Naturalists, natural history, and the nature of biological diversity

Abstract In this essay, I argue that natural history--observing the natural world and deciphering its patterns--is as essential today as it was during Darwin's lifetime to the continuing development of ecology and evolutionary biology. This tradition, which I illustrate through the example of E. O. Wilson's discovery of the taxon cycle 50 years ago, is still very much alive, but there is a growing tendency for observation to serve theory rather provide new insight or to test the predictions of theory. This tendency manifests itself in the failure of ideas about the diversity, distribution, and abundance of species to be informed by patterns in nature that are readily apparent. On the one hand, supporters of neutral theory have sidestepped the unrealistically slow dynamics of random processes in large metacommunities, and they have failed to note global correlations in species numbers and population sizes within taxa. On the other hand, proponents of niche theory have disregarded the implications of variation in distribution and abundance among close relatives, which implies population regulation largely by species-specific agents, such as pathogens. Nor has community niche theory addressed the independence of distribution and abundance with respect to number of close relatives (and presumed competitors). The diversity, abundances, and distributions of species represent the unfolding of many processes over a historically and geographically contingent landscape, for which experimental methods of scientific inquiry are poorly suited. To interpret patterns of diversity, we must continue to depend on inductive reasoning inspired by the data of natural history.     

The natural nature of biomembrane lipids: matches and bilayers

Ordinary matches were used in a class to illustrate the basic concepts underlying the organisation of biological membranes. The model was found to be very efficient in capturing students’ interest and in potentiating long-term memorisation of the subject matter.     

The incomplete natural history of mitochondria

Mitochondrial DNA (mtDNA) has been used to study molecular ecology and phylogeography for 25 years. Much important information has been gained in this way, but it is time to reflect on the biology of the mitochondrion itself and consider opportunities for evolutionary studies of the organelle itself and its ecology, biochemistry and physiology. This review has four sections. First, we review aspects of the natural history of mitochondria and their DNA to show that it is a unique molecule with specific characteristics that differ from nuclear DNA. We do not attempt to cover the plethora of differences between mitochondrial and nuclear DNA; rather we spotlight differences that can cause significant bias when inferring demographic properties of populations and/or the evolutionary history of species. We focus on recombination, effective population size and mutation rate. Second, we explore some of the difficulties in interpreting phylogeographical data from mtDNA data alone and suggest a broader use of multiple nuclear markers. We argue that mtDNA is not a sufficient marker for phylogeographical studies if the focus of the investigation is the species and not the organelle. We focus on the potential bias caused by introgression. Third, we show that it is not safe to assume a priori that mtDNA evolves as a strictly neutral marker because both direct and indirect selection influence mitochondria. We outline some of the statistical tests of neutrality that can, and should, be applied to mtDNA sequence data prior to making any global statements concerning the history of the organism. We conclude with a critical examination of the neglected biology of mitochondria and point out several surprising gaps in the state of our knowledge about this important organelle. Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance.     

Affirmative reaction: new formations of white masculinity

Within the politics of nationalism and nation-building, the emigration of ethnic and religious minorities, whether voluntary or involuntary, appears to be a commonly occurring practice. After the collapse of the Ottoman Empire in the early twentieth century, modern Turkey still carried the legacy of a multi-ethnic, multi-religious diversity in which its Armenian, Greek and Jewish communities had official minority status based upon the 1923 Treaty of Lausanne. However, throughout the twentieth century, Turkey's non-Muslim minority populations have undergone a mass emigration experience in which thousands of their numbers have migrated to various countries around the globe. While in the 1920s the population of non-Muslims in the country was close to 3 per cent of the total, today it has dropped to less than two per thousand. This article analyses the emigration of non-Muslim people from Turkey and relates this movement to the wider context of nation-building in the country.     

The natural history of nitrogen fixation

In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms-typically found within highly conserved operons-and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred into the bacterial domain.     

OpenUp! Creating a cross-domain pipeline for natural history data

Multimedia data held by Natural History Museums and Universities are presently not readily accessible, even within the natural history community itself. The EU project OpenUp! is an effort to mobilise scientific biological multimedia resources and open them to a wider audience using the EUROPEANA data standards and portal. The connection between natural history and EUROPEANA is accomplished using well established BioCASe and GBIF technologies. This is complemented with a system for data quality control, data transformation and semantic enrichment. With this approach, OpenUp! will provide at least 1,1 Million multimedia objects to EUROPEANA by 2014. Its lean infrastructure is sustainable within the natural history community and will remain functional and effective in the post-project phase.