Young adults’ accounts of scientific knowledge when responding to a television news report of contested science

This paper reports one aspect of a study of 28 young adults (18–26 years) engaging with the uncertain (contested) science of a television news report about recent research into mobile phone health risks. The aim of the study was to examine these young people’s ‘accounts of scientific knowledge’ in this context. Seven groups of friends responded to the news report, initially in focus group discussions. Later in semi-structured interviews they elaborated their understanding of the nature of science through their explanations of the scientists’ disagreement and described their mobile phone safety risk assessments. This paper presents their accounts in terms of their views of the nature of science and their concept understanding. Discussions were audio-recorded then analysed by coding the talk in terms of issues raised, which were grouped into themes and interpreted in terms of a moderate social constructionist theoretical framing. In this context, most participants expressed a ‘common sense’ view of the nature of science, describing it as an atheoretical, technical procedure of scientists testing their personal opinions on the issue, subject to the influence of funding sponsors. The roles of theory and data interpretation were largely ignored. It is argued that the nature of science understanding is crucial to engagement with contemporary socioscientific issues, particularly the roles of argumentation, theory, data interpretation, and the distinction of science from common sense. Implications for school science relate primarily to nature of science teaching and the inclusion of socioscientific issues in school science curricula. Future research directions are considered.

Defining the role of phytoene synthase in carotenoid accumulation of high provitamin A bananas

Vitamin A deficiency (VAD) is a serious problem in developing countries, affecting approximately 127 million children of preschool age and 7.2 million pregnant women each year. However, this deficiency is readily treated and prevented through adequate nutrition. This can potentially be achieved through genetically engineered biofortification of staple food crops to enhance provitamin A (pVA) carotenoid content. Bananas are the fourth most important food crop with an annual production of 100 million tonnes and are widely consumed in areas affected by VAD. However, the fruit pVA content of most widely consumed banana cultivars is low (~ 0.2 to 0.5 ìg/g dry weight). This includes cultivars such as the East African highland banana (EAHB), the staple crop in countries such as Uganda, where annual banana consumption is approximately 250 kg per person. This fact, in addition to the agronomic properties of staple banana cultivars such as vegetative reproduction and continuous cropping, make bananas an ideal target for pVA enhancement through genetic engineering. Interestingly, there are banana varieties known with high fruit pVA content (up to 27.8 ìg/g dry weight), although they are not widely consumed due to factors such as cultural preference and availability. The genes involved in carotenoid accumulation during banana fruit ripening have not been well studied and an understanding of the molecular basis for the differential capacity of bananas to accumulate carotenoids may impact on the effective production of genetically engineered high pVA bananas. The production of phytoene by the enzyme phytoene synthase (PSY) has been shown to be an important rate limiting determinant of pVA accumulation in crop systems such as maize and rice. Manipulation of this gene in rice has been used successfully to produce Golden Rice, which exhibits higher seed endosperm pVA levels than wild type plants. Therefore, it was hypothesised that differences between high and low pVA accumulating bananas could be due either to differences in PSY enzyme activity or factors regulating the expression of the psy gene. Therefore, the aim of this thesis was to investigate the role of PSY in accumulation of pVA in banana fruit of representative high (Asupina) and low (Cavendish) pVA banana cultivars by comparing the nucleic acid and encoded amino acid sequences of the banana psy genes, in vivo enzyme activity of PSY in rice callus and expression of PSY through analysis of promoter activity and mRNA levels. Initially, partial sequences of the psy coding region from five banana cultivars were obtained using reverse transcriptase (RT)-PCR with degenerate primers designed to conserved amino acids in the coding region of available psy sequences from other plants. Based on phylogenetic analysis and comparison to maize psy sequences, it was found that in banana, psy occurs as a gene family of at least three members (psy1, psy2a and psy2b). Subsequent analysis of the complete coding regions of these genes from Asupina and Cavendish suggested that they were all capable of producing functional proteins due to high conservation in the catalytic domain. However, inability to obtain the complete mRNA sequences of Cavendish psy2a, and isolation of two non-functional Cavendish psy2a coding region variants, suggested that psy2a expression may be impaired in Cavendish. Sequence analysis indicated that these Cavendish psy2a coding region variants may have resulted from alternate splicing. Evidence of alternate splicing was also observed in one Asupina psy1 coding region variant, which was predicted to produce a functional PSY1 isoform. The complete mRNA sequence of the psy2b coding regions could not be isolated from either cultivar. Interestingly, psy1 was cloned predominantly from leaf while psy2 was obtained preferentially from fruit, suggesting some level of tissue-specific expression. The Asupina and Cavendish psy1 and psy2a coding regions were subsequently expressed in rice callus and the activity of the enzymes compared in vivo through visual observation and quantitative measurement of carotenoid accumulation. The maize B73 psy1 coding region was included as a positive control. After several weeks on selection, regenerating calli showed a range of colours from white to dark orange representing various levels of carotenoid accumulation. These results confirmed that the banana psy coding regions were all capable of producing functional enzymes. No statistically significant differences in levels of activity were observed between banana PSYs, suggesting that differences in PSY activity were not responsible for differences in the fruit pVA content of Asupina and Cavendish. The psy1 and psy2a promoter sequences were isolated from Asupina and Cavendish gDNA using a PCR-based genome walking strategy. Interestingly, three Cavendish psy2a promoter clones of different sizes, representing possible allelic variants, were identified while only single promoter sequences were obtained for the other Asupina and Cavendish psy genes. Bioinformatic analysis of these sequences identified motifs that were previously characterised in the Arabidopsis psy promoter. Notably, an ATCTA motif associated with basal expression in Arabidopsis was identified in all promoters with the exception of two of the Cavendish psy2a promoter clones (Cpsy2apr2 and Cpsy2apr3). G1 and G2 motifs, linked to light-regulated responses in Arabidopsis, appeared to be differentially distributed between psy1 and psy2a promoters. In the untranscribed regulatory regions, the G1 motifs were found only in psy1 promoters, while the G2 motifs were found only in psy2a. Interestingly, both ATCTA and G2 motifs were identified in the 5’ UTRs of Asupina and Cavendish psy1. Consistent with other monocot promoters, introns were present in the Asupina and Cavendish psy1 5’ UTRs, while none were observed in the psy2a 5’ UTRs. Promoters were cloned into expression constructs, driving the â-glucuronidase (GUS) reporter gene. Transient expression of the Asupina and Cavendish psy1 and psy2a promoters in both Cavendish embryogenic cells and Cavendish fruit demonstrated that all promoters were active, except Cpsy2apr2 and Cpsy2apr3. The functional Cavendish psy2a promoter (Cpsy2apr1) appeared to have activity similar to the Asupina psy2a promoter. The activities of the Asupina and Cavendish psy1 promoters were similar to each other, and comparable to those of the functional psy2a promoters. Semi-quantitative PCR analysis of Asupina and Cavendish psy1 and psy2a transcripts showed that psy2a levels were high in green fruit and decreased during ripening, reinforcing the hypothesis that fruit pVA levels were largely dependent on levels of psy2a expression. Additionally, semi-quantitative PCR using intron-spanning primers indicated that high levels of unprocessed psy2a and psy2b mRNA were present in the ripe fruit of Cavendish but not in Asupina. This raised the possibility that differences in intron processing may influence pVA accumulation in Asupina and Cavendish. In this study the role of PSY in banana pVA accumulation was analysed at a number of different levels. Both mRNA accumulation and promoter activity of psy genes studied were very similar between Asupina and Cavendish. However, in several experiments there was evidence of cryptic or alternate splicing that differed in Cavendish compared to Asupina, although these differences were not conclusively linked to the differences in fruit pVA accumulation between Asupina and Cavendish. Therefore, other carotenoid biosynthetic genes or regulatory mechanisms may be involved in determining pVA levels in these cultivars. This study has contributed to an increased understanding of the role of PSY in the production of pVA carotenoids in banana fruit, corroborating the importance of this enzyme in regulating carotenoid production. Ultimately, this work may serve to inform future research into pVA accumulation in important crop varieties such as the EAHB and the discovery of avenues to improve such crops through genetic modification.

Voices of experience : opportunities to influence creatively the designing of school libraries

Using a critical ethnographic approach this study investigates the potential for multiple voices of experience, of educators, designers/architects, education facility planners and students/learners, to influence creatively the designing of school libraries. School libraries are considered as social and cultural entities within the contexts of school life and of wider society. It is proposed that school library designing is a social interaction of concern to those influenced by its practices and outcomes. School library designing is therefore of significance to educators and students as well as to those with professionally accredited involvement in school library designing, such as designers/architects and education facility planners. The study contends that current approaches to educational space designing, including school libraries, amplify the voices of accredited designers and diminish or silence the voices of the user participants. The study is conceptualised as creative processes of discovery, through which attention is paid to the voices of experience of user and designer participants, and is concerned with their understandings and experiences of school libraries and their understandings and experiences of designing. Grounded theory coding (Charmaz) is used for initial categorising of interview data. Critical discourse analysis (CDA, Fairclough) is used as analytical tool for reflection on the literature and for analysis of the small stories gathered through semi-structured interviews, field observations and documents. The critical interpretive stance taken through CDA, enables discussions of aspects of power associated with the understandings and experiences of participants, and for recognition of creative possibilities and creative influence within and beyond current conditions. Through an emphasis on prospects for educators and students as makers of the spaces and places of learning, in particular in school libraries, the study has the potential to inform education facility designing practices and design participant relationships, and to contribute more broadly to knowledge in the fields of education, design, architecture, and education facility planning.

Literacies programs: Debates and demands in cultural context

An introduction to the "four resources" model of literacy, where coding, semantics, pragmatic and critical text work are viewed as necessary components for literacy in contemporary society.

The complete mitochondrial genome of the gall-forming fly, Fergusonina taylori(Nelson and Yeates) (Diptera: Fergusoninidae)

The monogeneric family Fergusoninidae consists of gall-forming flies that, together with Fergusobia (Tylenchida: Neotylenchidae) nematodes, form the only known mutualistic association between insects and nematodes. In this study, the entire 16,000 bp mitochondrial genome of Fergusonina taylori Nelson and Yeates was sequenced. The circular genome contains one encoding region including 27 genes and one non-coding A þT-rich region. The arrangement of the proteincoding, ribosomal RNA (rRNA) and transfer RNA (tRNA) genes was the same as that found in the ancestral insect. Nucleotide composition is highly A þ T biased. All of the protein initiation codons are ATN, except for nad1 which begins with TTT. All 22 tRNA anticodons of F. taylori match those observed in Drosophila yakuba, and all form the typical cloverleaf structure except for tRNA-Ser (AGN) which lacks a dihydrouridine (DHU) arm. Secondary structural features of the rRNA genes of Fergusonina are similar to those proposed for other insects, with minor modifications. The mitochondrial genome of Fergusonina presented here may prove valuable for resolving the sister group to the Fergusoninidae, and expands the available mtDNA data sources for acalyptrates overall.

Quality metrics for assessing security-critical computer programs

Existing secure software development principles tend to focus on coding vulnerabilities, such as buffer or integer overflows, that apply to individual program statements, or issues associated with the run-time environment, such as component isolation. Here we instead consider software security from the perspective of potential information flow through a program’s object-oriented module structure. In particular, we define a set of quantifiable "security metrics" which allow programmers to quickly and easily assess the overall security of a given source code program or object-oriented design. Although measuring quality attributes of object-oriented programs for properties such as maintainability and performance has been well-covered in the literature, metrics which measure the quality of information security have received little attention. Moreover, existing securityrelevant metrics assess a system either at a very high level, i.e., the whole system, or at a fine level of granularity, i.e., with respect to individual statements. These approaches make it hard and expensive to recognise a secure system from an early stage of development. Instead, our security metrics are based on well-established compositional properties of object-oriented programs (i.e., data encapsulation, cohesion, coupling, composition, extensibility, inheritance and design size), combined with data flow analysis principles that trace potential information flow between high- and low-security system variables. We first define a set of metrics to assess the security quality of a given object-oriented system based on its design artifacts, allowing defects to be detected at an early stage of development. We then extend these metrics to produce a second set applicable to object-oriented program source code. The resulting metrics make it easy to compare the relative security of functionallyequivalent system designs or source code programs so that, for instance, the security of two different revisions of the same system can be compared directly. This capability is further used to study the impact of specific refactoring rules on system security more generally, at both the design and code levels. By measuring the relative security of various programs refactored using different rules, we thus provide guidelines for the safe application of refactoring steps to security-critical programs. Finally, to make it easy and efficient to measure a system design or program’s security, we have also developed a stand-alone software tool which automatically analyses and measures the security of UML designs and Java program code. The tool’s capabilities are demonstrated by applying it to a number of security-critical system designs and Java programs. Notably, the validity of the metrics is demonstrated empirically through measurements that confirm our expectation that program security typically improves as bugs are fixed, but worsens as new functionality is added.

Improved facial expression recognition via uni-hyperplane classification

Large margin learning approaches, such as support vector machines (SVM), have been successfully applied to numerous classification tasks, especially for automatic facial expression recognition. The risk of such approaches however, is their sensitivity to large margin losses due to the influence from noisy training examples and outliers which is a common problem in the area of affective computing (i.e., manual coding at the frame level is tedious so coarse labels are normally assigned). In this paper, we leverage the relaxation of the parallel-hyperplanes constraint and propose the use of modified correlation filters (MCF). The MCF is similar in spirit to SVMs and correlation filters, but with the key difference of optimizing only a single hyperplane. We demonstrate the superiority of MCF over current techniques on a battery of experiments.

The role of physical activity in the lives of people with lymphoedema following cancer treatment : a social constructionist study

Lymphoedema is a chronic condition predominantly affecting the limbs, although it can involve the trunk and other areas of the body. It is characterised by swelling due to excess accumulation of fluid in body tissues. Secondary lymphoedema, which arises following cancer treatment, is the more common form of lymphoedema in developed countries. At least 20% of those diagnosed with the most common cancers will develop lymphoedema. This is a concern in Australia as incidence of these cancers is increasing. Cancer survival rates are also increasing. Currently, this equates to 9 300 new cases of secondary lymphoedema diagnosed each year. Considerable physical and psychosocial impacts of lymphoedema have been reported and its subsequent impact on health-related quality of life can exacerbate other side effects of cancer treatment. Exercise following cancer treatment has been shown to significantly reduce the impact of treatment side effects, improve quality of life and physical status. While participating in exercise does not increase risk nor exacerbate existing lymphoedema, reductions in incidence of lymphoedema exacerbations and associated symptoms have been observed in women participating in regular weight lifting following breast cancer treatment. Despite these benefits, lymphoedema prevention and management advice cautions people with lymphoedema against „repetitive use. or „overuse. of their affected arm. It is possible that this advice creates a barrier to participation in physical activity; however, little is known about the relationship between physical activity and lymphoedema. In addition, the majority of studies examining the experiences of people living with lymphoedema and the impact of the condition have been predominantly conducted internationally and have focused on women following breast cancer. This study sought to explore firstly, how men and women construct their experience of living with lymphoedema following treatment for a range of cancers in the context of everyday life in Australia; and secondly, to analyse the role of physical activity in the lives of those living with lymphoedema following cancer treatment. A social constructivist grounded theory approach was taken to explore these objectives as it is acknowledged that human actions and the meanings associated with these actions are influenced by the interaction between the self and the social world. It is also acknowledged that the research process itself is a social construction between the researcher and participant. Purposive sampling techniques were used to recruit a total of 29 participants from a variety of sources. Telephone interviews and focus groups were conducted to collect data. Data were concurrently collected and analysed and analysis was conducted using the constant comparative method. The core category that developed in objective one was „sense of self‟. The self was defined by perceptions participants held of themselves and their identity prior to a lymphoedema diagnosis and changes to their perceptions and identity since diagnosis. Three conceptual categories which related to each other and to „sense of self‟ were developed through the process of coding that represented the process of how participants constructed their experiences living with secondary lymphoedema in the context of everyday life. Firstly, altered normalcy reflected the physical and psychosocial changes experienced and the effect it had on their lives. Secondly, „accidental journey‟ reflected participants‟ journey with the heath care system prior to diagnosis through to longer term management. Thirdly, renegotiating control revealed participants perceived control over lymphoedema and their ability to participate in daily activities previously enjoyed. These findings revealed the failure of the broader health system to recognise the significant and chronic nature of a lymphoedema diagnosis following cancer treatment with greater understanding, knowledge and support from health professionals being needed. The findings also reveal access to health professionals trained in lymphoedema management, a comprehensive approach encompassing both physical and psychosocial needs and provision of practical and meaningful guidelines supported by scientific evidence would contribute to improved treatment and management of the condition. The key findings for objective two were that people with lymphoedema define physical activity in different ways. Physical activity post-diagnosis was perceived as important by most for a variety of reasons ranging from everyday functioning, to physical and psychosocial health benefits. Issues relating to the impact of lymphoedema on physical activity related to the impact on peoples‟ ability to be physically active, confusion about acceptable forms of physical activity and barriers that lymphoedema presented to being physically active. A relationship between how people construct their experiences with lymphoedema and the role of physical activity was also established. The contribution of physical activity to the lives of people living with lymphoedema following cancer treatment appeared to be influenced by their sense of self as socially constructed through their experiences prior to diagnosis and following diagnosis with lymphoedema. The influence of pre-lymphoedema habits, norms and beliefs suggests the importance of effective health promotion messages to encourage physical activity among the general population and specific messages and guidelines particular to the needs of those diagnosed with lymphoedema following cancer treatment. The influence of participant.s social constructions on the lymphoedema experience highlights the importance of improving interactions between the overall health care system and patients, providing a clear treatment plan, providing evidence-based and clear advice about participation in appropriate physical activity, which in doing so will limit the physical and psychosocial effect of lymphoedema and providing comprehensive physical and psychosocial support to those living with the condition and their families. This study has contributed to a deep understanding of people.s experiences with lymphoedema following cancer treatment and the role of physical activity in the context of daily life in Australia. Findings from this study lead to recommendations for advocacy, a comprehensive approach to diagnosis, treatment and management, and specific areas for future research.

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations

Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the “reduced-bias” mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of nonhistorical signal, such as from compositional nonstationarity.

Evidence for time dependency of molecular rate estimates

Long-term changes in the genetic composition of a population occur by the fixation of new mutations, a process known as substitution. The rate at which mutations arise in a population and the rate at which they are fixed are expected to be equal under neutral conditions (Kimura, 1968). Between the appearance of a new mutation and its eventual fate of fixation or loss, there will be a period in which it exists as a transient polymorphism in the population (Kimura and Ohta, 1971). If the majority of mutations are deleterious (and nonlethal), the fixation probabilities of these transient polymorphisms are reduced and the mutation rate will exceed the substitution rate (Kimura, 1983). Consequently, different apparent rates may be observed on different time scales of the molecular evolutionary process (Penny, 2005; Penny and Holmes, 2001). The substitution rate of the mitochondrial protein-coding genes of birds and mammals has been traditionally recognized to be about 0.01 substitutions/site/million years (Myr) (Brown et al., 1979; Ho, 2007; Irwin et al., 1991; Shields and Wilson, 1987), with the noncoding D-loop evolving several times more quickly (e.g., Pesole et al., 1992; Quinn, 1992). Over the past decade, there has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al., 2003; Lambert et al., 2002; Mao et al., 2006; Mumm et al., 1997; Parsons et al., 1997; Santos et al., 2005). The immediate reaction to the first of these findings was that the polymorphisms generated by the elevated mutation rate are short-lived, perhaps extending back only a few hundred years (Gibbons, 1998; Macaulay et al., 1997). That is, purifying selection was thought to remove these polymorphisms very rapidly.

Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes

The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at ∼3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at ∼2.9 Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at ∼2.2 Mya, with R. rattus and R. tanezumi separating as recently as ∼0.4 Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.

Family-level relationships among the Australasian marsupial “herbivores” (Diprotodontia: Koala, wombats, kangaroos and possums)

The marsupial order Diprotodontia includes 10 extant families, which occupy all terrestrial habitats across Australia and New Guinea and have evolved remarkable dietary and locomotory diversity. Despite considerable attention, the interrelations of these families have for the most part remained elusive. In this study, we separately model mitochondrial RNA and protein-coding sequences in addition to nuclear protein-coding sequences to provide near-complete resolution of diprotodontian family-level phylogeny. We show that alternative topologies inferred in some previous studies are likely to be artifactual, resulting from branch-length and compositional biases. Subordinal groupings resolved herein include Vombatiformes (wombats and koala) and Phalangerida, which in turn comprises Petauroidea (petaurid gliders and striped, feathertail, ringtail and honey possums) and a clade whose plesiomorphic members possess blade-like premolars (phalangerid possums, kangaroos and their allies and most likely, pygmy possums). The topology resolved reveals ecological niche structuring among diprotodontians that has likely been maintained for more than 40 million years.

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

Despite recent methodological advances in inferring the time-scale of biological evolution from molecular data, the fundamental question of whether our substitution models are sufficiently well specified to accurately estimate branch-lengths has received little attention. I examine this implicit assumption of all molecular dating methods, on a vertebrate mitochondrial protein-coding dataset. Comparison with analyses in which the data are RY-coded (AG → R; CT → Y) suggests that even rates-across-sites maximum likelihood greatly under-compensates for multiple substitutions among the standard (ACGT) NT-coded data, which has been subject to greater phylogenetic signal erosion. Accordingly, the fossil record indicates that branch-lengths inferred from the NT-coded data translate into divergence time overestimates when calibrated from deeper in the tree. Intriguingly, RY-coding led to the opposite result. The underlying NT and RY substitution model misspecifications likely relate respectively to “hidden” rate heterogeneity and changes in substitution processes across the tree, for which I provide simulated examples. Given the magnitude of the inferred molecular dating errors, branch-length estimation biases may partly explain current conflicts with some palaeontological dating estimates.

Toward resolving deep neoaves phylogeny : data, signal enhancement, and priors

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed “WoodKing” (woodpeckers/rollers/kingfishers), “SCA” (owls/potoos/owlet-nightjars/hummingbirds/swifts), and “Conglomerati.” In general, the support is highly significant with just two exceptions, the owls move from the “SCA” group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the “Conglomerati”. Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.