the fifth being events in the Late Cretaceous, and the sixth starting at least 50,000 years ago (and is ongoing). Cretaceous/Tertiary boundary; the rise of birds and mammals. We have had a long-term interest (Cooper and Penny 1997) in designing tests to help evaluate whether the processes of microevolution are sufficient to explain macroevolution. The real challenge is to formulate hypotheses in a testable way. For example the numbers of lineages of birds and mammals that survive from the Cretaceous to the present is one test. Our first estimate was 22 for birds, and current work is tending to increase this value. This still does not consider lineages that survived into the Tertiary, and then went extinct later. Our initial suggestion was probably too narrow in that it lumped four models from Penny and Phillips (2004) into one model. This reduction is too simplistic in that we need to know about survival and ecological and morphological divergences during the Late Cretaceous, and whether Crown groups of avian or mammalian orders may have existed back into the Cretaceous. More recently (Penny and Phillips 2004) we have formalized hypotheses about dinosaurs and pterosaurs, with the prediction that interactions between mammals (and groundfeeding birds) and dinosaurs would be most likely to affect the smallest dinosaurs, and similarly interactions between birds and pterosaurs would particularly affect the smaller pterosaurs. There is now evidence for both classes of interactions, with the smallest dinosaurs and pterosaurs declining first, as predicted. Thus, testable models are now possible. Mass extinction number six: human impacts. On a broad scale, there is a good correlation between time of human arrival, and increased extinctions (Hurles et al. 2003; Martin 2005; Figure 1). However, it is necessary to distinguish different time scales (Penny 2005) and on a finer scale there are still large numbers of possibilities. In Hurles et al. (2003) we mentioned habitat modification (including the use of Geogenes III July 2006 31 fire), introduced plants and animals (including kiore) in addition to direct predation (the ‘overkill’ hypothesis). We need also to consider prey switching that occurs in early human societies, as evidenced by the results of Wragg (1995) on the middens of different ages on Henderson Island in the Pitcairn group. In addition, the presence of human-wary or humanadapted animals will affect the distribution in the subfossil record. A better understanding of human impacts world-wide, in conjunction with pre-scientific knowledge will make it easier to discuss the issues by removing ‘blame’. While continued spontaneous generation was accepted universally, there was the expectation that animals continued to reappear. New Zealand is one of the very best locations in the world to study many of these issues. Apart from the marine fossil record, some human impact events are extremely recent and the remains less disrupted by time.

‘Personal Response’ and English Teaching

A case study relating to secondary education, examining the teacher student relationship as it operates within the English classroom is the topic of this paper. It describes how a certain conception of 'personal response' to literature provided a means for the teacher/counsellor to form the ethical capacities of children. 'Personal response' is usually associated with the moment in which the child is freed to be most natural. But for all the emphasis upon the irreducibly individual nature of the 'genuinely felt response', this pedagogic exercise finds its place within a series of strategies designed both to cherish and correct the child, to nurture and to scrutinise, to guide and to reconstruct.

Resisting innovation talk in higher education teaching and learning

The exhortation to innovate is a pervasive one that occupies a central position across university mission statements, strategic plans, marketing literature and job titles. This paper locates a discourse of innovation within a history of Australian federal higher education policy, a history that may bear similarity with other national contexts. This paper names this discourse as an innovation talk that influences our teaching and learning practices, a discourse that can be reconfigured in a way that opens up the possibility for change. As such, this paper presents an analytical process used to resist taken-for-granted views of what constitutes valuable teaching practices. Suggestions for re-conceptualising how universities govern and support teaching and learning innovation are drawn from analysis of key federal policies that have influenced university practices in recent years.

Teaching in a nutshell : navigating your teacher education program as a stdent teacher

Teacher education programs bridge the interests of two worlds - the world of educational theory and the world of teaching practice. Despite teacher educators’ best attempts to convince pre-service teachers that theory and practice are linked, it is often during their practicum placements when pre-service teachers claim that their ‘real’ learning takes place. It is also on practicum when students teachers face (and are surprised by) the ‘extensive decision-making role of the teacher, the emotional aspects of teaching, and the sheer volume of work’ (p.4). Kosnick and Beck’s new book Teaching in a Nutshell utilises the authors’ extensive research with beginning teachers to help students ‘navigate’ their way through their programs. Identifying what they have found in their research to be the seven key priorities for teachers, each chapter follows a helpful structure beginning with an overview of current thinking in the priority area, followed by a case study of a beginning teacher showing how s/he implements the strategy...

Addressing quality teaching in hard to staff settings : the Exceptional Teachers for Disadvantaged Schools Project

This Exceptional Teachers for Disadvantaged Schools (ETDS) project sets out to design a new model of Australian teacher education responding to recent demands for quality education in low SES and disadvantaged schools. The project moves teacher education from the ‘missionary’ (Larabee, 2010) or deficit (Comber and Kamler 2004; Flessa, 2007) approaches, towards a focus on notions of quality and academic excellence. Rice (2008, p.1) argues for a need to place more of the “very best teachers into the most challenging schools”, yet the problem is not merely one of training more teachers, for disadvantaged schools already receive disproportionate numbers of beginning teachers (Connell, 1994; Vickers & Ferfolja, 2006). Rather, Grossman and Loeb (2010, p. 245) argue the problem centers on the common practice of “[p]lacing the least experienced teachers with the most needy students”. This paper reports on the first year trial of the project. The ETDS project is at present, the only mainstream Australian teacher education model that targets cohorts of academically high achieving pre-service teachers with the overt aim of preparing graduates of the program to teach in disadvantaged schools. At the end of its first year, the ETDS program graduated 20 new teachers, each of whom had over the previous 18 months engaged with a specialized curriculum and carefully monitored/scaffolded practicum placements in disadvantaged schools around Brisbane, Australia.

Microcosm study of ion mobilization and greenhouse gas evolution in soils of a plantation-forested subtropical coastal catchment

This study examined the potential for Fe mobilization and greenhouse gas (GHG, e.g. CO2, and CH4) evolution in SEQ soils associated with a range of plantation forestry practices and water-logged conditions. Intact, 30-cm-deep soil cores collected from representative sites were saturated and incubated for 35 days in the laboratory, with leachate and headspace gas samples periodically collected. Minimal Fe dissolution was observed in well-drained sand soils associated with mature, first-rotation Pinus and organic Fe complexation, whereas progressive Fe dissolution occurred over 14 days in clear-felled and replanted Pinus soils with low organic matter and non-crystalline Fe fractions. Both CO2 and CH4 effluxes were relatively lower in clear-felled and replanted soils compared with mature, first-rotation Pinus soils, despite the lack of statistically significant variations in total GHG effluxes associated with different forestry practices. Fe dissolution and GHG evolution in low-lying, water-logged soils adjacent to riparian and estuarine, native-vegetation buffer zones were impacted by mineral and physical soil properties. Highest levels of dissolved Fe and GHG effluxes resulted from saturation of riparian loam soils with high Fe and clay content, as well as abundant organic material and Fe-metabolizing bacteria. Results indicate Pinus forestry practices such as clear-felling and replanting may elevate Fe mobilization while decreasing CO2 and CH4 emissions from well-drained, SEQ plantation soils upon heavy flooding. Prolonged water-logging accelerates bacterially mediated Fe cycling in low-lying, clay-rich soils, leading to substantial Fe dissolution, organic matter mineralization, and CH4 production in riparian native-vegetation buffer zones.

Elementary teacher education in papua new guinea: towards a culturally connected perspective of teaching

Global and national agendas for quality education have led to reforms in Papua New Guinea’s (PNG) elementary education, but criticism of the learner-centred, Western pedagogies has emerged. One key influence on quality teacher education relates to perspectives of teaching. Existing research shows teachers’ beliefs and perceptions of teaching influence their practice, however to date little research has investigated perspectives of teaching for elementary education in PNG. This single exploratory case study investigated the perspectives of teaching for eighteen elementary teacher trainers as they studied for a Bachelor of Early Childhood (Teacher Education). The study, drawing on an interpretivist paradigm, analysed journals and course planning documents using a thematic approach. The findings revealed that while the trainers’ perspectives of teaching children tended to reflect a learning-centred perspective (focused on what the teacher does), their perspectives of teaching adults were both learning-centred and learner-centred (what the learner does). Based on these findings, a culturally connected perspective of teaching is advocated for PNG elementary teacher education. This perspective enables the co-existence of both the learning-centred and learner-centred perspectives of teaching in the PNG cultural context and has implications for teacher education and the communities involved in elementary education in general.

Reclaiming the art of teaching

This paper explores the art and craft of teaching in higher education. It presents a model of the relationship between art and craft drawn from the author’s theoretical and empirical work, and provides examples from the higher education context to illustrate the model. It discusses the characteristics of teaching as art and craft and critiques the move towards standardisation and conformity in favour of originality, creativity and innovation. It suggests that to see teaching as art is more holistic, satisfying and transformative than to see it as craft. It argues for reclaiming the art of teaching and provides strategies for encouraging and supporting artistic teaching.

Tracking the magmatic evolution of island arc volcanism : insights from a high-precision Pb isotope record of Montserrat, Lesser Antilles

The volcanic succession on Montserrat provides an opportunity to examine the magmatic evolution of island arc volcanism over a ∼2.5 Ma period, extending from the andesites of the Silver Hills center, to the currently active Soufrière Hills volcano (February 2010). Here we present high-precision double-spike Pb isotope data, combined with trace element and Sr-Nd isotope data throughout this period of Montserrat's volcanic evolution. We demonstrate that each volcanic center; South Soufrière Hills, Soufrière Hills, Centre Hills and Silver Hills, can be clearly discriminated using trace element and isotopic parameters. Variations in these parameters suggest there have been systematic and episodic changes in the subduction input. The SSH center, in particular, has a greater slab fluid signature, as indicated by low Ce/Pb, but less sediment addition than the other volcanic centers, which have higher Th/Ce. Pb isotope data from Montserrat fall along two trends, the Silver Hills, Centre Hills and Soufrière Hills lie on a general trend of the Lesser Antilles volcanics, whereas SSH volcanics define a separate trend. The Soufrière Hills and SSH volcanic centers were erupted at approximately the same time, but retain distinctive isotopic signatures, suggesting that the SSH magmas have a different source to the other volcanic centers. We hypothesize that this rapid magmatic source change is controlled by the regional transtensional regime, which allowed the SSH magma to be extracted from a shallower source. The Pb isotopes indicate an interplay between subduction derived components and a MORB-like mantle wedge influenced by a Galapagos plume-like source.