Global macroevolution and macroecology of passerine song

Studying the macroevolution of the songs of Passeriformes (perching birds) has proved challenging. The complexity of the task stems not just from the macroevolutionary and macroecological challenge of modeling so many species, but also from the difficulty in collecting and quantifying birdsong itself. Using machine learning techniques, we extracted songs from a large citizen science dataset, and then analyzed the evolution, and biotic and abiotic predictors of variation in birdsong across 578 passerine species. Contrary to expectations, we found few links between life‐history traits (monogamy and sexual dimorphism) and the evolution of song pitch (peak frequency) or song complexity (standard deviation of frequency). However, we found significant support for morphological constraints on birdsong, as reflected in a negative correlation between bird size and song pitch. We also found that broad‐scale biogeographical and climate factors such as net primary productivity, temperature, and regional species richness were significantly associated with both the evolution and present‐day distribution of bird song features. Our analysis integrates comparative and spatial modeling with newly developed data cleaning and curation tools, and suggests that evolutionary history, morphology, and present‐day ecological processes shape the distribution of song diversity in these charismatic and important birds.     

Dynamic macroecology and the future for biodiversity

Reliable projections of climate‐change impacts on biodiversity are vital in formulating conservation and management strategies that best retain biodiversity into the future. While recent modelling has focussed largely on individual species, macroecology has the potential to add significant value to these efforts, by incorporating important community‐level constraints and processes. Here we show how a new dynamic macroecological approach can project climate‐change impacts collectively across all species in a diverse taxonomic group, overcoming shortfalls in our knowledge of biodiversity, while incorporating the key processes of dispersal and community assembly. Our approach applies a recently published technique (DynamicFOAM) to predict the present composition of every community, which form the initial conditions for a new metacommunity model (M‐SET) that projects changes in composition over time, under specified climate and habitat scenarios. Applying this approach at fine resolution to plant biodiversity in Tasmania (2,051 species; 1,157,587 communities), we project high average turnover in community composition from 2010 to 2100 (mean Sorensen's dissimilarity = 0.71 (±7.0 × 10^?5)), with major reductions in species richness (32.9 (±0.02) species lost per community) and no plant species benefitting from climate change in the long term. We also demonstrate how our modelling approach can identify habitat likely to be of high value for retaining rare and poorly reserved species under climate change. Our analyses highlight the potential value of this dynamic macroecological approach, that incorporates key ecological processes in projecting climate change impacts for all species simultaneously and uses simple macroecological inputs that can be derived even for highly diverse and poorly studied taxa.     

Mississippian crinoid biodiversity,biogeography and macroevolution

Abstract: The biodiversity and biogeography of 217 genera of Mississippian crinoids from North America and the British Isles shed light on the macroevolutionary turnover between the Middle Palaeozoic and Late Palaeozoic Crinoid Evolutionary Faunas. This turnover resulted from steady differential extinction among clades during the middle Mississippian after crinoids reached their Phanerozoic peak of generic richness during the early Mississippian. This peak richness was primarily a function of Mississippian originations rather than Devonian–holdover taxa. North America had 100 per cent higher generic richness than the British Isles, but rarefaction analysis adjusts the difference to only 37 per cent higher. Rarefaction demonstrated that North America had increased biodiversity, compared to the British Isles, almost entirely among monobathrid camerates, disparids and primitive cladids. In contrast, diplobathrid camerates, advanced cladids and flexibles had the same generic biodiversity between regions, when compared using rarefaction. The early Mississippian radiation resulted from two primary causes: (1) the expansion of Tournaisian carbonate ramps following the Frasnian mass extinction of reef faunas and (2) the predatory release in the Tournaisian following the end‐Famennian Hangenberg extinction of durophagous fishes. A majority of crinoid genera from the British Isles are cosmopolitan. When combined with rarefaction analysis and evidence for more first occurrences in North America, this suggests higher origination rates in North America, especially when carbonate ramps were widespread. With the gradual reduction in the area of carbonate ramps from the early to late Mississippian, in conjunction with the radiation of new durophagous fishes, camerate crinoids in particular experienced continuous background extinction, without replacement, beginning during the earliest Viséan (late Osagean). By middle Viséan time (late Meramecian) advanced cladids were dominant in all settings. This resulted in the transition from the Middle Palaeozoic to the Late Palaeozoic Crinoid Macroevolutionary Fauna.     

Unifying ecology and macroevolution with individual‐based theory

A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage‐based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual‐based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.     

Animal memory: rats can answer unexpected questions about past events

A new study has found that rats are able to answer, in a hippocampus-dependent manner, unexpected questions about whether they recently ate food or not. The results highlight potential shared mechanisms for remembering personal events in rats and humans, and offer new insights into the nature of animal memory.     

Biology of cancer: some questions to answer

Though great advances in cancer biology have taken place through these years, some fundamental questions are still to be explained. Some observations in this regard are discussed in the present paper. In the course of experimental studies on hormonal stimulation of target cells, it was observed that goat granulosa cells showed differential proliferative response to sustained stimulation by oLH and hCG in culture. oLH caused cells to proliferate whereas hCG failed to stimulate the cells though both the gonadotropins have common receptors on the target cell. Further studies might throw some light on the mechanism of signal transduction in cell biology and neoplasia. A question is also posed as to how to interpret thermodynamically the sustained growth of cancer vis-a-vis the host.     

FiRe and microarrays: a fast answer to burning questions

FiRe is a user-friendly Excel macro designed to survey microarray data rapidly. This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression. Furthermore, macros bundled with FiRe can compare lists of genes, merge information from different spreadsheets, link candidates to information available from web-based databases, and produce heat-maps for easy visualization of microarray data. FiRe is freely available at http://www.unifr.ch/plantbio/FiRe/main.html .     

Taking physiology to the field: using physiological approaches to answer questions about animals in their environments

Both technological and conceptual advances continue to enhance our ability to evaluate physiological mechanisms in free-living animals. Although complex and uncontrolled natural environments may challenge our ability to define causal mechanistic relationships, they provide opportunities not available in more conventional laboratory settings. Among these opportunities are the ability to observe the interplay between physiology and behavior, the potential inspiration to physiological studies from novel observations in the field, and the ability to evaluate the extent to which particular physiological systems are challenged under natural conditions. As we accumulate information about physiological function in the field, we are often forced to reconsider established paradigms: hibernating bears may contract their muscles to maintain strength and tone, testosterone levels in male stonechats maintaining territories in winter are exceptionally low, wintering emperor penguins may risk overheating, and large desert mammals may eschew brain-cooling mechanisms. Measuring and quantifying the organismal response to a changing environment provides a link between mechanistic physiology and behavior, ecology, and evolution and gives us new tools to understand population, community, and ecosystem-level processes.     

Using ecological networks to answer questions in global biogeography and ecology

Ecological networks have classically been studied at site and landscape scales, yet recent efforts have been made to collate these data into global repositories. This offers an opportunity to integrate and upscale knowledge about ecological interactions from local to global scales to gain enhanced insights from the mechanistic information provided by these data. By drawing on existing research investigating patterns in ecological interactions at continental to global scales, we show how data on ecological networks, collected at appropriate scales, can be used to generate an improved understanding of many aspects of ecology and biogeography—for example, species distribution modelling, restoration ecology and conservation. We argue that by understanding the patterns in the structure and function of ecological networks across scales, it is possible to enhance our understanding of the natural world.     

Telomere biology of trypanosomatids: beginning to answer some questions

Studies of telomere structure and maintenance in trypanosomatids have provided insights into the evolutionary origin and conservation of some telomeric components shared by trypanosomes and vertebrates. For example, trypanosomatid telomeres are maintained by telomerase and consist of the canonical TTAGGG repeats, which in Trypanosoma brucei can form telomeric loops (t-loops). However, the telomeric chromatin of trypanosomatids is composed of organism-specific proteins and other proteins that share little sequence similarity with their vertebrate counterparts. Because telomere maintenance mechanisms are essential for genome stability, we propose that the particular features shown by the trypanosome telomeric chromatin hold the key for the design of antiparasitic drugs.     

Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model

There is growing interest in the integration of macroecology and palaeoecology towards a better understanding of past, present, and anticipated future biodiversity dynamics. However, the empirical basis for this integration has thus far been limited. Here we review prospects for a macroecology–palaeoecology integration in biodiversity analyses with a focus on marine microfossils [i.e. small (or small parts of) organisms with high fossilization potential, such as foraminifera, ostracodes, diatoms, radiolaria, coccolithophores, dinoflagellates, and ichthyoliths]. Marine microfossils represent a useful model system for such integrative research because of their high abundance, large spatiotemporal coverage, and good taxonomic and temporal resolution. The microfossil record allows for quantitative cross‐scale research designs, which help in answering fundamental questions about marine biodiversity, including the causes behind similarities in patterns of latitudinal and longitudinal variation across taxa, the degree of constancy of observed gradients over time, and the relative importance of hypothesized drivers that may explain past or present biodiversity patterns. The inclusion of a deep‐time perspective based on high‐resolution microfossil records may be an important step for the further maturation of macroecology. An improved integration of macroecology and palaeoecology would aid in our understanding of the balance of ecological and evolutionary mechanisms that have shaped the biosphere we inhabit today and affect how it may change in the future.     

Hubbell's fundamental biodiversity parameter and the Simpson diversity index

Central to Hubbell's neutral theory of biodiversity is a universal, dimensionless fundamental biodiversity parameter that is the product of community size and speciation rate. One of the most important discoveries of Hubbell's theory is that the species‐abundance distribution and the species–area relationship of the neutral metacommunity is completely determined by this fundamental biodiversity parameter, although the diversity patterns of the local community are collectively determined by the biodiversity parameter and migration. Using the relative abundance of species and following the concept of heterozygosity of population genetics, here we developed an analytical relationship between this biodiversity parameter and the well‐known Simpson diversity index. This relationship helps bridge the evolutionary aspect of biodiversity to the ecological and statistical aspect of the diversity. The relationship between these two parameters suggests that diversity patterns of the metacommunity can also be equally described by the Simpson index. This relationship provides an alternative approach to interpret and estimate the fundamental biodiversity parameter for the metacommunity.     

Dispersal is fundamental to biogeography and the evolution of biodiversity on oceanic islands

Vicariance biogeography emerged several decades ago from the fusion of cladistics and plate tectonics, and quickly came to dominate historical biogeography. The field has since been largely constrained by the notion that only processes of vicariance and not dispersal offer testable patterns and refutable hypotheses, dispersal being a random process essentially adding only noise to a vicariant system. A consequence of this thinking seems to have been a focus on the biogeography of continents and continental islands, considering the biogeography of oceanic islands less worthy of scientific attention because, being dependent on stochastic dispersal, it was uninteresting. However, the importance of dispersal is increasingly being recognized, and here we stress its fundamental role in the generation of biodiversity on oceanic islands that have been created in situ , never connected to larger land masses. Historical dispersal patterns resulting in modern distributions, once considered unknowable, are now being revealed in many plant and animal taxa, in large part through the analysis of polymorphic molecular markers. We emphasize the profound evolutionary insights that oceanic island biodiversity has provided, and the fact that, although small in area, oceanic islands harbour disproportionately high biodiversity and numbers of endemic taxa. We further stress the importance of continuing research on mechanisms generating oceanic island biodiversity, especially detection of general, non-random patterns of dispersal, and hence the need to acknowledge oceanic dispersal as significant and worthy of research.     

When one plus one equals three: Biochemistry and bioinformatics combine to answer complex questions

The availability of whole genome assemblies from evolutionarily distant species and iterative search algorithms has boosted ortholog analyses. However, orthology per se is not a sufficient predictor of a specific function. In a recent study, we have combined bioinformatic analysis and biochemistry to study the evolution of the multi-component SMN (Survival Motor Neuron)-complex. This macromolecular machinery performs essential steps during the assembly of spliceosomal UsnRNPs. By orthology, many factors constituting the SMN-complex in humans developed early in evolution. Some were secondarily lost in Drosophila. Compositional investigation of the Drosophila SMN-complex by biochemistry revealed the absence of two predicted orthologs although the complex was functional. Their bioinformatical re-assessment showed rapid sequence divergence indicating loss of evolutionary pressure in Drosophila. As a tool to better understand the function of individual proteins in multimeric molecular machineries, we therefore advocate iterative combination of bioinformatics with biochemical or functional assessment.