Three fundamental contributions of molecular genetics to avian ecology and evolution

Studies in molecular genetics are having revisionary impact in at least three broad areas of avian ecology and evolution: mating systems, geographic population structure and gene flow, and phylogenetic relationships among species and higher taxa. With regard to mating systems, genetic analyses of maternity and paternity have revealed unexpectedly high frequencies of extra-pair fertilization and intraspecific brood parasitism in numerous avian species (including those thought to be socially monogamous), and these discoveries are prompting a fundamental reshaping of mating system theory for birds. With regard to genetic structure, molecular markers have uncovered a great variety of depths and patterns in the phylogeographic histories of conspecific populations, and these findings provide novel perspectives on historical gene flow regimes and species concepts. With regard to evolutionary relationships among higher avian taxa, molecular findings have suggested several phylogenetic realignments, thus prompting renewed interest in the cross-comparative aspects of molecular and morphological evolution as well as of alternative procedures for molecular analysis.     

Phenotype recognition. Clinicians' contributions to molecular genetics.

Medullary cystic disease, Alport''s syndrome, and autosomal dominant polycystic kidney disease are inherited renal disorders whose genetic bases are better understood because of careful clinical observation. I explore the relationships among some clinical aspects of each of these conditions, the rapidly advancing field of molecular genetics, and the ethical issues that need to be addressed before gene identification becomes too widely applied as a diagnostic tool.     

Microbial biofilms: from ecology to molecular genetics.

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.     

The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools

Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.     

Early contributions of molecular phylogenetics to understanding the evolution of Rotifera

The past decade has seen the application of DNA sequence data to phylogenetic investigations of Rotifera, both expanding and challenging our understanding of the evolution of the phylum. Evidence that Acanthocephala, long regarded as a separate but closely related phylum, is a highly derived class of Rotifera demonstrates the potential of molecular analyses to suggest relationships not obvious from morphological analysis. Phylogenies based on the sequence of the gene for the small ribosomal RNA suggest that rotifers and acanthocephalans are associated with Platyhelminthes and Gastrotricha, perhaps in a clade with Gnathostomula and Cycliophora; at present, this group lacks a clear morphological synapomorphy. A more complete resolution of the molecular phylogeny of Rotifera will require surveying multiple genes and several species from each clade under investigation.     

Oxidative stress in ecology and evolution: lessons from avian studies

Although oxidative stress is a central topic in biochemical and medical research, the number of reports on its relevance in life‐history studies of non‐human animals is still low. Information about oxidative stress in wild birds may help describe functional interactions among the components of life‐history traits. Currently available evidence suggests that oxidative stress may impart an important physiological cost on longevity, reproduction, immune response or intense physical activity. Given the gaps in our present knowledge, it is still premature to attempt to draw definitive conclusions and basic questions (e.g. how is oxidative stress generated and how do organisms cope with it?) have yet to be fully explored under natural conditions. Therefore, caution is needed in developing hypotheses or drawing general conclusions until additional data become available to perform more rigorous comparative analyses.     

The ecology,genetics and evolution of bacteria in an experimental setting

Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University. He studies the ecology, genetics and evolution of bacteria in an experimental setting that enables him to observe the dynamical processes and outcomes across many generations. One of his experiments with Escherichia coli has passed 30,000 generations and is still on-going. A few years ago, he also began studying artificial life in the form of 'digital organisms' - computer programs that replicate, mutate, compete, and therefore evolve and adapt.     

Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time

Genetic time‐series data from historical samples greatly facilitate inference of past population dynamics and species evolution. Yet, although climate and landscape change are often touted as post‐hoc explanations of biological change, our understanding of past climate and landscape change influences on evolutionary processes is severely hindered by the limited application of methods that directly relate environmental change to species dynamics through time. Increased integration of spatiotemporal environmental and genetic data will revolutionize the interpretation of environmental influences on past population processes and the quantification of recent anthropogenic impacts on species, and vastly improve prediction of species responses under future climate change scenarios, yielding widespread revelations across evolutionary biology, landscape ecology and conservation genetics. This review encourages greater use of spatiotemporal landscape genetic analyses that explicitly link landscape, climate and genetic data through time by providing an overview of analytical approaches for integrating historical genetic and environmental data in five key research areas: population genetic structure, demography, phylogeography, metapopulation connectivity and adaptation. We also include a tabular summary of key methodological information, suggest approaches for mitigating the particular difficulties in applying these techniques to ancient DNA and palaeoclimate data, and highlight areas for future methodological development.     

Wilhelm Ludwig and his contributions to population genetics

This article reviews the life and work of the German biologist Wilhelm Ludwig (1901-1959), whose contributions to population genetics have been largely ignored. Ludwig's work was a rich tapestry of population biology, spanning investigations into population growth, biological asymmetries, sex ratio, and paternity analysis. He was ahead of his time in explicitly combining the theory of population ecology and population genetics. His classic paper on annidation showed the possibility of population differentiation in the face of gene flow, and his early studies demonstrated the importance of selection in evolutionary change. Much of his work spanned the period of the Second World War in Germany, and interesting questions remain about his life during this turbulent period.     

The molecular evolution of avian ultraviolet- and violet-sensitive visual pigments

The shortwave-sensitive SWS1 class of vertebrate visual pigments range in lambda(max) from the violet (385-445 nm) to the ultraviolet (UV) (365-355 nm), with UV-sensitivity almost certainly ancestral. In birds, however, the UV-sensitive pigments present in a number of species have evolved secondarily from an avian violet-sensitive (VS) pigment. All avian VS pigments expressed in vitro to date encode Ser86 whereas Phe86 is present in all non-avian ultraviolet sensitive (UVS) pigments. In this paper, we show by site directed mutagenesis of avian VS pigments that Ser86 is required in an avian VS pigment to maintain violet-sensitivity and therefore underlies the evolution of avian VS pigments. The major mechanism for the evolution of avian UVS pigments from an ancestral avian VS pigment is undoubtedly a Ser90Cys substitution. However, Phe86, as found in the Blue-crowned trogon, will also short-wave shift the pigeon VS pigment into the UV whereas Ala86 and Cys86 which are also found in natural avian pigments do not generate short-wave shifts when substituted into the pigeon pigment. From available data on avian SWS1 pigments, it would appear that UVS pigments have evolved on at least 5 separate occasions and utilize 2 different mechanisms for the short-wave shift.     

Integrating ecology and genetics to address Acari invasions

Because of their small size and tolerance to many of the control procedures used for a wide variety of commodities, Acari species have become one of the fastest, unwanted pest travelers since the beginning of this century. This special issue includes eleven studies on adventive and invasive Acari species affecting major crops and livestock around the world. The nucleus for this special issue is formed by the presentations in the symposium on invasive mites and ticks organized at the International Congress of Acarology in Recife, Brazil (ICA-13), in the summer of 2010. This special issue illustrates the increased concerns about domestic and international invasive mites and ticks worldwide.     

Applications of stable isotope analyses to avian ecology

In the past 20 years the use of stable isotope analysis has become increasingly common in ecological studies. In fact, in some instances these techniques have yielded remarkable insights into the foraging preferences and migrations of birds. Despite these advances and the potential of the approach, it is possibly still not as widely used as might be expected. In this paper we aim to illustrate the potential of the approach in the hope of encouraging more avian ecologists to think again about how these techniques might provide insights in the systems on which they work. We discuss some of the principles behind the approach, and review some of the more recent ornithological studies that have used stable isotope techniques to trace trophic pathways or infer migratory origins. We follow this by discussing some of the latest ideas on how stable isotopes may be used to generate community metrics and close by detailing the important assumptions and caveats that should be considered before undertaking any studies using this technique.     

Developmental phenotypic plasticity: Where ecology and evolution meet molecular biology

The plastic response of phenotypic traits to environmental change is a common research focus in several disciplines - from ecology and evolutionary biology to physiology and molecular genetics. The use of model systems such as the flowering plant Arabidopsis thaliana has facilitated a dialogue between developmental biologists asking how plasticity is controlled (proximate causes) and organismal biologists asking why plasticity exists (ultimate causes). Researchers studying ultimate causes and consequences are increasingly compelled to reject simplistic, ‘black box’ models, while those studying proximate causes and mechanisms are increasingly obliged to subject their interpretations to ecological ‘reality checks.’ We review the successful multidisciplinary efforts to understand the phytochrome-mediated shade-avoidance and light-seeking responses of flowering plants as a pertinent example of convergence between evolutionary and molecular biology. In this example, the two-way exchange between reductionist and holist camps has been essential to rapid and sustained progress. This should serve as a model for future collaborative efforts towards understanding the responses of organisms to their constantly changing environments.