Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification

Phylogenetic trees show a remarkable slowdown in the increase of number of lineages towards the present, a phenomenon which cannot be explained by the standard birth-death model of diversification with constant speciation and extinction rates. The birth-death model instead predicts a constant or accelerating increase in the number of lineages, which has been called the pull of the present. The observed slowdown has been attributed to nonconstancy of the speciation and extinction rates due to some form of diversity dependence (i.e., species-level density dependence), but the mechanisms underlying this are still unclear. Here, we propose an alternative explanation based on the simple concept that speciation takes time to complete. We show that this idea of "protracted" speciation can be incorporated in the standard birth-death model of diversification. The protracted birth-death model predicts a realistic slowdown in the rate of increase of number of lineages in the phylogeny and provides a compelling fit to four bird phylogenies with realistic parameter values. Thus, the effect of recognizing the generally accepted fact that speciation is not an instantaneous event is significant; even if it cannot account for all the observed patterns, it certainly contributes substantially and should therefore be incorporated into future studies.     

Polymorphisms past and present

Polymorphisms, particularly genetic variants of the red blood cell, have served as a major focus for the research of Frank B. Livingstone over the course of a long and productive career. Recent investigations confirm the value of key insights that he contributed to this area more than four decades ago. As Livingstone recognized, the same underlying evolutionary model that guides genetic studies in present populations also provides a productive framework for interpreting patterns of variation in the skeleton and dentition throughout past human evolution. Examples explored in detail here include polymorphisms in hominoid nasal bone shapes and fourth lower premolar roots. This work provides both empirical and theoretical contexts for investigating patterns of human variation over the last 6 to 8 million years.     

Chitosomes: past, present and future

José Ruiz-Herrera's discovery that chitin microfibrils could be made by a fungal extract paved the way for elucidating the intracellular location of chitin synthetase. In collaboration with Charles Bracker, chitosomes were identified as the major reservoir of chitin synthetase in fungi. Unique in size, buoyant density, and membrane thickness, chitosomes were found in a wide range of fungi. Their reversible dissociation into 16S subunits is another unique property of chitosomes. These 16S subunits are the smallest molecular entities known to retain chitin synthetase activity. Further dissociation leads to complete loss of activity. From studies with secretory mutants, yeast researchers concluded that chitosomes were components of the endocytosis pathway. However, key structural and enzymatic characteristics argue in favor of the chitosome being poised for exocytotic delivery rather than endocytotic recycling. The chitosome represents the main vehicle for delivering chitin synthetase to the cell surface. An immediate challenge is to elucidate chitosome ontogeny and the role of proteins encoded by the reported chitin synthetase genes in the structure or function of chitosomes. The ultimate challenge would be to understand how the chitosome integrates with the cell surface to construct the organized microfibrillar skeleton of the fungal cell wall.     

Growth hormone-releasing hormone: past and present

The discovery of hypothalamic hypophysiotropic factors confirmed the hypothesis of Green and Harris in the late 1940s. These hormones were isolated from their eutopic site of production (the hypothalamus) with the exception of growth hormone (GH)-releasing hormone (GHRH), which was isolated from an ectopic, tumoral site of production and found to be responsible for acromegaly. Following the isolation, characterization and synthesis of human GHRH, clinical studies were performed and are described below. Circulating levels of GHRH can be measured and provide the basis for the diagnosis of acromegaly related to the ectopic, tumoral production of GHRH. At present, GHRH is used as a test of GH secretion mainly as an adjunct to other agents which modify somatostatin status, or to GH-releasing peptides. Its therapeutic potential in children and the elderly is still under investigation. The role of GHRH in the pulsatile secretion of GH is described.     

Life: past, present and future

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote-centric (five-kingdoms) view of the planet to one that is peculiarly prokarote-centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen-using, carbon-eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such 'metabolic extremophily' forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.     

Schistosomiasis in Indonesia: past and present

Schistosomiasis is endemic in Indonesia in two isolated areas, Lindu valley and Napu valley, both located in the Province of Central Sulawesi. In 1940, a prevalence survey was initiated in Lake Lindu, which indicated a Schistosoma japonicum infection prevalence of 56% among the population of Anca, Tomado and Langko villages. Another survey was conducted in 1973 in Napu valley and very high infection prevalences of up to 72% were found among the population in Winowanga village. Since then, comprehensive studies on the epidemiology and the effects of control have been carried out in 24 endemic villages in both areas. Over the past six decades, schistosomiasis control has been implemented and the average prevalence is now much lower than before the control programme was launched. In 2006, it was 0.49% in 7 villages in Lindu valley. In Napu valley, the average infection prevalence among the population of 17 villages was 1.08% in the same year. Again in 2006, the prevalence of infection in snails ranged from 0 to 13.4% and from 0 to 9.1% in Napu and Lindu valleys, respectively. The highest prevalence among snails was found in Dodolo village. The prevalence of S. japonicum in the reservoir host Rattus spp. ranged from 0 to 20% and the highest prevalence was again found in Dodolo village. Contemporary data suggest that transmission of schistosomiasis is still ongoing in Indonesia despite regular surveillance and control activities covering the whole endemic area.     

Biodiversity: past, present and future

On 12-15 May 2011, a diverse group of students, researchers and practitioners from across Canada and around the world met in Banff, Alberta, to discuss the many facets of biodiversity science at the 6th Annual Meeting of the Canadian Society for Ecology and Evolution.     

Japanese tooth size: past and present

Mesial-distal and buccal-lingual crown measurements were made on male and female samples of recent Japanese teeth from three locations, Fukuoka, Kyoto, and Tokyo, and for Hokkaido Ainu and Koreans. Similar data were collected for prehistoric Middle-to-Late Jomon Japanese and from Yayoi specimens representing the first agriculturalists to appear in Japan. From a tooth-by-tooth comparison of cross-sectional areas, it was shown that the modern Japanese samples did not differ from one part of Japan to another. Korean tooth size also is not significantly different from Japanese, while Ainu have the smallest teeth recorded in Asia. The Yayoi who brought rice to Japan about 300 B.C. came in with teeth that were the same size as Chinese Neolithic teeth. They encountered a resident Jomon population whose teeth were 10% smaller. From tooth size measures alone, it is most economical to suggest that, if the rates of reduction observed elsewhere in the world applied in Japan, the recent Ainu would best be regarded as the direct descendants of the Jomon, while the modern Japanese are the results of in situ reduction from the incoming Yayoi. Other aspects of craniofacial morphology suggest that some Jomon was incorporated by the Yayoi. The modern Japanese, then, while predominantly derived from the Yayoi, would include a Jomon component.