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.

Review ["Telling the Evolutionary Time : Molecular Clocks and the Fossil Record" edited by Philip C. J. Donoghue and M. Paul Smith]

Determining the temporal scale of biological evolution has traditionally been the preserve of paleontology, with the timing of species originations and major diversifications all being read from the fossil record. However, the ages of the earliest (correctly identified) records will underestimate actual origins due to the incomplete nature of the fossil record and the necessity for lineages to have evolved sufficiently divergent morphologies in order to be distinguished. The possibility of inferring divergence times more accurately has been promoted by the idea that the accumulation of genetic change between modern lineages can be used as a molecular clock (Zuckerkandl and Pauling, 1965). In practice, though, molecular dates have often been so old as to be incongruent even with liberal readings of the fossil record. Prominent examples include inferred diversifications of metazoan phyla hundreds of millions of years before their Cambrian fossil record appearances (e.g., Nei et al., 2001) and a basal split between modern birds (Neoaves) that is almost double the age of their earliest recognizable fossils (e.g., Cooper and Penny, 1997).

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and divergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of autocorrelated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to divergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan divergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and divergence dates.

Relaxed phylogenetics and dating with confidence

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

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.

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas

The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early Cretaceous Teinolophos and Steropodon to the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion of Teinolophos and Steropodon and suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna–platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19–48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.

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.

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.

Perceiving and pursuing novelty : a grounded theory of adolescent creativity

Creativity plays an increasingly important role in our personal, social, educational, and community lives. For adolescents, creativity can enable self-expression, be a means of pushing boundaries, and assist learning, achievement, and completion of everyday tasks. Moreover, adolescents who demonstrate creativity can potentially enhance their capacity to face unknown future challenges, address mounting social and ecological issues in our global society, and improve their career opportunities and contribution to the economy. For these reasons, creativity is an essential capacity for young people in their present and future, and is highlighted as a priority in current educational policy nationally and internationally. Despite growing recognition of creativity’s importance and attention to creativity in research, the creative experience from the perspectives of the creators themselves and the creativity of adolescents are neglected fields of study. Hence, this research investigated adolescents’ self-reported experiences of creativity to improve understandings of their creative processes and manifestations, and how these can be supported or inhibited. Although some aspects of creativity have been extensively researched, there were no comprehensive, multidisciplinary theoretical frameworks of adolescent creativity to provide a foundation for this study. Therefore, a grounded theory methodology was adopted for the purpose of constructing a new theory to describe and explain adolescents’ creativity in a range of domains. The study’s constructivist-interpretivist perspective viewed the data and findings as interpretations of adolescents’ creative experiences, co-constructed by the participants and the researcher. The research was conducted in two academically selective high schools in Australia: one arts school, and one science, mathematics, and technology school. Twenty adolescent participants (10 from each school) were selected using theoretical sampling. Data were collected via focus groups, individual interviews, an online discussion forum, and email communications. Grounded theory methods informed a process of concurrent data collection and analysis; each iteration of analysis informed subsequent data collection. Findings portray creativity as it was perceived and experienced by participants, presented in a Grounded Theory of Adolescent Creativity. The Grounded Theory of Adolescent Creativity comprises a core category, Perceiving and Pursuing Novelty: Not the Norm, which linked all findings in the study. This core category explains how creativity involved adolescents perceiving stimuli and experiences differently, approaching tasks or life unconventionally, and pursuing novel ideas to create outcomes that are not the norm when compared with outcomes by peers. Elaboration of the core category is provided by the major categories of findings. That is, adolescent creativity entailed utilising a network of Sub-Processes of Creativity, using strategies for Managing Constraints and Challenges, and drawing on different Approaches to Creativity – adaptation, transfer, synthesis, and genesis – to apply the sub-processes and produce creative outcomes. Potentially, there were Effects of Creativity on Creators and Audiences, depending on the adolescent and the task. Three Types of Creativity were identified as the manifestations of the creative process: creative personal expression, creative boundary pushing, and creative task achievement. Interactions among adolescents’ dispositions and environments were influential in their creativity. Patterns and variations of these interactions revealed a framework of four Contexts for Creativity that offered different levels of support for creativity: high creative disposition–supportive environment; high creative disposition–inhibiting environment; low creative disposition–supportive environment; and low creative disposition–inhibiting environment. These contexts represent dimensional ranges of how dispositions and environments supported or inhibited creativity, and reveal that the optimal context for creativity differed depending on the adolescent, task, domain, and environment. This study makes four main contributions, which have methodological and theoretical implications for researchers, as well as practical implications for adolescents, parents, teachers, policy and curriculum developers, and other interested stakeholders who aim to foster the creativity of adolescents. First, this study contributes methodologically through its constructivist-interpretivist grounded theory methodology combining the grounded theory approaches of Corbin and Strauss (2008) and Charmaz (2006). Innovative data collection was also demonstrated through integration of data from online and face-to-face interactions with adolescents, within the grounded theory design. These methodological contributions have broad applicability to researchers examining complex constructs and processes, and with populations who integrate multimedia as a natural form of communication. Second, applicable to creativity in diverse domains, the Grounded Theory of Adolescent Creativity supports a hybrid view of creativity as both domain-general and domain-specific. A third major contribution was identification of a new form of creativity, educational creativity (ed-c), which categorises creativity for learning or achievement within the constraints of formal educational contexts. These theoretical contributions inform further research about creativity in different domains or multidisciplinary areas, and with populations engaged in formal education. However, the key contribution of this research is that it presents an original Theory and Model of Adolescent Creativity to explain the complex, multifaceted phenomenon of adolescents’ creative experiences.

Land fraud and inappropriate dealings in an electronic environment : An Australian and New Zealand perspective

The thesis presented in this paper is that the land fraud committed by Matthew Perrin in Queensland and inflicted upon Roger Mildenhall in Western Australia demonstrates the need for urgent procedural reform to the conveyancing process. Should this not occur, then calls to reform the substantive principles of the Torrens system will be heard throughout the jurisdictions that adopt title by registration, particularly in those places where immediate indefeasibility is still the norm. This paper closely examines the factual matrix behind both of these frauds, and asks what steps should have been taken to prevent them occurring. With 2012 bringing us Australian legislation embedding a national e-conveyancing system and a new Land Transfer Act for New Zealand we ask what legislative measures should be introduced to minimise the potential for such fraud. In undertaking this study, we reflect on whether the activities of Perrin and the criminals responsible for stealing Mildenhall's land would have succeeded under the present system for automated registration utilised in New Zealand.

Predictors of young people’s charitable intentions to donate money : an extended theory of planned behavior perspective

An extended theory of planned behavior (TPB) was used to predict young people’s intentions to donate money to charities in the future. Students (N = 210; 18-24 years) completed a questionnaire assessing their attitude, subjective norm, perceived behavioral control [PBC], moral obligation, past behavior and intentions toward donating money. Regression analyses revealed the extended TPB explained 61% of the variance in intentions to donate money. Attitude, PBC, moral norm, and past behavior predicted intentions, representing future targets for charitable giving interventions.

Genetic diversity in three redclaw crayfish (Cherax quadricarinatus, von Martens) lines developed in culture in China

The redclaw crayfish Cherax quadricarinatus (von Martens) accounts for the entire commercial production of freshwater crayfish in Australia. Two forms have been recognized, an 'Eastern' form in northern Queensland and a 'Western' form in the Northern Territory and far northern Western Australia. To date, only the Eastern form has been exported overseas for culture (including to China). The genetic structure of three Chinese redclaw crayfish culture lines from three different geographical locations in China (Xiamen in Fujian Province, Guangzhou in Guangdong Province and Chongming in Shanghai) were investigated for their levels and patterns of genetic diversity using microsatellite markers. Twenty-eight SSR markers were isolated and used to analyse genetic diversity levels in three redclaw crayfish culture lines in China. This study set out to improve the current understanding of the molecular genetic characteristics of imported strains of redclaw crayfish reared in China. Microsatellite analysis revealed moderate allelic and high gene diversity in all three culture lines. Polymorphism information content estimates for polymorphic loci varied between 0.1168 and 0.8040, while pairwise F ST values among culture lines were moderate (0.0020-0.1244). The highest estimate of divergence was evident between the Xiamen and Guangzhou populations.

Learning domain-specific sentiment lexicons for predicting product sales

Generic sentiment lexicons have been widely used for sentiment analysis these days. However, manually constructing sentiment lexicons is very time-consuming and it may not be feasible for certain application domains where annotation expertise is not available. One contribution of this paper is the development of a statistical learning based computational method for the automatic construction of domain-specific sentiment lexicons to enhance cross-domain sentiment analysis. Our initial experiments show that the proposed methodology can automatically generate domain-specific sentiment lexicons which contribute to improve the effectiveness of opinion retrieval at the document level. Another contribution of our work is that we show the feasibility of applying the sentiment metric derived based on the automatically constructed sentiment lexicons to predict product sales of certain product categories. Our research contributes to the development of more effective sentiment analysis system to extract business intelligence from numerous opinionated expressions posted to the Web

The Road to Whatever: Middle Class Cultgure and the Crisis of Adolescence

In this groundbreaking book, acclaimed sociologist and Pulitzer Prize finalist Elliott Currie draws on years of interviews to offer a profound investigation of what has gone wrong for so many “mainstream” American adolescents. Rejecting such predictable answers as TV violence, permissiveness, and inherent evil, Currie links this crisis to a pervasive “culture of exclusion” fostered by a society in which medications trump guidance and a punitive “zero tolerance” approach to adolescent misbehavior has become the norm. Broadening his inquiry, he dissects the changes in middle-class life that stratify the world into "winners" and "losers," imposing an extraordinarily harsh culture—and not just on kids. Vivid, compelling, and deeply empathetic, The Road to Whatever is a stark indictment of a society that has lost the will—or the capacity—to care.