Phylogenetic analysis of polyomaviruses based on their complete genomes

Perez-Losada et al. [1] analyzed 72 complete genomes corresponding to nine mammalian (67 strains) and 2 avian (5 strains) polyomavirus species using maximum likelihood and Bayesian methods of phylogenetic inference. Because some data of 2 genomes in their work are now not available in GenBank, in this work, we analyze the phylogenetic relationship of the remaining 70 complete genomes corresponding to nine mammalian (65 strains) and two avian (5 strains) polyomavirus species using a dynamical language model approach developed by our group (Yu et al., [26]). This distance method does not require sequence alignment for deriving species phylogeny based on overall similarities of the complete genomes. Our best tree separates the bird polyomaviruses (avian polyomaviruses and goose hemorrhagic polymaviruses) from the mammalian polyomaviruses, which supports the idea of splitting the genus into two subgenera. Such a split is consistent with the different viral life strategies of each group. In the mammalian polyomavirus subgenera, mouse polyomaviruses (MPV), simian viruses 40 (SV40), BK viruses (BKV) and JC viruses (JCV) are grouped as different branches as expected. The topology of our best tree is quite similar to that of the tree constructed by Perez-Losada et al.

An ecological assessment of secondary poisoning risk in the Australian sugarcane industry

Rodenticide use in agriculture can lead to the secondary poisoning of avian predators. Currently the Australian sugarcane industry has two rodenticides, Racumin® and Rattoff®, available for in-crop use but, like many agricultural industries, it lacks an ecologically-based method of determining the potential secondary poisoning risk the use of these rodenticides poses to avian predators. The material presented in this thesis addresses this by: a. determining where predator/prey interactions take place in sugar producing districts; b. quantifying the amount of rodenticide available to avian predators and the probability of encounter; and c. developing a stochastic model that allows secondary poisoning risk under various rodenticide application scenarios to be investigated. Results demonstrate that predator/prey interactions are highly constrained by environmental structure. Rodents used crops that provided high levels of canopy cover and therefore predator protection and poorly utilised open canopy areas. In contrast, raptors over-utilised areas with low canopy cover and low rodent densities, but which provided high accessibility to prey. Given this pattern of habitat use, and that industry baiting protocols preclude rodenticide application in open canopy crops, these results indicate that secondary poisoning can only occur if poisoned rodents leave closed canopy crops and become available for predation in open canopy areas. Results further demonstrate that after in-crop rodenticide application, only a small proportion of rodents available in open areas are poisoned and that these rodents carry low levels of toxicant. Coupled with the low level of rodenticide use in the sugar industry, the high toxic threshold raptors have to these toxicants and the low probability of encountering poisoned rodents, results indicate that the risk of secondary poisoning events occurring is minimal. A stochastic model was developed to investigate the effect of manipulating factors that might influence secondary poisoning hazard in a sugarcane agro-ecosystem. These simulations further suggest that in all but extreme scenarios, the risk of secondary poisoning is also minimal. Collectively, these studies demonstrate that secondary poisoning of avian predators associated with the use of the currently available rodenticides in Australian sugar producing districts is minimal. Further, the ecologically-based method of assessing secondary poisoning risk developed in this thesis has broader applications in other agricultural systems where rodenticide use may pose risks to avian predators.

Planning and evaluation

Introduction: The core business of public health is to protect and promote health in the population. Public health planning is the means to maximise these aspirations. Health professionals develop plans to address contemporary health priorities as the evidence about changing patterns of mortality and morbidity is presented. Officials are also alert to international trends in patterns of disease that have the potential to affect the health of Australians. Integrated planning and preparation is currently underway involving all emergency health services, hospitals and population health units to ensure Australia's quick and efficient response to any major infectious disease outbreak, such as avian influenza (bird flu). Public health planning for the preparations for the Sydney Olympics and Paralympic Games in 2000 took almost three years. ‘Its major components included increased surveillance of communicable disease; presentations to sentinel emergency departments; medical encounters at Olympic venues; cruise ship surveillance; environmental and food safety inspections; bioterrorism surveillance and global epidemic intelligence’ (Jorm et al 2003, 102). In other words, the public health plan was developed to ensure food safety, hospital capacity, safe crowd control, protection against infectious diseases, and an integrated emergency and disaster plan. We have national and state plans for vaccinating children against infectious diseases in childhood; plans to promote dental health for children in schools; and screening programs for cervical, breast and prostate cancer. An effective public health response to a change in the distribution of morbidity and mortality requires planning. All levels of government plan for the public’s health. Local governments (councils) ensure healthy local environments to protect the public’s health. They plan parks for recreation, construct traffic-calming devices near schools to prevent childhood accidents, build shade structures and walking paths, and even embed drafts/chess squares in tables for people to sit and play. Environmental Health officers ensure food safety in restaurants and measure water quality. These public health measures attempt to promote the quality of life of residents. Australian and state governments produce plans that protect and promote health through various policy and program initiatives and innovations. To be effective, program plans need to be evaluated. However, building an integrated evaluation plan into a program plan is often forgotten, as planning and evaluation are seen as two distinct entities. Consequently, it is virtually impossible to measure, with any confidence, the extent to which a program has achieved its goals and objectives. This chapter introduces you to the concepts of public health program planning and evaluation. Case studies and reflection questions are presented to illustrate key points. As various authors use different terminology to describe the same concepts/actions of planning and evaluation, the glossary at the back of this book will help you to clarify the terms used in this chapter.

Perception of affordances in multi-scale dynamics as an alternative explanation for equivalence of analogical and inferential reasoning in animals and humans

Recent claims of equivalence of animal and human reasoning are evaluated and a study of avian cognition serves as an exemplar of weaknesses in these arguments. It is argued that current research into neurobiological cognition lacks theoretical breadth to substantiate comparative analyses of cognitive function. Evaluation of a greater range of theoretical explanations is needed to verify claims of equivalence in animal and human cognition. We conclude by exemplifying how the notion of affordances in multi-scale dynamics can capture behavior attributed to processes of analogical and inferential reasoning in animals and humans.

Anticipated behaviours of emergency prehospital medical care providers during an influenza pandemic

Introduction: Emergency prehospital medical care providers are frontline health workers during emergencies. However, little is known about their attitudes, perceptions, and likely behaviors during emergency conditions. Understanding these attitudes and behaviors is crucial to mitigating the psychological and operational effects of biohazard events such as pandemic influenza, and will support the business continuity of essential prehospital services. ----- ----- Problem: This study was designed to investigate the association between knowledge and attitudes regarding avian influenza on likely behavioral responses of Australian emergency prehospital medical care providers in pandemic conditions. ----- ----- Methods: Using a reply-paid postal questionnaire, the knowledge and attitudes of a national, stratified, random sample of the Australian emergency prehospital medical care workforce in relation to pandemic influenza were investigated. In addition to knowledge and attitudes, there were five measures of anticipated behavior during pandemic conditions: (1) preparedness to wear personal protective equipment (PPE); (2) preparedness to change role; (3) willingness to work; and likely refusal to work with colleagues who were exposed to (4) known and (5) suspected influenza. Multiple logistic regression models were constructed to determine the independent predictors of each of the anticipated behaviors, while controlling for other relevant variables. ----- ----- Results: Almost half (43%) of the 725 emergency prehospital medical care personnel who responded to the survey indicated that they would be unwilling to work during pandemic conditions; one-quarter indicated that they would not be prepared to work in PPE; and one-third would refuse to work with a colleague exposed to a known case of pandemic human influenza. Willingness to work during a pandemic (OR = 1.41; 95% CI = 1.0–1.9), and willingness to change roles (OR = 1.44; 95% CI = 1.04–2.0) significantly increased with adequate knowledge about infectious agents generally. Generally, refusal to work with exposed (OR = 0.48; 95% CI = 0.3–0.7) or potentially exposed (OR = 0.43; 95% CI = 0.3–0.6) colleagues significantly decreased with adequate knowledge about infectious agents. Confidence in the employer’s capacity to respond appropriately to a pandemic significantly increased employee willingness to work (OR = 2.83; 95% CI = 1.9–4.1); willingness to change roles during a pandemic (OR = 1.52; 95% CI = 1.1–2.1); preparedness to wear PPE (OR = 1.68; 95% CI = 1.1–2.5); and significantly decreased the likelihood of refusing to work with colleagues exposed to (suspected) influenza (OR = 0.59; 95% CI = 0.4–0.9). ----- ----- Conclusions:These findings indicate that education and training alone will not adequately prepare the emergency prehospital medical workforce for a pandemic. It is crucial to address the concerns of ambulance personnel and the perceived concerns of their relationship with partners in order to maintain an effective prehospital emergency medical care service during pandemic conditions.

Attitudes to living and working in pandemic conditions among emergency prehospital medical care personnel

Introduction: Little is known about the risk perceptions and attitudes of healthcare personnel, especially of emergency prehospital medical care personnel, regarding the possibility of an outbreak or epidemic event. Problem: This study was designed to investigate pre-event knowledge and attitudes of a national sample of the emergency prehospital medical care providers in relation to a potential human influenza pandemic, and to determine predictors of these attitudes. Methods: Surveys were distributed to a random, cross-sectional sample of 20% of the Australian emergency prehospital medical care workforce (n = 2,929), stratified by the nine services operating in Australia, as well as by gender and location. The surveys included: (1) demographic information; (2) knowledge of influenza; and (3) attitudes and perceptions related to working during influenza pandemic conditions. Multiple logistic regression models were constructed to identify predictors of pandemic-related risk perceptions. Results: Among the 725 Australian emergency prehospital medical care personnel who responded, 89% were very anxious about working during pandemic conditions, and 85% perceived a high personal risk associated with working in such conditions. In general, respondents demonstrated poor knowledge in relation to avian influenza, influenza generally, and infection transmission methods. Less than 5% of respondents perceived that they had adequate education/training about avian influenza. Logistic regression analyses indicate that, in managing the attitudes and risk perceptions of emergency prehospital medical care staff, particular attention should be directed toward the paid, male workforce (as opposed to volunteers), and on personnel whose relationship partners do not work in the health industry. Conclusions: These results highlight the potentially crucial role of education and training in pandemic preparedness. Organizations that provide emergency prehospital medical care must address this apparent lack of knowledge regarding infection transmission, and procedures for protection and decontamination. Careful management of the perceptions of emergency prehospital medical care personnel during a pandemic is likely to be critical in achieving an effective response to a widespread outbreak of infectious disease.

Rodent blood-stage Plasmodium survive in dendritic cells that infect naive mice.

Plasmodium spp. parasites cause malaria in 300 to 500 million individuals each year. Disease occurs during the blood-stage of the parasite’s life cycle, where the parasite is thought to replicate exclusively within erythrocytes. Infected individuals can also suffer relapses after several years, from Plasmodium vivax and Plasmodium ovale surviving in hepatocytes. Plasmodium falciparum and Plasmodium malariae can also persist after the original bout of infection has apparently cleared in the blood, suggesting that host cells other than erythrocytes (but not hepatocytes) may harbor these blood-stage parasites, thereby assisting their escape from host immunity. Using blood stage transgenic Plasmodium berghei-expressing GFP (PbGFP) to track parasites in host cells, we found that the parasite had a tropism for CD317+ dendritic cells. Other studies using confocal microscopy, in vitro cultures, and cell transfer studies showed that blood-stage parasites could infect, survive, and replicate within CD317+ dendritic cells, and that small numbers of these cells released parasites infectious for erythrocytes in vivo. These data have identified a unique survival strategy for blood-stage Plasmodium, which has significant implications for understanding the escape of Plasmodium spp. from immune-surveillance and for vaccine development.

Policy analysis of disaster health management in China

Humankind has been dealing with all kinds of disasters since the dawn of time. The risk and impact of disasters producing mass casualties worldwide is increasing, due partly to global warming as well as to increased population growth, increased density and the aging population. China, as a country with a large population, vast territory, and complex climatic and geographical conditions, has been plagued by all kinds of disasters. Disaster health management has traditionally been a relatively arcane discipline within public health. However, SARS, Avian Influenza, and earthquakes and floods, along with the need to be better prepared for the Olympic Games in China has brought disasters, their management and their potential for large scale health consequences on populations to the attention of the public, the government and the international community alike. As a result significant improvements were made to the disaster management policy framework, as well as changes to systems and structures to incorporate an improved disaster management focus. This involved the upgrade of the Centres for Disease Control and Prevention (CDC) throughout China to monitor and better control the health consequences particularly of infectious disease outbreaks. However, as can be seen in the Southern China Snow Storm and Wenchuan Earthquake in 2008, there remains a lack of integrated disaster management and efficient medical rescue, which has been costly in terms of economics and health for China. In the context of a very large and complex country, there is a need to better understand whether these changes have resulted in effective management of the health impacts of such incidents. To date, the health consequences of disasters, particularly in China, have not been a major focus of study. The main aim of this study is to analyse and evaluate disaster health management policy in China and in particular, its ability to effectively manage the health consequences of disasters. Flood has been selected for this study as it is a common and significant disaster type in China and throughout the world. This information will then be used to guide conceptual understanding of the health consequences of floods. A secondary aim of the study is to compare disaster health management in China and Australia as these countries differ in their length of experience in having a formalised policy response. The final aim of the study is to determine the extent to which Walt and Gilson’s (1994) model of policy explains how disaster management policy in China was developed and implemented after SARS in 2003 to the present day. This study has utilised a case study methodology. A document analysis and literature search of Chinese and English sources was undertaken to analyse and produce a chronology of disaster health management policy in China. Additionally, three detailed case studies of flood health management in China were undertaken along with three case studies in Australia in order to examine the policy response and any health consequences stemming from the floods. A total of 30 key international disaster health management experts were surveyed to identify fundamental elements and principles of a successful policy framework for disaster health management. Key policy ingredients were identified from the literature, the case-studies and the survey of experts. Walt and Gilson (1994)’s policy model that focuses on the actors, content, context and process of policy was found to be a useful model for analysing disaster health management policy development and implementation in China. This thesis is divided into four parts. Part 1 is a brief overview of the issues and context to set the scene. Part 2 examines the conceptual and operational context including the international literature, government documents and the operational environment for disaster health management in China. Part 3 examines primary sources of information to inform the analysis. This involves two key studies: • A comparative analysis of the management of floods in China and Australia • A survey of international experts in the field of disaster management so as to inform the evaluation of the policy framework in existence in China and the criteria upon which the expression of that policy could be evaluated Part 4 describes the key outcomes of this research which include: • A conceptual framework for describing the health consequences of floods • A conceptual framework for disaster health management • An evaluation of the disaster health management policy and its implementation in China. The research outcomes clearly identified that the most significant improvements are to be derived from improvements in the generic management of disasters, rather than the health aspects alone. Thus, the key findings and recommendations tend to focus on generic issues. The key findings of this research include the following: • The health consequences of floods may be described in terms of time as ‘immediate’, ‘medium term’ and ‘long term’ and also in relation to causation as ‘direct’ and ‘indirect’ consequences of the flood. These two aspects form a matrix which in turn guides management responses. • Disaster health management in China requires a more comprehensive response throughout the cycle of prevention, preparedness, response and recovery but it also requires a more concentrated effort on policy implementation to ensure the translation of the policy framework into effective incident management. • The policy framework in China is largely of international standard with a sound legislative base. In addition the development of the Centres for Disease Control and Prevention has provided the basis for a systematic approach to health consequence management. However, the key weaknesses in the current system include: o The lack of a key central structure to provide the infrastructure with vital support for policy development, implementation and evaluation. o The lack of well-prepared local response teams similar to local government based volunteer groups in Australia. • The system lacks structures to coordinate government action at the local level. The result of this is a poorly coordinated local response and lack of clarity regarding the point at which escalation of the response to higher levels of government is advisable. These result in higher levels of risk and negative health impacts. The key recommendations arising from this study are: 1. Disaster health management policy in China should be enhanced by incorporating disaster management considerations into policy development, and by requiring a disaster management risk analysis and disaster management impact statement for development proposals. 2. China should transform existing organizations to establish a central organisation similar to the Federal Emergency Management Agency (FEMA) in the USA or the Emergency Management Australia (EMA) in Australia. This organization would be responsible for leading nationwide preparedness through planning, standards development, education and incident evaluation and to provide operational support to the national and local government bodies in the event of a major incident. 3. China should review national and local plans to reflect consistency in planning, and to emphasize the advantages of the integrated planning process. 4. Enhance community resilience through community education and the development of a local volunteer organization. China should develop a national strategy which sets direction and standards in regard to education and training, and requires system testing through exercises. Other initiatives may include the development of a local volunteer capability with appropriate training to assist professional response agencies such as police and fire services in a major incident. An existing organisation such as the Communist Party may be an appropriate structure to provide this response in a cost effective manner. 5. Continue development of professional emergency services, particularly ambulance, to ensure an effective infrastructure is in place to support the emergency response in disasters. 6. Funding for disaster health management should be enhanced, not only from government, but also from other sources such as donations and insurance. It is necessary to provide a more transparent mechanism to ensure the funding is disseminated according to the needs of the people affected. 7. Emphasis should be placed on prevention and preparedness, especially on effective disaster warnings. 8. China should develop local disaster health management infrastructure utilising existing resources wherever possible. Strategies for enhancing local infrastructure could include the identification of local resources (including military resources) which could be made available to support disaster responses. It should develop operational procedures to access those resources. Implementation of these recommendations should better position China to reduce the significant health consequences experienced each year from major incidents such as floods and to provide an increased level of confidence to the community about the country’s capacity to manage such events.

The future for public health

What is the future for public health in the twenty first century? Can we glean an idea about the future of public health from its past? As Winston Churchill once said ‘the further backward you look, the further forward you can see’. What then can we see in the history of public health that gives us an idea of where public health might be headed in the future? In the twentieth century there was substantial progress in public health in Australia. These improvements were brought about through a number of factors. In part, improvements were due to improved knowledge about the natural history of disease and its treatment. Added to this knowledge was a shifting focus from legislative measures to protect health, to the emergence of improved promotion and prevention strategies and a general improvement in social and economic conditions for people living in countries like Australia. The same could not, however, be said for poorer countries, many of whom have the most fundamental of sanitary and health protection issues still to deal with. For example, in sub-Saharan Africa and Russia, the decline in life expectancy may be an aberration or it may be related to a range of interconnected factors. In Russia, factors such as alcoholism, violence, suicide, accidents and cardiovascular disease could be contributing to the falling life expectancy (McMichael & Butler 2007). In sub-Saharan Africa, a range of issues such as HIV/AIDS, poverty, malaria, tuberculosis, undernutrition, totally inadequate infrastructure, gender inequality, conflict and violence, political taboos and a complete lack of political will, have all contributed to a dramatic drop in life expectancy (McMichael & Butler 2007).

Sri Lanka in global medical research: a scientific analysis of the Sri Lankan research output during 2000-2009

Background Scientific research is an essential component in guiding improvements in health systems. There are no studies examining the Sri Lankan medical research output at international level. The present study evaluated the Sri Lankan research performance in medicine as reflected by the research publications output between years 2000-2009. Methods This study was based on Sri Lankan medical research publication data, retrieved from the SciVerse Scopus® from January 2000 to December 2009. The process of article selection was as follows: Affiliation - 'Sri Lanka' or 'Ceylon', Publication year - 'January 2000 to December 2009' and Subject area - 'Life and Health Sciences'. The articles identified were classified according to disease, medical speciality, institutions, major international collaborators, authors and journals. Results Sri Lanka's cumulative medical publications output between years 2000-2009 was 1,740 articles published in 160 different journals. The average annual publication growth rate was 9.1%. Majority of the articles were published in 'International' (n = 950, 54.6%) journals. Most articles were descriptive studies (n = 611, 35.1%), letters (n-345, 19.8%) and case reports (n = 311, 17.9%). The articles were authored by 148 different Sri Lankan authors from 146 different institutions. The three most prolific local institutions were Universities of; Colombo (n = 547), Kelaniya (n = 246) and Peradeniya (n = 222). Eighty four countries were found to have published collaborative papers with Sri Lankan authors during the last decade. UK was the largest collaborating partner (n = 263, 15.1%). Malaria (n = 75), Diabetes Mellitus (n = 55), Dengue (n = 53), Accidental injuries (n = 42) and Lymphatic filariasis (n = 40) were the major diseases studied. The 1,740 publications were cited 9,708 times, with an average citation of 5.6 per paper. The most cited paper had 203 citations, while there were 597 publications with no citations. The Sri Lankan authors' contribution to the global medical research output during the last decade was only 0.086%. Conclusion The Sri Lankan medical research output during the last decade is only a small fraction of the global research output. There it is a necessity to setup an enabling environment for research, with a proper vision, support, funds and training. In addition, collaborations across the region need to be strengthened to face common regional health challenges. Keywords: Sri Lanka, Medical research, Publication, Analysis

Incidence and geographic distribution of endemic Burkitt lymphoma in northern Uganda revisited

Endemic Burkitt lymphoma (BL) is etiologically associated with Epstein-Barr virus (EBV) and ecologically linked to Plasmodium falciparum malaria. However, these infections imperfectly correlate with BL epidemiology. To obtain recent epidemiological data, we studied district- and county-specific BL incidence and standardized incidence ratios using data collected from 1997 through 2006 at Lacor Hospital in northern Uganda, where studies were last done more than 30 years ago. Among 500 patients, median age was 6 years (inter-quartile range 5-8) and male-to-female ratio was 1.8:1. Among those known, most presented with abdominal (56%, M: F 1.4:1) vs. only facial tumors (35%, M: F 3.0:1). Abdominal tumors occurred in older (mean age: 7.0 vs. 6.0 years; p<0.001) and more frequently in female children (68% vs. 50%; OR 2.2, 95% CI 1.5-3.5). The age-standardized incidence was 2.4 per 100,000, being 0.6 in 1-4 year olds, 4.1 in 5-9 year olds and 2.8 in 10-14 year olds and varied 3-4-fold across districts. The incidence was lower in districts that were far from Lacor and higher in districts that were close to Lacor. While districts close to Lacor were also more urbanized, the incidence was higher in the nearby perirural areas. We highlight high BL incidence and geographic variation in neighboring districts in northern Uganda. While distance from Lacor clearly influenced the patterns, the incidence was lower in municipal than in surrounding rural areas. Jaw tumors were characterized by young age and male gender, but presentation has shifted away from facial to mostly abdominal. Keywords: Africa, cancer, malaria, Epstein-Barr virus, clustering, epidemiology

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.

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.

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography

The ratite moa (Aves: Dinornithiformes) were a speciose group of massive graviportal avian herbivores that dominated the New Zealand (NZ) ecosystem until their extinction �600 years ago. The phylogeny and evolutionary history of this morphologically diverse order has remained controversial since their initial description in 1839. We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20–30 Ma. The data reveal that the patterns of genetic diversity within and between differentmoaclades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene (ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5–8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.

The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae)

Cockatoos are the distinctive family Cacatuidae, a major lineage of the order of parrots (Psittaciformes) and distributed throughout the Australasian region of the world. However, the evolutionary history of cockatoos is not well understood. We investigated the phylogeny of cockatoos based on three mitochondrial and three nuclear DNA genes obtained from 16 of 21 species of Cacatuidae. In addition, five novel mitochondrial genomes were used to estimate time of divergence and our estimates indicate Cacatuidae diverged from Psittacidae approximately 40.7 million years ago (95% CI 51.6–30.3 Ma) during the Eocene. Our data shows Cacatuidae began to diversify approximately 27.9 Ma (95% CI 38.1–18.3 Ma) during the Oligocene. The early to middle Miocene (20–10 Ma) was a significant period in the evolution of modern Australian environments and vegetation, in which a transformation from mainly mesic to xeric habitats (e.g., fire-adapted sclerophyll vegetation and grasslands) occurred. We hypothesize that this environmental transformation was a driving force behind the diversification of cockatoos. A detailed multi-locus molecular phylogeny enabled us to resolve the phylogenetic placements of the Palm Cockatoo (Probosciger aterrimus), Galah (Eolophus roseicapillus), Gang-gang Cockatoo (Callocephalon fimbriatum) and Cockatiel (Nymphicus hollandicus), which have historically been difficult to place within Cacatuidae. When the molecular evidence is analysed in concert with morphology, it is clear that many of the cockatoo species’ diagnostic phenotypic traits such as plumage colour, body size, wing shape and bill morphology have evolved in parallel or convergently across lineages.