Adaptation genomics: the next generation

Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?     

The precautionary approach in fisheries management: the devil is in the details

The William and Lenore Mote International Symposium 'Targets, thresholds and the burden of proof in fishery management' was held at the Mote Marine Laboratory, Sarasota, FL, USA, from 30 October to 2 November 2000.     

Visual processing: the devil is in the details

Ganglion cells convey information from the retina back to the brain. Recent experiments have examined how ganglion cell receptive fields are assembled from many incoming signals.     

Adaptation in the age of ecological genomics: insights from parallelism and convergence

Parallel phenotypic diversification in closely related species is a rigorous framework for testing the role of natural selection in evolution. Do parallel phenotypes always diversify by parallel genetic bases or does selection pave many alternative genomic routes to the same phenotypic ends? In this review, we show that the advent of next-generation sequencing technologies and the growing use of genomic approaches make it increasingly feasible to answer these fundamental questions using ecological and evolutionary 'non-model' populations of vertebrates in nature. While it is generally expected, and often observed, that closely related populations or species have parallel genetic bases to parallel phenotypes, exceptions are not rare and show that alternative genetic routes can result in similar phenotypes. Ultimately, this framework may illuminate the ecological conditions, evolutionary histories and genetic architectures that result in recurrent phenotypes and rapid adaptation.     

The genomics era is upon us

Alternative gene form discovery and candidate gene selection from gene indexing projectsBurke, J., Wang, H., Hide, W. and Davidson, D.B. (1998)Genome Res. 8, 276–290Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysisEisen, J.A. (1998)Genome Res. 8, 163–167     

Applied plant genomics: the secret is integration

Although concerted efforts to understand selected botanical models have been made, the resulting basic knowledge varies in its applicability to other diverse species including the major crops. Recent advances in high-throughput genomics are offering new avenues through which to exploit model systems for the study of botanical diversity, providing prospects for crop improvement. In particular, whole-genome sequencing has provided opportunities for the broader application of reverse genetics, expression profiling, and molecular mapping in diverse species.     

Centrosome function during stem cell division: the devil is in the details

Cell polarity is inherent to animal development and requires microtubules. In essentially all non-terminally differentiated somatic and male germ-line animal cells, microtubule organisation is governed by centrosomes. Animal development without centrosomes would therefore seem inconceivable. The claim of flies without centrosomes may appear to challenge this notion. Does it?     

The cost of reproduction: the devil in the details

The cost of reproduction is of fundamental importance in life-history evolution. However, our understanding of its mechanistic basis has been limited by a lack of detailed functional information at all biological levels. Here, we identify, evaluate and integrate recent studies in five areas examining the proximate mechanisms underlying the cost of reproduction. Rather than being alternate explanations, hormonal regulation and intermediary metabolism act in concert and have an overarching influence in shaping the cost of reproduction. Immune function is compromised by reproduction, as is resistance to environmental stress. These studies not only provide new information about mechanisms that comprise 'the cost', but also hint at an underlying evolutionarily conserved causal mechanism.     

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

The genomics revolution has initiated a new era of population genetics where genome‐wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high‐throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced‐representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long‐term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.     

Why genomics is more than genomes

A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004.